Photoexcited Energy Transfer in a Weakly Coupled Dimer.

PubMed

Alfonso Hernandez, Laura; Nelson, Tammie; Tretiak, Sergei; Fernandez-Alberti, Sebastian

2015-06-18

Nonadiabatic excited-state molecular dynamics (NA-ESMD) simulations have been performed in order to study the time-dependent exciton localization during energy transfer between two chromophore units of the weakly coupled anthracene dimer dithia-anthracenophane (DTA). Simulations are done at both low temperature (10 K) and room temperature (300 K). The initial photoexcitation creates an exciton which is primarily localized on a single monomer unit. Subsequently, the exciton experiences an ultrafast energy transfer becoming localized on either one monomer unit or the other, whereas delocalization between both monomers never occurs. In half of the trajectories, the electronic transition density becomes completely localized on the same monomer as the initial excitation, while in the other half, it becomes completely localized on the opposite monomer. In this article, we present an analysis of the energy transfer dynamics and the effect of thermally induced geometry distortions on the exciton localization. Finally, simulated fluorescence anisotropy decay curves for both DTA and the monomer unit dimethyl anthracene (DMA) are compared. Our analysis reveals that changes in the transition density localization caused by energy transfer between two monomers in DTA is not the only source of depolarization and exciton relaxation within a single DTA monomer unit can also cause reorientation of the transition dipole.

EFFECTS OF DOPAMINERGIC DRUGS ON WORKING AND REFERENCE MEMORY IN RATS

EPA Science Inventory

Occupational exposure to styrene monomer has been associated with cognitive dysfunction in humans, and changes in dopaminergic function have been suggested to underly effects of repeated exposure to styrene monomer in animals. his study was designed to determine whether styrene a...

[Reticulate evolution of parthenogenetic species of the Lacertidae rock lizards: inheritance of CLsat tandem repeats and anonymous RAPD markers].

PubMed

Chobanu, D; Rudykh, I A; Riabinina, N L; Grechko, V V; Kramerov, D A; Darevskiĭ, I S

2002-01-01

The genetic relatedness of several bisexual and of four unisexual "Lacerta saxicola complex" lizards was studied, using monomer sequences of the complex-specific CLsat tandem repeats and anonymous RAPD markers. Genomes of parthenospecies were shown to include different satellite monomers. The structure of each such monomer is specific for a certain pair of bisexual species. This fact might be interpreted in favor of co-dominant inheritance of these markers in bisexual species hybridogenesis. This idea is supported by the results obtained with RAPD markers; i.e., unisexual species genomes include only the loci characteristic of certain bisexual species. At the same time, in neither case parthenospecies possess specific, autoapomorphic loci that were not present in this or that bisexual species.

Small tandemly repeated DNA sequences of higher plants likely originate from a tRNA gene ancestor.

PubMed Central

Benslimane, A A; Dron, M; Hartmann, C; Rode, A

1986-01-01

Several monomers (177 bp) of a tandemly arranged repetitive nuclear DNA sequence of Brassica oleracea have been cloned and sequenced. They share up to 95% homology between one another and up to 80% with other satellite DNA sequences of Cruciferae, suggesting a common ancestor. Both strands of these monomers show more than 50% homology with many tRNA genes; the best homologies have been obtained with Lys and His yeast mitochondrial tRNA genes (respectively 64% and 60%). These results suggest that small tandemly repeated DNA sequences of plants may have evolved from a tRNA gene ancestor. These tandem repeats have probably arisen via a process involving reverse transcription of polymerase III RNA intermediates, as is the case for interspersed DNA sequences of mammalians. A model is proposed to explain the formation of such small tandemly repeated DNA sequences. Images PMID:3774553

pH-responsive fluorescence chemical sensor constituted by conjugated polymers containing pyridine rings.

PubMed

Adachi, Naoya; Kaneko, Yuki; Sekiguchi, Kazuki; Sugiyama, Hiroki; Sugeno, Masafumi

2015-12-01

Poly(p-pyridinium phenylene ethynylene)s (PPyPE) functionalized with alternating donor-acceptor repeat units were synthesized by a Pd-catalyzed Sonogashira coupling reaction between diethynyl monomer and di-iodopyridine for use as a pH-responsive fluorescence chemical sensor. The synthesized PPyPE, containing pyridine units, was characterized by FT-IR, (1)H and (13)C NMR, UV-visible and fluorescence spectroscopies. We investigated the relationship between changes of optical properties and protonation/deprotonation of PPyPE containing pyridine units in solution. Addition of HCl decreased and red-shifted the fluorescence intensity of the conjugated polymers that contained pyridine rings; fluorescence intensity of the polymers increased upon addition of NaOH solution. The synthesized PPyPE was found to be an effective and reusable chemical sensor for pH sensing. Copyright © 2015 John Wiley & Sons, Ltd.

A Helical Structural Nucleus Is the Primary Elongating Unit of Insulin Amyloid Fibrils

PubMed Central

Roessle, Manfred; Kastrup, Jette S; van de Weert, Marco; Flink, James M; Frokjaer, Sven; Gajhede, Michael; Svergun, Dmitri I

2007-01-01

Although amyloid fibrillation is generally believed to be a nucleation-dependent process, the nuclei are largely structurally uncharacterized. This is in part due to the inherent experimental challenge associated with structural descriptions of individual components in a dynamic multi-component equilibrium. There are indications that oligomeric aggregated precursors of fibrillation, and not mature fibrils, are the main cause of cytotoxicity in amyloid disease. This further emphasizes the importance of characterizing early fibrillation events. Here we present a kinetic x-ray solution scattering study of insulin fibrillation, revealing three major components: insulin monomers, mature fibrils, and an oligomeric species. Low-resolution three-dimensional structures are determined for the fibril repeating unit and for the oligomer, the latter being a helical unit composed of five to six insulin monomers. This helical oligomer is likely to be a structural nucleus, which accumulates above the supercritical concentration used in our experiments. The growth rate of the fibrils is proportional to the amount of the helical oligomer present in solution, suggesting that these oligomers elongate the fibrils. Hence, the structural nucleus and elongating unit in insulin amyloid fibrillation may be the same structural component above supercritical concentrations. A novel elongation pathway of insulin amyloid fibrils is proposed, based on the shape and size of the fibrillation precursor. The distinct helical oligomer described in this study defines a conceptually new basis of structure-based drug design against amyloid diseases. PMID:17472440

Architecture of polyglutamine-containing fibrils from time-resolved fluorescence decay.

PubMed

Röthlein, Christoph; Miettinen, Markus S; Borwankar, Tejas; Bürger, Jörg; Mielke, Thorsten; Kumke, Michael U; Ignatova, Zoya

2014-09-26

The disease risk and age of onset of Huntington disease (HD) and nine other repeat disorders strongly depend on the expansion of CAG repeats encoding consecutive polyglutamines (polyQ) in the corresponding disease protein. PolyQ length-dependent misfolding and aggregation are the hallmarks of CAG pathologies. Despite intense effort, the overall structure of these aggregates remains poorly understood. Here, we used sensitive time-dependent fluorescent decay measurements to assess the architecture of mature fibrils of huntingtin (Htt) exon 1 implicated in HD pathology. Varying the position of the fluorescent labels in the Htt monomer with expanded 51Q (Htt51Q) and using structural models of putative fibril structures, we generated distance distributions between donors and acceptors covering all possible distances between the monomers or monomer dimensions within the polyQ amyloid fibril. Using Monte Carlo simulations, we systematically scanned all possible monomer conformations that fit the experimentally measured decay times. Monomers with four-stranded 51Q stretches organized into five-layered β-sheets with alternating N termini of the monomers perpendicular to the fibril axis gave the best fit to our data. Alternatively, the core structure of the polyQ fibrils might also be a zipper layer with antiparallel four-stranded stretches as this structure showed the next best fit. All other remaining arrangements are clearly excluded by the data. Furthermore, the assessed dimensions of the polyQ stretch of each monomer provide structural evidence for the observed polyQ length threshold in HD pathology. Our approach can be used to validate the effect of pharmacological substances that inhibit or alter amyloid growth and structure. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Coarse-Grained and Atomistic Modeling of Polyimides

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Hinkley, Jeffrey A.

2004-01-01

A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

Characterization of a chromosome-specific chimpanzee alpha satellite subset: Evolutionary relationship to subsets on human chromosomes

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

Warburton, P.E.; Gosden, J.; Lawson, D.

1996-04-15

Alpha satellite DNA is a tandemly repeated DNA family found at the centromeres of all primate chromosomes examined. The fundamental repeat units of alpha satellite DNA are diverged 169- to 172-bp monomers, often found to be organized in chromosome-specific higher-order repeat units. The chromosomes of human (Homo sapiens (HSA)), chimpanzee (Pan troglodytes (PTR) and Pan paniscus), and gorilla (Gorilla gorilla) share a remarkable similarity and synteny. It is of interest to ask if alpha satellite arrays at centromeres of homologous chromosomes between these species are closely related (evolving in an orthologous manner) or if the evolutionary processes that homogenize andmore » spread these arrays within and between chromosomes result in nonorthologous evolution of arrays. By using PCR primers specific for human chromosome 17-specific alpha satellite DNA, we have amplified, cloned, and characterized a chromosome-specific subset from the PTR chimpanzee genome. Hybridization both on Southern blots and in situ as well as sequence analysis show that this subset is most closely related, as expected, to sequences on HSA 17. However, in situ hybridization reveals that this subset is not found on the homologous chromosome in chimpanzee (PTR 19), but instead on PTR 12, which is homologous to HSA 2p. 40 refs., 3 figs.« less

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

PubMed

Melters, Daniël P; Bradnam, Keith R; Young, Hugh A; Telis, Natalie; May, Michael R; Ruby, J Graham; Sebra, Robert; Peluso, Paul; Eid, John; Rank, David; Garcia, José Fernando; DeRisi, Joseph L; Smith, Timothy; Tobias, Christian; Ross-Ibarra, Jeffrey; Korf, Ian; Chan, Simon W L

2013-01-30

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

PubMed Central

2013-01-01

Background Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Results Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. Conclusions While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes. PMID:23363705

Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers.

PubMed

Kandeel, Mahmoud; Al-Taher, Abdulla; Li, Huifang; Schwingenschlogl, Udo; Al-Nazawi, Mohamed

2018-08-01

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulations were carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lower root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HRs, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer was modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the a and d positions of HR helices stabilize the whole system, with minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at the a and d positions of HR helix were strong stabilizers of HR recognition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop.

PubMed

Dembska, Anna; Juskowiak, Bernard

2015-01-01

In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit). Copyright © 2015 Elsevier B.V. All rights reserved.

40 CFR 723.250 - Polymers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... functional group. Fluorotelomers means the products of telomerization, which is the reaction of a telogen... relevant polymer-forming reaction used for the particular process. Monomer Unit means the reacted form of... monomer units but which, under the relevant reaction conditions used for the particular process, cannot...

Reactivity ratios and sequence structures of the copolymers prepared using photo-induced copolymerization of MMA with MTMP.

PubMed

Liu, Xiaoxuan; Zhang, Yongtao; Cui, Yanyan; Dong, Zhixian

2012-05-01

4-Methacryloyl-2,2,6,6-tetramethyl-piperidine (MTMP) was applied as reactive hindered amine piperidine. Photo-induced copolymerization of methyl methacrylate (MMA, M(1)) with MTMP (M(2)) was carried out in benzene solution at ambient temperature. The reactivity ratios for these monomers were measured by running a series of reactions at various feed ratios of initial monomers, and the monomer incorporation into copolymer was determined using (1)H NMR. Reactivity ratios of the MMA/MTMP system were measured to be r(1)= 0.37 and r(2)= 1.14 from extended Kelen-Tüdos method. The results show that monomer MTMP prefers homopolymerization to copolymerization in the system, whereas monomer MMA prefers copolymerization to homopolymerization. Sequence structures of the MMA/MTMP copolymers were characterized using (1)H NMR. The results show that the sequence structure for the main chain of the MMA/MTMP copolymers is mainly composed of a syndiotactic configuration, only with a little heterotactic configuration. Three kinds of the sequences of rr, rr', and lr' in the syndiotactic configuration are found. The sequence-length distribution in the MMA/MTMP copolymers is also obtained. For f(1)= 0.2, the monomer unit of MMA is mostly separated by MTMP units, and for f(1)= 0.6, the alternating tendency prevails and a large number of mono-sequences are formed; further up to f(1)= 0.8, the monomer unit of MTMP with the sequence of one unit is interspersed among the chain of MMA. Copyright © 2012 John Wiley & Sons, Ltd.

Chemoselective, Stereospecific, and Living Polymerization of Polar Divinyl Monomers by Chiral Zirconocenium Catalysts.

PubMed

Vidal, Fernando; Gowda, Ravikumar R; Chen, Eugene Y-X

2015-07-29

This contribution reports the first chemoselective, stereospecific, and living polymerization of polar divinyl monomers, enabled by chiral ansa-zirconocenium catalysts through an enantiomorphic-site controlled coordination-addition polymerization mechanism. Silyl-bridged-ansa-zirconocenium ester enolate 2 has been synthesized and structurally characterized, but it exhibits low to negligible activity and stereospecificity in the polymerization of polar divinyl monomers including vinyl methacrylate (VMA), allyl methacrylate (AMA), 4-vinylbenzyl methacrylate (VBMA), and N,N-diallyl acrylamide (DAA). In contrast, ethylene-bridged-ansa-zirconocenium ester enolate 1 is highly active and stereospecific in the polymerization of such monomers including AMA, VBMA, and DAA. The polymerization by 1 is perfectly chemoselective for all four polar divinyl monomers, proceeding exclusively through conjugate addition across the methacrylic C═C bond, while leaving the pendant C═C bonds intact. The polymerization of DAA is most stereospecific and controlled, producing essentially stereoperfect isotactic PDAA with [mmmm] > 99%, M(n) matching the theoretical value (thus a quantitative initiation efficiency), and a narrow molecular weight distribution (Đ = 1.06-1.16). The stereospecificity is slightly lower for the AMA polymerization but still leading to highly isotactic poly(allyl methacrylate) (PAMA) with 95-97% [mm]. The polymerization of VBMA is further less stereospecific, affording PVBMA with 90-94% [mm], while the polymerization VMA is least stereospecific. Several lines of evidence from both homo- and block copolymerization results have demonstrated living characteristics of the AMA polymerization by 1. Mechanistic studies of this polymerization have yielded a monometallic coordination-addition polymerization mechanism involving the eight-membered chelating intermediate. Post-functionalization of isotactic polymers bearing the pendant vinyl group on every repeating unit via the thiol-ene "click" reaction achieves a full conversion of all the pendant double bonds to the corresponding thioether bonds. Photocuring of such isotactic polymers is also successful, producing an elastic material readily characterizable by dynamic mechanical analysis.

Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen.

PubMed

Varma, Sameer; Botlani, Mohsen; Hammond, Jeff R; Scott, H Larry; Orgel, Joseph P R O; Schieber, Jay D

2015-10-01

A signature feature of collagen is its axial periodicity visible in TEM as alternating dark and light bands. In mature, type I collagen, this repeating unit, D, is 67 nm long. This periodicity reflects an underlying packing of constituent triple-helix polypeptide monomers wherein the dark bands represent gaps between axially adjacent monomers. This organization is visible distinctly in the microfibrillar model of collagen obtained from fiber diffraction. However, to date, no atomistic simulations of this diffraction model under zero-stress conditions have reported a preservation of this structural feature. Such a demonstration is important as it provides the baseline to infer response functions of physiological stimuli. In contrast, simulations predict a considerable shrinkage of the D-band (11-19%). Here we evaluate systemically the effect of several factors on D-band shrinkage. Using force fields employed in previous studies we find that irrespective of the temperature/pressure coupling algorithms, assumed salt concentration or hydration level, and whether or not the monomers are cross-linked, the D-band shrinks considerably. This shrinkage is associated with the bending and widening of individual monomers, but employing a force field whose backbone dihedral energy landscape matches more closely with our computed CCSD(T) values produces a small D-band shrinkage of < 3%. Since this force field also performs better against other experimental data, it appears that the large shrinkage observed in earlier simulations is a force-field artifact. The residual shrinkage could be due to the absence of certain atomic-level details, such as glycosylation sites, for which we do not yet have suitable data. © 2015 Wiley Periodicals, Inc.

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species.

PubMed

Kuhn, G C S; Teo, C H; Schwarzacher, T; Heslop-Harrison, J S

2009-05-01

Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM x DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.

Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor).

PubMed Central

Ishiai, M; Wada, C; Kawasaki, Y; Yura, T

1994-01-01

Replication of mini-F plasmid requires the plasmid-encoded RepE initiator protein and several host factors including DnaJ, DnaK, and GrpE, heat shock proteins of Escherichia coli. The RepE protein plays a crucial role in replication and exhibits two major functions: initiation of replication from the origin, ori2, and autogenous repression of repE transcription. One of the mini-F plasmid mutants that can replicate in the dnaJ-defective host produces an altered RepE (RepE54) with a markedly enhanced initiator activity but little or no repressor activity. RepE54 has been purified from cell extracts primarily in monomeric form, unlike the wild-type RepE that is recovered in dimeric form. Gel-retardation assays revealed that RepE54 monomers bind to ori2 (direct repeats) with a very high efficiency but hardly bind to the repE operator (inverted repeat), in accordance with the properties of RepE54 in vivo. Furthermore, the treatment of wild-type RepE dimers with protein denaturants enhanced their binding to ori2 but reduced binding to the operator: RepE dimers were partially converted to monomers, and the ori2 binding activity was uniquely associated with monomers. These results strongly suggest that RepE monomers represent an active form by binding to ori2 to initiate replication, whereas dimers act as an autogenous repressor by binding to the operator. We propose that RepE is structurally and functionally differentiated and that monomerization of RepE dimers, presumably mediated by heat shock protein(s), activates the initiator function and participates in regulation of mini-F DNA replication. Images PMID:8170998

Functional Degradable Polymers by Radical Ring-Opening Copolymerization of MDO and Vinyl Bromobutanoate: Synthesis, Degradability and Post-Polymerization Modification.

PubMed

Hedir, Guillaume G; Bell, Craig A; O'Reilly, Rachel K; Dove, Andrew P

2015-07-13

The synthesis of vinyl bromobutanoate (VBr), a new vinyl acetate monomer derivative obtained by the palladium-catalyzed vinyl exchange reaction between vinyl acetate (VAc) and 4-bromobutyric acid is reported. The homopolymerization of this new monomer using the RAFT/MADIX polymerization technique leads to the formation of novel well-defined and controlled polymers containing pendent bromine functional groups able to be modified via postpolymerization modification. Furthermore, the copolymerization of vinyl bromobutanoate with 2-methylene-1,3-dioxepane (MDO) was also performed to deliver a range of novel functional degradable copolymers, poly(MDO-co-VBr). The copolymer composition was shown to be able to be tuned to vary the amount of ester repeat units in the polymer backbone, and hence determine the degradability, while maintaining a control of the final copolymers' molar masses. The addition of functionalities via simple postpolymerization modifications such as azidation and the 1,3-dipolar cycloaddition of a PEG alkyne to an azide is also reported and proven by (1)H NMR spectroscopy, FTIR spectroscopy, and SEC analyses. These studies enable the formation of a novel class of hydrophilic functional degradable copolymers using versatile radical polymerization methods.

Optical isotropy and iridescence in a smectic 'blue phase'.

PubMed

Yamamoto, Jun; Nishiyama, Isa; Inoue, Miyoshi; Yokoyama, Hiroshi

2005-09-22

When liquid crystal molecules are chiral, the twisted structure competes with spatially uniform liquid crystalline orders, resulting in a variety of modulated liquid crystal phases, such as the cholesteric blue phase, twist grain boundary and smectic blue phases. Here we report a liquid crystal smectic blue phase (SmBP(iso)), formed from a two-component mixture containing a chiral monomer and a 'twin' containing two repeat units of the first molecule connected by a linear hydrocarbon spacer. The phase exhibits the simultaneous presence of finite local-order parameters of helices and smectic layers, without any discontinuity on a mesoscopic length scale. The anomalous softening of elasticity due to a strong reduction in entropy caused by mixing the monomer and the twin permits the seamless coexistence of these two competing liquid crystal orders. The new phase spontaneously exhibits an optically isotropic but uniformly iridescent colour and automatically acquires spherical symmetry, so that the associated photonic band gap maintains the same symmetry despite the local liquid crystalline order. We expect a range of unusual optical transmission properties based on this three-dimensional isotropic structure, and complete tunability due to the intrinsic softness and responsiveness of the liquid crystalline order against external fields.

Removal of metal ions from aqueous solution

DOEpatents

Jackson, Paul J.; Delhaize, Emmanuel; Robinson, Nigel J.; Unkefer, Clifford J.; Furlong, Clement

1990-01-01

A method of removing heavy metals from aqueous solution, a composition of matter used in effecting said removal, and apparatus used in effecting said removal. One or more of the polypeptides, poly (.gamma.-glutamylcysteinyl)glycines, is immobilized on an inert material in particulate form. Upon contact with an aqueous solution containing heavy metals, the polypeptides sequester the metals, removing them from the solution. There is selectivity of poly (.gamma.-glutamylcysteinyl)glycines having a particular number of monomer repeat units for particular metals. The polypeptides are easily regenerated by contact with a small amount of an organic acid, so that they can be used again to remove heavy metals from solution. This also results in the removal of the metals from the column in a concentrated form.

Removal of metal ions from aqueous solution

DOEpatents

Jackson, Paul J.; Delhaize, Emmanuel; Robinson, Nigel J.; Unkefer, Clifford J.; Furlong, Clement

1990-11-13

A method of removing heavy metals from aqueous solution, a composition of matter used in effecting said removal, and apparatus used in effecting said removal. One or more of the polypeptides, poly (.gamma.-glutamylcysteinyl)glycines, is immobilized on an inert material in particulate form. Upon contact with an aqueous solution containing heavy metals, the polypeptides sequester the metals, removing them from the solution. There is selectivity of poly (.gamma.-glutamylcysteinyl)glycines having a particular number of monomer repeat unit for particular metals. The polypeptides are easily regenerated by contact with a small amount of an organic acid, so that they can be used again to remove heayv metals from solution. This also results in the removal of the metals from the column in a concentrated form.

Compositions containing poly (.gamma.-glutamylcysteinyl)glycines

DOEpatents

Jackson, Paul J.; Delhaize, Emmanuel; Robinson, Nigel J.; Unkefer, Clifford J.; Furlong, Clement

1992-01-01

A method of removing heavy metals from aqueous solution, a composition of matter used in effecting said removal, and apparatus used in effecting said removal. One or more of the polypeptides, poly (.gamma.-glutamylcysteinyl)glycines, is immobilized on an inert material in particulate form. Upon contact with an aqueous solution containing heavy metals, the polypeptides sequester the metals, removing them from the solution. There is selectivity of poly (.gamma.-glutamylcysteinyl)glycines having a particular number of monomer repeat units for particular metals. The polypeptides are easily regenerated by contact with a small amount of an organic acid, so that they can be used again to remove heavy metals from solution. This also results in the removal of the metals from the column in a concentrated form.

A synthetic polymer system with repeatable chemical recyclability

NASA Astrophysics Data System (ADS)

Zhu, Jian-Bo; Watson, Eli M.; Tang, Jing; Chen, Eugene Y.-X.

2018-04-01

The development of chemically recyclable polymers offers a solution to the end-of-use issue of polymeric materials and provides a closed-loop approach toward a circular materials economy. However, polymers that can be easily and selectively depolymerized back to monomers typically require low-temperature polymerization methods and also lack physical properties and mechanical strengths required for practical uses. We introduce a polymer system based on γ-butyrolactone (GBL) with a trans-ring fusion at the α and β positions. Such trans-ring fusion renders the commonly considered as nonpolymerizable GBL ring readily polymerizable at room temperature under solvent-free conditions to yield a high–molecular weight polymer. The polymer has enhanced thermostability and can be repeatedly and quantitatively recycled back to its monomer by thermolysis or chemolysis. Mixing of the two enantiomers of the polymer generates a highly crystalline supramolecular stereocomplex.

Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates.

PubMed

Anderson, A J; Dawes, E A

1990-12-01

Polyhydroxyalkanoates (PHAs), of which polyhydroxybutyrate (PHB) is the most abundant, are bacterial carbon and energy reserve materials of widespread occurrence. They are composed of 3-hydroxyacid monomer units and exist as a small number of cytoplasmic granules per cell. The properties of the C4 homopolymer PHB as a biodegradable thermoplastic first attracted industrial attention more than 20 years ago. Copolymers of C4 (3-hydroxybutyrate [3HB]) and C5 (3-hydroxyvalerate [3HV]) monomer units have modified physical properties; e.g., the plastic is less brittle than PHB, whereas PHAs containing C8 to C12 monomers behave as elastomers. This family of materials is the centre of considerable commercial interest, and 3HB-co-3HV copolymers have been marketed by ICI plc as Biopol. The known polymers exist as 2(1) helices with the fiber repeat decreasing from 0.596 nm for PHB to about 0.45 nm for C8 to C10 polymers. Novel copolymers with a backbone of 3HB and 4HB have been obtained. The native granules contain noncrystalline polymer, and water may possibly act as a plasticizer. Although the biosynthesis and regulation of PHB are generally well understood, the corresponding information for the synthesis of long-side-chain PHAs from alkanes, alcohols, and organic acids is still incomplete. The precise mechanisms of action of the polymerizing and depolymerizing enzymes also remain to be established. The structural genes for the three key enzymes of PHB synthesis from acetyl coenzyme A in Alcaligenes eutrophus have been cloned, sequenced, and expressed in Escherichia coli. Polymer molecular weights appear to be species specific. The factors influencing the commercial choice of organism, substrate, and isolation process are discussed. The physiological functions of PHB as a reserve material and in symbiotic nitrogen fixation and its presence in bacterial plasma membranes and putative role in transformability and calcium signaling are also considered.

Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates.

PubMed Central

Anderson, A J; Dawes, E A

1990-01-01

Polyhydroxyalkanoates (PHAs), of which polyhydroxybutyrate (PHB) is the most abundant, are bacterial carbon and energy reserve materials of widespread occurrence. They are composed of 3-hydroxyacid monomer units and exist as a small number of cytoplasmic granules per cell. The properties of the C4 homopolymer PHB as a biodegradable thermoplastic first attracted industrial attention more than 20 years ago. Copolymers of C4 (3-hydroxybutyrate [3HB]) and C5 (3-hydroxyvalerate [3HV]) monomer units have modified physical properties; e.g., the plastic is less brittle than PHB, whereas PHAs containing C8 to C12 monomers behave as elastomers. This family of materials is the centre of considerable commercial interest, and 3HB-co-3HV copolymers have been marketed by ICI plc as Biopol. The known polymers exist as 2(1) helices with the fiber repeat decreasing from 0.596 nm for PHB to about 0.45 nm for C8 to C10 polymers. Novel copolymers with a backbone of 3HB and 4HB have been obtained. The native granules contain noncrystalline polymer, and water may possibly act as a plasticizer. Although the biosynthesis and regulation of PHB are generally well understood, the corresponding information for the synthesis of long-side-chain PHAs from alkanes, alcohols, and organic acids is still incomplete. The precise mechanisms of action of the polymerizing and depolymerizing enzymes also remain to be established. The structural genes for the three key enzymes of PHB synthesis from acetyl coenzyme A in Alcaligenes eutrophus have been cloned, sequenced, and expressed in Escherichia coli. Polymer molecular weights appear to be species specific. The factors influencing the commercial choice of organism, substrate, and isolation process are discussed. The physiological functions of PHB as a reserve material and in symbiotic nitrogen fixation and its presence in bacterial plasma membranes and putative role in transformability and calcium signaling are also considered. PMID:2087222

Non-fouling surfaces produced by gas phase pulsed plasma polymerization of an ultra low molecular weight ethylene oxide containing monomer.

PubMed

Wu; Timmons; Jen; Molock

2000-10-01

The pulsed plasma polymerization of low molecular weight molecules containing only one (ethylene oxide vinyl ether) and two (diethylene oxide vinyl ether) ethylene oxide units were investigated. The surface density of EO units retained in the polymer films increases sharply with decreasing average power input during deposition, particularly at very low plasma duty cycles. The protein adsorption properties of these plasma synthesized polymer were investigated using 125I-labeled albumin and fibrinogen. Surprisingly effective, non-fouling surfaces were observed with films synthesized from the monomer containing two ethylene oxide units; however, the monomer containing only one EO unit gave surfaces that were not particularly effective in preventing protein adsorptions. The results obtained show that ultra short chain length PEO modified surfaces can be biologically non-fouling. This, in turn, has interesting consequences in terms of trying to identify the basic reason for the effectiveness of EO units in preventing biomolecule adsorptions on surfaces.

A versatile platform for precise synthesis of asymmetric molecular brush in one shot.

PubMed

Xu, Binbin; Feng, Chun; Huang, Xiaoyu

2017-08-24

Asymmetric molecular brushes emerge as a unique class of nanostructured polymers, while their versatile synthesis keeps a challenge for chemists. Here we show the synthesis of well-defined asymmetric molecular double-brushes comprising two different side chains linked to the same repeat unit along the backbone by one-pot concurrent atom transfer radical polymerization (ATRP) and Cu-catalyzed azide/alkyne cycloaddition (CuAAC) reaction. The double-brushes are based on a poly(Br-acrylate-alkyne) homopolymer possessing an alkynyl for CuAAC reaction and a 2-bromopropionate initiating group for ATRP in each repeat unit. The versatility of this one-shot approach is demonstrated by CuAAC reaction of alkynyl/poly(ethylene oxide)-N 3 and ATRP of various monomers. We also show the quantitative conversion of pentafluorophenyl ester groups to amide groups in side chains, allowing for the further fabrication of diverse building blocks. This work provides a versatile platform for facile synthesis of Janus-type double-brushes with structural and functional control, in a minimum number of reactions.Producing well-defined polymer compositions and structures facilitates their use in many different applications. Here the authors show the synthesis of well-defined asymmetric double-brushes by a one-pot concurrent atom transfer radical polymerization and Cu-catalyzed Click reaction.

Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice.

PubMed

Ma, Jianxin; Jackson, Scott A

2006-02-01

The abundance of repetitive DNA varies greatly across centromeres within an individual or between different organisms. To shed light on the molecular mechanisms of centromere repeat proliferation, we performed structural analysis of LTR-retrotransposons, mostly centromere retrotransposons of rice (CRRs), and phylogenetic analysis of CentO satellite repeats harbored in the core region of the rice chromosome 4 centromere (CEN4). The data obtained demonstrate that the CRRs in the centromeric region we investigated have been enriched more significantly by recent rounds of segmental duplication than by original integration of active elements, suggesting that segmental duplication is an important process for CRR accumulation in the centromeric region. Our results also indicate that segmental duplication of large arrays of satellite repeats is primarily responsible for the amplification of satellite repeats, contributing to rapid reshuffling of CentO satellites. Intercentromere satellite homogenization was revealed by genome-wide comparison of CentO satellite monomers. However, a 10-bp duplication present in nearly half of the CEN4 monomers was found to be completely absent in rice centromere 8 (CEN8), suggesting that CEN4 and CEN8 may represent two different stages in the evolution of rice centromeres. These observations, obtained from the only complex eukaryotic centromeres to have been completely sequenced thus far, depict the evolutionary dynamics of rice centromeres with respect to the nature, timing, and process of centromeric repeat amplification.

Electrically conductive alternating copolymers

DOEpatents

Aldissi, M.; Jorgensen, B.S.

1987-08-31

Polymers which are soluble in common organic solvents and are electrically conductive, but which also may be synthesized in such a manner that they become nonconductive. Negative ions from the electrolyte used in the electrochemical synthesis of a polymer are incorporated into the polymer during the synthesis and serve as a dopant. A further electrochemical step may be utilized to cause the polymer to be conductive. The monomer repeat unit is comprised of two rings, a pyrrole molecule joined to a thienyl group, or a furyl group, or a phenyl group. The individual groups of the polymers are arranged in an alternating manner. For example, the backbone arrangement of poly(furylpyrrole) is -furan-pyrrole-furan-pyrrole- furan-pyrrole. An alkyl group or phenyl group may be substituted for either or both of the hydrogen atoms of the pyrrole ring.

About the activity and selectivity of less well-known metathesis catalysts during ADMET polymerizations

PubMed Central

Mutlu, Hatice; Montero de Espinosa, Lucas; Türünç, Oĝuz

2010-01-01

Summary We report on the catalytic activity of commercially available Ru-indenylidene and “boomerang” complexes C1, C2 and C3 in acyclic diene metathesis (ADMET) polymerization of a fully renewable α,ω-diene. A high activity of these catalysts was observed for the synthesis of the desired renewable polyesters with molecular weights of up to 17000 Da, which is considerably higher than molecular weights obtained using the same monomer with previously studied catalysts. Moreover, olefin isomerization side reactions that occur during the ADMET polymerizations were studied in detail. The isomerization reactions were investigated by degradation of the prepared polyesters via transesterification with methanol, yielding diesters. These diesters, representing the repeat units of the polyesters, were then quantified by GC-MS. PMID:21160555

Polymerization on the rocks: negatively-charged alpha-amino acids

NASA Technical Reports Server (NTRS)

Hill, A. R. Jr; Bohler, C.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

Oligomers of the negatively-charged amino acids, glutamic acid, aspartic acid, and O-phospho-L-serine are adsorbed by hydroxylapatite and illite with affinities that increase with oligomer length. In the case of oligo-glutamic acids adsorbed on hydroxylapatite, addition of an extra residue results in an approximately four-fold increase in the strength of adsorption. Oligomers much longer than the 7-mer are retained tenaciously by the mineral. Repeated incubation of short oligo-glutamic acids adsorbed on hydroxylapatite or illite with activated monomer leads to the accumulation of oligomers at least 45 units long. The corresponding reactions of aspartic acid and O-phospho-L-serine on hydroxylapatite are less effective in generating long oligomers, while illite fails to accumulate substantial amounts of long oligomers of aspartic acid or of O-phospho-L-serine.

Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum

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

Chen, Mo; Himmel, Michael E.; Wilson, David B.

Molecular dynamics (MD) simulations were used to study substrate recognition by the family 48 exocellulase CelF from Clostridium cellulolyticum. It was hypothesized that residues around the entrance of the active site tunnel of this enzyme might serve to recognize and bind the substrate through an affinity for the cellulose monomer repeat unit, ..beta..-d-glucopyranose. Simulations were conducted of the catalytic domain of this enzyme surrounded by a concentrated solution of ..beta..-d-glucopyranose, and the full three-dimensional probability distribution for finding sugar molecules adjacent to the enzyme was calculated from the trajectory. A significant probability of finding the sugar stacked against the planarmore » faces of Trp 310 and Trp 312 at the entrance of the active site tunnel was observed.« less

Compositions containing poly ([gamma]glutamylcysteinyl)glycines

DOEpatents

Jackson, P.J.; Delhaize, E.; Robinson, N.J.; Unkefer, C.J.; Furlong, C.

1992-02-18

A method of removing heavy metals from aqueous solution, a composition of matter used in effecting the removal, and the apparatus used in effecting the removal are described. One or more of the polypeptides, poly ([gamma]glutamylcysteinyl)glycines, is immobilized on an inert material in particulate form. Upon contact with an aqueous solution containing heavy metals, the polypeptides sequester the metals, removing them from the solution. There is selectivity of poly ([gamma]glutamylcysteinyl)glycines having a particular number of monomer repeat units for particular metals. The polypeptides are easily regenerated by contact with a small amount of an organic acid, so that they can be used again to remove heavy metals from solution. This also results in the removal of the metals from the column in a concentrated form. 1 figs.

Genetic and metabolic engineering for microbial production of poly-γ-glutamic acid.

PubMed

Cao, Mingfeng; Feng, Jun; Sirisansaneeyakul, Sarote; Song, Cunjiang; Chisti, Yusuf

2018-05-28

Poly-γ-glutamic acid (γ-PGA) is a natural biopolymer of glutamic acid. The repeating units of γ-PGA may be derived exclusively from d-glutamic acid, or l-glutamic acid, or both. The monomer units are linked by amide bonds between the α-amino group and the γ-carboxylic acid group. γ-PGA is biodegradable, edible and water-soluble. It has numerous existing and emerging applications in processing of foods, medicines and cosmetics. This review focuses on microbial production of γ-PGA via genetically and metabolically engineered recombinant bacteria. Strategies for improving production of γ-PGA include modification of its biosynthesis pathway, enhancing the production of its precursor (glutamic acid), and preventing loss of the precursor to competing byproducts. These and other strategies are discussed. Heterologous synthesis of γ-PGA in industrial bacterial hosts that do not naturally produce γ-PGA is discussed. Emerging trends and the challenges affecting the production of γ-PGA are reviewed. Copyright © 2018. Published by Elsevier Inc.

Purification and partial elucidation of the structure of an antioxidant carbohydrate biopolymer from the probiotic bacterium Bacillus coagulans RK-02.

PubMed

Kodali, Vidya P; Perali, Ramu S; Sen, R

2011-08-26

An exopolysaccharide (EPS) was isolated from Bacillus coagulans RK-02 and purified by size exclusion chromatography. The purified, homogeneous EPS had an average molecular weight of ∼3 × 10⁴ Da by comparison with FITC-labeled dextran standards. In vivo evaluations showed that, like other reported polysaccharides, this EPS displayed significant antioxidant activity. FTIR spectroscopy analysis showed the presence of hydroxy, carboxy, and α-glycosidic linkages and a mannose residue. GC analysis indicated that the EPS was a heteropolymer composed of glucose, mannose, galactose, glucosamine, and fucose as monomeric constituent units. Partial elucidation of the structure of the carbohydrate biopolymer based on GC-MS and NMR analysis showed the presence of two unique sets of tetrasaccharide repeating units that have 1→3 and 1→6 glycosidic linkages. This is also the first report of a Gram-positive bacterial polysaccharide with both fucose as a sugar monomer and 1→3 and 1→6 glycosidic linkages in the molecular backbone.

Effect of various visible light photoinitiators on the polymerization and color of light-activated resins.

PubMed

Arikawa, Hiroyuki; Takahashi, Hideo; Kanie, Takahito; Ban, Seiji

2009-07-01

The purpose of this study was to investigate effects of various visible light photoinitiators on the polymerization efficiency and color of the light-activated resins. Four photoinitiators, including camphorquinone, phenylpropanedione, monoacrylphosphine oxide (TPO), and bisacrylphosphine oxide (Ir819), were used. Each photoinitiator was dissolved in a Bis-GMA and TEGDMA monomer mixture. Materials were polymerized using dental quartz-tungsten halogen lamp (QTH), plasma-ark lamp and blue LED light-curing units, and a custom-made violet LED light unit. The degree of monomer conversion and CIE L*a*b* color values of the resins were measured using a FTIR and spectral transmittance meter. The degree of monomer conversions of TPO- and Ir819-containing resins polymerized with the violet-LED unit were higher than camphorquinone-containing resin polymerized with the QTH light-curing unit. The lowest color values were observed for the TPO-containing resin. Our results indicate that the TPO photoinitiator and the violet-LED light unit may provide a useful and improved photopolymerization system for dental light-activated resins.

Hyperbranched Polycarbosilanes via Nucleophilic Substitution Reactions

NASA Astrophysics Data System (ADS)

Interrante, L.; Shen, Q.

Nucleophilic substitution reactions involving organomagnesium (Grignard) [1] and organolithium reagents have been used extensively for many years to form Si—C bonds (see Reaction Scheme 12.1). However, their use for the construction of hyperbranched polymers whose backbone contains, as a major structural component, silicon—carbon bonds, i.e., polycarbosilanes [2] is relatively more recent. (12.1) begin{array}{l} {{R}}_3 {{SiX + MR'}} to {{R}}_3 {{SiR' + MX}} \\ left({{{R,R' = alkyl}} {{or aryl;}} {{M = Mg(X),}} {{Li,}} {{Na}};{{X = halogen, OR''}}} right) \\ This chapter focuses on the application of such nucleophilic substitution reactions toward the synthesis of hyperbranched polycarbosilanes, with particular emphasis on those preparations that have resulted in relatively well characterized products. These syntheses are organized by the type of ABn monomer unit used (see Section 1.2), where A and B refer to the (C)X and (Si)Xn, respectively, functional ends of the monomer unit and where the nature of the coupling reaction leads to entirely or primarily Si—C bond formation. In most cases, these are “one-pot” reactions that employ monomers that bear halogen or alkoxy groups on the C and Si ends of the unit. Indeed, hyperbranched polycarbosilanes have been described, in general, as “obtained in one synthetic step via a random, one-pot polymerization of multifunctional monomers of AB n type” [2]. Treatment of the ABn monomer with either elemental Mg or an organolithium reagent, ideally (but not always) forms a complexed carbanion (the nucleophile) by reaction with the C-X end of the monomer unit, resulting in an intermediate of the type, (XxM)CSiXn, where M = Mg or Li, X = halogen or alkoxy, and x = 1 (Mg) or 0 (Li). Self-coupling of this reagent via reactions of the type shown in Reaction Scheme 12.1 leads to oligomeric and polymeric products that are connected primarily through Si—C bonds and yield an inorganic MXx by-product.

Organization of 5S rDNA in species of the fish Leporinus: two different genomic locations are characterized by distinct nontranscribed spacers.

PubMed

Martins, C; Galetti, P M

2001-10-01

To address understanding the organization of the 5S rRNA multigene family in the fish genome, the nucleotide sequence and organization array of 5S rDNA were investigated in the genus Leporinus, a representative freshwater fish group of South American fauna. PCR, subgenomic library screening, genomic blotting, fluorescence in situ hybridization, and DNA sequencing were employed in this study. Two arrays of 5S rDNA were identified for all species investigated, one consisting of monomeric repeat units of around 200 bp and another one with monomers of 900 bp. These 5S rDNA arrays were characterized by distinct NTS sequences (designated NTS-I and NTS-II for the 200- and 900-bp monomers, respectively); however, their coding sequences were nearly identical. The 5S rRNA genes were clustered in two chromosome loci, a major one corresponding to the NTS-I sites and a minor one corresponding to the NTS-II sites. The NTS-I sequence was variable among Leporinus spp., whereas the NTS-II was conserved among them and even in the related genus Schizodon. The distinct 5S rDNA arrays might characterize two 5S rRNA gene subfamilies that have been evolving independently in the genome.

Interaction of Huntingtin Exon-1 Peptides with Lipid-Based Micellar Nanoparticles Probed by Solution NMR and Q-Band Pulsed EPR.

PubMed

Ceccon, Alberto; Schmidt, Thomas; Tugarinov, Vitali; Kotler, Samuel A; Schwieters, Charles D; Clore, G Marius

2018-05-23

Lipid-based micellar nanoparticles promote aggregation of huntingtin exon-1 peptides. Here we characterize the interaction of two such peptides, htt NT Q  7 and htt NT Q  10 comprising the N-terminal amphiphilic domain of huntingtin followed by 7 and 10 glutamine repeats, respectively, with 8 nm lipid micelles using NMR chemical exchange saturation transfer (CEST), circular dichroism and pulsed Q-band EPR. Exchange between free and micelle-bound htt NT Q  n peptides occurs on the millisecond time scale with a K D ∼ 0.5-1 mM. Upon binding micelles, residues 1-15 adopt a helical conformation. Oxidation of Met 7 to a sulfoxide reduces the binding affinity for micelles ∼3-4-fold and increases the length of the helix by a further two residues. A structure of the bound monomer unit is calculated from the backbone chemical shifts of the micelle-bound state obtained from CEST. Pulsed Q-band EPR shows that a monomer-dimer equilibrium exists on the surface of the micelles and that the two helices of the dimer adopt a parallel orientation, thereby bringing two disordered polyQ tails into close proximity which may promote aggregation upon dissociation from the micelle surface.

Parkinson-causing α-synuclein missense mutations shift native tetramers to monomers as a mechanism for disease initiation

PubMed Central

Dettmer, Ulf; Newman, Andrew J.; Soldner, Frank; Luth, Eric S.; Kim, Nora C.; von Saucken, Victoria E.; Sanderson, John B.; Jaenisch, Rudolf; Bartels, Tim; Selkoe, Dennis

2015-01-01

β-Sheet-rich α-synuclein (αS) aggregates characterize Parkinson's disease (PD). αS was long believed to be a natively unfolded monomer, but recent work suggests it also occurs in α-helix-rich tetramers. Crosslinking traps principally tetrameric αS in intact normal neurons, but not after cell lysis, suggesting a dynamic equilibrium. Here we show that freshly biopsied normal human brain contains abundant αS tetramers. The PD-causing mutation A53T decreases tetramers in mouse brain. Neurons derived from an A53T patient have decreased tetramers. Neurons expressing E46K do also, and adding 1-2 E46K-like mutations into the canonical αS repeat motifs (KTKEGV) further reduces tetramers, decreases αS solubility and induces neurotoxicity and round inclusions. The other three fPD missense mutations likewise decrease tetramer:monomer ratios. The destabilization of physiological tetramers by PD-causing missense mutations and the neurotoxicity and inclusions induced by markedly decreasing tetramers suggest that decreased α-helical tetramers and increased unfolded monomers initiate pathogenesis. Tetramer-stabilizing compounds should prevent this. PMID:26076669

Competitive adsorption of surfactants and polymers at the free water surface. A computer simulation study of the sodium dodecyl sulfate-poly(ethylene oxide) system.

PubMed

Darvas, Mária; Gilányi, Tibor; Jedlovszky, Pál

2011-02-10

Competitive adsorption of a neutral amphiphilic polymer, namely poly(ethylene oxide) (PEO) and an ionic surfactant, i.e., sodium dodecyl sulfate (SDS), is investigated at the free water surface by computer simulation methods at 298 K. The sampled equilibrium configurations are analyzed in terms of the novel identification of the truly interfacial molecules (ITIM) method, by which the intrinsic surface of the aqueous phase (i.e., its real surface corrugated by the capillary waves) instead of an ideally flat surface approximating its macroscopic surface plane, can be taken into account. In the simulations, the surface density of SDS is gradually increased from zero up to saturation, and the structural, dynamical, and energetic aspects of the gradual squeezing out of the PEO chains from the surface are analyzed in detail. The obtained results reveal that this squeezing out occurs in a rather intricate way. Thus, in the presence of a moderate amount of SDS the majority of the PEO monomer units, forming long bulk phase loops in the absence of SDS, are attracted to the surface of the solution. This synergistic effect of SDS of moderate surface density on the adsorption of PEO is explained by two factors, namely by the electrostatic attraction between the ionic groups of the surfactant and the moderately polar monomer units of the polymer, and by the increase of the conformational entropy of the polymer chain in the presence of the surfactant. This latter effect, thought to be the dominant one among the above two factors, also implies the formation of similar polymer/surfactant complexes at the interface than what are known to exist in the bulk phase of the solution. Finally, in the presence of a large amount of SDS the more surface active surfactant molecules gradually replace the PEO monomer units at the interfacial positions, and squeezing out the PEO molecules from the surface in a monomer unit by monomer unit manner.

Biochemical transformation of lignin for deriving valued commodities from lignocellulose

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

Gall, Daniel L.; Ralph, John; Donohue, Timothy J.

The biochemical properties of lignin present major obstacles to deriving societally beneficial entities from lignocellulosic biomass, an abundant and renewable feedstock. Similar to other biopolymers such as polysaccharides, polypeptides, and ribonucleic acids, lignin polymers are derived from multiple types of monomeric units. However, lignin’s renowned recalcitrance is largely attributable to its racemic nature and the variety of covalent inter-unit linkages through which its aromatic monomers are linked. Indeed, unlike other biopolymers whose monomers are consistently inter-linked by a single type of covalent bond, the monomeric units in lignin are linked via non-enzymatic, combinatorial radical coupling reactions that give rise tomore » a variety of inter-unit covalent bonds in mildly branched racemic polymers. Yet, despite the chemical complexity and stability of lignin, significant strides have been made in recent years to identify routes through which valued commodities can be derived from it. This paper discusses emerging biological and biochemical means through which degradation of lignin to aromatic monomers can lead to the derivation of commercially valuable products.« less

Biochemical transformation of lignin for deriving valued commodities from lignocellulose

DOE PAGES

Gall, Daniel L.; Ralph, John; Donohue, Timothy J.; ...

2017-03-24

The biochemical properties of lignin present major obstacles to deriving societally beneficial entities from lignocellulosic biomass, an abundant and renewable feedstock. Similar to other biopolymers such as polysaccharides, polypeptides, and ribonucleic acids, lignin polymers are derived from multiple types of monomeric units. However, lignin’s renowned recalcitrance is largely attributable to its racemic nature and the variety of covalent inter-unit linkages through which its aromatic monomers are linked. Indeed, unlike other biopolymers whose monomers are consistently inter-linked by a single type of covalent bond, the monomeric units in lignin are linked via non-enzymatic, combinatorial radical coupling reactions that give rise tomore » a variety of inter-unit covalent bonds in mildly branched racemic polymers. Yet, despite the chemical complexity and stability of lignin, significant strides have been made in recent years to identify routes through which valued commodities can be derived from it. This paper discusses emerging biological and biochemical means through which degradation of lignin to aromatic monomers can lead to the derivation of commercially valuable products.« less

Self-assembly of an amphiphilic macromolecule under spherical confinement: An efficient route to generate hollow nanospheres

NASA Astrophysics Data System (ADS)

Glagoleva, A. A.; Vasilevskaya, V. V.; Yoshikawa, K.; Khokhlov, A. R.

2013-12-01

In general, bio-macromolecules are composed of hydrophilic and hydrophobic moieties and are confined within small cavities, such as cell membranes and intracellular organelles. Here, we studied the self-organization of macromolecules having groups with different affinities to solvents under spherical nano-scale confinement by means of computer modeling. It is shown that depending on the interaction parameters of monomer units composed of side- and main-chain monomer groups along a single linear macromolecule and on cavity size, such amphiphilic polymers undergo the conformational transitions between hollow nanospheres, rod-like and folded cylindrical structures, and a necklace conformation with and without a particular ordering of beads. The diagram of the conformations in the variables the incompatibility parameter of monomer units and the cavity radius is constructed.

Characterization and serology of the matrix protein from a nuclear-polyhedrosis virus of Trichoplusia ni before and after degradation by an endogenous proteinase.

PubMed

Eppstein, D A; Thoma, J A

1977-11-01

The intact matrix protein from a nuclear-polyhedrosis virus of the cabbage looper (Trichoplusia ni), isolated after inhibition of an endogenous serine-type proteinase, was further purified by molecular-sieve chromatography. The matrix protein was associated with carbohydrate moieties, and the carbohydrate content was determined for the two major peptides isolated after proteolysis by the endogenous proteinase. The association-dissociation interactions of the intact and proteinase-hydrolysed monomer units were characterized at high and low pH. At pH1.9, proteinase-degraded matrix protein dissociated into two different peptide fractions, FI and FII. Fraction FII, a single peptide of 9400 daltons, comprised one-third of the monomer unit of 28 000 daltons. At pH9.5, the degraded peptides were tightly associated in units equivalent to the intact monomer. These monomer equivalents associated to form a series of interconverting aggregates. The predominant aggregate sedimented at 11S and had a mol.wt greater than or equal to 200 000. Two non-cross-reacting antigens were present in the aggregate mixture. The presence of these two antigens does not reflect the presence of two different matrix proteins; rather, the expression of the antigens correlates with the degree of aggregation of the matrix protein.

Self-assembly in densely grafted macromolecules with amphiphilic monomer units: diagram of states.

PubMed

Lazutin, A A; Vasilevskaya, V V; Khokhlov, A R

2017-11-22

By means of computer modelling, the self-organization of dense planar brushes of macromolecules with amphiphilic monomer units was addressed and their state diagram was constructed. The diagram of states includes the following regions: disordered position of monomer units with respect to each other, strands composed of a few polymer chains and lamellae with different domain spacing. The transformation of lamellae structures with different domain spacing occurred within the intermediate region and could proceed through the formation of so-called parking garage structures. The parking garage structure joins the lamellae with large (on the top of the brushes) and small (close to the grafted surface) domain spacing, which appears like a system of inclined locally parallel layers connected with each other by bridges. The parking garage structures were observed for incompatible A and B groups in selective solvents, which result in aggregation of the side B groups and dense packing of amphiphilic macromolecules in the restricted volume of the planar brushes.

Fluorescent Polymer Incorporating Triazolyl Coumarin Units for Cu2+ Detection via Planarization of Ict-Based Fluorophore

PubMed Central

Ngororabanga, Jean Marie Vianney; Du Plessis, Jacolien; Mama, Neliswa

2017-01-01

A novel fluorescent polymer with pendant triazolyl coumarin units was synthesized through radical polymerization. The polymer showed reasonable sensitivity and selectivity towards Cu2+ in acetonitrile in comparison to other tested metal ions with a significant quenching effect on fluorescence and blue shifting in the range of 20 nm. The blue shift was assigned to the conformation changes of the diethylamino group from the coumarin moiety which led to planarization of the triazolyl coumarin units. The possible binding modes for Cu2+ towards the polymer were determined through the comparison of the emission responses of the polymer, starting vinyl monomer and reference compound, and the triazole ring was identified as one of the possible binding sites for Cu2+. The detection limits of the polymer and vinyl monomer towards Cu2+ were determined from fluorescence titration experiments and a higher sensitivity (35 times) was observed for the polymer compared with its starting monomer. PMID:28867764

Fluorescent Polymer Incorporating Triazolyl Coumarin Units for Cu2+ Detection via Planarization of Ict-Based Fluorophore.

PubMed

Ngororabanga, Jean Marie Vianney; Du Plessis, Jacolien; Mama, Neliswa

2017-08-30

A novel fluorescent polymer with pendant triazolyl coumarin units was synthesized through radical polymerization. The polymer showed reasonable sensitivity and selectivity towards Cu 2+ in acetonitrile in comparison to other tested metal ions with a significant quenching effect on fluorescence and blue shifting in the range of 20 nm. The blue shift was assigned to the conformation changes of the diethylamino group from the coumarin moiety which led to planarization of the triazolyl coumarin units. The possible binding modes for Cu 2+ towards the polymer were determined through the comparison of the emission responses of the polymer, starting vinyl monomer and reference compound, and the triazole ring was identified as one of the possible binding sites for Cu 2+ . The detection limits of the polymer and vinyl monomer towards Cu 2+ were determined from fluorescence titration experiments and a higher sensitivity (35 times) was observed for the polymer compared with its starting monomer.

Silyl Ketene Acetals/B(C₆F₅)₃ Lewis Pair-Catalyzed Living Group Transfer Polymerization of Renewable Cyclic Acrylic Monomers.

PubMed

Hu, Lu; Zhao, Wuchao; He, Jianghua; Zhang, Yuetao

2018-03-15

This work reveals the silyl ketene acetal (SKA)/B(C₆F₅)₃ Lewis pair-catalyzed room-temperature group transfer polymerization (GTP) of polar acrylic monomers, including methyl linear methacrylate (MMA), and the biorenewable cyclic monomers γ-methyl-α-methylene-γ-butyrolactone (MMBL) and α-methylene-γ-butyrolactone (MBL) as well. The in situ NMR monitored reaction of SKA with B(C₆F₅)₃ indicated the formation of Frustrated Lewis Pairs (FLPs), although it is sluggish for MMA polymerization, such a FLP system exhibits highly activity and living GTP of MMBL and MBL. Detailed investigations, including the characterization of key reaction intermediates, polymerization kinetics and polymer structures have led to a polymerization mechanism, in which the polymerization is initiated with an intermolecular Michael addition of the ester enolate group of SKA to the vinyl group of B(C₆F₅)₃-activated monomer, while the silyl group is transferred to the carbonyl group of the B(C₆F₅)₃-activated monomer to generate the single-monomer-addition species or the active propagating species; the coordinated B(C₆F₅)₃ is released to the incoming monomer, followed by repeated intermolecular Michael additions in the subsequent propagation cycle. Such neutral SKA analogues are the real active species for the polymerization and are retained in the whole process as confirmed by experimental data and the chain-end analysis by matrix-assisted laser desorption/ionization time of flight mass spectroscopy (MALDI-TOF MS). Moreover, using this method, we have successfully synthesized well-defined PMMBL- b -PMBL, PMMBL- b -PMBL- b -PMMBL and random copolymers with the predicated molecular weights ( M n ) and narrow molecular weight distribution (MWD).

Molecular and chromosomal evidence for allopolyploidy in soybean.

PubMed

Gill, Navdeep; Findley, Seth; Walling, Jason G; Hans, Christian; Ma, Jianxin; Doyle, Jeff; Stacey, Gary; Jackson, Scott A

2009-11-01

Recent studies have documented that the soybean (Glycine max) genome has undergone two rounds of large-scale genome and/or segmental duplication. To shed light on the timing and nature of these duplication events, we characterized and analyzed two subfamilies of high-copy centromeric satellite repeats, CentGm-1 and CentGm-2, using a combination of computational and molecular cytogenetic approaches. These two subfamilies of satellite repeats mark distinct subsets of soybean centromeres and, in at least one case, a pair of homologs, suggesting their origins from an allopolyploid event. The satellite monomers of each subfamily are arranged in large tandem arrays, and intermingled monomers of the two subfamilies were not detected by fluorescence in situ hybridization on extended DNA fibers nor at the sequence level. This indicates that there has been little recombination and homogenization of satellite DNA between these two sets of centromeres. These satellite repeats are also present in Glycine soja, the proposed wild progenitor of soybean, but could not be detected in any other relatives of soybean examined in this study, suggesting the rapid divergence of the centromeric satellite DNA within the Glycine genus. Together, these observations provide direct evidence, at molecular and chromosomal levels, in support of the hypothesis that the soybean genome has experienced a recent allopolyploidization event.

Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker.

PubMed

Quinn, J S; Guglich, E; Seutin, G; Lau, R; Marsolais, J; Parna, L; Boag, P T; White, B N

1992-02-01

The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa.

Biodiversity of Exopolysaccharides Produced by Streptococcus thermophilus Strains Is Reflected in Their Production and Their Molecular and Functional Characteristics

PubMed Central

Vaningelgem, Frederik; Zamfir, Medana; Mozzi, Fernanda; Adriany, Tom; Vancanneyt, Marc; Swings, Jean; De Vuyst, Luc

2004-01-01

Twenty-six lactic acid bacterium strains isolated from European dairy products were identified as Streptococcus thermophilus and characterized by bacterial growth and exopolysaccharide (EPS)-producing capacity in milk and enriched milk medium. In addition, the acidification rates of the different strains were compared with their milk clotting behaviors. The majority of the strains grew better when yeast extract and peptone were added to the milk medium, although the presence of interfering glucomannans was shown, making this medium unsuitable for EPS screening. EPS production was found to be strain dependent, with the majority of the strains producing between 20 and 100 mg of polymer dry mass per liter of fermented milk medium. Furthermore, no straightforward relationship between the apparent viscosity and EPS production could be detected in fermented milk medium. An analysis of the molecular masses of the isolated EPS by gel permeation chromatography revealed a large variety, ranging from 10 to >2,000 kDa. A distinction could be made between high-molecular-mass EPS (>1,000 kDa) and low-molecular-mass EPS (<1,000 kDa). Based on the molecular size of the EPS, three groups of EPS-producing strains were distinguished. Monomer analysis of the EPS by high-performance anion-exchange chromatography with amperometric detection was demonstrated to be a fast and simple method. All of the EPS from the S. thermophilus strains tested were classified into six groups according to their monomer compositions. Apart from galactose and glucose, other monomers, such as (N-acetyl)galactosamine, (N-acetyl)glucosamine, and rhamnose, were also found as repeating unit constituents. Three strains were found to produce EPS containing (N-acetyl)glucosamine, which to our knowledge was never found before in an EPS from S. thermophilus. Furthermore, within each group, differences in monomer ratios were observed, indicating possible novel EPS structures. Finally, large differences between the consistencies of EPS solutions from five different strains were assigned to differences in their molecular masses and structures. PMID:14766570

Polyazomethines containing trifluoromethylbenzene units

NASA Technical Reports Server (NTRS)

Bryant, Robert G. (Inventor)

1995-01-01

Soluble, amorphous, aromatic polyazomethine polymers and copolymers were prepared by reacting a dialdehyde monomer with a diamine monomer containing trifluoromethylbenzene and various combinations thereof in a solvent, such as N,N-dimethylacetamide. The reaction was heated to reflux yielding a polyazomethine which, after cooling to room temperature, was precipitated. These polymers and copolymers may be used to make films, coatings, composites and adhesives.

Polyazomethines containing trifluoromethylbenzene units

NASA Technical Reports Server (NTRS)

Bryant, Robert G. (Inventor)

1996-01-01

Soluble, amorphous, aromatic polyazomethine polymers and copolymers were prepared by reacting a dialdehyde monomer with a diamine monomer containing trifluoromethylbenzene and various combinations thereof in a solvent, such as N,N-dimethylacetamide. The reaction was heated to reflux yielding a polyazomethine which, after cooling to room temperature, was precipitated. These polymers and copolymers may be used to make films, coatings, composites and adhesives.

Near-monodisperse sodium polymethacrylates: characterization by linear salt gradient anion-exchange chromatography

PubMed

Freydank; Krasia; Tiddy; Patrickios

2000-05-01

A family of six near-monodisperse homopolymers of sodium methacrylate (Mn = 1100, 3200, 5500, 7200, 14100, and 21000) is characterized by linear salt gradient anion-exchange chromatography. Although the retention times depend on the initial and final salt concentrations of the gradient, they are almost independent of the molecular weight of poly(sodium methacrylate). This suggests that anion-exchange chromatography is incapable of resolving mixtures of a given polyelectrolyte to their components of various molecular weights, and it is therefore impossible to identify the polydispersity of such a sample using this method. The independence of the retention times from molecular weight is also predicted by a theory based on stoichiometric mass-action ion-exchange. Using this theory and our experimental retention times, the equilibrium anion-exchange constant and the corresponding Gibbs free energy of anion-exchange of the monomer repeat unit are calculated to be around 2.1 and -1.8 kJ/mol, respectively.

Enhanced photophysics of conjugated polymers

DOEpatents

Chen, Liaohai [Argonne, IL; Xu, Su [Santa Clara, CA; McBranch, Duncan [Santa Fe, NM; Whitten, David [Santa Fe, NM

2003-05-27

The addition of oppositely charged surfactant to fluorescent ionic conjugated polymer forms a polymer-surfactant complex that exhibits at least one improved photophysical property. The conjugated polymer is a fluorescent ionic polymer that typically has at least one ionic side chain or moiety that interacts with the specific surfactant selected. The photophysical property improvements may include increased fluorescence quantum efficiency, wavelength-independent emission and absorption spectra, and more stable fluorescence decay kinetics. The complexation typically occurs in a solution of a polar solvent in which the polymer and surfactant are soluble, but it may also occur in a mixture of solvents. The solution is commonly prepared with a surfactant molecule:monomer repeat unit of polymer ratio ranging from about 1:100 to about 1:1. A polymer-surfactant complex precipitate is formed as the ratio approaches 1:1. This precipitate is recoverable and usable in many forms.

Flame retardant polyphosphazenes

NASA Technical Reports Server (NTRS)

Paciorek, K. L.; Karle, D. W.; Kratzer, R. H.

1976-01-01

Three processes for the preparation of polyphosphazenes were investigated: (1) the reaction of bisphosphines with diazides, (2) the condensation of bisdichlorophosphoranes with diamines; and (3) the treatment of bisphosphines with diamines in the presence of carbon tetrachloride followed by base dehydrohalogenation. All products obtained were of low molecular weight; the degree of polymerization did not exceed twelve repeating units. However, several compositions exhibited good thermal stability. No weight loss was observed up to 390 C when heated in air at 5 C/min. Treatment of bisphosphines with either an excess of a diazide or an excess of a diamine in the presence of carbon tetrachloride resulted in the production of difunctional phosphazenes which were respectively, azido and amino terminated. The reaction of these azido terminated extended monomers with bisphosphines did not produce high molecular weight materials. The bis-aminophosphazene prepared for the first time under this contract was successfully incorporated into a polyimide.

Montmorillonite, Oligonucleotides, RNA and Origin of Life

NASA Astrophysics Data System (ADS)

Ertem, Gözen

2004-12-01

Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer <3-mer <4-mer ... <7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).

Montmorillonite, oligonucleotides, RNA and origin of life

NASA Technical Reports Server (NTRS)

Ertem, Gozen

2004-01-01

Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer < 3-mer < 4-mer ... < 7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).

Development and validation of a sensitive UPLC-MS/MS instrumentation and alkaline nitrobenzene oxidation method for the determination of lignin monomers in wheat straw.

PubMed

Zheng, Mengjing; Gu, Shubo; Chen, Jin; Luo, Yongli; Li, Wenqian; Ni, Jun; Li, Yong; Wang, Zhenlin

2017-06-15

A method to determine the lignin monomers (p-hydroxybenzaldehyde, vanillin and syringaldehyde) in plant cell wall of wheat internode was developed and validated using a high-throughput nitrobenzene oxidation step and ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) for quantification. UPLC analyses were carried out using an reversed phase C 18 column (ACQUITY UPLC BEH, 1.7μm, 2.1×100mm) and gradient elution with water and acetonitrile. This method was completely validated in terms of analyzing speed, linearity, sensitivity, limits of detection (LODs) and limits of quantification (LOQs).The three lignin monomers were successfully separated within 6min and only 2min were required to regain its equilibrium. The method linearity with regression coefficients values (R2) greater than 0.997. Additionally, LODs ranged from 0.21 to 0.89μgL -1 and LOQs ranged from 0.69 to 2.95μgL -1 . The applicability of this analytical approach for determining the three lignin monomers was confirmed by the successful analysis of real samples of wheat stem internodes. The nitrobenzene oxidation method was used for the analysis of lignin monomers. We have optimized the treatment temperature (170°C, 1h) and realized the high-throughput using the microwave digestion instrument. Recovery of this extraction method ranged from 68.4% to 77.7%. The analysis result showed that the guaiacyl unit (G) was the major component of lignin and there was a higher content of the syringyl unit (S) than that of the hydroxybenzyl unit (H). Copyright © 2017. Published by Elsevier B.V.

Single chain technology: Toward the controlled synthesis of polymer nanostructures

NASA Astrophysics Data System (ADS)

Lyon, Christopher

A technique for fabricating advanced polymer nanostructures enjoying recent popularity is the collapse or folding of single polymer chains in highly dilute solution mediated by intramolecular cross-linking. We term the resultant structures single-chain nanoparticles (SCNP). This technique has proven particularly valuable in the synthesis of nanomaterials on the order of 5 -- 20 nm. Many different types of covalent and non-covalent chemistries have been used to this end. This dissertation investigates the use of so-called single-chain technology to synthesize nanoparticles using modular techniques that allow for easy incorporation of functionality or special structural or characteristic features. Specifically, the synthesis of linear polymers functionalized with pendant monomer units and the subsequent intramolecular polymerization of these monomer units is discussed. In chapter 2, the synthesis of SCNP using alternating radical polymerization is described. Polymers functionalized with pendant styrene and stilbene groups are synthesized via a modular post-polymerization Wittig reaction. These polymers were exposed to radical initiators in the presence (and absence) of maleic anhydride and other electron deficient monomers in order to form intramolecular cross-links. Chapter 3 discusses templated acyclic diene metathesis (ADMET) polymerization using single-chain technology, starting with the controlled ring-opening polymerization of a glycidyl ether functionalized with an ADMET monomer. This polymer was then exposed to Grubbs' catalyst to polymerize the ADMET monomer units. The ADMET polymer was hydrolytically cleaved from the template and separated. Upon characterization, it was found that the daughter ADMET polymer had a similar degree of polymerization, but did not retain the low dispersity of the template. Chapter 4 details the synthesis of aldehyde- and diol-functionalized polymers toward the synthesis of SCNP containing dynamic, acid-degradable acetal cross-links. SCNP fabrication with these materials is beyond the scope of this dissertation.

Structural Analysis of Succinoglycan Oligosaccharides from Sinorhizobium meliloti Strains with Different Host Compatibility Phenotypes

PubMed Central

Wood, Karl; Reuhs, Bradley L.

2013-01-01

Sinorhizobium meliloti NRG247 has a Fix+ phenotype on Medicago truncatula A20 and is Fix− on M. truncatula A17, and the phenotype is reversed with S. meliloti NRG185. As the succinoglycan was shown to impact host specificity, an analysis of the succinoglycan oligosaccharides produced by each strain was conducted. The symbiotically active succinoglycan trimeric oligosaccharides (STOs) from the two S. meliloti strains were compared by chromatography and mass spectrometry, and the analysis of the S. meliloti NRG247 oligosaccharides showed that this strain produces an abundance of STO trimer 1 (T1), containing no succinate (i.e., three nonsuccinylated repeats), yet the low-molecular-weight pool contained no nonsuccinylated monomers (potential repeats). This showed that STO T1 is likely to be the active signal on M. truncatula A20 and that the biosynthesis of the STOs is not a random polymerization of the monomer population. The results also suggest that the fully succinylated STO T7 is required for the infection of M. truncatula A17. PMID:23457246

Facile and high-efficient immobilization of histidine-tagged multimeric protein G on magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Lee, Jiho; Chang, Jeong Ho

2014-12-01

This work reports the high-efficient and one-step immobilization of multimeric protein G on magnetic nanoparticles. The histidine-tagged (His-tag) recombinant multimeric protein G was overexpressed in Escherichia coli BL21 by the repeated linking of protein G monomers with a flexible linker. High-efficient immobilization on magnetic nanoparticles was demonstrated by two different preparation methods through the amino-silane and chloro-silane functionalization on silica-coated magnetic nanoparticles. Three kinds of multimeric protein G such as His-tag monomer, dimer, and trimer were tested for immobilization efficiency. For these tests, bicinchoninic acid (BCA) assay was employed to determine the amount of immobilized His-tag multimeric protein G. The result showed that the immobilization efficiency of the His-tag multimeric protein G of the monomer, dimer, and trimer was increased with the use of chloro-silane-functionalized magnetic nanoparticles in the range of 98% to 99%, rather than the use of amino-silane-functionalized magnetic nanoparticles in the range of 55% to 77%, respectively.

Visualization of information with an established order

DOEpatents

Wong, Pak Chung [Richland, WA; Foote, Harlan P [Richmond, WA; Thomas, James J [Richland, WA; Wong, Kwong-Kwok [Sugar Land, TX

2007-02-13

Among the embodiments of the present invention is a system including one or more processors operable to access data representative of a biopolymer sequence of monomer units. The one or more processors are further operable to establish a pattern corresponding to at least one fractal curve and generate one or more output signals corresponding to a number of image elements each representative of one of the monomer units. Also included is a display device responsive to the one or more output signals to visualize the biopolymer sequence by displaying the image elements in accordance with the pattern.

Chemical synthesis of chiral conducting polymers

DOEpatents

Wang, Hsing-Lin [Los Alamos, NM; Li, Wenguang [Los Alamos, NM

2009-01-13

An process of forming a chiral conducting polymer, e.g., polyaniline, is provided including reacting a monomer, e.g., an aniline monomer, in the presence of a chiral dopant acid to produce a first reaction mixture by addition of a solution including a first portion of an oxidizing agent, the first portion of oxidizing agent characterized as insufficient to allow complete reaction of the monomer, and further reacting the first reaction mixture in the presence of the chiral dopant acid by addition of a solution including a second portion of the oxidizing agent, the second portion of oxidizing agent characterized as insufficient to allow complete reaction of the monomer, and repeating the reaction by addition of further portions of the oxidizing agent until the monomer reaction is complete to produce a chiral conducting polymer, e.g., polyaniline. A preferred process includes addition of a catalyst during the reaction, the catalyst selected from among the group consisting of phenylene diamine, aniline oligomers and amino-capped aniline oligomers and metal salts.The processes of the present invention further provide a resultant polyaniline product having a chirality level defined by a molar ellipticity of from about 40.times.10.sup.3 degree-cm.sup.2/decimole to about 700.times.10.sup.3 degree-cm.sup.2/decimole. The processes of the present invention further provide a resultant polyaniline product having a nanofiber structure with a diameter of from about 30 nanometers to about 120 nanometers and from about 1 micron to about 5 microns in length.

Donor polymer design enables efficient non-fullerene organic solar cells

PubMed Central

Li, Zhengke; Jiang, Kui; Yang, Guofang; Lai, Joshua Yuk Lin; Ma, Tingxuan; Zhao, Jingbo; Ma, Wei; Yan, He

2016-01-01

To achieve efficient organic solar cells, the design of suitable donor–acceptor couples is crucially important. State-of-the-art donor polymers used in fullerene cells may not perform well when they are combined with non-fullerene acceptors, thus new donor polymers need to be developed. Here we report non-fullerene organic solar cells with efficiencies up to 10.9%, enabled by a novel donor polymer that exhibits strong temperature-dependent aggregation but with intentionally reduced polymer crystallinity due to the introduction of a less symmetric monomer unit. Our comparative study shows that an analogue polymer with a C2 symmetric monomer unit yields highly crystalline polymer films but less efficient non-fullerene cells. Based on a monomer with a mirror symmetry, our best donor polymer exhibits reduced crystallinity, yet such a polymer matches better with small molecular acceptors. This study provides important insights to the design of donor polymers for non-fullerene organic solar cells. PMID:27782112

Crystallization and preliminary crystallographic investigation of a low-pH native insulin monomer with flexible behaviour.

PubMed

Zhang, Youshang; Whittingham, Jean L; Turkenburg, Johan P; Dodson, Eleanor J; Brange, Jens; Dodson, G Guy

2002-01-01

Insulin naturally aggregates as dimers and hexamers, whose structures have been extensively analysed by X-ray crystallography. Structural determination of the physiologically relevant insulin monomer, however, is an unusual challenge owing to the difficulty in finding solution conditions in which the concentration of insulin is high enough for crystallization yet the molecule remains monomeric. By utilizing solution conditions known to inhibit insulin assembly, namely 20% acetic acid, crystals of insulin in the monomeric state have been obtained. The crystals are strongly diffracting and a data set extending to 1.6 A has recently been collected. The crystals nominally belong to the space group I422, with unit-cell parameters a = b = 57.80, c = 54.61 A, giving rise to one molecule in the asymmetric unit. Preliminary electron-density maps show that whilst most of the insulin monomer is well ordered and similar in conformation to other insulin structures, parts of the B-chain C-terminus main chain adopt more than one conformation.

Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior

PubMed Central

Golji, Javad; Collins, Robert; Mofrad, Mohammad R. K.

2009-01-01

α-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks. As a crosslinker in the stressed cytoskeleton, α-actinin can retain conformation, function, and strength. α-Actinin has an actin binding domain and a calmodulin homology domain separated by a long rod domain. Using molecular dynamics and normal mode analysis, we suggest that the α-actinin rod domain has flexible terminal regions which can twist and extend under mechanical stress, yet has a highly rigid interior region stabilized by aromatic packing within each spectrin repeat, by electrostatic interactions between the spectrin repeats, and by strong salt bridges between its two anti-parallel monomers. By exploring the natural vibrations of the α-actinin rod domain and by conducting bending molecular dynamics simulations we also predict that bending of the rod domain is possible with minimal force. We introduce computational methods for analyzing the torsional strain of molecules using rotating constraints. Molecular dynamics extension of the α-actinin rod is also performed, demonstrating transduction of the unfolding forces across salt bridges to the associated monomer of the α-actinin rod domain. PMID:19436721

Genome-wide characterization of monomeric transcriptional regulators in Mycobacterium tuberculosis.

PubMed

Feng, Lipeng; Chen, Zhenkang; Wang, Zhongwei; Hu, Yangbo; Chen, Shiyun

2016-05-01

Gene transcription catalysed by RNA polymerase is regulated by transcriptional regulators, which play central roles in the control of gene transcription in both eukaryotes and prokaryotes. In regulating gene transcription, many regulators form dimers that bind to DNA with repeated motifs. However, some regulators function as monomers, but their mechanisms of gene expression control are largely uncharacterized. Here we systematically characterized monomeric versus dimeric regulators in the tuberculosis causative agent Mycobacterium tuberculosis. Of the >160 transcriptional regulators annotated in M. tuberculosis, 154 transcriptional regulators were tested, 22 % probably act as monomers and most are annotated as hypothetical regulators. Notably, all members of the WhiB-like protein family are classified as monomers. To further investigate mechanisms of monomeric regulators, we analysed the actions of these WhiB proteins and found that the majority interact with the principal sigma factor σA, which is also a monomeric protein within the RNA polymerase holoenzyme. Taken together, our study for the first time globally classified monomeric regulators in M. tuberculosis and suggested a mechanism for monomeric regulators in controlling gene transcription through interacting with monomeric sigma factors.

Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain

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

Nithianantham, Stanley; Xu, Minghua; Yamada, Mitsunori

2009-04-07

Many bacterial appendages have filamentous structures, often composed of repeating monomers assembled in a head-to-tail manner. The mechanisms of such linkages vary. We report here a novel protein oligomerization motif identified in the FadA adhesin from the Gram-negative bacterium Fusobacterium nucleatum. The 2.0 {angstrom} crystal structure of the secreted form of FadA (mFadA) reveals two antiparallel {alpha}-helices connected by an intervening 8-residue hairpin loop. Leucine-leucine contacts play a prominent dual intra- and intermolecular role in the structure and function of FadA. First, they comprise the main association between the two helical arms of the monomer; second, they mediate the head-to-tailmore » association of monomers to form the elongated polymers. This leucine-mediated filamentous assembly of FadA molecules constitutes a novel structural motif termed the 'leucine chain.' The essential role of these residues in FadA is corroborated by mutagenesis of selected leucine residues, which leads to the abrogation of oligomerization, filament formation, and binding to host cells.« less

Chemical synthesis of chiral conducting polymers

DOEpatents

Wang, Hsing-Lin; Li, Wenguang

2006-07-11

An process of forming a chiral conducting polymer, e.g., polyaniline, is provided including reacting a monomer, e.g., an aniline monomer, in the presence of a chiral dopant acid to produce a first reaction mixture by addition of a solution including a first portion of an oxidizing agent, the first portion of oxidizing agent characterized as insufficient to allow complete reaction of the monomer, and further reacting the first reaction mixture in the presence of the chiral dopant acid by addition of a solution including a second portion of the oxidizing agent, the second portion of oxidizing agent characterized as insufficient to allow complete reaction of the monomer, and repeating the reaction by addition of further portions of the oxidizing agent until the monomer reaction is complete to produce a chiral conducting polymer, e.g., polyaniline. A preferred process includes addition of a catalyst during the reaction, the catalyst selected from among the group consisting of phenylene diamine, aniline oligomers and amino-capped aniline oligomers and metal salts. The processes of the present invention further provide a resultant polyaniline product having a chirality level defined by a molar ellipticity of from about 40.times.10³ degree-cm²/decimole to about 700.times.10³ degree-cm²/decimole. The processes of the present invention further provide a resultant polyaniline product having a nanofiber structure with a diameter of from about 30 nanometers to about 120 nanometers and from about 1 micron to about 5 microns in length.

Water Transport in Bicontinuous, Phase-Separated Membranes Made from Reactive Block Copolymers

DTIC Science & Technology

2014-12-01

polyurethane foam impregnated with activated carbon, a design that allows perspiration to evaporate while chemical agents are adsorbed onto the activated... dispersed into a minimal volume (4–5 drops) of ethanol. The catalyst solution was then added to the polymer solution while stirring rapidly. The solution...substituted styrene monomer; one interior block with units of other styrene monomers which have been sulfonated; non- dispersible and solid in water

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide

NASA Technical Reports Server (NTRS)

Kanavarioti, A.; Bernasconi, C. F.; Alberas, D. J.; Baird, E. E.

1993-01-01

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.

Risk Assessment of residual monomer migrating from acrylic polymers and causing Allergic Contact Dermatitis during normal handling and use.

PubMed

Pemberton, Mark A; Lohmann, Barbara S

2014-08-01

Acrylic, Poly Methyl Methacrylate (PMMA) based polymers are found in many industrial, professional and consumer products and are of low toxicity, but do contain very low levels of residual monomers and process chemicals that can leach out during handling and use. Methyl Methacrylate, the principle monomer is of low toxicity, but is a recognized weak skin sensitizer. The risk of induction of contact allergy in consumers was determined using a method based upon the Exposure-based Quantitative Risk Assessment approach developed for fragrance ingredients. The No Expected Sensitization Induction Level (NESIL) was based on the threshold to induction of sensitization (EC3) in the Local Lymph Node Assay (LLNA) since no Human Repeat Insult Patch Test (HRIPT) data were available. Categorical estimation of Consumer Exposure Level was substituted with a worst case assumption based upon the quantitative determination of MMA monomer migration into simulants. Application of default and Chemical-Specific Adjustment Factors results in a Risk Characterization Ratio (RCR) of 10,000 and a high Margin of Safety for induction of Allergic Contact Dermatitis (ACD) in consumers handling polymers under conservative exposure conditions. Although there are no data available to derive a RCR for elicitation of ACD it is likely to be lower than that for induction. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

Biofilm formation in an experimental water distribution system: the contamination of non-touch sensor taps and the implication for healthcare.

PubMed

Moore, Ginny; Stevenson, David; Thompson, Katy-Anne; Parks, Simon; Ngabo, Didier; Bennett, Allan M; Walker, Jimmy T

2015-01-01

Hospital tap water is a recognised source of Pseudomonas aeruginosa. U.K. guidance documents recommend measures to control/minimise the risk of P. aeruginosa in augmented care units but these are based on limited scientific evidence. An experimental water distribution system was designed to investigate colonisation of hospital tap components. P. aeruginosa was injected into 27 individual tap 'assemblies'. Taps were subsequently flushed twice daily and contamination levels monitored over two years. Tap assemblies were systematically dismantled and assessed microbiologically and the effect of removing potentially contaminated components was determined. P. aeruginosa was repeatedly recovered from the tap water at levels above the augmented care alert level. The organism was recovered from all dismantled solenoid valves with colonisation of the ethylene propylene diene monomer (EPDM) diaphragm confirmed by microscopy. Removing the solenoid valves reduced P. aeruginosa counts in the water to below detectable levels. This effect was immediate and sustained, implicating the solenoid diaphragm as the primary contamination source.

Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

DOE PAGES

Larsen, Ross E.

2016-04-12

In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

Effects of various light curing methods on the leachability of uncured substances and hardness of a composite resin.

PubMed

Moon, H-J; Lee, Y-K; Lim, B-S; Kim, C-W

2004-03-01

The purpose of this study was to evaluate the effect of the various light curing units (plasma arc, halogen and light-emitting diodes) and irradiation methods (one-step, two-step and pulse) using different light energy densities on the leachability of unreacted monomers (Bis-GMA and UDMA) and the surface hardness of a composite resin (Z250, 3M). Leachability of the specimens immersed for 7 days in ethanol was analysed by HPLC. Vicker's hardness number (VHN) was measured immediately after curing (IC) and after immersion in ethanol for 7 days. Various irradiation methods with three curing units resulted in differences in the amount of leached monomers and VHN of IC when light energy density was lower than 17.0 J cm(-2) (P = 0.05). However, regardless of curing units and irradiation methods, these results were not different when the time or light energy density increased. When similar light energy density was irradiated (15.6-17.7 J cm(-2)), the efficiency of irradiation methods was different by the following order: one-step > or = two-step > pulse. These results suggest that the amount of leached monomers and VHN were influenced by forming polymer structure in activation and initiation stages of polymerization process with different light source energies and curing times.

Softening of the stiffness of bottle-brush polymers by mutual interaction

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

Bolisetty, S.; Airaud, C.; Rosenfeldt, S.

2007-04-15

We study bottle-brush macromolecules in a good solvent by small-angle neutron scattering (SANS), static light scattering (SLS), and dynamic light scattering (DLS). These polymers consist of a linear backbone to which long side chains are chemically grafted. The backbone contains about 1600 monomer units (weight average) and every second monomer unit carries side chains with approximately 60 monomer units. The SLS and SANS data extrapolated to infinite dilution lead to the form factor of the polymer that can be described in terms of a wormlike chain with a contour length of 380 nm and a persistence length of 17.5 nm.more » An analysis of the DLS data confirms these model parameters. The scattering intensities taken at finite concentration can be modeled using the polymer reference interaction site model. It reveals a softening of the bottle-brush polymers caused by their mutual interaction. We demonstrate that the persistence decreases from 17.5 nm down to 5 nm upon increasing the concentration from dilute solution to the highest concentration (40.59 g/l) under consideration. The observed softening of the chains is comparable to the theoretically predicted decrease of the electrostatic persistence length of linear polyelectrolyte chains at finite concentrations.« less

Thermoset polymers via ring opening metathesis polymerization of functionalized oils

DOEpatents

Larock, Richard C; Henna, Phillip H; Kessier, Michael R

2012-11-27

The invention provides a method for producing a thermosetting resin from renewable oils, the method comprising supplying renewable oil molecules containing strained ring alkene moieties; reacting the alkene moieties with cyclic alkenes to create a polymer; and repeating the above two steps until the resin having desired characteristics are obtained. Also provided is a thermoset resin comprising functionalized renewable oil polymerized with a co-monomer.

Non-strinking siloxane polymers

DOEpatents

Loy, Douglas A.; Rahimian, Kamyar

2001-01-01

Cross-linked polymers formed by ring-opening polymerization of a precursor monomer of the general formula R[CH.sub.2 CH(Si(CH.sub.3).sub.2).sub.2 O].sub.2, where R is a phenyl group or an alkyl group having at least two carbon atoms. A cross-linked polymer is synthesized by mixing the monomer with a co-monomer of the general formula CH.sub.2 CHR.sup.2 (SiMe.sub.2).sub.2 O in the presence of an anionic base to form a cross-linked polymer of recurring units of the general formula R(Me.sub.2 SiOCH.sub.2 CHSiMe.sub.2).sub.2 [CH.sub.2 CHR.sup.2 (SiMe.sub.2).sub.2 O].sub.n, where R.sup.2 is hydrogen, phenyl, ethyl, propyl or butyl. If the precursor monomer is a liquid, the polymer can be directly synthesized in the presence of an anionic base to a cross-linked polymer containing recurring units of the general formula R(Me.sub.2 SiOCH.sub.2 CHSiMe.sub.2).sub.2. The polymers have approximately less than 1% porosity and are thermally stable at temperatures up to approximately 500.degree. C. The conversion to the cross-linked polymer occurs by ring opening polymerization and results in shrinkage of less than approximately 5% by volume.

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil, E-mail: Anil.Shukla@pnnl.gov; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry (collision-induced dissociation with N{sub 2}). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi){sub n}Li{sup +}, (HCOOLi){sub n}Li{sub m}{sup m+}, (HCOOLi){sub n}HCOO{sup −}, and (HCOOLi){sub n}(HCOO){sub m}{sup m−}. Several magic number cluster (MNC) ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi){sub 3}Li{sup +} being the most abundant and stable cluster ion. Fragmentations ofmore » singly charged positive clusters proceed first by the loss of a dimer unit ((HCOOLi){sub 2}) followed by the loss of monomer units (HCOOLi) although the former remains the dominant dissociation process. In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi){sub 3}Li{sup +} as the most abundant fragment ion at higher collision energies which then fragments further to dimer and monomer ions at lower abundances. In the negative ion mode, however, singly charged clusters dissociated via sequential loss of monomer units. Multiply charged clusters in both positive and negative ion modes dissociated mainly via Coulomb repulsion. Quantum chemical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the central lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

Solubility enhancement of dioxins and PCBs by surfactant monomers and micelles quantified with polymer depletion techniques.

PubMed

Schacht, Veronika J; Grant, Sharon C; Escher, Beate I; Hawker, Darryl W; Gaus, Caroline

2016-06-01

Partitioning of super-hydrophobic organic contaminants (SHOCs) to dissolved or colloidal materials such as surfactants can alter their behaviour by enhancing apparent aqueous solubility. Relevant partition constants are, however, challenging to quantify with reasonable accuracy. Partition constants to colloidal surfactants can be measured by introducing a polymer (PDMS) as third phase with known PDMS-water partition constant in combination with the mass balance approach. We quantified partition constants of PCBs and PCDDs (log KOW 5.8-8.3) between water and sodium dodecyl sulphate monomers (KMO) and micelles (KMI). A refined, recently introduced swelling-based polymer loading technique allowed highly precise (4.5-10% RSD) and fast (<24 h) loading of SHOCs into PDMS, and due to the miniaturisation of batch systems equilibrium was reached in <5 days for KMI and <3 weeks for KMO. SHOC losses to experimental surfaces were substantial (8-26%) in monomer solutions, but had a low impact on KMO (0.10-0.16 log units). Log KMO for PCDDs (4.0-5.2) were approximately 2.6 log units lower than respective log KMI, which ranged from 5.2 to 7.0 for PCDDs and 6.6-7.5 for PCBs. The linear relationship between log KMI and log KOW was consistent with more polar and moderately hydrophobic compounds. Apparent solubility increased with increasing hydrophobicity and was highest in micelle solutions. However, this solubility enhancement was also considerable in monomer solutions, up to 200 times for OCDD. Given the pervasive presence of surfactant monomers in typical field scenarios, these data suggest that low surfactant concentrations may be effective long-term facilitators for subsurface transport of SHOCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular recognition at methyl methacrylate/n-butyl acrylate (MMA/nBA) monomer unit boundaries of phospholipids at p-MMA/nBA copolymer surfaces.

PubMed

Yu, Min; Urban, Marek W; Sheng, Yinghong; Leszczynski, Jerzy

2008-09-16

Lipid structural features and their interactions with proteins provide a useful vehicle for further advances in membrane proteins research. To mimic one of potential lipid-protein interactions we synthesized poly(methyl methacrylate/ n-butyl acrylate) (p-MMA/nBA) colloidal particles that were stabilized by phospholipid (PLs). Upon the particle coalescence, PL stratification resulted in the formation of surface localized ionic clusters (SLICs). These entities are capable of recognizing MMA/nBA monomer interfaces along the p-MMA/nBA copolymer backbone and form crystalline SLICs at the monomer interface. By utilizing attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and selected area electron diffraction (SAD) combined with ab initio calculations, studies were conducted that identified the origin of SLICs as well as their structural features formed on the surface of p-MMA/nBA copolymer films stabilized by 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) PL. Specific entities responsible for SLIC formation are selective noncovalent bonds of anionic phosphate and cationic quaternary ammonium segments of DLPC that interact with two neighboring carbonyl groups of nBA and MMA monomers of the p-MMA/nBA polymer backbone. To the best of our knowledge this is the first example of molecular recognition facilitated by coalescence of copolymer colloidal particles and the ability of PLs to form SLICs at the boundaries of the neighboring MMA and nBA monomer units of the p-MMA/nBA chain. The dominating noncovalent bonds responsible for the molecular recognition is a combination of H-bonding and electrostatic interactions.

An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon).

PubMed

Ba, Hengxing; Wu, Lang; Liu, Zongyue; Li, Chunyi

2016-01-01

Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.

The residual monomer content and mechanical properties of CAD\\CAM resins used in the fabrication of complete dentures as compared to heat cured resins

PubMed Central

Ayman, Al-Dharrab

2017-01-01

Background The utilization of computer-assisted designing and computer-assisted milling CAD\\CAM resins in the fabrication of removable prostheses is a modern-day concept that offers many advantages over the use of the traditional polymethylmethacrylate (PMMA). Aim This study instigated some of the mechanical properties of CAD\\CAM denture base resin including the amount of residual monomer. Methods This study was conducted at the Faculty of Dentistry, King Abdulaziz University from October 2016 to February 2017. A total of seventy rectangular specimens were fabricated (group A: 35 heat-cured PMMA and group B: 35 CAD/CAM pre-polymerized acrylic resin blocks). The flexural strength and surface hardness were tested while the residual monomer content at baseline, two-day and seven-day intervals was estimated using gas chromatography (GC). Means and standard deviations were determined for each group as well as independent-samples t-test and ANOVA with repeated measures for comparison between the groups and subgroups of varying time intervals. Results Heat cured PMMA (A), displayed higher flexural strength and low value flexural modulus compared to CAD/CAM acrylic resin denture base material (B). Student t-test indicated highly significant differences (p<0.001) of the flexural strength (t=37.911) and flexural modulus (t=88.559). The surface hardness of group (B) was significantly higher compared to group (A) as indicated by the t-test (t=20.430). Higher release of the monomer content was detected by GC in group (A) at different time intervals with a statistically significant difference (p<0.001) in residual monomer content. Conclusion CAD/CAM resin may be considered suitable for use in the construction of denture bases. PMID:28894533

Proton and metal ion binding to natural organic polyelectrolytes-I. Studies with synthetic model compounds

USGS Publications Warehouse

Marinsky, J.A.; Reddy, M.M.

1984-01-01

A unified physico-chemical model, based on a modified Henderson-Hasselbalch equation, for the analysis of ion complexation reactions involving charged polymeric systems is presented and verified. In this model pH = pKa+p(??Ka) + log(??/1 - ??) where Ka is the intrinsic acid dissociation constant of the ionizable functional groups on the polymer, ??Ka is the deviation of the intrinsic constant due to electrostatic interaction between the hydrogen ion and the polyanion, and alpha (??) is the polyacid degree of ionization. Using this approach pKa values for repeating acidic units of polyacrylic (PAA) and polymethacrylic (PMA) acids were found to be 4.25 ?? 0.03 and 4.8 ?? 0.1, respectively. The polyion electrostatic deviation term derived from the potentiometric titration data (i.e. p(??Ka)) is used to calculate metal ion concentration at the complexation site on the surface of the polyanion. Intrinsic cobalt-polycarboxylate binding constants (7.5 for PAA and 5.6 for PMA), obtained using this procedure, are consistent with the range of published binding constants for cobalt-monomer carboxylate complexes. In two phase systems incorporation of a Donnan membrane potential term allows determination of the intrinsic pKa of a cross-linked PMA gel, pKa = 4.83, in excellent agreement with the value obtained for the linear polyelectrolyte and the monomer. Similarly, the intrinsic stability constant for cobalt ion binding to a PMA-gel (??CoPMA+ = 11) was found to be in agreement with the linear polyelectrolyte analogue and the published data for cobalt-carboxylate monodentate complexes. ?? 1984.

Versatile Tandem Ring-Opening/Ring-Closing Metathesis Polymerization: Strategies for Successful Polymerization of Challenging Monomers and Their Mechanistic Studies.

PubMed

Park, Hyeon; Kang, Eun-Hye; Müller, Laura; Choi, Tae-Lim

2016-02-24

Tandem ring-opening/ring-closing metathesis (RO/RCM) results in extremely fast living polymerization; however, according to previous reports, only monomers containing certain combinations of cycloalkenes, terminal alkynes, and nitrogen linkers successfully underwent tandem polymerization. After examining the polymerization pathways, we proposed that the relatively slow intramolecular cyclization might lead to competing side reactions such as intermolecular cross metathesis reactions to form inactive propagating species. Thus, we developed two strategies to enhance tandem polymerization efficiency. First, we modified monomer structures to accelerate tandem RO/RCM cyclization by enhancing the Thorpe-Ingold effect. This strategy increased the polymerization rate and suppressed the chain transfer reaction to achieve controlled polymerization, even for challenging syntheses of dendronized polymers. Alternatively, reducing the reaction concentration facilitated tandem polymerization, suggesting that the slow tandem RO/RCM cyclization step was the main reason for the previous failure. To broaden the monomer scope, we used monomers containing internal alkynes and observed that two different polymer units with different ring sizes were produced as a result of nonselective α-addition and β-addition on the internal alkynes. Thorough experiments with various monomers with internal alkynes suggested that steric and electronic effects of the alkyne substituents influenced alkyne addition selectivity and the polymerization reactivity. Further polymerization kinetics studies revealed that the rate-determining step of monomers containing certain internal alkynes was the six-membered cyclization step via β-addition, whereas that for other monomers was the conventional intermolecular propagation step, as observed in other chain-growth polymerizations. This conclusion agrees well with all those polymerization results and thus validates our strategies.

Initial Reactivity of Linkages and Monomer Rings in Lignin Pyrolysis Revealed by ReaxFF Molecular Dynamics.

PubMed

Zhang, Tingting; Li, Xiaoxia; Guo, Li

2017-10-24

The initial conversion pathways of linkages and their linked monomer units in lignin pyrolysis were investigated comprehensively by ReaxFF MD simulations facilitated by the unique VARxMD for reaction analysis. The simulated molecular model contains 15 920 atoms and was constructed on the basis of Adler's softwood lignin model. The simulations uncover the initial conversion ratio of various linkages and their linked aryl monomers. For linkages and their linked monomer aryl rings of α-O-4, β-O-4 and α-O-4 & β-5, the C α /C β ether bond cracking dominates the initial pathway accounting for at least up to 80% of their consumption. For the linkage of β-β & γ-O-α, both the C α -O ether bond cracking and its linked monomer aryl ring opening are equally important. Ring-opening reactions dominate the initial consumption of other 4-O-5, 5-5, β-1, β-2, and β-5 linkages and their linked monomers. The ether bond cracking of C α -O and C β -O occurs at low temperature, and the aryl ring-opening reactions take place at relatively high temperature. The important intermediates leading to the stable aryl ring opening are the phenoxy radicals, the bridged five-membered and three-membered rings and the bridged six-membered and three-membered rings. In addition, the reactivity of a linkage and its monomer aryl ring may be affected by other linkages. The ether bond cracking of α-O-4 and β-O-4 linkages can activate its neighboring linkage or monomer ring through the formed phenoxy radicals as intermediates. The important intermediates revealed in this article should be of help in deepening the understanding of the controlling mechanism for producing aromatic chemicals from lignin pyrolysis.

Biocatalytic synthesis and polymerization via ROMP of new biobased phenolic monomers: a greener process towards sustainable antioxidant polymers

NASA Astrophysics Data System (ADS)

Diot-Néant, Florian; Migeot, Loïs; Hollande, Louis; Reano, Felix A.; Domenek, Sandra; Allais, Florent

2017-12-01

Antioxidant norbornene-based monomers bearing biobased sterically hindered phenols (SHP) - NDF (norbornene dihydroferulate) and NDS (norbornene dihydrosinapate) - have been successfully prepared through biocatalysis from naturally occurring ferulic and sinapic acids, respectively, in presence of Candida antarctica Lipase B (Cal-B). The ring opening metathesis polymerization (ROMP) of these monomers was investigated according to ruthenium catalyst type (GI) vs. (HGII) and monomer to catalyst molar ratio ([M]/[C]). The co-polymerization of antioxidant functionalized monomer (NDF or NDS) and non-active norbornene (N) has also been performed in order to adjust the number of SHP groups present per weight unit and tune the antioxidant activity of the copolymers. The polydispersity of the resulting copolymers was readily improved by a simple acetone wash to provide antioxidant polymers with well-defined structures. After hydrogenation with p-toluenesulfonylhydrazine (p-TSH), the radical scavenging ability of the resulting saturated polymers was evaluated using α,α-diphenyl-β-picrylhydrazyl (DPPH) analysis. Results demonstrated that polymers bearing sinapic acid SHP exhibited higher antiradical activity than the polymer bearing ferulic acid SHP. In addition it was also shown that only a small SHP content was needed in the copolymers to exhibit a potent antioxidant activity.

Abiotic formation of RNA-like oligomers by montmorillonite catalysis: part II

NASA Astrophysics Data System (ADS)

Ertem, Gözen; Snellinger-O'Brien, Ann M.; Ertem, M. C.; Rogoff, D. A.; Dworkin, Jason P.; Johnston, Murray V.; Hazen, Robert M.

2008-01-01

This work is an extension of our previous studies carried out to investigate the possible catalytic role of minerals in the abiotic synthesis of biologically important molecules. In the presence of montmorillonite, a member of the phyllosilicate group minerals that are abundant on Earth and identified on Mars, activated RNA monomers, namely 5‧-phosphorimidazolides of nucleosides (ImpNs), undergo condensation reactions in aqueous electrolyte solution producing oligomers with similar structures to short RNA fragments. Analysis of the linear trimer isomers formed in the reaction of a mixture of activated adenosine and cytidine monomers (ImpA and ImpC, respectively) employing high-performance liquid chromatography, selective enzymatic hydrolysis and matrix-assisted laser desorption/ionization mass spectroscopy molecular weight measurements demonstrate that montmorillonite catalysis facilitates the formation of hetero-isomers containing 56% A- and 44% C-monomer incorporated in their structure. The results also show that 56% of the monomer units are linked together by RNA-like 3‧, 5‧-phosphodiester bonds. These results follow the same trend observed in our most recent work studying the reaction of activated adenosine and uridine monomers, and support Bernal's hypothesis proposing the possible catalytic role of minerals in the abiotic processes in the course of chemical evolution.

MS/MS Digital Readout: Analysis of Binary Information Encoded in the Monomer Sequences of Poly(triazole amide)s.

PubMed

Amalian, Jean-Arthur; Trinh, Thanh Tam; Lutz, Jean-François; Charles, Laurence

2016-04-05

Tandem mass spectrometry was evaluated as a reliable sequencing methodology to read codes encrypted in monodisperse sequence-coded oligo(triazole amide)s. The studied oligomers were composed of monomers containing a triazole ring, a short ethylene oxide segment, and an amide group as well as a short alkyl chain (propyl or isobutyl) which defined the 0/1 molecular binary code. Using electrospray ionization, oligo(triazole amide)s were best ionized as protonated molecules and were observed to adopt a single charge state, suggesting that adducted protons were located on every other monomer unit. Upon collisional activation, cleavages of the amide bond and of one ether bond were observed to proceed in each monomer, yielding two sets of complementary product ions. Distribution of protons over the precursor structure was found to remain unchanged upon activation, allowing charge state to be anticipated for product ions in the four series and hence facilitating their assignment for a straightforward characterization of any encoded oligo(triazole amide)s.

TEGDMA and UDMA monomers released from composite dental material polymerized with diode and halogen lamps.

PubMed

Wacławczyk, Agnieszka; Postek-Stefańska, Lidia; Pietraszewska, Daria; Birkner, Ewa; Zalejska-Fiolka, Jolanta; Wysoczańska-Jankowicz, Iwona

2018-03-20

More than 35 substances released from composite fillings have been identified. Among these, basic monomers and the so-called co-monomers are most often reported. The substances released from polymer-based materials demonstrate allergenic, cytotoxic, genotoxic, mutagenic, embryotoxic, teratogenic, and estrogenic properties. The aim of this study was to measure the amounts of triethylene glycol dimethacrylate (TEGDMA) and urethane dimethacrylate (UDMA) monomers released from composite dental fillings to citrate-phosphate buffer with the pH of 4, 6, 8 after 24 h and 6 months from the polymerization. Ten samples for each polymerization method had been made from the composite material (Filtek Supreme XT, 3M ESPE, St. Paul, USA), which underwent polymerization using the following lamps: halogen lamp (Translux CL, Heraeus Kulzer, Hanau, Germany) (sample H) and diode lamp (Elipar Freelight 2, 3M ESPE), with soft start function (group DS) and without that function (group DWS). It has been demonstrated that the type of light-curing units has a significant impact on the amount of TEGDMA and UDMA released. The amount of UDMA and TEGDMA monomers released from composite fillings differed significantly depending on the source of polymerization applied, as well as the pH of the solution and sample storage time. Elution of the monomers from composite material polymerized using halogen lamp was significantly greater as compared to curing with diode lamps.

Structural and biophysical properties of h-FANCI ARM repeat protein.

PubMed

Siddiqui, Mohd Quadir; Choudhary, Rajan Kumar; Thapa, Pankaj; Kulkarni, Neha; Rajpurohit, Yogendra S; Misra, Hari S; Gadewal, Nikhil; Kumar, Satish; Hasan, Syed K; Varma, Ashok K

2017-11-01

Fanconi anemia complementation groups - I (FANCI) protein facilitates DNA ICL (Inter-Cross-link) repair and plays a crucial role in genomic integrity. FANCI is a 1328 amino acids protein which contains armadillo (ARM) repeats and EDGE motif at the C-terminus. ARM repeats are functionally diverse and evolutionarily conserved domain that plays a pivotal role in protein-protein and protein-DNA interactions. Considering the importance of ARM repeats, we have explored comprehensive in silico and in vitro approach to examine folding pattern. Size exclusion chromatography, dynamic light scattering (DLS) and glutaraldehyde crosslinking studies suggest that FANCI ARM repeat exist as monomer as well as in oligomeric forms. Circular dichroism (CD) and fluorescence spectroscopy results demonstrate that protein has predominantly α- helices and well-folded tertiary structure. DNA binding was analysed using electrophoretic mobility shift assay by autoradiography. Temperature-dependent CD, Fluorescence spectroscopy and DLS studies concluded that protein unfolds and start forming oligomer from 30°C. The existence of stable portion within FANCI ARM repeat was examined using limited proteolysis and mass spectrometry. The normal mode analysis, molecular dynamics and principal component analysis demonstrated that helix-turn-helix (HTH) motif present in ARM repeat is highly dynamic and has anti-correlated motion. Furthermore, FANCI ARM repeat has HTH structural motif which binds to double-stranded DNA.

Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat.

PubMed

Tek, Ahmet L; Kashihara, Kazunari; Murata, Minoru; Nagaki, Kiyotaka

2011-11-01

The centromere plays an essential role for proper chromosome segregation during cell division and usually harbors long arrays of tandem repeated satellite DNA sequences. Although this function is conserved among eukaryotes, the sequences of centromeric DNA repeats are variable. Most of our understanding of functional centromeres, which are defined by localization of a centromere-specific histone H3 (CENH3) protein, comes from model organisms. The components of the functional centromere in legumes are poorly known. The genus Astragalus is a member of the legumes and bears the largest numbers of species among angiosperms. Therefore, we studied the components of centromeres in Astragalus sinicus. We identified the CenH3 homolog of A. sinicus, AsCenH3 that is the most compact in size among higher eukaryotes. A CENH3-based assay revealed the functional centromeric DNA sequences from A. sinicus, called CentAs. The CentAs repeat is localized in A. sinicus centromeres, and comprises an AT-rich tandem repeat with a monomer size of 20 nucleotides.

Genomic, RNAseq, and Molecular Modeling Evidence Suggests That the Major Allergen Domain in Insects Evolved from a Homodimeric Origin

PubMed Central

Randall, Thomas A.; Perera, Lalith; London, Robert E.; Mueller, Geoffrey A.

2013-01-01

The major allergen domain (MA) is widely distributed in insects. The crystal structure of a single Bla g 1 MA revealed a novel protein fold in which the fundamental structure was a duplex of two subsequences (monomers), which had diverged over time. This suggested that the evolutionary origin of the MA structure may have been a homodimer of this smaller subsequence. Using publicly available genomic data, the distribution of the basic unit of this class of proteins was determined to better understand its evolutionary history. The duplication and divergence is examined at three distinct levels of resolution: 1) within the orders Diptera and Hymenoptera, 2) within one genus Drosophila, and 3) within one species Aedes aegypti. Within the family Culicidae, we have found two separate occurrences of monomers as independent genes. The organization of the gene family in A. aegypti shows a common evolutionary origin for its monomer and several closely related MAs. Molecular modeling of the A. aegypti monomer with the unique Bla g 1 fold confirms the distant evolutionary relationship and supports the feasibility of homodimer formation from a single monomer. RNAseq data for A. aegypti confirms that the monomer is expressed in the mosquito similar to other A. aegypti MAs after a blood meal. Together, these data support the contention that the detected monomer shares similar functional characteristics to related MAs in other insects. An extensive search for this domain outside of Insecta confirms that the MAs are restricted to insects. PMID:24253356

40 CFR 63.12005 - What definitions apply to this subpart?

Code of Federal Regulations, 2012 CFR

2012-07-01

... venting episode that is associated with a single unit operation. A unit operation may have more than one... characterized by a two-step anhydrous polymerization process: the formation of small resin particles in a pre... of the resin particles in a post-polymerization reactor using additional vinyl chloride monomer...

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry. Singly as well as multiply charged clusters were formed with the general formulae, (HCOOLi)nLi+, (HCOOLi)nLimm+, (HCOOLi)nHCOO- and (HCOOLi)n(HCOO)mm-. Several magic number cluster ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi)3Li+ being the most abundant and stable cluster ions. Fragmentations of singly charged clusters proceed first by the loss of a dimer unit ((HCOOLi)2) followed by sequential loss of monomer units (HCOOLi). In the case ofmore » positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi)3Li+ at higher collision energies which later fragments to dimer and monomer ions in lower abundance. Quantum mechanical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

Rational Design of High-Performance Wide-Bandgap (≈2 eV) Polymer Semiconductors as Electron Donors in Organic Photovoltaics Exhibiting High Open Circuit Voltages (≈1 V).

PubMed

Chochos, Christos L; Katsouras, Athanasios; Gasparini, Nicola; Koulogiannis, Chrysanthos; Ameri, Tayebeh; Brabec, Christoph J; Avgeropoulos, Apostolos

2017-01-01

Systematic optimization of the chemical structure of wide-bandgap (≈2.0 eV) "donor-acceptor" copolymers consisting of indacenodithiophene or indacenodithieno[3,2-b]thiophene as the electron-rich unit and thieno[3,4-c]pyrrole-4,6-dione as the electron-deficient moiety in terms of alkyl side chain engineering and distance of the electron-rich and electron-deficient monomers within the repeat unit of the polymer chain results in high-performance electron donor materials for organic photovoltaics. Specifically, preliminary results demonstrate extremely high open circuit voltages (V oc s) of ≈1.0 V, reasonable short circuit current density (J sc ) of around 11 mA cm -2 , and moderate fill factors resulting in efficiencies close to 6%. All the devices are fabricated in an inverted architecture with the photoactive layer processed by doctor blade equipment, showing the compatibility with roll-to-roll large-scale manufacturing processes. From the correlation of the chemical structure-optoelectronic properties-photovoltaic performance, a rational guide toward further optimization of the chemical structure in this family of copolymers, has been achieved. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biocatalytic synthesis of maltodextrin-based acrylates from starch and α-cyclodextrin.

PubMed

Kloosterman, Wouter M J; Spoelstra-van Dijk, Gerda; Loos, Katja

2014-09-01

Novel 2-(β-maltooligooxy)-ethyl (meth)acrylate monomers are successfully synthesized by CGTase from Bacillus macerans catalyzed coupling of 2-(β-glucosyloxy)-ethyl acrylate and methacrylate with α-cyclodextrin or starch. HPLC-UV analysis shows that the CGTase catalyzed reaction yields 2-(β-maltooligooxy)-ethyl acrylates with 1 to 15 glucopyranosyl units. (1) H NMR spectroscopy reveals that the β-linkage in the acceptor molecule is preserved during the CGTase catalyzed coupling reaction, whereas the newly introduced glucose units are attached by α-(1,4)-glycosidic linkages. The synthesized 2-(β-maltooligooxy)-ethyl acrylate monomers are successfully polymerized by aqueous free radical polymerization to yield the comb-shaped glycopolymer poly(2-(β-maltooligooxy)-ethyl acrylate). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of surface preparation on the failure load of a highly filled composite bonded to the polymer-monomer matrix of a fiber-reinforced composite.

PubMed

Shimizu, Hiroshi; Tsue, Fumitake; Chen, Zhao-Xun; Takahashi, Yutaka

2009-04-01

The purpose of the present study was to evaluate the effect of surface preparation on the maximum fracture load value of a highly filled composite bonded to the polymer-monomer matrix of a fiber-reinforced composite. A polymer-monomer matrix was made by mixing urethane dimethacrylate and triethyleneglycol dimethacrylate at a ratio of 1:1 with camphorquinone and 2-dimethylaminoethyl methacrylate as a light initiator. The matrix was then polymerized in a disk-shaped silicone mold with a light-polymerizing unit. The flat surfaces of the polymer-monomer matrix disk were prepared in one of the following ways: (1) without preparation; (2) application of silane coupling agent; or (3) application of matrix liquid and prepolymerization. A highly filled composite material was applied and polymerized with a light-polymerizing unit. Additional test specimens made entirely of the polymer-monomer matrix were fabricated as references; the disk and cylinder were fabricated in one piece using a mold specially made for the present study (group 4). Half the specimens were thermocycled up to 10,000 times in water with a 1-minute dwell time at each temperature (5 degrees C and 55 degrees C). The maximum fracture load values were determined using a universal testing machine (n = 10). The maximum fracture loads for group 3 were significantly enhanced both before and after thermocycling, whereas the maximum fracture loads of group 2 were significantly enhanced before thermocycling (p < 0.05); however, the failure loads decreased for all groups after thermocycling (p < 0.05). All the specimens in groups 1 and 2 debonded during thermocycling. The failure load of group 3 was significantly lower than that of group 4 both before and after thermocycling (p < 0.05). Within the limitations of the current in vitro study, the application and prepolymerization of a mixed dimethacrylate resin liquid prior to the application of a highly filled composite was an effective surface preparation for the polymer-monomer matrix of a fiber-reinforced composite; however, the bond durability may be insufficient.

Synthesis of Energetic Polymers.

DTIC Science & Technology

1981-10-15

demonstrated by a single peak in the gc analysis (injector temperature 2500 C). The reaction will be repeated in a different solvent to avoid the formation of...glass column packed with 10% OV-101 on chrom Q, with n-decane as an internal standard. Rates of polymerization were calculated using the assumption...the Kelen-Tudos method. The disappearance of monomer was monitored by gas chromatography, using a glass column packed with 10% OV-101 on Chrom Q

Structure of the intact ATM/Tel1 kinase

NASA Astrophysics Data System (ADS)

Wang, Xuejuan; Chu, Huanyu; Lv, Mengjuan; Zhang, Zhihui; Qiu, Shuwan; Liu, Haiyan; Shen, Xuetong; Wang, Weiwu; Cai, Gang

2016-05-01

The ataxia-telangiectasia mutated (ATM) protein is an apical kinase that orchestrates the multifaceted DNA-damage response. Normally, ATM kinase is in an inactive, homodimer form and is transformed into monomers upon activation. Besides a conserved kinase domain at the C terminus, ATM contains three other structural modules, referred to as FAT, FATC and N-terminal helical solenoid. Here we report the first cryo-EM structure of ATM kinase, which is an intact homodimeric ATM/Tel1 from Schizosaccharomyces pombe. We show that two monomers directly contact head-to-head through the FAT and kinase domains. The tandem N-terminal helical solenoid tightly packs against the FAT and kinase domains. The structure suggests that ATM/Tel1 dimer interface and the consecutive HEAT repeats inhibit the binding of kinase substrates and regulators by steric hindrance. Our study provides a structural framework for understanding the mechanisms of ATM/Tel1 regulation as well as the development of new therapeutic agents.

Genetic loci simultaneously controlling lignin monomers and biomass digestibility of rice straw.

PubMed

Hu, Zhen; Zhang, Guifen; Muhammad, Ali; Samad, Rana Abdul; Wang, Youmei; Walton, Jonathan D; He, Yuqing; Peng, Liangcai; Wang, Lingqiang

2018-02-26

Lignin content and composition are crucial factors affecting biomass digestibility. Exploring the genetic loci simultaneously affecting lignin-relevant traits and biomass digestibility is a precondition for lignin genetic manipulation towards energy crop breeding. In this study, a high-throughput platform was employed to assay the lignin content, lignin composition and biomass enzymatic digestibility of a rice recombinant inbred line population. Correlation analysis indicated that the absolute content of lignin monomers rather than lignin content had negative effects on biomass saccharification, whereas the relative content of p-hydroxyphenyl unit and the molar ratio of p-hydroxyphenyl unit to guaiacyl unit exhibited positive roles. Eight QTL clusters were identified and four of them affecting both lignin composition and biomass digestibility. The additive effects of clustered QTL revealed consistent relationships between lignin-relevant traits and biomass digestibility. Pyramiding rice lines containing the above four positive alleles for increasing biomass digestibility were selected and showed comparable lignin content, decreased syringyl or guaiacyl unit and increased molar percentage of p-hydroxyphenyl unit, the molar ratio of p-hydroxyphenyl unit to guaiacyl unit and sugar releases. More importantly, the lodging resistance and eating/cooking quality of pyramiding lines were not sacrificed, indicating the QTL information could be applied to select desirable energy rice lines.

Probing solvation decay length in order to characterize hydrophobicity-induced bead-bead attractive interactions in polymer chains.

PubMed

Das, Siddhartha; Chakraborty, Suman

2011-08-01

In this paper, we quantitatively demonstrate that exponentially decaying attractive potentials can effectively mimic strong hydrophobic interactions between monomer units of a polymer chain dissolved in aqueous solvent. Classical approaches to modeling hydrophobic solvation interactions are based on invariant attractive length scales. However, we demonstrate here that the solvation interaction decay length may need to be posed as a function of the relative separation distances and the sizes of the interacting species (or beads or monomers) to replicate the necessary physical interactions. As an illustrative example, we derive a universal scaling relationship for a given solute-solvent combination between the solvation decay length, the bead radius, and the distance between the interacting beads. With our formalism, the hydrophobic component of the net attractive interaction between monomer units can be synergistically accounted for within the unified framework of a simple exponentially decaying potential law, where the characteristic decay length incorporates the distinctive and critical physical features of the underlying interaction. The present formalism, even in a mesoscopic computational framework, is capable of incorporating the essential physics of the appropriate solute-size dependence and solvent-interaction dependence in the hydrophobic force estimation, without explicitly resolving the underlying molecular level details.

Precision Aliphatic Polyesters with Alternating Microstructures via Cross-Metathesis Polymerization: An Event of Sequence Control.

PubMed

Li, Zi-Long; Zeng, Fu-Rong; Ma, Ji-Mei; Sun, Lin-Hao; Zeng, Zhen; Jiang, Hong

2017-06-01

Sequence-regulated polymerization is realized upon sequential cross-metathesis polymerization (CMP) and exhaustive hydrogenation to afford precision aliphatic polyesters with alternating sequences. This strategy is particularly suitable for the arrangement of well-known monomer units including glycolic acid, lactic acid, and caprolactic acid on polymer chain in a predetermined sequence. First of all, structurally asymmetric monomers bearing acrylate and α-olefin terminuses are generated in an efficient and straightforward fashion. Subsequently, cross-metathesis (co)polymerization of M1 and M2 using the Hoveyda-Grubbs second-generation catalyst (HG-II) furnishes P1-P3, respectively. Finally, hydrogenation yields the desired saturated polyesters HP1-HP3. It is noteworthy that the ε-caprolactone-derived unit is generated in situ rather than introduced to tailor-made monomers prior to CMP. NMR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) results verify the microstructural periodicity of these precision polyesters. Differential scanning calorimetry (DSC) results reflect that polyesters without methyl side groups exhibit crystallinity, and unsaturated polyester samples show higher glass transition temperatures than their hydrogenated counterparts owing to structural rigidity. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and characterization of organic-inorganic polymers from new methacrylate monomers and silane derivatives

NASA Astrophysics Data System (ADS)

Nicolescu, F. Adriana; Jerca, Victor V.; Albu, Ana M.; Vasilescu, D. Sorin; Vuluga, D. Mircea

2009-09-01

We report the synthesis of five new hybrid polymeric structures obtained by free radical copolymerization of some organic azo-based methacrylate monomers and 3-methacryloxypropyl trimethoxysilane (MEMO). The copolymers are soluble in common solvents like methylene chloride, chloroform, dichlorbenzene, dimethylsulfoxide, dimethylformamide. The copolymeric structures might be interesting from the point of view of nonlinear optical response due to a rich content in chromophoric units determined by H-NMR spectroscopy. The structures were also characterized by FT-IR spectroscopy, TGA and SEC analysis.

Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis

PubMed Central

Vyas, Rajan; Kumar, Vijay; Panjikar, Santosh; Karthikeyan, Subramanian; Kishan, K. V. Radha; Tewari, Rupinder; Weiss, Manfred S.

2008-01-01

Aspartate semialdehyde dehydrogenase from Mycobacterium tuberculosis (Asd, ASADH, Rv3708c), which is the second enzyme in the lysine/homoserine-biosynthetic pathways, has been expressed heterologously in Escherichia coli. The enzyme was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Preliminary diffraction data analysis suggested the presence of up to four monomers in the asymmetric unit of the orthorhombic crystal form A and of one or two monomers in the cubic crystal form B. PMID:18323599

Acidity of the amidoxime functional group in aqueous solution. A combined experimental and computational study

DOE PAGES

Mehio, Nada; Lashely, Mark A.; Nugent, Joseph W.; ...

2015-01-26

Poly(acrylamidoxime) adsorbents are often invoked in discussions of mining uranium from seawater. It has been demonstrated repeatedly in the literature that the success of these materials is due to the amidoxime functional group. While the amidoxime-uranyl chelation mode has been established, a number of essential binding constants remain unclear. This is largely due to the wide range of conflicting pK a values that have been reported for the amidoxime functional group in the literature. To resolve this existing controversy we investigated the pK a values of the amidoxime functional group using a combination of experimental and computational methods. Experimentally, wemore » used spectroscopic titrations to measure the pK a values of representative amidoximes, acetamidoxime and benzamidoxime. Computationally, we report on the performance of several protocols for predicting the pK a values of aqueous oxoacids. Calculations carried out at the MP2 or M06-2X levels of theory combined with solvent effects calculated using the SMD model provide the best overall performance with a mean absolute error of 0.33 pK a units and 0.35 pK a units, respectively, and a root mean square deviation of 0.46 pK a units and 0.45 pK a units, respectively. Finally, we employ our two best methods to predict the pK a values of promising, uncharacterized amidoxime ligands. Hence, our study provides a convenient means for screening suitable amidoxime monomers for future generations of poly(acrylamidoxime) adsorbents used to mine uranium from seawater.« less

Effect of grafted oligopeptides on friction.

PubMed

Iarikov, Dmitri D; Ducker, William A

2013-05-14

Frictional and normal forces in aqueous solution at 25 °C were measured between a glass particle and oligopeptide films grafted from a glass plate. Homopeptide molecules consisting of 11 monomers of either glutamine, leucine, glutamic acid, lysine, or phenylalanine and one heteropolymer were each "grafted from" an oxidized silicon wafer using microwave-assisted solid-phase peptide synthesis. The peptide films were characterized using X-ray photoelectron spectroscopy and secondary ion mass spectrometry. Frictional force measurements showed that the oligopeptides increased the magnitude of friction compared to that on a bare hydrophilic silicon wafer but that the friction was a strong function of the nature of the monomer unit. Overall we find that the friction is lower for more hydrophilic films. For example, the most hydrophobic monomer, leucine, exhibited the highest friction whereas the hydrophilic monomer, polyglutamic acid, exhibited the lowest friction at zero load. When the two surfaces had opposite charges, there was a strong attraction, adhesion, and high friction between the surfaces. Friction for all polymers was lower in phosphate-buffered saline than in pure water, which was attributed to lubrication via hydrated salt ions.

Models for mirror symmetry breaking via β-sheet-controlled copolymerization: (i) mass balance and (ii) probabilistic treatment.

PubMed

Blanco, Celia; Hochberg, David

2012-12-06

Experimental mechanisms that yield the growth of homochiral copolymers over their heterochiral counterparts have been advocated by Lahav and co-workers. These chiral amplification mechanisms proceed through racemic β-sheet-controlled polymerization operative in both surface crystallites as well as in solution. We develop two complementary theoretical models for these template-induced desymmetrization processes leading to multicomponent homochiral copolymers. First, assuming reversible β-sheet formation, the equilibrium between the free monomer pool and the polymer strand within the template is assumed. This yields coupled nonlinear mass balance equations whose solutions are used to calculate enantiomeric excesses and average lengths of the homochiral chains formed. The second approach is a probabilistic treatment based on random polymerization. The occlusion probabilities depend on the polymerization activation energies for each monomer species and are proportional to the concentrations of the monomers in solution in the constant pool approximation. The monomer occlusion probabilities are represented geometrically in terms of unit simplexes from which conditions for maximizing or minimizing the likelihood for mirror symmetry breaking can be determined.

Expression, purification, crystallization and preliminary crystallographic study of isolated modules of the mouse coactivator-associated arginine methyltransferase 1

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

Troffer-Charlier, Nathalie; Cura, Vincent; Hassenboehler, Pierre

2007-04-01

Isolated modules of mouse coactivator-associated arginine methyltransferase 1 encompassing the protein arginine N-methyltransferase catalytic domain have been overexpressed, purified and crystallized. X-ray diffraction data have been collected and have enabled determination of the structures by multiple isomorphous replacement using anomalous scattering. Coactivator-associated arginine methyltransferase 1 (CARM1) plays a crucial role in gene expression as a coactivator of several nuclear hormone receptors and also of non-nuclear receptor systems. Its recruitment by the transcriptional machinery induces protein methylation, leading to chromatin remodelling and gene activation. CARM1{sub 28–507} and two structural states of CARM1{sub 140–480} were expressed, purified and crystallized. Crystals of CARM1{submore » 28–507} belong to space group P6{sub 2}22, with unit-cell parameters a = b = 136.0, c = 125.3 Å; they diffract to beyond 2.5 Å resolution using synchrotron radiation and contain one monomer in the asymmetric unit. The structure of CARM1{sub 28–507} was solved by multiple isomorphous replacement and anomalous scattering methods. Crystals of apo CARM1{sub 140–480} belong to space group I222, with unit-cell parameters a = 74.6, b = 99.0, c = 207.4 Å; they diffract to beyond 2.7 Å resolution and contain two monomers in the asymmetric unit. Crystals of CARM1{sub 140–480} in complex with S-adenosyl-l-homocysteine belong to space P2{sub 1}2{sub 1}2, with unit-cell parameters a = 74.6, b = 98.65, c = 206.08 Å; they diffract to beyond 2.6 Å resolution and contain four monomers in the asymmetric unit. The structures of apo and holo CARM1{sub 140–480} were solved by molecular-replacement techniques from the structure of CARM1{sub 28–507}.« less

Synthesis and characterization of branched polymers from lipase-catalyzed trimethylolpropane copolymerizations.

PubMed

Kulshrestha, Ankur S; Gao, Wei; Fu, Hongyong; Gross, Richard A

2007-06-01

Lipase-catalyzed terpolymerizations were performed with the monomers trimethylolpropane (B3), 1,8-octanediol (B2), and adipic acid (A2). Polymerizations were performed in bulk, at 70 degrees C, for 42 h, using immobilized lipase B from Candida antartica (Novozyme-435) as a catalyst. To determine the substitution pattern of trimethylolpropane (TMP) in copolymers, model compounds with variable degrees of acetylation were synthesized. Inverse-gated 13C NMR spectra were recorded to first determine the chemical shift positions for mono-, di-, and trisubstituted TMP units and, subsequently, to determine substitution of TMP units along chains. Variation of TMP in the monomer feed gave copolymers with degrees of branching (DB) from 20% to 67%. In one example, a hyperbranched copolyester with 53 mol % TMP adipate units was formed in 80% yield, with Mw 14 100 (relative to polystyrene standards), Mw/Mn 5.3, and DB 36%. Thermal and crystalline properties of the copolyesters were studied by thermogravimetric analysis and differential scanning calorimetry.

Simultaneous UPLC-MS/MS analysis of native catechins and procyanidins and their microbial metabolites in intestinal contents and tissues of male Wistar Furth inbred rats.

PubMed

Goodrich, Katheryn M; Neilson, Andrew P

2014-05-01

Procyanidins have been extensively investigated for their potential health protective activities. However, the potential bioactivities of procyanidins are limited by their poor bioavailability. The majority of the ingested dose remains unabsorbed and reaches the colon where extensive microbial metabolism occurs. Most existing analytical methods measure either native compounds (catechins and procyanidins), or their microbial metabolites. The objectives of this study were to develop a high-throughput extraction and UPLC-MS/MS method for simultaneous measurement of both native procyanidins and their metabolites, facilitating high-throughput analysis of native and metabolite profiles in various regions of the colon. The present UPLC-MS/MS method facilitates simultaneous resolution and detection of authentic standards of 14 native catechin monomers and procyanidins, as well as 24 microbial metabolites. Detection and resolution of an additional 3 procyanidin dimers and 10 metabolites for which standards were not available was achieved. Elution and adequate resolution of both native compounds and metabolites were achieved within 10min. The intraday repeatability for native compounds was between 1.1 and 16.5%, and the interday repeatability for native compounds was between 2.2 and 25%. Intraday and interday repeatability for metabolites was between 0.6 and 24.1% and 1 and 23.9%, respectively. Observed lower limits of quantification for native compounds were ∼9-350fmol on-column, and for the microbial metabolites were ∼0.8-12,000fmol on-column. Observed lower limits of detection for native compounds were ∼4.5-190fmol on-column, and for metabolites were 0.304-6020fmol on-column. For native monomers and procyanidins, extraction recoveries ranged from 38 to 102%. Extraction recoveries for the 9 microbial metabolites tested ranged from 41 to 95%. Data from tissue analysis of rats gavaged with grape seed extract indicate fairly high accumulation of native compounds, primarily monomers and dimers, in the cecum and colon. Metabolite data indicate the progressive nature of microbial metabolism as the digesta moves through the lower GI tract. This method facilitates the high-throughput, sensitive, and simultaneous analysis of both native compounds and their microbial metabolites in biological samples and provides a more efficient means of extraction and analysis than previous methods. Copyright © 2014 Elsevier B.V. All rights reserved.

MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information

NASA Astrophysics Data System (ADS)

Charles, Laurence; Cavallo, Gianni; Monnier, Valérie; Oswald, Laurence; Szweda, Roza; Lutz, Jean-François

2017-06-01

In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner. [Figure not available: see fulltext.

Antibacterial Activity of Geminized Amphiphilic Cationic Homopolymers.

PubMed

Wang, Hui; Shi, Xuefeng; Yu, Danfeng; Zhang, Jian; Yang, Guang; Cui, Yingxian; Sun, Keji; Wang, Jinben; Yan, Haike

2015-12-22

The current study is aimed at investigating the effect of cationic charge density and hydrophobicity on the antibacterial and hemolytic activities. Two kinds of cationic surfmers, containing single or double hydrophobic tails (octyl chains or benzyl groups), and the corresponding homopolymers were synthesized. The antimicrobial activity of these candidate antibacterials was studied by microbial growth inhibition assays against Escherichia coli, and hemolysis activity was carried out using human red blood cells. It was interestingly found that the homopolymers were much more effective in antibacterial property than their corresponding monomers. Furthermore, the geminized homopolymers had significantly higher antibacterial activity than that of their counterparts but with single amphiphilic side chains in each repeated unit. Geminized homopolymers, with high positive charge density and moderate hydrophobicity (such as benzyl groups), combine both advantages of efficient antibacterial property and prominently high selectivity. To further explain the antibacterial performance of the novel polymer series, the molecular interaction mechanism is proposed according to experimental data which shows that these specimens are likely to kill microbes by disrupting bacterial membranes, leading them unlikely to induce resistance.

Multimerized CHR-derived peptides as HIV-1 fusion inhibitors.

PubMed

Nomura, Wataru; Hashimoto, Chie; Suzuki, Takaharu; Ohashi, Nami; Fujino, Masayuki; Murakami, Tsutomu; Yamamoto, Naoki; Tamamura, Hirokazu

2013-08-01

To date, several HIV-1 fusion inhibitors based on the carboxy-terminal leucine/isoleucine heptad repeat (CHR) region of an HIV-1 envelope protein gp41 have been discovered. We have shown that a synthetic peptide mimetic of a trimer form of the CHR-derived peptide C34 has potent inhibitory activity against the HIV-1 fusion mechanism, compared to a monomer C34 peptide. The present study revealed that a dimeric form of C34 is evidently structurally critical for fusion inhibitors, and that the activity of multimerized CHR-derived peptides in fusion inhibition is affected by the properties of the unit peptides C34, SC34EK, and T20. The fluorescence-based study suggested that the N36-interactive sites of the C34 trimer, including hydrophobic residues, are exposed outside the trimer and that trimerization of C34 caused a remarkable increase in fusion inhibitory activity. The present results could be useful in the design of fusion inhibitors against viral infections which proceed via membrane fusion with host cells. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural determination of a 5-acetamido-3,5,7, 9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulos onic acid-containing homopolysaccharide isolated from Sinorhizobium fredii HH103.

PubMed Central

Gil-Serrano, A M; Rodríguez-Carvajal, M A; Tejero-Mateo, P; Espartero, J L; Menendez, M; Corzo, J; Ruiz-Sainz, J E; BuendíA-Clavería, A M

1999-01-01

The structure of a polysaccharide from Sinorhizobium fredii HH103 has been determined. This polysaccharide was isolated by following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, matrix-assisted laser desorption ionization MS, electron-impact high-resolution MS, one-dimensional (1)H-NMR and (13)C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a homopolymer of a 3:1 mixture of 5-acetamido-3,5,7, 9-tetradeoxy-7-[(R)- and (S)-3-hydroxybutyramido]-l-glycero-l-manno-nonulosonic acid. The sugar residues are attached via a glycosidic linkage to the OH group of the 3-hydroxybutyramido substituent and thus the monomers are linked via both glycosidic and amidic linkages. In contrast with the Sinorhizobium K-antigens previously reported, which are composed of a disaccharide repeating unit, the K-antigen polysacharide of S. fredii HH103 is a homopolysaccharide. PMID:10477263

Bicomponent Block Copolymers Derived from One or More Random Copolymers as an Alternative Route to Controllable Phase Behavior

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

Ashraf, Arman R.; Ryan, Justin J.; Satkowski, Michael M.

Block copolymers have been extensively studied due to their ability to spontaneously self-organize into a wide variety of morphologies that are valuable in energy-, medical- and conservation-related (nano)technologies. While the phase behavior of bicomponent diblock and triblock copolymers is conventionally governed by temperature and individual block masses, we demonstrate that their phase behavior can alternatively be controlled through the use of blocks with random monomer sequencing. Block random copolymers (BRCs), i.e., diblock copolymers wherein one or both blocks is a random copolymer comprised of A and B repeat units, have been synthesized, and their phase behavior, expressed in terms ofmore » the order-disorder transition (ODT), has been investigated. Our results establish that, depending on the block composition contrast and molecular weight, BRCs can microphase-separate. We also report that the predicted ODT can be generated at relatively constant molecular weight and temperature with these new soft materials. This sequence-controlled synthetic strategy is extended to thermoplastic elastomeric triblock copolymers differing in chemistry and possessing a random-copolymer midblock.« less

Controllable synthesis, crystal structure and magnetic properties of Monomer-Dimer Cocrystallized MnIII Salen-type composite material

NASA Astrophysics Data System (ADS)

Wu, Qiong; Wu, Wei; Wu, Yongmei; Li, Weili; Qiao, Yongfeng; Wang, Ying; Wang, Baoling

2018-04-01

By the reaction of manganese-Schiff-base complexes with penta-anionic Anderson heteropolyanion, a new supramolecular architecture [Mn2(Salen)2(H2O)2][Mn(Salen)(H2O)2]2Na[IMo6O24]·8H2O (1) (salen = N,N‧-ethylene-bis (salicylideneiminate) has been isolated. Compound 1 was characterized by the single-crystal X-ray diffraction, elemental, IR and thermal gravimetric analyses. Structural analysis reveals that the unit cell simultaneously contains MnIII-Salen dimer and monomer cation fragments, for which the Anderson-type polyanions serve as counter anions. In the packing arrangement, all the MnIII dimers are well separated by polyoxometalate units and form tertiary structure together with MnIII monomers. Interestingly, different from the previous work, in the exact same reaction conditions, we are able to template MnIII-Salen complexes into different configurations by varying the charge state of polyanions. Besides, the magnetic properties of 1 were also examined by using both dc and ac magnetic field of the superconducting quantum interference devices. Most importantly, our fitting of the experimental data to a Heisenberg-type spin model shows that there exists a ferromagnetic exchange interaction ∼5 K between the spins (S = 2) on MnIII in the dimer, while antiferromagnetic ones exist among monomers and dimer (∼2 K). This meta-magnetic state could induce a slight spin frustration at low temperature, which would in turn affect the magnetic behavior. In addition, our ac field measurement of the susceptibilities suggests a typical signature for a single-molecule magnet.

Efficient and Tunable Three-Dimensional Functionalization of Fully Zwitterionic Antifouling Surface Coatings.

PubMed

Lange, Stefanie C; van Andel, Esther; Smulders, Maarten M J; Zuilhof, Han

2016-10-11

To enhance the sensitivity and selectivity of surface-based (bio)sensors, it is of crucial importance to diminish background signals that arise from the nonspecific binding of biomolecules, so-called biofouling. Zwitterionic polymer brushes have been shown to be excellent antifouling materials. However, for sensing purposes, antifouling does not suffice but needs to be combined with the possibility to efficiently modify the brush with recognition units. So far this has been achieved only at the expense of either antifouling properties or binding capacity. Herein we present a conceptually new approach by integrating both characteristics into a single tailor-made monomer: a novel sulfobetaine-based zwitterionic monomer equipped with a clickable azide moiety. Copolymerization of this monomer with a well-established standard sulfobetaine monomer results in highly antifouling surface coatings with a large yet tunable number of clickable groups present throughout the entire brush. Subsequent functionalization of the azido brushes via widely used strain-promoted alkyne azide click reactions yields fully zwitterionic 3D-functionalized coatings with a recognition unit of choice that can be tailored for any specific application. Here we show a proof of principle with biotin-functionalized brushes on Si 3 N 4 that combine excellent antifouling properties with specific avidin binding from a protein mixture. The signal-to-noise ratio is significantly improved over that of traditional chain-end modification of sulfobetaine polymer brushes, even if the azide content is lowered to 1%. This therefore offers a viable approach to the development of biosensors with greatly enhanced performance on any surface.

Three-dimensional modeling of glucose-6-phosphate dehydrogenase-deficient variants from German ancestry.

PubMed

Kiani, Farooq; Schwarzl, Sonja; Fischer, Stefan; Efferth, Thomas

2007-07-18

Loss of function of dimeric glucose-6-phosphate dehydrogenase (G6PD) represents the most common inborn error of metabolism throughout the world affecting an estimated 400 million people. In Germany, this enzymopathy is very rare. On the basis of G6PD crystal structures, we have analyzed six G6PD variants of German ancestry by three-dimensional modeling. All mutations present in the German population are either close to one of the three G6P or NADP(+) units or to the interface of the two monomers. Two of the three mutated amino acids of G6PD Vancouver are closer to the binding site of NADP(+). The G6PD Aachen mutation is also closer to the second NADP(+) unit. The G6PD Wayne mutation is closer to the G6P binding region. These mutations may affect the binding of G6P and NADP(+) units. Three mutations, i.e. G6PD Munich, G6PD Riverside and G6PD Gastonia, lie closer to the interface of the two monomers. These may also affect the interface of two monomers. None of these G6PD variants share mutations with the common G6PD variants known from the Mediterranean, Near East, or Africa indicating that they have developed independently. The G6PD variants have been compared with mutants from other populations and the implications for survival of G6PD variants from natural selection have been discussed.

Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus.

PubMed

Rajagopal, J; Das, S; Khurana, D K; Srivastava, P S; Lakshmikumaran, M

1999-10-01

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.

Isolation and characterisation of the biological repeating unit of cepacian, the exopolysaccharide produced by bacteria of the Burkholderia cepacia complex.

PubMed

Cescutti, Paola; Foschiatti, Michela; Furlanis, Linda; Lagatolla, Cristina; Rizzo, Roberto

2010-07-02

The repeating unit of cepacian, the exopolysaccharide produced by the majority of the microorganisms belonging to the Burkholderia cepacia complex, was isolated from inner bacterial membranes and investigated by mass spectrometry, with and without prior derivatisation. Interpretation of the mass spectra led to the determination of the biological repeating unit primary structure, thus disclosing the nature of the oligosaccharide produced in vivo. Moreover, mass spectra recorded on the native sample revealed that acetyl substitution was very variable, producing a mixture of repeating units containing zero to four acyl groups. At the same time, finding acetylated oligosaccharides showed that binding of these substituents occurred in the cellular periplasmic space, before the polymerisation process took place. In the chromatographic peak containing the repeating unit, oligosaccharides shorter than the repeating unit co-eluted. Mass spectrometric analysis showed that they were biosynthetic intermediates of the repeating unit and further investigation revealed the biosynthetic sequence of cepacian building block. Copyright 2010 Elsevier Ltd. All rights reserved.

Synthesis and Characterization of Polymers for Fuel Cells Application

NASA Technical Reports Server (NTRS)

Tytko, Stephen F.

2003-01-01

The goal of this summer research is to prepare Polymer Exchange Membranes (PEM s) for fuel cell application. Several high temperature polymers such as polybenzimidazoles and polyether ketones were known to possess good high temperature stability and had been investigated by post-sulfonation to yield sulfonated polymers. The research project will involve two approaches: 1. Synthesis of polybenzimidazoles and then react with alkyl sultonse to attach an aliphatic sulfonic groups. 2. Synthesis of monomers containing sulfonic acid units either on a aromatic ring or on an aliphatic chain and then polymerize the monomers to form high molecular weight sulfonate polymers.

Nucleoside-O-Methyl-(H)-Phosphinates: Novel Monomers for the Synthesis of Methylphosphonate Oligonucleotides Using H-Phosphonate Chemistry.

PubMed

Kostov, Ondřej; Páv, Ondřej; Rosenberg, Ivan

2017-09-18

This unit comprises the straightforward synthesis of protected 2'-deoxyribonucleoside-O-methyl-(H)-phosphinates in both 3'- and 5'-series. These compounds represent a new class of monomers compatible with the solid-phase synthesis of oligonucleotides using H-phosphonate chemistry and are suitable for the preparation of both 3'- and 5'-O-methylphosphonate oligonucleotides. The synthesis of 4-toluenesulfonyloxymethyl-(H)-phosphinic acid as a new reagent for the preparation of O-methyl-(H)-phosphinic acid derivatives is described. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers

DOE PAGES

Olek, Anna T.; Rayon, Catherine; Makowski, Lee; ...

2014-07-10

Cellulose microfibrils are para-crystalline arrays of several dozen linear (1→4)-β-d-glucan chains synthesized at the surface of the cell membrane by large, multimeric complexes of synthase proteins. Recombinant catalytic domains of rice ( Oryza sativa) CesA8 cellulose synthase form dimers reversibly as the fundamental scaffold units of architecture in the synthase complex. Specificity of binding to UDP and UDP-Glc indicates a properly folded protein, and binding kinetics indicate that each monomer independently synthesizes single glucan chains of cellulose, i.e., two chains per dimer pair. In contrast to structure modeling predictions, solution x-ray scattering studies demonstrate that the monomer is a two-domain,more » elongated structure, with the smaller domain coupling two monomers into a dimer. The catalytic core of the monomer is accommodated only near its center, with the plant-specific sequences occupying the small domain and an extension distal to the catalytic domain. This configuration is in stark contrast to the domain organization obtained in predicted structures of plant CesA. As a result, the arrangement of the catalytic domain within the CesA monomer and dimer provides a foundation for constructing structural models of the synthase complex and defining the relationship between the rosette structure and the cellulose microfibrils they synthesize.« less

Effect of increased exposure times on amount of residual monomer released from single-step self-etch adhesives.

PubMed

Altunsoy, Mustafa; Botsali, Murat Selim; Tosun, Gonca; Yasar, Ahmet

2015-10-16

The aim of this study was to evaluate the effect of increased exposure times on the amount of residual Bis-GMA, TEGDMA, HEMA and UDMA released from single-step self-etch adhesive systems. Two adhesive systems were used. The adhesives were applied to bovine dentin surface according to the manufacturer's instructions and were polymerized using an LED curing unit for 10, 20 and 40 seconds (n = 5). After polymerization, the specimens were stored in 75% ethanol-water solution (6 mL). Residual monomers (Bis-GMA, TEGDMA, UDMA and HEMA) that were eluted from the adhesives (after 10 minutes, 1 hour, 1 day, 7 days and 30 days) were analyzed by high-performance liquid chromatography (HPLC). The data were analyzed using 1-way analysis of variance and Tukey HSD tests. Among the time periods, the highest amount of released residual monomers from adhesives was observed in the 10th minute. There were statistically significant differences regarding released Bis-GMA, UDMA, HEMA and TEGDMA between the adhesive systems (p<0.05). There were no significant differences among the 10, 20 and 40 second polymerization times according to their effect on residual monomer release from adhesives (p>0.05). Increasing the polymerization time did not have an effect on residual monomer release from single-step self-etch adhesives.

The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers.

PubMed

Olek, Anna T; Rayon, Catherine; Makowski, Lee; Kim, Hyung Rae; Ciesielski, Peter; Badger, John; Paul, Lake N; Ghosh, Subhangi; Kihara, Daisuke; Crowley, Michael; Himmel, Michael E; Bolin, Jeffrey T; Carpita, Nicholas C

2014-07-01

Cellulose microfibrils are para-crystalline arrays of several dozen linear (1→4)-β-d-glucan chains synthesized at the surface of the cell membrane by large, multimeric complexes of synthase proteins. Recombinant catalytic domains of rice (Oryza sativa) CesA8 cellulose synthase form dimers reversibly as the fundamental scaffold units of architecture in the synthase complex. Specificity of binding to UDP and UDP-Glc indicates a properly folded protein, and binding kinetics indicate that each monomer independently synthesizes single glucan chains of cellulose, i.e., two chains per dimer pair. In contrast to structure modeling predictions, solution x-ray scattering studies demonstrate that the monomer is a two-domain, elongated structure, with the smaller domain coupling two monomers into a dimer. The catalytic core of the monomer is accommodated only near its center, with the plant-specific sequences occupying the small domain and an extension distal to the catalytic domain. This configuration is in stark contrast to the domain organization obtained in predicted structures of plant CesA. The arrangement of the catalytic domain within the CesA monomer and dimer provides a foundation for constructing structural models of the synthase complex and defining the relationship between the rosette structure and the cellulose microfibrils they synthesize. © 2014 American Society of Plant Biologists. All rights reserved.

Monomer Release from Resin Based Dental Materials Cured With LED and Halogen Lights

PubMed Central

Ak, Asli Topaloglu; Alpoz, A. Riza; Bayraktar, Oguz; Ertugrul, Fahinur

2010-01-01

Objectives: To measure the release of TEGDMA and BisGMA from two commercially available composite resins; Filtek Z 250 (3M ESPE, Germany), Leaddent (Leaddent, Germany) and two fissure sealants; Helioseal F (3M ESPE, Germany) Enamel Loc (Premiere Rev, USA) over 1, 3 and 7 days after polymerization with standard quartz-tungsten halogen Coltolux II (QHL) (Coltene Switzerland) and a standard blue light emitting diode Elipar Freelight 2 (3M ESPE, Germany). Methods: 9 samples of each material were placed in disc shaped specimens in 1 mm of thickness and 10 mm in diameter (n=36). Each material was polymerized using LED for 20 s (n=12), 40 s (n=12) and halogen for 40 s (n=12), respectively. High Performance Liquid Chromatography (HPLC) was used to measure the amount of monomers released over 1, 3 and 7 days. Data was analyzed using one way ANOVA and Bonferroni test for multiple comparisons with a significance level of .05. Results: LED 20 sec group showed the highest release of monomers at 1, 3 and 7 days in sealant groups. Halogen 40 sec group resulted highest release of monomers for Leaddent at all time intervals (P<.05) Conclusions: Efficiency of the curing unit and applying the recommended curing time of the light activated resin based dental materials is very important to protect the patient from potential hazards of residual monomers. PMID:20046478

High Temperature Degradation of 5250-4 Polymer Resin

DTIC Science & Technology

2007-06-01

fragments. The pieces were then repeatedly crushed between two stainless steel plates with a Wabash 30 Ton Press. After this process, the pieces...the BMI powder. Two stainless steel ASTM test sieves, with mesh sizes of 45 and 90 µm, were used to collect only the powder in the 45 to 90 µm range...The o,o’-diallylbisphenol A ( BPA ) monomer in Figure 1 is not a bismaleimide, but it is often used in BMI polymers to make otherwise brittle BMIs

PALS Free Volume Measurements of Fractionated Hydrido- Silsesquioxane Resin.

NASA Astrophysics Data System (ADS)

Madani, Mahmoud M.; Granata, Richard D.; Pernisz, Udo C.

1997-03-01

Hydrido-Silsesquioxane (HSQ) is a resinous polymer with monomer unit formula (HSiO_3/2)_n. For n=8...16, it forms cages which in turn cross-link to yield a resin with a broad molecular weight distribution. It is soluble and forms thin films that may be converted to low-density silica with excellent dielectric properties. These, and the HSQ solubility, depend on molecular structure and size distribution of the cages. Samples of different molecular weight fractions were prepared from HSQ by SCF and the free volume of several cuts was measured by PALS in a conventional fast-fast system. POSITRONFIT and CONTIN programs were used to analyze the spectra. Three separate lifetime regions were identified with free volume regimes that correlate strongly with the molecular weight. The lowest is identified with the monomer cage unit, the larger values with intramolecular separation.

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.

PubMed

Hirsh, Layla; Paladin, Lisanna; Piovesan, Damiano; Tosatto, Silvio C E

2018-05-09

RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poorly annotated class of non-globular proteins carrying heterogeneous functions. RepeatsDB-lite extends the prediction to all TR types and strongly improves the performance both in terms of computational time and accuracy over previous methods, with precision above 95% for solenoid structures. The algorithm exploits an improved TR unit library derived from the RepeatsDB database to perform an iterative structural search and assignment. The web interface provides tools for analyzing the evolutionary relationships between units and manually refine the prediction by changing unit positions and protein classification. An all-against-all structure-based sequence similarity matrix is calculated and visualized in real-time for every user edit. Reviewed predictions can be submitted to RepeatsDB for review and inclusion.

A comparative evaluation of effect of modern-curing lights and curing modes on conventional and novel-resin monomers

PubMed Central

Roy, Konda Karthik; Kumar, Kanumuru Pavan; John, Gijo; Sooraparaju, Sujatha Gopal; Nujella, Surya Kumari; Sowmya, Kyatham

2018-01-01

Aim: The aim of this study is to compare and to evaluate effect of curing light and curing modes on the nanohybrid composite resins with conventional Bis-GMA and novel tricyclodecane (TCD) monomers. Methodology: Two nanohybrid composites, IPS empress direct and charisma diamond were used in this study. Light-emitting diode (LED)-curing unit and quartz-tungsten-halogen (QTH)-curing unit which were operated into two different modes: continuous and soft start. Based on the composite resin, curing lights, and mode of curing used, the samples were divided into 8 groups. After polymerization, the samples were stored for 48 h in complete darkness at 37°C and 100% humidity. The Vickers hardness (VK) of the surface was determined with Vickers indenter by the application of 200 g for 15 s. Three VK readings were recorded for each sample surface both on top and bottom surfaces. For all the specimens, the three hardness values for each surface were averaged and reported as a single value. The mean VK and hardness ratio were calculated. The depth of cure was assessed based on the hardness ratio. Results: Comparison of mean hardness values and hardness ratios was done using ANOVA with post hoc Tukey's test. Conclusion: Both QTH- and LED-curing units had shown the adequate depth of cure. Soft-start-curing mode in both QTH- and LED-curing lights had effectively increased microhardness than the continuous mode of curing. TCD monomer had shown higher hardness values compared with conventional Bis-GMA-containing resin. PMID:29628651

Amphiphilic polymeric micelle as pseudostationary phase in electrokinetic chromatography for analysis of eight corticosteroids in cosmetics.

PubMed

Xu, Xiaojin; Ni, Xinjiong; Cao, Yuhua; Zhuo, Xiaolu; Yang, Xiaoxiao; Cao, Guangqun

2014-03-01

Amphiphilic polymeric micelle, as a novel pseudostationary phase in EKC was used to determine eight kinds of corticosteroids namely hydrocortisone, prednisolone, hydrocortisone acetate, prednisone, cortisone acetate, prednisolone acetate, dexamethasone, and triamcinolone acetonide in cosmetics. Amphiphilic random copolymer poly(methyl methacrylate-co-methacrylic acid) (P(MMA-co-MAA)) was micellizated via neutralization in alkaline aqueous solution. The influences of the molar ratio of monomer MMA to MAA, the concentration of polymer and pH on the polymeric micelle microstructure and EKC performances were investigated. As molar ratio of MMA to MAA in P(MMA-co-MAA) increased, both CMC and environmental polarity of the inner core in polymeric micelle decreased dramatically. With increasing monomer ratio, the size of polymeric micelles increased firstly, and then decreased, finally increased again. ζ potential of the micelle had a slight decline trend. As increment of polymer concentration, the size of the polymeric micelle increased steadily. By optimizing the monomer ratio, the polymer concentration, and pH of the running buffer, as well as operation conditions such as separation voltage and temperature, the eight analytes could be separated within 16.5 min using 7.5 mg/mL polymer with the monomer ratio of 7:3 dissolved in pH 9.2 borax buffer as the running buffer. The method has been used for analysis of corticosteroids in cosmetic samples with simple extraction; the recoveries for eight analytes were between 85.9 and 106%. This method was of accuracy, repeatability, pretreatment simplicity, and could be applied to the quality control of cosmetics. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymerization on the rocks: theoretical introduction

NASA Technical Reports Server (NTRS)

Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

It is difficult if not impossible to synthesize long polymers of amino acids, nucleotides, etc., in homogeneous aqueous solution. We suggest that long polymers were synthesized on the surface of minerals in a prebiotic process analogous to solid-phase synthesis. Provided that the affinity of a mineral for an oligomer increases with the length of the oligomer, adsorption must become essentially irreversible for sufficiently long oligomers. Irreversibly adsorbed oligomers may be elongated indefinitely by repeated cycles in which the mineral with its adsorbed oligomers is first incubated with activated monomers and then washed free of deactivated monomer and side-products. We discuss in some detail the formation of oligomers of negatively-charged amino acids such as glutamic acid on anion-exchange minerals such as hydroxylapatite or illite. We show that the average length of adsorbed oligomers at steady state, n, depends on the balance between the rate of chain elongation and the rate of hydrolysis, and we derive a very approximate formula for n.

Sulfonated macro-RAFT agents for the surfactant-free synthesis of cerium oxide-based hybrid latexes.

PubMed

Garnier, Jérôme; Warnant, Jérôme; Lacroix-Desmazes, Patrick; Dufils, Pierre-Emmanuel; Vinas, Jérôme; van Herk, Alex

2013-10-01

Three types of amphiphatic macro-RAFT agents were employed as compatibilizers to promote the polymerization reaction at the surface of nanoceria for the synthesis of CeO2-based hybrid latexes. Macro-RAFT copolymers and terpolymers were first synthesized employing various combinations of butyl acrylate as a hydrophobic monomer and acrylic acid (AA) and/or 2-acrylamido-2-methylpropane sulfonic acid (AMPS) as hydrophilic monomers. After characterizing the adsorption of these macro-RAFT agents at the cerium oxide surface by UV-visible spectrometry, emulsion copolymerization reactions of styrene and methyl acrylate were then carried out in the presence of the surface-modified nanoceria. Dynamic Light Scattering and cryo-Transmission Electron Microscopy were employed to confirm the hybrid structure of the final CeO2/polymer latexes, and proved that the presence of acrylic acid units in amphiphatic macro-RAFT agents enabled an efficient formation of hybrid structures, while the presence of AMPS units, when combined with AA units, resulted in a better distribution of cerium oxide nanoclusters between latex particles. Copyright © 2013 Elsevier Inc. All rights reserved.

Precise control of surface electrostatic forces on polymer brush layers with opposite charges for resistance to protein adsorption.

PubMed

Sakata, Sho; Inoue, Yuuki; Ishihara, Kazuhiko

2016-10-01

Various molecular interaction forces are generated during protein adsorption process on material surfaces. Thus, it is necessary to control them to suppress protein adsorption and the subsequent cell and tissue responses. A series of binary copolymer brush layers were prepared via surface-initiated atom transfer radical polymerization, by mixing the cationic monomer unit and anionic monomer unit randomly in various ratios. Surface characterization revealed that the constructed copolymer brush layers exhibited an uniform super-hydrophilic nature and different surface potentials. The strength of the electrostatic interaction forces operating on these mixed-charge copolymer brush surfaces was evaluated quantitatively using force-versus-distance (f-d) curve measurements by atomic force microscopy (AFM) and probes modified by negatively charged carboxyl groups or positively charged amino groups. The electrostatic interaction forces were determined based on the charge ratios of the copolymer brush layers. Notably, the surface containing equivalent cationic/anionic monomer units hardly interacted with both the charged groups. Furthermore, the protein adsorption force and the protein adsorption mass on these surfaces were examined by AFM f-d curve measurement and surface plasmon resonance measurement, respectively. To clarify the influence of the electrostatic interaction on the protein adsorption behavior on the surface, three kinds of proteins having negative, positive, and relatively neutral net charges under physiological conditions were used in this study. We quantitatively demonstrated that the amount of adsorbed proteins on the surfaces would have a strong correlation with the strength of surface-protein interaction forces, and that the strength of surface-protein interaction forces would be determined from the combination between the properties of the electrostatic interaction forces on the surfaces and the charge properties of the proteins. Especially, the copolymer brush surface composed of equivalent cationic/anionic monomer units exhibited no significant interaction forces, and dramatically suppressed the adsorption of proteins regardless of their charge properties. We conclude that the established methodology could elucidate relationship between the protein adsorption behavior and molecular interaction, especially the electrostatic interaction forces, and demonstrated that the suppression of the electrostatic interactions with the ionic functional groups would be important for the development of new polymeric biomaterials with a high repellency of protein adsorption. Copyright © 2016 Elsevier Ltd. All rights reserved.

Occupational exposure to acrylamide in closed system production plants: air levels and biomonitoring.

PubMed

Moorman, William J; Reutman, Susan S; Shaw, Peter B; Blade, Leo Michael; Marlow, David; Vesper, Hubert; Clark, John C; Schrader, Steven M

2012-01-01

The aim of this study was to evaluate biomarkers of acrylamide exposure, including hemoglobin adducts and urinary metabolites in acrylamide production workers. Biomarkers are integrated measures of the internal dose, and it is total acrylamide dose from all routes and sources that may present health risks. Workers from three companies were studied. Workers potentially exposed to acrylamide monomer wore personal breathing-zone air samplers. Air samples and surface-wipe samples were collected and analyzed for acrylamide. General-area air samples were collected in chemical processing units and control rooms. Hemoglobin adducts were isolated from ethylenediamine teraacetic acid (EDTA)-whole blood, and adducts of acrylamide and glycidamide, at the N-terminal valines of hemoglobin, were cleaved from the protein chain by use of a modified Edman reaction. Full work-shift, personal breathing zone, and general-area air samples were collected and analyzed for particulate and acrylamide monomer vapor. The highest general-area concentration of acrylamide vapor was 350 μg/cm(3) in monomer production. Personal breathing zone and general-area concentrations of acrylamide vapor were found to be highest in monomer production operations, and lower levels were in the polymer production operations. Adduct levels varied widely among workers, with the highest in workers in the monomer and polymer production areas. The acrylamide adduct range was 15-1884 pmol/g; glycidamide adducts ranged from 17.8 to 1376 p/mol/g. The highest acrylamide and glycidamide adduct levels were found among monomer production process operators. The primary urinary metabolite N-acetyl-S-(2-carbamoylethyl) cysteine (NACEC) ranged from the limit of detection to 15.4 μg/ml. Correlation of workplace exposure and sentinel health effects is needed to determine and control safe levels of exposure for regulatory standards.

Ultrafast endothermic transfer of non-radiative exciplex state to radiative excitons in polyfluorene random copolymer for blue electroluminescence

NASA Astrophysics Data System (ADS)

Moghe, Dhanashree A.; Dey, Amrita; Johnson, Kerr; Lu, L.-P.; Friend, Richard H.; Kabra, Dinesh

2018-04-01

We report a blue-emitting random copolymer (termed modified Aryl-F8) consisting of three repeat units of polydioctylfluorene (F8), Aryl-polydioctylfluorene (Aryl-F8), and an aromatic amine comonomer unit, poly(bis-N,Ν'-(4-butylphenyl)-bis-N,N'-phenyl-1,4 phenylenediamine) chemically linked to get an improved charge carrier balance without compromising on the photoluminescence (PL) quantum yield with respect to the Aryl-F8 homo-polymer. The measured photoluminescence quantum efficiency (˜70%) of the blue-emitting polymer is comparable to or greater than the individual monomer units. The time resolved PL spectra from the modified Aryl-F8 are similar to those of Arylated-poly(9,9'-dioctylfluorene-co-bis-N,N'-(4-butylphenyl)-bis-N,N'-phenyl-1,4 phenylenediamine) (PFB) even at a time scale of 100-250 ps, indicating an ultrafast energy transfer from the (Aryl-F8 or F8):Arylated-PFB interface to Arylated-PFB, i.e., endothermic transfer of non-radiative exciplex to a radiative molecular exciton. Furthermore, the presence of non-radiative exciplex is confirmed by the photoluminescence decay profile and temperature dependent PL spectra. The luminance efficiency achieved for the modified Aryl-F8 polymer light-emitting diodes is ˜11 cd A-1 with an external quantum efficiency (EQE) of ˜4.5%, whereas it is 0.05 cd/A with an EQE of ˜0.025% for Aryl-F8. Almost two orders of higher efficiency is achieved due to the improved charge carrier balance from the random copolymer without compromising on the photoluminescence yield.

High Dynamic Range (Δn) Two-Stage Photopolymers via Enhanced Solubility of a High Refractive Index Acrylate Writing Monomer.

PubMed

Alim, Marvin D; Glugla, David J; Mavila, Sudheendran; Wang, Chen; Nystrom, Philip D; Sullivan, Amy C; McLeod, Robert R; Bowman, Christopher N

2018-01-10

Holographic photopolymers capable of high refractive index modulation (Δn) on the order of 10 -2 are integral for the fabrication of functional holographic optical elements that are useful in a myriad of optical applications. In particular, to address the deficiency of suitable high refractive index writing monomers for use in two-stage holographic formulations, here we report a novel high refractive index writing monomer, 1,3-bis(phenylthio)-2-propyl acrylate (BPTPA), simultaneously possessing enhanced solubility in a low refractive index (n = 1.47) urethane matrix. When examined in comparison to a widely used high refractive index monomer, 2,4,6-tribromophenyl acrylate, BPTPA exhibited superior solubility in a stage 1 urethane matrix of approximately 50% with a 20% higher refractive index increase per unit amount of the writing monomer for stage 2 polymerizations. Formulations with 60 wt % loading of BPTPA exhibit a peak-to-mean holographic Δn ≈ 0.029 without obvious deficiencies in transparency, color, or scatter. To the best of our knowledge, this value is the highest reported in the peer-reviewed literature for a transmission hologram. The capabilities and versatility of BPTPA-based formulations are demonstrated at varying length scales via demonstrative refractive index gradient structure examples including direct laser write, projection mask lithography of a 1″ diameter Fresnel lens, and ∼100% diffraction efficiency volume transmission holograms with a 1 μm fringe spacing in 11 μm thick samples.

Polymer-gel formation and reformation on irradiation of tertiary-butyl acrylate

NASA Astrophysics Data System (ADS)

Yao, Tiantian; Denkova, Antonia G.; Warman, John M.

2014-04-01

The purpose of the present research was to provide a radiation-chemical basis for the use of tertiary-butyl acrylate gels in radio-fluorogenic dose-imaging applications (Warman et al. 2011a,b, 2013a,b). The radiation-induced polymerization of tertiary-butyl acrylate (TBA) results in the formation of a transparent gel with an optical density lower than 0.1 cm-1 from 600 nm down to 315 nm. The fractional monomer-to-polymer conversion, CM, determined gravimetrically, increases super-linearly with dose, D Gy. Up to CM≈40%, and over the dose rate range D‧=3.5 to 49 cGy s-1, the dose dependence is given by CM=[1+ACM]KD/√D‧ with K=1.43×10-3 Gy-0.5 s-0.5 and A=0.70. For D‧=3.5 cGy s-1 the average polymer size is estimated to be 1.2×105 monomer units or 17 megadalton. For CM≥10% the gel is quasi-rigid, displaying little tendency to flow on a timescale of an hour or more. After removal of monomer by evacuation, the gel can be reformed by adding a volume of monomer to the remaining polymer equal to that removed and allowing this to swell for several days. The dose and dose rate dependence of radiation-induced monomer conversion in the reformed gel show no evidence of a discontinuity caused by the intervening evacuation and reformation procedures.

Analysis of tandem repeat units of the promoter of capsanthin/capsorubin synthase (Ccs) gene in pepper fruit.

PubMed

Tian, Shi-Lin; Li, Zheng; Li, Li; Shah, S N M; Gong, Zhen-Hui

2017-07-01

Capsanthin/capsorubin synthase ( Ccs ) gene is a key gene that regulates the synthesis of capsanthin and the development of red coloration in pepper fruits. There are three tandem repeat units in the promoter region of Ccs , but the potential effects of the number of repetitive units on the transcriptional regulation of Ccs has been unclear. In the present study, expression vectors carrying different numbers of repeat units of the Ccs promoter were constructed, and the transient expression of the β-glucuronidase ( GUS ) gene was used to detect differences in expression levels associated with the promoter fragments. These repeat fragments and the plant expression vector PBI121 containing the 35s CaMV promoter were ligated to form recombinant vectors that were transfected into Agrobacterium tumefaciens GV3101. A fluorescence spectrophotometer was used to analyze the expression associated with the various repeat units. It was concluded that the constructs containing at least one repeat were associated with GUS expression, though they did not differ from one another. This repeating unit likely plays a role in transcription and regulation of Ccs expression.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

PubMed

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Promoter Engineering Reveals the Importance of Heptameric Direct Repeats for DNA Binding by Streptomyces Antibiotic Regulatory Protein-Large ATP-Binding Regulator of the LuxR Family (SARP-LAL) Regulators in Streptomyces natalensis.

PubMed

Barreales, Eva G; Vicente, Cláudia M; de Pedro, Antonio; Santos-Aberturas, Javier; Aparicio, Jesús F

2018-05-15

The biosynthesis of small-size polyene macrolides is ultimately controlled by a couple of transcriptional regulators that act in a hierarchical way. A Streptomyces antibiotic regulatory protein-large ATP-binding regulator of the LuxR family (SARP-LAL) regulator binds the promoter of a PAS-LuxR regulator-encoding gene and activates its transcription, and in turn, the gene product of the latter activates transcription from various promoters of the polyene gene cluster directly. The primary operator of PimR, the archetype of SARP-LAL regulators, contains three heptameric direct repeats separated by four-nucleotide spacers, but the regulator can also bind a secondary operator with only two direct repeats separated by a 3-nucleotide spacer, both located in the promoter region of its unique target gene, pimM A similar arrangement of operators has been identified for PimR counterparts encoded by gene clusters for different antifungal secondary metabolites, including not only polyene macrolides but peptidyl nucleosides, phoslactomycins, or cycloheximide. Here, we used promoter engineering and quantitative transcriptional analyses to determine the contributions of the different heptameric repeats to transcriptional activation and final polyene production. Optimized promoters have thus been developed. Deletion studies and electrophoretic mobility assays were used for the definition of DNA-binding boxes formed by 22-nucleotide sequences comprising two conserved heptameric direct repeats separated by four-nucleotide less conserved spacers. The cooperative binding of PimR SARP appears to be the mechanism involved in the binding of regulator monomers to operators, and at least two protein monomers are required for efficient binding. IMPORTANCE Here, we have shown that a modulation of the production of the antifungal pimaricin in Streptomyces natalensis can be accomplished via promoter engineering of the PAS-LuxR transcriptional activator pimM The expression of this gene is controlled by the Streptomyces antibiotic regulatory protein-large ATP-binding regulator of the LuxR family (SARP-LAL) regulator PimR, which binds a series of heptameric direct repeats in its promoter region. The structure and importance of such repeats in protein binding, transcriptional activation, and polyene production have been investigated. These findings should provide important clues to understand the regulatory machinery that modulates antibiotic biosynthesis in Streptomyces and open new possibilities for the manipulation of metabolite production. The presence of PimR orthologues encoded by gene clusters for different secondary metabolites and the conservation of their operators suggest that the improvements observed in the activation of pimaricin biosynthesis by Streptomyces natalensis could be extrapolated to the production of different compounds by other species. Copyright © 2018 Barreales et al.

Signature of hydrophobic hydration in a single polymer

PubMed Central

Li, Isaac T. S.; Walker, Gilbert C.

2011-01-01

Hydrophobicity underpins self-assembly in many natural and synthetic molecular and nanoscale systems. A signature of hydrophobicity is its temperature dependence. The first experimental evaluation of the temperature and size dependence of hydration free energy in a single hydrophobic polymer is reported, which tests key assumptions in models of hydrophobic interactions in protein folding. Herein, the hydration free energy required to extend three hydrophobic polymers with differently sized aromatic side chains was directly measured by single molecule force spectroscopy. The results are threefold. First, the hydration free energy per monomer is found to be strongly dependent on temperature and does not follow interfacial thermodynamics. Second, the temperature dependence profiles are distinct among the three hydrophobic polymers as a result of a hydrophobic size effect at the subnanometer scale. Third, the hydration free energy of a monomer on a macromolecule is different from a free monomer; corrections for the reduced hydration free energy due to hydrophobic interaction from neighboring units are required. PMID:21911397

Effect of Sequence Blockiness on the Morphologies of Surface-grafted Elastin-like Polypeptides

NASA Astrophysics Data System (ADS)

Albert, Julie; Sintavanon, Kornkanok; Mays, Robin; MacEwan, Sarah; Chilkoti, Ashutosh; Genzer, Jan

2014-03-01

The inter- and intra- molecular interactions among monomeric units of copolymers and polypeptides depend strongly on monomer sequence distribution and dictate the phase behavior of these species both in solution and on surfaces. To study the relationship between sequence and phase behavior, we have designed a series of elastin-like polypeptides (ELPs) with controlled monomer sequences that mimic copolymers with various co-monomer sequence distributions and attached them covalently to silicon substrates from buffer solutions at temperatures below and above the bulk ELPs' lower critical solution temperatures (LCSTs). The dependence of ELP grafting density on solution temperature was examined by ellipsometry and the resultant surface morphologies were examined in air and under water with atomic force microscopy. Depositions performed above the LCST resulted in higher grafting densities and greater surface roughness of ELPs relative to depositions carried out below the LCST. In addition, we are using gradient substrates to examine the effect of ELP grafting density on temperature responsiveness.

Lignin dimers: Structures, distribution, and potential geochemical applications

NASA Astrophysics Data System (ADS)

Goñi, Miguel A.; Hedges, John I.

1992-11-01

An extensive suite of thirty lignin-derived phenolic dimers and fourteen additional monomers has been identified among the CuO reaction products of twenty-four different vascular plant tissues. The various lignin dimers are characterized by five different types of linkages between phenolic units, including direct 5,5'-ring-ring bonding, as well as β,1-diketone, α,1-monoketone, α,5-monoketone, and α,2-methyl sidechain-ring couplings. The new lignin-derived monomeric CuO reaction products include vanillyl and syringyl glyoxalic acids and vanillyl phenols with formyl and carboxyl functional groups attached at various ring positions. The distribution of all these novel compounds in twenty-four different vascular plant tissues indicates important differences in the structure and chemical composition of the lignin macromolecule among these sources. The abundances of these compounds in a selected set of sedimentary samples suggest that the lignin dimers and novel lignin monomers can characterize the ultrastructure, sources, and diagenetic state of sedimentary lignin in ways not possible from the routinely utilized lignin monomers alone.

High degree of polymerization in a fullerene-containing supramolecular polymer.

PubMed

Isla, Helena; Pérez, Emilio M; Martín, Nazario

2014-05-26

Supramolecular polymers based on dispersion forces typically show lower molecular weights (MW) than those based on hydrogen bonding or metal-ligand coordination. We present the synthesis and self-assembling properties of a monomer featuring two complementary units, a C60 derivative and an exTTF-based macrocycle, that interact mainly through π-π, charge-transfer, and van der Waals interactions. Thanks to the preorganization in the host part, a remarkable log K(a)=5.1±0.5 in CHCl3 at room temperature is determined for the host-guest couple. In accordance with the large binding constant, the monomer self-assembles in the gas phase, in solution, and in the solid state to form linear supramolecular polymers with a very high degree of polymerization. A MW above 150 kDa has been found experimentally in solution, while in the solid state the monomer forms extraordinarily long, straight, and uniform fibers with lengths reaching several microns. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New Insights Toward Quantitative Relationships between Lignin Reactivity to Monomers and Their Structural Characteristics.

PubMed

Ma, Ruoshui; Zhang, Xiumei; Wang, Yi; Zhang, Xiao

2018-04-27

The heterogeneous and complex structural characteristics of lignin present a significant challenge to predict its processability (e.g. depolymerization, modifications etc) to valuable products. This study provides a detailed characterization and comparison of structural properties of seven representative biorefinery lignin samples derived from forest and agricultural residues, which were subjected to representative pretreatment methods. A range of wet chemistry and spectroscopy methods were applied to determine specific lignin structural characteristics such as functional groups, inter-unit linkages and peak molecular weight. In parallel, oxidative depolymerization of these lignin samples to either monomeric phenolic compounds or dicarboxylic acids were conducted, and the product yields were quantified. Based on these results (lignin structural characteristics and monomer yields), we demonstrated for the first time to apply multiple-variable linear estimations (MVLE) approach using R statistics to gain insight toward a quantitative correlation between lignin structural properties and their conversion reactivity toward oxidative depolymerization to monomers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Low Dielectric Polymers

NASA Technical Reports Server (NTRS)

Venumbaka, Sreenivasulu R.; Cassidy, Patrick E.

2002-01-01

This report summarizes results obtained from research funded through Research Cooperative Agreement No. NCC-1-01033-"Low Dielectric Polymers" (from 5/10/01 through 5/09/02). Results are reported in three of the proposed research areas (Tasks 1-3 in the original proposal): (1) Repeat and confirm the preparation and properties of the new alkyl-substituted PEK, 6HC17-PEK, (2) Prepare and evaluate polymers derived from a highly fluorinated monomer, and (3) Prepare and evaluate new silicon and/or fluorine-containing polymers expected to retain useful properties at low temperature.

A metal-linked gapped zipper model is proposed for the 90 kDa heat shock protein-estrogen receptor interface.

PubMed

Schwartz, J A; Mizukami, H

1991-06-01

A novel arrangement is proposed for the association of the 90 kDa heat shock protein (hsp 90) dimer and the human estrogen receptor (hER) monomer. Secondary structure analyses of the hsp 90 molecule reveal the presence of a cysteine-containing, leucine-rich, heptad repeat, which we refer to as region C. Similar analyses on the hER, at its hormone binding domain (HBD), have indicated the presence of a central subdomain bordered by 2 alpha-helical flanking segments which also display the heptad substructure. Due to its predicted potential for conformational change (1) we refer to this central subdomain as the Helix Conversion Unit or HCU. It contains an HX5C peptide and shares significant homology with the metal-binding domain of a gag-encoded HIV-LAV protein (2). We predict that, by virtue of its presence in duplicate, region C may be capable of simultaneous leucine zipper-like pairing with the hER at its flanking helices, as well as the formation of a shared CCHC-box-type metal binding link with the same hER at the putative HCU which lies in between.

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

PubMed Central

Arai, Shigeki; Yonezawa, Yasushi; Ishibashi, Matsujiro; Matsumoto, Fumiko; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko; Blaber, Michael; Tokunaga, Masao; Kuroki, Ryota

2014-01-01

Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1–4 M NaCl). In order to clarify the structural basis of its halophilic characteristics and its wide-range adaptation to salt concentration, the tertiary structure of HaAP was determined by X-ray crystallography to 2.1 Å resolution. The unit cell of HaAP contained one dimer unit corresponding to the biological unit. The monomer structure of HaAP contains a domain comprised of an 11-stranded β-sheet core with 19 surrounding α-helices similar to those of APs from other species, and a unique ‘crown’ domain containing an extended ‘arm’ structure that participates in formation of a hydrophobic cluster at the entrance to the substrate-binding site. The HaAP structure also displays a unique distribution of negatively charged residues and hydrophobic residues in comparison to other known AP structures. AP from Vibrio sp. G15-21 (VAP; a slight halophile) has the highest similarity in sequence (70.0% identity) and structure (Cα r.m.s.d. of 0.82 Å for the monomer) to HaAP. The surface of the HaAP dimer is substantially more acidic than that of the VAP dimer (144 exposed Asp/Glu residues versus 114, respectively), and thus may enable the solubility of HaAP under high-salt conditions. Conversely, the monomer unit of HaAP formed a substantially larger hydrophobic interior comprising 329 C atoms from completely buried residues, whereas that of VAP comprised 264 C atoms, which may maintain the stability of HaAP under low-salt conditions. These characteristics of HaAP may be responsible for its unique functional adaptation permitting activity over a wide range of salt concentrations. PMID:24598750

Impact of solvent selection on graft polymerization of acrylamide onto starch

USDA-ARS?s Scientific Manuscript database

The impact on polymer properties [molecular weight, monomer conversion, graft content, graft efficiency and anhydroglucose units between grafts (AGU/graft)] that result from changing the solvent for the graft co-polymerization of acrylamide onto starch from water to dimethylsulfoxide (DMSO) was eval...

Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation

PubMed Central

Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

2016-01-01

Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy—combining sequential and modular concepts—enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain. PMID:27901024

Effect of leaving group on the oligomerization of 5'-AMP on montmorillonite. [Abstract only

NASA Technical Reports Server (NTRS)

Prabahar, K. Joseph; Ferris, James P.

1994-01-01

The oligomerization of imidazole derivative of 5'-AMP (ImpA) in the presence of montmorillonite clay yields oligomers containing up to 10 monomer units. In these reactions, the heterocyclic base, imidazole is the leaving group. In our present study, we synthesized a series of activated nucleotides of 5'AMP using other leaving groups such as pyrazole, 1,2,4-triazole, piperidine, morpholine, 4-aminopyridine, 4-methylaminopyridine, 4-dimethylaminopyridine, 2-aminobenzimidazole etc. to determine the effect of amine leaving group on the products of the oligomerization reaction. Earlier results from our laboratory showed that the presence AppA in the clay reaction of ImpA enhances the oligomerization reaction to yield higher oligomers. We also studied the effect of AppA in the clay mediated oligomerization reaction of the activated nucleotides. Oligomerization of 2-amino-benzimidazole derivative of 5'-AMP gave higher oligomers containing up to nine monomer units in the presence of AppA.

The Crystal and Molecular Structure of an Asymmetric Diacetylene Monomer, 6-(2-methyl-4-nitroanilino)-2,4-hexadiyne-1-ol

NASA Technical Reports Server (NTRS)

Vlasse, Marcus; Paley, Mark S.

1993-01-01

The crystal and molecular structure of an asymmetric diacetylene monomer has been determined from x-ray diffraction data. The crystals, obtained from an acetone/pentane solution, are orthorhombic, Fdd2 with Z = 16 in a unit cell having dimensions of a = 42.815(6) A, b = 22.224(5) A, c = 4.996(l) A. The structure was solved by direct methods and refined by least- squares techniques to an R(sub F) of 6.4% for 988 reflections and 171 variables. The diacetylene chains are disposed in the unit cell in a complex manner in order to satisfy the hydrogen- bonding, crystal packing, and symmetry requirements of the system. The solid state polymerization mechanism is discussed with respect to the geometric disposition of the diacetylene chains. These chains are far apart and incorrectly oriented with respect to each other to permit polymerization in the crystal by means of 1,4-addition, consistent with the Baughman mechanistic model.

Crosslinked wholly aromatic polyether membranes based on quinoline derivatives and their application in high temperature polymer electrolyte membrane fuel cells

NASA Astrophysics Data System (ADS)

Kallitsis, K. J.; Nannou, R.; Andreopoulou, A. K.; Daletou, M. K.; Papaioannou, D.; Neophytides, S. G.; Kallitsis, J. K.

2018-03-01

An AB type difunctional quinoline based monomer bearing a pentafluorophenyl unit combined with a phenol functionality is being synthesized and homopolymerized to create linear aromatic polyethers as polymer electrolytes for HT-PEM FCs applications. Several conditions are tested for the optimized synthesis of the monomer and homopolymer. Additionally, covalent crosslinking through aromatic polyether bond formation enables the creation of wholly aromatic crosslinked polymeric electrolyte membranes. More specifically, the perfluorophenyl units are crosslinked with other hydroxyl end functionalized moieties, providing membranes with enhanced chemical and mechanical properties that are moreover easily doped with phosphoric acid even at ambient temperatures. All membranes are evaluated for their structural and thermal characteristics and their doping ability with phosphoric acid. Selected crosslinked membranes are further tested in terms of their single cell performance at the temperature range 160 °C-200 °C showing promising performance and high conductivity values even up to 0.2 S cm-1 in some cases.

Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation.

PubMed

Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

2016-11-30

Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy-combining sequential and modular concepts-enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain.

Nitrogen Containing Organic Compounds and Oligomers in Secondary Organic Aerosol Formed by Photooxidation of Isoprene

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

Nguyen, Tran B.; Laskin, Julia; Laskin, Alexander

2011-07-06

Electrospray ionization high-resolution mass spectrometry (ESI HR-MS) was used to probe molecular structures of oligomers in secondary organic aerosol (SOA) generated in laboratory experiments on isoprene photooxidation at low- and high-NOx conditions. Up to 80-90% of the observed products are oligomers and up to 33% are nitrogen-containing organic compounds (NOC). We observe oligomers with up to 8 monomer units in length. Tandem mass spectrometry (MSn) confirms NOC compounds are organic nitrates and elucidates plausible chemical building blocks contributing to oligomer formation. Most organic nitrates are comprised of methylglyceric acid units. Other important multifunctional C2-C5 monomer units are identified including methylglyoxal,more » hydroxyacetone, hydroxyacetic acid, glycolaldehyde, and 2-methyltetrols. The majority of the NOC oligomers contain only one nitrate moiety resulting in a low average N:C ratio of 0.019. Average O:C ratios of the detected SOA compounds are 0.54 under the low-NOx conditions and 0.83 under the high-NOx conditions. Our results underscore the importance of isoprene photooxidation as a source of NOC in organic particulate matter.« less

Proteins containing expanded polyglutamine tracts and neurodegenerative disease

PubMed Central

Adegbuyiro, Adewale; Sedighi, Faezeh; Pilkington, Albert W.; Groover, Sharon; Legleiter, Justin

2017-01-01

Several hereditary neurological and neuromuscular diseases are caused by an abnormal expansion of trinucleotide repeats. To date, there have been ten of these trinucleotide repeat disorders associated with an expansion of the codon CAG encoding glutamine (Q). For these polyglutamine (polyQ) diseases, there is a critical threshold length of the CAG repeat required for disease, and further expansion beyond this threshold is correlated with age of onset and symptom severity. PolyQ expansion in the translated proteins promotes their self-assembly into a variety of oligomeric and fibrillar aggregate species that accumulate into the hallmark proteinaceous inclusion bodies associated with each disease. Here, we review aggregation mechanisms of proteins with expanded polyQ-tracts, structural consequences of expanded polyQ ranging from monomers to fibrillar aggregates, the impact of protein context and post translational modifications on aggregation, and a potential role for lipids membranes in aggregation. As the pathogenic mechanisms that underlie these disorders are often classified as either a gain of toxic function or loss of normal protein function, some toxic mechanisms associated with mutant polyQ tracts will also be discussed. PMID:28170216

Structure of the E2 DNA-binding domain from human papillomavirus serotype 31 at 2.4 A.

PubMed

Bussiere, D E; Kong, X; Egan, D A; Walter, K; Holzman, T F; Lindh, F; Robins, T; Giranda, V L

1998-11-01

The papillomaviruses are a family of small double-stranded DNA viruses which exclusively infect epithelial cells and stimulate the proliferation of those cells. A key protein within the papillomavirus life-cycle is known as the E2 (Early 2) protein and is responsible for regulating viral transcription from all viral promoters as well as for replication of the papillomavirus genome in tandem with another protein known as E1. The E2 protein itself consists of three functional domains: an N-terminal trans-activation domain, a proline-rich linker, and a C-terminal DNA-binding domain. The first crystal structure of the human papillomavirus, serotype 31 (HPV-31), E2 DNA-binding domain has been determined at 2.4 A resolution. The HPV DNA-binding domain monomer consists of two beta-alpha-beta repeats of approximately equal length and is arranged as to have an anti-parallel beta-sheet flanked by the two alpha-helices. The monomers form the functional in vivo dimer by association of the beta-sheets of each monomer so as to form an eight-stranded anti-parallel beta-barrel at the center of the dimer, with the alpha-helices lining the outside of the barrel. The overall structure of HVP-31 E2 DNA-binding domain is similar to both the bovine papillomavirus E2-binding domain and the Epstein-Barr nuclear antigen-1 DNA-binding domain.

The Targeted Sequencing of Alpha Satellite DNA in Cercopithecus pogonias Provides New Insight into the Diversity and Dynamics of Centromeric Repeats in Old World monkeys.

PubMed

Cacheux, Lauriane; Ponger, Loïc; Gerbault-Seureau, Michèle; Loll, François; Gey, Delphine; Richard, Florence Anne; Escudé, Christophe

2018-06-01

Alpha satellite is the major repeated DNA element of primate centromeres. Specific evolutionary mechanisms have led to a great diversity of sequence families with peculiar genomic organization and distribution, which have till now been studied mostly in great apes. Using high throughput sequencing of alpha satellite monomers obtained by enzymatic digestion followed by computational and cytogenetic analysis, we compare here the diversity and genomic distribution of alpha satellite DNA in two related Old World monkey species, Cercopithecus pogonias and Cercopithecus solatus, which are known to have diverged about seven million years ago. Two main families of monomers, called C1 and C2, are found in both species. A detailed analysis of our datasets revealed the existence of numerous subfamilies within the centromeric C1 family. Although the most abundant subfamily is conserved between both species, our FISH experiments clearly show that some subfamilies are specific for each species and that their distribution is restricted to a subset of chromosomes, thereby pointing to the existence of recurrent amplification/homogenization events. The pericentromeric C2 family is very abundant on the short arm of all acrocentric chromosomes in both species, pointing to specific mechanisms that lead to this distribution. Results obtained using two different restriction enzymes are fully consistent with a predominant monomeric organization of alpha satellite DNA which coexists with higher order organization patterns in the Cercopithecus pogonias genome. Our study suggests a high dynamics of alpha satellite DNA in Cercopithecini, with recurrent apparition of new sequence variants and interchromosomal sequence transfer.

Analytical method for the simultaneous determination of polyfunctional amines used as monomers in the manufacture of food packaging materials.

PubMed

Paseiro-Cerrato, R; de Quirós, A Rodríguez-Bernaldo; Sendón, Raquel; Bustos, Juana; Ruíz, E; Cruz, J M; Paseiro-Losada, P

2011-10-07

This paper describes the development of a multi-analyte method for the determination of polyfunctional amines commonly used as monomers in the manufacture of food contact materials. Amines were analyzed by high-performance-liquid chromatography with diode-array detection (HPLC-DAD) after derivatization with dansyl chloride. The chromatographic analysis and the derivatization conditions were optimized. The proposed method was validated in terms of linearity, limits of detection and repeatabilities. The method showed an excellent sensitivity (LOD≤0.05 μg/mL) and appropriate repeatabilites (RSD (n=7)≤5%)). LC-MS/MS was used as a confirmatory technique. The stability of the amines in five food simulants (distilled water, 3% acetic acid, 10% ethanol, 50% ethanol and olive oil) under the most common testing conditions (10 days at 40 °C) was also studied. Results showed that amines had an acceptable stability in aqueous simulants but in the olive oil a loss of 100% was observed for all analytes. Copyright © 2011. Published by Elsevier B.V.

Mechanism for controlling the monomer-dimer conversion of SARS coronavirus main protease.

PubMed

Wu, Cheng Guo; Cheng, Shu Chun; Chen, Shiang Chuan; Li, Juo Yan; Fang, Yi Hsuan; Chen, Yau Hung; Chou, Chi Yuan

2013-05-01

The Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M(pro)) cleaves two virion polyproteins (pp1a and pp1ab); this essential process represents an attractive target for the development of anti-SARS drugs. The functional unit of M(pro) is a homodimer and each subunit contains a His41/Cys145 catalytic dyad. Large amounts of biochemical and structural information are available on M(pro); nevertheless, the mechanism by which monomeric M(pro) is converted into a dimer during maturation still remains poorly understood. Previous studies have suggested that a C-terminal residue, Arg298, interacts with Ser123 of the other monomer in the dimer, and mutation of Arg298 results in a monomeric structure with a collapsed substrate-binding pocket. Interestingly, the R298A mutant of M(pro) shows a reversible substrate-induced dimerization that is essential for catalysis. Here, the conformational change that occurs during substrate-induced dimerization is delineated by X-ray crystallography. A dimer with a mutual orientation of the monomers that differs from that of the wild-type protease is present in the asymmetric unit. The presence of a complete substrate-binding pocket and oxyanion hole in both protomers suggests that they are both catalytically active, while the two domain IIIs show minor reorganization. This structural information offers valuable insights into the molecular mechanism associated with substrate-induced dimerization and has important implications with respect to the maturation of the enzyme.

Effects of a low-shrinkage methacrylate monomer and monoacylphosphine oxide photoinitiator on curing efficiency and mechanical properties of experimental resin-based composites.

PubMed

Manojlovic, Dragica; Dramićanin, Miroslav D; Milosevic, Milos; Zeković, Ivana; Cvijović-Alagić, Ivana; Mitrovic, Nenad; Miletic, Vesna

2016-01-01

This study investigated the degree of conversion, depth of cure, Vickers hardness, flexural strength, flexural modulus and volumetric shrinkage of experimental composite containing a low shrinkage monomer FIT-852 (FIT; Esstech Inc.) and photoinitiator 2,4,6-trimethylbenzoyldiphenylphosphine oxide (TPO; Sigma Aldrich) compared to conventional composite containing Bisphenol A-glycidyl methacrylate (BisGMA) and camphorquinone-amine photoinitiator system. The degree of conversion was generally higher in FIT-based composites (45-64% range) than in BisGMA-based composites (34-58% range). Vickers hardness, flexural strength and modulus were higher in BisGMA-based composites. A polywave light-curing unit was generally more efficient in terms of conversion and hardness of experimental composites than a monowave unit. FIT-based composite containing TPO showed the depth of cure below 2mm irrespective of the curing light. The depth of cure of FIT-based composite containing CQ and BisGMA-based composites with either photoinitiator was in the range of 2.8-3.0mm. Volumetric shrinkage of FIT-based composite (0.9-5.7% range) was lower than that of BisGMA-based composite (2.2-12% range). FIT may be used as a shrinkage reducing monomer compatible with the conventional CQ-amine system as well as the alternative TPO photoinitiator. However, the depth of cure of FIT_TPO composite requires boosting to achieve clinically recommended thickness of 2mm. Copyright © 2015 Elsevier B.V. All rights reserved.

Elucidation of neurophysin/bioligand interactions from molecular modeling.

PubMed

Kaźmierkiewicz, R; Czaplewski, C; Ciarkowski, J

1997-01-01

This is a review of our recent modeling work aimed at: (i) development and assessment of techniques for reliable refinement of low-resolution protein structures and (ii) using these techniques, at solving specific problems pertinent to neurophysin-bioligand interactions. Neurophysins I and II (NPI and NPII) serve in the neurosecretory granules of the posterior pituitary as carrier proteins for the neurophyseal hormones oxytocin (OT) and vasopressin (VP), respectively, until the latter are released into blood. NPs are homologous two-domain, sulphur rich small proteins (93-95 residues, 7 disulphide bridges per monomer), capable of being aggregated. The C2 symmetrical NPI2 and NPII2 homodimers, and the (NPI/OT)2 and (NPII/VP)2 heterotetramers, all believed to be the smallest functional units, were modeled using low-resolution structure information, i.e. the C alpha-carbon coordinates of the homologous NPII/dipeptide complex as a template. The all-atom representations of the models were obtained using the SYBYL suite of programs (by Tripos, Inc.). Subsequently, they were relaxed, using a constrained simulated annealing (CSA) protocol, and submitted to about 100 ps molecular dynamics (MD) in water, using the AMBER 4.1 force field. The (NPI/OT)2 and (NPII/VP)2 structures, averaged after the last 20 ps of MD, were remarkably similar to those recently reported either for NPII/dipeptide or NPII/oxytocin complex in the solid state (Chen et al., 1991, Proc. Natl. Acad. Sci., U.S.A. 88, 4240-4244; Rose et al., 1996, Nature Struct. Biol. 3, 163-169). The results indicate that the 3(10) helices (terminating the amino domains) and the carboxyl domains are more mobile than the remainder of the NP monomers. The hormones become anchored by residues 1-3 and 6 to the host, leaving residues 4-5 and 7-9 exposed on the surface and free to move. A cluster of attractive interactions, extending from the ligand binding site, Tyr-24-Ile-26 of unit 1(2), to the inter-monomer interface Val-36 of unit 1(2), Cys-79 and Ile-72 of unit 2(1), is clearly seen. We suggest that both these interactions as well as the increased mobility of the 3(10) helix and the carboxyl domain may contribute to the allosteric communication between the ligand and the unit1-unit2 interface.

Single molecule force spectroscopy reveals the adhesion mechanism of hydrophobins

NASA Astrophysics Data System (ADS)

Cao, Yi; Li, Bing; Qin, Meng; Wang, Wei

Hydrophobins are a special class of amphiphilic proteins produced by filamentous fungi. They show outstanding interfacial self-assembly and adhesion properties, which are critical to their biological function. Such feature also inspires their broad applications in bio-engineering, surface modification, and nanotechnology. However, the biophysical properties of hydrophobins are not well understood. We combined atomic force microscopy based single molecule force spectroscopy and protein engineering to directly quantify the adhesion strength of a hydorphobin (HFB1) to various surfaces in both the monomer and oligomer states to reveal the molecular determinant of the adhesion strength of hydrophobins. We found that the monomer HFB1 showed distinct adhesion properties towards hydrophobic and hydrophilic surfaces. The adhesion to hydrophobic surfaces (i.e. graphite and gold) was significantly higher than that to the hydrophilic ones (e.g. mica and silicon). However, when self-assembled monolayers were formed, the adhesion strengths to various surfaces were similar and were ubiquitously stronger than the monomer cases. We hypothesized that the interactions among hydrophobins in the monolayer played significant roles for the enhance adhesion strengths. Extracting any single hydrophobin monomers from the surface required the break of interactions not only with the surface but also with the neighboring units. We proposed that such a mechanism may be widely explored in nature for many biofilms for surface adhesion. May also inspire the design of novel adhesives.

Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats.

PubMed

Urvoas, Agathe; Guellouz, Asma; Valerio-Lepiniec, Marie; Graille, Marc; Durand, Dominique; Desravines, Danielle C; van Tilbeurgh, Herman; Desmadril, Michel; Minard, Philippe

2010-11-26

Repeat proteins have a modular organization and a regular architecture that make them attractive models for design and directed evolution experiments. HEAT repeat proteins, although very common, have not been used as a scaffold for artificial proteins, probably because they are made of long and irregular repeats. Here, we present and validate a consensus sequence for artificial HEAT repeat proteins. The sequence was defined from the structure-based sequence analysis of a thermostable HEAT-like repeat protein. Appropriate sequences were identified for the N- and C-caps. A library of genes coding for artificial proteins based on this sequence design, named αRep, was assembled using new and versatile methodology based on circular amplification. Proteins picked randomly from this library are expressed as soluble proteins. The biophysical properties of proteins with different numbers of repeats and different combinations of side chains in hypervariable positions were characterized. Circular dichroism and differential scanning calorimetry experiments showed that all these proteins are folded cooperatively and are very stable (T(m) >70 °C). Stability of these proteins increases with the number of repeats. Detailed gel filtration and small-angle X-ray scattering studies showed that the purified proteins form either monomers or dimers. The X-ray structure of a stable dimeric variant structure was solved. The protein is folded with a highly regular topology and the repeat structure is organized, as expected, as pairs of alpha helices. In this protein variant, the dimerization interface results directly from the variable surface enriched in aromatic residues located in the randomized positions of the repeats. The dimer was crystallized both in an apo and in a PEG-bound form, revealing a very well defined binding crevice and some structure flexibility at the interface. This fortuitous binding site could later prove to be a useful binding site for other low molecular mass partners. Copyright © 2010 Elsevier Ltd. All rights reserved.

IR investigation on silicon oxycarbide structure obtained from precursors with 1:1 silicon to carbon atoms ratio and various carbon atoms distribution

NASA Astrophysics Data System (ADS)

Niemiec, Wiktor; Szczygieł, Przemysław; Jeleń, Piotr; Handke, Mirosław

2018-07-01

Silicon oxycarbide is a material with a number of advantageous properties that strongly depend on its structure. The most common approach to its tailoring is based on varying the silicon to carbon atoms ratio in the preceramic polymeric precursor. This work is the first comparison of the materials obtained from precursors with the same Si to C atoms ratio, but with various distribution of these atoms in the preceramic polymer. In addition to standard mixtures of monomers containing single silicon atom, a number of monomers with high molar masses and well defined structure was used. The IR was used to investigate the structure of the precursors and materials obtained after their annealing in 800 °C. The results show, that not only the distribution of carbon containing groups among the monomers is important, but also the (in)ability of these groups to end up in each other vicinity in the precursor as well as the degree of condensation of each structural unit.

Regulation of AQP0 water permeability is enhanced by cooperativity

PubMed Central

Németh-Cahalan, Karin L.; Clemens, Daniel M.

2013-01-01

Aquaporin 0 (AQP0), essential for lens clarity, is a tetrameric protein composed of four identical monomers, each of which has its own water pore. The water permeability of AQP0 expressed in Xenopus laevis oocytes can be approximately doubled by changes in calcium concentration or pH. Although each monomer pore functions as a water channel, under certain conditions the pores act cooperatively. In other words, the tetramer is the functional unit. In this paper, we show that changes in external pH and calcium can induce an increase in water permeability that exhibits either a positive cooperativity switch-like increase in water permeability or an increase in water permeability in which each monomer acts independently and additively. Because the concentrations of calcium and hydrogen ions increase toward the center of the lens, a concentration signal could trigger a regulatory change in AQP0 water permeability. It thus seems plausible that the cooperative modes of water permeability regulation by AQP0 tetramers mediated by decreased pH and elevated calcium are the physiologically important ones in the living lens. PMID:23440275

Structures of ω repressors bound to direct and inverted DNA repeats explain modulation of transcription

PubMed Central

Weihofen, Wilhelm Andreas; Cicek, Aslan; Pratto, Florencia; Alonso, Juan Carlos; Saenger, Wolfram

2006-01-01

Repressor ω regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. ω belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel β-sheet for DNA major groove binding. Homodimeric ω2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5′-A/TATCACA/T-3′, symbolized by →) in palindromic inverted, converging (→←) or diverging (←→) orientation and also, unique to ω2 and contrasting other RHH2 repressors, to non-palindromic direct (→→) repeats. Here we investigate with crystal structures how ω2 binds specifically to heptads in minimal operators with (→→) and (→←) repeats. Since the pseudo-2-fold axis relating the monomers in ω2 passes the central C–G base pair of each heptad with ∼0.3 Å downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (→→), ∼0.6 Å shorter in (→←) but would be ∼0.6 Å longer in (←→). These variations grade interactions between adjacent ω2 and explain modulations in cooperative binding affinity of ω2 to operators with different heptad orientations. PMID:16528102

Push-pull quinoidal porphyrins.

PubMed

Smith, Martin J; Blake, Iain M; Clegg, William; Anderson, Harry L

2018-05-01

A family of push-pull quinoidal porphyrin monomers has been prepared from a meso-formyl porphyrin by bromination, thioacetal formation, palladium-catalyzed coupling with malononitrile and oxidation with DDQ. Attempts at extending this synthesis to a push-pull quinoidal/cumulenic porphyrin dimer were not successful. The crystal structures of the quinoidal porphyrins indicate that there is no significant contribution from singlet biradical or zwitterionic resonance forms. The crystal structure of an ethyne-linked porphyrin dimer shows that the torsion angle between the porphyrin units is only about 3°, in keeping with crystallographic results on related compounds, but contrasting with the torsion angle of about 35° predicted by computational studies. The free-base quinoidal porphyrin monomers form tightly π-stacked layer structures, despite their curved geometries and bulky aryl substituents.

Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko

2014-01-01

One of the β-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077

A catalytic surface for amyloid fibril formation

NASA Astrophysics Data System (ADS)

Hammarström, P.; Ali, M. M.; Mishra, R.; Svensson, S.; Tengvall, P.; Lundström, I.

2008-03-01

A hydrophobic surface incubated in a solution of protein molecules (insulin monomers) was made into a catalytic surface for amyloid fibril formation by repeatedly incubate, rinse and dry the surface. The present contribution describes how this unexpected transformation occurred and its relation to rapid fibrillation of insulin solutions in contact with the surface. A tentative model of the properties of the catalytic surface is given, corroborated by ellipsometric measurements of the thickness of the organic layer on the surface and by atomic force microscopy. The surfaces used were spontaneously oxidized silicon made hydrophobic through treatment in dichlorodimethylsilane.

Hydrophobic folding units derived from dissimilar monomer structures and their interactions.

PubMed

Tsai, C J; Nussinov, R

1997-01-01

We have designed an automated procedure to cut a protein into compact hydrophobic folding units. The hydrophobic units are large enough to contain tertiary non-local interactions, reflecting potential nucleation sites during protein folding. The quality of a hydrophobic folding unit is evaluated by four criteria. The first two correspond to visual characterization of a structural domain, namely, compactness and extent of isolation. We use the definition of Zehfus and Rose (Zehfus MH, Rose GD, 1986, Biochemistry 25:35-340) to calculate the compactness of a cut protein unit. The isolation of a unit is based on the solvent accessible surface area (ASA) originally buried in the interior and exposed to the solvent after cutting. The third quantity is the hydrophobicity, equivalent to the fraction of the buried non-polar ASA with respect to the total non-polar ASA. The last criterion in the evaluation of a folding unit is the number of segments it includes. To conform with the rationale of obtaining hydrophobic units, which may relate to early folding events, the hydrophobic interactions are implicitly and explicitly applied in their generation and assessment. We follow Holm and Sander (Holm L, Sander C, 1994, Proteins 19:256-268) to reduce the multiple cutting-point problem to a one-dimensional search for all reasonable trial cuts. However, as here we focus on the hydrophobic cores, the contact matrix used to obtain the first non-trivial eigenvector contains only hydrophobic contracts, rather than all, hydrophobic and hydrophilic, interactions. This dataset of hydrophobic folding units, derived from structurally dissimilar single chain monomers, is particularly useful for investigations of the mechanism of protein folding. For cases where there are kinetic data, the one or more hydrophobic folding units generated for a protein correlate with the two or with the three-state folding process observed. We carry out extensive amino acid sequence order independent structural comparisons to generate a structurally non-redundant set of hydrophobic folding units for fold recognition and for statistical purposes.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed

Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed Central

Rehm, Charlotte; Wurmthaler, Lena A.; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S.

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria. PMID:26695179

Micromechanics Fatigue Damage Analysis Modeling for Fabric Reinforced Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Min, J. B.; Xue, D.; Shi, Y.

2013-01-01

A micromechanics analysis modeling method was developed to analyze the damage progression and fatigue failure of fabric reinforced composite structures, especially for the brittle ceramic matrix material composites. A repeating unit cell concept of fabric reinforced composites was used to represent the global composite structure. The thermal and mechanical properties of the repeating unit cell were considered as the same as those of the global composite structure. The three-phase micromechanics, the shear-lag, and the continuum fracture mechanics models were integrated with a statistical model in the repeating unit cell to predict the progressive damages and fatigue life of the composite structures. The global structure failure was defined as the loss of loading capability of the repeating unit cell, which depends on the stiffness reduction due to material slice failures and nonlinear material properties in the repeating unit cell. The present methodology is demonstrated with the analysis results evaluated through the experimental test performed with carbon fiber reinforced silicon carbide matrix plain weave composite specimens.

Evolution of Protein Domain Repeats in Metazoa

PubMed Central

Schüler, Andreas; Bornberg-Bauer, Erich

2016-01-01

Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a significant fraction of noteworthy volatile outliers with very high indel rates. Analysis of structural data indicates that repeats with an open structure and independently folding units are more volatile and more likely to be intrinsically disordered. Such disordered repeats are also significantly enriched in sites with a high functional potential such as linear motifs. Furthermore, the most volatile repeats have a high sequence similarity between their units. Since many volatile repeats also show signs of recombination, we conclude they are often shaped by concerted evolution. Intriguingly, many of these conserved yet volatile repeats are involved in host-pathogen interactions where they might foster fast but subtle adaptation in biological arms races. Key Words: protein evolution, domain rearrangements, protein repeats, concerted evolution. PMID:27671125

A nonaqueous potentiometric titration study of the dissociation of t-butyl methacrylate-methacrylic acid copolymers.

PubMed

Nakatani, Kiyoharu; Yamashita, Jun; Sekine, Tomomi; Toriumi, Minoru; Itani, Toshiro

2003-05-01

The dissociation of t-butyl methacrylate-methacrylic acid copolymers in dimethyl sulfoxide was analyzed by a nonaqueous potentiometric titration technique. The negative logarithm of the dissociation constant of the monomer unit of a methacrylic acid (MAA) monotonously increased with the increasing degree of dissociation corresponding to the titrant/MAA amount ratio, and was highly influenced by the copolymerization ratio. The results are discussed in terms of the suppression of the dissociation of MAA by a neighboring charged methacrylate anion unit.

Dipole moment, solution, and solid state structure (-)-epicatechin, a monomer unit of procyanidin polymers

Treesearch

Frank R. Fronczek; Garret Gannuch; Wayne L. Mattice; Fred L. Tobiason; Jeff L. Broker; Richard W. Hemingway

1984-01-01

The structure of (-)-epicatechin has been determined in the crystalline state. Crystals are orthorhombic. P212121, a=670.8(1), b=1329.1 (3), c=1426.2(4) pm, Z=4. Dc=1.516 g cm-3, R=0.041 for 1624 observations. Intramolecular hydrogen bonds are absent. The...

Crystallization and preliminary X-ray diffraction analysis of three myotoxic phospholipases A2 from Bothrops brazili venom

PubMed Central

Fernandes, Carlos A. H.; Gartuzo, Elaine C. G.; Pagotto, Ivan; Comparetti, Edson J.; Huancahuire-Vega, Salomón; Ponce-Soto, Luis Alberto; Costa, Tássia R.; Marangoni, Sergio; Soares, Andreimar M.; Fontes, Marcos R. M.

2012-01-01

Two myotoxic and noncatalytic Lys49-phospholipases A2 (braziliantoxin-II and MT-II) and a myotoxic and catalytic phospholipase A2 (braziliantoxin-III) from the venom of the Amazonian snake Bothrops brazili were crystallized. The crystals diffracted to resolutions in the range 2.56–2.05 Å and belonged to space groups P3121 (braziliantoxin-II), P6522 (braziliantoxin-III) and P21 (MT-II). The structures were solved by molecular-replacement techniques. Both of the Lys49-phospholipases A2 (braziliantoxin-II and MT-II) contained a dimer in the asymmetric unit, while the Asp49-phospholipase A2 braziliantoxin-III contained a monomer in its asymmetric unit. Analysis of the quaternary assemblies of the braziliantoxin-II and MT-II structures using the PISA program indicated that both models have a dimeric conformation in solution. The same analysis of the braziliantoxin-III structure indicated that this protein does not dimerize in solution and probably acts as a monomer in vivo, similar to other snake-venom Asp49-phospholipases A2. PMID:22869126

Bond durability of adhesives containing modified-monomer with/without-fluoride after aging in artificial saliva and under intrapulpal pressure simulation.

PubMed

El-Deeb, H A; Al Sherbiney, H H; Mobarak, E H

2013-01-01

To evaluate the dentin bond strength durability of adhesives containing modified-monomer with/without-fluoride after storage in artificial saliva and under intrapulpal pressure simulation (IPPS). The occlusal enamel of 48 freshly extracted teeth was trimmed to expose midcoronal dentin. Roots were sectioned to expose the pulp chamber and to connect the specimens to the pulpal-pressure assembly. Specimens were assigned into four groups (n=12) according to adhesive system utilized: a two-step etch-and-rinse adhesive system (SB, Adper Single Bond 2, 3M ESPE), a two-step self-etch adhesive system (CSE, Clearfil SE Bond, Kuraray Medical Inc), and two single-step self-etch adhesives with the same modified monomer (bis-acrylamide)-one with fluoride (AOF, AdheSE One F, Ivoclar-Vivadent) and the other without (AO, AdheSE One, Ivoclar-Vivadent). Bonding was carried out while the specimens were subjected to 15-mm Hg IPPS. Resin composite (Valux Plus, 3M ESPE) buildups were made. After curing, specimens were aged in artificial saliva and under 20-mm Hg IPPS at 37°C in a specially constructed incubator either for 24 hours or six months prior to testing. Bonded specimens (n=6/group) were sectioned into sticks (n=24/group) with a cross section of 0.9 ± 0.01 mm(2) and subjected to microtensile bond strength (μTBS) testing using a universal testing machine. Data were statistically analyzed using two-way analysis of variance (ANOVA) with repeated measures, one-way ANOVA tests, and a t-test (p<0.05). Failure modes were determined using a scanning electron microscope. The μTBS values of SB and CSE fell significantly after six-month storage in artificial saliva and under IPPS, yet these values remained significantly higher than those for the other two adhesives with modified monomers. There was no significant difference in the bond strength values between fluoride-containing and fluoride-free self-etch adhesive systems (AOF and AO) after 24 hours or six months. Modes of failure were mainly adhesive and mixed. Based on the results of this study, 1) Fluoride addition did not affect dentin bond durability; and 2) despite the fact that the single-step adhesive system with modified monomer showed stability, bond strengths associated with these systems remained lower than those of multistep adhesive systems.

Repeater F-waves are signs of motor unit pathology in polio survivors.

PubMed

Hachisuka, Akiko; Komori, Tetsuo; Abe, Tatsuya; Hachisuka, Kenji

2015-05-01

The purpose of this study was to determine whether F-waves reveal electrophysiological features of anterior horn cells in polio survivors. Forty-three polio survivors and 20 healthy controls underwent motor nerve conduction studies of the median and tibial nerves bilaterally, including sampling of F-waves elicited by 100 stimuli and the determination of motor unit number estimation (MUNE). A significant increase in abnormally stereotyped ("repeater") F-waves and a reduction of F-wave persistence were observed in both nerves in the polio group as compared with the control group. Repeater F-waves had a negative correlation with MUNE. These trends in F-wave persistence and repeater F-waves after motor unit loss are characteristic findings in polio survivors. Repeater F-waves are a sign of motor unit pathology. © 2014 The Authors. Muscle & Nerve Published by Wiley Periodicals, Inc.

High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events

PubMed Central

Wolfgruber, Thomas K.; Nakashima, Megan M.; Schneider, Kevin L.; Sharma, Anupma; Xie, Zidian; Albert, Patrice S.; Xu, Ronghui; Bilinski, Paul; Dawe, R. Kelly; Ross-Ibarra, Jeffrey; Birchler, James A.; Presting, Gernot G.

2016-01-01

The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR) has presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here, we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 × 10−6 and 5 × 10−5 for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb from the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length CR from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB) repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. In many cases examined here, DSB repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to efficiently repair frequent DSBs in centromeres. PMID:27047500

Preparation of membranes using solvent-less vapor deposition followed by in-situ polymerization

DOEpatents

O'Brien, Kevin C [San Ramon, CA; Letts, Stephan A [San Ramon, CA; Spadaccini, Christopher M [Oakland, CA; Morse, Jeffrey C [Pleasant Hill, CA; Buckley, Steven R [Modesto, CA; Fischer, Larry E [Los Gatos, CA; Wilson, Keith B [San Ramon, CA

2012-01-24

A system of fabricating a composite membrane from a membrane substrate using solvent-less vapor deposition followed by in-situ polymerization. A first monomer and a second monomer are directed into a mixing chamber in a deposition chamber. The first monomer and the second monomer are mixed in the mixing chamber providing a mixed first monomer and second monomer. The mixed first monomer and second monomer are solvent-less vapor deposited onto the membrane substrate in the deposition chamber. The membrane substrate and the mixed first monomer and second monomer are heated to produce in-situ polymerization and provide the composite membrane.

Preparation of membranes using solvent-less vapor deposition followed by in-situ polymerization

DOEpatents

O'Brien, Kevin C [San Ramon, CA; Letts, Stephan A [San Ramon, CA; Spadaccini, Christopher M [Oakland, CA; Morse, Jeffrey C [Pleasant Hill, CA; Buckley, Steven R [Modesto, CA; Fischer, Larry E [Los Gatos, CA; Wilson, Keith B [San Ramon, CA

2010-07-13

A system of fabricating a composite membrane from a membrane substrate using solvent-less vapor deposition followed by in-situ polymerization. A first monomer and a second monomer are directed into a mixing chamber in a deposition chamber. The first monomer and the second monomer are mixed in the mixing chamber providing a mixed first monomer and second monomer. The mixed first monomer and second monomer are solvent-less vapor deposited onto the membrane substrate in the deposition chamber. The membrane substrate and the mixed first monomer and second monomer are heated to produce in-situ polymerization and provide the composite membrane.

Key role of amino acid residues in the dimerization and catalytic activation of the autolysin LytA, an important virulence factor in Streptococcus pneumoniae.

PubMed

Romero, Patricia; López, Rubens; García, Ernesto

2007-06-15

LytA, the main autolysin of Streptococcus pneumoniae, was the first member of the bacterial N-acetylmuramoyl-l-alanine amidase (NAM-amidase) family of proteins to be well characterized. This autolysin degrades the peptidoglycan bonds of pneumococcal cell walls after anchoring to the choline residues of the cell wall teichoic acids via its choline-binding module (ChBM). The latter is composed of seven repeats (ChBRs) of approximately 20 amino acid residues. The translation product of the lytA gene is the low-activity E-form of LytA (a monomer), which can be "converted" (activated) in vitro by choline into the fully active C-form at low temperature. The C-form is a homodimer with a boomerang-like shape. To study the structural requirements for the monomer-to-dimer modification and to clarify whether "conversion" is synonymous with dimerization, the biochemical consequences of replacing four key amino acid residues of ChBR6 and ChBR7 (the repeats involved in dimer formation) were determined. The results obtained with a collection of 21 mutated NAM-amidases indicate that Ile-315 is a key amino acid residue in both LytA activity and folding. Amino acids with a marginal position in the solenoid structure of the ChBM were of minor influence in dimer stability; neither the size, polarity, nor aromatic nature of the replacement amino acids affected LytA activity. In contrast, truncated proteins were drastically impaired in their activity and conversion capacity. The results indicate that dimerization and conversion are different processes, but they do not answer the questions of whether conversion can only be achieved after a dimer formation step.

Unique and Highly Selective Anticytomegalovirus Activities of Artemisinin-Derived Dimer Diphenyl Phosphate Stem from Combination of Dimer Unit and a Diphenyl Phosphate Moiety

PubMed Central

He, Ran; Forman, Michael; Mott, Bryan T.; Venkatadri, Rajkumar; Posner, Gary H.

2013-01-01

We report that the artemisinin-derived dimer diphenyl phosphate (DPP; dimer 838) is the most selective inhibitor of human cytomegalovirus (CMV) replication among a series of artemisinin-derived monomers and dimers. Dimer 838 was also unique in being an irreversible CMV inhibitor. The peroxide unit within artemisinins' chemical structures is critical to their activities, and its absence results in loss of anti-CMV activities. Surprisingly, the deoxy dimer of 838 retained modest anti-CMV activity, suggesting that the DPP moiety of dimer 838 contributes to its anti-CMV activities. DPP alone did not inhibit CMV replication, but triphenyl phosphate (TPP) had modest CMV inhibition, although its selectivity index was low. Artemisinin DPP derivatives dimer 838 and monomer diphenyl phosphate (compound 558) showed stronger CMV inhibition and a higher selectivity index than their analogs lacking the DPP unit. An add-on and removal assay revealed that removing DPP derivatives (compounds 558 and 838) but not the non-DPP backbones (artesunate and compound 606) at 24 h postinfection (hpi) already resulted in dominant CMV inhibition. CMV inhibition was fully irreversible with 838 and partially irreversible with 558, while non-DPP artemisinins were reversible inhibitors. While all artemisinin derivatives and TPP reduced the expression of the CMV immediate early 2 (IE2), UL44, and pp65 proteins at or after 48 hpi, only TPP inhibited the expression of both IE1 and IE2. Combination of a non-DPP dimer (compound 606) with TPP was synergistic in CMV inhibition, while ganciclovir and TPP were additive. Although TPP shared structural similarity with monomer DPP (compound 558) and dimer DPP (compound 838), its pattern of CMV inhibition was significantly different from the patterns of the artemisinins. These findings demonstrate that the DPP group contributes to the unique activities of compound 838. PMID:23774439

Mass and molecular composition of vesicular stomatitis virus: a scanning transmission electron microscopy analysis.

PubMed

Thomas, D; Newcomb, W W; Brown, J C; Wall, J S; Hainfeld, J F; Trus, B L; Steven, A C

1985-05-01

Dark-field scanning transmission electron microscopy was used to perform mass analyses of purified vesicular stomatitis virions, pronase-treated virions, and nucleocapsids, leading to a complete self-consistent account of the molecular composition of vesicular stomatitis virus. The masses obtained were 265.6 +/- 13.3 megadaltons (MDa) for the native virion, 197.5 +/- 8.4 MDa for the pronase-treated virion, and 69.4 +/- 4.9 MDa for the nucleocapsid. The reduction in mass effected by pronase treatment, which corresponds to excision of the external domains (spikes) of G protein, leads to an average of 1,205 molecules of G protein per virion. The nucleocapsid mass, after compensation for the RNA (3.7 MDa) and residual amounts of other proteins, yielded a complement of 1,258 copies of N protein. Calibration of the amounts of M, NS, and L proteins relative to N protein by biochemical quantitation yielded values of 1,826, 466, and 50 molecules, respectively, per virion. Assuming that the remaining virion mass is contributed by lipids in the viral envelope, we obtained a value of 56.1 MDa for its lipid content. In addition, four different electron microscopy procedures were applied to determine the nucleocapsid length, which we conclude to be 3.5 to 3.7 micron. The nucleocapsid comprises a strand of repeating units which have a center-to-center spacing of 3.3 nm as measured along the middle of the strand. We show that these repeating units represent monomers of N protein, each of which is associated with 9 +/- 1 bases of single-stranded RNA. From scanning transmission electron microscopy images of negatively stained nucleocapsids, we inferred that N protein has a wedge-shaped, bilobed structure with dimensions of approximately 9.0 nm (length), approximately 5.0 nm (depth), and approximately 3.3 nm (width, at the midpoint of its long axis). In the coiled configuration of the in situ nucleocapsid, the long axis of N protein is directed radially, and its depth corresponds to the pitch of the nucleocapsid helix.

Mass and molecular composition of vesicular stomatitis virus: a scanning transmission electron microscopy analysis.

PubMed Central

Thomas, D; Newcomb, W W; Brown, J C; Wall, J S; Hainfeld, J F; Trus, B L; Steven, A C

1985-01-01

Dark-field scanning transmission electron microscopy was used to perform mass analyses of purified vesicular stomatitis virions, pronase-treated virions, and nucleocapsids, leading to a complete self-consistent account of the molecular composition of vesicular stomatitis virus. The masses obtained were 265.6 +/- 13.3 megadaltons (MDa) for the native virion, 197.5 +/- 8.4 MDa for the pronase-treated virion, and 69.4 +/- 4.9 MDa for the nucleocapsid. The reduction in mass effected by pronase treatment, which corresponds to excision of the external domains (spikes) of G protein, leads to an average of 1,205 molecules of G protein per virion. The nucleocapsid mass, after compensation for the RNA (3.7 MDa) and residual amounts of other proteins, yielded a complement of 1,258 copies of N protein. Calibration of the amounts of M, NS, and L proteins relative to N protein by biochemical quantitation yielded values of 1,826, 466, and 50 molecules, respectively, per virion. Assuming that the remaining virion mass is contributed by lipids in the viral envelope, we obtained a value of 56.1 MDa for its lipid content. In addition, four different electron microscopy procedures were applied to determine the nucleocapsid length, which we conclude to be 3.5 to 3.7 micron. The nucleocapsid comprises a strand of repeating units which have a center-to-center spacing of 3.3 nm as measured along the middle of the strand. We show that these repeating units represent monomers of N protein, each of which is associated with 9 +/- 1 bases of single-stranded RNA. From scanning transmission electron microscopy images of negatively stained nucleocapsids, we inferred that N protein has a wedge-shaped, bilobed structure with dimensions of approximately 9.0 nm (length), approximately 5.0 nm (depth), and approximately 3.3 nm (width, at the midpoint of its long axis). In the coiled configuration of the in situ nucleocapsid, the long axis of N protein is directed radially, and its depth corresponds to the pitch of the nucleocapsid helix. Images PMID:2985822

Spectral-fluorescent study of the interaction of the polymethine dye probe Cyan 2 with chondroitin-4-sulfate

NASA Astrophysics Data System (ADS)

Tatikolov, Alexander S.; Akimkin, Timofey M.; Panova, Ina G.; Yarmoluk, Sergiy M.

2017-04-01

The noncovalent interaction of the polymethine dye probe 3,3‧,9-trimethylthiacarbocyanine iodide (Cyan 2) with chondroitin-4-sulfate (C4S) in buffer solutions with different pH and in water in the absence of buffers has been studied by spectral-fluorescent methods. It has been shown that in all media studied, at relatively high concentrations, the dye is bound to C4S mainly as a monomer, which is accompanied by a steep rise of fluorescence (the intermediate formation of dye aggregates on the biopolymer is also observed). From the dependence of the fluorescence quantum yield on the concentration of C4S, the parameters of binding of the dye monomer to C4S were obtained: the effective binding constant K, the number of the monomeric C4S units n per one dye monomer bound to C4S, and the fluorescence quantum yield of the bound dye monomer Φfb. The dependence of Φfb (and K) on pH of the medium is not monotonic: it has a minimum in the region of neutral pH and a growth in the regions of acid and basic pH. This can be explained by changing the charge of a C4S macromolecule as a function of pH and related conformational alterations in the biopolymer, which can affect the rigidity of a dye molecule and the energy of its interaction with the biopolymer.

Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study.

PubMed

Borkar, Aditi Narendra; Rout, Manoj Kumar; Hosur, Ramakrishna V

2011-01-01

Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR) was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH) solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH reveal that the PR denaturation begins by separation of dimer into intact monomers and it is only after this separation that the monomer units start denaturing. The denaturation of the monomers is flagged off by the loss of crucial interactions between the α-helix at C-terminal and surrounding β-strands. This causes the structure to transit from the equilibrium dynamics to random non-equilibrating dynamics. Residence time calculations indicate that denaturation occurs via direct interaction of the acetic acid molecules with certain regions of the protein in 9 M AcOH. All these observations have helped to decipher a picture of the early events in acetic acid denaturation of PR and have illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function.

Characterisation of polyhydroxyalkanoate copolymers with controllable four-monomer composition.

PubMed

Dai, Yu; Lambert, Lynette; Yuan, Zhiguo; Keller, Jurg

2008-03-20

Polyhydroxyalkanoate (PHA) copolymers comprising the four monomers 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), 3-hydroxy-2-methylvalerate (3HMV) and 3-hydroxy-2-methylbutyrate (3HMB) were generated using the recently discovered Defluviicoccus vanus-related glycogen accumulating organisms (DvGAOs) under anaerobic conditions without applying any nutrient limitations. The composition could be manipulated in a defined range by modifying the ratio of propionate and acetate provided in the feed stream. The PHAs produced were characterised as random copolymers (from propionate alone) or a mixture of random copolymers (from mixture of propionate and acetate) through microstructure analysis using 13C NMR spectroscopy. The sequence distribution of all eight comonomer pairs in the carbonyl region of 3HB and 3HV was identified and assigned with confidence utilising two-dimensional heteronuclear multiple bond coherence (HMBC) spectroscopy. Weight average molecular weights were in the range 390-560 kg/mol. Differential scanning calorimetry (DSC) traces showed that the melting temperature (Tm) varied between 70 and 161 degrees C and glass transition temperature (Tg) ranged from -8 to 0 degrees C. The incorporation of considerable amounts of 3HMV and 3HMB monomer units introduced additional "defects" into the PHBV copolymer structure and hence greatly lowered the crystallinity. The data indicate the potential of these four-monomer PHAs to be employed for practical applications, considering their favourable properties and the cost-effective production process using a mixed culture and simple carbon sources.

Synthesis, characterization and fluorescent properties of water-soluble glycopolymer bearing curcumin pendant residues.

PubMed

Zhang, Haisong; Yu, Meng; Zhang, Hailei; Bai, Libin; Wu, Yonggang; Wang, Sujuan; Ba, Xinwu

2016-08-01

Curcumin is a potential natural anticancer drug with low oral bioavailability because of poor water solubility. The aqueous solubility of curcumin is enhanced by means of modification with the carbohydrate units. Polymerization of the curcumin-containing monomer with carbohydrate-containing monomer gives the water-soluble glycopolymer bearing curcumin pendant residues. The obtained copolymers (P1 and P2) having desirable water solubility were well-characterized by infrared spectroscopy (IR), nuclear magnetic resonance (NMR), gel permeation chromatography (GPC), UV-Vis absorption spectroscopy, and photoluminescence spectroscopy. The copolymer P2 with a molar ratio of 1:6 (curcumin/carbohydrate) calculated from the proton NMR results exhibits a similar anticancer activity compared to original curcumin, which may serve as a potential chemotherapeutic agent in the field of anticancer medicine.

Photoinduced Reversible Morphological Transformation of Azobenzene-Containing Pseudo-2D Polymers.

PubMed

Li, Zili; Tang, Miao; Jiang, Chen; Bai, Ruke; Bai, Wei

2018-05-02

2D polymer sheets containing azobenzene are successfully prepared by a facile strategy of "2D self-assembly polymerization (2DSP)" via free radical polymerization in solution. A bola amphiphile containing azobenzene as a novel monomer is designed and synthesized. The results indicate that single-layer covalent pseudo-2D polymers on a micrometer scale are obtained after polymerization with vinyl monomers. Moreover, the 2D polymer sheets are highly sensitive to UV light due to incorporation of azobenzene groups into the polymer. Upon alternative irradiation with UV and visible light, the morphological transformation between sheets and rolled-up nanotubes can be achieved based on the reversible trans-to-cis photoisomerization of azobenzene units in the 2D polymer sheets. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bond cleavage of lignin model compounds into aromatic monomers using supported metal catalysts in supercritical water

PubMed Central

Yamaguchi, Aritomo; Mimura, Naoki; Shirai, Masayuki; Sato, Osamu

2017-01-01

More efficient use of lignin carbon is necessary for carbon-efficient utilization of lignocellulosic biomass. Conversion of lignin into valuable aromatic compounds requires the cleavage of C–O ether bonds and C–C bonds between lignin monomer units. The catalytic cleavage of C–O bonds is still challenging, and cleavage of C–C bonds is even more difficult. Here, we report cleavage of the aromatic C–O bonds in lignin model compounds using supported metal catalysts in supercritical water without adding hydrogen gas and without causing hydrogenation of the aromatic rings. The cleavage of the C–C bond in bibenzyl was also achieved with Rh/C as a catalyst. Use of this technique may greatly facilitate the conversion of lignin into valuable aromatic compounds. PMID:28387304

Electromyographic analysis of repeated bouts of eccentric exercise.

PubMed

McHugh, M P; Connolly, D A; Eston, R G; Gartman, E J; Gleim, G W

2001-03-01

The repeated bout effect refers to the protective effect provided by a single bout of eccentric exercise against muscle damage from a similar subsequent bout. The aim of this study was to determine if the repeated bout was associated with an increase in motor unit activation relative to force production, an increased recruitment of slow-twitch motor units or increased motor unit synchronization. Surface electromyographic (EMG) signals were recorded from the hamstring muscles during two bouts of submaximal isokinetic (2.6 rad x s(-1)) eccentric (11 men, 9 women) or concentric (6 men, 4 women) contractions separated by 2 weeks. The EMG per unit torque and median frequency were analysed. The initial bout of eccentric exercise resulted in strength loss, pain and muscle tenderness, while the repeated eccentric bout resulted in a slight increase in strength, no pain and no muscle tenderness (bout x time effects, P < 0.05). Strength, pain and tenderness were unaffected by either bout of concentric exercise. The EMG per unit torque and median frequency were not different between the initial and repeated bouts of eccentric exercise. The EMG per unit torque and median frequency increased during both bouts of eccentric exercise (P < 0.01) but did not change during either concentric bout. In conclusion, there was no evidence that the repeated bout effect was due to a neural adaptation.

The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA

PubMed Central

Gully, Benjamin S.; Cowieson, Nathan; Stanley, Will A.; Shearston, Kate; Small, Ian D.; Barkan, Alice; Bond, Charles S.

2015-01-01

The pentatricopeptide repeat (PPR) protein family is a large family of RNA-binding proteins that is characterized by tandem arrays of a degenerate 35-amino-acid motif which form an α-solenoid structure. PPR proteins influence the editing, splicing, translation and stability of specific RNAs in mitochondria and chloroplasts. Zea mays PPR10 is amongst the best studied PPR proteins, where sequence-specific binding to two RNA transcripts, atpH and psaJ, has been demonstrated to follow a recognition code where the identity of two amino acids per repeat determines the base-specificity. A recently solved ZmPPR10:psaJ complex crystal structure suggested a homodimeric complex with considerably fewer sequence-specific protein–RNA contacts than inferred previously. Here we describe the solution structure of the ZmPPR10:atpH complex using size-exclusion chromatography-coupled synchrotron small-angle X-ray scattering (SEC-SY-SAXS). Our results support prior evidence that PPR10 binds RNA as a monomer, and that it does so in a manner that is commensurate with a canonical and predictable RNA-binding mode across much of the RNA–protein interface. PMID:25609698

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence.

PubMed

Lahr, Roni M; Mack, Seshat M; Héroux, Annie; Blagden, Sarah P; Bousquet-Antonelli, Cécile; Deragon, Jean-Marc; Berman, Andrea J

2015-09-18

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence

DOE PAGES

Lahr, Roni M.; Mack, Seshat M.; Heroux, Annie; ...

2015-07-22

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. Amore » putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. Ultimately, these studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.« less

Co-polymer Films for Sensors

NASA Technical Reports Server (NTRS)

Ryan, Margaret A. (Inventor); Jewell, April D. (Inventor); Taylor, Charles (Inventor); Yen, Shiao-Pin S. (Inventor); Kisor, Adam (Inventor); Manatt, Kenneth S. (Inventor); Blanco, Mario (Inventor); Goddard, William A. (Inventor); Homer, Margie L. (Inventor); Shevade, Abhijit V. (Inventor)

2012-01-01

Embodiments include a sensor comprising a co-polymer, the co-polymer comprising a first monomer and a second monomer. For some embodiments, the first monomer is poly-4-vinyl pyridine, and the second monomer is poly-4-vinyl pyridinium propylamine chloride. For some embodiments, the first monomer is polystyrene and the second monomer is poly-2-vinyl pyridinium propylamine chloride. For some embodiments, the first monomer is poly-4-vinyl pyridine, and the second monomer is poly-4-vinyl pyridinium benzylamine chloride. Other embodiments are described and claimed.

Co-polymer films for sensors

NASA Technical Reports Server (NTRS)

Ryan, Margaret A. (Inventor); Homer, Margie L. (Inventor); Yen, Shiao-Pin S. (Inventor); Kisor, Adam (Inventor); Jewell, April D. (Inventor); Shevade, Abhijit V. (Inventor); Manatt, Kenneth S. (Inventor); Taylor, Charles (Inventor); Blanco, Mario (Inventor); Goddard, William A. (Inventor)

2010-01-01

Embodiments include a sensor comprising a co-polymer, the co-polymer comprising a first monomer and a second monomer. For some embodiments, the first monomer is poly-4-vinyl pyridine, and the second monomer is poly-4-vinyl pyridinium propylamine chloride. For some embodiments, the first monomer is polystyrene and the second monomer is poly-2-vinyl pyridinium propylamine chloride. For some embodiments, the first monomer is poly-4-vinyl pyridine, and the second monomer is poly-4-vinyl pyridinium benzylamine chloride. Other embodiments are described and claimed.

Hybrid molecularly imprinted polymers synthesized with 3-aminopropyltriethoxysilane-methacrylic acid monomer for miniaturized solid-phase extraction: A new and economical sample preparation strategy for determination of acyclovir in urine.

PubMed

Yan, Hongyuan; Wang, Mingyu; Han, Yehong; Qiao, Fengxia; Row, Kyung Ho

2014-06-13

The miniaturized molecularly imprinted solid-phase extraction (mini-MISPE) coupled with high-performance liquid chromatography was proposed for the determination of acyclovir in urine. 1.5-mL tapered plastic centrifuge tube filled with hybrid molecularly imprinted polymers (HMIPs) was used as the cartridge of mini-MISPE, and the HMIPs synthesized with 3-aminopropyltriethoxy silane-methacrylic acid as monomer exhibited good recognition and selectivity for acyclovir. Under the optimized condition, good linear calibration was obtained in a range of 0.5-15μgmL(-1) with the correlation coefficient of 0.9994, and the recoveries at three spiked levels were 91.6-103.3% in urine with the relative standard deviation (RSD) of ≤3.5%. Excellent intra-day and inter-day repeatability were achieved with RSD of ≤2.6% and 4.0% in three different concentrations. This method combined the advantages of HMIPs and mini-MISPE, and it could become an alternative tool for analyzing the residues of acyclovir in complex urine matrices. Copyright © 2014 Elsevier B.V. All rights reserved.

Polyphenolic compounds in date fruit seed (Phoenix dactylifera): characterisation and quantification by using UPLC-DAD-ESI-MS.

PubMed

Habib, Hosam M; Platat, Carine; Meudec, Emmanuelle; Cheynier, Veronique; Ibrahim, Wissam H

2014-04-01

Date fruit seeds have been demonstrated to possess high antioxidant activities due to their high content of flavonoids and phenolic compounds. The objective of this work was to identify and quantify the phenolic composition of date seeds. Two UPLC-DAD-ESI-MS analyses were performed on the seed of the Khalas variety as follows: (1) an analysis of simple phenolic compounds [phenolic acids, hydroxycinnamic acids, flavonols, flavones, flavan-3-ols (monomers, dimers and trimers)]; and (2) an analysis of all flavan-3-ols (monomers, and proanthocyanidin oligomers and polymers) after depolymerisation. The amount of total phenolic compounds before depolymerisation was found to be 2.194 ± 0.040 g kg(-1) date seed. The analysis of flavan-3-ol monomers and constitutive units of proanthocyanidins after depolymerisation revealed 50.180 ± 1.360 g kg(-1) flavan-3-ols with 46.800 ± 1.012 g kg(-1) epicatechin and 3.380 ± 0.349 g kg(-1) catechin. The results indicate that date seeds are a very rich source of bioactive compounds, thus constituting strong candidates for functional food additives and nutraceuticals. © 2013 Society of Chemical Industry.

A novel antibacterial orthodontic cement containing a quaternary ammonium monomer dimethylaminododecyl methacrylate

PubMed Central

Melo, Mary A.S.; Wu, Junling; Weir, Michael D.; Xu, Hockin H. K.

2015-01-01

Demineralized lesions in tooth enamel around orthodontic brackets are caused by acids from cariogenic biofilm. This study aimed to develop a novel antibacterial orthodontic cement by incorporating a quaternary ammonium monomer dimethylaminododecyl methacrylate (DMADDM) into a commercial orthodontic cement, and to investigate the effects on microcosm biofilm response and enamel bond strength. DMADDM, a recently-synthetized antibacterial monomer, was incorporated into orthodontic cement at 0%, 1.5%, 3% and 5% mass fractions. Bond strength of brackets to enamel was measured. A microcosm biofilm model was used to measure metabolic activity, lactic acid production, and colony-forming units (CFU) on orthodontic cements. Shear bond strength was not reduced at 3% DAMDDM (p > 0.1), but was slightly reduced at 5% DMADDM, compared to 0% DMADDM. Biofilm viability was substantially inhibited when in contact with orthodontic cement containing 3% DMADDM. Biofilm metabolic activity, lactic acid production, and CFU were much lower on orthodontic cement containing DMADDM than control cement (p < 0.05). Therefore, the novel antibacterial orthodontic cement containing 3% DMADDM inhibited oral biofilms without compromising the enamel bond strength, and is promising to reduce or eliminate demineralization in enamel around orthodontic brackets. PMID:25035230

Increase in 4-coumaryl alcohol units during lignification in alfalfa (Medicago sativa) alters the extractability and molecular weight of lignin.

PubMed

Ziebell, Angela; Gracom, Kristen; Katahira, Rui; Chen, Fang; Pu, Yunqiao; Ragauskas, Art; Dixon, Richard A; Davis, Mark

2010-12-10

The lignin content of biomass can impact the ease and cost of biomass processing. Lignin reduction through breeding and genetic modification therefore has potential to reduce costs in biomass-processing industries (e.g. pulp and paper, forage, and lignocellulosic ethanol). We investigated compositional changes in two low-lignin alfalfa (Medicago sativa) lines with antisense down-regulation of p-coumarate 3-hydroxylase (C3H) or hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT). We investigated whether the difference in reactivity during lignification of 4-coumaryl alcohol (H) monomers versus the naturally dominant sinapyl alcohol and coniferyl alcohol lignin monomers alters the lignin structure. Sequential base extraction readily reduced the H monomer content of the transgenic lines, leaving a residual lignin greatly enriched in H subunits; the extraction profile highlighted the difference between the control and transgenic lines. Gel permeation chromatography of isolated ball-milled lignin indicated significant changes in the weight average molecular weight distribution of the control versus transgenic lines (CTR1a, 6000; C3H4a, 5500; C3H9a, 4000; and HCT30a, 4000).

The industrial production and use of 1,3-butadiene.

PubMed Central

Morrow, N L

1990-01-01

This presentation provides a brief overview of the production and use of 1,3-butadiene in the United States. Starting as a coproduct of ethylene, the 1,3-butadiene monomer is extracted and purified, then transferred to consumers. Major uses of 1,3-butadiene include the manufacture of styrene-butadiene rubber, polybutadiene rubber, and adiponitrile. PMID:2205493

Implications of the fluorescence for the conformational analysis of polymeric profisetinidins and procyanidins

Treesearch

Carin A. Helfer; Joo-Sang Sun; Mark A. Matties; Wayne L. Mattice; Richard W. Hemingway; Jan P. Steynberg; Lisa A. Kelly

1995-01-01

The common monomeric units in the polymeric proeyanidins are catechin and epicatechin, which have a hydroxyl group at C(5). This hydroxyl group is absent in the profisetinidins. The fluorescence properties have been characterized for the profisetinidin monomer and dimers, and compared with previous results for the procyanidins. There is a measurable heterogeneity in...

Implications of the fluorescence for the conformational analysis of polymeric profisentinidins and procyanidins

Treesearch

Carin A. Heifer; Joo-Sang Sun; Mark A. Matties; Wayne L. Mattice; Richard W. Hemingway; Jan P. Steynberg; Lisa A. Kelly

1995-01-01

The common monomeric units in the polymeric procyanidins are catechin and epicatechin, which have a hydroxyl group at C(5). this hydroxyl group is absent in the profisetinidins. The fluorescence properties have been characterized for the profisentinidin monomer and dimers, and compared with previous results for the procyanidins. There is a measurable heterogeneity in...

Concerted evolution of the tandem array encoding primate U2 snRNA occurs in situ, without changing the cytological context of the RNU2 locus.

PubMed Central

Pavelitz, T; Rusché, L; Matera, A G; Scharf, J M; Weiner, A M

1995-01-01

In primates, the tandemly repeated genes encoding U2 small nuclear RNA evolve concertedly, i.e. the sequence of the U2 repeat unit is essentially homogeneous within each species but differs somewhat between species. Using chromosome painting and the NGFR gene as an outside marker, we show that the U2 tandem array (RNU2) has remained at the same chromosomal locus (equivalent to human 17q21) through multiple speciation events over > 35 million years leading to the Old World monkey and hominoid lineages. The data suggest that the U2 tandem repeat, once established in the primate lineage, contained sequence elements favoring perpetuation and concerted evolution of the array in situ, despite a pericentric inversion in chimpanzee, a reciprocal translocation in gorilla and a paracentric inversion in orang utan. Comparison of the 11 kb U2 repeat unit found in baboon and other Old World monkeys with the 6 kb U2 repeat unit in humans and other hominids revealed that an ancestral U2 repeat unit was expanded by insertion of a 5 kb retrovirus bearing 1 kb long terminal repeats (LTRs). Subsequent excision of the provirus by homologous recombination between the LTRs generated a 6 kb U2 repeat unit containing a solo LTR. Remarkably, both junctions between the human U2 tandem array and flanking chromosomal DNA at 17q21 fall within the solo LTR sequence, suggesting a role for the LTR in the origin or maintenance of the primate U2 array. Images PMID:7828589

Thermally crosslinked polymeric compositions and methods of making the same

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

Koros, William John; Kratochvil, Adam Michal

2014-03-04

The various embodiments of the present disclosure relate generally to thermally crosslinked polymeric compositions and methods of making thermally crosslinked polymeric compositions. An embodiment of the present invention comprises a composition comprising: a first polymer comprising a first repeat unit, the first repeat unit comprising a carboxyl group, wherein the first polymer crosslinks to a second polymer formed from a second repeat unit, and wherein the first polymer crosslinks to the second polymer without formation of an ester group.

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PubMed

Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

2017-04-01

There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

An Intriguing Method for Fabricating Arbitrarily Shaped “Matreshka” Hydrogels Using a Self-Healing Template

PubMed Central

Sato, Takeshi; Uto, Koichiro; Aoyagi, Takao; Ebara, Mitsuhiro

2016-01-01

This work describes an intriguing strategy for the creation of arbitrarily shaped hydrogels utilizing a self-healing template (SHT). A SHT was loaded with a photo-crosslinkable monomer, PEG diacrylate (PEGDA), and then ultraviolet light (UV) crosslinked after first shaping. The SHT template was removed by simple washing with water, leaving behind the hydrogel in the desired physical shape. A hierarchical 3D structure such as “Matreshka” boxes were successfully prepared by simply repeating the “self-healing” and “photo-irradiation” processes. We have also explored the potential of the SHT system for the manipulation of cells. PMID:28773983

A Thermally Re-mendable Cross-Linked Polymeric Material

NASA Astrophysics Data System (ADS)

Chen, Xiangxu; Dam, Matheus A.; Ono, Kanji; Mal, Ajit; Shen, Hongbin; Nutt, Steven R.; Sheran, Kevin; Wudl, Fred

2002-03-01

We have developed a transparent organic polymeric material that can repeatedly mend or ``re-mend'' itself under mild conditions. The material is a tough solid at room temperature and below with mechanical properties equaling those of commercial epoxy resins. At temperatures above 120°C, approximately 30% (as determined by solid-state nuclear magnetic resonance spectroscopy) of ``intermonomer'' linkages disconnect but then reconnect upon cooling, This process is fully reversible and can be used to restore a fractured part of the polymer multiple times, and it does not require additional ingredients such as a catalyst, additional monomer, or special surface treatment of the fractured interface.

Diffusion of residual monomer in polymer resins.

PubMed Central

Piver, W T

1976-01-01

A simplified mathematical model which made use of Fick's laws of diffusion written in spherical coordinates was developed to describe the rate of diffusion of residual monomers from polymer resins. The properties of the monomer-polymer system which influenced the amount of monomer remaining in the polymer as a function of time were the diffusivity and solubility of the monomer in the polymer, and the particle size of the polymer resin. This model was used to analyze literature data on the diffusion of residual vinyl chloride monomer in polyvinyl chloride resins made by the suspension process. It was concluded that particle size of the resin was a significant parameter which should be taken advantage of in process equipment designed to remove residual monomer from PVC resins. The diffusivity of the monomer in the polymer was a function of the solubility of the monomer in the polymer. Monomer solubility can be determined from Henry's law. It was suggested that this model could be adapted to describe diffusion of monomers from any monomer-polymer system, and would be a useful approach to modeling the transport of nonreactive chemical additives from plastics. PMID:1026410

Stability, denaturation and refolding of Mycobacterium tuberculosis MfpA, a DNA mimicking protein that confers antibiotic resistance

PubMed Central

Khrapunov, Sergei; Brenowitz, Michael

2011-01-01

MfpA from Mycobacterium tuberculosis is a founding member of the pentapeptide repeat class of proteins (PRP) that is believed to confer bacterial resistance to the drug fluoroquinolone by mimicking the size, shape and surface charge of duplex DNA. We show that phenylalanine side chain stacking stabilizes the N-terminus of MfpA’s pentapeptide thus extending the DNA mimicry analogy. The Lumry-Eyring model was applied to multiple spectral measures of MfpA denaturation revealing that the MfpA dimer dissociates to monomers which undergo a structural transition that leads to aggregation. MfpA retains high secondary and tertiary structure content under denaturing conditions. Dimerization stabilizes MfpA’s pentapeptide repeat fold. The high Arrhenius activation energy of the barrier to aggregate formation rationalizes its stability. The mechanism of MfpA denaturation and refolding is a ‘double funnel’ energy landscape where the ‘native’ and ‘aggregate’ funnels are separated by the high barrier that is not overcome during in vitro refolding. PMID:21605934

Method for fabricating carbon/lithium-ion electrode for rechargeable lithium cell

NASA Technical Reports Server (NTRS)

Attia, Alan I. (Inventor); Halpert, Gerald (Inventor); Huang, Chen-Kuo (Inventor); Surampudi, Subbarao (Inventor)

1995-01-01

The method includes steps for forming a carbon electrode composed of graphitic carbon particles adhered by an ethylene propylene diene monomer binder. An effective binder composition is disclosed for achieving a carbon electrode capable of subsequent intercalation by lithium ions. The method also includes steps for reacting the carbon electrode with lithium ions to incorporate lithium ions into graphitic carbon particles of the electrode. An electrical current is repeatedly applied to the carbon electrode to initially cause a surface reaction between the lithium ions and to the carbon and subsequently cause intercalation of the lithium ions into crystalline layers of the graphitic carbon particles. With repeated application of the electrical current, intercalation is achieved to near a theoretical maximum. Two differing multi-stage intercalation processes are disclosed. In the first, a fixed current is reapplied. In the second, a high current is initially applied, followed by a single subsequent lower current stage. Resulting carbon/lithium-ion electrodes are well suited for use as an anode in a reversible, ambient temperature, lithium cell.

The study on mechanism of holographic recording in photopolymer with dual monomer

NASA Astrophysics Data System (ADS)

Zhai, Qianli; Tao, Shiquan; Wang, Dayong

2010-06-01

In this paper we study the dynamics of refractive index modulation in a dual-monomer photopolymer through grating growth under different experiment stages. By using different sets of parameters for vinyl monomers (NVC) and acrylate monomers (POEA) respectively, a composite dual-monomer model, extended from the uniform post-exposure (UPE) model for single monomer photopolymer, is proposed and fitted with the experiment data very well. Further discussions indicate that the dominant contribution to the total index modulation is made by NVC monomers, and a brief explanation of the function of POEA monomers is given.

Polymers containing borane or carborane cage compounds and related applications

DOEpatents

Bowen, III, Daniel E; Eastwood, Eric A

2013-04-23

Polymers comprising residues of cage compound monomers having at least one polyalkoxy silyl substituent are provided. The cage compound monomers are selected from borane cage compound monomers comprising at least 7 cage atoms and/or carborane cage compound monomers comprising 7 to 11 cage compound monomers. Such polymers can further comprise one or more reactive matrices and/or co-monomers covalently bound with the cage compound monomer residues. Articles of manufacture comprising such polymers are also disclosed.

Efficient production of artificially designed gelatins with a Bacillus brevis system.

PubMed

Kajino, T; Takahashi, H; Hirai, M; Yamada, Y

2000-01-01

Artificially designed gelatins comprising tandemly repeated 30-amino-acid peptide units derived from human alphaI collagen were successfully produced with a Bacillus brevis system. The DNA encoding the peptide unit was synthesized by taking into consideration the codon usage of the host cells, but no clones having a tandemly repeated gene were obtained through the above-mentioned strategy. Minirepeat genes could be selected in vivo from a mixture of every possible sequence encoding an artificial gelatin by randomly ligating the mixed sequence unit and transforming it into Escherichia coli. Larger repeat genes constructed by connecting minirepeat genes obtained by in vivo selection were also stable in the expression host cells. Gelatins derived from the eight-unit and six-unit repeat genes were extracellularly produced at the level of 0.5 g/liter and easily purified by ammonium sulfate fractionation and anion-exchange chromatography. The purified artificial gelatins had the predicted N-terminal sequences and amino acid compositions and a solgel property similar to that of the native gelatin. These results suggest that the selection of a repeat unit sequence stable in an expression host is a shortcut for the efficient production of repetitive proteins and that it can conveniently be achieved by the in vivo selection method. This study revealed the possible industrial application of artificially designed repetitive proteins.

Synergetic interaction between neighbouring platinum monomers in CO2 hydrogenation

NASA Astrophysics Data System (ADS)

Li, Hongliang; Wang, Liangbing; Dai, Yizhou; Pu, Zhengtian; Lao, Zhuohan; Chen, Yawei; Wang, Menglin; Zheng, Xusheng; Zhu, Junfa; Zhang, Wenhua; Si, Rui; Ma, Chao; Zeng, Jie

2018-05-01

Exploring the interaction between two neighbouring monomers has great potential to significantly raise the performance and deepen the mechanistic understanding of heterogeneous catalysis. Herein, we demonstrate that the synergetic interaction between neighbouring Pt monomers on MoS2 greatly enhanced the CO2 hydrogenation catalytic activity and reduced the activation energy relative to isolated monomers. Neighbouring Pt monomers were achieved by increasing the Pt mass loading up to 7.5% while maintaining the atomic dispersion of Pt. Mechanistic studies reveal that neighbouring Pt monomers not only worked in synergy to vary the reaction barrier, but also underwent distinct reaction paths compared with isolated monomers. Isolated Pt monomers favour the conversion of CO2 into methanol without the formation of formic acid, whereas CO2 is hydrogenated stepwise into formic acid and methanol for neighbouring Pt monomers. The discovery of the synergetic interaction between neighbouring monomers may create a new path for manipulating catalytic properties.

Chlorine resistant desalination membranes based on directly sulfonated poly(arylene ether sulfone) copolymers

DOEpatents

McGrath, James E [Blacksburg, VA; Park, Ho Bum [Austin, TX; Freeman, Benny D [Austin, TX

2011-10-04

The present invention provides a membrane, kit, and method of making a hydrophilic-hydrophobic random copolymer membrane. The hydrophilic-hydrophobic random copolymer membrane includes a hydrophilic-hydrophobic random copolymer. The hydrophilic-hydrophobic random copolymer includes one or more hydrophilic monomers having a sulfonated polyarylsulfone monomer and a second monomer and one or more hydrophobic monomers having a non-sulfonated third monomer and a fourth monomer. The sulfonated polyarylsulfone monomer introduces a sulfonate into the hydrophilic-hydrophobic random copolymer prior to polymerization.

Correlation Between the Extent of Catalytic Activity and Charge Density of Montmorillonites

PubMed Central

Steudel, Annett; Emmerich, Katja; Lagaly, Gerhard; Schuhmann, Rainer

2010-01-01

Abstract The clay mineral montmorillonite is a member of the phyllosilicate group of minerals, which has been detected on martian soil. Montmorillonite catalyzes the condensation of activated monomers to form RNA-like oligomers. Extent of catalysis, that is, the yield of oligomers, and the length of the longest oligomer formed in these reactions widely varies with the source of montmorillonite (i.e., the locality where the mineral is mined). This study was undertaken to establish whether there exists a correlation between the extent of catalytic property and the charge density of montmorillonites. Charge density was determined by saturating the montmorillonites with alkyl ammonium cations that contained increasing lengths of alkyl chains, [CH3-(CH2)n-NH3]+, where n = 3–16 and 18, and then measuring d(001), interlayer spacing of the resulting montmorillonite-alkyl ammonium-montmorillonite complex by X-ray diffractometry (XRD). Results demonstrate that catalytic activity of montmorillonites with lower charge density is superior to that of higher charge density montmorillonite. They produce longer oligomers that contain 9 to 10 monomer units, while montmorillonite with high charge density catalyzes the formation of oligomers that contain only 4 monomer units. The charge density of montmorillonites can also be calculated from the chemical composition if elemental analysis data of the pure mineral are available. In the next mission to Mars, CheMin (Chemistry and Mineralogy), a combined X-ray diffraction/X-ray fluorescence instrument, will provide information on the mineralogical and elemental analysis of the samples. Possible significance of these results for planning the future missions to Mars for the search of organic compounds and extinct or extant life is discussed. Key Words: Mars—Origin of life—Montmorillonite—Mineral catalysis—Layer charge density—X–ray diffractometry. Astrobiology 10, 743–749. PMID:20854214

Correlation between the extent of catalytic activity and charge density of montmorillonites.

PubMed

Ertem, Gözen; Steudel, Annett; Emmerich, Katja; Lagaly, Gerhard; Schuhmann, Rainer

2010-09-01

The clay mineral montmorillonite is a member of the phyllosilicate group of minerals, which has been detected on martian soil. Montmorillonite catalyzes the condensation of activated monomers to form RNA-like oligomers. Extent of catalysis, that is, the yield of oligomers, and the length of the longest oligomer formed in these reactions widely varies with the source of montmorillonite (i.e., the locality where the mineral is mined). This study was undertaken to establish whether there exists a correlation between the extent of catalytic property and the charge density of montmorillonites. Charge density was determined by saturating the montmorillonites with alkyl ammonium cations that contained increasing lengths of alkyl chains, [CH₃-(CH₂)(n)-NH₃](+), where n = 3-16 and 18, and then measuring d(₀₀₁), interlayer spacing of the resulting montmorillonite-alkyl ammonium-montmorillonite complex by X-ray diffractometry (XRD). Results demonstrate that catalytic activity of montmorillonites with lower charge density is superior to that of higher charge density montmorillonite. They produce longer oligomers that contain 9 to 10 monomer units, while montmorillonite with high charge density catalyzes the formation of oligomers that contain only 4 monomer units. The charge density of montmorillonites can also be calculated from the chemical composition if elemental analysis data of the pure mineral are available. In the next mission to Mars, CheMin (Chemistry and Mineralogy), a combined X-ray diffraction/X-ray fluorescence instrument, will provide information on the mineralogical and elemental analysis of the samples. Possible significance of these results for planning the future missions to Mars for the search of organic compounds and extinct or extant life is discussed.

Nitroxyl-mediated oxidation of lignin and polycarboxylated products

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

Stahl, Shannon S.; Rafiee, Mohammad

Methods of selectively modifying lignin, polycarboxylated products thereof, and methods of deriving aromatic compounds therefrom. The methods comprise electrochemically oxidizing lignin using stable nitroxyl radicals to selectively oxidize primary hydroxyls on .beta.-O-4 phenylpropanoid units to corresponding carboxylic acids while leaving the secondary hydroxyls unchanged. The oxidation results in polycarboxylated lignin in the form of a polymeric .beta.-hydroxy acid. The polymeric .beta.-hydroxy acid has a high loading of carboxylic acid and can be isolated in acid form, deprotonated, and/or converted to a salt. The .beta.-hydroxy acid, anion, or salt can also be subjected to acidolysis to generate various aromatic monomers ormore » oligomers. The initial oxidation of lignin to the polycarboxylated form renders the lignin more susceptible to acidolysis and thereby enhances the yield of aromatic monomers and oligomers obtained through acidolysis.« less

Identification of proanthocyanidin dimers and trimers, flavone C-Glycosides, and antioxidants in Ficus deltoidea , a malaysian herbal tea.

PubMed

Omar, Maizatul Hasyima; Mullen, William; Crozier, Alan

2011-02-23

Phenolic compounds in an aqueous infusion of leaves of Ficus deltoidea (Moraceae), a well-known herbal tea in Malaysia, were analyzed by HPLC coupled to photodiode array and fluorescence detectors and an electrospray ionization tandem mass spectrometer. Following chromatography of extracts on a reversed phase C(12) column, 25 flavonoids were characterized and/or tentatively identified with the main constituents being flavan-3-ol monomers, proanthocyanidins, and C-linked flavone glycosides. The proanthocyanidins were dimers and trimers comprising (epi)catechin and (epi)afzelechin units. No higher molecular weight proanthocyanidin polymers were detected. The antioxidant activity of F. deltoidea extract was analyzed using HPLC with online antioxidant detection. This revealed that 85% of the total antioxidant activity of the aqueous F. deltoidea infusion was attributable to the flavan-3-ol monomers and the proanthocyanidins.

Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form

PubMed Central

Zheng, Heping; Mandal, Arabinda; Shumilin, Igor A.; Chordia, Mahendra D.; Panneerdoss, Subbarayalu; Herr, John C.; Minor, Wladek

2016-01-01

Sperm Lysozyme-Like Protein 1 (SLLP1) is one of the lysozyme-like proteins predominantly expressed in mammalian testes that lacks bacteriolytic activity, localizes in the sperm acrosome, and exhibits high affinity for an oolemmal receptor, SAS1B. The crystal structure of mouse SLLP1 (mSLLP1) was determined at 2.15Å resolution. mSLLP1 monomer adopts a structural fold similar to that of chicken/mouse lysozymes retaining all four canonical disulfide bonds. mSLLP1 is distinct from c-lysozyme by substituting two essential catalytic residues (E35T/D52N), exhibiting different surface charge distribution, and by forming helical filaments approximately 75Å in diameter with a 25Å central pore comprised of six monomers per helix turn repeating every 33Å. Cross-species alignment of all reported SLLP1 sequences revealed a set of invariant surface regions comprising a characteristic fingerprint uniquely identifying SLLP1 from other c-lysozyme family members. The fingerprint surface regions reside around the lips of the putative glycan binding groove including three polar residues (Y33/E46/H113). A flexible salt bridge (E46-R61) was observed covering the glycan binding groove. The conservation of these regions may be linked to their involvement in oolemmal protein binding. Interaction between SLLP1 monomer and its oolemmal receptor SAS1B was modeled using protein-protein docking algorithms, utilizing the SLLP1 fingerprint regions along with the SAS1B conserved surface regions. This computational model revealed complementarity between the conserved SLLP1/SAS1B interacting surfaces supporting the experimentally-observed SLLP1/SAS1B interaction involved in fertilization. PMID:26198801

Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form.

PubMed

Zheng, H; Mandal, A; Shumilin, I A; Chordia, M D; Panneerdoss, S; Herr, J C; Minor, W

2015-07-01

Sperm lysozyme-like protein 1 (SLLP1) is one of the lysozyme-like proteins predominantly expressed in mammalian testes that lacks bacteriolytic activity, localizes in the sperm acrosome, and exhibits high affinity for an oolemmal receptor, SAS1B. The crystal structure of mouse SLLP1 (mSLLP1) was determined at 2.15 Å resolution. mSLLP1 monomer adopts a structural fold similar to that of chicken/mouse lysozymes retaining all four canonical disulfide bonds. mSLLP1 is distinct from c-lysozyme by substituting two essential catalytic residues (E35T/D52N), exhibiting different surface charge distribution, and by forming helical filaments approximately 75 Å in diameter with a 25 Å central pore comprised of six monomers per helix turn repeating every 33 Å. Cross-species alignment of all reported SLLP1 sequences revealed a set of invariant surface regions comprising a characteristic fingerprint uniquely identifying SLLP1 from other c-lysozyme family members. The fingerprint surface regions reside around the lips of the putative glycan-binding groove including three polar residues (Y33/E46/H113). A flexible salt bridge (E46-R61) was observed covering the glycan-binding groove. The conservation of these regions may be linked to their involvement in oolemmal protein binding. Interaction between SLLP1 monomer and its oolemmal receptor SAS1B was modeled using protein-protein docking algorithms, utilizing the SLLP1 fingerprint regions along with the SAS1B conserved surface regions. This computational model revealed complementarity between the conserved SLLP1/SAS1B interacting surfaces supporting the experimentally observed SLLP1/SAS1B interaction involved in fertilization. © 2015 American Society of Andrology and European Academy of Andrology.

Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

PubMed

Beauparlant, Marc A; Drouin, Guy

2014-02-01

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

Enhanced molecular recognition for imprinted monolithic column containing polyhedral oligomeric silsesquioxanes by dendritic effect of mesoporous molecular sieve scaffolds.

PubMed

Yang, Fang-Fang; Li, Zai-Xuan; Xu, Yu-Jing; Huang, Yan-Ping; Liu, Zhao-Sheng

2018-06-07

The dendritic effect of nano mesoporous molecular sieve was first used to enhance molecular recognition of molecularly imprinted polymers (MIPs)-based polyhedral oligomeric silsesquioxanes (POSS). In this study, the MIPs were made using S-naproxen (S-NAP) as template molecule, 4-vinylpyridine (4-VP) as functional monomer, ethylene glycol dimethacrylate as cross-linker, 1-butyl-3-methylimidazoliumtetrafluoroborate ([BMIM]BF 4 )/DMSO as binary porogens, 1-propylmethacrylate-heptaisobutyl substituted as POSS monomer, and mesoporous molecular sieve (Mobil composition of matter No. 41, MCM-41) as dendritic scaffold. The influence of synthesis parameters on the imprinting effect, including the content of POSS monomer and derivatized MCM-41-MPS, the ratio of template to monomer, and the ratio of binary porogens were also investigated, respectively. The morphology of the polymers was characterized by scanning electron microscopy, nitrogen adsorption, and X-ray powder diffraction. The results showed that POSS&MCM-41-MPS MIP had a stronger imprinting effect with an imprinting factor 6.86, which is approximately 2.4, 2.3, and 3 times than that of POSS MIP, MCM-41-MPS MIP, and conventional MIP, respectively. The increase of affinity might be attributed to impediment of the chain motion of polymer due to improved POSS aggregation and the dipole interaction between the POSS units by introduce of MCM-41-MPS as scaffolds. The resulting POSS&MCM-41-MPS MIP was used as adsorbent for the enrichment of S-NAP in solid-phase extraction with a high recovery of 97.65% and the value of RSD was 0.94%.

Elution of monomer from different bulk fill dental composite resins.

PubMed

Cebe, Mehmet Ata; Cebe, Fatma; Cengiz, Mehmet Fatih; Cetin, Ali Rıza; Arpag, Osman Fatih; Ozturk, Bora

2015-07-01

The purpose of this study was to evaluate the elution of Bis-GMA, TEGDMA, HEMA, and Bis-EMA monomers from six bulk fill composite resins over four different time periods, using HPLC. Six different composite resin materials were used in the present study: Tetric Evo Ceram Bulk Fill (Ivoclar Vivadent, Amherst, NY), X-tra Fill (VOCO, Cuxhaven, Germany), Sonic Fill (Kerr, Orange, CA, USA), Filtek Bulk Fill (3M ESPE Dental Product, St. Paul, MN), SDR (Dentsply, Konstanz, Germany), EQUIA (GC America INC, Alsip, IL). The samples (4mm thickness, 5mm diameter) were prepared and polymerized for 20s with a light emitted diode unit. After fabrication, each sample was immediately immersed in 75wt% ethanol/water solution used as extraction fluid and stored in the amber colored bottles at room temperature. Ethanol/water samples were taken (0.5mL) at predefined time intervals:10m (T1), 1h (T2), 24h (T3) and 30 days (T4). These samples were analyzed by HPLC. The obtained data were analyzed with one-way ANOVA and Tukey HSD at significance level of p<0.05. Amount of eluted Bis-EMA and Bis-GMA from Tetric Evo Ceram Bulk Fill and amount of eluted TEGDMA and HEMA from X-tra Fill higher than others composites (p<0.05). Residual monomers were eluted from bulk fill composite resins in all time periods and the amount of eluted monomers was increased with time. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Synthesis of Metal Phthalocyanine Sheet Polymers

NASA Technical Reports Server (NTRS)

Achar, B. N.; Fohlen, G. M.; Parker, J. A.

1986-01-01

New method for synthesizing metal phthalocyanine tetracarboxylic acids (MPTCA's) yields high purity end product. In addition, high-purity metal phthalocyanine sheet polymers synthesized from compounds. Monomer formed into sheet polymer by heating. Units of polymer linked in manner similar to phenyl-group linkages in biphenyl: Conjugation extends throughout macromolecule, thereby increasing delocalization of TT-electrons. Increases conductivity and thermal stability of polymer.

Method for polymer synthesis in a reaction well

DOEpatents

Brennan, Thomas M.

1998-01-01

A method of synthesis for building a polymer chain, oligonucleotides in particular, by sequentially adding monomer units to at least one solid support for growing and immobilizing a polymer chain thereon in a liquid reagent solution. The method includes the step of: A) depositing a liquid reagent in a reaction well (26) in contact with at least one solid support and at least one monomer unit of the polymer chain affixed to the solid support. The well (26) includes at least one orifice (74) extending into the well (26), and is of a size and dimension to form a capillary liquid seal to retain the reagent solution in the well (26) to enable polymer chain growth on the solid support. The method further includes the step of B) expelling the reagent solution from the well (26), while retaining the polymer chain therein. This is accomplished by applying a first gas pressure to the reaction well such that a pressure differential between the first gas pressure and a second gas pressure exerted on an exit (80) of the orifice (74) exceeds a predetermined amount sufficient to overcome the capillary liquid seal and expel the reagent solution from the well (26) through the orifice exit (80).

Method for polymer synthesis in a reaction well

DOEpatents

Brennan, T.M.

1998-09-29

A method of synthesis is described for building a polymer chain, oligonucleotides in particular, by sequentially adding monomer units to at least one solid support for growing and immobilizing a polymer chain thereon in a liquid reagent solution. The method includes the step of: (A) depositing a liquid reagent in a reaction well in contact with at least one solid support and at least one monomer unit of the polymer chain affixed to the solid support. The well includes at least one orifice extending into the well, and is of a size and dimension to form a capillary liquid seal to retain the reagent solution in the well to enable polymer chain growth on the solid support. The method further includes the step of (B) expelling the reagent solution from the well, while retaining the polymer chain therein. This is accomplished by applying a first gas pressure to the reaction well such that a pressure differential between the first gas pressure and a second gas pressure exerted on an exit of the orifice exceeds a predetermined amount sufficient to overcome the capillary liquid seal and expel the reagent solution from the well through the orifice exit. 9 figs.

Tuning the structural and electronic properties of novel thiophene-pyrrole based 1,2,3,4-tetrazine

NASA Astrophysics Data System (ADS)

Dutta, Rakesh; Kalita, Dhruba Jyoti

2017-04-01

Here, we have studied the structural and optoelectronic behaviour of a series of conjugated heterocyclic polymers. The basic monomer unit of the conjugated polymers contains a backbone of novel thiophene and pyrrole based 1,2,3,4-tetrazine. The other oligomers are designed by substituting the basic monomer unit with different electron-donating and electron-withdrawing groups at the nitrogen and the 3rd C-atom of the pyrrole and the thiophene ring respectively. We have calculated dihedral angles, HOMO-LUMO gaps, excitation energies and oscillator strengths by employing TD-DFT method. Our study reveals that compounds having bulky substituents exhibit larger dihedral angles. This in turn renders an increase in the band gaps (ΔH - L). Presence of the electron-withdrawing substituents also increases the ΔH - L values of the oligomers. However, the electron-donating groups decrease the ΔH - L values of the oligomers. Therefore, small electron-donating substituents have an overwhelming effect on the optoelectronic properties of the conjugated polymers which in turn makes them interesting materials with good conduction properties for fabrication of optoelectronic devices such as OLEDs, OFETs and solar cells.

Does the copolymer poly(vinylidene cyanide-tricyanoethylene) possess piezoelectricity?

PubMed

Wang, Zhi-Yin; Su, Ke-He; Xu, Qiong

2012-10-01

The geometry, energy, internal rotation barrier, dipole moment, and molecular polarizability of the α- and β-chain models of poly(vinylidene cyanide-tricyanoethylene) [P(VDCN-TrCN)] were studied with density functional theory at the B3PW91/6-31G(d) level. The effects of the chain length and the TrCN content on the copolymer chain stability, the chain conformation, and the electrical properties of P(VDCN-TrCN) were examined and compared with those of poly(vinylidene fluoride-trifluoroethylene) and PVDCN to gauge whether P(VDCN-TrCN) would be expected to possess substantial piezoelectricity. The results of this study showed that the stability of the β conformation increases and the energy difference per monomer unit between the β- and α-chains decreases with increasing TrCN. However, introducing TrCN into VDCN will not significantly enhance the radius of curvature of the P(VDCN-TrCN) chains. The average dipole moment per monomer unit in the β-chain is affected by the chain curvature and the TrCN content. The amount of piezoelectricity present in P(VDCN-TrCN) is slightly smaller than that in PVDCN, and is less than that in poly(vinylidene fluoride-trifluoroethylene).

Crystallization and preliminary X-ray analysis of the isomerase domain of glucosamine-6-phosphate synthase from Candida albicans

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

Olchowy, Jaroslaw; Jedrzejczak, Robert; Milewski, Slawomir

2005-11-01

The isomerase domain of glucosamine-6-phosphate synthase from C. albicans has been crystallized and X-ray diffraction data have been collected. Preliminary analysis of the data reveals the oligomeric structure of the eukaryotic synthase to be a ‘dimer’ of prokaryotic-like dimers. Glucosamine-6-phosphate synthase (EC 2.6.1.16) catalyses the first and practically irreversible step in the hexosamine metabolism pathway, the end product of which, uridine 5′-diphospho-N-acetyl d-glucosamine, is an essential substrate for assembly of the cell wall. The isomerase domain, consisting of residues 346–712 (42 kDa), of glucosamine-6-phosphate synthase from Candida albicans has been crystallized. X-ray analysis revealed that the crystals belonged to spacemore » group I4, with unit-cell parameters a = b = 149, c = 103 Å. Diffraction data were collected to 3.8 Å. Preliminary results from molecular replacement using the homologous bacterial monomer reveal that the asymmetric unit contains two monomers that resemble a bacterial dimer. The crystal lattice consists of pairs of such symmetry-related dimers forming elongated tetramers.« less

Enhanced production of longer side-chain polyhydroxyalkanoic acid with omega-aromatic group substitution in phaZ-disrupted Pseudomonas fluorescens BM07 mutant through unrelated carbon source cometabolism and salicylic acid beta-oxidation inhibition.

PubMed

Choi, Mun Hwan; Xu, Ju; Rho, Jong Kook; Zhao, Xu Ping; Yoon, Sung Chul

2010-06-01

The deletion of the intracellular polyhydroxyalkanoate (PHA) depolymerase gene (phaZ) in Pseudomonas fluorescens BM07 was found to increase more efficiently the levels of longer medium-chain-length (MCL) omega-aromatic monomer-units than in the wild-type strain when the cells were grown with a mixture of fructose and MCL omega-aromatic fatty acid in the presence of salicylic acid that is known as a beta-oxidation inhibitor in BM07 strain. When 11-phenoxyundecanoic acid was used as co-carbon source, the longest monomer-unit 3-hydroxy-11-phenoxyundecanoate, not reported in literature yet, was incorporated into the polymer chain up to approximately 10 mol%. An advantage of salicylic acid inhibition technique is that salicylic acid is not metabolized in BM07 strain, thus, the effective concentration of the inhibitor remaining constant throughout the cultivation. In conclusion, this new technique could be exploited for the enhanced production of side-chain modulated functional MCL-PHA with improved physicochemical properties in P. fluorescens BM07. (c) 2010 Elsevier Ltd. All rights reserved.

Crystal structure of Plasmodium falciparum phosphoglycerate kinase: Evidence for anion binding in the basic patch

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

Smith, Craig D.; Chattopadhyay, Debasish; Pal, Biswajit

2012-11-09

3-Phosphoglycerate kinase (EC 2.7.2.3) is a key enzyme in the glycolytic pathway and catalyzes an important phosphorylation step leading to the production of ATP. The crystal structure of Plasmodium falciparum phosphoglycerate kinase (PfPGK) in the open conformation is presented in two different groups, namely I222 and P6{sub 1}22. The structure in I222 space group is solved using MAD and refined at 3 {angstrom} whereas that in P6{sub 1}22A is solved using MR and refined at 2.7 {angstrom}. I222 form has three monomers in asymmetric unit whereas P6{sub 1}22 form has two monomers in the asymmetric unit. In both crystal formsmore » a sulphate ion is located at the active site where ATP binds, but no Mg{sup 2+} ion is observed. For the first time another sulphate ion is found at the basic patch where the 3-phosphate of 1,3-biphosphoglycerate normally binds. This was found in both chains of P6{sub 1}22 form but only in chain A of I222 form.« less

Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

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

Liao, D.; Weiner, A.M.

1995-12-10

The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to studymore » the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.« less

Synthesis and characterization of antibacterial dental monomers and composites

PubMed Central

Xu, Xiaoming; Wang, Yapin; Liao, Sumei; Wen, Zezhang T.; Fan, Yuwei

2012-01-01

The objective of this study is to synthesize antibacterial methacrylate and methacrylamide monomers and formulate antibacterial fluoride-releasing dental composites. Three antibacterial methacrylate or methacrylamide monomers containing long-chain quaternary ammonium fluoride, 1,2-methacrylamido-N,N,N-trimethyldodecan-1-aminium fluoride (monomer I), N-benzyl-11-(methacryloyloxy)-N,N-dimethylundecan-1-aminium fluoride (monomer II), and methacryloxyldecylpyridinium fluoride (monomer III) have been synthesized and analyzed by nuclear magnetic resonance (NMR) and mass spectrometry (MS). The cytotoxicity test and bactericidal test against Streptococcus mutans indicate that antibacterial monomer II is superior to monomers I and III. A series of dental composites containing 0–6% of antibacterial monomer II have been formulated and tested for degree of conversion (DC), flexure strength, water sorption, solubility, and inhibition of S. mutans biofilms. An antibacterial fluoride-releasing dental composite has also been formulated and tested for flexure strength and fluoride release. The dental composite containing 3% of monomer II has a significant effect against S. mutans biofilm formation without major adverse effects on its physical and mechanical properties. The new antibacterial monomers can be used together with the fluoride-releasing monomers containing a ternary zirconiun- fluoride chelate to formulate a new antibacterial fluoride- releasing dental composite. Such a new dental composite is expected to have higher anticaries efficacy and longer service life. PMID:22447582

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

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

Arai, Shigeki; Yonezawa, Yasushi; Ishibashi, Matsujiro

2014-03-01

In order to clarify the structural basis of the halophilic characteristics of an alkaline phosphatase derived from the moderate halophile Halomonas sp. 593 (HaAP), the tertiary structure of HaAP was determined to 2.1 Å resolution by X-ray crystallography. The structural properties of surface negative charge and core hydrophobicity were shown to be intermediate between those characteristic of halophiles and non-halophiles, and may explain the unique functional adaptation to a wide range of salt concentrations. Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1–4 M NaCl). Inmore » order to clarify the structural basis of its halophilic characteristics and its wide-range adaptation to salt concentration, the tertiary structure of HaAP was determined by X-ray crystallography to 2.1 Å resolution. The unit cell of HaAP contained one dimer unit corresponding to the biological unit. The monomer structure of HaAP contains a domain comprised of an 11-stranded β-sheet core with 19 surrounding α-helices similar to those of APs from other species, and a unique ‘crown’ domain containing an extended ‘arm’ structure that participates in formation of a hydrophobic cluster at the entrance to the substrate-binding site. The HaAP structure also displays a unique distribution of negatively charged residues and hydrophobic residues in comparison to other known AP structures. AP from Vibrio sp. G15-21 (VAP; a slight halophile) has the highest similarity in sequence (70.0% identity) and structure (C{sup α} r.m.s.d. of 0.82 Å for the monomer) to HaAP. The surface of the HaAP dimer is substantially more acidic than that of the VAP dimer (144 exposed Asp/Glu residues versus 114, respectively), and thus may enable the solubility of HaAP under high-salt conditions. Conversely, the monomer unit of HaAP formed a substantially larger hydrophobic interior comprising 329 C atoms from completely buried residues, whereas that of VAP comprised 264 C atoms, which may maintain the stability of HaAP under low-salt conditions. These characteristics of HaAP may be responsible for its unique functional adaptation permitting activity over a wide range of salt concentrations.« less

Synthesis of π-conjugated polymer consisting of pyrrole and fluorene units by Ru-catalyzed site-selective direct arylation polycondensation.

PubMed

Lu, Wei; Kuwabara, Junpei; Kanbara, Takaki

2013-07-25

Polycondensation of 1-(2-pyrimidinyl)pyrrole with 2,7-dibromo-9,9-dioctylfluorene via Ru-catalyzed direct arylation gives the corresponding conjugated polymer with a molecular weight of 19 800 in 86% yield. The introduction of directing group, 2-pyrimidinyl substituent, into the pyrrole monomer induces ortho-metalation and provides the site-selective direct arylation polycondensation at the α-position of pyrrole unit without the protection of β-position. The removal of 2-pyrimidinyl substituent on the pyrrole unit proceeds efficiently and results in the enhancement of coplanarity along the main chain of the polymer. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oligomerization State of CXCL4 Chemokines Regulates G Protein-Coupled Receptor Activation.

PubMed

Chen, Ya-Ping; Wu, Hsin-Li; Boyé, Kevin; Pan, Chen-Ya; Chen, Yi-Chen; Pujol, Nadège; Lin, Chun-Wei; Chiu, Liang-Yuan; Billottet, Clotilde; Alves, Isabel D; Bikfalvi, Andreas; Sue, Shih-Che

2017-11-17

CXCL4 chemokines have antiangiogenic properties, mediated by different mechanisms, including CXCR3 receptor activation. Chemokines have distinct oligomerization states that are correlated with their biological functions. CXCL4 exists as a stable tetramer under physiological conditions. It is unclear whether the oligomerization state impacts CXCL4-receptor interaction. We found that the CXCL4 tetramer is sensitive to pH and salt concentration. Residues Glu28 and Lys50 were important for tetramer formation, and the first β-strand and the C-terminal helix are critical for dimerization. By mutating the critical residues responsible for oligomerization, we generated CXCL4 mutants that behave as dimers or monomers under neutral/physiological conditions. The CXCL4 monomer acts as the minimal active unit for interacting CXCR3A, and sulfation of N-terminal tyrosine residues on the receptor is important for binding. Noticeably, CXCL4L1, a CXCL4 variant that differs by three residues in the C-terminal helix, could activate CXCR3A. CXCL4L1 showed a higher tendency to dissociate into monomers, but native CXCL4 did not. This result indicates that monomeric CXCL4 behaves like CXCL4L1. Thus, in this chemokine family, being in the monomeric state seems critical for interaction with CXCR3A.

Dehaloperoxidase-Hemoglobin from Amphitrite ornata Is Primarily a Monomer in Solution

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

M Thompson; S Franzen; M Davis

2011-12-31

The crystal structures of the dehaloperoxidase-hemoglobin from A. ornata (DHP A) each report a crystallographic dimer in the unit cell. Yet, the largest dimer interface observed is 450 {angstrom}{sup 2}, an area significantly smaller than the typical value of 1200-2000 {angstrom}{sup 2} and in contrast to the extensive interface region of other known dimeric hemoglobins. To examine the oligomerization state of DHP A in solution, we used gel permeation by fast protein liquid chromatography and small-angle X-ray scattering (SAXS). Gel permeation experiments demonstrate that DHP A elutes as a monomer (15.5 kDa) and can be separated from green fluorescent protein,more » which has a molar mass of 27 kDa, near the 31 kDa expected for the DHP A dimer. By SAXS, we found that DHP A is primarily monomeric in solution, but with a detectable level of dimer (10%), under all conditions studied up to a protein concentration of 3.0 mM. These concentrations are likely 10-100-fold lower than the K{sub d} for dimer formation. Additionally, there was no significant effect either on the overall conformation of DHP A or its monomer-dimer equilibrium upon addition of the DHP A inhibitor, 4-iodophenol.« less

Evidence and Function Relevance of Native DOR-MOR Heteromers.

PubMed

Cahill, Catherine M; Ong, Edmund

2018-04-10

Opioid receptors are the sites of action for morphine and most other clinically used opioid drugs. Abundant evidence now demonstrates that different opioid receptor types can physically associate to form heteromers. Owing to their constituent monomers' involvement in analgesia, mu/delta opioid receptor (M/DOR) heteromers have been a particular focus of attention. Understandings of the physiological relevance and indisputable proof of M/DOR formation in vivo are still evolving. This aspect of the field has been slow to progress in large part by the limitations of most available experimental models; recently however, promising progress is being made. As a result, the long-repeated promise of opioid receptor heteromers as selective therapeutic targets is now being realized.

Mini-thin filaments regulated by troponin–tropomyosin

PubMed Central

Gong, Huiyu; Hatch, Victoria; Ali, Laith; Lehman, William; Craig, Roger; Tobacman, Larry S.

2005-01-01

Striated muscle thin filaments contain hundreds of actin monomers and scores of troponins and tropomyosins. To study the cooperative mechanism of thin filaments, “mini-thin filaments” were generated by isolating particles nearly matching the minimal structural repeat of thin filaments: a double helix of actin subunits with each strand approximately seven actins long and spanned by a troponin–tropomyosin complex. One end of the particles was capped by a gelsolin (segment 1–3)–TnT fusion protein (substituting for normal TnT), and the other end was capped by tropomodulin. EM showed that the particles were 46 ± 9 nm long, with a knob-like mass attributable to gelsolin at one end. Average actin, tropomyosin, and gelsolin–troponin composition indicated one troponin–tropomyosin attached to each strand of the two-stranded actin filament. The minifilaments thus nearly represent single regulatory units of thin filaments. The myosin S1 MgATPase rate stimulated by the minifilaments was Ca2+-sensitive, indicating that single regulatory length particles are sufficient for regulation. Ca2+ bound cooperatively to cardiac TnC in conventional thin filaments but noncooperatively to cardiac TnC in minifilaments in the absence of myosin. This suggests that thin filament Ca2+-binding cooperativity reflects indirect troponin–troponin interactions along the long axis of conventional filaments, which do not occur in minifilaments. Despite noncooperative Ca2+ binding to minifilaments in the absence of myosin, Ca2+ cooperatively activated the myosin S1-particle ATPase rate. Two-stranded single regulatory units therefore may be sufficient for myosin-mediated Ca2+-binding cooperativity. Functional mini-thin filaments are well suited for biochemical and structural analysis of thin-filament regulation. PMID:15644437

Simultaneous covalent and noncovalent hybrid polymerizations

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

Yu, Z.; Tantakitti, F.; Yu, T.

Covalent and supramolecular polymers are two distinct forms of soft matter, composed of long chains of covalently and noncovalently linked structural units, respectively. We report a hybrid system formed by simultaneous covalent and supramolecular polymerizations of monomers. The process yields cylindrical fibers of uniform diameter that contain covalent and supramolecular compartments, a morphology not observed when the two polymers are formed independently. The covalent polymer has a rigid aromatic imine backbone with helicoidal conformation, and its alkylated peptide side chains are structurally identical to the monomer molecules of supramolecular polymers. In the hybrid system, covalent chains grow to higher averagemore » molar mass relative to chains formed via the same polymerization in the absence of a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure, suggesting soft materials with novel delivery or repair functions.« less

Stereospecificity of {beta}-O-4 lignin oligomers

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

Faulon, J.L.; Pohl, P.I.

1995-12-01

Lignin, a complex macromolecule of vascular plants is a cross-linked polymer of glyceryl methoxyphenol units. The major type of linkage between the monomers is the {beta}-O-4 bond. We have studied the conformations of {beta}-O-4 lignin oligomers in a vacuum, and in the presence of water, cations, and cellulosic materials. There are several stereoisomers of {beta}-O-4 lignin oligomers because lignin monomers contain chiral atoms. We have constructed the stereoisomers using a stochastic chemical structure generator (the SIGNATURE program). The potential energies of the resulting structures were calculated using several force fields (MM2, DREIDING, CVFF), and several semiempirical codes (AM1, PM3). Themore » conformational space of the stereoisomers were investigated using Monte Carlo and simulated annealing modeling techniques. It was observed that the lowest energies were obtained for the stereospecific all-three and all-erythro isomers independently of the degree of polymerization.« less

Development of flame resistant treatment for Nomex fibrous structures

NASA Technical Reports Server (NTRS)

Toy, M. S.

1977-01-01

Flame resistant fibrous materials for space shuttle application were developed through chemical modification of commercially available aromatic polyamide fibrous products. The new surface treatment was achieved in the laboratory by ultraviolet activation of the fabric in the presence of fluoroolefin monomers and a diluent gas. The monomers grafted under these conditions provide the improved properties of the fabric in flame resistance, chemical inertness, and nonwettability without the sacrifice of color or physical properties. The laboratory reaction vessel was scaled-up to a batch continuous process, which treats ten yards of the commercial width textiles. The treated commercial width Nomex (HT-10-41) from the scaled-up reactor is self-extinguishing in an oxygen-enriched environment, water-repellent, soft, silky, and improved in chemical resistance. Unlike most textile processes, the grafting unit operates under dry conditions and no chemical by-products have to be washed out of the finished product.

The changing world of G protein-coupled receptors: from monomers to dimers and receptor mosaics with allosteric receptor-receptor interactions.

PubMed

Fuxe, Kjell; Marcellino, Daniel; Borroto-Escuela, Dasiel Oscar; Frankowska, Malgorzata; Ferraro, Luca; Guidolin, Diego; Ciruela, Francisco; Agnati, Luigi F

2010-10-01

Based on indications of direct physical interactions between neuropeptide and monoamine receptors in the early 1980s, the term receptor-receptor interactions was introduced and later on the term receptor heteromerization in the early 1990s. Allosteric mechanisms allow an integrative activity to emerge either intramolecularly in G protein-coupled receptor (GPCR) monomers or intermolecularly via receptor-receptor interactions in GPCR homodimers, heterodimers, and receptor mosaics. Stable heteromers of Class A receptors may be formed that involve strong high energy arginine-phosphate electrostatic interactions. These receptor-receptor interactions markedly increase the repertoire of GPCR recognition, signaling and trafficking in which the minimal signaling unit in the GPCR homomers appears to be one receptor and one G protein. GPCR homomers and GPCR assemblies are not isolated but also directly interact with other proteins to form horizontal molecular networks at the plasma membrane.

Thio-amide functionalized polymers via polymerization or post-polymerization modification

NASA Astrophysics Data System (ADS)

Ozcam, Ali; Henke, Adam; Stibingerova, Iva; Srogl, Jiri; Genzer, Jan

2011-03-01

Decreasing supplies of fresh water and increasing population necessitates development of advanced water cleaning technologies, which would facilitate the removal of water pollutants. Amongst the worst of such contaminants are heavy metals and cyanides, infamous for their high toxicity. To assist the water purification processes, we aim to synthesize functionalized macromolecules that would contribute in the decontamination processes by scavenging detrimental chemicals. Epitomizing this role thio-amide unit features remarkable chemical flexibility that facilitates reversible catch-release of the ions, where the behavior controlled by subtle red-ox changes in the environment. Chemical tunability of the thio-amide moiety enables synthesis of thio-amide based monomers and post-polymerization modification agents. Two distinct synthetic pathways, polymerization and post-polymerization modification, have been exploited, leading to functional thioamide-based macromolecules: thioamide-monomers were copolymerized with N-isopropylacrylamide and post-polymerization modifications of poly(dimethylaminoethyl methacrylate) and poly(propargyl methacrylate) were accomplished via quarternization and ``click'' reactions, respectively.

Electroactive polymers containing 3-arylcarbazolyl units as hole transporting materials for OLEDs

NASA Astrophysics Data System (ADS)

Krucaite, G.; Liu, L.; Tavgeniene, D.; Peciulyte, L.; Grazulevicius, J. V.; Xie, Z.; Zhang, B.; Grigalevicius, S.

2015-04-01

Monomers and their polymers containing 3-arylcarbazolyl electrophores have been synthesized by the multi-step synthetic route. The materials were characterized by thermo-gravimetric analysis, differential scanning calorimetry and electron photoemission technique. The polymers represent materials of high thermal stability having initial thermal degradation temperatures in the range of 331-411 °C. The glass transition temperatures of the amorphous polymeric materials were in the rage of 148-175 °C. The electron photoemission spectra of thin layers of monomers showed ionization potentials in the range of 5.6-5.65 eV. Hole-transporting properties of the polymers were tested in the structures of organic light emitting diodes with Alq3 as the green emitter. The device containing hole-transporting layers of polyether with 3-naphthylcarbazolyl groups exhibited the best overall performance with a maximum current efficiency of 3.3 cd/A and maximum brightness of about 1000 cd/m2.

Alcoholysis: A Promising Technology for Conversion of Lignocellulose and Platform Chemicals.

PubMed

Zhu, Shanhui; Guo, Jing; Wang, Xun; Wang, Jianguo; Fan, Weibin

2017-06-22

In the catalytic conversion of lignocellulose to valuable products, the first entry point is to break down these biopolymers to sugar units or aromatic monomers, which is conventionally achieved by hydrolysis in water medium. Recent years have seen tremendous progress in the alcoholysis process, which has remarkable advantages, such as the avoidance of treating waste water, suppression of humins or chars, and enhancement of reaction rate and product yield. Advances have been focused on the alcoholysis of cellulose, hemicellulose, and lignin to alkyl glucosides, xylosides, and aromatic monomers, respectively. Alcoholysis of the platform molecule furfuryl alcohol (FAL) to alkyl levulinate (AL) and integrated alcoholysis of cellulose and furfural into AL are also summarized. This Minireview highlights the comparisons between alcoholysis and hydrolysis, the reaction mechanism of alcoholysis, and future challenges for industrial applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Homopolymer Micelles in Heterogeneous Solvent Mixtures

PubMed Central

Basu, Subhadeep; Vutukuri, Dharma Rao

2008-01-01

Amphiphilic homopolymers containing a hydrophilic and a hydrophobic functionality in each monomer unit have been shown to form polar or apolar containers depending on the solvent environment. When presented with a mixture of solvents, these polymeric containers are capable of releasing certain guest molecules. The fundamental mechanism behind these properties is investigated and the utility of these assemblies in separations has been demonstrated with an example. PMID:16316219

Powder-based adsorbents having high adsorption capacities for recovering dissolved metals and methods thereof

DOEpatents

Janke, Christopher J.; Dai, Sheng; Oyola, Yatsandra

2016-05-03

A powder-based adsorbent and a related method of manufacture are provided. The powder-based adsorbent includes polymer powder with grafted side chains and an increased surface area per unit weight to increase the adsorption of dissolved metals, for example uranium, from aqueous solutions. A method for forming the powder-based adsorbent includes irradiating polymer powder, grafting with polymerizable reactive monomers, reacting with hydroxylamine, and conditioning with an alkaline solution. Powder-based adsorbents formed according to the present method demonstrated a significantly improved uranium adsorption capacity per unit weight over existing adsorbents.

Foam-based adsorbents having high adsorption capacities for recovering dissolved metals and methods thereof

DOEpatents

Janke, Christopher J.; Dai, Sheng; Oyola, Yatsandra

2015-06-02

Foam-based adsorbents and a related method of manufacture are provided. The foam-based adsorbents include polymer foam with grafted side chains and an increased surface area per unit weight to increase the adsorption of dissolved metals, for example uranium, from aqueous solutions. A method for forming the foam-based adsorbents includes irradiating polymer foam, grafting with polymerizable reactive monomers, reacting with hydroxylamine, and conditioning with an alkaline solution. Foam-based adsorbents formed according to the present method demonstrated a significantly improved uranium adsorption capacity per unit weight over existing adsorbents.

Guest-Release Control in Enzyme-Sensitive, Amphiphilic-Dendrimer-Based Nanoparticles through Photochemical Crosslinking

PubMed Central

Raghupathi, Krishna R.; Azagarsamy, Malar A.; Thayumanavan, S.

2012-01-01

Stimuli sensitive, facially amphiphilic dendrimers have been synthesized and their enzyme-responsive nature has been determined with dual fluorescence responses of both covalently conjugated and non-covalently bound reporter units. These dual responses are correlated to ascertain the effect of enzymatic action on micellar aggregates and the consequential guest release. The release of the guest molecule is conveniently tuned by stabilizing the micellar aggregates through photochemical crosslinking of hydrophobic coumarin units. This photo-crosslinking is also utilized as a tool to investigate the mode of enzyme-substrate interaction in the context of aggregate-monomer equilibrium. PMID:21887830

Novel (meth)acrylate monomers for ultrarapid polymerization and enhanced polymer properties

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

Beckel, E. R.; Berchtold, K. A.; Nie, J.

2002-01-01

Ultraviolet light is known to be one of the most efficient methods to initiatc polymeric reactions in the presence of a photonitiator. Photopolymerizations are advantageous because the chemistry of the materials can be tailored to design liquid monomers for ultrarapid polymerization into a solid polymer material. One way to achieve rapid photopolymerizations is to utilize multifunctional (meth)acrylate monomers. which form highly crosslinked polymers; however, these monomers typically do not achieve complete functional group conversion. Recently, Decker et al. developed novel monovinyl acrylate monomers that display polyriicrization kinetics that rival those of multifunctional acrylate monomers. These novel acrylate monomers incorporate secondarymore » functionalities and end groups such as carbonates, carbamates, cyclic carbonates and oxazolidone which promote the increased polymerization kinetics of these monomers. In addition to thc polynierization kinetics, these novel monovinyl monomers form crosslinked polymers, which are characterized by having high strength and high flexibility. Unfortunately, the exact mechanism or mechanisms responsible for the polymerization kinetics and crosslinking are not well understood.« less

Synthesis and Properties of Cross-Linked Polyamide Aerogels

NASA Technical Reports Server (NTRS)

Williams, Jarrod; Meador, Mary Ann; McCorkle, Linda

2014-01-01

We report our ongoing research on polyamide aerogels made by step growth polymerization using a combination of terephthaloyl chloride, isophthaloyl chloride and m-phenylenediamine. Crosslinking of the amine capped polymer chains with 1,3,5-benzenetricarbonyl trichloride causes gelation in as little as two to five minutes. Removing the reaction solvent is accomplished through solvent exchange, followed by drying using supercritical CO2 extraction to give colorless aerogels with densities ranging from 0.07 to 0.33 grams per cubic centimeter and surface areas as high as 440 square meters per gram. Statistical experimental design methodology has been utilized to investigate dependence of properties of these aerogels, such as density, compressive modulus, and surface area, on changes in fabrication parameters including formulated number of amide oligomer repeat units (n-value), acid chloride (meta, para or combination), and solids concentration of solution used for gelation. For example, the density of these materials was found to be dependent on the acid chloride type and the solids concentration, but n was not a significant variable. However, surface area was significantly influenced by all three parameters. The polyamide aerogels represent a potential cost savings over previously reported polyimide aerogels, since monomers are all inexpensive and commercially available. Surface area and density were both highest when 100 terephthaloyl chloride was used but a combination of 5 solid concentration, 100 terephthaloyl chloride and n of 20 gave the best combination of properties.

Retraction Note: Catalytic living ring-opening metathesis polymerization

NASA Astrophysics Data System (ADS)

Nagarkar, Amit A.; Kilbinger, Andreas F. M.

2018-05-01

We the authors are retracting this Article because of our failure to reproduce the molecular weight dispersities (PDI) shown in Fig. 4 using the chain-transfer agent described in the paper (CTA1). While the degenerate chain-transfer mechanism described in Fig. 3 is correct, the best molecular weight dispersities that could be reproduced with the chain-transfer agent shown in the Article are much larger (PDI > 2.0) than reported.We have since studied the kinetics of CTA1 in comparison with several other chain-transfer agents we are currently investigating and we now understand that the reactivity of CTA1 towards propagating ruthenium alkylidene complexes is very low. Very long monomer addition times would therefore have been necessary to gain control over the molecular weight distribution. Such long addition times would exceed the lifetime of the Grubbs catalyst in solution. Faster addition of the monomer has since repeatedly been shown to broaden the molecular weight dispersity.Additionally, the best chain-transfer agents we are currently investigating are orders of magnitude more reactive than CTA1 but give broader molecular weight dispersities than reported in Fig. 4. Molecular weight and dispersity control as shown in Fig. 4 is therefore an inappropriate claim for CTA1.The authors deeply regret these errors and apologize to the community.

Effect of a functional monomer (MDP) on the enamel bond durability of single-step self-etch adhesives.

PubMed

Tsuchiya, Kenji; Takamizawa, Toshiki; Barkmeier, Wayne W; Tsubota, Keishi; Tsujimoto, Akimasa; Berry, Thomas P; Erickson, Robert L; Latta, Mark A; Miyazaki, Masashi

2016-02-01

The present study aimed to determine the effect of the functional monomer, 10-methacryloxydecyl dihydrogen phosphate (MDP), on the enamel bond durability of single-step self-etch adhesives through integrating fatigue testing and long-term water storage. An MDP-containing self-etch adhesive, Clearfil Bond SE ONE (SE), and an experimental adhesive, MDP-free (MF), which comprised the same ingredients as SE apart from MDP, were used. Shear bond strength (SBS) and shear fatigue strength (SFS) were measured with or without phosphoric acid pre-etching. The specimens were stored in distilled water for 24 h, 6 months, or 1 yr. Although similar SBS and SFS values were obtained for SE with pre-etching and for MF after 24 h of storage in distilled water, SE with pre-etching showed higher SBS and SFS values than MF after storage in water for 6 months or 1 yr. Regardless of the pre-etching procedure, SE showed higher SBS and SFS values after 6 months of storage in distilled water than after 24 h or 1 yr. To conclude, MDP might play an important role in enhancing not only bond strength but also bond durability with respect to repeated subcritical loading after long-term water storage. © 2015 Eur J Oral Sci.

Investigating the Structural Impact of the Glutamine Repeat in Huntingtin Assembly

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

Perevozchikova, Tatiana; Stanley, Christopher B; McWilliams-Koeppen, Helen P

2014-01-01

Acquiring detailed structural information about the various aggregation states of the huntingtin-exon1 protein (Htt-exon1) is crucial not only for identifying the true nature of the neurotoxic species responsible for Huntington s disease (HD) but also for designing effective therapeutics. Using time-resolved small-angle neutron scattering (TR-SANS), we followed the conformational changes that occurred during fibrillization of the pathologic form of Htt-exon1 (NtQ42P10) and compared the results with those obtained for the wild-type (NtQ22P10). Our results show that the aggregation pathway of NtQ22P10 is very different from that of NtQ42P10, as the initial steps require a monomer to 7-mer transition stage. Inmore » contrast, the earliest species identified for NtQ42P10 are monomer and dimer. The divergent pathways ultimately result in NtQ22P10 fibrils that possess a pack- ing arrangement consistent with the common amyloid sterical zipper model, whereas NtQ42P10 fibrils present a better fit to the Perutz b-helix structural model. The structural details obtained by TR-SANS should help to delineate the key mechanisms that underpin Htt-exon1 aggregation leading to HD.« less

Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

PubMed Central

Lee, Tong Geon; Kumar, Indrajit; Diers, Brian W; Hudson, Matthew E

2015-01-01

The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1. PMID:25735447

Correlating Charge Transport with Structure in Deconstructed Diketopyrrolopyrrole Oligomers: A Case Study of a Monomer in Field-Effect Transistors.

PubMed

Pickett, Alec; Torkkeli, Mika; Mukhopadhyay, Tushita; Puttaraju, Boregowda; Laudari, Amrit; Lauritzen, Andreas E; Bikondoa, Oier; Kjelstrup-Hansen, Jakob; Knaapila, Matti; Patil, Satish; Guha, Suchismita

2018-06-13

Copolymers based on diketopyrrolopyrrole (DPP) cores have attracted a lot of attention because of their high p-type as well as n-type carrier mobilities in organic field-effect transistors (FETs) and high power conversion efficiencies in solar cell structures. We report the structural and charge transport properties of n-dialkyl side-chain-substituted thiophene DPP end-capped with a phenyl group (Ph-TDPP-Ph) monomer in FETs which were fabricated by vacuum deposition and solvent coating. Grazing-incidence X-ray diffraction (GIXRD) from bottom-gate, bottom-contact FET architectures was measured with and without biasing. Ph-TDPP-Ph reveals a polymorphic structure with π-conjugated stacking direction oriented in-plane. The unit cell comprises either one monomer with a = 20.89 Å, b = 13.02 Å, c = 5.85 Å, α = 101.4°, β = 90.6°, and γ = 94.7° for one phase (TR1) or two monomers with a = 24.92 Å, b = 25.59 Å, c = 5.42 Å, α = 80.3°, β = 83.5°, and γ = 111.8° for the second phase (TR2). The TR2 phase thus signals a shift from a coplanar to herringbone orientation of the molecules. The device performance is sensitive to the ratio of the two triclinic phases found in the film. Some of the best FET performances with p-type carrier mobilities of 0.1 cm 2 /V s and an on/off ratio of 10 6 are for films that comprise mainly the TR1 phase. GIXRD from in operando FETs demonstrates the crystalline stability of Ph-TDPP-Ph.

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

Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.

α 1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based onmore » biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found inWT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo polymerization showing a surprising diversity of polymer topography. PLOS« less

Poly(ferulic acid-co-tyrosine): Effect of the Regiochemistry on the Photophysical and Physical Properties en Route to Biomedical Applications

PubMed Central

2015-01-01

The photophysical and mechanical properties of novel poly(carbonate-amide)s derived from two biorenewable resources, ferulic acid (FA) and l-tyrosine ethyl ester, were evaluated in detail. From these two bio-based precursors, a series of four monomers were generated (having amide and/or carbonate coupling units with remaining functionalities to allow for carbonate formation) and transformed to a series of four poly(carbonate-amide)s. The simplest monomer, which was biphenolic and was obtained in a single amidation synthetic step, displayed bright, visible fluorescence that was twice brighter than FA. Multidimensional fluorescence spectroscopy of the polymers in solution highlighted the strong influence that regioselectivity and the degree of polymerization have on their photophysical properties. The regiochemistry of the system had little effect on the wettability, surface free energy, and Young’s modulus (ca. 2.5 GPa) in the solid state. Confocal imaging of solvent-cast films of each polymer revealed microscopically flat surfaces with fluorescent emission deep into the visible region. Fortuitously, one of the two regiorandom polymers (obtainable from the biphenolic monomer in only an overall two synthetic steps from FA and l-tyrosine ethyl ester) displayed the most promising fluorescent properties both in the solid state and in solution, allowing for the possibility of translating this system as a self-reporting or imaging agent in future applications. To further evaluate the potential of this polymer as a biodegradable material, hydrolytic degradation studies at different pH values and temperatures were investigated. Additionally, the antioxidant properties of the degradation products of this polymer were compared with its biphenolic monomer and FA. PMID:25364040

Interference of functional monomers with polymerization efficiency of adhesives.

PubMed

Hanabusa, Masao; Yoshihara, Kumiko; Yoshida, Yasuhiro; Okihara, Takumi; Yamamoto, Takatsugu; Momoi, Yasuko; Van Meerbeek, Bart

2016-04-01

The degree of conversion (DC) of camphorquinone/amine-based adhesives is affected by acidic functional monomers as a result of inactivation of the amine co-initiator through an acid-base reaction. During bonding, functional monomers of self-etch adhesives chemically interact with hydroxyapatite (HAp). Here, we tested in how far the latter interaction of functional monomers with HAp counteracts the expected reduction in DC of camphorquinone/amine-based adhesives. The DC of three experimental adhesive formulations, containing either of the two functional monomers [10-methacryloyloxydecyl dihydrogen phosphate (10-MDP) or 4-methacryloxyethyl trimellitic acid anhydride (4-META)] or no functional monomer (no-FM; control), was measured with and without HAp powder added to the adhesive formulations. Both the variables 'functional monomer' and 'HAp' were found to be significant, with the functional monomer reducing the DC and HAp counteracting this effect. It is concluded that the functional monomers 10-MDP and 4-META interfere with the polymerization efficiency of adhesives. This interference is less prominent in the presence of HAp, which would clinically correspond to when these two functional monomers of the adhesive simultaneously interact with HAp in tooth tissue. © 2016 Eur J Oral Sci.

Crystallization and X-ray data analysis of the 10 kDa C-terminal lid subdomain from Caenorhabditis elegans Hsp70

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

Worrall, Liam; Walkinshaw, Malcolm D., E-mail: m.walkinshaw@ed.ac.uk

Crystals of the C-terminal 10 kDa lid subdomain from the C. elegans chaperone Hsp70 have been obtained that diffract X-rays to ∼3.5 Å and belong to space group I2{sub 1}2{sub 1}2{sub 1}. Analysis of X-ray data and initial heavy-atom phasing reveals 24 monomers in the asymmetric unit related by 432 non-crystallographic symmetry. Hsp70 is an important molecular chaperone involved in the regulation of protein folding. Crystals of the C-terminal 10 kDa helical lid domain (residues 542–640) from a Caenorhabditis elegans Hsp70 homologue have been produced that diffract X-rays to ∼3.4 Å. Crystals belong to space group I2{sub 1}2{sub 1}2{sub 1},more » with unit-cell parameters a = b = 197, c = 200 Å. The Matthews coefficient, self-rotation function and Patterson map indicate 24 monomers in the asymmetric unit, showing non-crystallographic 432 symmetry. Molecular-replacement studies using the corresponding domain from rat, the only eukaryotic homologue with a known structure, failed and a mercury derivative was obtained. Preliminary MAD phasing using SHELXD and SHARP for location and refinement of the heavy-atom substructure and SOLOMON for density modification produced interpretable maps with a clear protein–solvent boundary. Further density-modification, model-building and refinement are currently under way.« less

Synthesis of the diazonium (perfluoroalkyl) benzenesulfonimide monomer from Nafion monomer for proton exchange membrane fuel cells

NASA Astrophysics Data System (ADS)

Mei, Hua; D'Andrea, Dan; Nguyen, Tuyet-Trinh; Nworie, Chima

2014-02-01

One diazonium (perfluoroalkyl) benzenesulfonimide monomer, perfluoro-3, 6-dioxa-4-methyl-7-octene benzenesulfonyl imide, has been synthesized from Nafion monomer for the first time. With trifluorovinyl ether and diazonium precursors, the partially-fluorinated diazonium PFSI monomer can be polymerized and will provide chemically bonding with carbon electrode in proton exchange membrane fuel cells. A systematic study of the synthesis and characterization of this diazonium PFSI monomer has been conducted by varying reaction conditions. The optimized synthesis method has been established in the lab.

Mutational Analysis of the Stability of the H2A and H2B Histone Monomers

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

The eukaryotic histone heterodimer H2A-H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The H2A and H2B monomers exhibit free energies of unfolding of 2.5 and 2.9 kcal mol−1, respectively; at 10 μM, the sum of the stability of the monomers is ~60% of the stability of the native dimer. The helical content, stability and m values indicate that H2B has a more stable, compact structure than H2A. The monomer m values are larger than expected for the extended histone fold motif, suggesting that the monomers adopt an overly-collapsed structure. Stopped-flow refolding—initiated from urea-denatured monomers or the partially folded monomers populated at low denaturant concentrations—yielded essentially identical rates, indicating that monomer folding is productive in the rapid association and folding of the heterodimer. A series of Ala and Gly mutations were introduced into H2A and H2B to probe the importance of helix propensity on the structure and stability of the monomers. The mutational studies show that the central α-helix of the histone fold, which makes extensive inter-monomer contacts, is structured in H2B but only partially folded in H2A. PMID:18976667

Modeling the Growth Rates of Tetragonal Lysozyme Crystal Faces

NASA Technical Reports Server (NTRS)

Li, Meirong; Nadarajah, Arunan; Pusey, Marc L.

1998-01-01

The measured macroscopic growth rates of the (110) and (101) faces of tetragonal lysozyme show an unexpectedly complex dependence on the supersaturation. The growth rates decay asymptotically to zero when the supersaturation is lowered to zero and increase rapidly when the supersaturation is increased. When supersaturations are increased still further the growth rates attain a maximum before starting to decrease. However, growth of these crystals is known to proceed by the classical dislocation and 2D nucleation growth mechanisms. This anomaly can be explained if growth is assumed to occur not by monomer units but by lysozyme aggregates. Analysis of the molecular packing of these crystals revealed that they were constructed of strongly bonded 4(sub 3) helices, while weaker bonds were responsible for binding the helices to each other. It follows that during crystal growth the stronger bonds are formed before the weaker ones. Thus, the growth of these crystals could be viewed as a two step process: aggregate growth units corresponding to the 4(sub 3) helix are first formed in the bulk solution by stronger intermolecular bonds and then attached to the crystal face by weaker bonds on dislocation hillocks or 2D islands. This will lead to a distribution of aggregates in the solution with monomers and lower order aggregates being predominant at low supersaturations and higher order aggregates being predominant at high supersaturations. If the crystal grows mostly by higher order aggregates, such as tetramers and octamers, it would explain the anomalous dependence of the growth rates on the supersaturation. Besides the analysis of molecular packing, a comprehensive analysis of the measured (110) and (101) growth rates was also undertaken in this study. The distribution of aggregates in lysozyme nutrient solutions at various solution conditions were determined from reversible aggregation reactions at equilibrium. The supersaturation was defined for each aggregate species with respect to its concentration at saturation in order to apply growth rate models to this process. The measured growth rates were then compared with the predicted ones from several dislocation and 2D nucleation growth models, employing tetramer and octamer growth units in polydisperse solutions and monomer units in monodisperse solutions. For the (110) face, the calculations consistently showed that the measured growth rates followed the expected model relations with octamer growth units. For the (101) face, it is not possible to obtain a clear agreement between the predicted and measured growth rates for a single growth unit as done for the (110) face. However, the calculations do indicate that the average size of the growth unit is between a tetramer and an octamer. This suggests that tetramers, octamers and other intermediate size growth units all participate in the growth process for this face. These calculations show that it is possible to model the macroscopic protein crystal growth rates if the molecular level processes can be account for, particularly protein aggregation processes in the bulk solution. Our recent investigations of tetragonal lysozyme crystals employing high resolution atomic force microscopy scans have further confirmed the growth of these crystals by aggregate growth units corresponding to 4(sub 3) helices.

Cofilin promotes stimulus-induced lamellipodium formation by generating an abundant supply of actin monomers

PubMed Central

Kiuchi, Tai; Ohashi, Kazumasa; Kurita, Souichi; Mizuno, Kensaku

2007-01-01

Cofilin stimulates actin filament disassembly and accelerates actin filament turnover. Cofilin is also involved in stimulus-induced actin filament assembly during lamellipodium formation. However, it is not clear whether this occurs by replenishing the actin monomer pool, through filament disassembly, or by creating free barbed ends, through its severing activity. Using photoactivatable Dronpa-actin, we show that cofilin is involved in producing more than half of all cytoplasmic actin monomers and that the rate of actin monomer incorporation into the tip of the lamellipodium is dependent on the size of this actin monomer pool. Finally, in cofilin-depleted cells, stimulus-induced actin monomer incorporation at the cell periphery is attenuated, but the incorporation of microinjected actin monomers is not. We propose that cofilin contributes to stimulus-induced actin filament assembly and lamellipodium extension by supplying an abundant pool of cytoplasmic actin monomers. PMID:17470633

Length and sequence heterogeneity in 5S rDNA of Populus deltoides.

PubMed

Negi, Madan S; Rajagopal, Jyothi; Chauhan, Neeti; Cronn, Richard; Lakshmikumaran, Malathi

2002-12-01

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.

An exploration of risk for recurrent falls in two geriatric care settings

PubMed Central

2013-01-01

Background Fall events were examined in two distinct geriatric populations to identify factors associated with repeat fallers, and to examine whether patients who use gait aids, specifically a walker, were more likely to experience repeat falls. Each unit already had a generic program for falls prevention in place. Methods Secondary data analysis was conducted on information collected during the pilot testing of a new quality assurance Incident Reporting Tool between October 2006 and September 2008. The study settings included an in-patient geriatric rehabilitation unit (GRU) and a long stay veterans’ unit (LSVU) in a rehabilitation and long-stay hospital in Ontario. Participants were two hundred and twenty three individuals, aged 65 years or older on these two units, who experienced one or more fall incidents during the study period. Results Logistic regression analyses showed that on the GRU age was significantly associated with repeat falls. On the LSVU first falls in the morning or late evening were associated with repeat falling. Walker as a gait aid listed at time of first fall was not associated with repeat falls. Conclusions This study suggests that different intervention may be necessary in different geriatric settings to identify, for secondary prevention, certain individuals for which the generic programs prove inadequate. Information collection with a specific focus on the issue of repeat falls may be necessary for greater insight. PMID:24106879

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation

NASA Astrophysics Data System (ADS)

Dimzon, Ian Ken; Trier, Xenia; Frömel, Tobias; Helmus, Rick; Knepper, Thomas P.; de Voogt, Pim

2016-02-01

High resolution mass spectrometry (HRMS) was successfully applied to elucidate the structure of a polyfluorinated polyether (PFPE)-based formulation. The mass spectrum generated from direct injection into the MS was examined by identifying the different repeating units manually and with the aid of an instrument data processor. Highly accurate mass spectral data enabled the calculation of higher-order mass defects. The different plots of MW and the nth-order mass defects (up to n = 3) could aid in assessing the structure of the different repeating units and estimating their absolute and relative number per molecule. The three major repeating units were -C2H4O-, -C2F4O-, and -CF2O-. Tandem MS was used to identify the end groups that appeared to be phosphates, as well as the possible distribution of the repeating units. Reversed-phase HPLC separated of the polymer molecules on the basis of number of nonpolar repeating units. The elucidated structure resembles the structure in the published manufacturer technical data. This analytical approach to the characterization of a PFPE-based formulation can serve as a guide in analyzing not just other PFPE-based formulations but also other fluorinated and non-fluorinated polymers. The information from MS is essential in studying the physico-chemical properties of PFPEs and can help in assessing the risks they pose to the environment and to human health.

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation.

PubMed

Dimzon, Ian Ken; Trier, Xenia; Frömel, Tobias; Helmus, Rick; Knepper, Thomas P; de Voogt, Pim

2016-02-01

High resolution mass spectrometry (HRMS) was successfully applied to elucidate the structure of a polyfluorinated polyether (PFPE)-based formulation. The mass spectrum generated from direct injection into the MS was examined by identifying the different repeating units manually and with the aid of an instrument data processor. Highly accurate mass spectral data enabled the calculation of higher-order mass defects. The different plots of MW and the nth-order mass defects (up to n = 3) could aid in assessing the structure of the different repeating units and estimating their absolute and relative number per molecule. The three major repeating units were -C2H4O-, -C2F4O-, and -CF2O-. Tandem MS was used to identify the end groups that appeared to be phosphates, as well as the possible distribution of the repeating units. Reversed-phase HPLC separated of the polymer molecules on the basis of number of nonpolar repeating units. The elucidated structure resembles the structure in the published manufacturer technical data. This analytical approach to the characterization of a PFPE-based formulation can serve as a guide in analyzing not just other PFPE-based formulations but also other fluorinated and non-fluorinated polymers. The information from MS is essential in studying the physico-chemical properties of PFPEs and can help in assessing the risks they pose to the environment and to human health. Graphical Abstract ᅟ.

Development of new resist materials for 193-nm dry and immersion lithography

NASA Astrophysics Data System (ADS)

Sasaki, Takashi; Shirota, Naoko; Takebe, Yoko; Yokokoji, Osamu

2006-03-01

We earlier developed new monocyclic fluoropolymers (FUGU) for F II resist materials. But, it is necessary for FUGU to improve of their characteristics, especially the dry-etching resistance, in order to apply for ArF lithography at fine design rules. We have tried to combine FUGUs with Adamntyl methacrylates based conventional ArF resist polymer. In this paper, we have investigated the role of cyclic fluorinated unit, FUGU, in 193 nm resist polymers by analyzing the dissolution behavior. We found that FGEAM showed high sensitivity and good dissolution contrast, compared with acrylate based conventional samples at low PEB temperature (100 °C). And this difference of sensitivity was clearly found when weak acidity PAGs were used. From the dissolution behaviors of FGEAM, FUGU unit can work to improve the resist sensitivity in acrylate based ArF resist polymers. And we also found that FGEAM showed long acid diffusion length on PEB process, compared with Conventional samples. These result show that FUGU unit has a unique characteristics of the sensitivity with 193nm exposure and the acid diffusion behavior. We also investigated a new series of fluorinated copolymers for 193-nm lithography, combination of FUGU monomer and acrylate units which are used in conventional ArF resist. Six ter-polymers of FUGU, combination of FUGU monomers and EAdMA, GBLMA and HAdMA were prepared. We found that FUGU ter-polymers had a good dry etching resistance keeping high transparency at 193nm. And FUGU ter-polymers showed high sensitivity toward 193nm exposure. FUGU ter-polymers also had a high hydrophobic properties compared conventional type ArF resist polymers. So we also expect FUGU ter-polymers to be useful for ArF dry and immersion lithography.

Recombination hot spot in 3.2-kb region of the Charcot-Marie Tooth type 1A repeat sequences: New tools for molecular diagnosis of hereditary neuropathy with liability to pressure palsies and of Charcot-Marie-Tooth type 1A

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

Lopes, J.; LeGuern, E.; Gouider, R.

1996-06-01

Charcot-Marie-Tooth type 1A (CMT1A) disease and hereditary neuropathy with liability to pressure palsies (HNPP) are autosomal dominant neuropathies, associated, respectively, with duplications and deletions of the same 1.5-Mb region on 17p11.2-p12. These two rearrangements are the reciprocal products of an unequal meiotic crossover between the two chromosome 17 homologues, caused by the misalignment of the CMT1A repeat sequences (CMT1A-REPs), the homologous sequences flanking the 1.5-Mb CMT1A/HNPP monomer unit. In order to map recombination breakpoints within the CMT1A-REPs, a 12.9-kb restriction map was constructed from cloned EcoRI fragments of the proximal and distal CMT1A-REPs. Only 3 of the 17 tested restrictionmore » sites were present in the proximal CMT1A-REP but absent in the distal CMT1A-REP, indicating a high degree of homology between these sequences. The rearrangements were mapped in four regions of the CMT1A-REPs by analysis of 76 CMT1A index cases and 38 HNPP patients, who were unrelated. A hot spot of crossover breakpoints located in a 3.2-kb region accounted for three-quarters of the rearrangements, detected after EcoRI/SacI digestion, by the presence of 3.2-kb and 7.8-kb junction fragments in CMT1A and HNPP patients, respectively. These junction fragments, which can be detected on classical Southern blots, permit molecular diagnosis. Other rearrangements can also be detected by gene dosage on the same Southern blots. 25 refs., 4 figs., 2 tabs.« less

Feasibility of the Simultaneous Determination of Monomer Concentrations and Particle Size in Emulsion Polymerization Using in Situ Raman Spectroscopy

PubMed Central

2015-01-01

An immersion Raman probe was used in emulsion copolymerization reactions to measure monomer concentrations and particle sizes. Quantitative determination of monomer concentrations is feasible in two-monomer copolymerizations, but only the overall conversion could be measured by Raman spectroscopy in a four-monomer copolymerization. The feasibility of measuring monomer conversion and particle size was established using partial least-squares (PLS) calibration models. A simplified theoretical framework for the measurement of particle sizes based on photon scattering is presented, based on the elastic-sphere-vibration and surface-tension models. PMID:26900256

Computational analysis for biodegradation of exogenously depolymerizable polymer

NASA Astrophysics Data System (ADS)

Watanabe, M.; Kawai, F.

2018-03-01

This study shows that microbial growth and decay in a biodegradation process of exogenously depolymerizable polymer are controlled by consumption of monomer units. Experimental outcomes for residual polymer were incorporated in inverse analysis for a degradation rate. The Gauss-Newton method was applied to an inverse problem for two parameter values associated with the microbial population. A biodegradation process of polyethylene glycol was analyzed numerically, and numerical outcomes were obtained.

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

Nata, Iryanti Fatyasari, E-mail: yanti_tkunlam@yahoo.com; Irawan, Chairul; Mardina, Primata

Highly sulfonated carbonaceous spheres with diameter of 100–500 nm can be generated by hydrothermal carbonization of glucose in the presence of hydroxyethylsulfonic acid and acrylic acid at 180 °C for 4 h. The acidity of the prepared carbonaceous sphere C4-SO{sub 3}H can reach 2.10 mmol/g. It was used as a solid acid catalyst for the hydrolysis of cornstarch. Total reducing sugar (TRS) concentration of 19.91 mg/mL could be obtained by hydrolyzing 20 mg/mL cornstarch at 150 °C for 6 h using C4-SO{sub 3}H as solid acid catalyst. The solid acid catalyst demonstrated good stability that only 9% decrease in TRSmore » concentration was observed after five repeat uses. The as-prepared carbon-based solid acid catalyst can be an environmentally benign replacement for homogeneous catalyst. - Highlights: • Carbon solid acid was successfully prepared by one-step hydrothermal carbonization. • The acrylic acid as monomer was effectively reduce the diameter size of particle. • The solid acid catalyst show good catalytic performance of starch hydrolysis. • The solid acid catalyst is not significantly deteriorated after repeated use.« less

Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies

NASA Astrophysics Data System (ADS)

Kwon, Ah-Young; Nam, Gi-Moon; Johner, Albert; Kim, Seyong; Hong, Seok-Cheol; Lee, Nam-Kyung

2016-02-01

Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC) n repeats or (TG) n repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC) n sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG) n sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.

Template properties of oligocytidylates formed in the montmorillonite catalyzed condensation of ImpC. [Abstract only

NASA Technical Reports Server (NTRS)

Ferris, James P.; Ertem, Goezen

1994-01-01

In an attempt to investigate the prebiotic formation of phosphodiester bond in RNA, we have studied the self condensation of 5'-phosphorimidazolide of adenosine (ImpA), in aqueous solutions containing 0.2 M sodium chloride and 0.075 M magnesium chloride at pH 8 using clay minerals as catalyst. In the presence of certain montmorillonites, oligomers containing up to ten monomer units in their chain were formed, while in control experiments, where no catalyst was added, the major product was 5',5'-diadenosine diphosphate, A(sup 5')ppA. In reactions carried out with ImpA: A(sup 5')ppA mixtures at 9:1 mole ratio, oligomers of the type A(sup 5')p(pA)(sub n) and (A(sup 5')p)(sub n)A(sup 5')ppA(pA)(sub n) formed at the expense of (pA)(sub n) type oligomers. Addition of A(sup 5')ppA to the reaction mixture increased the regiospecifity of 3',5'-link formation from 67% to 79%. The condensation of the 5'-phosphorimidazolide of cytidine, ImpC, was also carried out in the presence and absence of A(sup 5')ppA under the same conditions and oligomers containing up to twelve monomer units were obtained.

Combinatorial Synthesis of Structurally Diverse Triazole-Bridged Flavonoid Dimers and Trimers.

PubMed

Sum, Tze Han; Sum, Tze Jing; Galloway, Warren R J D; Collins, Súil; Twigg, David G; Hollfelder, Florian; Spring, David R

2016-09-16

Flavonoids are a large family of compounds associated with a broad range of biologically useful properties. In recent years, synthetic compounds that contain two flavonoid units linked together have attracted attention in drug discovery and development projects. Numerous flavonoid dimer systems, incorporating a range of monomers attached via different linkers, have been reported to exhibit interesting bioactivities. From a medicinal chemistry perspective, the 1,2,3-triazole ring system has been identified as a particularly attractive linker moiety in dimeric derivatives (owing to several favourable attributes including proven biological relevance and metabolic stability) and triazole-bridged flavonoid dimers possessing anticancer and antimalarial activities have recently been reported. However, there are relatively few examples of libraries of triazole-bridged flavonoid dimers and the diversity of flavonoid subunits present within these is typically limited. Thus, this compound type arguably remains underexplored within drug discovery. Herein, we report a modular strategy for the synthesis of novel and biologically interesting triazole-bridged flavonoid heterodimers and also very rare heterotrimers from readily available starting materials. Application of this strategy has enabled step-efficient and systematic access to a library of structurally diverse compounds of this sort, with a variety of monomer units belonging to six different structural subclasses of flavonoid successfully incorporated.

Organometallic macromolecules with piano stool coordination repeating units: chain configuration and stimulated solution behaviour.

PubMed

Cao, Kai; Ward, Jonathan; Amos, Ryan C; Jeong, Moon Gon; Kim, Kyoung Taek; Gauthier, Mario; Foucher, Daniel; Wang, Xiaosong

2014-09-11

Theoretical calculations illustrate that organometallic macromolecules with piano stool coordination repeating units (Fe-acyl complex) adopt linear chain configuration with a P-Fe-C backbone surrounded by aromatic groups. The macromolecules show molecular weight-dependent and temperature stimulated solution behaviour in DMSO.

Designing occupancy studies: general advice and allocating survey effort

USGS Publications Warehouse

MacKenzie, D.I.; Royle, J. Andrew

2005-01-01

1. The fraction of sampling units in a landscape where a target species is present (occupancy) is an extensively used concept in ecology. Yet in many applications the species will not always be detected in a sampling unit even when present, resulting in biased estimates of occupancy. Given that sampling units are surveyed repeatedly within a relatively short timeframe, a number of similar methods have now been developed to provide unbiased occupancy estimates. However, practical guidance on the efficient design of occupancy studies has been lacking. 2. In this paper we comment on a number of general issues related to designing occupancy studies, including the need for clear objectives that are explicitly linked to science or management, selection of sampling units, timing of repeat surveys and allocation of survey effort. Advice on the number of repeat surveys per sampling unit is considered in terms of the variance of the occupancy estimator, for three possible study designs. 3. We recommend that sampling units should be surveyed a minimum of three times when detection probability is high (> 0.5 survey-1), unless a removal design is used. 4. We found that an optimal removal design will generally be the most efficient, but we suggest it may be less robust to assumption violations than a standard design. 5. Our results suggest that for a rare species it is more efficient to survey more sampling units less intensively, while for a common species fewer sampling units should be surveyed more intensively. 6. Synthesis and applications. Reliable inferences can only result from quality data. To make the best use of logistical resources, study objectives must be clearly defined; sampling units must be selected, and repeated surveys timed appropriately; and a sufficient number of repeated surveys must be conducted. Failure to do so may compromise the integrity of the study. The guidance given here on study design issues is particularly applicable to studies of species occurrence and distribution, habitat selection and modelling, metapopulation studies and monitoring programmes.

Topological characteristics of helical repeat proteins.

PubMed

Groves, M R; Barford, D

1999-06-01

The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem repeats of an alpha-helical structural unit, creating extended superhelical structures that are ideally suited to create a protein recognition interface.

Effects of electronics, aromaticity, and solvent polarity on the rate of azaquinone-methide-mediated depolymerization of aromatic carbamate oligomers.

PubMed

Robbins, Jessica S; Schmid, Kyle M; Phillips, Scott T

2013-04-05

This paper uses physical-organic studies on well-defined oligomers to establish design principles for creating aromatic poly(carbamates) that depolymerize from head-to-tail in low dielectric constant environments when exposed to specific applied signals. We show that either increasing electron density or decreasing the aromaticity of aromatic repeating units in poly(carbamates) increase the overall depolymerization rate. For example, a methoxybenzene-based repeating unit provides depolymerization rates that are 143× faster than oligomers that contain a benzene-based repeating unit. Furthermore, the rate of depolymerization in the methoxybenzene-based system is tolerant to low dielectric environments, whereas the benzene-based oligomers are not.

Atomistic Model for the Polyamide Formation from β-Lactam Catalyzed by Candida Antarctica Lipase B

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

Baum, Iris; Elsasser, Brigitta M.; Schwab, Leendert

2011-04-01

Candida antarctica lipase B (CALB) is an established biocatalyst for a variety of transesterification, amidation, and polymerization reactions. In contrast to polyesters, polyamides are not yet generally accessible via enzymatic polymerization. In this regard, an enzyme-catalyzed ring-opening polymerization of {beta}-lactam (2-azetidinone) using CALB is the first example of an enzymatic polyamide formation yielding unbranched poly({beta}-alanine), nylon 3. The performance of this polymerization, however, is poor, considering the maximum chain length of 18 monomer units with an average length of 8, and the molecular basis of the reaction so far is not understood. We have employed molecular modeling techniques using dockingmore » tools, molecular dynamics, and QM/MM procedures to gain insight into the mechanistic details of the various reaction steps involved. As a result, we propose a catalytic cycle for the oligomerization of {beta}-lactam that rationalizes the activation of the monomer, the chain elongation by additional {beta}-lactam molecules, and the termination of the polymer chain. In addition, the processes leading to a premature chain termination are studied. Particularly, the QM/MM calculation enables an atomistic description of all eight steps involved in the catalytic cycle, which features an in situ-generated {beta}-alanine as the elongating monomer and which is compatible with the experimental findings.« less

A mathematical model for regulating monomer composition of the microbially synthesized polyhydroxyalkanoate copolymers.

PubMed

Xu, Jun; Guo, Baohua; Zhang, Zengmin; Wu, Qiong; Zhou, Quan; Chen, Jinchun; Chen, Guoqiang; Li, Guodong

2005-06-30

A mathematical model is proposed for predicting the copolymer composition of the microbially synthesized polyhydroxyalkanoate (PHA) copolymers. Based on the biochemical reactions involved in the precursor formation and polymerization pathways, the model correlates the copolymer composition with the cultivation conditions, the enzyme levels and selectivity, and the metabolic pathways. It suggests the following points: (1) in the case of a sole carbon source, the copolymer composition depends mainly on the topology of the metabolic pathways and the selectivity of both the enzymes involved in the precursor formation and the polymerization route; (2) the copolymer composition can be varied in a wide range via alteration of the flux ratio of different types of monomers channeled from two or more independent and simultaneous pathways; (3) the enzymes which should be over-expressed or inhibited to obtain the desired copolymer composition can be predicted. For example, inhibition of the beta-oxidation pathway will increase the content of the monomer units with longer chain length. To test the model, various experiments were envisaged by varying cultivation time, concentration and chain length of the sole carbon source, and molar ratio of the cosubstrates. The predictions from the model agree well with the experimental results. Therefore, the proposed model will be useful in predicting the PHA copolymer composition under different biochemical reaction conditions. In other words, it can provide a guide for the synthesis of desired PHA copolymers.

Exposing Differences in Monomer Exchange Rates of Multicomponent Supramolecular Polymers in Water.

PubMed

Baker, Matthew B; Gosens, Ronald P J; Albertazzi, Lorenzo; Matsumoto, Nicholas M; Palmans, Anja R A; Meijer, E W

2016-02-02

The formation of multicomponent and bioactive supramolecular polymers is a promising strategy for the formation of biomaterials that match the dynamic and responsive nature of biological systems. In order to fully realize the potential of this strategy, knowledge of the location and behavior of bioactive components within the system is crucial. By employing synthetic strategies to create multifunctional monomers, coupled with FRET and STORM techniques, we have investigated the formation and behavior of a bioactive and multicomponent supramolecular polymer. By creating a peptide-dye-monomer conjugate, we were able to measure high degrees of monomer incorporation and to visualize the equal distribution of monomers within the supramolecular polymer. Furthermore, by tracking the movement of monomers, we uncovered small differences in the dynamics of the bioactive monomers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Human exposures to monomers resulting from consumer contact with polymers.

PubMed

Leber, A P

2001-06-01

Many consumer products are composed completely, or in part, of polymeric materials. Direct or indirect human contact results in potential exposures to monomers as a result of migrations of trace amounts from the polymeric matrix into foods, into the skin or other bodily surfaces. Typically, residual monomer levels in these polymers are <100 p.p.m., and represent exposures well below those observable in traditional toxicity testing. These product applications thus require alternative methods for evaluating health risks relating to monomer exposures. A typical approach includes: (a) assessment of potential human contacts for specific polymer uses; (b) utilization of data from toxicity testing of pure monomers, e.g. cancer bioassay results; and (c) mathematical risk assessment methods. Exposure potentials are measured in one of two analytical procedures: (1) migration of monomer from polymer into a simulant solvent (e.g. alcohol, acidic water, vegetable oil) appropriate for the intended use of the product (e.g. beer cans, food jars, packaging adhesive, dairy hose); or (2) total monomer content of the polymer, providing worse-case values for migratable monomer. Application of toxicity data typically involves NOEL or benchmark values for non-cancer endpoints, or tumorigenicity potencies for monomers demonstrated to be carcinogens. Risk assessments provide exposure 'safety margin' ratios between levels that: (1) are projected to be safe according to toxicity information, and (2) are potential monomer exposures posed by the intended use of the consumer product. This paper includes an example of a health risk assessment for a chewing gum polymer for which exposures to trace levels of butadiene monomer occur.

A direct and fast method to monitor lipid oxidation progress in model fatty acid methyl esters by high-performance size-exclusion chromatography.

PubMed

Márquez-Ruiz, G; Holgado, F; García-Martínez, M C; Dobarganes, M C

2007-09-21

A new method based on high-performance size-exclusion chromatography (HPSEC) is proposed to quantitate primary and secondary oxidation compounds in model fatty acid methyl esters (FAMEs). The method consists on simply injecting an aliquot sample in HPSEC, without preliminary isolation procedures neither addition of standard internal. Four groups of compounds can be quantified, namely, unoxidised FAME, oxidised FAME monomers including hydroperoxides, FAME dimers and FAME polymers. Results showed high repeatability and sensitivity, and substantial advantages versus determination of residual substrate by gas-liquid chromatography. Applicability of the method is shown through selected data obtained by numerous oxidation experiments on pure FAME, mainly methyl linoleate, at ambient and moderate temperatures.

40 CFR 721.10082 - Amine modified monomer acrylate (generic).

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Amine modified monomer acrylate... Specific Chemical Substances § 721.10082 Amine modified monomer acrylate (generic). (a) Chemical substance... amine modified monomer acrylate (PMN P-06-29) is subject to reporting under this section for the...

40 CFR 721.10082 - Amine modified monomer acrylate (generic).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Amine modified monomer acrylate... Specific Chemical Substances § 721.10082 Amine modified monomer acrylate (generic). (a) Chemical substance... amine modified monomer acrylate (PMN P-06-29) is subject to reporting under this section for the...

Structural investigation of the exopolysaccharide produced by Pseudomonas flavescens strain B62--degradation by a fungal cellulase and isolation of the oligosaccharide repeating unit.

PubMed

Cescutti, P; Toffanin, R; Fett, W F; Osman, S F; Pollesello, P; Paoletti, S

1998-02-01

Pseudomonas flavescens strain B62 (NCPPB 3063) is a recently described bacterium isolated from walnut blight cankers. This strain has been designated as the type strain of a Pseudomonas rRNA group-I species. Strain B62 produced a mixture of two exopolysaccharides, differing in weight average relative molecular mass and composition. Only the most abundant exopolysaccharide (90% by mass), corresponding to the one with the lower molecular mass, was investigated by use of methylation analysis, partial acid hydrolysis, and NMR spectroscopy. The polysaccharide was depolymerised by the action of the cellulase produced by Penicillum funiculosum and the oligosaccharide obtained, corresponding to the repeating unit, was characterised by NMR spectroscopy and ion-spray mass spectrometry. The repeating unit of the B62 exopolysaccharide is [structure in text] where X is glucose (75%) or mannose (25%), and Lac is lactate. The O-acetyl groups are present only on 75% of the repeating units, and they are linked to the C6 of the hexose residues in non-stoichiometric amounts.

Qualitative Beam Profiling of Light Curing Units for Resin Based Composites.

PubMed

Haenel, Thomas; Hausnerová, Berenika; Steinhaus, Johannes; Moeginger, Ing Bernhard

2016-12-01

This study investigates two technically simple methods to determine the irradiance distribution of light curing units that governs the performance of a visible-light curing resin-based composites. Insufficient light irradiation leads to under-cured composites with poor mechanical properties and elution of residual monomers. The unknown irradiance distribution and its effect on the final restoration are the main critical issues requiring highly sophisticated experimental equipment. The study shows that irradiance distributions of LCUs can easily be determined qualitatively with generally available equipment. This significantly helps dentists in practices to be informed about the homogeneity of the curing lights. Copyright© 2016 Dennis Barber Ltd.

Molecular weight-dependent degradation of D-lactate-containing polyesters by polyhydroxyalkanoate depolymerases from Variovorax sp. C34 and Alcaligenes faecalis T1.

PubMed

Sun, Jian; Matsumoto, Ken'ichiro; Tabata, Yuta; Kadoya, Ryosuke; Ooi, Toshihiko; Abe, Hideki; Taguchi, Seiichi

2015-11-01

Polyhydroxyalkanoate depolymerase derived from Variovorax sp. C34 (PhaZVs) was identified as the first enzyme that is capable of degrading isotactic P[67 mol% (R)-lactate(LA)-co-(R)-3-hydroxybutyrate(3HB)] [P(D-LA-co-D-3HB)]. This study aimed at analyzing the monomer sequence specificity of PhaZVs for hydrolyzing P(LA-co-3HB) in comparison with a P(3HB) depolymerase from Alcaligenes faecalis T1 (PhaZAf) that did not degrade the same copolymer. Degradation of P(LA-co-3HB) by action of PhaZVs generated dimers, 3HB-3HB, 3HB-LA, LA-3HB, and LA-LA, and the monomers, suggesting that PhaZVs cleaved the linkages between LA and 3HB units and between LA units. To provide a direct evidence for the hydrolysis of these sequences, the synthetic methyl trimers, 3HB-3HB-3HB, LA-LA-3HB, LA-3HB-LA, and 3HB-LA-LA, were treated with the PhaZs. Unexpectedly, not only PhaZVs but also PhaZAf hydrolyzed all of these substrates, namely PhaZAf also cleaved LA-LA linkage. Considering the fact that both PhaZs did not degrade P[(R)-LA] (PDLA) homopolymer, the cleavage capability of LA-LA linkage by PhaZs was supposed to depend on the length of the LA-clustering region in the polymer chain. To test this hypothesis, PDLA oligomers (6 to 40 mer) were subjected to the PhaZ assay, revealing that there was an inverse relationship between molecular weight of the substrates and their hydrolysis efficiency. Moreover, PhaZVs exhibited the degrading activity toward significantly longer PDLA oligomers compared to PhaZAf. Therefore, the cleaving capability of PhaZs used here toward the D-LA-based polymers containing the LA-clustering region was strongly associated with the substrate length, rather than the monomer sequence specificity of the enzyme.

Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli.

PubMed

Cupp-Vickery, Jill R; Silberg, Jonathan J; Ta, Dennis T; Vickery, Larry E

2004-04-16

IscA, an 11 kDa member of the hesB family of proteins, binds iron and [2Fe-2S] clusters, and participates in the biosynthesis of iron-sulfur proteins. We report the crystal structure of the apo-protein form of IscA from Escherichia coli to a resolution of 2.3A. The crystals belong to the space group P3(2)21 and have unit cell dimensions a=b=66.104 A, c=150.167 A (alpha=beta=90 degrees, gamma=120 degrees ). The structure was solved using single-wavelength anomalous dispersion (SAD) phasing of a selenomethionyl derivative, and the IscA model was refined to R=21.4% (Rfree=25.4%). IscA exists as an (alpha1alpha2)2 homotetramer with the (alpha1alpha2) dimer comprising the asymmetric unit. Cys35, implicated in Fe-S cluster assembly, is located in a central cavity formed at the tetramer interface with the gamma-sulfur atoms of residues from the alpha1 and alpha2' monomers (and alpha1'alpha2) positioned close to one another (approximately equal 7 A). C-terminal residues 99-107 are disordered, and the exact positions of Cys99 and Cys101 could not be determined. However, computer modeling of C-terminal residues in the tetramer suggests that Cys99 and Cys101 in the alpha1 monomer and those of the alpha1' monomer (or alpha2 and alpha2') are positioned sufficiently close to coordinate [2Fe-2S] clusters between the two dimers, whereas this is not possible within the (alpha1alpha2) or (alpha1'alpha2') dimer. This symmetrical arrangement allows for binding of two [2Fe-2S] clusters on opposite sides of the tetramer. Modeling further reveals that Cys101 is positioned sufficiently close to Cys35 to allow Cys35 to participate in cluster assembly, formation, or transfer.

β-Hairpin-Mediated Formation of Structurally Distinct Multimers of Neurotoxic Prion Peptides

PubMed Central

Gill, Andrew C.

2014-01-01

Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109–122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109–122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109–122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106–126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies. PMID:24498083

Insights into the Aggregation Mechanism of PolyQ Proteins with Different Glutamine Repeat Lengths.

PubMed

Yushchenko, Tetyana; Deuerling, Elke; Hauser, Karin

2018-04-24

Polyglutamine (polyQ) diseases, including Huntington's disease, result from the aggregation of an abnormally expanded polyQ repeat in the affected protein. The length of the polyQ repeat is essential for the disease's onset; however, the molecular mechanism of polyQ aggregation is still poorly understood. Controlled conditions and initiation of the aggregation process are prerequisites for the detection of transient intermediate states. We present an attenuated total reflection Fourier-transform infrared spectroscopic approach combined with protein immobilization to study polyQ aggregation dependent on the polyQ length. PolyQ proteins were engineered mimicking the mammalian N-terminus fragment of the Huntingtin protein and containing a polyQ sequence with the number of glutamines below (Q11), close to (Q38), and above (Q56) the disease threshold. A monolayer of the polyQ construct was chemically immobilized on the internal reflection element of the attenuated total reflection cell, and the aggregation was initiated via enzymatic cleavage. Structural changes of the polyQ sequence were monitored by time-resolved infrared difference spectroscopy. We observed faster aggregation kinetics for the longer sequences, and furthermore, we could distinguish β-structured intermediates for the different constructs, allowing us to propose aggregation mechanisms dependent on the repeat length. Q11 forms a β-structured aggregate by intermolecular interaction of stretched monomers, whereas Q38 and Q56 undergo conformational changes to various β-structured intermediates, including intramolecular β-sheets. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Ordered mapping of 3 alphoid DNA subsets on human chromosome 22

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

Antonacci, R.; Baldini, A.; Archidiacono, N.

1994-09-01

Alpha satellite DNA consists of tandemly repeated monomers of 171 bp clustered in the centromeric region of primate chromosomes. Sequence divergence between subsets located in different human chromosomes is usually high enough to ensure chromosome-specific hybridization. Alphoid probes specific for almost every human chromosome have been reported. A single chromosome can carry different subsets of alphoid DNA and some alphoid subsets can be shared by different chromosomes. We report the physical order of three alphoid DNA subsets on human chromosome 22 determined by a combination of low and high resolution cytological mapping methods. Results visually demonstrate the presence of threemore » distinct alphoid DNA domains at the centromeric region of chromosome 22. We have measured the interphase distances between the three probes in three-color FISH experiments. Statistical analysis of the results indicated the order of the subsets. Two color experiments on prometaphase chromosomes established the order of the three domains relative to the arms of chromosome 22 and confirmed the results obtained using interphase mapping. This demonstrates the applicability of interphase mapping for alpha satellite DNA orderering. However, in our experiments, interphase mapping did not provide any information about the relationship between extremities of the repeat arrays. This information was gained from extended chromatin hybridization. The extremities of two of the repeat arrays were seen to be almost overlapping whereas the third repeat array was clearly separated from the other two. Our data show the value of extended chromatin hybridization as a complement of other cytological techniques for high resolution mapping of repetitive DNA sequences.« less

Recovery of olefin monomers

DOEpatents

Golden, Timothy Christoph; Weist, Jr., Edward Landis; Johnson, Charles Henry

2004-03-16

In a process for the production of a polyolefin, an olefin monomer is polymerised said polyolefin and residual monomer is recovered. A gas stream comprising the monomer and nitrogen is subjected to a PSA process in which said monomer is adsorbed on a periodically regenerated silica gel or alumina adsorbent to recover a purified gas stream containing said olefin and a nitrogen rich stream containing no less than 99% nitrogen and containing no less than 50% of the nitrogen content of the gas feed to the PSA process.

Amino acid sequence analysis of the annexin super-gene family of proteins.

PubMed

Barton, G J; Newman, R H; Freemont, P S; Crumpton, M J

1991-06-15

The annexins are a widespread family of calcium-dependent membrane-binding proteins. No common function has been identified for the family and, until recently, no crystallographic data existed for an annexin. In this paper we draw together 22 available annexin sequences consisting of 88 similar repeat units, and apply the techniques of multiple sequence alignment, pattern matching, secondary structure prediction and conservation analysis to the characterisation of the molecules. The analysis clearly shows that the repeats cluster into four distinct families and that greatest variation occurs within the repeat 3 units. Multiple alignment of the 88 repeats shows amino acids with conserved physicochemical properties at 22 positions, with only Gly at position 23 being absolutely conserved in all repeats. Secondary structure prediction techniques identify five conserved helices in each repeat unit and patterns of conserved hydrophobic amino acids are consistent with one face of a helix packing against the protein core in predicted helices a, c, d, e. Helix b is generally hydrophobic in all repeats, but contains a striking pattern of repeat-specific residue conservation at position 31, with Arg in repeats 4 and Glu in repeats 2, but unconserved amino acids in repeats 1 and 3. This suggests repeats 2 and 4 may interact via a buried saltbridge. The loop between predicted helices a and b of repeat 3 shows features distinct from the equivalent loop in repeats 1, 2 and 4, suggesting an important structural and/or functional role for this region. No compelling evidence emerges from this study for uteroglobin and the annexins sharing similar tertiary structures, or for uteroglobin representing a derivative of a primordial one-repeat structure that underwent duplication to give the present day annexins. The analyses performed in this paper are re-evaluated in the Appendix, in the light of the recently published X-ray structure for human annexin V. The structure confirms most of the predictions and shows the power of techniques for the determination of tertiary structural information from the amino acid sequences of an aligned protein family.

Formation of Novel Polydiacetylenes: Synthesis of Poly(iodoethynyliododiacetylene) and Towards the Formation of Conjugated Ladder Polydiacetylenes

NASA Astrophysics Data System (ADS)

Freitag, Matthew

Polydiacetylenes (PDAs) are 1-dimensional polymers with a carbon-rich ene-yne backbone. Materials scientists are interested in PDAs because they are semiconductors, they have large multiphoton absorptions, and they can be prepared as ordered assemblies in the solid-state. Polydiacetylenes are formed from the topochemical 1,4-polymerization of a monomer unit made up of at least two sequential alkynes. This work describes attempts to form novel polydiacetylenes from several higher order polyyne monomers, as well as efforts to alter the morphology of known polydiacetylenes into thin films. The first project described here examined the formation of cocrystals of diiodohexatriyne with a bis(alkylnitrile) oxalamide host. Diiodohexatriyne undergoes 1,4-topochemical polymerization, with mild heating, to form poly(iodoethynyliododiacetylene), PIEDA. Polymerization was followed by extensive characterization through Raman spectroscopy, solid-state 13C MAS-NMR, and X-ray crystallography. This work represents the first ordered single-crystal to single-crystal 1,4-topochemical polymerization of a triyne, demonstrated through X-ray diffraction. The second project described efforts towards post-polymerization modification on PIEDA. Despite some success in model studies, isolated PIEDA was found to be too unstable to undergo controlled post-polymerization modification. The third project of this work described the demonstration of the formation of thin films of another PDA, polydiiododiacetylene (PIDA). Thin films of PIDA cocrystals could serve as components in solar cells or photovoltaic devices. Using lower concentration and allowing evaporation to occur in a fume hood, nanometer thick films were formed. However, thin films of PIDA cocrystals were too heterogeneous to be used within devices. The fourth project described here examined the preparation of cocrystals of bis(iodobutadiynyl)benzene monomer with several oxalamide hosts. The goal of this project is formation of conjugated ladder polydiacetylenes which have been theorized to have a lower band-gap than analogous linear polydiacetylenes. Cocrystals of monomer bis(iodobutadiynyl)benzene were formed with a variety of oxalamide hosts. Monomer cocrystals were heated at high temperatures and gave Raman signal consistent with polydiacetylene formation. Attempts to analyze heated cocrystals through single crystal X-ray diffraction have failed due to increased mosaicity. Other methods of inducing polymerization have been investigated but no ordered polymerization could be demonstrated. Halogen bonding has been demonstrated to be a reliable interaction for aligning these monomers. However, the polymerization and characterization of resultant polymer remains challenging due to the multiple reaction pathways of these materials.

Development of a novel oxirane-acrylate composite restorative resin material

NASA Astrophysics Data System (ADS)

Sripathi Panditaradhyula, Anuhya

The need for resin with a long clinical life can be satiated through the novel formulation of varying concentrations of oxirane and acrylate monomers with an increase in filler loading in the sample, which will allow the creation of a resin that is less susceptible to chemical degradation along with improved mechanical properties. Various concentrations of oxirane and acrylate monomers with a three-component photoinitiation system, which is capable of both free radical (acrylate) and cationic (oxirane) initiation, are used. The resin composites were placed in the Speedmixer for 30 seconds and gravitation convection oven for one minute, repeated 5-7 times. The resin composites were used to create a 9.525 mm diameter * 1.5875 mm thick resin mold. The mold was then photocured for twenty seconds on both sides using VALO blue LED light. The Rockwell hardness and shore D durometer hardness served as relative measures of bonding between the monomers. The ideal formulation of oxirane and acrylate concentrations were used to perform the Instron 3 point bend test, as well as contact angle determination. The goal is to identify a resin with a clinical life twice that of the resins being used in practice. Potential findings include ideal oxirane and acrylate concentrations with the highest shore D durometer hardness, Rockwell hardness, contact angle values, and Instron 3 point bend test values. Ideal color, transparency and properties of the resin are taken into account. Optimization of oxirane and acrylate monomers, impact while using various filler components (salination, number of fillers), filler particle size variations and variations in using different filler concentrations are observed. Results of using micro and nano-sized monomers are also studied. Addition of fluorinated acrylate monomer to the micro and nano composite was the next goal. A comparison of all the above stated compositions to the control group 70/30 BisTEG was done. A study on the degradation behavior of these specimens were done by placing the respective specimens in distilled water, ascorbic acid (pH=1.5) and NaOH (pH=13). These resins were not fully cured with filler apart from filled 25:75 oxirane: acrylate cured best. Replacing 4-(Octyloxy) phenyl] phenyl iodonium SbF6 (OPPI) with 4-Isopropyl-4'- methyldiphenyl iodonium Tetrakis (pentafluorophenyl borate (Borate) initiator enhanced 24hr oxirane cure. Formulations had greater hardness compared with the controls. The increase in hardness was due to Increase in oxirane functionality, Increase in filler loading and use of acrylate-salinated filler. Modulus and ultimate transverse strength are greater than controls, but did not have statistically significance energy to break. Thus, these composites are as tough as controls and less brittle. They have the higher hydrophobicity than BisGMA: TEGDMA controls. Furthermore, other means of increasing hydrophobicity was explored, because higher the hydrophobicity, higher the resistance to hydrolytic degradation. Further research observations, such as dynamic mechanical analysis, should be carried out in order to determine the molecular interactions and usage of multi-walled, white carbon nanotubes as filler material.

Glucose Electrodes Based on Cross-Linked (Os(bpy)2CI)+/2+ Complexed Poly(1-Vinylimidazole) Films

DTIC Science & Technology

1993-05-24

oxidase (GOX) through covalent bonding in the cross-linking step, glucose was electrooxidized at 250 mV (SCE). The characteristics of these... electrooxidation currents were independent of the polymers’ osmium content in the studied (3 - 10 osmium S_ _ centers per monomer unit ) range, Electrodes...glucose was electrooxidized at 250 mV (SCE). The characteristics of these electrodes depended on the GOX concentration, film thickness, 02

21 CFR 888.4220 - Cement monomer vapor evacuator.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Cement monomer vapor evacuator. 888.4220 Section... (CONTINUED) MEDICAL DEVICES ORTHOPEDIC DEVICES Surgical Devices § 888.4220 Cement monomer vapor evacuator. (a) Identification. A cement monomer vapor evacuator is a device intended for use during surgery to contain or remove...

21 CFR 888.4220 - Cement monomer vapor evacuator.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Cement monomer vapor evacuator. 888.4220 Section... (CONTINUED) MEDICAL DEVICES ORTHOPEDIC DEVICES Surgical Devices § 888.4220 Cement monomer vapor evacuator. (a) Identification. A cement monomer vapor evacuator is a device intended for use during surgery to contain or remove...

21 CFR 888.4220 - Cement monomer vapor evacuator.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Cement monomer vapor evacuator. 888.4220 Section... (CONTINUED) MEDICAL DEVICES ORTHOPEDIC DEVICES Surgical Devices § 888.4220 Cement monomer vapor evacuator. (a) Identification. A cement monomer vapor evacuator is a device intended for use during surgery to contain or remove...

21 CFR 888.4220 - Cement monomer vapor evacuator.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Cement monomer vapor evacuator. 888.4220 Section... (CONTINUED) MEDICAL DEVICES ORTHOPEDIC DEVICES Surgical Devices § 888.4220 Cement monomer vapor evacuator. (a) Identification. A cement monomer vapor evacuator is a device intended for use during surgery to contain or remove...

21 CFR 888.4220 - Cement monomer vapor evacuator.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cement monomer vapor evacuator. 888.4220 Section... (CONTINUED) MEDICAL DEVICES ORTHOPEDIC DEVICES Surgical Devices § 888.4220 Cement monomer vapor evacuator. (a) Identification. A cement monomer vapor evacuator is a device intended for use during surgery to contain or remove...

Scattering Studies of Hydrophobic Monomers in Liposomal Bilayers: An Expanding Shell Model of Monomer Distribution

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

Richter, Andrew; Dergunov, Sergey; Ganus, Bill

2011-01-01

Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scatteringmore » (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.« less

Scattering Studies of Hydrophobic Monomers in Liposomal Bilayers: An Expanding Shell Model of Monomer Distribution

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

Richter, Andrew G.; Dergunov, Sergey A.; Ganus, Bill

2011-03-10

Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scatteringmore » (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Finally, pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.« less

Interfacially polymerized layers for oxygen enrichment: a method to overcome Robeson's upper-bound limit.

PubMed

Tsai, Ching-Wei; Tsai, Chieh; Ruaan, Ruoh-Chyu; Hu, Chien-Chieh; Lee, Kueir-Rarn

2013-06-26

Interfacial polymerization of four aqueous phase monomers, diethylenetriamine (DETA), m-phenylenediamine (mPD), melamine (Mela), and piperazine (PIP), and two organic phase monomers, trimethyl chloride (TMC) and cyanuric chloride (CC), produce a thin-film composite membrane of polymerized polyamide layer capable of O2/N2 separation. To achieve maximum efficiency in gas permeance and O2/N2 permselectivity, the concentrations of monomers, time of interfacial polymerization, number of reactive groups in monomers, and the structure of monomers need to be optimized. By controlling the aqueous/organic monomer ratio between 1.9 and 2.7, we were able to obtain a uniformly interfacial polymerized layer. To achieve a highly cross-linked layer, three reactive groups in both the aqueous and organic phase monomers are required; however, if the monomers were arranged in a planar structure, the likelihood of structural defects also increased. On the contrary, linear polymers are less likely to result in structural defects, and can also produce polymer layers with moderate O2/N2 selectivity. To minimize structural defects while maximizing O2/N2 selectivity, the planar monomer, TMC, containing 3 reactive groups, was reacted with the semirigid monomer, PIP, containing 2 reactive groups to produce a membrane with an adequate gas permeance of 7.72 × 10(-6) cm(3) (STP) s(-1) cm(-2) cm Hg(-1) and a high O2/N2 selectivity of 10.43, allowing us to exceed the upper-bound limit of conventional thin-film composite membranes.

Survey of commercially available chocolate- and cocoa-containing products in the United States. 2. Comparison of flavan-3-ol content with nonfat cocoa solids, total polyphenols, and percent cacao.

PubMed

Miller, Kenneth B; Hurst, W Jeffrey; Flannigan, Nancy; Ou, Boxin; Lee, C Y; Smith, Nancy; Stuart, David A

2009-10-14

A survey of a broad range of chocolate- and cocoa-containing products marketed in the United States was conducted to provide a more detailed analysis of flavan-3-ol monomers, oligomers, and polymers, which can be grouped into a class of compounds called procyanidins. Samples consisted of the three or four top-selling products within the following six categories: natural cocoa powder, unsweetened baking chocolate, dark chocolate, semisweet baking chips, milk chocolate, and chocolate syrup. Composite samples were characterized for percent fat (% fat), percent nonfat cocoa solids (% NFCS), antioxidant level by ORAC, total polyphenols, epicatechin, catechin, total monomers, and flavan-3-ol oligomers and polymers (procyanidins). On a gram weight basis epicatechin and catechin content of the products follow in decreasing order: cocoa powder > baking chocolate > dark chocolate = baking chips > milk chocolate > chocolate syrup. Analysis of the monomer and oligomer profiles within product categories shows there are two types of profiles: (1) products that have high monomers with decreasing levels of oligomers and (2) products in which the level of dimers is equal to or greater than the monomers. Results show a strong correlation (R(2) = 0.834) of epicatechin to the level of % NFCS and also very good correlations for N = 2-5 oligomers to % NFCS. A weaker correlation was observed for catechin to % NFCS (R(2) = 0.680). Other analyses show a similar high degree of correlation with epicatechin and N = 2-5 oligomers to total polyphenols, with catechin being less well correlated to total polyphenols. A lesser but still good correlation exists between the calculated percent cacao (calcd % cacao) content, a proxy for percent cacao, and these same flavanol measures, with catechin again showing a lesser degree of correlation to calcd % cacao. Principal component analysis (PCA) shows that the products group discretely into five classes: (1) cocoa powder, (2) baking chocolate, (3) dark chocolate and semisweet chips, (4) milk chocolates, and (5) syrup. PCA also shows that most factors group closely together including the antioxidant activity, total polyphenols, and the flavan-3-ol measures with the exception of catechin and % fat in the product, which group separately. Because catechin distribution appears to be different from the other flavan-3-ol measures, an analysis of the epicatechin to catechin ratio was done, indicating there is a >5-fold variation in this measure across the products studied. The cocoa-containing products tested range from cocoa powder with 227.34 +/- 17.23 mg of procyanidins per serving to 25.75 +/- 9.91 mg of procyanidins per serving for chocolate syrup. These results are discussed with respect to other studies on commercial products, the bioavailability of the flavanols, and the possible role of processing on the amount of catechin in products.

Silicone Oil Microdroplets and Protein Aggregates in Repackaged Bevacizumab and Ranibizumab: Effects of Long-term Storage and Product Mishandling

PubMed Central

Liu, Lu; Ammar, David A.; Ross, Lindsey A.; Mandava, Naresh; Kahook, Malik Y.

2011-01-01

Purpose. To quantify levels of subvisible particles and protein aggregates in repackaged bevacizumab obtained from compounding pharmacies, as well as in samples of bevacizumab and ranibizumab tested in controlled laboratory experiments. Methods. Repackaged bevacizumab was purchased from four external compounding pharmacies. For controlled laboratory studies, bevacizumab and placebo were drawn into plastic syringes and incubated at −20°C, 4°C, and room temperature (with and without exposure to light) for 12 weeks. In addition, mechanical shock occurring during shipping was mimicked with syringes containing bevacizumab. Particle counts and size distributions were quantified by particle characterization technology. Levels of monomer and soluble aggregates of bevacizumab were determined with size-exclusion high-performance liquid chromatography (SE-HPLC). Results. Repackaged bevacizumab from the compounding pharmacies had a wide range of particle counts (89,006 ± 56,406 to 602,062 ± 18,349/mL). Bevacizumab sampled directly from the original glass vial had particle counts of 63,839 ± 349/mL. There was up to a 10% monomer loss in the repackaged bevacizumab. Laboratory samples of repackaged bevacizumab and placebo had initial particle counts, respectively, of 283,675 ± 60,494/mL and 492,314 ± 389,361/mL. Freeze-thawing of both bevacizumab and placebo samples led to >1.2 million particles/mL. In all repackaged samples, most of the particles were due to silicone oil. SE-HPLC showed no significant differences for repackaged samples incubated in the laboratory under various conditions, compared with bevacizumab directly from vial. However, repeated freeze-thawing caused a more than 10% monomer loss. Conclusions. Bevacizumab repackaged in plastic syringes could contain protein aggregates and is contaminated by silicone oil microdroplets. Freeze-thawing or other mishandling can further increase levels of particle contaminants. PMID:21051703

Aqueous phase oligomerization of α,β-unsaturated carbonyls and acids investigated using ion mobility spectrometry coupled to mass spectrometry (IMS-MS)

NASA Astrophysics Data System (ADS)

Renard, Pascal; Tlili, Sabrine; Ravier, Sylvain; Quivet, Etienne; Monod, Anne

2016-04-01

One of the current essential issues to unravel our ability to forecast future climate change and air quality, implies a better understanding of natural processes leading to secondary organic aerosol (SOA) formation, and in particular the formation and fate of oligomers. The difficulty in characterizing macromolecules is to discern between large oxygenated molecules from series of oligomers containing repeated small monomers of diverse structures. In the present study, taking advantage from previously established radical vinyl oligomerization of methyl vinylketone (MVK) in the aqueous phase, where relatively simple oligomers containing up to 14 monomers were observed, we have investigated the same reactivity on several other unsaturated water soluble organic compounds (UWSOCs) and on a few mixtures of these precursor compounds. The technique used to characterize the formed oligomers was a traveling wave ion mobility spectrometry coupled to a hybrid quadrupole - time of flight mass spectrometer (IMS-MS) fitted with an electrospray source and ultra-high performance liquid chromatography (UPLC). The technique allows for an additional separation, especially for large ions, containing long carbon chains. We have shown the efficiency of the IMS-mass spectrometry technique to detect oligomers derived from MVK photooxidation in the aqueous phase. The results were then compared to other oligomers, derived from ten other individual biogenic UWSOCs. The technique allowed distinguishing between different oligomers arising from different precursors. It also clearly showed that compounds bearing a non-conjugated unsaturation did not provide oligomerization. Finally, it was shown that the IMS-mass spectrometry technique, applied to mixtures of unsaturated conjugated precursors, exhibited the ability of these precursors to co-oligomerize, i.e. forming only one complex oligomer system bearing monomers of different structures. The results are discussed in terms of atmospheric implications for the detection of oligomers in complex chamber and/or field samples.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

PubMed

Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

2018-05-01

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

Circularly Polarized Luminescence from a Pyrene-Cyclodextrin Supra-Dendron.

PubMed

Zhang, Yuening; Yang, Dong; Han, Jianlei; Zhou, Jin; Jin, Qingxian; Liu, Minghua; Duan, Pengfei

2018-05-22

Soft nanomaterials with circularly polarized luminescence (CPL) have been currently attracting great interest. Here, we report a pyrene-containing π-peptide dendron hydrogel, which shows 1D and 2D nanostructures with varied CPL activities. It was found that the individual dendrons formed hydrogels in a wide pH range (3-12) and self-assembled into helices with pH-tuned pitches. Through chirality transfer, the pyrene unit could show CPL originated from both the monomer and excimer bands. When cyclodextrin was introduced, different supra-dendrons were obtained with β-cyclodextrin (PGAc@β-CD) and γ-cyclodextrin (PGAc@γ-CD) through host-guest interactions, respectively. Interestingly, the PGAc@β-CD and PGAc@γ-CD supra-dendrons self-assembled into 2D nanosheet and entangled nanofibers, respectively, showing cyclodextrin induced circularly polarized emission from both the monomer and excimer bands of the pyrene moiety. Thus, through a simple host-guest interaction, both the nanostructures and the chiroptical activities could be modulated.

Cooperativity in self-limiting equilibrium self-associating systems

NASA Astrophysics Data System (ADS)

Freed, Karl F.

2012-11-01

A wide variety of highly cooperative self-assembly processes in biological and synthetic systems involve the assembly of a large number (m) of units into clusters, with m narrowly peaked about a large size m0 ≫ 1 and with a second peak centered about the m = 1 unassembled monomers. While very specific models have been proposed for the assembly of, for example, viral capsids and core-shell micelles of ß-casein, no available theory describes a thermodynamically general mechanism for this double peaked, highly cooperative equilibrium assembly process. This study provides a general mechanism for these cooperative processes by developing a minimal Flory-Huggins type theory. Beginning from the simplest non-cooperative, free association model in which the equilibrium constant for addition of a monomer to a cluster is independent of cluster size, the new model merely allows more favorable growth for clusters of intermediate sizes. The theory is illustrated by computing the phase diagram for cases of self-assembly on cooling or heating and for the mass distribution of the two phases.

Higher cytotoxicity of divalent antibody-toxins than monovalent antibody-toxins

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

Won, JaeSeon; Nam, PilWon; Lee, YongChan

2009-04-24

Recombinant antibody-toxins are constructed via the fusion of a 'carcinoma-specific' antibody fragment to a toxin. Due to the high affinity and high selectivity of the antibody fragments, antibody-toxins can bind to surface antigens on cancer cells and kill them without harming normal cells [L.H. Pai, J.K. Batra, D.J. FitzGerald, M.C. Willingham, I. Pastan, Anti-tumor activities of immunotoxins made of monoclonal antibody B3 and various forms of Pseudomonas exotoxin, Proc. Natl. Acad. Sci. USA 88 (1991) 3358-3362]. In this study, we constructed the antibody-toxin, Fab-SWn-PE38, with SWn (n = 3, 6, 9) sequences containing n-time repeated (G{sub 4}S) between the Fabmore » fragment and PE38 (38 kDa truncated form of Pseudomonas exotoxin A). The SWn sequence also harbored one cysteine residue that could form a disulfide bridge between two Fab-SWn-PE38 monomers. We assessed the cytotoxicity of the monovalent (Fab-SWn-PE38), and divalent ([Fab-SWn-PE38]{sub 2}) antibody-toxins. The cytotoxicity of the dimer against the CRL1739 cell line was approximately 18.8-fold higher than that of the monomer on the ng/ml scale, which was approximately 37.6-fold higher on the pM scale. These results strongly indicate that divalency provides higher cytotoxicity for an antibody-toxin.« less

Spectrophotometric determination of fluoxetine by molecularly imprinted polypyrrole and optimization by experimental design, artificial neural network and genetic algorithm

NASA Astrophysics Data System (ADS)

Nezhadali, Azizollah; Motlagh, Maryam Omidvar; Sadeghzadeh, Samira

2018-02-01

A selective method based on molecularly imprinted polymer (MIP) solid-phase extraction (SPE) using UV-Vis spectrophotometry as a detection technique was developed for the determination of fluoxetine (FLU) in pharmaceutical and human serum samples. The MIPs were synthesized using pyrrole as a functional monomer in the presence of FLU as a template molecule. The factors that affecting the preparation and extraction ability of MIP such as amount of sorbent, initiator concentration, the amount of monomer to template ratio, uptake shaking rate, uptake time, washing buffer pH, take shaking rate, Taking time and polymerization time were considered for optimization. First a Plackett-Burman design (PBD) consists of 12 randomized runs were applied to determine the influence of each factor. The other optimization processes were performed using central composite design (CCD), artificial neural network (ANN) and genetic algorithm (GA). At optimal condition the calibration curve showed linearity over a concentration range of 10- 7-10- 8 M with a correlation coefficient (R2) of 0.9970. The limit of detection (LOD) for FLU was obtained 6.56 × 10- 9 M. The repeatability of the method was obtained 1.61%. The synthesized MIP sorbent showed a good selectivity and sensitivity toward FLU. The MIP/SPE method was used for the determination of FLU in pharmaceutical, serum and plasma samples, successfully.

Concise chemical synthesis of a tetrasaccharide repeating unit of the O-antigen of Hafnia alvei 10457.

PubMed

Kumar, Rishi; Maulik, Prakas R; Misra, Anup Kumar

2008-08-01

Concise chemical synthesis of a tetrasaccharide repeating unit of the O-antigen of Hafnia alvei 10457 is reported. Construction of the tetrasaccharide as its 4-methoxyphenyl glycoside was achieved by condensation of less abundant monosaccharide units such as, D-galactofuranose, N-acetyl-D-galactosamine and N-acetylneuraminic acid. The synthetic strategy consists of the preparation of suitably protected required monosaccharide intermediates from the commercially available reducing sugars and high yielding glycosylation reactions.

Genetic Studies of the Prp17 Gene of Saccharomyces Cerevisiae: A Domain Essential for Function Maps to a Nonconserved Region of the Protein

PubMed Central

Seshadri, V.; Vaidya, V. C.; Vijayraghavan, U.

1996-01-01

The PRP17 gene product is required for the second step of pre-mRNA splicing reactions. The C-terminal half of this protein bears four repeat units with homology to the β transducin repeat. Missense mutations in three temperature-sensitive prp17 mutants map to a region in the N-terminal half of the protein. We have generated, in vitro, 11 missense alleles at the β transducin repeat units and find that only one affects function in vivo. A phenotypically silent missense allele at the fourth repeat unit enhances the slow-growing phenotype conferred by an allele at the third repeat, suggesting an interaction between these domains. Although many missense mutations in highly conserved amino acids lack phenotypic effects, deletion analysis suggests an essential role for these units. Only mutations in the N-terminal nonconserved domain of PRP17 are synthetically lethal in combination with mutations in PRP16 and PRP18, two other gene products required for the second splicing reaction. A mutually allele-specific interaction between prp17 and snr7, with mutations in U5 snRNA, was observed. We therefore suggest that the functional region of Prp17p that interacts with Prp18p, Prp16p, and U5 snRNA is in the N terminal region of the protein. PMID:8722761

Residual monomers and degree of conversion of partially bioresorbable fiber-reinforced composite.

PubMed

Väkiparta, Marju; Puska, Mervi; Vallittu, Pekka K

2006-01-01

The aim of this study was to evaluate the total quantity of residual monomer (bis-phenyl glycidyl dimethacrylate, i.e. Bis-GMA, and triethylene glycol dimethacrylate, i.e. TEGDMA), residual monomer release into water and the degree of monomer conversion (DC%) of glass fiber-reinforced composites (FRC) with a partially bioresorbable polymer matrix. Another aim was to find out whether the curing mode affects the quantity of residual monomer and degree of conversion. Glass fibers were preimpregnated with a bioresorbable poly(hydroxyproline) amide and non-resorbable Bis-GMA-TEGDMA resin system. Specimens were immersed in water for 1, 3 or 7 days (37 degrees C) to determine the quantity of leached residual monomers, or in the solvent tetrahydrofuran for 3 days to determine the total quantity of residual monomers by high performance liquid chromatography. DC% was measured by Fourier transform infrared spectroscopy. The quantity of residual monomer of the specimens decreased when the specimens contained glass fibers, and/or poly(hydroxyproline) amide, and/or when it was post-cured. The majority of the residual monomers were leached out during the first 24 h of immersion in water. The DC% of the specimens increased when post-cured. Also glass fibers in the composite increased the DC% in contrast to Bis-GMA-TEGDMA resin only. In conclusion, use of poly(hydroxyproline) amide as a sizing of the glass fibers in FRC does not increase the quantity of residual monomers. These results suggest that this new kind of partially bioresorbable FRC has potential for biomedical applications.

Effect of Laser-assisted and Conventional In-office Bleaching on Monomer Release from Microhybrid and Nanohybrid Composite.

PubMed

Omrani, Ladan Ranjbar; Farjadfar, Shayan; Pedram, Parham; Sadray, Sima; Kamangar, Sedighe Sadat Hashemi; Chiniforoush, Nasim

2017-06-30

Bleaching might affect structural properties of composite materials, and lead to monomer release. This study aimed to evaluate the effect of Laser-assisted and conventional in-office bleaching on the release of BIS-GMA, TEGDMA, and UDMA monomers from a nanohybrid and a microhybrid BIS-GMA based composite. 32 samples of each composite, were divided into 4 subgroups; subgroup 1: Conventional in-office bleaching (CIB) with the Opalescence Boost PF 38% gel, subgroup 2: Laser-assisted bleaching (LBO) with the Opalescence Boost PF 38% gel, subgroup 3: Laser-assisted bleaching (LBH) with the JW Power bleaching gel, subgroup 4: (CO) control without bleaching. All the samples were immersed in tubes of 2cc Ethanol 75% medium. The released monomers were analyzed using the high performance liquid chromatography (HPLC) method 24 h, 7, and 28 days. Data's were analyzed by Univariate Analysis of Variance test followed by Tukeys HSD. The amount of TEGDMA monomer released was not significant. However, nanohybrid composites showed significantly more monomer release than microhybrid composites (P < 0.05). For UDMA the interaction was significant only after 1 week. In microhybrid composites, the CO subgroup showed more monomer release than LBH and LBO. In nanohybrid composites, LBH showed more monomer release than CIB and CO subgroups. For BIS-GMA monomers the interaction was significant at all time periods and the LBH subgroup of nanohybrid composite had significantly more BIS_GMA release in comparison to other subgroups. Bleaching by laser with JW Power Bleaching gel led to more monomer release in nanohybrid composite.

Fibrin monomer increases platelet adherence to tumor cells in a flowing system: a possible role in metastasis?

PubMed

Biggerstaff, J P; Seth, N B; Meyer, T V; Amirkhosravi, A; Francis, J L

1998-12-15

Considerable evidence exists linking hemostasis and malignancy. Platelet adhesion to tumor cells has been implicated in the metastatic process. Plasma fibrinogen (Fg) and fibrin (Fn) monomer, increased in cancer, may play a role in tumor biology. Binding of Fn monomer to tumor cells and its effect on platelet-tumor cell adhesion in a flowing system were studied. Fn monomer was produced by adding thrombin (1 micro/mL) to FXIII- and plasminogen-free Fg in the presence of Gly-Pro-Arg-Pro (GPRP) amide. Fn monomer binding to live A375 cells was visualized by confocal laser scanning microscopy (CLSM). Adherent cells were perfused for 1h with Fn monomer, washed and stained in situ with anti-human Fn (American Biogenetic Sciences, Inc.) followed by goat anti-mouse IgG(FITC). Platelet adherence to Fn monomer treated A375 cells was performed under flow conditions by passing platelets (5x10(4)/microl 0.25 mL/min; labeled with the carbocyanine dye DiI) over the tumor cells for 30 min. CLSM images were obtained after washing. There was considerable binding of Fn monomer, but not Fg alone. Platelets adhered relatively weakly to untreated A375 cells and this was not significantly affected by pre-treatment of the tumor cells with fibrinogen or thrombin. However, pre-treatment with Fn monomer resulted in extensive platelet binding to tumor cells, suggesting that coagulation activation and the subsequent increase in circulating Fn monomer may enhance platelet adhesion to circulating tumor cells and thereby facilitate metastatic spread.

Heat resistant polymers of oxidized styrylphosphine

NASA Technical Reports Server (NTRS)

Paciorek, K. J. L. (Inventor)

1978-01-01

Homopolymers, copolymers and terpolymers of a styrene based monomer are prepared by polymerizing at least one oxidized styrylphosphine monomer or by polymerizing p-diphenylphosphinestyrene and then oxidizing the polymerized monomer with an organoazide. Copolymers can also be prepared by copolymerizing styrene with at least one oxidized styrylphosphine monomer. Flame resistant vinyl based polymers whose degradation products are non toxic and non corrosive are obtained.

Modeling phase separation in mixtures of intrinsically-disordered proteins

NASA Astrophysics Data System (ADS)

Gu, Chad; Zilman, Anton

Phase separation in a pure or mixed solution of intrinsically-disordered proteins (IDPs) and its role in various biological processes has generated interest from the theoretical biophysics community. Phase separation of IDPs has been implicated in the formation of membrane-less organelles such as nucleoli, as well as in a mechanism of selectivity in transport through the nuclear pore complex. Based on a lattice model of polymers, we study the phase diagram of IDPs in a mixture and describe the selective exclusion of soluble proteins from the dense-phase IDP aggregates. The model captures the essential behaviour of phase separation by a minimal set of coarse-grained parameters, corresponding to the average monomer-monomer and monomer-protein attraction strength, as well as the protein-to-monomer size ratio. Contrary to the intuition that strong monomer-monomer interaction increases exclusion of soluble proteins from the dense IDP aggregates, our model predicts that the concentration of soluble proteins in the aggregate phase as a function of monomer-monomer attraction is non-monotonic. We corroborate the predictions of the lattice model using Langevin dynamics simulations of grafted polymers in planar and cylindrical geometries, mimicking various in-vivo and in-vitro conditions.

Solid-support Electron Paramagnetic Resonance (EPR) Studies of Aβ40 Monomers Reveal a Structured State with Three Ordered Segments*

PubMed Central

Gu, Lei; Ngo, Sam; Guo, Zhefeng

2012-01-01

Alzheimer disease is associated with the pathological accumulation of amyloid-β peptide (Aβ) in the brain. Soluble Aβ oligomers formed during early aggregation process are believed to be neurotoxins and causative agents in Alzheimer disease. Aβ monomer is the building block for amyloid assemblies. A comprehensive understanding of the structural features of Aβ monomer is crucial for delineating the mechanism of Aβ oligomerization. Here we investigated the structures of Aβ40 monomer using a solid-support approach, in which Aβ40 monomers are tethered on the solid support via an N-terminal His tag to prevent further aggregation. EPR spectra of tethered Aβ40 with spin labels at 18 different positions show that Aβ40 monomers adopt a completely disordered structure under denaturing conditions. Under native conditions, however, EPR spectra suggest that Aβ40 monomers adopt both a disordered state and a structured state. The structured state of Aβ40 monomer has three more ordered segments at 14–18, 29–30, and 38–40. Interactions between these segments may stabilize the structured state, which likely plays an important role in Aβ aggregation. PMID:22277652

[Study on the choice of functional monomer before preparation of myclobutanil molecularly imprinted polymer].

PubMed

Gao, Wen-Hui; Liu, Bo; Li, Xing-Feng; Han, Jun-Hua; Jia, Ying-Min

2014-03-01

To prepare myclobutanil molecularly imprinted polymer, a method was established for the choice of the appropriate functional monomer and its dosage. UV spectra was applied to study the combination form, the effect intensity, the optimal concentration ratio and the numbers of binding sites between myclobutanil and methyl acrylic acid (MAA) or acrylamide (AM) functional monomer. The results showed that hydrogen-bonding interaction could be formed between myclobutanil and methyl acrylic acid (MAA) or acrylamide (AM) functional monomer. The pi electron of the triazole ring conjugated double bond in my clobutanil could transit to pi* conjugate antibonding orbital when it absorbed energy. The formation of hydrogen bond could make pi-->pi* absorption band transit. Maximum absorption wavelength produced red shift with the increase in the functional monomer concentration in the system. The research revealed that the optimal concentration ratios between myclobutanil and the two monomers were c(M):c(MAA) = 1:4, c(M):c(AM) = 1:2. Myclobutanil and the both the functional monomers had the bonding ability, and strong bonding force. The prepared molecularly imprinted polymer using AM as a functional monomer had better stability and specificity of recognition for myclobutanil.

Method for nanoencapsulation of aerogels and nanoencapsulated aerogels produced by such method

NASA Technical Reports Server (NTRS)

Sullivan, Thomas A. (Inventor)

2007-01-01

A method for increasing the compressive modulus of aerogels comprising: providing aerogel substrate comprising a bubble matrix in a chamber; providing monomer to the chamber, the monomer comprising vapor phase monomer which polymerizes substantially free of polymerization byproducts; depositing monomer from the vapor phase onto the surface of the aerogel substrate under deposition conditions effective to produce a vapor pressure sufficient to cause the vapor phase monomer to penetrate into the bubble matrix and deposit onto the surface of the aerogel substrate, producing a substantially uniform monomer film; and, polymerizing the substantially uniform monomer film under polymerization conditions effective to produce polymer coated aerogel comprising a substantially uniform polymer coating substantially free of polymerization byproducts.Polymer coated aerogel comprising aerogel substrate comprising a substantially uniform polymer coating, said polymer coated aerogel comprising porosity and having a compressive modulus greater than the compressive modulus of the aerogel substrate, as measured by a 100 lb. load cell at 1 mm/minute in the linear range of 20% to 40% compression.

Monomer-dependent secondary nucleation in amyloid formation.

PubMed

Linse, Sara

2017-08-01

Secondary nucleation of monomers on the surface of an already existing aggregate that is formed from the same kind of monomers may lead to autocatalytic amplification of a self-assembly process. Such monomer-dependent secondary nucleation occurs during the crystallization of small molecules or proteins and self-assembled materials, as well as in protein self-assembly into fibrous structures. Indications of secondary nucleation may come from analyses of kinetic experiments starting from pure monomers or monomers supplemented with a low concentration of pre-formed aggregates (seeds). More firm evidence requires additional experiments, for example those employing isotope labels to distinguish new aggregates arising from the monomer from those resulting from fragmentation of the seed. In cases of amyloid formation, secondary nucleation leads to the formation of toxic oligomers, and inhibitors of secondary nucleation may serve as starting points for therapeutic developments. Secondary nucleation displays a high degree of structural specificity and may be enhanced by mutations or screening of electrostatic repulsion.

Plant chromosomes from end to end: telomeres, heterochromatin and centromeres.

PubMed

Lamb, Jonathan C; Yu, Weichang; Han, Fangpu; Birchler, James A

2007-04-01

Recent evidence indicates that heterochromatin in plants is composed of heterogeneous sequences, which are usually composed of transposable elements or tandem repeat arrays. These arrays are associated with chromatin modifications that produce a closed configuration that limits transcription. Centromere sequences in plants are usually composed of tandem repeat arrays that are homogenized across the genome. Analysis of such arrays in closely related taxa suggests a rapid turnover of the repeat unit that is typical of a particular species. In addition, two lines of evidence for an epigenetic component of centromere specification have been reported, namely an example of a neocentromere formed over sequences without the typical repeat array and examples of centromere inactivation. Although the telomere repeat unit is quite prevalent in the plant kingdom, unusual repeats have been found in some families. Recently, it was demonstrated that the introduction of telomere sequences into plants cells causes truncation of the chromosomes, and that this technique can be used to produce artificial chromosome platforms.

Reactivity of vinyl ethers and vinyl ribosides in UV-initiated free radical copolymerization with acceptor monomers.

PubMed

Pichavant, Loic; Guillermain, Céline; Coqueret, Xavier

2010-09-13

The reactivity of various vinyl ethers and vinyloxy derivatives of ribose in the presence of diethyl fumarate or diethyl maleate was investigated for evaluating the potential of donor-acceptor-type copolymerization applied to unsaturated monomers derived from renewable feedstock. The photochemically induced polymerization of model monomer blends in the bulk state was monitored by infrared spectroscopy. The method allowed us to examine the influence of monomer pair structure on the kinetic profiles. The simultaneous consumption of both monomers was observed, supporting an alternating copolymerization mechanism. A lower reactivity of the blends containing maleates compared with fumarates was confirmed. The obtained kinetic data revealed a general correlation between the initial polymerization rate and the Hansen parameter δ(H) associated with the H-bonding aptitude of the donor monomer.

Enantioselective cyclization of racemic supramolecular polymers.

PubMed

ten Cate, A Tessa; Dankers, Patricia Y W; Kooijman, Huub; Spek, Anthony L; Sijbesma, Rint P; Meijer, E W

2003-06-11

Homochiral hydrogen-bonded cyclic assemblies are formed in dilute solutions of racemic supramolecular polymers based on the quadruple hydrogen bonding 2-ureido-4[1H]-pyrimidinone unit, as observed by 1H NMR and SEC experiments. Preorganization of the monomers and the combined binding strength of the eight hydrogen bonds result in a very high stability of the cyclic aggregates with pronounced selectivity between homochiral and heterochiral cyclic species, usually only observed in crystalline or liquid crystalline phases.

A conservation and biophysics guided stochastic approach to refining docked multimeric proteins.

PubMed

Akbal-Delibas, Bahar; Haspel, Nurit

2013-01-01

We introduce a protein docking refinement method that accepts complexes consisting of any number of monomeric units. The method uses a scoring function based on a tight coupling between evolutionary conservation, geometry and physico-chemical interactions. Understanding the role of protein complexes in the basic biology of organisms heavily relies on the detection of protein complexes and their structures. Different computational docking methods are developed for this purpose, however, these methods are often not accurate and their results need to be further refined to improve the geometry and the energy of the resulting complexes. Also, despite the fact that complexes in nature often have more than two monomers, most docking methods focus on dimers since the computational complexity increases exponentially due to the addition of monomeric units. Our results show that the refinement scheme can efficiently handle complexes with more than two monomers by biasing the results towards complexes with native interactions, filtering out false positive results. Our refined complexes have better IRMSDs with respect to the known complexes and lower energies than those initial docked structures. Evolutionary conservation information allows us to bias our results towards possible functional interfaces, and the probabilistic selection scheme helps us to escape local energy minima. We aim to incorporate our refinement method in a larger framework which also enables docking of multimeric complexes given only monomeric structures.

Manipulation of Guaiacyl and Syringyl Monomer Biosynthesis in an Arabidopsis Cinnamyl Alcohol Dehydrogenase Mutant Results in Atypical Lignin Biosynthesis and Modified Cell Wall Structure

PubMed Central

Anderson, Nickolas A.; Tobimatsu, Yuki; Ciesielski, Peter N.; Ximenes, Eduardo; Ralph, John; Donohoe, Bryon S.; Ladisch, Michael; Chapple, Clint

2015-01-01

Modifying lignin composition and structure is a key strategy to increase plant cell wall digestibility for biofuel production. Disruption of the genes encoding both cinnamyl alcohol dehydrogenases (CADs), including CADC and CADD, in Arabidopsis thaliana results in the atypical incorporation of hydroxycinnamaldehydes into lignin. Another strategy to change lignin composition is downregulation or overexpression of ferulate 5-hydroxylase (F5H), which results in lignins enriched in guaiacyl or syringyl units, respectively. Here, we combined these approaches to generate plants enriched in coniferaldehyde-derived lignin units or lignins derived primarily from sinapaldehyde. The cadc cadd and ferulic acid hydroxylase1 (fah1) cadc cadd plants are similar in growth to wild-type plants even though their lignin compositions are drastically altered. In contrast, disruption of CAD in the F5H-overexpressing background results in dwarfism. The dwarfed phenotype observed in these plants does not appear to be related to collapsed xylem, a hallmark of many other lignin-deficient dwarf mutants. cadc cadd, fah1 cadc cadd, and cadd F5H-overexpressing plants have increased enzyme-catalyzed cell wall digestibility. Given that these CAD-deficient plants have similar total lignin contents and only differ in the amounts of hydroxycinnamaldehyde monomer incorporation, these results suggest that hydroxycinnamaldehyde content is a more important determinant of digestibility than lignin content. PMID:26265762

Investigating the compatibility of PEEK polymer for the fabrication of sample cells for use in muon spin spectroscopy

NASA Astrophysics Data System (ADS)

Chandrasena, L.; McKenzie, I.; Brodovitch, J.-C.; Mozafari, M.; Cottrell, S. P.; Percival, P. W.

2014-12-01

Polyether ether ketone (PEEK) is a thermoplastic polymer with a wide range of applications due to its chemical inertness and thermal stability, and for these reasons sample cells for gas and liquid phase μSR have been constructed from PEEK. Muon levelcrossing resonance (μLCR) studies of PEEK revealed a broad, strong μLCR signal that, we hypothesize, is due to multiple overlapping resonances from the various muonium (Mu) adducts of PEEK. To investigate this, two monomer units from PEEK (4,4'-dihydroxybenzophenone and para-dimethoxybenzene) were studied in solution using transverse-field muon spin rotation (TF-μSR) and μLCR. Two different muoniated radicals were formed by Mu addition to 4,4/- dihydroxybenzophenone and one radical was formed in para-dimethoxybenzene. The μSR spectra were assigned by comparing the experimentally measured muon and proton hyperfine coupling constants with values calculated for the possible structures using Gaussian-09 software with the B3LYP functional and 6-31G basis set. Good agreement was found for cyclohexadienyl- type radicals formed by Mu addition to the benzene rings of the monomer units. We can also infer that these radicals are being formed in PEEK, and based on this we conclude that sample cells made of PEEK are unsuitable for many types of μSR experiment.

NMR characterization of altered lignins extracted from tobacco plants down-regulated for lignification enzymes cinnamylalcohol dehydrogenase and cinnamoyl-CoA reductase.

PubMed

Ralph, J; Hatfield, R D; Piquemal, J; Yahiaoui, N; Pean, M; Lapierre, C; Boudet, A M

1998-10-27

Homologous antisense constructs were used to down-regulate tobacco cinnamyl-alcohol dehydrogenase (CAD; EC 1.1.1.195) and cinnamoyl-CoA reductase (CCR; EC 1.2.1.44) activities in the lignin monomer biosynthetic pathway. CCR converts activated cinnamic acids (hydroxycinnamoyl-SCoAs) to cinnamaldehydes; cinnamaldehydes are then reduced to cinnamyl alcohols by CAD. The transformations caused the incorporation of nontraditional components into the extractable tobacco lignins, as evidenced by NMR. Isolated lignin of antisense-CAD tobacco contained fewer coniferyl and sinapyl alcohol-derived units that were compensated for by elevated levels of benzaldehydes and cinnamaldehydes. Products from radical coupling of cinnamaldehydes, particularly sinapaldehyde, which were barely discernible in normal tobacco, were major components of the antisense-CAD tobacco lignin. Lignin content was reduced in antisense-CCR tobacco, which displayed a markedly reduced vigor. That lignin contained fewer coniferyl alcohol-derived units and significant levels of tyramine ferulate. Tyramine ferulate is a sink for the anticipated build-up of feruloyl-SCoA, and may be up-regulated in response to a deficit of coniferyl alcohol. Although it is not yet clear whether the modified lignins are true structural components of the cell wall, the findings provide further indications of the metabolic plasticity of plant lignification. An ability to produce lignin from alternative monomers would open new avenues for manipulation of lignin by genetic biotechnologies.

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, Kap; Ho, Joseph X.; Keeling, Kim; Gilliland, Gary L.; Ji, Xinhua; Rueker, Florian; Carter, Daniel C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

The structure of the exopolysaccharide of Pseudomonas fluorescens strain H13.

PubMed

Osman, S F; Fett, W F; Irwin, P; Cescutti, P; Brouillette, J N; O'Connor, J V

1997-05-19

An acidic exopolysaccharide was isolated from P. fluorescens strain H13. The structure of the polysaccharide repeating unit was determined using chemical methods and 1D and 2D NMR techniques. The repeating unit was characterized as a trisaccharide composed of D-glucose, 2-acetamido-2-deoxy-D-glucose and 4-O-acetyl-2-acetamido-2-deoxy-D-mannuronic acid.

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming.

PubMed

Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der

2017-11-06

Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives.

PubMed

Li, Wan; Bian, Xin; Evivie, Smith Etareri; Huo, Gui-Cheng

2016-09-01

The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.

AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

DOE PAGES

Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; ...

2016-03-23

α 1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based onmore » biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found inWT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo polymerization showing a surprising diversity of polymer topography. PLOS« less

The Structure of the Protonated Serine Octamer.

PubMed

Scutelnic, Valeriu; Perez, Marta A S; Marianski, Mateusz; Warnke, Stephan; Gregor, Aurelien; Rothlisberger, Ursula; Bowers, Michael T; Baldauf, Carsten; von Helden, Gert; Rizzo, Thomas R; Seo, Jongcheol

2018-06-20

The amino acid serine has long been known to form a protonated "magic-number" cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a Ser 8 H + structure that is in agreement with all experimental observations. Here, we present the structure of Ser 8 H + determined by a combination of infrared spectroscopy and ab initio molecular dynamics simulations. The three-dimensional structure that we determine is ∼25 kcal mol -1 more stable than the previous most stable published structure and explains both the homochiral preference and the experimentally observed facile replacement of two serine units.

Effect of monomer composition of polymer matrix on flexural properties of glass fibre-reinforced orthodontic archwire.

PubMed

Ohtonen, J; Vallittu, P K; Lassila, L V J

2013-02-01

To compare force levels obtained from glass fibre-reinforced composite (FRC) archwires. Specifically, FRC wires were compared with polymer matrices having different dimethacrylate monomer compositions. FRC material (E-glass provided by Stick Tech Ltd, Turku, Finland) with continuous unidirectional glass fibres and four different types of dimethacrylate monomer compositions for the resin matrix were tested. Cross-sectionally round FRC archwires fitting into the 0.3 mm slot of a bracket were divided into 16 groups with six specimens in each group. Glass fibres were impregnated by the manufacturer, and they were initially light-cured by hand light-curing unit or additionally post-cured in light-curing oven. The FRC archwire specimens were tested at 37°C according to a three-point bending test in dry and wet conditions using a span length of 10 mm and a crosshead speed of 1.0 mm/minute. The wires were loaded until final failure. The data were statistically analysed using analysis of variance (ANOVA). The dry FRC archwire specimens revealed higher load values than water stored ones, regardless of the polymer matrix. A majority of the FRC archwires showed higher load values after being post-cured. ANOVA revealed that the polymer matrix, curing method, and water storage had a significant effect (P < 0.05) on the flexural behaviour of the FRC archwire. Polymer matrix composition, curing method, and water storage affected the flexural properties and thus, force level and working range which could be obtained from the FRC archwire.

The effect of the polymerization initiator and light source on the elution of residual Bis-GMA and TEGDMA monomers: A study using liquid chromatography with UV detection.

PubMed

Denis, Aline B; Diagone, Cristina A; Plepis, Ana M G; Viana, Rommel B

2015-12-05

A method for the extraction and quantification of two residual monomers, bisphenol glycidyl dimethacrylate (Bis-GMA) and triethylene glycol dimethacrylate (TEGDMA), that were evaluated using high efficiency liquid chromatography with UV detection was developed and validated in this study. Three types of solvents were applied in the extraction of the monomers (methanol, ethanol and acetonitrile), where the highest extraction efficiency was obtained using acetonitrile. The different resins were prepared by photoactivation of Bis-GMA and TEGDMA monomers. Additionally, the effects of the addition of two photoinitiators (camphorquinone (CQ) and phenyl propanodione (PPD) and that of a co-initiator (N,N-dimethyl-p-toluidine) were also analyzed. When only the CQ photoinitiator was used, a smaller amount of residual monomers was obtained, whereas a larger amount was obtained with PPD. When the two photoinitiators were used in the same matrix, however, no significant changes were observed in relation to the amount of residual TEGDMA monomers. For the addition of the co-initiator, there were no large changes in the extraction of residual monomers. The effect of the two photoactivation sources (halogen lamp and LED) led to small differences in the elution of the two monomers, although all of the resins differed significantly when photoactivated with a LED. Quantum chemical calculations using Density Functional Theory were carried out to characterize several molecular properties of each monomer. Copyright © 2015 Elsevier B.V. All rights reserved.

Chemical synthesis of water-soluble, chiral conducting-polymer complexes

DOEpatents

Wang, Hsing-Lin; McCarthy, Patrick A.; Yang, Sze Cheng

2003-01-01

The template-guided synthesis of water-soluble, chiral conducting polymer complexes is described. Synthesis of water-soluble polyaniline complexes is achieved by carefully controlling the experimental parameters such as; acid concentration, ionic strength, monomer/template ratio, total reagent concentration, and order of reagent addition. Chiral (helical) polyaniline complexes can be synthesized by addition of a chiral inducing agent (chiral acid) prior to polymerization, and the polyaniline helix can be controlled by the addition of the (+) or (-) form of the chiral acid. Moreover the quantity of chiral acid and the salt content has a significant impact on the degree of chirality in the final polymer complexes. The polyaniline and the template have been found to be mixed at the molecular level which results in chiral complexes that are robust through repeated doping and dedoping cycles.

Radiation-induced polymerization of cyclophosphazene trimers. Final report, 1 September 1985-30 September 1988

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

Stannett, V.T.

1989-01-04

Hexachlorophosphazene was irradiated in bulk and in solution after various methods of purification. When rigorously dried and purified, good yields of polymer were obtained. Poor reproducibility was found in the bulk but reasonably good results were obtained in decalin solution. The best yields and highest molecular weights were obtained after the addition of small amounts of the bulky electron acceptor pyromellitic dianhydride. Hexachlorocyclotriphosphazene was purified by recrystallization for various times from dried heptane. The trimer was then further purified by repeated sublimation steps under high vacuum. Finally the trimer was dried in the melt over rigorously baked out barium oxide.more » The monomer was then transferred to ampules or the NMR tubes for radiation and subsequent determination of the polymer content.« less

Di(hydroxyphenyl)- benzimidazole monomers

NASA Technical Reports Server (NTRS)

Connell, John W. (Inventor); Hergenrother, Paul M. (Inventor); Smith, Joseph G. (Inventor)

1993-01-01

Di(hydroxyphenyl)benzimidazole monomers were prepared from phenyl-hydroxybenzoate and aromatic bis(o-diamine)s. These monomers were used in the synthesis of soluble polybenzimidazoles. The reaction involved the aromatic nucleophilic displacement of various di(hydroxyphenyl)benzimidazole monomers with activated aromatic dihalides or activated aromatic dinitro compounds in the presence of an alkali metal base. These polymers exhibited lower glass transition temperatures, improved solubility, and better compression moldability over their commercial counterparts.

Flash evaporation of liquid monomer particle mixture

DOEpatents

Affinito, John D.; Darab, John G.; Gross, Mark E.

1999-01-01

The present invention is a method of making a first solid composite polymer layer. The method has the steps of (a) mixing a liquid monomer with particles substantially insoluble in the liquid monomer forming a monomer particle mixture; (b) flash evaporating the particle mixture and forming a composite vapor; and (c) continuously cryocondensing said composite vapor on a cool substrate and cross-linking the cryocondensed film thereby forming the polymer layer.

Rational computational design for the development of andrographolide molecularly imprinted polymer

NASA Astrophysics Data System (ADS)

Krishnan, Hemavathi; Islam, K. M. Shafiqul; Hamzah, Zainab; Ahmad, Mohd Noor

2017-10-01

Andrographolide is a popular medicinal compound derived from Andrographis Paniculata (AP). Molecularly Imprint Polymer (MIP) is a "Lock and Key" approach, where MIP is the lock and Andrographolide is the key which fits to the MIP lock by both physically and chemically. MIP will be used as selective extraction tool to enrich Andrographolide bioactive compound. Pre-polymerization step is crucial to design MIP. This work investigates molecular interactions and the Gibbs free binding energies on the development of MIP. The structure of Andrographolide (template) and functional monomers were drawn in HyperChem 8.0.10. A hybrid quantum chemical model was used with a few functional monomers. Possible conformations of template and functional monomer as 1:n (n < 4) were designed and simulated to geometrically optimize the complex to the lowest energy in gas phase. The Gibbs free binding energies of each conformation were calculated using semi-empirical PM3 simulation method. Results proved that functional monomers that contain carboxylic group shows higher binding energy compared to those with amine functional group. Itaconic acid (IA) chosen as the best functional monomer at optimum ratio (1:3) of template: monomer to prepare andrographolide MIP. This study demonstrates the importance of studying intermolecular interaction among template, functional monomer and template-monomer ratio in developing MIP.

Effect of the combination of dithiooctanoate monomers and acidic adhesive monomers on adhesion to precious metals, precious metal alloys and non-precious metal alloys.

PubMed

Ikemura, Kunio; Kojima, Katsunori; Endo, Takeshi; Kadoma, Yoshinori

2011-01-01

This study investigated the effect of the combination of a dithiooctanoate monomer and an acidic adhesive monomer on adhesion to precious metals, precious and non-precious metal alloys. From a selection of four dithiooctanoate monomers and six acidic adhesive monomers, 14 experimental primers containing a combination of 5.0 wt% of a dithiooctanoate monomer and 1.0 wt% of an acidic adhesive monomer in acetone were prepared. Tensile bond strengths (TBSs) of MMA-PMMA/TBBO resin to nine kinds of precious metals, precious metal alloys, and non-precious metal alloys after 2,000 thermal cycles were measured. Results showed that there were no significant differences in TBS among the primers to all the precious and non-precious metal adherends tested (p>0.05). Highest TBS values (46.5-55.8 MPa) for bonding to Au alloy, Au-Ag-Pd alloy, Co-Cr alloy, and Ni-Cr alloy were achieved with the primer which contained 5.0 wt% 10-methacryloyloxydecyl 6,8-dithiooctanoate (10-MDDT) and 1.0 wt% 6-methacryloyloxyhexyl phosphonoacetate (6-MHPA). Therefore, 5.0 wt% 10-MDDT and 1.0 wt% 6-MHPA was determined as the optimal combination for bonding to precious metals, precious and non-precious metal alloys.

Shear sensitive monomer-polymer laminate structure and method of using same

NASA Technical Reports Server (NTRS)

Singh, Jag J. (Inventor); Eftekhari, Abe (Inventor); Parmar, Devendra S. (Inventor)

1993-01-01

Monomer cholesteric liquid crystals have helical structures which result in a phenomenon known as selective reflection, wherein incident white light is reflected in such a way that its wavelength is governed by the instantaneous pitch of the helix structure. The pitch is dependent on temperature and external stress fields. It is possible to use such monomers in flow visualization and temperature measurement. However, the required thin layers of these monomers are quickly washed away by a flow, making their application time dependent for a given flow rate. The laminate structure according to the present invention comprises a liquid crystal polymer substrate attached to a test surface of an article. A light absorbing coating is applied to the substrate and is thin enough to permit bonding steric interaction between the liquid crystal polymer substrate and an overlying liquid crystal monomer thin film. Light is directed through and reflected by the liquid crystal monomer thin film and unreflected light is absorbed by the underlying coating. The wavelength of the reflected light is indicative of the shear stress experienced by the test surface. Novel aspects of the invention include its firm bonding of a liquid crystal monomer to a model and its use of a coating to reduce interference from light unreflected by the monomer helical structure.

47 CFR 90.247 - Mobile repeater stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... of the mobile unit and an automatic time-delay device that de-activates the transmitter after any... 47 Telecommunication 5 2010-10-01 2010-10-01 false Mobile repeater stations. 90.247 Section 90.247... MOBILE RADIO SERVICES Non-Voice and Other Specialized Operations § 90.247 Mobile repeater stations. A...

Comparison of small molecules and oligonucleotides that target a toxic, non-coding RNA.

PubMed

Costales, Matthew G; Rzuczek, Suzanne G; Disney, Matthew D

2016-06-01

Potential RNA targets for chemical probes and therapeutic modalities are pervasive in the transcriptome. Oligonucleotide-based therapeutics are commonly used to target RNA sequence. Small molecules are emerging as a modality to target RNA structures selectively, but their development is still in its infancy. In this work, we compare the activity of oligonucleotides and several classes of small molecules that target the non-coding r(CCUG) repeat expansion (r(CCUG)(exp)) that causes myotonic dystrophy type 2 (DM2), an incurable disease that is the second-most common cause of adult onset muscular dystrophy. Small molecule types investigated include monomers, dimers, and multivalent compounds synthesized on-site by using RNA-templated click chemistry. Oligonucleotides investigated include phosphorothioates that cleave their target and vivo-morpholinos that modulate target RNA activity via binding. We show that compounds assembled on-site that recognize structure have the highest potencies amongst small molecules and are similar in potency to a vivo-morpholino modified oligonucleotide that targets sequence. These studies are likely to impact the design of therapeutic modalities targeting other repeats expansions that cause fragile X syndrome and amyotrophic lateral sclerosis, for example. Copyright © 2016. Published by Elsevier Ltd.

Capillary gel electrophoresis for the quantification and purity determination of recombinant proteins in inclusion bodies.

PubMed

Espinosa-de la Garza, Carlos E; Perdomo-Abúndez, Francisco C; Campos-García, Víctor R; Pérez, Néstor O; Flores-Ortiz, Luis F; Medina-Rivero, Emilio

2013-09-01

In this work, a high-resolution CGE method for quantification and purity determination of recombinant proteins was developed, involving a single-component inclusion bodies (IBs) solubilization solution. Different recombinant proteins expressed as IBs were used to show method capabilities, using recombinant interferon-β 1b as the model protein for method validation. Method linearity was verified in the range from 0.05 to 0.40 mg/mL and a determination coefficient (r(2) ) of 0.99 was obtained. The LOQs and LODs were 0.018 and 0.006 mg/mL, respectively. RSD for protein content repeatability test was 2.29%. In addition, RSD for protein purity repeatability test was 4.24%. Method accuracy was higher than 90%. Specificity was confirmed, as the method was able to separate recombinant interferon-β 1b monomer from other aggregates and impurities. Sample content and purity was demonstrated to be stable for up to 48 h. Overall, this method is suitable for the analysis of recombinant proteins in IBs according to the attributes established on the International Conference for Harmonization guidelines. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cutin and suberin monomers are membrane perturbants.

PubMed

Douliez, Jean-Paul

2004-03-15

The interaction between cutin and suberin monomers, i.e., omega -hydroxylpalmitic acid, alpha, omega -hexadecanedioic acid, alpha, omega --hexadecanediol, 12-hydroxylstearic acid, and phospholipid vesicles biomimicking the lipid structure of plant cell membranes has been studied by optical and transmission electron microscopy, quasielastic light scattering, differential scanning calorimetry, and (31)P solid-state NMR. Monomers were shown to penetrate model membranes until a molar ratio of 30%, modulating their gel to fluid-phase transition, after which monomer crystals also formed in solution. These monomers induced a decrease of the phospholipid vesicle size from several micrometers to about 300 nm. The biological implications of these findings are discussed.

Method for molding ceramic powders using a water-based gel casting

DOEpatents

Janney, Mark A.; Omatete, Ogbemi O.

1991-07-02

A method for molding ceramic powders comprises forming a slurry mixture including ceramic powder, a dispersant, and a monomer solution. The monomer solution includes at least one monofunctional monomer and at least one difunctional monomer, a free-radical initiator, and a aqueous solvent. The slurry mixture is transferred to a mold, and the mold containing the slurry mixture is heated to polymerize and crosslink the monomer and form a firm polymer-solvent gel matrix. The solid product any be removed from the mold and heated to first remove the solvent and subsequently remove the polymer, whereafter the product may be sintered.

Method for molding ceramic powders using a water-based gel casting process

DOEpatents

Jenny, Mark A.; Omalete, Ogbemi O.

1992-09-08

A method for molding ceramic powders comprises forming a slurry mixture including ceramic powder, a dispersant, and a monomer solution. The monomer solution includes at least one monofunctional monomer and at least one difunctional monomer, a free-radical initiator, and a aqueous solvent. The slurry mixture is transferred to a mold, and the mold containing the slurry mixture is heated to polymerize and crosslink the monomer and form a firm polymer-solvent gel matrix. The solid product may be removed from the mold and heated to first remove the solvent and subsequently remove the polymer, whereafter the product may be sintered.

Expression, purification and preliminary biochemical and structural characterization of the leucine rich repeat namesake domain of leucine rich repeat kinase 2.

PubMed

Vancraenenbroeck, Renée; Lobbestael, Evy; Weeks, Stephen D; Strelkov, Sergei V; Baekelandt, Veerle; Taymans, Jean-Marc; De Maeyer, Marc

2012-03-01

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease. Much research effort has been directed towards the catalytic core region of LRRK2 composed of GTPase (ROC, Ras of complex proteins) and kinase domains and a connecting COR (C-terminus of ROC) domain. In contrast, the precise functions of the protein-protein interaction domains, such as the leucine-rich repeat (LRR) domain, are not known. In the present study, we modeled the LRRK2 LRR domain (LRR(LRRK2)) using a template assembly approach, revealing the presence of 14 LRRs. Next, we focused on the expression and purification of LRR(LRRK2) in Escherichia coli. Buffer optimization revealed that the protein requires the presence of a zwitterionic detergent, namely Empigen BB, during solubilization and the subsequent purification and characterization steps. This indicates that the detergent captures the hydrophobic surface patches of LRR(LRRK2) thereby suppressing its aggregation. Circular dichroism (CD) spectroscopy measured 18% α-helices and 21% β-sheets, consistent with predictions from the homology model. Size exclusion chromatography (SEC) and dynamic light scattering measurements showed the presence of a single species, with a Stokes radius corresponding to the model dimensions of a protein monomer. Furthermore, no obvious LRR(LRRK2) multimerization was detected via cross-linking studies. Finally, the LRR(LRRK2) clinical mutations did not influence LRR(LRRK2) secondary, tertiary or quaternary structure as determined via SEC and CD spectroscopy. We therefore conclude that these mutations are likely to affect putative LRR(LRRK2) inter- and intramolecular interactions. Copyright © 2011 Elsevier B.V. All rights reserved.

Discordant expression and variable numbers of neighboring GGA- and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene.

PubMed Central

Koch, K S; Gleiberman, A S; Aoki, T; Leffert, H L; Feren, A; Jones, A L; Fodor, E J

1995-01-01

An unusual S1-nuclease sensitive microsatellite (STMS) has been found in the single copy, rat polymeric immunoglobulin receptor gene (PIGR) terminal exon. In Fisher rats, elements within or beyond the STMS are expressed variably in the 3' untranslated regions (3'UTRs) of two 'Groups' of PIGR-encoded hepatic mRNAs (pIg-R) during liver regeneration. STMS elements include neighboring constant regions (a 60-bp d[GA]-rich tract with a chi-like octamer, followed by 15 tandem d[GGA] repeats) that merge directly with 36 or 39 tandem d[GAA] repeats (Fisher or Wistar strains, respectively) interrupted by d[AA] between their 5th-6th repeat units. The Wistar STMS is flanked upstream by two regions of nearly contiguous d[CA] or d[CT] repeats in the 3' end of intron 8; and downstream, by a 283 bp 'unit' containing several inversions at its 5' end, and two polyadenylation signals at its 3' end. The 283 nt unit is expressed in Group 1 pIg-R mRNAs; but it is absent in the Group 2 family so that their GAA repeats merge with their poly A tails. In contrast to genomic sequence, GGA triplet repeats are amplified (n > or = 24-26), whereas GAA triplet repeats are truncated variably (n < or = 9-37) and expressed uninterruptedly in both mRNA Groups. These results suggest that 3' end processing of the rat PIGR gene may involve misalignment, slippage and premature termination of RNA polymerase II. The function of this unusual processing and possible roles of chi-like octamers in quiescent or extrahepatic tissues are discussed. Images PMID:7739889

High Regional Variation in Urethroplasty in the United States

PubMed Central

Figler, Bradley D.; Gore, John L.; Holt, Sarah K.; Voelzke, Bryan B.; Wessells, Hunter

2015-01-01

Purpose We identified clinical and regional factors associated with the use of urethroplasty vs repeat endoscopic management for urethral stricture disease. Materials and Methods We analyzed claims for patients 18 to 65 years old in the 2007 to 2011 MarketScan ® Commercial Claims and Encounters Database with a diagnosis of urethral stricture. The primary outcome was treatment with urethroplasty vs repeat endoscopic management, defined as more than 2 dilations or direct vision internal urethrotomies. The likelihood of urethroplasty vs repeat endoscopic management was determined for each major metropolitan area in the United States. Multivariate logistic regression was done to identify factors associated with urethroplasty. Results We identified 41,056 patients with urethral stricture, yielding a diagnosis rate of 296/100,000 men in MarketScan. Repeat endoscopic management and urethroplasty were performed in 2,700 and 1,444 patients, respectively. Compared to patients treated with repeat endoscopic management those with urethroplasty were younger (median age 44 vs 54 years) and more likely to have a Charlson comorbidity score of 0 (84% vs 77%), have traveled out of a metropolitan area for care (34% vs 17%) and have a reconstructive urologist in the treatment metropolitan area (76% and 62%, each p < 0.001). When controlling for age and Charlson comorbidity score, travel out of a metropolitan area (OR 2.7, 95% CI 2.2–3.3) and a reconstructive urologist in the treatment metropolitan area (OR 2.0, 95% CI 1.7–2.5) were associated with a greater likelihood of urethroplasty vs repeat endoscopic management. Conclusions Despite the well established benefits of urethroplasty compared to repeat endoscopic management a strong bias for repeat endoscopic management exists in many regions in the United States. PMID:25072180

A Kinetic Study of DDGS Hemicellulose Acid Hydrolysis and NMR Characterization of DDGS Hydrolysate.

PubMed

Chen, Hanchi; Liu, Shijie

2015-09-01

Liquid hot water (LHW) extraction was used as a pretreatment method to separate the hemicellulose fraction from dried distiller's grain with solubles (DDGS) into liquid phase. Acid hydrolysis using 3.264 % w/w sulfuric acid at 130 °C was performed to convert polysaccharides in LHW extract to monosaccharides. The structure characterization of DDGS in anomeric carbon region based on proton NMR and heteronuclear single quantum coherence (HSQC) during acid hydrolysis was studied in this work. It reveals that the sugar units in DDGS hemicelluloses are constructed with (1-4)-β-D-xylopyranose and α-L-arabinofuranosyl residues. A kinetic model is included to explain the changing concentration of monomer, oligomer, and sugar units. The model was further tested based on the changing concentration of five carbon sugar units during hydrolysis.

Solid polymeric electrolytes for lithium batteries

DOEpatents

Angell, Charles A.; Xu, Wu; Sun, Xiaoguang

2006-03-14

Novel conductive polyanionic polymers and methods for their preparion are provided. The polyanionic polymers comprise repeating units of weakly-coordinating anionic groups chemically linked to polymer chains. The polymer chains in turn comprise repeating spacer groups. Spacer groups can be chosen to be of length and structure to impart desired electrochemical and physical properties to the polymers. Preferred embodiments are prepared from precursor polymers comprising the Lewis acid borate tri-coordinated to a selected ligand and repeating spacer groups to form repeating polymer chain units. These precursor polymers are reacted with a chosen Lewis base to form a polyanionic polymer comprising weakly coordinating anionic groups spaced at chosen intervals along the polymer chain. The polyanionic polymers exhibit high conductivity and physical properties which make them suitable as solid polymeric electrolytes in lithium batteries, especially secondary lithium batteries.

Flash evaporation of liquid monomer particle mixture

DOEpatents

Affinito, J.D.; Darab, J.G.; Gross, M.E.

1999-05-11

The present invention is a method of making a first solid composite polymer layer. The method has the steps of (a) mixing a liquid monomer with particles substantially insoluble in the liquid monomer forming a monomer particle mixture; (b) flash evaporating the particle mixture and forming a composite vapor; and (c) continuously cryocondensing said composite vapor on a cool substrate and cross-linking the cryocondensed film thereby forming the polymer layer. 3 figs.

Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

PubMed Central

2017-01-01

Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular biodynamers are commonly produced in aqueous media under mild or even physiological conditions to suit their biorelated applications. In contrast to static biopolymers emphasizing structural stability and unity by using irreversible covalent bonds, molecular biodynamers are seeking relative structural adaptability and diversity through the formation of reversible covalent bonds. Based on these considerations, molecular biodynamers are capable of reorganizing their monomers, generating, identifying, and amplifying the fittest structures in response to environmental factors. Hence, molecular biodynamers have received considerable research attention over the past decades. Accordingly, the construction of molecular biodynamers through equilibrium polymerization of nucleobase-, carbohydrate- or amino-acid-based monomers can lead to the fabrication of dynamic analogues of nucleic acids (DyNAs), polysaccharides (glycodynamers), or proteins (dynamic proteoids), respectively. In this Account, we summarize recent advances in developing different types of molecular biodynamers as structural or functional biomimetics of biopolymers, including DyNAs, glycodynamers, and dynamic proteoids. We introduce how chemists utilize various reversible reactions to generate molecular biodynamers with specific sequences and well-ordered structures in aqueous medium. We also discuss and list their potential applications in various research fields, such as drug delivery, drug discovery, gene sensing, cancer diagnosis, and treatment. PMID:28169527

High internal free volume compositions for low-k dielectric and other applications

NASA Technical Reports Server (NTRS)

Bouffard, Jean (Inventor); Swager, Timothy M. (Inventor)

2010-01-01

The present invention provides materials, devices, and methods involving new heterocyclic, shape-persistent monomeric units with internal free volume. In some cases, materials the present invention may comprise monomers, oligomers, or polymers that incorporate a heterocyclic, shape-persistent iptycene. The present invention may provide materials having low dielectric constants and improved stability at high operating temperatures due to the electron-poor character of materials. In addition, compositions of the invention may be easily synthesized and readily modified to suit a particular application.

Phenoxazine Based Units- Synthesis, Photophysics and Electrochemistry

PubMed Central

Nowakowska-Oleksy, Anna; Cabaj, Joanna

2010-01-01

A few new phenoxazine-based conjugated monomers were synthesized, characterized, and successfully used as semiconducting materials. The phenoxazine-based oligomers have low ionization potentials or high-lying HOMO levels (~4.7 eV), which were estimated from cyclic voltammetry. Conjugated oligomers offer good film—forming, mechanical and optical properties connected with their wide application. These results demonstrate that phenoxazine-based conjugated mers are a promising type of semiconducting and luminescent structures able to be used as thin films in organic electronics. PMID:20625802

Peptoid architectures: elaboration, actuation, and application.

PubMed

Yoo, Barney; Kirshenbaum, Kent

2008-12-01

Peptoids are peptidomimetic oligomers composed of N-substituted glycine units. Their convenient synthesis enables strict control over the sequence of highly diverse monomers and is capable of generating extensive compound libraries. Recent studies are beginning to explore the relationship between peptoid sequence, structure and function. We describe new approaches to direct the conformation of the peptoid backbone, leading to secondary structures such as helices, loops, and turns. These advances are enabling the discovery of bioactive peptoids and will establish modules for the design and assembly of protein mimetics.

The vibrational spectra and structure of 4-methyl oxaloacetate (carbomethoxypyruvic acid)

NASA Astrophysics Data System (ADS)

Schiering, David W.; Katon, J. E.

1986-04-01

The vibrational spectra of solid 4-methyl oxalocetate have been recorded. Infrared spectra were collected at ambient and liquid nitrogen temperatures; Raman spectra were collected at ambient temperature only. A tentative vibrational assignment of the solid is proposed based on a dimer structure composed of two enolic monomer units hydrogen bonded through the carboxylic acid group. 4-Methyl oxaloacetate was found to undergo keto—enol tautomerization in solution, and the solvent dependency of this equilibrium was demonstrated.

Identification and characterization of functional centromeres of the common bean.

PubMed

Iwata, Aiko; Tek, Ahmet L; Richard, Manon M S; Abernathy, Brian; Fonsêca, Artur; Schmutz, Jeremy; Chen, Nicolas W G; Thareau, Vincent; Magdelenat, Ghislaine; Li, Yupeng; Murata, Minoru; Pedrosa-Harand, Andrea; Geffroy, Valérie; Nagaki, Kiyotaka; Jackson, Scott A

2013-10-01

In higher eukaryotes, centromeres are typically composed of megabase-sized arrays of satellite repeats that evolve rapidly and homogenize within a species' genome. Despite the importance of centromeres, our knowledge is limited to a few model species. We conducted a comprehensive analysis of common bean (Phaseolus vulgaris) centromeric satellite DNA using genomic data, fluorescence in situ hybridization (FISH), immunofluorescence and chromatin immunoprecipitation (ChIP). Two unrelated centromere-specific satellite repeats, CentPv1 and CentPv2, and the common bean centromere-specific histone H3 (PvCENH3) were identified. FISH showed that CentPv1 and CentPv2 are predominantly located at subsets of eight and three centromeres, respectively. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of CentPv1 and CentPv2 at centromeres. Genomic analysis revealed several interesting features of CentPv1 and CentPv2: (i) CentPv1 is organized into an higher-order repeat structure, named Nazca, of 528 bp, whereas CentPv2 is composed of tandemly organized monomers; (ii) CentPv1 and CentPv2 have undergone chromosome-specific homogenization; and (iii) CentPv1 and CentPv2 are not likely to be commingled in the genome. These findings suggest that two distinct sets of centromere sequences have evolved independently within the common bean genome, and provide insight into centromere satellite evolution. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Qualitative and quantitative analysis of monomers in polyesters for food contact materials.

PubMed

Brenz, Fabrian; Linke, Susanne; Simat, Thomas

2017-02-01

Polyesters (PESs) are gaining more importance on the food contact material (FCM) market and the variety of properties and applications is expected to be wide. In order to acquire the desired properties manufacturers can combine several FCM-approved polyvalent carboxylic acids (PCAs) and polyols as monomers. However, information about the qualitative and quantitative composition of FCM articles is often limited. The method presented here describes the analysis of PESs with the identification and quantification of 25 PES monomers (10 PCA, 15 polyols) by HPLC with diode array detection (HPLC-DAD) and GC-MS after alkaline hydrolysis. Accurate identification and quantification were demonstrated by the analysis of seven different FCM articles made of PESs. The results explained between 97.2% and 103.4% w/w of the polymer composition whilst showing equal molar amounts of PCA and polyols. Quantification proved to be precise and sensitive with coefficients of variation (CVs) below 6.0% for PES samples with monomer concentrations typically ranging from 0.02% to 75% w/w. The analysis of 15 PES samples for the FCM market revealed the presence of five different PCAs and 11 different polyols (main monomers, co-monomers, non-intentionally added substances (NIAS)) showing the wide variety of monomers in modern PESs. The presented method provides a useful tool for commercial, state and research laboratories as well as for producers and distributors facing the task of FCM risk assessment. It can be applied for the identification and quantification of migrating monomers and the prediction of oligomer compositions from the identified monomers, respectively.

In situ polymerization of monomers for polyphenylquinoxaline-graphite fiber composites

NASA Technical Reports Server (NTRS)

Serafini, T. T.; Delvigs, P.; Vannucci, R. D.

1974-01-01

In situ polymerization of monomers was used to prepare graphite-fiber-reinforced polyphenylquinoxaline composites. Six different monomer combinations were investigated. Composite mechanical property retention characteristics were determined at 316 C (600 F) over an extended time period.

Novel variants of the 5S rRNA genes in Eruca sativa.

PubMed

Singh, K; Bhatia, S; Lakshmikumaran, M

1994-02-01

The 5S ribosomal RNA (rRNA) genes of Eruca sativa were cloned and characterized. They are organized into clusters of tandemly repeated units. Each repeat unit consists of a 119-bp coding region followed by a noncoding spacer region that separates it from the coding region of the next repeat unit. Our study reports novel gene variants of the 5S rRNA genes in plants. Two families of the 5S rDNA, the 0.5-kb size family and the 1-kb size family, coexist in the E. sativa genome. The 0.5-kb size family consists of the 5S rRNA genes (S4) that have coding regions similar to those of other reported plant 5S rDNA sequences, whereas the 1-kb size family consists of the 5S rRNA gene variants (S1) that exist as 1-kb BamHI tandem repeats. S1 is made up of two variant units (V1 and V2) of 5S rDNA where the BamHI site between the two units is mutated. Sequence heterogeneity among S4, V1, and V2 units exists throughout the sequence and is not limited to the noncoding spacer region only. The coding regions of V1 and V2 show approximately 20% dissimilarity to the coding regions of S4 and other reported plant 5S rDNA sequences. Such a large variation in the coding regions of the 5S rDNA units within the same plant species has been observed for the first time. Restriction site variation is observed between the two size classes of 5S rDNA in E. sativa.(ABSTRACT TRUNCATED AT 250 WORDS)

Repeating Patterns in Kindergarten: Findings from Children's Enactments of Two Activities

ERIC Educational Resources Information Center

Tsamir, Pessia; Tirosh, Dina; Levenson, Esther S.; Barkai, Ruthi; Tabach, Michal

2017-01-01

This paper describes kindergarten children's engagement with two patterning activities. The first activity includes two tasks in which children are asked to choose possible ways for extending two different repeating patterns and the second activity calls for comparing different pairs of repeating patterns. Children's recognition of the unit of…

Insensitive explosive composition and method of fracturing rock using an extrudable form of the composition

DOEpatents

Davis, Lloyd L

2013-11-05

Insensitive explosive compositions were prepared by reacting di-isocyanate and/or poly-isocyanate monomers with an explosive diamine monomer. Prior to a final cure, the compositions are extrudable. The di-isocyanate monomers tend to produce tough, rubbery materials while polyfunctional monomers (i.e. having more than two isocyanate groups) tend to form rigid products. The extrudable form of the composition may be used in a variety of applications including rock fracturing.

Insensitive explosive composition and method of fracturing rock using an extrudable form of the composition

DOEpatents

Davis, Lloyd L.

2015-07-28

Insensitive explosive compositions were prepared by reacting di-isocyanate and/or poly-isocyanate monomers with an explosive diamine monomer. Prior to a final cure, the compositions are extrudable. The di-isocyanate monomers tend to produce tough, rubbery materials while polyfunctional monomers (i.e. having more than two isocyanate groups) tend to form rigid products. The extrudable form of the composition may be used in a variety of applications including rock fracturing.

Proline Substitution of Dimer Interface β-strand Residues as a Strategy for the Design of Functional Monomeric Proteins

PubMed Central

Joseph, Prem Raj B.; Poluri, Krishna Mohan; Gangavarapu, Pavani; Rajagopalan, Lavanya; Raghuwanshi, Sandeep; Richardson, Ricardo M.; Garofalo, Roberto P.; Rajarathnam, Krishna

2013-01-01

Proteins that exist in monomer-dimer equilibrium can be found in all organisms ranging from bacteria to humans; this facilitates fine-tuning of activities from signaling to catalysis. However, studying the structural basis of monomer function that naturally exists in monomer-dimer equilibrium is challenging, and most studies to date on designing monomers have focused on disrupting packing or electrostatic interactions that stabilize the dimer interface. In this study, we show that disrupting backbone H-bonding interactions by substituting dimer interface β-strand residues with proline (Pro) results in fully folded and functional monomers, by exploiting proline’s unique feature, the lack of a backbone amide proton. In interleukin-8, we substituted Pro for each of the three residues that form H-bonds across the dimer interface β-strands. We characterized the structures, dynamics, stability, dimerization state, and activity using NMR, molecular dynamics simulations, fluorescence, and functional assays. Our studies show that a single Pro substitution at the middle of the dimer interface β-strand is sufficient to generate a fully functional monomer. Interestingly, double Pro substitutions, compared to single Pro substitution, resulted in higher stability without compromising native monomer fold or function. We propose that Pro substitution of interface β-strand residues is a viable strategy for generating functional monomers of dimeric, and potentially tetrameric and higher-order oligomeric proteins. PMID:24048001

Hydrophobic Coatings on Cotton Obtained by in Situ Plasma Polymerization of a Fluorinated Monomer in Ethanol Solutions.

PubMed

Molina, Ricardo; Teixidó, Josep Maria; Kan, Chi-Wai; Jovančić, Petar

2017-02-15

Plasma polymerization using hydrophobic monomers in the gas phase is a well-known technology to generate hydrophobic coatings. However, synthesis of functional hydrophobic coatings using plasma technology in liquids has not yet been accomplished. This work is consequently focused on polymerization of a liquid fluorinated monomer on cotton fabric initiated by atmospheric plasma in a dielectric barrier discharge configuration. Functional hydrophobic coatings on cotton were successfully achieved using in situ atmospheric plasma-initiated polymerization of fluorinated monomer dissolved in ethanol. Gravimetric measurements reveal that the amount of polymer deposited on cotton substrates can be modulated with the concentration of monomer in ethanol solution, and cross-linking reactions occur during plasma polymerization of a fluorinated monomer even without the presence of a cross-linking agent. FTIR and XPS analysis were used to study the chemical composition of hydrophobic coatings and to get insights into the physicochemical processes involved in plasma treatment. SEM analysis reveals that at high monomer concentration, coatings possess a three-dimensional pattern with a characteristic interconnected porous network structure. EDX analysis reveals that plasma polymerization of fluorinated monomers takes place preferentially at the surface of cotton fabric and negligible polymerization takes place inside the cotton fabric. Wetting time measurements confirm the hydrophobicity of cotton coatings obtained although equilibrium moisture content was slightly decreased. Additionally, the abrasion behavior and resistance to washing of plasma-coated cotton has been evaluated.

Lessons that Bear Repeating and Repeating that Bears Lessons: An Interdisciplinary Unit on Principles of Minimalism in Modern Music, Art, and Poetry (Grades 4-8)

ERIC Educational Resources Information Center

Smigel, Eric; McDonald, Nan L.

2012-01-01

This theory-to-practice article focuses on interdisciplinary classroom activities based on principles of minimalism in modern music, art, and poetry. A lesson sequence was designed for an inner-city Grades 4 and 5 general classroom of English language learners, where the unit was taught, assessed, and documented by the authors. Included in the…

Photochemically Synthesized Polyimides

NASA Technical Reports Server (NTRS)

Meador, Michael A.; Tyson, Daniel S.

2008-01-01

An alternative to the conventional approach to synthesis of polyimides involves the use of single monomers that are amenable to photopolymerization. Heretofore, the synthesis of polyimides has involved multiple-monomer formulations and heating to temperatures that often exceed 250 C. The present alternative approach enables synthesis under relatively mild conditions that can include room temperature. The main disadvantages of the conventional approach are the following: Elevated production temperatures can lead to high production costs and can impart thermal stresses to the final products. If the proportions of the multiple monomeric ingredients in a given batch are not exactly correct, the molecular weight and other physical properties of the final material could be reduced from their optimum or desired values. To be useful in the alternative approach, a monomer must have a molecular structure tailored to exploit Diels-Alder trapping of a photochemically generated ortho-quinodimethane. (In a Diels-Alder reaction, a diene combines with a dienophile to form molecules that contain six-membered rings.) In particular, a suitable monomer (see figure) contains ortho-methylbenzophenone connected to a dienophile (in this case, a maleimide) through a generic spacer group. Irradiation with ultraviolet light gives rise to a photochemical intermediate the aforementioned ortho-quinodimethane from the ortho-methylbenzophenone. This group may react with the dienophile on another such monomer molecule to produce an oligomer that, in turn may react in a stepgrowth manner to produce a polyimide. This approach offers several advantages in addition to those mentioned above: The monomer can be stored for a long time because it remains unreactive until exposed to light. Because the monomer is the only active starting ingredient, there is no need for mixing, no concern for ensuring correct proportions of monomers, and the purity of the final product material is inherently high. The use of solvents is optional: The synthesis can be performed using the neat monomer or the monomer mixed with one or more solvent(s) in dilute or concentrated solution. The solubility of the monomer and the physical and chemical properties of the final polymer can be tailored through selection of the spacer group.

Tempered mlo broad-spectrum resistance to barley powdery mildew in an Ethiopian landrace

PubMed Central

Ge, Xintian; Deng, Weiwei; Lee, Zheng Zhou; Lopez-Ruiz, Francisco J.; Schweizer, Patrick; Ellwood, Simon R.

2016-01-01

Recessive mutations in the Mlo gene confer broad spectrum resistance in barley (Hordeum vulgare) to powdery mildew (Blumeria graminis f. sp. hordei), a widespread and damaging disease. However, all alleles discovered to date also display deleterious pleiotropic effects, including the naturally occurring mlo-11 mutant which is widely deployed in Europe. Recessive resistance was discovered in Eth295, an Ethiopian landrace, which was developmentally controlled and quantitative without spontaneous cell wall appositions or extensive necrosis and loss of photosynthetic tissue. This resistance is determined by two copies of the mlo-11 repeat units, that occur upstream to the wild-type Mlo gene, compared to 11–12 in commonly grown cultivars and was designated mlo-11 (cnv2). mlo-11 repeat unit copy number-dependent DNA methylation corresponded with cytological and macroscopic phenotypic differences between copy number variants. Sequence data indicated mlo-11 (cnv2) formed via recombination between progenitor mlo-11 repeat units and the 3′ end of an adjacent stowaway MITE containing region. mlo-11 (cnv2) is the only example of a moderated mlo variant discovered to date and may have arisen by natural selection against the deleterious effects of the progenitor mlo-11 repeat unit configuration. PMID:27404990

Testing the Predictive Capability of the High-Fidelity Generalized Method of Cells Using an Efficient Reformulation

NASA Technical Reports Server (NTRS)

Arnold, Steven M. (Technical Monitor); Bansal, Yogesh; Pindera, Marek-Jerzy

2004-01-01

The High-Fidelity Generalized Method of Cells is a new micromechanics model for unidirectionally reinforced periodic multiphase materials that was developed to overcome the original model's shortcomings. The high-fidelity version predicts the local stress and strain fields with dramatically greater accuracy relative to the original model through the use of a better displacement field representation. Herein, we test the high-fidelity model's predictive capability in estimating the elastic moduli of periodic composites characterized by repeating unit cells obtained by rotation of an infinite square fiber array through an angle about the fiber axis. Such repeating unit cells may contain a few or many fibers, depending on the rotation angle. In order to analyze such multi-inclusion repeating unit cells efficiently, the high-fidelity micromechanics model's framework is reformulated using the local/global stiffness matrix approach. The excellent agreement with the corresponding results obtained from the standard transformation equations confirms the new model's predictive capability for periodic composites characterized by multi-inclusion repeating unit cells lacking planes of material symmetry. Comparison of the effective moduli and local stress fields with the corresponding results obtained from the original Generalized Method of Cells dramatically highlights the original model's shortcomings for certain classes of unidirectional composites.

Mechanical properties of regular porous biomaterials made from truncated cube repeating unit cells: Analytical solutions and computational models.

PubMed

Hedayati, R; Sadighi, M; Mohammadi-Aghdam, M; Zadpoor, A A

2016-03-01

Additive manufacturing (AM) has enabled fabrication of open-cell porous biomaterials based on repeating unit cells. The micro-architecture of the porous biomaterials and, thus, their physical properties could then be precisely controlled. Due to their many favorable properties, porous biomaterials manufactured using AM are considered as promising candidates for bone substitution as well as for several other applications in orthopedic surgery. The mechanical properties of such porous structures including static and fatigue properties are shown to be strongly dependent on the type of the repeating unit cell based on which the porous biomaterial is built. In this paper, we study the mechanical properties of porous biomaterials made from a relatively new unit cell, namely truncated cube. We present analytical solutions that relate the dimensions of the repeating unit cell to the elastic modulus, Poisson's ratio, yield stress, and buckling load of those porous structures. We also performed finite element modeling to predict the mechanical properties of the porous structures. The analytical solution and computational results were found to be in agreement with each other. The mechanical properties estimated using both the analytical and computational techniques were somewhat higher than the experimental data reported in one of our recent studies on selective laser melted Ti-6Al-4V porous biomaterials. In addition to porosity, the elastic modulus and Poisson's ratio of the porous structures were found to be strongly dependent on the ratio of the length of the inclined struts to that of the uninclined (i.e. vertical or horizontal) struts, α, in the truncated cube unit cell. The geometry of the truncated cube unit cell approaches the octahedral and cube unit cells when α respectively approaches zero and infinity. Consistent with those geometrical observations, the analytical solutions presented in this study approached those of the octahedral and cube unit cells when α approached respectively 0 and infinity. Copyright © 2015 Elsevier B.V. All rights reserved.

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences.

PubMed

Kapila, R; Das, S; Srivastava, P S; Lakshmikumaran, M

1996-08-01

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

Absorbing states in a catalysis model with anti-Arrhenius behavior.

PubMed

de Andrade, M F; Figueiredo, W

2012-04-28

We study a model of heterogeneous catalysis with competitive reactions between two monomers A and B. We assume that reactions are dependent on temperature and follow an anti-Arrhenius mechanism. In this model, a monomer A can react with a nearest neighbor monomer A or B, however, reactions between monomers of type B are not allowed. We assume attractive interactions between nearest neighbor monomers as well as between monomers and the catalyst. Through mean-field calculations, at the level of site and pair approximations, and extensive Monte Carlo simulations, we determine the phase diagram of the model in the plane y(A) versus temperature, where y(A) is the probability that a monomer A reaches the catalyst. The model exhibits absorbing and active phases separated by lines of continuous phase transitions. We calculate the static, dynamic, and spreading exponents of the model, and despite the absorbing state be represented by many different microscopic configurations, the model belongs to the directed percolation universality class in two dimensions. Both reaction mechanisms, Arrhenius and anti-Arrhenius, give the same set of critical exponents and do not change the nature of the universality class of the catalytic models.

Enzymatic Specific Production and Chemical Functionalization of Phenylpropanone Platform Monomers from Lignin

PubMed Central

Hasegawa, Ryoichi; Kurosawa, Kanako; Maeda, Allyn H.; Koizumi, Toshio; Nishimura, Hiroshi; Okada, Hitomi; Qu, Chen; Saito, Kaori; Watanabe, Takashi; Hatada, Yuji

2016-01-01

Abstract Enzymatic catalysis is an ecofriendly strategy for the production of high‐value low‐molecular‐weight aromatic compounds from lignin. Although well‐definable aromatic monomers have been obtained from synthetic lignin‐model dimers, enzymatic‐selective synthesis of platform monomers from natural lignin has not been accomplished. In this study, we successfully achieved highly specific synthesis of aromatic monomers with a phenylpropane structure directly from natural lignin using a cascade reaction of β‐O‐4‐cleaving bacterial enzymes in one pot. Guaiacylhydroxylpropanone (GHP) and the GHP/syringylhydroxylpropanone (SHP) mixture are exclusive monomers from lignin isolated from softwood (Cryptomeria japonica) and hardwood (Eucalyptus globulus). The intermediate products in the enzymatic reactions show the capacity to accommodate highly heterologous substrates at the substrate‐binding sites of the enzymes. To demonstrate the applicability of GHP as a platform chemical for bio‐based industries, we chemically generate value‐added GHP derivatives for bio‐based polymers. Together with these chemical conversions for the valorization of lignin‐derived phenylpropanone monomers, the specific and enzymatic production of the monomers directly from natural lignin is expected to provide a new stream in “white biotechnology” for sustainable biorefineries. PMID:27878983

Modification of the lithium metal surface by nonionic polyether surfactants. 2. Investigations with microelectrode voltammetry and in situ quartz crystal microbalance

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

Naoi, Katsuhiko; Mori, Mitsuhiro; Inoue, Masahiro

2000-03-01

Li metal has a high specific capacity, and films formed on the surface of Li metal must thus be stabilized in some way. The authors used a nonionic surfactant resembling poly(ethylene glycol) dimethyl ether (PEGDME) to achieve this stabilization. The success of this stabilization as a function of the molecular weight of the polyether (Mw 90 to 2,000) was investigated with microelectrode voltammetry (MEV) and the in situ quartz crystal microbalance method. In 1 mol dm{sup {minus}3} LiClO{sub 4}/PC, the activation energy ({Delta}G{asterisk}) for charge transfer of the Li/Li{sup +} couple (as obtained from MEV measurements) increased by 11 tomore » 60 kJ mol{sup {minus}1} as the molecular weight (g mol{sup {minus}1}) was increased from 90 to 400, and remained almost unchanged as it was increased from 400 to 2,000. The variation of {Delta}G{asterisk} indicates that Li ions were preferentially coordinated with ethylene oxide (EO) chains and were taken into the helix structures of the EO chains when PEGDME (which possesses repeated EO units in the range of 180 to 2,000 Mw) was added to electrolytes. As for the stoichiometry, the surface film formed in the presence of PEGDME with Mw {ge} 180 causes no accumulation during the Li deposition and dissolution cycles. Such a stable film including a few EO units eventually functioned as a uniform path for Li ions in both deposition and dissolution processes. the extent of inactivation of the deposited Li for various molecular weights of the PEGDME was consistent with the change of solvation state and surface chemistry. Namely, the inactivation for the PEGDME-added (with Mw {ge} 180) systems was diminished markedly (by ca. 40 to 65%) as compared with surfactant-free and monomer (Mw 90)-added systems.« less

21 CFR 181.32 - Acrylonitrile copolymers and resins.

Code of Federal Regulations, 2011 CFR

2011-04-01

... acrylonitrile monomer extraction for finished food-contact articles, determined by using the method of analysis titled “Gas-Solid Chromatographic Procedure for Determining Acrylonitrile Monomer in Acrylonitrile... or fat. (c) Acrylonitrile monomer may present a hazard to health when ingested. Accordingly, any food...

Compounds containing meta-biphenylenedioxy moieties and polymers therefrom

NASA Technical Reports Server (NTRS)

St.clair, Terry L. (Inventor); Pratt, John Richard (Inventor)

1993-01-01

Two monomers containing meta-biphenylenedioxy moieties were prepared. One monomer, a diamine, is used to prepare polyimide, polyamide, and epoxy polymers. The other monomer, a dianhydride, was used to prepare polyimide polymers. These polymers are used to make films, coatings, and selective membranes.

Process for Preparing Epoxy-Reinforced Silica Aerogels

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B (Inventor)

2016-01-01

One-pot reaction process for preparing epoxy-reinforced monolithic silica aerogels comprising the reaction of at least one silicon compound selected from the group consisting of alkoxysilanes, orthosilicates and combination thereof in any ratio with effective amounts of an epoxy monomer and an aminoalkoxy silane to obtain an epoxy monomer-silica sol in solution, subsequently preparing an epoxy-monomer silica gel from said silica sol solution followed by initiating polymerization of the epoxy monomer to obtain the epoxy-reinforced monolithic silica aerogel.

Prevalence of Huntington's disease gene CAG trinucleotide repeat alleles in patients with bipolar disorder.

PubMed

Ramos, Eliana Marisa; Gillis, Tammy; Mysore, Jayalakshmi S; Lee, Jong-Min; Alonso, Isabel; Gusella, James F; Smoller, Jordan W; Sklar, Pamela; MacDonald, Marcy E; Perlis, Roy H

2015-06-01

Huntington's disease is a neurodegenerative disorder characterized by motor, cognitive, and psychiatric symptoms that are caused by huntingtin gene (HTT) CAG trinucleotide repeat alleles of 36 or more units. A greater than expected prevalence of incompletely penetrant HTT CAG repeat alleles observed among individuals diagnosed with major depressive disorder raises the possibility that another mood disorder, bipolar disorder, could likewise be associated with Huntington's disease. We assessed the distribution of HTT CAG repeat alleles in a cohort of individuals with bipolar disorder. HTT CAG allele sizes from 2,229 Caucasian individuals diagnosed with DSM-IV bipolar disorder were compared to allele sizes in 1,828 control individuals from multiple cohorts. We found that HTT CAG repeat alleles > 35 units were observed in only one of 4,458 chromosomes from individuals with bipolar disorder, compared to three of 3,656 chromosomes from control subjects. These findings do not support an association between bipolar disorder and Huntington's disease. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The organization of repeating units in mitochondrial DNA from yeast petite mutants.

PubMed

Bos, J L; Heyting, C; Van der Horst, G; Borst, P

1980-04-01

We have reinvestigated the linkage orientation of repeating units in mtDNAs of yeast ρ(-) petite mutants containing an inverted duplication. All five petite mtDNAs studied contain a continuous segment of wild-type mtDNA, part of which is duplicated and present in inverted form in the repeat. We show by restriction enzyme analysis that the non-duplicated segments between the inverted duplications are present in random orientation in all five petite mtDNAs. There is no segregation of sub-types with unique orientation. We attribute this to the high rate of intramolecular recombination between the inverted duplications. The results provide additional evidence for the high rate of recombination of yeast mtDNA even in haploid ρ(-) petite cells.We conclude that only two types of stable sequence organization exist in petite mtDNA: petites without an inverted duplication have repeats linked in straight head-to-tail arrangement (abcabc); petites with an inverted duplication have repeats in which the non-duplicated segments are present in random orientation.

Low-Resolution Structure of the Full-Length Barley (Hordeum vulgare) SGT1 Protein in Solution, Obtained Using Small-Angle X-Ray Scattering

PubMed Central

Taube, Michał; Pieńkowska, Joanna R.; Jarmołowski, Artur; Kozak, Maciej

2014-01-01

SGT1 is an evolutionarily conserved eukaryotic protein involved in many important cellular processes. In plants, SGT1 is involved in resistance to disease. In a low ionic strength environment, the SGT1 protein tends to form dimers. The protein consists of three structurally independent domains (the tetratricopeptide repeats domain (TPR), the CHORD- and SGT1-containing domain (CS), and the SGT1-specific domain (SGS)), and two less conserved variable regions (VR1 and VR2). In the present study, we provide the low-resolution structure of the barley (Hordeum vulgare) SGT1 protein in solution and its dimer/monomer equilibrium using small-angle scattering of synchrotron radiation, ab-initio modeling and circular dichroism spectroscopy. The multivariate curve resolution least-square method (MCR-ALS) was applied to separate the scattering data of the monomeric and dimeric species from a complex mixture. The models of the barley SGT1 dimer and monomer were formulated using rigid body modeling with ab-initio structure prediction. Both oligomeric forms of barley SGT1 have elongated shapes with unfolded inter-domain regions. Circular dichroism spectroscopy confirmed that the barley SGT1 protein had a modular architecture, with an α-helical TPR domain, a β-sheet sandwich CS domain, and a disordered SGS domain separated by VR1 and VR2 regions. Using molecular docking and ab-initio protein structure prediction, a model of dimerization of the TPR domains was proposed. PMID:24714665

Spectrophotometric determination of fluoxetine by molecularly imprinted polypyrrole and optimization by experimental design, artificial neural network and genetic algorithm.

PubMed

Nezhadali, Azizollah; Motlagh, Maryam Omidvar; Sadeghzadeh, Samira

2018-02-05

A selective method based on molecularly imprinted polymer (MIP) solid-phase extraction (SPE) using UV-Vis spectrophotometry as a detection technique was developed for the determination of fluoxetine (FLU) in pharmaceutical and human serum samples. The MIPs were synthesized using pyrrole as a functional monomer in the presence of FLU as a template molecule. The factors that affecting the preparation and extraction ability of MIP such as amount of sorbent, initiator concentration, the amount of monomer to template ratio, uptake shaking rate, uptake time, washing buffer pH, take shaking rate, Taking time and polymerization time were considered for optimization. First a Plackett-Burman design (PBD) consists of 12 randomized runs were applied to determine the influence of each factor. The other optimization processes were performed using central composite design (CCD), artificial neural network (ANN) and genetic algorithm (GA). At optimal condition the calibration curve showed linearity over a concentration range of 10 -7 -10 -8 M with a correlation coefficient (R 2 ) of 0.9970. The limit of detection (LOD) for FLU was obtained 6.56×10 -9 M. The repeatability of the method was obtained 1.61%. The synthesized MIP sorbent showed a good selectivity and sensitivity toward FLU. The MIP/SPE method was used for the determination of FLU in pharmaceutical, serum and plasma samples, successfully. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystal Structure of a Bacterial Signal Peptide Peptidase

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

Kim,A.; Oliver, D.; Paetzel, M.

2008-01-01

Signal peptide peptidase (Spp) is the enzyme responsible for cleaving the remnant signal peptides left behind in the membrane following Sec-dependent protein secretion. Spp activity appears to be present in all cell types, eukaryotic, prokaryotic and archaeal. Here we report the first structure of a signal peptide peptidase, that of the Escherichia coli SppA (SppAEC). SppAEC forms a tetrameric assembly with a novel bowl-shaped architecture. The bowl has a dramatically hydrophobic interior and contains four separate active sites that utilize a Ser/Lys catalytic dyad mechanism. Our structural analysis of SppA reveals that while in many Gram-negative bacteria as well asmore » characterized plant variants, a tandem duplication in the protein fold creates an intact active site at the interface between the repeated domains, other species, particularly Gram-positive and archaeal organisms, encode half-size, unduplicated SppA variants that could form similar oligomers to their duplicated counterparts, but using an octamer arrangement and with the catalytic residues provided by neighboring monomers. The structure reveals a similarity in the protein fold between the domains in the periplasmic Ser/Lys protease SppA and the monomers seen in the cytoplasmic Ser/His/Asp protease ClpP. We propose that SppA may, in addition to its role in signal peptide hydrolysis, have a role in the quality assurance of periplasmic and membrane-bound proteins, similar to the role that ClpP plays for cytoplasmic proteins.« less

Monolithic column based on a poly(glycidyl methacrylate-co-4-vinylphenylboronic acid-co-ethylene dimethacrylate) copolymer for capillary liquid chromatography of small molecules and proteins.

PubMed

Lin, Zian; Huang, Hui; Sun, Xiaobo; Lin, Yao; Zhang, Lan; Chen, Guonan

2012-07-13

A new polymer monolith with three modes of reverse-phase, hydrophilic and cation-exchange interaction was synthesized in 100 μm i.d. fused-silica capillary by in situ polymerization procedure. The pre-polymerization mixture consisted of glycidyl methacrylate (GMA) and 4-vinylphenylboronic acid (VPBA) as bifunctional monomers, ethylene dimethacrylate (EDMA) as crosslinker, 1,4-butanediol (BDO) and diethylene glycol (DEG) as binary porogenic solvents, and azobisisobutyronitrile (AIBN) as initiator. The resulting poly(GMA-co-VPBA-co-EDMA) monolith showed a relatively homogeneous monolithic structure, good permeability and mechanical stability. Different ratios of monomers and porogens were used for optimizing the properties of monolithic column. The column performance was assessed by the separation of a series of neutral solutes, charge solutes, phenols and anilines. Compared with poly(GMA-co-EDMA) monolith, the proposed monolith exhibited more flexible adjustment of selectivity in terms of hydrophobic, hydrophilic, as well as cation-exchange interaction in the same chromatographic conditions. High column efficiencies for benzene derivatives with 70,000-102,000 theoretical plates/m could be obtained at a linear velocity of 0.265 mm/s. The run-to-run, column-to-column, and batch-to-batch repeatabilities of the retention times were less than 8.23%. Additionally, the purposed monolith was also applied to efficient separation of alkaloids and proteins for demonstrating its potential in biomolecule separation. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Aminothienopyridazines and Methylene Blue Affect Tau Fibrillization via Cysteine Oxidation*

PubMed Central

Crowe, Alex; James, Michael J.; Lee, Virginia M.-Y.; Smith, Amos B.; Trojanowski, John Q.; Ballatore, Carlo; Brunden, Kurt R.

2013-01-01

Alzheimer disease and several other neurodegenerative disorders are characterized by the accumulation of intraneuronal fibrils comprised of the protein Tau. Tau is normally a soluble protein that stabilizes microtubules, with splice isoforms that contain either three (3-R) or four (4-R) microtubule binding repeats. The formation of Tau fibrils is thought to result in neuronal damage, and inhibitors of Tau fibrillization may hold promise as therapeutic agents. The process of Tau fibrillization can be replicated in vitro, and a number of small molecules have been identified that inhibit Tau fibril formation. However, little is known about how these molecules affect Tau fibrillization. Here, we examined the mechanism by which the previously described aminothieno pyridazine (ATPZ) series of compounds inhibit Tau fibrillization. Active ATPZs were found to promote the oxidation of the two cysteine residues within 4-R Tau by a redox cycling mechanism, resulting in the formation of a disulfide-containing compact monomer that was refractory to fibrillization. Moreover, the ATPZs facilitated intermolecular disulfide formation between 3-R Tau monomers, leading to dimers that were capable of fibrillization. The ATPZs also caused cysteine oxidation in molecules unrelated to Tau. Interestingly, methylene blue, an inhibitor of Tau fibrillization under evaluation in Alzheimer disease clinical trials, caused a similar oxidation of cysteines in Tau and other molecules. These findings reveal that the ATPZs and methylene blue act by a mechanism that may affect their viability as potential therapeutic agents. PMID:23443659

Processes for microemulsion polymerization employing novel microemulsion systems

DOEpatents

Beckman, Eric J.; Smith, Richard D.; Fulton, John L.

1990-06-12

This invention is directed to a microemulsion system comprising a first phase including a low-polarity fluid material which is a gas at standard temperature and pressure, and which has a cloud-point density. It also includes a second phase including a polar fluid, typically water, a monomer, preferably a monomer soluble in the polar fluid, and a microemulsion promoter for facilitating the formation of micelles including the monomer in the system. In the subject process, micelles including the monomer are formed in the first phase. A polymerization initiator is introduced into the micelles in the microemulsion system. The monomer is then polymerized in the micelles, preferably in the core of the micelle, to produce a polymeric material having a relatively high molecular weight.

Biodegradation of dimethylsilanediol in soils.

PubMed Central

Sabourin, C L; Carpenter, J C; Leib, T K; Spivack, J L

1996-01-01

The biodegradation potential of [14C]dimethylsilanediol, the monomer unit of polydimethylsiloxane, in soils was investigated. Dimethylsilanediol was found to be biodegraded in all of the tested soils, as monitored by the production of 14CO2. When 2-propanol was added to the soil as a carbon source in addition to [14C]dimethylsilanediol, the production of 14CO2 increased. A method for the selection of primary substrates that support cometabolic degradation of a target compound was developed. By this method, the activity observed in the soils was successfully transferred to liquid culture. A fungus, Fusarium oxysporum Schlechtendahl, and a bacterium, an Arthrobacter species, were isolated from two different soils, and both microorganisms were able to cometabolize [14C]dimethylsilanediol to 14CO2 in liquid culture. In addition, the Arthrobacter sp. that was isolated grew on dimethylsulfone, and we believe that this is the first reported instance of a microorganism using dimethylsulfone as its primary carbon source. Previous evidence has shown that polydimethylsiloxane is hydrolyzed in soil to the monomer, dimethylsilanediol. Now, biodegradation of dimethylsilanediol in soil has been demonstrated. PMID:8953708

Proanthocyanidin profile of cowpea (Vigna unguiculata) reveals catechin-O-glucoside as the dominant compound.

PubMed

Ojwang, Leonnard O; Yang, Liyi; Dykes, Linda; Awika, Joseph

2013-08-15

Proanthocyanidin (PA) profile and content can have important nutritional and health implications on plant foods. Six diverse cowpea phenotypes (black, red, green, white, light-brown and golden-brown) were investigated for PA composition using normal-phase HPLC and reversed-phase UPLC-TQD-MS. Catechin and (epi)afzelechin were the major flavan-3-ol units. Unusual composition was observed in all cowpea phenotypes with significant degrees of glycosylation in the monomers and dimers. The PA content of cowpea (dry basis) ranged between 2.2 and 6.3 mg/g. Monomeric flavan-3-ols were the largest group of PA (36-69%) in cowpea, with catechin-7-O-glucoside accounting for most (about 88%) of the monomers. The oligomers with degree of polymerization (DP) 2-4 ranged from 0.41 to 1.3 mg/g (15-20%), whereas DP>10 polymers accounted for only 13.5% of PA. Future studies that highlight the impact of the unusual cowpea PA profile on nutritional and bioactive properties of this important legume are warranted. Copyright © 2013 Elsevier Ltd. All rights reserved.

Rationalization and in vitro modeling of the chemical mechanisms of the enzymatic oxidation of phenolic compounds in planta: from flavonols and stilbenoids to lignins.

PubMed

Cottyn, Betty; Kollmann, Albert; Waffo-Teguo, Pierre; Ducrot, Paul-Henri

2011-06-20

Enzymatic oxidation of phenolic compounds is a widespread phenomenon in plants. It is responsible for the formation of many oligomers and polymers, which are generally described as the result of a combinatorial coupling of the different radicals formed through oxidation of the phenol group and delocalization of the radical. We focused our interest on several phenolic compounds that are present in plants and known to form, under enzymatic oxidation, oligomers with different type of linkages between monomers. To explain this diversity of inter-monomer linkages and their variation according to the experimental procedure used for the enzymatic oxidation, we report an alternative mechanistic pathway involving dismutation of the radicals, leading to the formation of carbocations which, thereafter, react with nucleophilic species present in the medium. This alternative pathway allows the understanding of peculiar linkages between monomeric units in the oligomer and offers new insights for understanding the formation of phenolic biopolymers in plants. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Toxicity of an α-Pore-forming Toxin Depends on the Assembly Mechanism on the Target Membrane as Revealed by Single Molecule Imaging*

PubMed Central

Subburaj, Yamunadevi; Ros, Uris; Hermann, Eduard; Tong, Rudi; García-Sáez, Ana J.

2015-01-01

α-Pore-forming toxins (α-PFTs) are ubiquitous defense tools that kill cells by opening pores in the target cell membrane. Despite their relevance in host/pathogen interactions, very little is known about the pore stoichiometry and assembly pathway leading to membrane permeabilization. Equinatoxin II (EqtII) is a model α-PFT from sea anemone that oligomerizes and forms pores in sphingomyelin-containing membranes. Here, we determined the spatiotemporal organization of EqtII in living cells by single molecule imaging. Surprisingly, we found that on the cell surface EqtII did not organize into a unique oligomeric form. Instead, it existed as a mixture of oligomeric species mostly including monomers, dimers, tetramers, and hexamers. Mathematical modeling based on our data supported a new model in which toxin clustering happened in seconds and proceeded via condensation of EqtII dimer units formed upon monomer association. Furthermore, altering the pathway of EqtII assembly strongly affected its toxic activity, which highlights the relevance of the assembly mechanism on toxicity. PMID:25525270

The low-lying electronic states of pentacene and their roles in singlet fission.

PubMed

Zeng, Tao; Hoffmann, Roald; Ananth, Nandini

2014-04-16

We present a detailed study of pentacene monomer and dimer that serves to reconcile extant views of its singlet fission. We obtain the correct ordering of singlet excited-state energy levels in a pentacene molecule (E (S1) < E (D)) from multireference calculations with an appropriate active orbital space and dynamical correlation being incorporated. In order to understand the mechanism of singlet fission in pentacene, we use a well-developed diabatization scheme to characterize the six low-lying singlet states of a pentacene dimer that approximates the unit cell structure of crystalline pentacene. The local, single-excitonic diabats are not directly coupled with the important multiexcitonic state but rather mix through their mutual couplings with one of the charge-transfer configurations. We analyze the mixing of diabats as a function of monomer separation and pentacene rotation. By defining an oscillator strength measure of the coherent population of the multiexcitonic diabat, essential to singlet fission, we find this population can, in principle, be increased by small compression along a specific crystal direction.

Synthesis of Poly(N-isopropylacrylamide) Microcapsules for Drug Delivery Applications via UV Aerosol Photopolymerization

NASA Astrophysics Data System (ADS)

Roberson, Nicole; Denmark, Daniel; Witanachchi, Sarath

Hybrid drug delivery systems composed of thermoresponsive polymers and magnetic nanoparticles have been developed using chemical methods to deliver controlled amounts of a biotherapeutic to target tissue. These methods can be expensive, time intensive, and produce impure composites due to the use of surfactants during polymer synthesis. In this study, UV aerosol photopolymerization is used to synthesize N-isoplopylacrylamide (NIPAM) monomers, N,N-methylenebisacrylamide (MBA) crosslinker, and irgacure 2959 photoinitiator into the transporting microcapsule for drug delivery. The method of UV aerosol photopolymerization allows for the continuous, cost effective, and time efficient synthesis of a high concentration of pure polymers in a short amount of time; toxic surfactants are not necessary. Optimal NIPAM monomer, MBA crosslinker, and irgacure 2959 photoinitiator concentrations were tested and analyzed to synthesize a microcapsule with optimal conditions for controlled drug delivery. Scanning Electron Microscope (SEM) imaging reveals that synthesis of polymer microcapsules of about 30 micrometers in size is effective through UV aerosol photopolymerization. Findings will contribute greatly to the field of emergency medicine. This work was supported by the United States Army (Grant No. W81XWH1020101/3349).

Copper(I)-induced amplification of a [2]catenane in a virtual dynamic library of macrocyclic alkenes.

PubMed

Berrocal, José Augusto; Nieuwenhuizen, Marko M L; Mandolini, Luigi; Meijer, E W; Di Stefano, Stefano

2014-08-28

Olefin cross-metathesis of diluted dichloromethane solutions (≤0.15 M) of the 28-membered macrocyclic alkene C1, featuring a 1,10-phenanthroline moiety in the backbone, as well as of catenand 1, composed of two identical interlocked C1 units, generates families of noninterlocked oligomers Ci. The composition of the libraries is strongly dependent on the monomer concentration, but independent of whether C1 or 1 is used as feedstock, as expected for truly equilibrated systems. Accordingly, the limiting value 0.022 M approached by the equilibrium concentration of C1 when the total monomer concentration approaches the critical value, as predicted by the Jacobson-Stockmayer theory, provides a reliable estimate of the thermodynamically effective molarity. Catenand 1 behaves as a virtual component of the dynamic libraries, in that there is no detectable trace of its presence in the equilibrated mixtures, but becomes the major component - in the form of its copper(I) complex - when olefin cross-metathesis is carried out in the presence of a copper(I) salt.

Hierarchical on-surface synthesis and electronic structure of carbonyl-functionalized one- and two-dimensional covalent nanoarchitectures

NASA Astrophysics Data System (ADS)

Steiner, Christian; Gebhardt, Julian; Ammon, Maximilian; Yang, Zechao; Heidenreich, Alexander; Hammer, Natalie; Görling, Andreas; Kivala, Milan; Maier, Sabine

2017-03-01

The fabrication of nanostructures in a bottom-up approach from specific molecular precursors offers the opportunity to create tailored materials for applications in nanoelectronics. However, the formation of defect-free two-dimensional (2D) covalent networks remains a challenge, which makes it difficult to unveil their electronic structure. Here we report on the hierarchical on-surface synthesis of nearly defect-free 2D covalent architectures with carbonyl-functionalized pores on Au(111), which is investigated by low-temperature scanning tunnelling microscopy in combination with density functional theory calculations. The carbonyl-bridged triphenylamine precursors form six-membered macrocycles and one-dimensional (1D) chains as intermediates in an Ullmann-type coupling reaction that are subsequently interlinked to 2D networks. The electronic band gap is narrowed when going from the monomer to 1D and 2D surface-confined π-conjugated organic polymers comprising the same building block. The significant drop of the electronic gap from the monomer to the polymer confirms an efficient conjugation along the triphenylamine units within the nanostructures.

Chitosan in Molecularly-Imprinted Polymers: Current and Future Prospects.

PubMed

Xu, Long; Huang, Yun-An; Zhu, Qiu-Jin; Ye, Chun

2015-08-07

Chitosan is widely used in molecular imprinting technology (MIT) as a functional monomer or supporting matrix because of its low cost and high contents of amino and hydroxyl functional groups. The various excellent properties of chitosan, which include nontoxicity, biodegradability, biocompatibility, and attractive physical and mechanical performances, make chitosan a promising alternative to conventional functional monomers. Recently, chitosan molecularly-imprinted polymers have gained considerable attention and showed significant potential in many fields, such as curbing environmental pollution, medicine, protein separation and identification, and chiral-compound separation. These extensive applications are due to the polymers' desired selectivity, physical robustness, and thermal stability, as well as their low cost and easy preparation. Cross-linkers, which fix the functional groups of chitosan around imprinted molecules, play an important role in chitosan molecularly-imprinted polymers. This review summarizes the important cross-linkers of chitosan molecularly-imprinted polymers and illustrates the cross-linking mechanism of chitosan and cross-linkers based on the two glucosamine units. Finally, some significant attempts to further develop the application of chitosan in MIT are proposed.

Polyimides containing meta-biphenylenedioxy moieties and articles prepared therefrom

NASA Technical Reports Server (NTRS)

St.clair, Terry L. (Inventor); Pratt, Richard (Inventor)

1995-01-01

Two monomers containing meta-biphenylenedioxy moieties were prepared. One monomer, a diamine, is used to prepare polyimide, polyamide, and epoxy polymers. The other monomer, a dianhydride, was used to prepared polyimide polymers. These polymers are used to make films, coatings, and selective membranes.

Effect of a Polymercaptan Material on the Electro-Optical Properties of Polymer-Dispersed Liquid Crystal Films.

PubMed

Sun, Yujian; Zhang, Cuihong; Zhou, Le; Fang, Hua; Huang, Jianhua; Ma, Haipeng; Zhang, Yi; Yang, Jie; Zhang, Lan-Ying; Song, Ping; Gao, Yanzi; Xiao, Jiumei; Li, Fasheng; Li, Kexuan

2016-12-30

Polymer-dispersed liquid crystal (PDLC) films were prepared by the ultraviolet-light-induced polymerization of photopolymerizable monomers in nematic liquid crystal/chiral dopant/thiol-acrylate reaction monomer composites. The effects of the chiral dopant and crosslinking agents on the electro-optical properties of the PDLC films were systematically investigate. While added the chiral dopant S811 into the PDLC films, the initial off-state transmittance of the films was decreased. It was found that the weight ratio among acrylate monomers, thiol monomer PETMP and the polymercaptan Capcure 3-800 showed great influence on the properties of the fabricated PDLC films because of the existence of competition between thiol-acrylate reaction and acrylate monomer polymerization reaction. While adding polymercaptans curing agent Capcure 3-800 with appropriate concentration into the PDLC system, lower driven voltage and higher contrast ratio were achieved. This made the polymer network and electro-optical properties of the PDLC films easily tunable by the introduction of the thiol monomers.

Conformational alteration in alpha-toxin from Staphylococcus aureus concomitant with the transformation of the water-soluble monomer to the membrane oligomer.

PubMed

Ikigai, H; Nakae, T

1985-07-16

The membrane-damaging alpha-toxin aggregate of Staphylococcus aureus was characterized physicochemically. The aggregate weight of the toxin formed by various methods appeared to be 6 times higher than the molecular weight of the monomer as determined by the laser light scattering technique, suggesting the presence of a hexamer in the membrane. The aggregates fluoresced 20 to 50% more than the monomer at 336 nm. Circular dichroism measurements revealed that both the monomer and the oligomer showed essentially beta-sheet structure with the maximum ellipticity about -8,400 deg.cm2.dmol-1 at 215 nm. Circular dichroism spectrum of the oligomers showed ellipticity difference of -6,600, -44 and +84 deg.cm2.dmol-1, at 200, 250 and 280 nm, respectively, compared with the monomer. All these results suggest that the conformational change in the toxin molecule occurs concomitant with the transformation of the water-soluble monomer to the membrane-embedded hexamer.

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of DHNA synthetase from Geobacillus kaustophilus

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

Kanaujia, Shankar Prasad; Ranjani, Chellamuthu Vasuki; Jeyakanthan, Jeyaraman

2007-02-01

DHNA synthetase from G. kaustophilus has been cloned, expressed, purified and crystallized. The aerobic Gram-positive bacterium Geobacillus kaustophilus is a bacillus species that was isolated from deep-sea sediment from the Mariana Trench. 1,4-Dihydroxy-2-naphthoate (DHNA) synthetase plays a vital role in the biosynthesis of menaquinone (vitamin K{sub 2}) in this bacterium. DHNA synthetase from Geobacillus kaustophilus was crystallized in the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 77.01, b = 130.66, c = 131.69 Å. The crystal diffracted to a resolution of 2.2 Å. Preliminary studies and molecular-replacement calculations reveal the presence of three monomers in the asymmetricmore » unit.« less

Structural study of the exopolysaccharide produced by a clinical isolate of Burkholderia cepacia.

PubMed

Cescutti, P; Bosco, M; Picotti, F; Impallomeni, G; Leitão, J H; Richau, J A; Sá-Correia, I

2000-07-14

The primary structure of the exopolysaccharide produced by a clinical isolate of the bacterium Burkholderia cepacia was studied by means of methylation analysis, selective degradation, NMR spectroscopy, and electrospray mass spectrometry. The resulting data showed that the parent repeating unit of the exopolysaccharide is a highly branched heptasaccharide with the following structure: Two acetyl groups are present per repeating unit, as noncarbohydrate substituents. Copyright 2000 Academic Press.

Intratypic variability of a tandem repeat locus within the DNA polymerase gene of human herpes simplex virus type 2.

PubMed

Sun, Yongjiang; Chan, Roy Kum Wah; Tan, Suat Hoon

2004-01-01

In this study, the irntratypic variability of a tandem repeat locus within the DNA polymerase (pol) gene of human herpes simplex virus type 2 (HSV2) was uncovered. The locus contained variable numbers of tandem dodecanucleotide (5'-GAC GAG GAC GGG-3') repetitive units. Our result showed that approximately 95% of analyzed HSV2 clinical isolates and the current GenBank HSV2 strains contained two copies of the repetitive units. From genital herpes specimens, three new HSV2 strains, which respectively contained 1, 3, and 4 copies of the repetitive units, were identified. This variable number of tandem repeat (VNTR) locus is absent in HSV1, and thus it also contributes to the intertypic variability of HSV1 and HSV2. The intratypic variability of the locus may be useful for HSV2 strain genotyping and this application is discussed.

Evaluation of Antimicrobial Efficiency of New Polymers Comprised by Covalently Attached and/or Electrostatically Bound Bacteriostatic Species, Based on Quaternary Ammonium Compounds.

PubMed

Kougia, Efstathia; Tselepi, Maria; Vasilopoulos, Gavriil; Lainioti, Georgia Ch; Koromilas, Nikos D; Druvari, Denisa; Bokias, Georgios; Vantarakis, Apostolos; Kallitsis, Joannis K

2015-12-01

In the present work a detailed study of new bacteriostatic copolymers with quaternized ammonium groups introduced in the polymer chain through covalent attachment or electrostatic interaction, was performed. Different copolymers have been considered since beside the active species, the hydrophobic/hydrophilic nature of the co-monomer was also evaluated in the case of covalently attached bacteriostatic groups, aiming at achieving permanent antibacterial activity. Homopolymers with quaternized ammonium/phosphonium groups were also tested for comparison reasons. The antimicrobial activity of the synthesized polymers after 3 and 24 h of exposure at 4 and 22 °C was investigated on cultures of Gram-negative (P. aeruginosa, E. coli) and Gram-positive (S. aureus, E. faecalis) bacteria. It was found that the combination of the hydrophilic monomer acrylic acid (AA), at low contents, with the covalently attached bacteriostatic group vinyl benzyl dimethylhexadecylammonium chloride (VBCHAM) in the copolymer P(AA-co-VBCHAM88), resulted in a high bacteriostatic activity against P. aeruginosa and E. faecalis (6 log reduction in certain cases). Moreover, the combination of covalently attached VBCHAM units with electrostatically bound cetyltrimethylammonium 4-styrene sulfonate (SSAmC16) units in the P(SSAmC16-co-VBCHAMx) copolymers led to efficient antimicrobial materials, especially against Gram-positive bacteria, where a log reduction between 4.9 and 6.2 was verified. These materials remain remarkably efficient even when they are incorporated in polysulfone membranes.

NMR characterization of altered lignins extracted from tobacco plants down-regulated for lignification enzymes cinnamylalcohol dehydrogenase and cinnamoyl-CoA reductase

PubMed Central

Ralph, John; Hatfield, Ronald D.; Piquemal, Joël; Yahiaoui, Nabila; Pean, Michel; Lapierre, Catherine; Boudet, Alain M.

1998-01-01

Homologous antisense constructs were used to down-regulate tobacco cinnamyl-alcohol dehydrogenase (CAD; EC 1.1.1.195) and cinnamoyl-CoA reductase (CCR; EC 1.2.1.44) activities in the lignin monomer biosynthetic pathway. CCR converts activated cinnamic acids (hydroxycinnamoyl–SCoAs) to cinnamaldehydes; cinnamaldehydes are then reduced to cinnamyl alcohols by CAD. The transformations caused the incorporation of nontraditional components into the extractable tobacco lignins, as evidenced by NMR. Isolated lignin of antisense-CAD tobacco contained fewer coniferyl and sinapyl alcohol-derived units that were compensated for by elevated levels of benzaldehydes and cinnamaldehydes. Products from radical coupling of cinnamaldehydes, particularly sinapaldehyde, which were barely discernible in normal tobacco, were major components of the antisense-CAD tobacco lignin. Lignin content was reduced in antisense-CCR tobacco, which displayed a markedly reduced vigor. That lignin contained fewer coniferyl alcohol-derived units and significant levels of tyramine ferulate. Tyramine ferulate is a sink for the anticipated build-up of feruloyl–SCoA, and may be up-regulated in response to a deficit of coniferyl alcohol. Although it is not yet clear whether the modified lignins are true structural components of the cell wall, the findings provide further indications of the metabolic plasticity of plant lignification. An ability to produce lignin from alternative monomers would open new avenues for manipulation of lignin by genetic biotechnologies. PMID:9788995

Manipulation of Guaiacyl and Syringyl Monomer Biosynthesis in an Arabidopsis Cinnamyl Alcohol Dehydrogenase Mutant Results in Atypical Lignin Biosynthesis and Modified Cell Wall Structure.

PubMed

Anderson, Nickolas A; Tobimatsu, Yuki; Ciesielski, Peter N; Ximenes, Eduardo; Ralph, John; Donohoe, Bryon S; Ladisch, Michael; Chapple, Clint

2015-08-01

Modifying lignin composition and structure is a key strategy to increase plant cell wall digestibility for biofuel production. Disruption of the genes encoding both cinnamyl alcohol dehydrogenases (CADs), including CADC and CADD, in Arabidopsis thaliana results in the atypical incorporation of hydroxycinnamaldehydes into lignin. Another strategy to change lignin composition is downregulation or overexpression of ferulate 5-hydroxylase (F5H), which results in lignins enriched in guaiacyl or syringyl units, respectively. Here, we combined these approaches to generate plants enriched in coniferaldehyde-derived lignin units or lignins derived primarily from sinapaldehyde. The cadc cadd and ferulic acid hydroxylase1 (fah1) cadc cadd plants are similar in growth to wild-type plants even though their lignin compositions are drastically altered. In contrast, disruption of CAD in the F5H-overexpressing background results in dwarfism. The dwarfed phenotype observed in these plants does not appear to be related to collapsed xylem, a hallmark of many other lignin-deficient dwarf mutants. cadc cadd, fah1 cadc cadd, and cadd F5H-overexpressing plants have increased enzyme-catalyzed cell wall digestibility. Given that these CAD-deficient plants have similar total lignin contents and only differ in the amounts of hydroxycinnamaldehyde monomer incorporation, these results suggest that hydroxycinnamaldehyde content is a more important determinant of digestibility than lignin content. © 2015 American Society of Plant Biologists. All rights reserved.

Proline substitution of dimer interface β-strand residues as a strategy for the design of functional monomeric proteins.

PubMed

Joseph, Prem Raj B; Poluri, Krishna Mohan; Gangavarapu, Pavani; Rajagopalan, Lavanya; Raghuwanshi, Sandeep; Richardson, Ricardo M; Garofalo, Roberto P; Rajarathnam, Krishna

2013-09-17

Proteins that exist in monomer-dimer equilibrium can be found in all organisms ranging from bacteria to humans; this facilitates fine-tuning of activities from signaling to catalysis. However, studying the structural basis of monomer function that naturally exists in monomer-dimer equilibrium is challenging, and most studies to date on designing monomers have focused on disrupting packing or electrostatic interactions that stabilize the dimer interface. In this study, we show that disrupting backbone H-bonding interactions by substituting dimer interface β-strand residues with proline (Pro) results in fully folded and functional monomers, by exploiting proline's unique feature, the lack of a backbone amide proton. In interleukin-8, we substituted Pro for each of the three residues that form H-bonds across the dimer interface β-strands. We characterized the structures, dynamics, stability, dimerization state, and activity using NMR, molecular dynamics simulations, fluorescence, and functional assays. Our studies show that a single Pro substitution at the middle of the dimer interface β-strand is sufficient to generate a fully functional monomer. Interestingly, double Pro substitutions, compared to single Pro substitution, resulted in higher stability without compromising native monomer fold or function. We propose that Pro substitution of interface β-strand residues is a viable strategy for generating functional monomers of dimeric, and potentially tetrameric and higher-order oligomeric proteins. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Virtual imprinting as a tool to design efficient MIPs for photosynthesis-inhibiting herbicides.

PubMed

Breton, Florent; Rouillon, Regis; Piletska, Elena V; Karim, Kal; Guerreiro, Antonio; Chianella, Iva; Piletsky, Sergey A

2007-04-15

Molecular modelling and computational screening were used to identify functional monomers capable of interacting with several different photosynthesis-inhibiting herbicides. The process involved the design of a virtual library of molecular models of functional monomers containing polymerizable residues and residues able to interact with the template through electrostatic, hydrophobic, Van der Waals forces and dipole-dipole interactions. Each of the entries in the virtual library was probed for its possible interactions with molecular models of the template molecules. It was anticipated that the monomers giving the highest binding score would represent good candidates for the preparation of affinity polymers. Strong interactions were computationally determined between acidic functional monomers like methacrylic acid (MAA) or itaconic acid (IA) with triazines, and between vinylimidazole with bentazone and bromoxynil. Nevertheless, weaker interactions were seen with phenylureas. The corresponding blank polymers were prepared using the selected monomers and tested in the solid phase extraction (SPE) of herbicides from chloroform solutions. A good correlation was found between the binding score of the monomers and the affinities of the corresponding polymers. The use of computationally designed blanks can potentially eliminate the need for molecular imprinting, (adding a template to the monomer mixture to create specific binding sites). Data also showed that some monomers have a natural selectivity for some herbicides, which can be further enhanced by imprinting. Thus, in regard to retention on the blank polymer, we can estimate if the resulting imprinted polymer will be effective or not.

The evolution and function of protein tandem repeats in plants.

PubMed

Schaper, Elke; Anisimova, Maria

2015-04-01

Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

A Cesium Rare-Earth Silicate Cs3 RESi6 O15 (RE=Dy-Lu, Y, In): The Parent of an Unusual Structural Class Featuring a Remarkable 57 Å Unit Cell Axis.

PubMed

Terry, Rylan; Vinton, Daniel; McMillen, Colin D; Kolis, Joseph W

2018-02-19

The structure of Cs 3 RESi 6 O 15 , where RE=Dy-Lu, Y, In, is unusual in that it contains octahedrally coordinated rare-earth ions; their relative orientation dictates the structure, as they rotate about the c-axis supported by the cyclic Si 6 O 15 framework. The repeat unit of the rotation is eight units generating a very long (ca. 57 Å) unit cell axis. This unusual repeat unit is created by the structural flexibility of the hexasilicate ring, which is in turn affected by the size of the rare earth ion as well as the size of alkali ion residing within the silicate layers. Previous work showed for the smaller Sc 3+ ion, the rotation of the octahedra is not sufficient to achieve closure at an integral repeat unit and an incommensurate structure results. The products are prepared as large, high quality single crystals using a high-temperature (650 °C) hydrothermal method with CsOH and F - mineralizers. The presence of fluoride is essential to the formation of the product. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monomers, polymers and articles containing the same from sugar derived compounds

DOEpatents

Gallagher, James; Reineke, Theresa; Hillmyer, Marc A.

2016-11-29

Disclosed herein are monomers formed by reacting a sugar derived compound(s) comprising a lactone and two hydroxyls with a compound(s) comprising an isocyanate and an acrylate or methacrylate. Polymers formed from such monomers, and articles formed from the polymers are also disclosed.

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7

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

Quesada, Odayme; Gurda, Brittney; Govindasamy, Lakshmanan

2007-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids have been produced which diffract X-rays to ∼3.0 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to ∼3.0 Å resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 Å in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R{sub merge} of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of amore » capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.« less

High-throughput approach for the identification of anilinium-based ionic liquids that are suitable for electropolymerisation.

PubMed

Abdelhamid, Muhammad E; Murdoch, Timothy; Greaves, Tamar L; O'Mullane, Anthony P; Snook, Graeme A

2015-07-21

We report the synthesis of new protic ionic liquids (PILs) based on aniline derivatives and the use of high-throughput (HT) techniques to screen possible candidates. In this work, a simple HT method was applied to rapidly screen different aniline derivatives against different acids in order to identify possible combinations that produce PILs. This was followed by repeating the HT process with a Chemspeed robotic synthesis platform for more accurate results. One of the successful combinations were then chosen to be synthesised on a larger scale for further analysis. The new PILs are of interest to the fields of ionic liquids, energy storage and especially, conducting polymers as they serve as solvents, electrolytes and monomers at the same time for possible electropolymerisation (i.e. a self-contained polymer precursor).

Photopatternable electrochromic materials from oxetane precursors.

PubMed

Leliège, Antoine; Barik, Satyananda; Skene, W G

2014-05-14

Conjugated thiophenoazomethine triads containing an acid sensitive oxetane group were prepared. The solution processable monomers were immobilized on glass and ITO coated glass substrates by photoacid induced cationic ring-opening polymerization (CROP) of the oxetane moiety. Photolithography using a photoacid generator and photosensitizer were used to pattern an electroactive polymer. Micro- and macroscale patterns ranging between 20 μm and 50 mm were possible with the electrochromic materials. The photopolymerized azomethine remained electroactive, and it could be repeatedly switched electrochemically between its neutral (mauve, λmax=535 nm) and oxidized (blue, λmax=585 nm) states without degradation. The electrochromic properties were evaluated in a simulated device where the colors were successfully cycled between blue (oxidized) and purple (neutral) states with applied biases of +0.6 V and -0.6 V vs Fc/Fc+ under ambient conditions without significant color fatigue or degradation.

21 CFR 177.1030 - Acrylonitrile/butadiene/styrene/methyl methacrylate copolymer.

Code of Federal Regulations, 2011 CFR

2011-04-01

... monomer content of the finished copolymer articles is not more than 11 parts per million as determined by a gas chromatographic method titled “Determination of Residual Acrylonitrile and Styrene Monomers... article shall yield not more than 0.0025 milligram per square inch of acrylonitrile monomer when exposed...

46 CFR 151.50-34 - Vinyl chloride (vinyl chloride monomer).

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 5 2011-10-01 2011-10-01 false Vinyl chloride (vinyl chloride monomer). 151.50-34 Section 151.50-34 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS... chloride (vinyl chloride monomer). (a) Copper, aluminum, magnesium, mercury, silver, and their alloys shall...

46 CFR 151.50-34 - Vinyl chloride (vinyl chloride monomer).

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 5 2010-10-01 2010-10-01 false Vinyl chloride (vinyl chloride monomer). 151.50-34... chloride (vinyl chloride monomer). (a) Copper, aluminum, magnesium, mercury, silver, and their alloys shall... equipment that may come in contact with vinyl chloride liquid or vapor. (b) Valves, flanges, and pipe...

Homogeneous reactions of hydrocarbons, silane, and chlorosilanes in radiofrequency plasmas at low pressures

NASA Technical Reports Server (NTRS)

Avni, R.; Carmi, U.; Inspektor, A.; Rosenthal, I.

1984-01-01

The ion-molecule and radical-molecule mechanisms are responsible for the dissociation of hydrocarbon, silane, and chlorosilane monomers and the formation of polymerized species, respectively, in an RF plasma discharge. In a plasma containing a mixture of monomer and argon the rate-determining step for both dissociation and polymerization is governed by an ion-molecule type of interaction. Adding hydrogen or ammonia to the monomer-argon mixture transforms the rate-determining step from an ion-molecule interaction to a radical-molecule interaction for both monomer dissociation and polymerization.

Status review of PMR polyimides. [Polymerization of Monomer Reactants

NASA Technical Reports Server (NTRS)

Serafini, T. T.

1979-01-01

In the NASA developed PMR (polymerization of monomer reactants) the reinforcing fibers are impregnated with a solution containing a mixture of monomers dissolved in a low boiling point alkyl alcohol solvent, with the monomers reacting in situ at elevated temperatures to form a thermo-oxidatively stable polyimide matrix. The current status of first and second generation PMR polyimides is reviewed, considering synthesis and properties, processing, and applications. It is concluded that the PMR approach offers various significant advantages, especially superior high temperature properties and processing versatility, to fabricators and users of polyimide/fiber composites.

Effects of Monomer Structure on Their Organization and Polymerization in a Smectic Liquid Crystal

PubMed

Guymon; Hoggan; Clark; Rieker; Walba; Bowman

1997-01-03

Photopolymerizable diacrylate monomers dissolved in fluid-layer smectic A and smectic C liquid crystal (LC) hosts exhibited significant spatial segregation and orientation that depend strongly on monomer structure. Small, flexible monomers such as 1,6-hexanediol diacrylate (HDDA) oriented parallel to the smectic layers and intercalated, whereas rod-shaped mesogen-like monomers such as 1,4-di-(4-(6-acryloyloxyhexyloxy)benzoyloxy)-2-methylbenzene (C6M) oriented normal to the smectic layers and collected within them. Such spatial segregation caused by the smectic layering dramatically enhanced photopolymerization rates; for HDDA, termination rates were reduced, whereas for C6M, both the termination and propagation rates were increased. These polymerization precursor structures suggest novel materials-design paradigms for gel LCs and nanophase-separated polymer systems.

AFM study of the morphologic change of HDPE surface photografted with glycidyl methacrylate.

PubMed

Wang, Huiliang; Han, Jianmei

2009-05-01

The UV-induced grafting of glycidyl methacrylate (GMA) onto high-density polyethylene (HDPE) and the atomic force microscopy (AFM) study of the morphologic change of the grafted surface are reported. The grafting was carried out in GMA acetone solutions with different monomer concentrations. Grafting was much faster in a solution with a higher monomer concentration. FTIR analyses proved that GMA had been successfully grafted onto HDPE. The morphologies of grafted HDPE surfaces changed with UV irradiation time. The monomer concentration had a significant effect on the morphologies of the grafted HDPE surfaces. The HDPE surface grafted in a solution with a higher monomer concentration was much rougher than that grafted in a solution with a lower monomer concentration. The growth models of the grafted granules or clusters are also proposed.

Synthesis and photopolymerization of low shrinkage methacrylate monomers containing bulky substituent groups.

PubMed

Ge, Junhao; Trujillo, Marianela; Stansbury, Jeffrey

2005-12-01

This study was conducted to determine whether novel photopolymerizable formulations based on dimethacrylate monomers with bulky substituent groups could provide low polymerization shrinkage without sacrifice to degree of conversion, and mechanical properties of the polymers. Relatively high molecular weight dimethacrylate monomers were prepared from rigid bisphenol A core groups. Photopolymerization kinetics and shrinkage as well as flexural strength and glass transition temperatures were evaluated for various comonomer compositions. Copolymerization of the bulky monomers with TEGDMA show higher conversion but similar shrinkage compared with Bis-GMA/TEGDMA controls. The resulting polymers have suitable mechanical strength properties for potential dental restorative materials applications. When copolymerized with PEGDMA, the bulky monomers show lower shrinkage, comparable conversion, and more homogeneous polymeric network structures compared with Bis-EMA/PEGDMA systems. The novel dimethacrylate monomers with reduced reactive group densities can decrease the polymerization shrinkage as anticipated, but there is no significant evidence that the bulky substituent groups have any additional effect on reducing shrinkage based on the physical interactions as polymer side chains. The bulky groups improve the double bond conversion and help maintain the mechanical properties of the resulting polymer, which would otherwise decrease rapidly due to the reduced crosslinking density. Further, it was found that bulky monomers help produce more homogeneous copolymer networks.

Residual methyl methacrylate monomer, water sorption, and water solubility of hypoallergenic denture base materials.

PubMed

Pfeiffer, Peter; Rosenbauer, Ernst-Ulrich

2004-07-01

Denture base materials have the potential to cause irritation and allergic reaction to the oral mucosa. Water sorption and water solubility of denture base resins affect dimensional behavior and denture stability. A correlation between residual monomer and water sorption exists. This in vitro study compared the amount of residual monomer, quantity of water sorption, and solubility of 4 denture base materials purported to be hypoallergenic with those of a polymethyl methacrylate-based (PMMA) heat-polymerizing acrylic resin. The denture base resins Sinomer (heat-polymerized, modified methacrylate), Polyan (thermoplastic, modified methacrylate), Promysan (thermoplastic, enterephthalate-based), and Microbase (microwave polymerized, polyurethane-based), which are purported to be hypoallergenic, and Paladon 65 (heat-polymerized, methacrylate, control group) were examined. Specimens of each material were tested for residual methyl methacrylate (MMA) monomer (% wt, n=3), amount of water sorption (microg/mm3, n=5) and water solubility (microg/mm3, n=5), according to ISO 1567:2000. The residual MMA monomer concentrations were determined by gas chromatography (GC). The data were analyzed with 1-way ANOVA and the Bonferroni-Dunn multiple comparisons post hoc analysis for each test variable (alpha=.05). Significantly lower residual MMA monomer was shown for Sinomer and Polyan compared to the PMMA control group (0.90 +/- 0.20% wt, P<.05). Sinomer contained 0.31% +/- 0.00% wt MMA monomer, and Polyan exhibited residual MMA monomer content of 0.44% +/- 0.01% wt. Promysan and Microbase did not contain detectable residual MMA. Water sorption of Promysan (16.21 +/- 0.96 microg/mm3) was significantly lower than Paladon 65 (23.04 +/- 3.13 microg/mm3, P<.0001), whereas water solubility of the hypoallergenic denture base materials (0.34-0.84 +/- 0.05-0.09 microg/mm3) was not significantly lower than the PMMA material (0.40 +/- 0.06 microg/mm3, P>.05). Except for Sinomer, the tested denture base resins passed the requirements of ISO 1567 regarding residual MMA monomer (<2.2% wt). Sinomer failed to comply with the requirements for residual MMA monomer because the manufacturer claimed that the material did not contain any MMA. The tested denture base materials fulfilled the requirements regarding water sorption (<32 microg/mm3) and solubility (<1.6 microg/mm3). The tested hypoallergenic denture base materials exhibited significantly lower residual monomer content than PMMA. Promysan and Microbase showed no detectable residual MMA.

Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

PubMed

Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

1997-12-01

Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R.

Monomers of cutin biopolymer: sorption and esterification on montmorillonite surfaces

NASA Astrophysics Data System (ADS)

Olshansky, Yaniv; Polubesova, Tamara; Chefetz, Benny

2013-04-01

One of the important precursors for soil organic matter is plant cuticle, a thin layer of predominantly lipids that cover all primary aerial surfaces of vascular plants. In most plant species cutin biopolymer is the major component of the cuticle (30-85% weight). Therefore cutin is the third most abundant plant biopolymer (after lignin and cellulose). Cutin is an insoluble, high molecular weight bio-polyester, which is constructed of inter-esterified cross linked hydroxy-fatty acids and hydroxyepoxy-fatty acids. The most common building blocks of the cutin are derivatives of palmitic acid, among them 9(10),16 dihydroxy palmitic acid (diHPA) is the main component. These fatty acids and their esters are commonly found in major organo-mineral soil fraction-humin. Hence, the complexes of cutin monomers with minerals may serve as model of humin. Both cutin and humin act as adsorption efficient domains for organic contaminants. However, only scarce information is available about the interactions of cutin with soil mineral surfaces, in particular with common soil mineral montmorillonite. The main hypothesize of the study is that adsorbed cutin monomers will be reconstituted on montmorillonite surface due to esterification and oligomerization, and that interactions of cutin monomers with montmorillonite will be affected by the type of exchangeable cation. Cutin monomers were obtained from the fruits of tomato (Lycopersicon esculentum). Adsorption of monomers was measured for crude Wyoming montmorillonites and montmorillonites saturated with Fe3+ and Ca2+. To understand the mechanism of monomer-clay interactions and to evaluate esterification on the clay surface, XRD and FTIR analyses of the montmorillonite-monomers complexes were performed. Our results demonstrated that the interactions of cutin monomers with montmorillonite are affected by the type of exchangeable cation. Isotherms of adsorption of cutin monomers on montmorillonites were fitted by a dual mode model of sorption, which combines site specific adsorption mechanism (Langmuir) and partitioning mechanism. Adsorption of monomers by Fe3+-montmorillonite was higher than for Ca2+ and crude -montmorillonites. XRD measurements showed expansion of d-spacing of montmorillonite samples with the increase in diHPA loading from 12.32, 12.66 and 12.17 Å for Fe3+- Ca2+- and crude-montmorillonite up to 16.84, 16.62 and 16.79 Å for organo-clay complexes of Fe3+-, Ca2+- and crude-montmorillonites respectively. This significant expansion of d-spacing suggests interlayer, and probably, multilayer diHPA adsorption by montmorillonite. Based on FTIR data we suggest that diHPA forms inner-sphere complexes with Fe3+-montmorillonite surface but not with Ca2+ and crude-montmorillonites. However all montmorillonite samples induce esterification and oligomerization of the monomers, which was demonstrated by FTIR spectra of the organo-montmorillonite complexes and by LC-MS analysis of the organic material extracted from organo-clay complexes. These results confirmed our hypothesis about oligomerization of cuticular monomers on mineral surfaces. We assume that esterification and oligomerization of monomers on montmorillonite surfaces simulate similar soil processes, which result in the formation of soil organo-mineral complexes and humin.

Leishmania infantum: Lipophosphoglycan intraspecific variation and interaction with vertebrate and invertebrate hosts.

PubMed

Coelho-Finamore, J M; Freitas, V C; Assis, R R; Melo, M N; Novozhilova, N; Secundino, N F; Pimenta, P F; Turco, S J; Soares, R P

2011-03-01

Interspecies variations in lipophosphoglycan (LPG) have been the focus of intense study over the years due its role in specificity during sand fly-Leishmania interaction. This cell surface glycoconjugate is highly polymorphic among species with variations in sugars that branch off the conserved Gal(β1,4)Man(α1)-PO(4) backbone of repeat units. However, the degree of intraspecies polymorphism in LPG of Leishmania infantum (syn. Leishmania chagasi) is not known. In this study, intraspecific variation in the repeat units of LPG was evaluated in 16 strains of L. infantum from Brazil, France, Algeria and Tunisia. The structural polymorphism in the L. infantum LPG repeat units was relatively slight and consisted of three types: type I does not have side chains; type II has one β-glucose residue that branches off the disaccharide-phosphate repeat units and type III has up to three glucose residues (oligo-glucosylated). The significance of these modifications was investigated during in vivo interaction of L. infantum with Lutzomyia longipalpis, and in vitro interaction of the parasites and respective LPGs with murine macrophages. There were no consequential differences in the parasite densities in sand fly midguts infected with Leishmania strains exhibiting type I, II and III LPGs. However, higher nitric oxide production was observed in macrophages exposed to glucosylated type II LPG. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Synthesis and study of the vibrational spectra of a first generation phosphorus-containing dendrimer with pyridyl functional groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Tripathi, V.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2018-06-01

A new phosphorus-containing dendrimer of the first-generation with potential pharmacological activity was synthesized and studied by spectral methods. The FTIR, FT Raman, 1H and 31P NMR spectra of the first generation dendrimer G1 with a cyclotriphosphazene core, six branches sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd P(S) < and twelve 4-oxyphenethylamidopyridyl end groups sbnd Osbnd C6H4sbnd (CH2)2sbnd NHsbnd COsbnd C5NH4 were recorded. Amide groups of the dendrimer participate in the formation of an intermolecular hydrogen bond. Structure, geometric parameters, the frequency and intensity of the bands in the vibrational spectra were calculated using DFT with PBE functional and TZ2P basis set. Spectral characteristics, charge distribution and reactivity of the core, repeating units and terminal groups of the dendrimer were determined. The first-generation dendrimer molecule has the shape of a concave lens with a slightly non-planar cyclotriphosphazene core and flat repeating units. Repeating units are arranged symmetrically on three on each side of the core, there are no steric hindrances in it and the end groups are able to enter into subsequent reactions and dendrimer has a sufficiently large cavity for accommodating guest molecules. The HOMO covers the repeating units with a noticeable conjugation and the LUMO belongs to the terminal groups.

Ligand-Binding Properties and Conformational Dynamics of Autolysin Repeat Domains in Staphylococcal Cell Wall Recognition

PubMed Central

Zoll, Sebastian; Schlag, Martin; Shkumatov, Alexander V.; Rautenberg, Maren; Svergun, Dmitri I.; Götz, Friedrich

2012-01-01

The bifunctional major autolysin Atl plays a key role in staphylococcal cell separation. Processing of Atl yields catalytically active amidase (AM) and glucosaminidase (GL) domains that are each fused to repeating units. The two repeats of AM (R1 and R2) target the enzyme to the septum, where it cleaves murein between dividing cells. We have determined the crystal structure of R2, which reveals that each repeat folds into two half-open β-barrel subunits. We further demonstrate that lipoteichoic acid serves as a receptor for the repeats and that this interaction depends on conserved surfaces in each subunit. Small-angle X-ray scattering of the mature amidase reveals the presence of flexible linkers separating the AM, R1, and R2 units. Different levels of flexibility for each linker provide mechanistic insights into the conformational dynamics of the full-length protein and the roles of its components in cell wall association and catalysis. Our analysis supports a model in which the repeats direct the catalytic AM domain to the septum, where it can optimally perform the final step of cell division. PMID:22609916

Thermostability of photosystem I trimers and monomers from the cyanobacterium Thermosynechococcus elongatus

NASA Astrophysics Data System (ADS)

Shubin, Vladimir V.; Terekhova, Irina V.; Bolychevtseva, Yulia V.; El-Mohsnawy, Eithar; Rögner, Matthias; Mäntele, Werner; Kopczak, Marta J.; Džafić, Enela

2017-05-01

The performance of solar energy conversion into alternative energy sources in artificial systems highly depends on the thermostability of photosystem I (PSI) complexes Terasaki et al. (2007), Iwuchukwu et al. (2010), Kothe et al. (2013) . To assess the thermostability of PSI complexes from the thermophilic cyanobacterium Thermosynechococcus elongatus heating induced perturbations on the level of secondary structure of the proteins were studied. Changes were monitored by Fourier transform infrared (FT-IR) spectra in the mid-IR region upon slow heating (1 °C per minute) of samples in D2O phosphate buffer (pD 7.4) from 20 °C to 100 °C. These spectra showed distinct changes in the Amide I region of PSI complexes as a function of the rising temperature. Absorbance at the Amide I maximum of PSI monomers (centered around 1653 cm- 1), gradually dropped in two temperature intervals, i.e. 60-75 and 80-90 °C. In contrast, absorbance at the Amide I maximum of PSI trimers (around 1656 cm- 1) dropped only in one temperature interval 80-95 °C. The thermal profile of the spectral shift of α-helices bands in the region 1656-1642 cm- 1 confirms the same two temperature intervals for PSI monomers and only one interval for trimers. Apparently, the observed absorbance changes at the Amide I maximum during heating of PSI monomers and trimers are caused by deformation and unfolding of α-helices. The absence of absorbance changes in the interval of 20-65 °C in PSI trimers is probably caused by a greater stability of protein secondary structure as compared to that in monomers. Upon heating above 80 °C a large part of α-helices both in trimers and monomers converts to unordered and aggregated structures. Spectral changes of PSI trimers and monomers heated up to 100 °C are irreversible due to protein denaturation and non-specific aggregation of complexes leading to new absorption bands at 1618-1620 cm- 1. We propose that monomers shield the denaturation sensitive sides at the monomer/monomer interface within a trimer, making the oligomeric structure more stable against thermal stress.

Biomimetic poly(amidoamine) hydrogels as synthetic materials for cell culture

PubMed Central

Jacchetti, Emanuela; Emilitri, Elisa; Rodighiero, Simona; Indrieri, Marco; Gianfelice, Antonella; Lenardi, Cristina; Podestà, Alessandro; Ranucci, Elisabetta; Ferruti, Paolo; Milani, Paolo

2008-01-01

Background Poly(amidoamine)s (PAAs) are synthetic polymers endowed with many biologically interesting properties, being highly biocompatible, non toxic and biodegradable. Hydrogels based on PAAs can be easily modified during the synthesis by the introduction of functional co-monomers. Aim of this work is the development and testing of novel amphoteric nanosized poly(amidoamine) hydrogel film incorporating 4-aminobutylguanidine (agmatine) moieties to create RGD-mimicking repeating units for promoting cell adhesion. Results A systematic comparative study of the response of an epithelial cell line was performed on hydrogels with agmatine and on non-functionalized amphoteric poly(amidoamine) hydrogels and tissue culture plastic substrates. The cell adhesion on the agmatine containing substrates was comparable to that on plastic substrates and significantly enhanced with respect to the non-functionalized controls. Interestingly, spreading and proliferation on the functionalized supports are slower than on plastic exhibiting the possibility of an easier control of the cell growth kinetics. In order to favor the handling of the samples, a procedure for the production of bi-layered constructs was also developed by means the deposition via spin coating of a thin layer of hydrogel on a pre-treated cover slip. Conclusion The obtained results reveal that PAAs hydrogels can be profitably functionalized and, in general, undergo physical and chemical modifications to meet specific requirements. In particular the incorporation of agmatine warrants good potential in the field of cell culturing and the development of supported functionalized hydrogels on cover glass are very promising substrates for applications in cell screening devices. PMID:19014710

Synthesis and evaluation of novel siloxane-methacrylate monomers used as dentin adhesives

PubMed Central

Ge, Xueping; Ye, Qiang; Song, Linyong; Misra, Anil; Spencer, Paulette

2014-01-01

Objectives The objectives of this study were to synthesize two new siloxane-methacrylate (SM) monomers for application in dentin adhesives and to investigate the influence of different functionality of the siloxane-containing monomers on the adhesive photopolymerization, water sorption, and mechanical properties. Materials and method Two siloxane-methacrylate monomers (SM1 and SM2) with four and eight methacrylate groups were synthesized. Dentin adhesives containing BisGMA, HEMA and the siloxane-methacrylate monomers were photo-polymerized. The experimental adhesives were compared with the control adhesive (HEMA/BisGMA 45/55 w/w) and characterized with regard to degree of conversion (DC), water miscibility of the liquid resin, water sorption and dynamic mechanical analysis (DMA). Results The experimental adhesives exhibited improved water miscibility as compared to the control. When cured in the presence of 12 wt % water to simulate the wet environment of the mouth, the SM-containing adhesives showed DC comparable to the control. The experimental adhesives showed higher rubbery modulus than the control under dry conditions. Under wet conditions, the mechanical properties of the formulations containing SM monomer with increased functionality were comparable with the control, even with more water sorption. Significance The concentration and functionality of the newly synthesized siloxane-methacrylate monomers affected the water miscibility, water sorption and mechanical properties of the adhesives. The experimental adhesives show improved water compatibility compared with the control. The mechanical properties were enhanced with an increase of the functionality of the siloxane-containing monomers. The results provide critical structure/property relationships and important information for future development of durable, versatile siloxane-containing dentin adhesives. PMID:24993811

Monomeric Nucleoprotein of Influenza A Virus

PubMed Central

Chenavas, Sylvie; Estrozi, Leandro F.; Slama-Schwok, Anny; Delmas, Bernard; Di Primo, Carmelo; Baudin, Florence; Li, Xinping; Crépin, Thibaut; Ruigrok, Rob W. H.

2013-01-01

Isolated influenza A virus nucleoprotein exists in an equilibrium between monomers and trimers. Samples containing only monomers or only trimers can be stabilized by respectively low and high salt. The trimers bind RNA with high affinity but remain trimmers, whereas the monomers polymerise onto RNA forming nucleoprotein-RNA complexes. When wild type (wt) nucleoprotein is crystallized, it forms trimers, whether one starts with monomers or trimers. We therefore crystallized the obligate monomeric R416A mutant nucleoprotein and observed how the domain exchange loop that leads over to a neighbouring protomer in the trimer structure interacts with equivalent sites on the mutant monomer surface, avoiding polymerisation. The C-terminus of the monomer is bound to the side of the RNA binding surface, lowering its positive charge. Biophysical characterization of the mutant and wild type monomeric proteins gives the same results, suggesting that the exchange domain is folded in the same way for the wild type protein. In a search for how monomeric wt nucleoprotein may be stabilized in the infected cell we determined the phosphorylation sites on nucleoprotein isolated from virus particles. We found that serine 165 was phosphorylated and conserved in all influenza A and B viruses. The S165D mutant that mimics phosphorylation is monomeric and displays a lowered affinity for RNA compared with wt monomeric NP. This suggests that phosphorylation may regulate the polymerisation state and RNA binding of nucleoprotein in the infected cell. The monomer structure could be used for finding new anti influenza drugs because compounds that stabilize the monomer may slow down viral infection. PMID:23555270

Synthesis and evaluation of novel siloxane-methacrylate monomers used as dentin adhesives.

PubMed

Ge, Xueping; Ye, Qiang; Song, Linyong; Misra, Anil; Spencer, Paulette

2014-09-01

The objectives of this study were to synthesize two new siloxane-methacrylate (SM) monomers for application in dentin adhesives and to investigate the influence of different functionality of the siloxane-containing monomers on the adhesive photopolymerization, water sorption, and mechanical properties. Two siloxane-methacrylate monomers (SM1 and SM2) with four and eight methacrylate groups were synthesized. Dentin adhesives containing BisGMA, HEMA and the siloxane-methacrylate monomers were photo-polymerized. The experimental adhesives were compared with the control adhesive (HEMA/BisGMA, 45/55, w/w) and characterized with regard to degree of conversion (DC), water miscibility of the liquid resin, water sorption and dynamic mechanical analysis (DMA). The experimental adhesives exhibited improved water miscibility as compared to the control. When cured in the presence of 12 wt% water to simulate the wet environment of the mouth, the SM-containing adhesives showed DC comparable to the control. The experimental adhesives showed higher rubbery modulus than the control under dry conditions. Under wet conditions, the mechanical properties of the formulations containing SM monomer with increased functionality were comparable with the control, even with more water sorption. The concentration and functionality of the newly synthesized siloxane-methacrylate monomers affected the water miscibility, water sorption and mechanical properties of the adhesives. The experimental adhesives show improved water compatibility compared with the control. The mechanical properties were enhanced with an increase of the functionality of the siloxane-containing monomers. The results provide critical structure/property relationships and important information for future development of durable, versatile siloxane-containing dentin adhesives. Published by Elsevier Ltd.

Does Topology Drive Fiber Polymerization?

PubMed Central

2015-01-01

We have developed new procedures to examine the early steps in fibrin polymerization. First, we isolated fibrinogen monomers from plasma fibrinogen by gel filtration. Polymerization of fibrinogen monomers differed from that of plasma fibrinogen. The formation of protofibrils was slower and the transformation of protofibrils to fibers faster for the fibrinogen monomers. Second, we used formaldehyde to terminate the polymerization reactions. The formaldehyde-fixed products obtained at each time point were examined by dynamic light scattering and transmission electron microscopy (TEM). The data showed the formaldehyde-fixed products were stable and representative of the reaction intermediates. TEM images showed monomers, short oligomers, protofibrils, and thin fibers. The amount and length of these species varied with time. Short oligomers were less than 5% of the molecules at all times. Third, we developed models that recapitulate the TEM images. Fibrin monomer models were assembled into protofibrils, and protofibrils were assembled into two-strand fibers using Chimera software. Monomers were based on fibrinogen crystal structures, and the end-to-end interactions between monomers were based on D-dimer crystal structures. Protofibrils assembled from S-shaped monomers through asymmetric D:D interactions were ordered helical structures. Fibers were modeled by duplicating a protofibril and rotating the duplicate 120° around its long axis. No specific interactions were presumed. The two protofibrils simply twisted around one another to form a fiber. This model suggests that the conformation of the protofibril per se promotes the assembly into fibers. These findings introduce a novel mechanism for fibrin assembly that may be relevant to other biopolymers. PMID:25419972

The minisatellite of the GPI/AMF/NLK/MF gene: interspecies conservation and transcriptional activity.

PubMed

Williams, R R; Hassan-Walker, A F; Lavender, F L; Morgan, M; Faik, P; Ragoussis, J

2001-05-16

Minisatellites are tandemly repeated DNA sequences found throughout the genomes of all eukaryotes. They are regions often prone to instability and hence hypervariability; thus repeat unit sequence is generally not conserved beyond closely related species. We have studied the minisatellite located in intron 9 of the human glucose phosphate isomerase (GPI) gene (also known as neuroleukin, autocrine motility factor, maturation and differentiation factor) and have found, by Zoo blotting coupled with PCR amplification and DNA sequencing, that similar repeat units are present in seven other species of mammal. There is also evidence for the presence of the minisatellite in chicken. The repeat unit does not appear to be present at any other locus in these genomes. Minisatellite DNA has been reported to be involved in recombination activity, control of gene expression of nearby gene(s) (both transcriptional and translational), whilst others form protein coding regions. The high level of conservation exhibited by the GPI minisatellite, coupled with the unique location, strongly suggests a functional role. Our results from transient and stable transfections using luciferase reporter constructs have shown that the GPI minisatellite region can act to increase transcription from the SV40 promoter, CMV promoter and the human GPI promoter.

Polymers containing borane or carborane cage compounds and related applications

DOEpatents

Bowen, III, Daniel E.; Eastwood, Eric A [Raymore, MO

2012-06-05

Polymers comprising residues of borane and/or carborane cage compound monomers having at least one polyalkoxy silyl substituent. Such polymers can further comprise one or more reactive matrices and/or co-monomers covalently bound with the cage compound monomer residues. Methods of making and applications for using such polymers are also disclosed.

Polymer solutions

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

Krawczyk, Gerhard Erich; Miller, Kevin Michael

2011-07-26

There is provided a method of making a polymer solution comprising polymerizing one or more monomer in a solvent, wherein said monomer comprises one or more ethylenically unsaturated monomer that is a multi-functional Michael donor, and wherein said solvent comprises 40% or more by weight, based on the weight of said solvent, one or more multi-functional Michael donor.

Synthesis and polymerization of vinyl triazolium ionic liquids

DOEpatents

Luebke, David; Nulwala, Hunaid; Matyjaszewski, Krzysztof; Adzima, Brian

2018-05-15

Herein, we describe polymerized ionic liquids, demonstrate the synthesis of polymerized ionic liquids, and demonstrate the polymerization of triazolium monomers. One embodiment shows the polymeriazation of the triazolium monomers with bis(trifluoromethanesulfonyl)imide anions. In another embodiment we show the feasibility of copolymerizing with commodity monomers such as styrene using free radical polymerization techniques.

Determination of residual monomers resulting from the chemical polymerization process of dental materials

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

Boboia, S.; Moldovan, M.; Ardelean, I.

The residual monomer present in post-polymerized dental materials encourages premature degradation of the reconstructed tooth. That is why the residual monomer should be quantified in a simple, fast, accurate and reproducible manner. In our work we propose such an approach for accurate determination of the residual monomer in dental materials which is based on low-field nuclear magnetic resonance (NMR) relaxometry. The results of the NMR approach are compared with those of the high performance liquid chromatography (HPLC) technique. The samples under study contain the main monomers (2,2-bis[4-(2-hydroxy-3-methacryloyloxypropoxy)phenyl]propane and triethylene glycol dimethacrylate) constituting the liquid phase of most dental materials andmore » an initiator. Two samples were analyzed with different ratios of chemical initiation systems: N,N-dimethyl-p-toluide: benzoyl peroxide (1:2 and 0.7:1.2). The results obtained by both techniques highlight that by reducing the initiator the polymerization process slows down and the amount of residual monomer reduces. This prevents the premature degradation of the dental fillings and consequently the reduction of the biomaterial resistance.« less

Controlled grafting of vinylic monomers on polyolefins: a robust mathematical modeling approach

PubMed Central

Saeb, Mohammad Reza; Rezaee, Babak; Shadman, Alireza; Formela, Krzysztof; Ahmadi, Zahed; Hemmati, Farkhondeh; Kermaniyan, Tayebeh Sadat; Mohammadi, Yousef

2017-01-01

Abstract Experimental and mathematical modeling analyses were used for controlling melt free-radical grafting of vinylic monomers on polyolefins and, thereby, reducing the disturbance of undesired cross-linking of polyolefins. Response surface, desirability function, and artificial intelligence methodologies were blended to modeling/optimization of grafting reaction in terms of vinylic monomer content, peroxide initiator concentration, and melt-processing time. An in-house code was developed based on artificial neural network that learns and mimics processing torque and grafting of glycidyl methacrylate (GMA) typical vinylic monomer on high-density polyethylene (HDPE). Application of response surface and desirability function enabled concurrent optimization of processing torque and GMA grafting on HDPE, through which we quantified for the first time competition between parallel reactions taking place during melt processing: (i) desirable grafting of GMA on HDPE; (ii) undesirable cross-linking of HDPE. The proposed robust mathematical modeling approach can precisely learn the behavior of grafting reaction of vinylic monomers on polyolefins and be placed into practice in finding exact operating condition needed for efficient grafting of reactive monomers on polyolefins. PMID:29491797

A radiation-sensitive monomer of 2,4-hexadiyn-1,6-bis(p-toluene sulphonyl urethane) in PVA as a radiochromic film dosimeter

NASA Astrophysics Data System (ADS)

Soliman, Yasser S.; Abdel-Fattah, A. A.; Hamed, A. A.; Bayomi, A. M. M.

2018-03-01

A conjugated monomer 2,4-hexadiyn-1,6-bis(p-toluene sulphonyl urethane) (HDTU) was synthesized. Thereafter, it was incorporated into polyvinyl alcohol (PVA), and coated on self-adhesive sheet, thus to prepare film dosimeters. The monomer and films were analyzed using X-ray diffraction (XRD), FTIR spectroscopy and specular reflectance colorimetry. This monomer polymerizes in the films by radiation and turns progressively blue in proportion to absorbed dose, indicating the formation of π-conjugated colored poly-HDTU. Color development was investigated at 480 nm and 610 nm for dose monitoring ranging from 10 Gy to 15 kGy. HDTU in PVA film is highly ordered and crystalline and, upon irradiation, it forms a semi-crystalline polymer with nearly the same interplanar distances as the monomer, indicating the occurrence of topochemical polymerization. During irradiation, polymerization of the monomer is nearly independent of humidity in the range of 0-53% and temperature in the range of 25-45 °C. The uncertainty of this system is 5.16% at 95% confidence level.

Controlled grafting of vinylic monomers on polyolefins: a robust mathematical modeling approach.

PubMed

Saeb, Mohammad Reza; Rezaee, Babak; Shadman, Alireza; Formela, Krzysztof; Ahmadi, Zahed; Hemmati, Farkhondeh; Kermaniyan, Tayebeh Sadat; Mohammadi, Yousef

2017-01-01

Experimental and mathematical modeling analyses were used for controlling melt free-radical grafting of vinylic monomers on polyolefins and, thereby, reducing the disturbance of undesired cross-linking of polyolefins. Response surface, desirability function, and artificial intelligence methodologies were blended to modeling/optimization of grafting reaction in terms of vinylic monomer content, peroxide initiator concentration, and melt-processing time. An in-house code was developed based on artificial neural network that learns and mimics processing torque and grafting of glycidyl methacrylate (GMA) typical vinylic monomer on high-density polyethylene (HDPE). Application of response surface and desirability function enabled concurrent optimization of processing torque and GMA grafting on HDPE, through which we quantified for the first time competition between parallel reactions taking place during melt processing: (i) desirable grafting of GMA on HDPE; (ii) undesirable cross-linking of HDPE. The proposed robust mathematical modeling approach can precisely learn the behavior of grafting reaction of vinylic monomers on polyolefins and be placed into practice in finding exact operating condition needed for efficient grafting of reactive monomers on polyolefins.

The binding of glucose to yeast hexokinase monomers is independent of ionic strength.

PubMed

Mayes, E L; Hoggett, J G; Kellett, G L

1982-05-01

Hoggett & Kellett [Eur. J. Biochem. 66, 65-77 (1976)] have reported that the binding of glucose to the monomer of hexokinase PII isoenzyme is independent of ionic strength, in contrast to the subsequent claim of Feldman & Kramp [Biochemistry 17, 1541-1547 (1978)] that the binding is strongly dependent on ionic strength. Since measurements with native hexokinase P forms are complicated by the fact that the enzyme exists in a monomer-dimer association-dissociation equilibrium, we have now studied the binding of glucose to the proteolytically-modified S forms which are monomeric. At pH 8.5, the affinity of glucose for both SI and SII monomers is independent of salt concentration over the range of KCl concentrations 0-1.0 mol . dm-3 and is in good agreement with that of the corresponding P forms in both low and high salt. These observations confirm that the binding of glucose to hexokinase P monomers is independent of ionic strength and that the affinity of glucose for the hexokinase PII monomer is about an order of magnitude greater than that for the dimer.

The binding of glucose to yeast hexokinase monomers is independent of ionic strength.

PubMed Central

Mayes, E L; Hoggett, J G; Kellett, G L

1982-01-01

Hoggett & Kellett [Eur. J. Biochem. 66, 65-77 (1976)] have reported that the binding of glucose to the monomer of hexokinase PII isoenzyme is independent of ionic strength, in contrast to the subsequent claim of Feldman & Kramp [Biochemistry 17, 1541-1547 (1978)] that the binding is strongly dependent on ionic strength. Since measurements with native hexokinase P forms are complicated by the fact that the enzyme exists in a monomer-dimer association-dissociation equilibrium, we have now studied the binding of glucose to the proteolytically-modified S forms which are monomeric. At pH 8.5, the affinity of glucose for both SI and SII monomers is independent of salt concentration over the range of KCl concentrations 0-1.0 mol . dm-3 and is in good agreement with that of the corresponding P forms in both low and high salt. These observations confirm that the binding of glucose to hexokinase P monomers is independent of ionic strength and that the affinity of glucose for the hexokinase PII monomer is about an order of magnitude greater than that for the dimer. PMID:7052060

(1→3)-β-d-Glucan oligosaccharides monomers purification and its H2O2 induction effect study.

PubMed

Fu, Yunbin; Wang, Mengyu; Wang, Wenxia; Tuo, Yaqin; Guo, Zhimou; Du, Yuguang; Yin, Heng

2015-11-01

In order to produce highly purified (1→3)-β-d-glucan oligosaccharides ((1→3)-β-d-GOS) monomers, a hydrophilic interaction liquid chromatography (HILIC) system with X-Amide stationary phase was performed. Nine (1→3)-β-d-GOS monomers with degree of polymerization (DP) from 2 to 10 were successfully separated. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) demonstrated that these monomers were with high purity. Furthermore, a hydrogen peroxide (H2O2) online detection method was established to monitor H2O2 releases in tobacco cells. This is the first report on nine consecutive (1→3)-β-d-GOS monomers purification and its effect upon H2O2-releasing in plants. It was found that (1→3)-β-d-GOS monomers with higher DP induced stronger defense responses in plants, which will pave the way for elucidating the relationship between (1→3)-β-d-GOS and biological activities. Copyright © 2015 Elsevier B.V. All rights reserved.

Structure-function relationships in Gan42B, an intracellular GH42 β-galactosidase from Geobacillus stearothermophilus.

PubMed

Solomon, Hodaya V; Tabachnikov, Orly; Lansky, Shifra; Salama, Rachel; Feinberg, Hadar; Shoham, Yuval; Shoham, Gil

2015-12-01

Geobacillus stearothermophilus T-6 is a Gram-positive thermophilic soil bacterium that contains a battery of degrading enzymes for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. A 9.4 kb gene cluster has recently been characterized in G. stearothermophilus that encodes a number of galactan-utilization elements. A key enzyme of this degradation system is Gan42B, an intracellular GH42 β-galactosidase capable of hydrolyzing short β-1,4-galactosaccharides into galactose units, making it of high potential for various biotechnological applications. The Gan42B monomer is made up of 686 amino acids, and based on sequence homology it was suggested that Glu323 is the catalytic nucleophile and Glu159 is the catalytic acid/base. In the current study, the detailed three-dimensional structure of wild-type Gan42B (at 2.45 Å resolution) and its catalytic mutant E323A (at 2.50 Å resolution), as determined by X-ray crystallography, are reported. These structures demonstrate that the three-dimensional structure of the Gan42B monomer generally correlates with the overall fold observed for GH42 proteins, consisting of three main domains: an N-terminal TIM-barrel domain, a smaller mixed α/β domain, and the smallest all-β domain at the C-terminus. The two catalytic residues are located in the TIM-barrel domain in a pocket-like active site such that their carboxylic functional groups are about 5.3 Å from each other, consistent with a retaining mechanism. The crystal structure demonstrates that Gan42B is a homotrimer, resembling a flowerpot in general shape, in which each monomer interacts with the other two to form a cone-shaped tunnel cavity in the centre. The cavity is ∼35 Å at the wide opening and ∼5 Å at the small opening and ∼40 Å in length. The active sites are situated at the interfaces between the monomers, so that every two neighbouring monomers participate in the formation of each of the three active sites of the trimer. They are located near the small opening of the cone tunnel, all facing the centre of the cavity. The biological relevance of this trimeric structure is supported by independent results obtained from gel-permeation chromatography. These data and their comparison to the structural data of related GH42 enzymes are used for a more general discussion concerning structure-activity aspects in this GH family.

Clamping characteristics study on different types of clamping unit

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

Jiao, Zhiwei; Liu, Haichao; Xie, Pengcheng

2015-05-22

Plastic products are becoming more and more widely used in aerospace, IT, digital electronics and many other fields. With the development of technology, the requirement of product precision is getting higher and higher. However, type and working performance of clamping unit play a decisive role in product precision. Clamping characteristics of different types of clamping unit are discussed in this article, which use finite element numerical analysis method through the software ABAQUS to study the clamping uniformity, and detect the clamping force repeatability precision. The result shows that compared with toggled three-platen clamping unit, clamping characteristics of internal circulation two-platenmore » clamping unit are better, for instance, its mold cavity deformation and force that bars and mold parting surface suffered are more uniform, and its clamping uniformity and repeatability precision is also better.« less

Engineering Human Immunodeficiency Virus 1 Protease Heterodimers as Macromolecular Inhibitors of Viral Maturation

NASA Astrophysics Data System (ADS)

McPhee, Fiona; Good, Andrew C.; Kuntz, Irwin D.; Craik, Charles S.

1996-10-01

Dimerization of human immunodeficiency virus type 1 protease (HIV-1 PR) monomers is an essential prerequisite for viral proteolytic activity and the subsequent generation of infectious virus particles. Disruption of the dimer interface inhibits this activity as does formation of heterodimers between wild-type and defective monomers. A structure-based approach was used to identify amino acid substitutions at the dimer interface of HIV-1 PR that facilitate preferential association of heterodimers and inhibit self-association of the defective monomers. Expression of the designed PR monomers inhibits activity of wild-type HIV-1 PR and viral infectivity when assayed in an ex vivo model system. These results show that it is possible to design PR monomers as macromolecular inhibitors that may provide an alternative to small molecule inhibitors for the treatment of HIV infection.

Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality.

PubMed

Wang, Xiao-Gang; Carrington, Tucker

2017-03-14

In this paper, we present new ideas for computing rovibrational energy levels of molecules composed of two components and apply them to H 2 O-Cl - . When both components are themselves molecules, Euler angles that specify their orientation with respect to an axis system attached to the inter-monomer vector are used as vibrational coordinates. For H 2 O-Cl - , there is only one set of Euler angles. Using Euler angles as intermolecular vibrational coordinates is advantageous because in many cases coupling between them and coordinates that describe the shape of the monomers is unimportant. The monomers are not assumed to be rigid. In the most efficient calculation, vibrational wavefunctions of the monomers are used as contracted basis functions. Energy levels are calculated using the Lanczos algorithm.

Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2017-03-01

In this paper, we present new ideas for computing rovibrational energy levels of molecules composed of two components and apply them to H2O-Cl-. When both components are themselves molecules, Euler angles that specify their orientation with respect to an axis system attached to the inter-monomer vector are used as vibrational coordinates. For H2O-Cl-, there is only one set of Euler angles. Using Euler angles as intermolecular vibrational coordinates is advantageous because in many cases coupling between them and coordinates that describe the shape of the monomers is unimportant. The monomers are not assumed to be rigid. In the most efficient calculation, vibrational wavefunctions of the monomers are used as contracted basis functions. Energy levels are calculated using the Lanczos algorithm.

Resin adhesion strengths to zirconia ceramics after primer treatment with silane coupling monomer or oligomer.

PubMed

Okada, Masahiro; Inoue, Kazusa; Irie, Masao; Taketa, Hiroaki; Torii, Yasuhiro; Matsumoto, Takuya

2017-09-26

Resin bonding to zirconia ceramics is difficult to achieve using the standard methods for conventional silica-based dental ceramics, which employ silane coupling monomers as primers. The hypothesis in this study was that a silane coupling oligomer -a condensed product of silane coupling monomers- would be a more suitable primer for zirconia. To prove this hypothesis, the shear bond strengths between a composite resin and zirconia were compared after applying either a silane coupling monomer or oligomer. The shear bond strength increased after applying a non-activated ethanol solution of the silane coupling oligomer compared with that achieved when applying the monomer. Thermal treatment of the zirconia at 110°C after application of the silane coupling agents was essential to improve the shear bond strength between the composite resin cement and zirconia.

Synthesis of Side Chain Liquid Crystal Polymers by Living Ring Opening Metathesis Polymerization. 3. Influence of Molecular Weight, Interconnecting Unit and Substituent on the Mesomorphic behavior of Polymers with Laterally Attached Mesogens

DTIC Science & Technology

1992-04-08

polymethylsiloxanes, 6 -7 polyacrylates ,2,4,5 polymethacrylates, 1 ,3 and polychloroacrylates, 5 exhibit only nematic mesophases regardless of the...corresponding carboxyl chloride. Potassium bicyclo[2.2.1]hept-2-ene-5- carboxylate was prepared by titrating a methanolic solution of the carboxylic acid...Esterification of the Corresponding Benzyl Bromides. Monomers 1I-n were prepared in 47-88% yield using the following procedure. A mixture of potassium bicyclo

The neighbourhood polynomial of some families of dendrimers

NASA Astrophysics Data System (ADS)

Nazri Husin, Mohamad; Hasni, Roslan

2018-04-01

The neighbourhood polynomial N(G,x) is generating function for the number of faces of each cardinality in the neighbourhood complex of a graph and it is defined as (G,x)={\\sum }U\\in N(G){x}|U|, where N(G) is neighbourhood complex of a graph, whose vertices of the graph and faces are subsets of vertices that have a common neighbour. A dendrimers is an artificially manufactured or synthesized molecule built up from branched units called monomers. In this paper, we compute this polynomial for some families of dendrimer.

Rhubarb Antagonizes Matrix Metalloproteinase-9-induced Vascular Endothelial Permeability

PubMed Central

Cui, Yun-Liang; Zhang, Sheng; Tian, Zhao-Tao; Lin, Zhao-Fen; Chen, De-Chang

2016-01-01

Background: Intact endothelial structure and function are critical for maintaining microcirculatory homeostasis. Dysfunction of the latter is an underlying cause of various organ pathologies. In a previous study, we showed that rhubarb, a traditional Chinese medicine, protected intestinal mucosal microvascular endothelial cells in rats with metastasizing septicemia. In this study, we investigated the effects and mechanisms of rhubarb on matrix metalloproteinase-9 (MMP9)-induced vascular endothelial (VE) permeability. Methods: Rhubarb monomers were extracted and purified by a series of chromatography approaches. The identity of these monomers was analyzed by hydrogen-1 nuclear magnetic resonance (NMR), carbon-13 NMR, and distortionless enhancement by polarization transfer magnetic resonance spectroscopy. We established a human umbilical vein endothelial cell (HUVEC) monolayer on a Transwell insert. We measured the HUVEC permeability, proliferation, and the secretion of VE-cadherin into culture medium using fluorescein isothiocyanate-dextran assay, 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide assay, and enzyme-linked immunosorbent assay, respectively, in response to treatment with MMP9 and/or rhubarb monomers. Results: A total of 21 rhubarb monomers were extracted and identified. MMP9 significantly increased the permeability of the HUVEC monolayer, which was significantly reduced by five individual rhubarb monomer (emodin, 3,8-dihydroxy-1-methyl-anthraquinone-2-carboxylic acid, 1-O-caffeoyl-2-(4-hydroxyl-O-cinnamoyl)-β-D-glucose, daucosterol linoleate, and rhein) or a combination of all five monomers (1 μmol/L for each monomer). Mechanistically, the five-monomer mixture at 1 μmol/L promoted HUVEC proliferation. In addition, MMP9 stimulated the secretion of VE-cadherin into the culture medium, which was significantly inhibited by the five-monomer mixture. Conclusions: The rhubarb mixture of emodin, 3,8-dihydroxy-1-methyl-anthraquinone-2-carboxylic acid, 1-O-caffeoyl-2-(4-hydroxyl-O-cinnamoyl)-β-D-glucose, daucosterol linoleate, and rhein, at a low concentration, antagonized the MMP9-induced HUVEC monolayer permeability by promoting HUVEC proliferation and reducing extracellular VE-cadherin concentrations. PMID:27411464

In situ oligomerization of 2-(thiophen-3-yl)acetate intercalated into Zn{sub 2}Al layered double hydroxide

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

Tronto, Jairo, E-mail: jairotronto@ufv.br; Pinto, Frederico G.; Costa, Liovando M. da

2015-01-15

A layered double hydroxide (LDH) with cation composition Zn{sub 2}Al was intercalated with 2-(thiophen-3-yl)acetate (3-TA) monomers. To achieve in situ polymerization and/or oligomerization of the intercalated monomers, soft thermal treatments were carried out, and subsequent hybrid LDH materials were analyzed by means of several characterization techniques using powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), {sup 13}C CP–MAS nuclear magnetic resonance (NMR), electron spin resonance (EPR), scanning electron microscopy (SEM), and transmission electron microscopy (TEM), inductively coupled plasma optical emission spectroscopy (ICP–OES), and elemental analysis. PXRD analysis suggested that the intercalated monomers formed a bilayer. Thermalmore » treatment of the hybrid LDH assembly above 120 °C provokes partially the breakdown of the layered structure, generating the phase zincite. EPR results indicated that vicinal monomers (oligomerization) were bound to each other after hydrothermal or thermal treatment, leading to a polaron response characteristic of electron conductivity localized on a restricted number of thiophene-based monomer segments. Localized unpaired electrons exist in the material and interact with the {sup 27}Al nuclei of the LDH layers by superhyperfine coupling. These unpaired electrons also interact with the surface of ZnO (O{sup 2−} vacancies), formed during the thermal treatments. - Graphical abstract: We synthesized a layered double hydroxide (LDH) with cation composition Zn{sub 2}Al, intercalated with 2-(thiophen-3-yl)acetate (3-TA) monomers, by coprecipitation at constant pH. We thermally treated the material, to achieve in situ polymerization and/or oligomerization of the intercalated monomers. - Highlights: • A Zn{sub 2}Al–LDH was intercalated with 2-(thiophen-3-yl)acetate monomers. • To achieve in situ oligomerization of the monomers, thermal treatments were made. • Thermal treatment above 120 °C causes partially breakdown of the LDH structure. • ESR results indicated a polaron response characteristic of electron conductivity.« less

Detection of p75NTR Trimers: Implications for Receptor Stoichiometry and Activation

PubMed Central

Barker, Phillip A.; Chao, Moses V.

2015-01-01

The p75 neurotrophin receptor (p75NTR) is a multifunctional receptor that participates in many critical processes in the nervous system, ranging from apoptosis to synaptic plasticity and morphological events. It is a member of the tumor necrosis factor receptor (TNFR) superfamily, whose members undergo trimeric oligomerization. Interestingly, p75NTR interacts with dimeric ligands (i.e., proneurotrophins or mature neurotrophins), but several of the intracellular adaptors that mediate p75NTR signaling are trimeric (i.e., TNFR-associated factor 6 or TRAF6). Consequently, the active receptor signaling unit remains uncertain. To identify the functional receptor complex, we evaluated its oligomerization in vitro and in mice brain tissues using a combination of biochemical techniques. We found that the most abundant homotypic arrangement for p75NTR is a trimer and that monomers and trimers coexist at the cell surface. Interestingly, trimers are not required for ligand-independent or ligand-dependent p75NTR activation in a growth cone retraction functional assay. However, monomers are capable of inducing acute morphological effects in neurons. We propose that p75NTR activation is regulated by its oligomerization status and its levels of expression. These results indicate that the oligomeric state of p75NTR confers differential responses and offers an explanation for the diverse and contradictory actions of this receptor in the nervous system. SIGNIFICANCE STATEMENT The p75 neurotrophin receptor (p75NTR) regulates a wide range of cellular functions, including apoptosis, neuronal processes remodeling, and synaptic plasticity. The goal of our work was to inquire whether oligomers of the receptor are required for function. Here we report that p75NTR predominantly assembles as a trimer, similar to other tumor necrosis factor receptors. Interestingly, monomers and trimers coexist at the cell surface, but trimers are not required for p75NTR activation in a functional assay. However, monomers are capable of inducing acute morphological effects in neurons. Identification of the oligomerization state of p75NTR begins to provide insights to the mechanisms of signal initiation of this noncatalytic receptor, as well as to develop therapeutic interventions to diminish its activity. PMID:26311773

Detection of p75NTR Trimers: Implications for Receptor Stoichiometry and Activation.

PubMed

Anastasia, Agustin; Barker, Phillip A; Chao, Moses V; Hempstead, Barbara L

2015-08-26

The p75 neurotrophin receptor (p75(NTR)) is a multifunctional receptor that participates in many critical processes in the nervous system, ranging from apoptosis to synaptic plasticity and morphological events. It is a member of the tumor necrosis factor receptor (TNFR) superfamily, whose members undergo trimeric oligomerization. Interestingly, p75(NTR) interacts with dimeric ligands (i.e., proneurotrophins or mature neurotrophins), but several of the intracellular adaptors that mediate p75(NTR) signaling are trimeric (i.e., TNFR-associated factor 6 or TRAF6). Consequently, the active receptor signaling unit remains uncertain. To identify the functional receptor complex, we evaluated its oligomerization in vitro and in mice brain tissues using a combination of biochemical techniques. We found that the most abundant homotypic arrangement for p75(NTR) is a trimer and that monomers and trimers coexist at the cell surface. Interestingly, trimers are not required for ligand-independent or ligand-dependent p75(NTR) activation in a growth cone retraction functional assay. However, monomers are capable of inducing acute morphological effects in neurons. We propose that p75(NTR) activation is regulated by its oligomerization status and its levels of expression. These results indicate that the oligomeric state of p75(NTR) confers differential responses and offers an explanation for the diverse and contradictory actions of this receptor in the nervous system. The p75 neurotrophin receptor (p75(NTR)) regulates a wide range of cellular functions, including apoptosis, neuronal processes remodeling, and synaptic plasticity. The goal of our work was to inquire whether oligomers of the receptor are required for function. Here we report that p75(NTR) predominantly assembles as a trimer, similar to other tumor necrosis factor receptors. Interestingly, monomers and trimers coexist at the cell surface, but trimers are not required for p75(NTR) activation in a functional assay. However, monomers are capable of inducing acute morphological effects in neurons. Identification of the oligomerization state of p75(NTR) begins to provide insights to the mechanisms of signal initiation of this noncatalytic receptor, as well as to develop therapeutic interventions to diminish its activity. Copyright © 2015 the authors 0270-6474/15/3511911-10$15.00/0.

Vogel-Fulcher dependence of relaxation rates in a nematic monomer and elastomer

NASA Astrophysics Data System (ADS)

Shenoy, D.; Filippov, S.; Aliev, F.; Keller, P.; Thomsen, D.; Ratna, B.

2000-12-01

Dielectric relaxation spectroscopy is used to study the relaxation processes in a nematic monomer and the corresponding cross-linked polymer nematic liquid crystal (elastomer). In the frequency window 10 mHz to 2 GHz the monomer liquid crystal shows a single relaxation whereas the polymer exhibits three relaxation processes, two of which are quantitatively analyzed. The temperature dependence of relaxation times in both the monomer and polymer follows a Vogel-Fulcher behavior. The relaxation processes are identified with specific molecular motions and activation energies are calculated in a linear approximation for comparison with literature data.

Method for molding ceramic powders

DOEpatents

Janney, Mark A.

1990-01-01

A method for molding ceramic powders comprises forming a slurry mixture including ceramic powder, a dispersant for the metal-containing powder, and a monomer solution. The monomer solution includes at least one multifunctional monomer, a free-radical initiator, and an organic solvent. The slurry mixture is transferred to a mold, and the mold containing the slurry mixture is heated to polymerize and crosslink the monomer and form a firm polymer-solvent gel matrix. The solid product may be removed from the mold and heated to first remove the solvent and subsequently remove the polymer, whereafter the product may be sintered.

Method for molding ceramic powders

DOEpatents

Janney, M.A.

1990-01-16

A method for molding ceramic powders comprises forming a slurry mixture including ceramic powder, a dispersant for the metal-containing powder, and a monomer solution. The monomer solution includes at least one multifunctional monomer, a free-radical initiator, and an organic solvent. The slurry mixture is transferred to a mold, and the mold containing the slurry mixture is heated to polymerize and crosslink the monomer and form a firm polymer-solvent gel matrix. The solid product may be removed from the mold and heated to first remove the solvent and subsequently remove the polymer, where after the product may be sintered.

Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

PubMed Central

Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P.

2016-01-01

Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

A Legionella pneumophila collagen-like protein encoded by a gene with a variable number of tandem repeats is involved in the adherence and invasion of host cells.

PubMed

Vandersmissen, Liesbeth; De Buck, Emmy; Saels, Veerle; Coil, David A; Anné, Jozef

2010-05-01

Legionella pneumophila is a Gram-negative, facultative intracellular pathogen and the causative agent of Legionnaires' disease, a severe pneumonia in humans. Analysis of the Legionella sequenced genomes revealed a gene with a variable number of tandem repeats (VNTRs), whose number varies between strains. We examined the strain distribution of this gene among a collection of 108 clinical, environmental and hot spring serotype I strains. Twelve variants were identified, but no correlation was observed between the number of repeat units and clinical and environmental strains. The encoded protein contains the C-terminal consensus motif of outer membrane proteins and has a large region of collagen-like repeats that is encoded by the VNTR region. We have therefore annotated this protein Lcl for Legionella collagen-like protein. Lcl was shown to contribute to the adherence and invasion of host cells and it was demonstrated that the number of repeat units present in lcl had an influence on these adhesion characteristics.