Identification of protein interaction regions of VINC/NEAT1/Men epsilon RNA

The virus inducible non-coding RNA (VINC) was detected initially in the brain of mice infected with Japanese encephalitis virus (JEV) and rabies virus. VINC is also known as NEAT1 or Men epsilon RNA. It is localized in the nuclear paraspeckles of several murine as well as human cell lines and is essential for paraspeckle formation. We demonstrate that VINC interacts with the paraspeckle protein, P54nrb through three different protein interaction regions (PIRs) one of which (PIR-1) is localized near the 50 end while the other two (PIR-2, PIR-3) are localized near the 30 region of VINC. Our studies suggest that VINC may interact with P54nrb through a novel mechanism which is different from that reported for protein coding RNAs. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

Observation of a chiral smectic phase in azobenzene-linked bolaamphiphiles containing free sugars

Amphiphilic sugars exhibit both lyotropic and thermotropic liquid-crystalline behavior. Interestingly, in spite of the abundance of chiral centers in amphiphilic sugars, their liquid-crystalline phases do not exhibit macroscopic chirality. Herein, we report on the first observation of macroscopic chirality in sugar-based bolaamphiphiles containing free hydroxyl groups. The manifestation of the chiral smectic C* phase in these bolaamphiphiles has been observed to be critically dependent on the presence of the azobenzene moiety and the suitable length of the methylene spacer. These results imply that by suitable selection of linker groups, mesogenic bolaamphiphiles possessing macroscopic chirality can be designed using a variety of naturally available sugar derivatives.

Unfolding of Plasmodium falciparum Triosephosphate Isomerase in Urea and Guanidinium Chloride: Evidence for a Novel Disulfide Exchange Reaction in a Covalently Cross-Linked Mutant†

The conformational stability of Plasmodium falciparum triosephosphate isomerase (TIMWT) enzyme has been investigated in urea and guanidinium chloride (GdmCl) solutions using circular dichroism, fluorescence, and size-exclusion chromatography. The dimeric enzyme is remarkably stable in urea solutions. It retains considerable secondary, tertiary, and quaternary structure even in 8 M urea. In contrast, the unfolding transition is complete by 2.4 M GdmCl. Although the secondary as well as the tertiary interactions melt before the perturbation of the quaternary structure, these studies imply that the dissociation of the dimer into monomers ultimately leads to the collapse of the structure, suggesting that the interfacial interactions play a major role in determining multimeric protein stability. The C-m(urea)/C-m(GdmCl) ratio (where C-m is the concentration of the denaturant required at the transition midpoint) is unusually high for triosephosphate isomerase as compared to other monomeric and dimeric proteins. A disulfide crosslinked mutant protein (Y74C) engineered to form two disulfide cross-links across the interface (13-74') and (13'-74) is dramatically destablized in urea. The unfolding transition is complete by 6 M urea and involves a novel mechanism of dimer dissociation through intramolecular thiol-disulfide exchange.

Prediction of estrus cyclicity in Asian elephants (Elephas maximus) through estimation of fecal progesterone metabolite: development of an enzyme-linked immuno-sorbent assay

Asian elephants (Dephas maximus), prominent ``flagship species'', arelisted under the category of endangered species (EN - A2c, ver. 3.1, IUCN Red List 2009) and there is a need for their conservation This requires understanding demographic and reproductive dynamics of the species. Monitoring reproductive status of any species is traditionally being carried out through invasive blood sampling and this is restrictive for large animals such as wild or semi-captive elephants due to legal. ethical, and practical reasons Hence. there is a need for a non-invasive technique to assess reproductive cyclicity profiles of elephants. which will help in the species' conservation strategies In this study. we developed an indirect competitive enzyme linked immuno-sorbent assay (ELISA) to estimate the concentration of one of the progesterone-metabolites i.e, allopregnanolone (5 alpha-P-3OH) in fecal samples of As elephants We validated the assay which had a sensitivity of 0.25 mu M at 90% binding with an EC50 value of 1 37 mu M Using female elephants. kept under semi-captive conditions in the forest camps of Mudumalar Wildlife Sanctuary, Tamil Nadu and Bandipur National Park, Karnataka, India. we measured fecal progesterone-metabolite (5 alpha-P-3OH) concentrations in six an and showed their clear correlation with those of scrum progesterone measured by a standard radio-immuno assay. Statistical analyses using a Linear Mixed Effect model showed a positive correlation (P < 0 1) between the profiles of fecal 5 alpha-P-3OH (range 0 5-10 mu g/g) and serum progesterone (range: 0 1-1 8 ng/mL) Therefore, our studies show, for the first time, that the fecal progesterone-metabolite assay could be exploited to predict estrus cyclicity and to potentially assess the reproductive status of captive and free-ranging female Asian elephants, thereby helping to plan their breeding strategy (C) 2010 Elsevier Inc.All rights reserved.

Enzymatic Degradation of Poly(soybean oil-g-methyl methacrylate)

This study discusses grafting of methyl methacrylate units from thepolymeric soybean oil peroxide to produce poly(soybean oil-graft-methyl methacrylate) (PSO-g-PMMA). The degradation of this copolymer in solution was evaluated in the presence of different lipases, viz Candida rugosa (CR), Lipolase 100T (LP), Novozym 435 (N435) and Porcine pancreas (PP), at different temperatures The copolymer degraded by specific chain end scission and the mass fraction of the specific product evolved was determined The degradation was modeled using continuous distribution kinetics to determine the rate coefficients ofmenzymatic chain end scission and deactivation of the enzyme The enzymes, CR. LP and N435 exhibited maximum activity for the degradation of PSO-g-PMMA at 60 degrees C, while PP was most active at 50 degrees C. The thermal degradability of the copolymer, assessed by thermo-gravimetry, indicated that the activation energy of degradation of the copolymer was 154 kJ mol(-1), which was lesser than that of the PMMA homopolymer.

Adsorption of anionic dyes on chitosan grafted poly(alkyl methacrylate)s

Chitosan grafted poly(alkyl methacrylate)s (namely chitosan grafted poly(methyl methacrylate) (ChgPMMA), chitosan grafted poly(ethyl methacrylate)(ChgPEMA), chitosan grafted poly(butyl methacrylate) (ChgPBMA) and chitosan grafted poly(hexyl methacrylate) (ChgPHMA)) were synthesized and characterized by using FT-IR and C-13 NMR techniques. The adsorption batch experiments on these grafted copolymers were conducted by using an anionic sulfonated dye. Orange-G. A pseudo-second-order kinetic model was used to determine the kinetics of adsorption. The effect of grafting, effect of process variables and the effect of different sulfonated anionic dyes (Orange-C, Congo Red, Remazol Brill Blue R and Methyl Blue) on the adsorption kinetics was determined. The Langmuir and Freundlich models were used to fit the adsorption isotherms and from the values of correlation coefficients (R-2), it was observed that the experimental data fits very well to the Langmuir model. The values of the maximum adsorption capacity of the adsorbents follow the order: ChgPMMA > ChgPEMA > ChgPBMA > ChgPHMA > chitosan. (C) 2010 Elsevier B.V. All rights reserved.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa

Purpose: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. Methods: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. Results: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease.

Main chain and segmental dynamics of semi interpenetrating based on polyisoprene and poly(methyl methacrylate)

Main chain and segmental dynamics of polyisoprene (PI) and poly(methyl methacrylate)(PMMA) chains in semi IPNs were systematically studied over a wide range of temperatures (above and below T-g of both polymers) as a function of composition, crosslink density, and molecular weight. The immiscible polymers retained most of its characteristic molecular motion; however, the semi IPN synthesis resulted in dramatic changes in the motional behavior of both polymers due to the molecular level interpenetration between two polymer chains. ESR spin probe method was found to be sensitive to the concentration changes of PMMA in semi IPNs. Low temperature spectra showed the characteristics of rigid limit spectra, and in the range of 293-373 K.complex spectra were obtained with the slow component mostly arisingout of the PMMA rich regions and fast component from the PI phase. We found that the rigid PMMA chains closely interpenetrated into thehighly mobile PI network imparts motional restriction in nearby PI chains, and the highly mobile PI chains induce some degree of flexibility in highly rigid PMMA chains. Molecular level interchain mixing was found to be more efficient at a PMMA concentration of 35 wt.%. Moreover, the strong interphase formed in the above mentionedsemi IPN contributed to the large slow component in the ESR spectra at higher temperature. The shape of the spectra along with the data obtained from the simulations of spectra was correlated to the morphology of the semi IPNs. The correlation time measurement detected the motional region associated with the glass transition of PI and PMMA, and these regions were found to follow the same pattern of shifts in a-relaxation of PI and PMMA observed in DMA analysis. Activation energies associated with the T-g regions were also calculated. T-50G was found to correlate with the T-g of PMMA, and the volume of polymer segments undergoing glass transitional motion was calculated to be 1.7 nm(3).C-13 T-1 rho measurements of PMMA carbons indicate that the molecular level interactions were strong in semi IPN irrespective of the immiscible nature of polymers. The motional characteristics of H atoms attached to carbon atoms in both polymers were analyzed using 2D WISE NMR. Main relaxations of both components shifted inward, and both SEM and TEM analysis showed the development of a nanometer sized morphology in the case of highly crosslinked semi IPN. (C) 2010 Elsevier Ltd. All rights reserved.

Ultrasonic degradation of poly (styrene-co-alkyl methacrylate) copolymers

The ultrasonic degradation of poly (styrene-co-methyl methacrylate) (SMMA), poly (styrene-co-ethyl methacrylate) (SEMA) and poly (styrene-co-butyl methacrylate) (SBMA) copolymers of different compositions was studied. The copolymers were synthesized and NMR spectroscopy was used to determine the composition, and the glass transition temperatures were determined by DSC. The reactivity ratios were determined by the Kelen-Tudos method and it indicated that the copolymers were random. The effect of solvent, temperature and copolymer composition on the ultrasonic degradation rate of these copolymers was investigated. A model based on continuous distribution kinetics was employed to study the degradation kinetics. The degradation rate coefficients of the copolymers decreased with an increase in the styrene content in the copolymer. At any particular copolymer composition the rate of degradation follows the order: SBMA >SEMA > SMMA. Thermogravimetric analysis (TGA) of the copolymers was carried in order to assess their thermal stability. The same order of degradation was observed for the thermal degradation of the copolymers as that observed for ultrasonic degradation. (C) 2010 Elsevier B.V. All rights reserved.

Degradation Kinetics of Poly(HDDA-co-MMA)

1,6-hexanediol diacrylate (HDDA) and methyl methacrylate (MMA) were copolymerized in different weight ratios using UV light induced photo-polymerization to give poly(HDDA-co-MMA). Differential scanning calorimetry shows that copolymer was formed. The thermogravimetric and differential scanning calorimetric studies with different heating rates were carried out on these copolymers to understand the nature of degradation and to determine its kinetics. Different kinetic models were adopted to evaluate various parameters like the activation energy, the order, and the frequency factor. These analyses are important to study the binder removal from 3D-shaped ceramic objects made by techniques like Solid free form fabrication. (C) 2010 Wiley Periodicals, Inc. J Appl Polym Sci 117: 2444-2453, 2010.

Hardness of approximation results for the problem of finding the stopping distance in Tanner graphs

Tanner Graph representation of linear block codes is widely used by iterative decoding algorithms for recovering data transmitted across a noisy communication channel from errors and erasures introduced by the channel. The stopping distance of a Tanner graph T for a binary linear block code C determines the number of erasures correctable using iterative decoding on the Tanner graph T when data is transmitted across a binary erasure channel using the code C. We show that the problem of finding the stopping distance of a Tanner graph is hard to approximate within any positive constant approximation ratio in polynomial time unless P = NP. It is also shown as a consequence that there can be no approximation algorithm for the problem achieving an approximation ratio of 2(log n)(1-epsilon) for any epsilon > 0 unless NP subset of DTIME(n(poly(log n))).

Synthesis of Poly(1,4-Divinylbenzene Peroxide)

Polymeric peroxides have received renewed attention in the recent past, in view of some significant explorations of their physical and chemical properties. The potential of polymeric peroxides as a class, as specialized fuel, and the need to synthesize such new materials have been reported in the literature. So far, this class of polymers is constituted only by a dozen or so polyperoxides. From the point of view of their use in propellant applications, the importance lies in making materials which are easy to handle etc., unlike the earlier reported poly(styrene peroxide) (PSP), a sticky semi-solid mass. However, judging from the better combustion characteristics, exploring aromatic monomers was thought worthwhile. In this preliminary communication, the synthesis of a new polymeric peroxide made from 1,4-divinylbenzene is reported. The polymer obtained was in powder form and had an exothermic heat of degradation approximately equal to that of PSP. 4 ref.--AA

Effect of plasticizers on magnesium-poly(ethyleneoxide) polymer electrolyte

Solid polymer electrolytes (SPEs) of poly(ethyleneoxide) and magnesium triflate, which are plasticized with propylene carbonate (PC), ethylene carbonate (EC) and a mixture of PC and EC, are studied for their conductivity, ac impedance of the Mg I SPE interface, cyclic voltammetry, infrared spectroscopy and differential scanning calorimetry. in the presence of plasticizers, the ionic conductivity (a) increases from a value of 1 x 10(-8) S cm(-1) to about 1 x 10(-4) S cm(-1) at ambient temperature. The a is found to follow a VTF relationship with temperature. The values of the activation energy, pre-exponential factor and equilibrium glass transition temperature are shown to depend on the concentration of plasticizer. Ac impedance studies indicate lower interfacial impedance of Mg/plasticized SPE than stainless steel/plasticized SPE. The impedance spectra are analyzed using a non-linear least square curve fitting technique and the interfacial resistance of Mg/plasticized SPE is evaluated. The cyclic voltammetric results suggest a quasireversible type of Mg/Mg2+ couple in plasticized SPE. (C) 2000 Elsevier Science B.V. All rights reserved.

Characterization of poly(ADP-ribosyl)ated domains of rat pachytene chromatin

Poly(ADP-ribosyl)ation of nuclear proteins was several-fold higher in the pachytene spermatocytes than in the premeiotic germ cells of the rat. Among the histones of the pachytene nucleus, histone subtypes H2A, H1 and H3 were poly(ADP-ribosyl)ated. Based on the immunoaffinity fractionation procedure of Malik, Miwa, Sugimara & Smulson [(1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2554-2558] we have fractionated DNAase-II-solubilized chromatin into poly(ADP-ribosyl)ated chromatin (PAC) and non-poly(ADP-ribosyl)ated chromatin (non-PAC) domains on an anti-[poly(ADP-ribose)] IgG affinity matrix. Approx. 2.5% of the pachytene chromatin represented the PAC domains. A significant amount of [alpha-32P]dATP-labelled pachytene chromatin (labelled in vitro) was bound to the affinity matrix. The DNA of pachytene PAC domains had internal strand breaks, significant length of gaps and ligatable ends, namely 5'-phosphoryl and 3'-hydroxyl termini. On the other hand, the PAC domains from 18 h regenerating liver had very few gaps, if any. The presence of gaps in the pachytene PAC DNA was also evident from thermal denaturation studies. Although many of the polypeptides were common to the PAC domains of both pachytene and regenerating liver, the DNA sequences associated with these domains were quite different. A 20 kDa protein and the testis-specific histone H1t were selectively enriched in the pachytene PAC domains. The pachytene PAC domains also contained approx. 10% of the messenger coding sequences present in the DNAase-II-solubilized chromatin. The pachytene PAC domains, therefore, may represent highly enriched DNA-repair domains of the pachytene nucleus.

Peroxomonosulphate initiated graft copolymerization of aniline onto poly(propylene) fibre - A kinetic approach

Graft copolymerization of poly(aniline) (PANI) onto poly(propylene) (PP) fibre was carried out in aqueous acidic medium under nitrogen atmosphere by using peroxomonosulphate (PMS) as a lone initiator. The non-conducting fibre was now made into a conducting one through the chemical grafting of PANI units onto the PP fibre backbone. The content of PANI in the backbone was found to vary while varying the [ANI], [PMS] and amount of PP fibre. Various graft parameters were evaluated. The chemical grafting of PANI onto PP fibre was confirmed by conductivity measurements.