Estimation of ^{3}J_{HN\hbox{-}H\alpha} and ^{3}J_{H\alpha\hbox{-}H\beta} coupling constants from heteronuclear TOCSY spectra

(3)J proton-proton coupling constants bear information on the intervening dihedral angles. Methods have been developed to derive this information from NMR spectra of proteins. Using series expansion of the time dependent density matrix, and exploiting the simple topology of amino acid spin-systems, formulae for estimation of (3)J(HN-Halpha) and (3)J(Halpha-Hbeta) from HSQC-TOCSY spectra are derived. The results obtained on a protein entailing both alpha-helix and beta-sheet secondary structure elements agree very well with J-coupling constants computed from the X-ray structure. The method compares well with existing methods and requires only 2D spectra which would be typically otherwise recorded for structural studies.     

Endor characterization and D2O exchange in the \begin{array}{*{20}c} {\mathop Z\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array} /{\kern 1pt} \begin{array}{*{20}c} {\mathop D\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array} radical in photosystem II

The early suggestion by Lozier and Butler (Photochem. Photobiol. 17, 133–137 (1973)) that EPR Signal II arises from radicals associated with the water-splitting process in PSII has been confirmed and extended over the intervening years. Recent work has identified the Signal II radicals, \(\begin{array}{*{20}c} {\mathop D\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array}\) and \(\begin{array}{*{20}c} {\mathop Z\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array}\) , with plastosemiquinone cation species. In the experiments presented here we have used ENDOR spectroscopy and D₂O/H₂O exchange to characterize these paramagnets in more detail. The ENDOR matrix region, which arises from protons which interact weakly with the unpaired electron spin, is well-resolved at 4 K and at least seven resonances are apparent. A number of hyperfine couplings in the 3–8 MHz range are observed and are suggested to arise from methyl or hydroxyl protons which occur as substituents on the plastosemiquinone cation ring or from amino acid protons hydrogen-bonded to the 1,4-hydroxyl groups. Orientation selection experiments are consistent with these possibilities. D₂O/H₂O exchange shows that the D⁺/Z⁺ site is accessible to solvent. However, the exchange occurs slowly and is not complete even after 72 hours which suggests that the free radicals are functionally isolated from solvent water.     

Numerical integration of the equations of motion describing the acceleration of plasma particles in Syrovatski $$\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\smile}$}}{l} $$ 's model of the dynamic current sheet

The acceleration of solar-wind protons in a current sheet in the Earth's magnetotail, in which the geomagnetic field lines reconnect, is investigated numerically using the dynamic current sheet model proposed by S.I. Syrovatski $\overset{\lower0.5em\hbox{$\overset{\lower0.5em\hbox{ . The dynamics of current sheets in the Earth's magnetotail is analyzed. In addition to the known solutions, the solution describing a contracting current sheet is derived. The time evolution of the magnetic field structure in Syrovatski $\overset{\lower0.5em\hbox{$\overset{\lower0.5em\hbox{ 's model is calculated numerically. The energy spectrum of the protons that are accelerated in the sheet by induction electric fields during rapid changes in the sheet topology is calculated and analyzed. A study is made of proton acceleration up to the time when the current sheet ruptures in the course of its evolution.     

Cloning,characterization and expression of \emph{OsFMO}_{{\mathbf{(}\emph{t}\mathbf{)}}} in rice encoding a flavin monooxygenase

Flavin monooxygenases (FMO) play a key role in tryptophan (Trp)-dependent indole-acetic acid (IAA) biosynthesis in plants and regulate plant growth and development. In this study, the full-length genomic DNA and cDNA of OsFMO _(t), a FMO gene that was originally identified from a rolled-leaf mutant in rice, was isolated and cloned from wild type of the rolled-leaf mutant. OsFMO _(t) was found to have four exons and three introns, and encode a protein with 422 amino acid residues that contains two basic conserved motifs, with a ‘G×G××G’ characteristic structure. OsFMO_(t) showed high amino acid sequence identity with FMO proteins from other plants, in particular with YUCCA from Arabidopsis, FLOOZY from Petunia, and OsYUCCA1 from rice. Our phylogenetic analysis showed that OsFMO_(t) and the homologous FMO proteins belong to the same clade in the evolutionary tree. Overexpression of OsFMO _(t) in transformed rice calli produced IAA-excessive phenotypes that showed browning and lethal effects when exogenous auxins such as naphthylacetic acid (NAA) were added to the medium. These results suggested that the OsFMO_(t) protein is involved in IAA biosynthesis in rice and its overexpression could lead to the malformation of calli. Spatio-temporal expression analysis using RT-PCR and histochemical analysis for GUS activity revealed that expression of OsFMO _(t) was totally absent in the rolled-leaf mutant. However, in the wild type variety, this gene was expressed at different levels temporally and spatially, with the highest expression observed in tissues with fast growth and cell division such as shoot apexes, tender leaves and root tips. Our results demonstrated that IAA biosynthesis regulated by OsFMO _(t) is likely localized and might play an essential role in shaping local IAA concentrations which, in turn, is critical for regulating normal growth and development in rice.     

Coupling of secondary active transport with\Delta \tilde \mu _{H^ + }

Most nutrients and ions in bacteria, yeasts, algae, and plants are transported uphill at the expense of a gradient of the electrochemical potential of protons deltamu-H+ (a type of secondary active transport). Diagnosis of such transports rests on the determination of the transmembrane electrical potential difference deltapsi and the difference of pH at the two membrane sides. The behavior of kinetic parameters K(T) (the half-saturation constant) and J(max), (the maximum rate of transport) upon changing driving ion concentrations and electrical potentials may be used to determine the molecular details of the transport reaction. Equilibrium accumulation ratios of driven solutes are expected to be in agreement with the deltapsi and deltapH measured independently, as well as with the Haldane-type expression involving K(T) and J(max). Different stoichiometries of H+/solute, as well as intramembrane effects of pH and deltapsi, may account for some of the observed inconsistencies.     

N$_{3}^{-}$ azide anion confined inside finite-size carbon nanotubes

In this work, the confinement of an N\(_{3}^{-}\) azide anion inside finite-size single-wall zigzag and armchair carbon nanotubes of different diameters has been studied by wave function and density functional theory. Unrelaxed and relaxed interaction energies have been computed, resulting in a favorable interaction between the guest and host system. In particular, the largest interaction has been observed for the confinement in an armchair (5,5) carbon nanotube, for which a natural population analysis as well as an investigation based on the molecular electrostatic potential has been carried out. The nature of the interaction between the two fragments appears to be mainly electrostatic, favored by the enhanced polarizability of the nanotube wall treated as a finite system and passivated by hydrogen atoms. The results obtained are promising for possible applications of this complex as a starting point for the stabilization of larger polynitrogen compounds, suitable as a high-energy density material.     

Further comments on replication in\left( {\mathfrak{M},\Re } \right)-systems-systems

A number of inaccuracies in previous papers are pointed out and amended, and some implications of the correct situation are outlined.     

{Omega}-oxidation of {alpha}-chlorinated fatty acids: identification of {alpha}-chlorinated dicarboxylic acids

Myeloperoxidase-derived HOCl targets tissue- and lipoprotein-associated plasmalogens to generate α-chlorinated fatty aldehydes, including 2-chlorohexadecanal. Under physiological conditions, 2-chlorohexadecanal is oxidized to 2-chlorohexadecanoic acid (2-ClHA). This study demonstrates the catabolism of 2-ClHA by ω-oxidation and subsequent β-oxidation from the ω-end. Mass spectrometric analyses revealed that 2-ClHA is ω-oxidized in the presence of liver microsomes with initial ω-hydroxylation of 2-ClHA. Subsequent oxidation steps were examined in a human hepatocellular cell line (HepG2). Three different α-chlorinated dicarboxylic acids, 2-chlorohexadecane-(1,16)-dioic acid, 2-chlorotetradecane-(1,14)-dioic acid, and 2-chloroadipic acid (2-ClAdA), were identified. Levels of 2-chlorohexadecane-(1,16)-dioic acid, 2-chlorotetradecane-(1,14)-dioic acid, and 2-ClAdA produced by HepG2 cells were dependent on the concentration of 2-ClHA and the incubation time. Synthetic stable isotope-labeled 2-ClHA was used to demonstrate a precursor-product relationship between 2-ClHA and the α-chlorinated dicarboxylic acids. We also report the identification of endogenous 2-ClAdA in human and rat urine and elevations in stable isotope-labeled urinary 2-ClAdA in rats subjected to intraperitoneal administration of stable isotope-labeled 2-ClHA. Furthermore, urinary 2-ClAdA and plasma 2-ClHA levels are increased in LPS-treated rats. Taken together, these data show that 2-ClHA is ω-oxidized to generate α-chlorinated dicarboxylic acids, which include α-chloroadipic acid that is excreted in the urine.     

sRNAbase: A Web Resource for Small RNAs in Enterobacteriaceae\m{1}

Bacterial small RNAs (sRNAs) have gained considerable attention due to their multivalent roles in the survival and pathogenesis of bacteria and mostly identified through bio-computational methods. A manually curated web-resource, sRNAbase has been constructed to give comprehensive and exhaustive information on non-coding small RNAs excluding tRNAs and rRNAs in Enterobacteriaceae family. The sRNA entries curated in sRNAbase contain experimentally verified small RNAs available in the literature and their partial/non-homologs reported within the related genomes from our earlier studies. The sRNAbase aims to facilitate the scientific community by providing information on the physical genomic location of the non-coding small RNAs, its alias names, sequences, strand orientation, gene identification numbers of the conserved genes that sandwiches the particular sRNA with possible functional role and a link to the PubMed literatures. Currently, sRNAbase holding information on 1986 entries belongs to 80 sRNA families spread over 45 Enterobacteriaceae genomes. The sRNAbase is accessible on the web at http://bicmku.in:8081/srnabase/.     

p38 MAPK mediates renal tubular cell TNF-{alpha} production and TNF-{alpha}-dependent apoptosis during simulated ischemia

Ischemia causes renal tubular cellloss through apoptosis; however, the mechanisms of this processremain unclear. Using the renal tubular epithelial cell lineLLC-PK₁, we developed a model of simulated ischemia(SI) to investigate the role of p38 MAPK (mitogen-activated proteinkinase) in renal cell tumor necrosis factor- (TNF-) mRNAproduction, protein bioactivity, and apoptosis. Resultsdemonstrate that 60 min of SI induced maximal TNF- mRNA productionand bioactivity. Furthermore, 60 min of ischemia induced renaltubular cell apoptosis at all substrate replacement time pointsexamined, with peak apoptotic cell death occurring after either 24 or 48 h. p38 MAPK inhibition abolished TNF- mRNA production andTNF- bioactivity, and both p38 MAPK inhibition and TNF- neutralization (anti-porcine TNF- antibody) preventedapoptosis after 60 min of SI. These results constitute theinitial demonstration that 1) renal tubular cells produceTNF- mRNA and biologically active TNF- and undergoapoptosis in response to SI, and 2) p38 MAPKmediates renal tubular cell TNF- production and TNF--dependent apoptosis after SI.