Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases

The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.

UNIQUENESS OF SOLUTIONS TO SCHRODINGER EQUATIONS ON H-TYPE GROUPS

This paper deals with the Schrodinger equation i partial derivative(s)u(z, t; s) - Lu(z, t; s) = 0; where L is the sub-Laplacian on the Heisenberg group. Assume that the initial data f satisfies vertical bar f(z, t)vertical bar less than or similar to q(alpha)(z, t), where q(s) is the heat kernel associated to L. If in addition vertical bar u(z, t; s(0))vertical bar less than or similar to q(beta)(z, t), for some s(0) is an element of R \textbackslash {0}, then we prove that u(z, t; s) = 0 for all s is an element of R whenever alpha beta < s(0)(2). This result holds true in the more general context of H-type groups. We also prove an analogous result for the Grushin operator on Rn+1.

Synthesis of novel poly[(2,5-dimethoxy-p-phenylene)vinylene] precursors having two eliminatable groups: An approach for the control of conjugation length

Poly[(2,5-dimethoxy-p-phenylene)vinylene] (DMPPV) of varying conjugation length was synthesized by selective elimination of organic soluble precursor polymers that contained two eliminatable groups, namely, methoxy and acetate groups. These precursor copolymers were in turn synthesized by competitive nucleophilic substitution of the sulfonium polyelectrolyte precursor (generated by the standard Wessling route) using methanol and sodium acetate in acetic acid. The composition of the precursor copolymer, in terms of the relative amounts of methoxy and acetate groups, was controlled by varying the composition of the reaction mixture during nucleophilic substitution. Thermal elimination of these precursor copolymers at 250 degrees C, yielded partially conjugated polymers, whose color varied from light yellow to deep red. FT-IR studies confirmed that, while essentially all the acetate groups were eliminated, the methoxy groups were intact and caused the interruption in conjugation. Preliminary photoluminescence studies of the partially eliminated DMPPV samples showed a gradual shift in the emission maximum from 498 to 598 nm with increasing conjugation lengths, suggesting that the color of LED devices fabricated from such polymers can, in principle, be fine-tuned.

Identification of amino groups in the carbohydrate binding activity of winged bean acidic agglutinin

Chemical modification studies reveal that the modification of amino groups in WBA II leads to a complete loss in the hemagglutinating and saccharide binding activities. Since WBA II is a dimeric molecule and contains two binding sites, one amino group in each of the binding sites is inferred to be essential for its activity. The presence of amino group which has a potential to form hydrogen bonded interactions with the ligand, substantiates our observation regarding the forces involved in WBA II-receptor and WBA II-simple sugar interactions.

Working group report: Quantum chromodynamics sub-group

This is the report of the QCD working sub-group at the Tenth Workshop on High Energy Physics Phenomenology (WHEPP-X).

Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Background: Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results: The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion: The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

On-Chip Clock Network Skew Measurement using Sub-Sampling

We present a technique for an all-digital on-chip delay measurement system to measure the skews in a clock distribution network. It uses the principle of sub-sampling. Measurements from a prototype fabricated in a 65 nm industrial process, indicate the ability to measure delays with a resolution of 0.5ps and a DNL of 1.2 ps.

Gauge theory of a group of diffeomorphisms. II. The conformal and de Sitter groups

The extension of Hehl's Poincaré gauge theory to more general groups that include space-time diffeomorphisms is worked out for two particular examples, one corresponding to the action of the conformal group on Minkowski space, and the other to the action of the de Sitter group on de Sitter space, and the effect of these groups on physical fields.

Algebraic and geometric intersection numbers for free groups

We show that the algebraic intersection number of Scott and Swarup for splittings of free groups Coincides With the geometric intersection number for the sphere complex of the connected sum of copies of S-2 x S-1. (C) 2009 Elsevier B.V. All rights reserved.

Choice of the End Functional Groups in Tri(p-phenylenevinylene) Derivatives Controls Its Physical Gelation Abilities

New supramolecular organogels based on all-trans-tri(p-phenylenevinylene) (TPV) systems possessing different terminal groups, e.g., oxime, hydrazone, phenylhydrazone, and semicarbazone have been synthesized. The self-assembly properties of the compounds that gelate in specific organic solvents and the aggregation motifs of these molecules in the organogels were investigated using UV−vis, fluorescence, FT-IR, and 1H NMR spectroscopy, electron microscopy, differential scanning calorimetry (DSC), and rheology. The temperature variable UV−vis and fluorescence spectroscopy in different solvents clearly show the aggregation pattern of the self-assemblies promoted by hydrogen bonding, aromatic π-stacking, and van der Waals interactions among the individual TPV units. Gelation could be controlled by variation in the number of hydrogen-bonding donors and acceptors in the terminal functional groups of this class of gelators. Also wherever gelation is observed, the individual fibers in gels change to other types of networks in their aggregates depending on the number of hydrogen-bonding sites in the terminal functions. Comparison of the thermal stability of the gels obtained from DSC data of different gelators demonstrates higher phase transition temperature and enthalpy for the hydrazone-based gelator. Rheological studies indicate that the presence of more hydrogen-bonding donors in the periphery of the gelator molecules makes the gel more viscoelastic solidlike. However, in the presence of more numbers of hydrogen-bonding donor/acceptors at the periphery of TPVs such as with semicarbazone a precipitation as opposed to gelation was observed. Clearly, the choice of the end functional groups and the number of hydrogen-bonding groups in the TPV backbone holds the key and modulates the effective length of the chromophore, resulting in interesting optical properties.

Embedding Of Non-Simple Lie-Groups, Coupling-Constant Relations And Non-Uniqueness Of Models Of Unification

A general derivation of the coupling constant relations which result on embedding a non-simple group like SU L (2) @ U(1) in a larger simple group (or graded Lie group) is given. It is shown that such relations depend only on the requirement (i) that the multiplet of vector fields form an irreducible representation of the unifying algebra and (ii) the transformation properties of the fermions under SU L (2). This point is illustrated in two ways, one by constructing two different unification groups containing the same fermions and therefore have same Weinberg angle; the other by putting different SU L (2) structures on the same fermions and consequently have different Weinberg angles. In particular the value sin~0=3/8 is characteristic of the sequential doublet models or models which invoke a large number of additional leptons like E 6, while addition of extra charged fermion singlets can reduce the value of sin ~ 0 to 1/4. We point out that at the present time the models of grand unification are far from unique.

On the reactivity of carboxyl groups of ribonuclease-A in anhydrous methanol

The esterification of Ribonuclease-A in methanol/0.1 M hydrochloric acid has been studied by measuring the decrease in the number of titratable groups of the protein and estimating the amount of methanol incorporated. Esterification of nearly five of the 11 free carboxyl groups of the protein resulted in almost complete inactivation of the enzyme. The initial products of esterification have been chromatographed on Amberlite columns, and five partially active methyl ester derivatives of Ribonuclease-A have been isolated. The dimethyl ester, the initial product of esterification with reduced catalytic activity, has the carboxyl groups of Glu-49 and Asp-53 modified. Even in the non-aqueous solvent, as in the native structure of the protein in aqueous solution, these carboxyl groups are the fast reacting ones. Subsquently, the esterification reaction appears to proceed preferentially at the C-terminal region of the molecule. Comparison of the reactivities of carboxyl groups of Ribonuclease-A in acidic methanol to that known in aqueous solutions (with carbodiimides) suggests that the structure of Ribonuclease-A in the non-aqueous solvent resembles, at least in part, the structure in aqueous environment.

Synthesis of a one-dimensional coordination polymer containing pendant hydrosulfide groups

In view of the recent interest in compounds containing M-SH units, an organotin hydrosulfide compound, Me2Sn(SH)(O2CMe) (1) was prepared by controlled hydrolysis of the diorganotin thioacetate. Under similar mild hydrolytic conditions the corresponding benzoate could not be isolated. Instead, the thiobenzoate complex, Me2Sn(SOCPh)(2) (3) was obtained in excellent yields indicating that there was no hydrolysis. Both 1 and 3 were characterized by X-ray crystallography. Some properties of the polymeric compound 1, such as spectral, electrical conductivity and NLO response were also studied. The reactivity and properties were explained using density functional calculations.

Synthetic polypeptide with antifreeze activity

MUCH information has been gathered in recent years on the so-called 'antifreeze' proteins which lower the freezing point of the serum of certain marine fishes living in sub-zero water temperatures1−4. The proteins from the Antarctic fish Trematomus borchgrevinki are glycoproteins with a repeating alanyl-alanyl-threonyl tripeptide sequence, the threonyl residue being linked to a disaccharide1,2. In contrast, the antifreeze protein from the winter flounder Pseudopleuronectus americanus in the North American Atlantic coastal region is made up of eight ammo acids with no apparent repeating sequence of the residues and no sugar moiety (ref. 4 and unpublished work of C. L. Hew, C. C. Yip & G. Fletcher). The antifreeze activity of these proteins is not compatible with the known colligative properties of solutes in solution and the mechanism of their action is not yet fully understood. But a common feature of both types of the antifreeze proteins is the preponderance of alanine which accounts for over 60% of the total amino residues. This fact, together with the absence of the carbohydrate in the protein from the winter flounder, prompted us to attempt the synthesis of polypeptide analogues having comparable proportions of alanine in them along with suitable other amino acids. As a first step, we made use of the lack of any obvious periodicity in the distribution of the alanyl residues in the flounder's protein and attempted the synthesis of a random copolypeptide containing about 65 mol % of alanine and 35 mol % of aspartic acid. The choice of aspartic acid was made on the basis of its being the next major amino acid in the flounder's protein3,4 and on the expectation that its polar character will help the water-solubility of the alanine-rich copolypeptide, as in other studies on alanine-containing random copolymers. In addition, Duman and DeVries4 have earlier indicated the involvement of carboxyl groups on the antifreeze activity by chemical modification studies. We report here the synthesis of this polypeptide and show that it possesses antifreeze activity.

Preparation of Palladium(II) Complexes of Isonitrosoacetylacetoneimines Having O- and N-Coordinated Isonitroso Groups

Methods for the preparation of palladium(II) complexes of the type Pd(R-IAI)(IAI'), where IAI' is the anion of isonitrosoacetylacetoneimine and R-IAI, its N-alkyl or N-aryl derivative, are given.