Isolation of an 800 kb contiguous DNA fragment encompassing a 3.5-cM region of chromosome 1 in Arabidopsis using YAC clones

The apetalal mutation of Arabidopsis affects floral meristem identity and the development of sepal and petal primordia of the flower. We mapped the available RFLP markers on chromosome 1 that are in the general vicinity of apetalal on a fine structure map and then chose the closest RFLP as a starting point for contiguous DNA (contig) generation. We report here a contig of about 800 kilobases (kb) that spans a 3.5 cM region of chromosome 1. We used genomic libraries of Arabidopsis prepared in yeast artificial chromosome (YAC) vectors and the detailed characterization of 19 YACs is reported. RFLPs displayed by the end fragments from the walk were mapped to align and correlate the genetic and physical maps for this region of chromosome 1. In this segment of the genome, 1 cM corresponds to a little over 200 kb of physical distance.

Primary structure of a cytotoxin-like basic protein from Naja naja naja (Indian Cobra) venom

The complete amino acid sequence of a cytotoxin-like basic protein (CLBP) from the venom of Naja naja naja (Indian Cobra) was determined by manual degradation using a 4-dimethylaminoazobenzene-4'-isothiocyanate double-coupling method. Peptide fragments obtained by chemical cleavage with cyanogen bromide and enzymic cleavages with trypsin and Staphylococcus aureus proteases for sequence analysis were purified by reversed-phase chromatography. The total number of amino acid residues was 61, with leucine as the C-terminal residue. (C) Munksgaard 1995.

Simulation and modelling of orbital debris environment by equivalent breakups

It is well known that the increasing space activities pose a serious threat to future missions. This is mainly due to the presence of spent stages, rockets spacecraft and fragments which can lead to collisions. The calculation of the collision probability of future space vehicles with the orbital debris is necessary for estimating the risk. There is lack of adequately catalogued and openly available detailed information on the explosion characteristics of trackable and untrackable debris data. Such a situation compels one to develop suitable mathematical modelling of the explosion and the resultant debris environment. Based on a study of the available information regarding the fragmentation, subsequent evolution and observation, it turns out to be possible to develop such a mathematical model connecting the dynamical features of the fragmentation with the geometrical/orbital characteristics of the debris and representing the environment through the idea of equivalent breakup. (C) 1997 COSPAR.

Molecular structure and reactions of 1,1 '-bi(acenaphthen-1-ylidene)-2,2 '-dione

The molecular structure of 1,1'-bi(acenaphthen-1-ylidene)-2,2'-dione 1, a potential building-block for the synthesis of fullerene fragments, has been investigated by X-ray crystallography and semi-empirical (AM1 and PM3) calculations. There is a good agreement between the calculated and crystal structure which is essentially planar and has E-configuration. In the solid state, molecules of 1 pack in an interesting manner as corrugated sheets sustained by a network of C-H ... O hydrogen bonds and resulting in the formation of tetrameric loops. While steric factors limit the reactivity of the carbonyl groups in 1, the ene double bond of the ene-dione moiety present in it exhibits propensity toward [4 + 2]-cycloadditions to furnish novel and highly compressed polycycles 8-10.

Nematogens with more flexible chains than aromatic rings in the core

Mesogens containing four rings in the main core can accommodate one terminal and two nearby lateral chains on each outside aromatic ring. These compounds containing six chains present an enantiotropic nematic range which is influenced by the rigidity of the links. The conformational behaviour of the first methyleneoxy group within the chains was investigated by one and two dimensional C-13 NMR. The sign of the jump in chemical shifts when entering the nematic phase indicates the folding of each lateral branch. Dipolar oscillations during cross-polarization contact provide the values of the bond order parameter. The two First lateral fragments do not behave in the same way, demonstrating the influence of the fragment along which the chain is back: folded.

PDB Goodies - a web-based GUI to manipulate the Protein Data Bank file

PDB Goodies is a web-based graphical user interface (GUI) to manipulate the Protein Data Bank file containing the three-dimensional atomic coordinates of protein structures. The program also allows users to save the manipulated three-dimensional atomic coordinate file on their local client system. These fragments are used in various stages of structure elucidation and analysis. This software is incorporated with all the three-dimensional protein structures available in the Protein Data Bank, which presently holds approximately 18 000 structures. In addition, this program works on a three-dimensional atomic coordinate file (Protein Data Bank format) uploaded from the client machine. The program is written using CGI/PERL scripts and is platform independent. The program PDB Goodies can be accessed over the World Wide Web at http:// 144.16.71.11/pdbgoodies/.

The absolute orientation of a molecule in space: Extension of the 'CIP' system

A scheme for denoting the absolute spatial orientation of molecules and molecular fragments is presented; this is based on three angular deviations - one for each spatial dimension - with respect to a reference orientation, which is itself defined with the help of certain features of the Cahn-Ingold-Prelog stereochemical notation. The new scheme helps in reconstructing the three-dimensional characteristics of molecules from purely verbal descriptors, and may thus find application in various information storage and retrieval processes (e.,-. encrypting holograms, etc.).

Cretaceous-Tertiary diversification among select Scolopendrid centipedes of South India

Given that peninsular India was part of the Gondwanan super continent, part of its current biota has Gondwanan origin. To determine the Gondwanan component of the peninsular Indian biota, a large number of species spanning diverse taxonomic groups need to be sampled from multiple, if not all, of the former Gondwanan fragments. Such a large scale phylogenetic approach will be time consuming and resource intensive. Here, we explore the utility of a limited sampling approach, wherein sampling is confined to one of the Gondwanan fragments (peninsular India), in identifying putative Gondwanan elements. To this end, samples of Scolopendrid centipedes from Western Ghats region of peninsular India were subjected to molecular phylogenetic and dating analyses. The resulting phylogenetic tree supported monophyly of the family Scolopendridae which was in turn split into two clades constituting tribes Otostigmini and Scolopendrini-Asanadini. Bayesian divergence date estimates suggested that the earliest diversifications within various genera were between 86 and 73 mya, indicating that these genera might have Gondwanan origin. In particular, at least four genera of Scolopendrid centipedes, Scolopendra, Cormocephalus, Rhysida and Digitipes, might have undergone diversification on the drifting peninsular India during the Late Cretaceous. These putative Gondwanan taxa can be subjected to more extensive sampling to confirm their Gondwanan origin. (C) 2011 Elsevier Inc. All rights reserved.

Crucible Steel in South India-Preliminary Investigations on Crucibles from Some Newly Identified Sites

European accounts from the 17th century onwards have referred to the repute and manufacture of “wootz’, a traditional crucible steel made especially in parts of southern India in the former provinces of Golconda, Mysore and Salem. Pliny's Natural History mentions the import of iron and steel from the Seres which have been thought to refer to the ancient southern Indian kingdom of the Cheras. As yet the scale of excavations and surface surveys is too limited to link the literary accounts to archaeometallurgical evidence, although pioneering exploratory investigations have been made by scholars, especially on the pre-industrial production sites of Konasamudram and Gatihosahalli discussed in 18th-19th century European accounts. In 1991–2 during preliminary surveys of ancient base metal mining sites, Srinivasan came across unreported dumps with crucible fragments at Mel-Siruvalur in Tamil Nadu, and Tintini and Machnur in Karnataka and she collected surface specimens from these sites as well as from the known site of Gatihosahalli. She was also given crucible fragments by the Tamil University, Tanjavur, from an excavated megalithic site at Kodumanal, dated to ca 2nd c. Bc, mentioned in Tamil Sangam literature (ca 3rd c. BC-3rd c. AD), and very near Karur, the ancient capital of the Sangam Cheras. Analyses of crucible fragments from the surface collection at Mel-Siruvalur showed several iron prills with a uniform pearlitic structure of high-carbon hypereutectoid steel (∼1–1.5% C) suggesting that the end product was uniformly a high-carbon steel of a structure consistent with those of high-carbon steels used successfully to experimentally replicate the watered steel patterns on ‘Damascus’ swords. Investigations indicate that the process was of carburisation of molten low carbon iron (m.p. 1400° C) in crucibles packed with carbonaceous matter. The fabric of crucibles from all the above mentioned sites appears similar. Preliminary investigations on these crucibles are thus reported to establish their relationship to crucible production of carbon steel and to thereby extend the known horizons of this technology further.

Synthesis, biological studies of linear and branched arabinofuranoside-containing glycolipids and their interaction with surfactant protein A

Oligoarabinofuranoside-containing glycolipids relevant to mycobacterial cell wall components were synthesized in order to understand the functional roles of such glycolipids. A series of linear tetra-, hexa-, octa-and a branched heptasaccharide oligoarabinofuranosides, with 1 -> 2 and 1 -> 5 a-linkages between the furanoside residues, were synthesized by chemical methods from readily available monomer building blocks. Upon the synthesis of glycolipids, constituted with a double alkyl chain-substituted sn-glycerol core and oligosaccharide fragments, biological studies were performed to identify the effect of synthetic glycolipids on the biofilm formation and sliding motilities of Mycobacterium smegmatis. Synthetic glycolipids and arabinofuranosides displayed an inhibitory effect on the growth profile, but mostly on the biofilm formation and maturation. Similarly, synthetic compounds also influenced the sliding motility of the bacteria. Further, biophysical studies were undertaken, so as to identify the interactions of the glycolipids with a pulmonary surfactant protein, namely surfactant protein A (SP-A), with the aid of the surface plasmon resonance technique. Specificities of each glycolipid interacting with SP-A were thus evaluated. From this study, glycolipids were found to exhibit higher apparent association constants than the corresponding oligosaccharide portion alone, without the double alkyl group-substituted glycerol core.

Severe wear of a near eutectic aluminium-silicon alloy

The severe wear of a near eutectic aluminium silicon alloy is explored using a range of electron microscopic, spectroscopic and diffraction techniques to identify the residually strained and unstrained regions, microcracks and oxidized regions in the subsurface. In severe wear the contact pressure exceeds the elastic shakedown limit. Under this condition the primary and eutectic silicon particles fragment drastically. The fragments are transported by the matrix as it undergoes incremental straining with each cyclic contact at the asperity level. The grains are refined from similar to 2000 nm in the bulk to 30 nm in the near surface region. A large reduction in the interparticle distance compared with that for a milder stage of wear gives rise to high strain gradients which contribute to an enhancement of the dislocation density. The resulting regions of very high strain in the boundaries of the recrystallized grains as well as within the subgrains lead to the formation of microvoidskracks. This is accompanied by the formation of brittle oxides at these subsurface interfaces due to enhanced diffusion of oxygen. We believe that the abundance of such microcracks in the near surface region, primed by severe plastic deformation, is what distinguishes a severe wear regime from mild wear. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

10 Years of Click Chemistry: Synthesis and Applications of Ferrocene-Derived Triazoles

Click chemistry has played a significant role as a rapid and versatile strategy for conjugating two molecular fragments under very mild reaction conditions. Introduction of ferrocene-derived triazole systems using click chemistry has attracted enormous interest in various fields due to its potential applications in electrochemical techniques for detection and sensing. The present discussion focuses on the synthesis of ferrocene-triazole and the importance of using a CuAAC reaction for such conjugation. Applications of ferrocene-based click reactions in conjugate chemistry, asymmetric catalysis, medicinal chemistry, host-guest interactions, and materials chemistry have been highlighted.

Stability of domain structures in multi-domain proteins

Multi-domain proteins have many advantages with respect to stability and folding inside cells. Here we attempt to understand the intricate relationship between the domain-domain interactions and the stability of domains in isolation. We provide quantitative treatment and proof for prevailing intuitive ideas on the strategies employed by nature to stabilize otherwise unstable domains. We find that domains incapable of independent stability are stabilized by favourable interactions with tethered domains in the multi-domain context. Stability of such folds to exist independently is optimized by evolution. Specific residue mutations in the sites equivalent to inter-domain interface enhance the overall solvation, thereby stabilizing these domain folds independently. A few naturally occurring variants at these sites alter communication between domains and affect stability leading to disease manifestation. Our analysis provides safe guidelines for mutagenesis which have attractive applications in obtaining stable fragments and domain constructs essential for structural studies by crystallography and NMR.

Phenylboronic acids in crystal engineering: Utility of the energetically unfavorable syn,syn-conformation in co-crystal design

Phenylboronic acids can exist, in principle, in three different conformers (syn,syn; syn,anti and anti,anti) with distinct energy profiles. In their native state, these compounds prefer the energetically favored syn, anti-conformation. In molecular complexes, however, the functionality exhibits conformational diversity. In this paper we report a series of co-crystals, with N-donor compounds, prepared by a design strategy involving the synthons based on the syn, syn-conformation of the boronic acid functionality. For this purpose, we employed compounds with the 1,2-diazo fragment (alprazolam, 1H-tetrazole, acetazolamide and benzotriazole), 1,10-phenanthroline and 2,2'-bipyridine for the co-crystallization experiments. However, our study shows that the mere presence of the 1,2-diazo fragment in the coformer does not guarantee the successful formation of co-crystals with a syn, syn-conformation of the boronic acid. [GRAPHICS] The -B(OH)(2) fragment makes unsymmetrical O-H center dot center dot center dot N heterosynthons with alprazolam (ALP) and 1,10-phenanthroline (PHEN). In the co-crystals of phenylboronic acids with 1H-tetrazole (TETR) and 2,2'-bipyridine (BPY), the symmetrical boronic acid dimer is the major synthon. In the BPY complex, boronic acid forms linear chains and the pyridine compound interacts with the lateral OH of boronic acid dimers that acts as a connector, thus forming a ladder structure. In the TETR complex, each heterocycle interacts with three boronic acids. While two boronic acids interact using the phenolic group, the third molecule generates O-H center dot center dot center dot N hydrogen bonds using the extra OH group, of -B(OH)(2) fragment, left after the dimer formation. Thus, although molecules were selected retrosynthetically with the 1,2-diazo fragment or with nearby hetero-atoms to induce co-crystal formation using the syn,syn-orientation of the -B(OH)(2) functionality, co-crystal formation is in fact selective and is probably driven by energy factors. Acetazolamide (ACET) contains self-complementary functional groups and hence creates stable homosynthons. Phenylboronic acids being weak competitors fail to perturb the homosynthons and hence the components crystallize separately. Therefore, besides the availability of possible hydrogen bond acceptors in the required position and orientation, the ability of the phenyl-boronic acid to perturb the existing interactions is also a prerequisite to form co-crystals. This is illustrated in the table below. In the case of ALP, PHEN and BPY, the native structures are stabilized by weak interactions and may be influenced by the boronic acid fragment. Thus phenylboronic acids can attain co-crystals with those compounds, wherein the cyclic O-H center dot center dot center dot N hydrogen bonds are stronger than the individual homo-interactions. This can lower the lattice energy of the molecular complex as compared with the individual crystals. [GRAPHICS] Phenylboronic acids show some selectivity in the formation of co-crystals with N-heterocycles. The differences in solubility of the components fall short to provide a possible reason for the selective formation of co-crystals only with certain compounds. These compounds, being weak acids, do not follow the Delta pK(a) analysis and hence fail to provide any conclusive observation. Theoretical results show that of the three conformers possible, the syn,anti conformer is the most stable. The relative stabilities of the three conformers syn,anti,syn,syn and anti,anti are 0.0, 2.18 and 3.14 kcal/mol, respectively. The theoretical calculations corroborate the fact that only energetically favorable synthons can induce the formation of heterosynthons, as in ALP and PHEN complexes. From a theoretical and structural analysis it is seen that phenylboronic acids will form interactions with those molecules wherein the heterocyclic and acidic fragments can interrupt the homosynthons. However, the energy profile is shallow and can be perturbed easily by the presence of competing functional groups (such as OH and COOH) in the vicinity. [GRAPHICS] .

NMR Structure Implications of Enhanced Efficacy of Obestatin Fragment Analogs

Obestatin is a more recently discovered hormone that is encoded by the ghrelin gene and produced in the stomach and gut. We report NMR analysis on synthetic Obestatin (OB23), a 23 residue peptide, along with three overlapping fragments of the same in methanol solvent as a first step towards structure activity relationship. Selective substitutions on the promising N-terminal and middle fragments of obestatin have been carried out in order to improve the efficacy and potency. In the N-terminal fragment two peptides were obtained by the replacement of Gly (8) with a-aminoisobutyric acid (Aib, U) and Phe (F5) with Cyclohexylalanine (Cha). In case of the middle fragment both Gly (3) and Gly (8) were replaced with Aib residues. The rationale being, these unusual amino acids could provide protection from immediate degradation and aid structure stabilization. Our previous studies showed that the N-terminal and the middle fragment were unstructured and hence this substitution would directly evaluate the effect of structure on the activity of these fragment analogs. Detailed NMR analysis clearly demonstrates formation of helical secondary structure in all the peptide analogues and provides justification for relative activities reported by our group previously (Nagaraj et al. 2009).