Large cryptic internal sequence repeats in protein structures from Homo sapiens

Amino acid sequences are known to constantly mutate and diverge unless there is a limiting condition that makes such a change deleterious. However, closer examination of the sequence and structure reveals that a few large, cryptic repeats are nevertheless sequentially conserved. This leads to the question of why only certain repeats are conserved at the sequence level. It would be interesting to find out if these sequences maintain their conservation at the three-dimensional structure level. They can play an active role in protein and nucleotide stability, thus not only ensring proper functioning but also potentiating malfunction and disease. Therefore, insights into any aspect of the repeats - be it structure, function or evolution - would prove to be of some importance. This study aims to address the relationship between protein sequence and its three-dimensional structure, by examining if large cryptic sequence repeats have the same structure.

Enantiodiscrimination and extraction of short and long range homo- and hetero-nuclear residual dipolar couplings by a spin selective correlation experiment

A two dimensional correlation experiment for the measurement of short and long range homo- and hetero- nuclear residual dipolar couplings (RDCs) from the broad and featureless proton NMR spectra including C-13 satellites is proposed. The method employs a single natural abundant C-13 spin as a spy nucleus to probe all the coupled protons and permits the determination of RDCs of negligible strengths. The technique has been demonstrated for the study of organic chiral molecules aligned in chiral liquid crystal, where additional challenge is to unravel the overlapped spectrum of enantiomers. The significant advantage of the method is demonstrated in better chiral discrimination using homonuclear RDCs as additional parameters. (C) 2010 Elsevier B.V. All rights reserved.

Karyotype instability in the ponerine ant genus Diacamma

The queenless ponerine ant Diacamma ceylonense and a population of Diacamma from the Nilgiri hills which we refer to as `nilgiri', exhibit interesting similarities as well as dissimilarities. Molecular phylogenetic study of these morphologically almost similar taxa has shown that D ceylonense is closely related to `nilgiri' and indicates that `nilgiri' is a recent diversion in the Diacamma phylogenetic tree. However, there is a striking behavioural difference in the way reproductive monopoly is maintained by the respective gamergates (mated egg laying workers), and there is evidence that they are genetically differentiated, suggesting a lack of gene flow To develop a better understanding of the mechanism involved in speciation of Diacamma, we have analysed karyotypes of D. ceylonense and `nilgiri' In both, we found surprising inter-individual and intra-individual karyotypic mosaicism. The observed numerical variability, both at intra-individual and inter-individual levels, does not appear to have hampered the sustainability of the chromosomal diversity in each population under study Since the related D. indicum, displays no such intra-individual or inter-Individual variability whatsoever under identical experimental conditions, these results are unlikely to he artifacts. Although no known mechanisms can account for the observed karyotypic variability of this nature, we believe that the present findings on the ants under study would provide opportunities for exciting new discoveries concerning the origin, maintenance and significance of intra-individual and inter-individual karyotypic mosaicism.

Use of 2-pyrimidineamidoxime to generate polynuclear homo-/heterometallic assemblies: synthesis, crystal structures and magnetic study with theoretical investigations on the exchange mechanism

Three new transition metal complexes using 2-pyrimidineamidoxime (pmadH(2)) as multidentate chelating and/or bridging ligand have been synthesized and characterized. The ligand pmadH(2) has two potential bridging functional groups mu-O and mu-(N-O)] and consequently shows several coordination modes. While a polymeric 1D Cu-II complex Cu(pmadH(2))(2)(NO3)](NO3) (1) was obtained upon treatment of Cu(NO3)(2)center dot 3H(2)O with pmadH(2) at room temperature in the absence of base, a high temperature reaction in the presence of base yielded a tetranuclear Cu-II-complex Cu-4(pmad)(2)(pmadH)(2)(NO3)](NO3)(H2O) (2). One of the Cu-II centers is in a square pyramidal environment while the other three are in a square planar geometry. Reaction of the same ligand with an equimolar mixture of both Cu(NO3)(2)center dot 3H(2)O and NiCl2 center dot 6H(2)O yielded a tetranuclear heterometallic (Cu2Ni2II)-Ni-II complex Cu2Ni2(pmad)(2)(pmadH)(2)Cl-2]center dot H2O (3) containing both square planar (Ni-II) and square pyramidal (Cu-II) metal centers. Complexes 1-3 represent the first examples of polynuclear metal complexes of 2-pyrimidineamidoxime. The analysis of variable temperature magnetic susceptibility data of 2 reveals that both ferromagnetic and antiferromagnetic interactions exist in this complex (J(1) = +10.7 cm(-1) and J(2) = -2.7 cm(-1) with g = 2.1) leading to a resultant ferromagnetic behavior. Complex 3 shows expected antiferromagnetic interaction between two Cu-II centers through -N-O- bridging pathway with J(1) = -3.4 cm(-1) and g = 2.08. DFT calculations have been used to corroborate the magnetic results.

Visualization of enantiomers and determination of homo- and hetero-nuclear residual dipolar and scalar couplings: The natural abundant C-13 edited J/D-resolved NMR techniques

The simple two dimensional C-13-satellite J/D-resolved experiments have been proposed for the visualization of enantiomers, extraction of homo- and hetero-nuclear residual dipolar couplings and also H-1 chemical shift differences between the enantiomers in the anisotropic medium. The significant advantages of the techniques are in the determination of scalar couplings of bigger organic molecules. The scalar couplings specific to a second abundant spin such as F-19 can be selectively extracted from the severely overlapped spectrum. The methodologies are demonstrated on a chiral molecule aligned in the chiral liquid crystal medium and two different organic molecules in the isotropic solutions. (C) 2010 Elsevier B.V. All rights reserved.

Analysis of geometric and strain effects in homo-Diels-Alder reactions

Molecular mechanics calculations have been carried out to quantify the key geometric and strain effects which are likely to control the homo-Diels-Alder reactivity of 1,4-dienes. The criteria considered include C1..C5 and C2..C4 distances in the diene, twist angle of the two pi units, and the magnitude of strain increase as a result of cycloaddition. By first considering these factors in a number of non-conjugated dienes with known reactivity, the ranges of values within which the reaction is favoured are proposed. Calculations are also reported on several substrates which have not been investigated so far. Promising systems for experimental study are suggested which, in addition to being intrinsically interesting, would place the present proposals on a firm basis.

Role of Hetero-Halogen (F center dot center dot center dot X, X = Cl, Br, and I) or Homo-Halogen (X center dot center dot center dot X, X = F, Cl, Br, and I) Interactions in Substituted Benzanilides

A series of halogen-substituted benzanilides have been synthesized and characterized, and crystallization studies directed toward generation of polymorphs have been performed to delineate the importance of interactions involving halogens. The effect of halogen substitution on the molecular conformation and supramolecular packing has been investigated. The N-H center dot center dot center dot O H-bond is a key structure-directing element acting in conjunction with C-H center dot center dot center dot O and C-H center dot center dot center dot pi interactions. In addition, it is of importance to note that organic fluorine prefers Type I F center dot center dot center dot F contacts, whereas Cl, Br, and I prefer Type II contacts. Hetero-halogen center dot center dot center dot halogen interactions on the other hand are predominately of Type II geometry, and this is due to the greater polarizability of the electron density associated with the heavier halogens. It is of importance to evaluate the contributing role of these interactions in crystal structure packing and the co-operativity associated with such interactions in the solid state.

Thermal analysis studies on hydroxobridged homo and hetero trinuclear cobalt(III) complexes

The synthesis and thermal analysis studies of several hydroxobridged homo and hetero trinuclear cobalt(III) complexes are reported. The complexes are of the type [M(H2O)(x) {(OH)(2)Co(en)(2)}(2)](SO4)(2). nH(2)O and [M(H2O)(x){(OH)(2)Co(NH3)(4)}(2)] (SO4)(2). nH(2)O where en denotes ethylenediamine and M =Co(II), Ni(II), Cu(II) and Zn(II) with x=0 for Cu(II), and 2 for other metal ions, and n =3, 4 or 5. The TG and DTA studies of these compounds show that one or more intermediate compounds are formed in each case before the metal oxides are produced.

A new parasitic bee of the genus Braunsapis from India (Hymenoptera : Apidae : Allodapini)

A new species of allodapine bee (Apidae, Xylocopinae, Allodapini), Braunsapis bislensis, is described from southern India. To judge by its reduced mouthparts and scopa, it is a social parasite, perhaps in nests of B. puangensis (Cockerell).

The diatom genus Gomphonema Ehrenberg in India: Checklist and description of three new species

We have compiled a checklist of Gomphonema Ehrenberg taxa reported previously from India. From forty-nine references, over 100 Gomphonema taxa have been reported, including 39 new taxon descriptions. In addition to these previous reports of Gomphonema taxa, we describe three new species. G. gandhii Karthick & Kociolek, sp. nov., G. difformum Karthick & Kociolek, sp. nov. and G. diminutum Karthick & Kociolek, sp. nov., all from hill streams of Western Ghats, India. Frustule morphology, as studied in light and scanning electron microscopy, is compared with that of other recently described Gomphonema species from Africa and Asia. All three Indian species have distinctly dilated proximal raphe ends, in addition to differentiated apical pore fields, septa, pseudosepta and a round external stigma! opening. Gomphonema gandhii is linear-lanceolate-clavate, has a wide axial area, and is 19-51 mu m long, 3-7 mu m broad. Gomphonema difformum is smaller than G. gandhii, and has a hyaline area around the headpole. Gomphonema diminuta is much smaller and narrower than the other two species. These species are distinct from their closest congeners by their sizes, shape and structure of the head pole, and striae densities. All these species were described from low nutrient, neutral, low ionic content streams of Western Ghats. As most other species described from tropical region these three species appear to be endemic to India. Moreover, within India they have hitherto only been found in Western Ghats, one of the twelve biodiversity hotspots of the World.

Testing concordance in species boundaries using acoustic, morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea, Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species-specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency.

Inhibition of Mycobacterium tuberculosis RNA Polymerase by Binding of a Gre Factor Homo log to the Secondary Channel

Because of its essential nature, each step of transcription, viz., initiation, elongation, and termination, is subjected to elaborate regulation. A number of transcription factors modulate the rates of transcription at these different steps, and several inhibitors shut down the process. Many modulators, including small molecules and proteinaceous inhibitors, bind the RNA polymerase (RNAP) secondary channel to control transcription. We describe here the first small protein inhibitor of transcription in Mycobacterium tuberculosis. Rv3788 is a homolog of the Gre factors that binds near the secondary channel of RNAP to inhibit transcription. The factor also affected the action of guanosine pentaphosphate (pppGpp) on transcription and abrogated Gre action, indicating its function in the modulation of the catalytic center of RNAP. Although it has a Gre factor-like domain organization with the conserved acidic residues in the N terminus and retains interaction with RNAP, the factor did not show any transcript cleavage stimulatory activity. Unlike Rv3788, another Gre homolog from Mycobacterium smegmatis, MSMEG_6292 did not exhibit transcription-inhibitory activities, hinting at the importance of the former in influencing the lifestyle of M. tuberculosis.

Modeling of room temperature current-voltage measurements on homo-junction HgCdTe diodes exhibiting nonequilibrium effects

HgCdTe mid wave infrared (MWIR) n(+)/nu/p(+) homo-junction photodiodes with planar architecture are designed, fabricated, and measured at room temperature. An improved analytical I-V model is reported by incorporating trap assisted tunneling and electric field enhanced Shockley-Read-Hall generation recombination process due to dislocations. Tunneling currents are fitted before and after the Auger suppression of carriers with energy level of trap (E-t), trap density (N-t), and the doping concentrations of n(+) and nu regions as fitting parameters. Values of E-t and N-t are determined as 0.79 E-g and similar to 9 x 10(14) cm(-3), respectively, in all cases. Doping concentration of nu region was found to exhibit nonequilibrium depletion from a value of 2 x 10(16) to 4 x 10(15) cm(-3) for n(+) doping of 2 x 10(17) cm(-3). Pronounced negative differential resistance is observed in the homo-junction HgCdTe diodes. (C) 2012 American Institute of Physics. [doi:10.1063/1.3682483]

Homo- or Heterosynthon? A Crystallographic Study on a Series of New Cocrystals Derived from Pyrazinecarboxamide and Various Carboxylic Acids Equipped with Additional Hydrogen Bonding Sites

Four new cocrystals of a well studied active pharmaceutical ingredient (API), namely, pyrazinecarboxamide (PZA), with various monocarboxylic acids equipped with additional hydrogen bonding sites such as vanillic acid (VA), gallic acid (GA), 1-hydroxy-2-naphthoic acid (1HNA), and indole-2-carboxylic acid (I2CA) have been successfully prepared and characterized by FTIR, H-1 NMR, differential scanning calorimetry (DSC), and single crystal and powder X-ray diffraction (SXRD and PXRD, respectively) techniques. In the majority of the cases, preferential occurrence amide amide and acid acid homosynthons has been observed. Since the heterosynthon is energetically preferred to homosynthon, such unusual occurrence of homosynthon in these cocrystals is intriguing.