Diversity of DNA methyltransferases that recognize asymmetric target sequences

DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

Diversity of DNA methyltransferases that recognize asymmetric target sequences

DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

Characterization of foot-and-mouth disease virus types Ο and Asia 1 RNA

Foot-and-mouth disease is an acute and highly contagious febrile disease affecting cloven-footed animals. Identification of the foot-and-mouth disease virus (FMDV), the causative agent of the disease, posed problems because of the occurrence of many types and subtypes of the virus. A molecular approach based on oligonucleotide mapping of FMDV RNA has been used for the identification and characterization of virus isolates obtained in a disease outbreak (King et al., 1981). One-dimensional oligonucleotide mapping was used for rapid analysis of FMDV RNA (LaTorre et al., 1982). FMDV types Ο and Asia 1 of Indian origin are being routinely used for vaccine production in India. This report presents the differences between FMDV types Ο and Asia 1 at molecular level based on one-dimensional oligonucleotide mapping of virus-induced poly (A) RNA.

Scientometric analysis of some disciplines: Comparison of Indian institutions with other international institutions

We have carried out a three-part study comparing the research performance of Indian institutions with that of other international institutions. In the first part, the publication profiles of various Indian institutions were examined and ranked based on the h-index and p-index. We found that the institutions of national importance contributed the highest in terms of publications and citations per institution. In the second part of the study, we looked at the publication profiles of various Indian institutions in the high-impact journals and compared these profiles against that of the top Asian and US universities. We found that the number of papers in these journals from India was miniscule compared to the US universities. Recognizing that the publication profiles of various institutions depend on the field/departments, we studied the publication profiles of many science and engineering departments at the Indian Institute of Science (IISc), Bangalore, the Indian Institutes of Technology, as well as top Indian universities. Because the number of faculty in each department varies widely, we have computed the publications and citations per faculty per year for each department. We have also compared this with other departments in various Asian and US universities. We found that the top Indian institution based on various parameters in various disciplines was IISc, but overall even the top Indian institutions do not compare favourably with the top US or Asian universities.

Integrated modelling approaches to analysis of climate change impacts on forests and forest management

This paper reviews integrated economic and ecological models that address impacts and adaptation to climate change in the forest sector. Early economic model studies considered forests as one out of many possible impacts of climate change, while ecological model studies tended to limit the economic impacts to fixed price-assumptions. More recent studies include broader representations of both systems, but there are still few studies which can be regarded fully integrated. Full integration of ecological and economic models is needed to address forest management under climate change appropriately. The conclusion so far is that there are vast uncertainties about how climate change affects forests. This is partly due to the limited knowledge about the global implications of the social and economical adaptation to the effects of climate change on forests.

Analysis of the effects of amino-acid-sequence on the structure of proteins

The conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues.

Self-assembly of neutral and cationic Pd-II organometallic molecular rectangles: synthesis, characterization and nitroaromatic sensing

Design and synthesis of three novel 2 + 2] self-assembled molecular rectangles 1-3 via coordination driven self-assembly of predesigned Pd(II) ligands is reported. 1,8-Diethynylanthracene was assembled with trans-Pd(PEt3)(2)Cl-2 in the presence of CuCl catalyst to yield a neutral rectangle 1 via Pd-C bond formation. Complex 1 represents the first example of a neutral molecular rectangle obtained via C-Pd coordination driven self-assembly. A new Pd-2(II) organometallic building block with 180 degrees bite-angle 1,4-bistrans-(ethynyl)Pd(PEt3)(2)(NO3)] benzene (M-2) containing ethynyl functionality was synthesized in reasonable yield by employing Sonagashira coupling reaction. Self-assembly of M-2 with two organic clip-type donors (L-2-L-3) afforded 2 + 2] self-assembled molecular rectangles 2 and 3, respectively L-2 = 1,8-bis(4-pyridylethynyl) anthracene; L-3 = 1,3-bis(3-pyridyl) isophthalamide]. The macrocycles 1-3 were fully characterized by multinuclear NMR and ESI-MS spectroscopic techniques, and in case of 1 the structure was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of Pd-ethynyl bonds helped to make the assemblies p-electron rich and fluorescent in nature. Complexes 1-2 showed quenching of fluorescence intensity in solution in presence of nitroaromatics, which are the chemical signatures of many commercially available explosives.

Rudiments of complexity theory for scientists and engineers

Complexity theory is an important and growing area in computer science that has caught the imagination of many researchers in mathematics, physics and biology. In order to reach out to a large section of scientists and engineers, the paper introduces elementary concepts in complexity theory in a informal manner, motivating the reader with many examples.

Molecular organization of the gene encoding Xenopus laevis transforming growth factor-beta 5

Transforming growth factor-beta s (TGF-beta 5) are multifunctional polypeptides, known to influence proliferation and differentiation of many cell types. TGF-beta 5 cDNA was cloned from Xenopus laevis and this isoform is unique to the amphibians. Here, we report the isolation and characterization of the TGF-beta 5 genomic clones to determine the structure of TGF-beta 5 gene. The gene consists of seven exons and all intron-exon boundaries follow the GT-AG consensus. The organization of TGF-beta 5 gene was identical to that of the mammalian TGF-beta isoforms, with the exception of position of the first splice junction. We determined the size of TGF-beta 5 gene to be approximately 20 kb.

Gene Expression Profiling of Preovulatory Follicle in the Buffalo Cow: Effects of Increased IGF-I Concentration on Periovulatory Events

The preovulatory follicle in response to gonadotropin surge undergoes dramatic biochemical, and morphological changes orchestrated by expression changes in hundreds of genes. Employing well characterized bovine preovulatory follicle model, granulosa cells (GCs) and follicle wall were collected from the preovulatory follicle before, 1, 10 and 22 h post peak LH surge. Microarray analysis performed on GCs revealed that 450 and 111 genes were differentially expressed at 1 and 22 h post peak LH surge, respectively. For validation, qPCR and immunocytochemistry analyses were carried out for some of the differentially expressed genes. Expression analysis of many of these genes showed distinct expression patterns in GCs and the follicle wall. To study molecular functions and genetic networks, microarray data was analyzed using Ingenuity Pathway Analysis which revealed majority of the differentially expressed genes to cluster within processes like steroidogenesis, cell survival and cell differentiation. In the ovarian follicle, IGF-I is established to be an important regulator of the above mentioned molecular functions. Thus, further experiments were conducted to verify the effects of increased intrafollicular IGF-I levels on the expression of genes associated with the above mentioned processes. For this purpose, buffalo cows were administered with exogenous bGH to transiently increase circulating and intrafollicular concentrations of IGF-I. The results indicated that increased intrafollicular concentrations of IGF-I caused changes in expression of genes associated with steroidogenesis (StAR, SRF) and apoptosis (BCL-2, FKHR, PAWR). These results taken together suggest that onset of gonadotropin surge triggers activation of various biological pathways and that the effects of growth factors and peptides on gonadotropin actions could be examined during preovulatory follicle development.

Phenobarbitone-mediated translocation of the cytosolic proteins interacting with the 5 '-proximal region of rat liver CYP2B1/B2 gene into the nucleus

The positive element (PE) (-69 to -98 bp) within the 5'-proximal region of the CYP2B1B2 gene (+1 to -179 bp) of rat liver is essential for phenobarbitone (PB) response and gives a single major complex with the rat liver cytosol in gel shift analysis. This complex corresponds to complex I (top) of the three complexes given by the nuclear extracts. PB treatment of rats leads to a decrease in complex I formation with the cytosol and PE and an increase in the same with the nuclear extract in gel shift analysis. Both the changes are counteracted by simultaneous okadaic acid administration. The nuclear protein giving rise to complex I has been isolated and has an M-r of 26 kDa. The cytosolic counterpart consists of two species, 26 and 28 kDa, as revealed by Southwestern blot analysis using labeled PE. It is concluded that PB treatment leads to the translocation accompanied by processing of the cytosolic protein species into the nucleus that requires protein dephosphorylation. It is suggested that PB may exert a global regulation on the transcription of many genes by modulating the phosphorylation status of different protein factors involved in transcriptional regulation. (C) 2002 Elsevier Science (USA).

The origin of degeneracies and crossings in the 1d Hubbard model

The paper is devoted to the connection between integrability of a finite quantum system and degeneracies of its energy levels. In particular, we analyse in detail the energy spectra of finite Hubbard chains. Heilmann and Lieb demonstrated that in these systems there are crossings of levels of the same parameter-independent symmetry. We show that this apparent violation of the Wigner-von Neumann noncrossing rule follows directly from the existence of nontrivial conservation laws and is a characteristic signature of quantum integrability. The energy spectra of Hubbard chains display many instances of permanent (at all values of the coupling) twofold degeneracies that cannot be explained by parameter-independent symmetries. We relate these degeneracies to the different transformation properties of the conserved currents under spatial reflections and the particle-hole transformation and estimate the fraction of doubly degenerate states. We also discuss multiply degenerate eigenstates of the Hubbard Hamiltonian. The wavefunctions of many of these states do not depend on the coupling, which suggests the existence of an additional parameter-independent symmetry.

Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large [Delta]Cp's

Maltose binding protein (MBP) is a large, monomeric two domain protein containing 370 amino acids. In the absence of denaturant at neutral pH, the protein is in the native state, while at pH 3.0 it forms a molten globule. The molten globule lacks a tertiary circular dichroism signal but has secondary structure similar to that of the native state. The molten globule binds 8-anilino-1-naphthalene sulfonate (ANS). The unfolding thermodynamics of MBP at both pHs were measured by carrying out a series of isothermal urea melts at temperatures ranging from 274–329 K. At 298 K, values of [Delta]G°, [Delta]Cp, and Cm were 3.1 ± 0.2 kcal mol−1, 5.9 ± 0.8 kcal mol−1 K−1 (15.9 cal (mol-residue)−1 K−1), and 0.8 M, respectively, at pH 3.0 and 14.5 ± 0.4 kcal mol−1, 8.3 ± 0.7 kcal mol−1 K−1 (22.4 kcal (mol-residue)−1 K−1), and 3.3 M, respectively, at pH 7.1. Guanidine hydrochloride denaturation at pH 7.1 gave values of [Delta]G° and [Delta]Cp similar to those obtained with urea. The m values for denaturation are strongly temperature dependent, in contrast to what has been previously observed for small globular proteins. The value of [Delta]Cp per mol-residue for the molten globule is comparable to corresponding values of [Delta]Cp for the unfolding of typical globular proteins and suggests that it is a highly ordered structure, unlike molten globules of many small proteins. The value of [Delta]Cp per mol-residue for the unfolding of the native state is among the highest currently known for any protein.

Compiler Assisted Leakage Energy Optimization for Clustered VLIW Architectures

Miniaturization of devices and the ensuing decrease in the threshold voltage has led to a substantial increase in the leakage component of the total processor energy consumption. Relatively simpler issue logic and the presence of a large number of function units in the VLIW and the clustered VLIW architectures attribute a large fraction of this leakage energy consumption in the functional units. However, functional units are not fully utilized in the VLIW architectures because of the inherent variations in the ILP of the programs. This underutilization is even more pronounced in the context of clustered VLIW architectures because of the contentions for the limited number of slow intercluster communication channels which lead to many short idle cycles.In the past, some architectural schemes have been proposed to obtain leakage energy bene .ts by aggressively exploiting the idleness of functional units. However, presence of many short idle cycles cause frequent transitions from the active mode to the sleep mode and vice-versa and adversely a ffects the energy benefits of a purely hardware based scheme. In this paper, we propose and evaluate a compiler instruction scheduling algorithm that assist such a hardware based scheme in the context of VLIW and clustered VLIW architectures. The proposed scheme exploits the scheduling slacks of instructions to orchestrate the functional unit mapping with the objective of reducing the number of transitions in functional units thereby keeping them off for a longer duration. The proposed compiler-assisted scheme obtains a further 12% reduction of energy consumption of functional units with negligible performance degradation over a hardware-only scheme for a VLIW architecture. The benefits are 15% and 17% in the context of a 2-clustered and a 4-clustered VLIW architecture respectively. Our test bed uses the Trimaran compiler infrastructure.

Effect of shear deformation on interfacial stresses in plated beams subjected to arbitrary loading

Bonding a fibre reinforced polymer (FRP) composite or metallic plate to the soffit of a reinforced concrete (RC), timber or metallic beam can significantly increase its strength and other aspects of structural performance. These hybrid beams are often found to fail due to premature debonding of the plate from the original beam in a brittle manner. This has led to the development of many analytical solutions over the last two decades to quantify the interfacial shear and normal stresses between the adherends. The adherends are subjected to axial, bending and shear deformations. However, most analytical solutions have neglected the influence of shear deformation of the adherends. For the few solutions which consider this effect in an approximate manner, their applicability is limited to one or two specific load cases. This paper presents a general analytical solution for the interfacial stresses in plated beams under an arbitrary loading with the shear deformation of the adherends duly considered. The shear stress distribution is assumed to be parabolic through the depth of the adherends in predicting the interfacial shear stress and Timoshenko's beam theory is adopted in predicting interfacial normal stress to account for the shear deformation. The solution is applicable to a beam of arbitrary prismatic cross-section bonded symmetrically or asymmetrically with a thin or thick plate, both having linear elastic material properties. The effect of shear deformation is illustrated through an example beam. The influence of material and geometric parameters of the adherends and adhesive on the interfacial stress concentrations at the plate end is discussed. (C) 2011 Elsevier Ltd. All rights reserved.