Cardiac remodeling in Drosophila arises from changes in actin gene expression and from a contribution of lymph gland-like cells to the heart musculature

Understanding the basis of normal heart remodeling can provide insight into the plasticity of the cardiac state, and into the potential for treating diseased tissue. In Drosophila, the adult heart arises during metamorphosis from a series of events, that include the remodeling of an existing cardiac tube, the elaboration of new inflow tracts, and the addition of a layer of longitudinal muscle fibers. We have identified genes active in all these three processes, and studied their expression in order to characterize in greater detail normal cardiac remodeling. Using a Transglutaminase-lacZ transgenic line, that is expressed in the inflow tracts of the larval and adult heart, we confirm the existence of five inflow tracts in the adult structure. In addition, expression of the Actin87E actin gene is initiated in the remodeling cardiac tube, but not in the longitudinal fibers, and we have identified an Act87E promoter fragment that recapitulates this switch in expression. We also establish that the longitudinal fibers are multinucleated, characterizing these cells as specialized skeletal muscles. Furthermore, we have defined the origin of the longitudinal fibers, as a subset of lymph gland cells associated with the larval dorsal vessel. These studies underline the myriad contributors to the formation of the adult Drosophila heart, and provide new molecular insights into the development of this complex organ. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Structural proteins of mycobacteriophage I3: cloning, expression and sequence analysis of a gene encoding a 70-kDa structural protein

The structural proteins of mycobacteriophage I3 have been analysed by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis (SDS-PAGE), radioiodination and immunoblotting. Based on their abundance the 34- and 70-kDa bands appeared to represent the major structural proteins. Successful cloning and expression of the 70-kDa protein-encoding gene of phage I3 in Escherichia coli and its complete nucleotide sequence determination have been accomplished, A second (partial) open reading frame following the stop codon for the 70-kDa protein was also identified within the cloned fragment. The deduced amino-acid sequence of the 70-kDa protein and the codon usage patterns indicated the preponderance of codons, as predicted from the high G+C content of the genomic DNA of phage I3.

Topology of wolfgram proteins and 2?, 3?-cyclic nucleotide 3?-phosphodiesterase in CNS myelin: Studies with proteases

The topological disposition of Wolfgram proteins (WP) and their relationship with 2', 3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) in human, rat, sheep, bovine, guinea pig and chicken CNS myelin was investigated. Controlled digestion of myelin with trypsin gave a 35KDa protein band (WP-t) when electrophoresed on dodecyl sulfate-polyacrylamide gel in all species. Western blot analysis showed that the WP-t was derived from WP. WP-t was also formed when rat myelin was treated with other proteases such as kallikrein, thermolysin and leucine aminopeptidase. Staining for CNPase activity on nitrocellulose blots showed that WP-t is enzymatically active. Much of the CNPase activity remained with the membrane fraction even after treatment with high concentrations of trypsin when WP were completely hydrolysed and no protein bands with M.W > 14KDa were detected on the gels. Therefore protein fragments of WP with M.W < 14KDa may contain CNPase activity. From these results, it is suggested that the topological disposition of all the various WP is such that a 35KDa fragment is embedded in the lipid bilayer and the remaining fragment exposed at the intraperiod line in the myelin structure which may play a role in the initiation of myelinogenesis.

Monte Carlo simulation of network formation based on structural fragments in epoxy-anhydride systems

A method combining the Monte Carlo technique and the simple fragment approach has been developed for simulating network formation in amine-catalysed epoxy-anhydride systems. The method affords a detailed insight into the nature and composition of the network, showing the distribution of various fragments. It has been used to characterize the network formation in the reaction of the diglycidyl ester of isophthalic acid with hexahydrophthalic anhydride, catalysed by benzyldimethylamine. Pre-gel properties like number and weight distributions and average molecular weights have been calculated as a function of epoxy conversion, leading to a prediction of the gel-point conversion. Analysis of the simulated network further yields other characteristic properties such as concentration of crosslink points, distribution and concentration of elastically active chains, average molecular weight between crosslinks, sol content and mass fraction of pendent chains. A comparison has been made of the properties obtained through simulation with those predicted by the fragment approach alone, which, however, gives only average properties. The Monte Carlo simulation results clearly show that loops and other cyclic structures occur in the gel. This may account for the differences observed between the results of the simulation and the fragment model in the post-gel phase. Copyright (C) 1996 Elsevier Science Ltd.

DNA Condensation by the Rat Spermatidal Protein TP2 Shows GC-Rich Sequence Preference and Is Zinc Dependent

Transition protein-2 (TP2), isolated from rat testes, was recently shown to be a zinc metalloprotein. We have now carried out a detailed analysis of the DNA condensing properties of TP2 with various polynucleotides using circular dichroism spectroscopy. The condensation of the alternating copolymers by TP2 (incubated with 10 mu M ZnSO4), namely, poly(dG-dC). poly(dG-dC) and poly(dA-dT). poly(dA-dT), was severalfold higher than condensation of either of the homoduplexes poly(dG). poly-(dC) and poly(dA). poly(dT) or rat oligonucleosomal DNA. Between the two alternating copolymers, poly(dG-dC). poly(dG-dC) was condensed 3.2-fold more effectively than poly(dA-dT). poly(dA-dT). Preincubation of TP2 with 5 mM EDTA significantly reduced its DNA-condensing property. Interestingly, condensation of the alternating copolymer poly(dI-dC). poly(dI-dC) by TP2 was much less as compared to that of poly(dG-dC). poly(dG-dC). The V8 protease-derived N-terminal fragment (88 aa) condensed poly(dA-dT). poly(dA-dT) to a very small extent but did not have any effect on poly(dG-dC). poly-(dG-dC). The C-terminal fragment (28 aa) was able to condense poly(dA-dT) . poly(dA-dT) more effectively than poly(dG-dC). poly(dG-dC). These results suggest that TP2 in its zinc-coordinated form condenses GC-rich polynucleotides much more effectively than other types of polynucleotides. Neither the N-terminal two-thirds of TP2 which is the zinc-binding domain nor the C-terminal basic domain are as effective as intact TP2 in bringing about condensation of DNA.

BSSB: BLAST Server for Structural Biologists

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence-structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

Preferential condensation of SAR-DNA by histone H1 and its SPKK containing octapeptide repeat motif

Linker histone H1 binds preferentially the scaffold associated region (SAR) DNA elements that contain characteristic oligo dA . dT tracts. In the present study, we have compared the condensation brought about by histone H1 of a SAR DNA fragment in the histone spacer region of Drosophila melanogaster with that of a random DNA (pBR322 EcoRI-SalI) fragment by circular dichroism spectroscopy. The condensation of the SAR DNA fragment by histone H1 is 3-4-fold higher than that of the random DNA fragment. A 16-mer peptide, ATPKKSTKKTPKKAKK, the sequence that is present in the C-terminus of histone H1d, which has recently been shown to possess DIVA and chromatin condensing properties, also condenses the SAR DNA fragment preferentially in a highly cooperative manner. We have proposed a model for the dynamics of chromatin structure involving histone H1-SAR DNA interaction through SPKK containing peptide motifs and its competition by AT-hook peptides present in the nonhistone chromosomal proteins like HMG-I and HMG-Y.

Crystal structure of nonadentate tricompartmental ligand derived from pyridine-2,6-dicarboxylic acid: Spectroscopic, electrochemical and thermal investigations of its transition metal(II) complexes

The coordinating behavior of a new dihydrazone ligand, 2,6-bis(3-methoxysalicylidene) hydrazinocarbonyl]pyridine towards manganese(II), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) has been described. The metal complexes were characterized by magnetic moments, conductivity measurements, spectral (IR, NMR, UV-Vis, FAB-Mass and EPR) and thermal studies. The ligand crystallizes in triclinic system, space group P-1, with alpha=98.491(10)degrees, beta=110.820(10)degrees and gamma=92.228(10)degrees. The cell dimensions are a=10.196(7)angstrom, b=10.814(7)angstrom, c=10.017(7)angstrom, Z=2 and V=1117.4(12). IR spectral studies reveal the nonadentate behavior of the ligand. All the complexes are neutral in nature and possess six-coordinate geometry around each metal center. The X-band EPR spectra of copper(II) complex at both room temperature and liquid nitrogen temperature showed unresolved broad signals with g(iso) = 2.106. Cyclic voltametric studies of copper(II) complex at different scan rates reveal that all the reaction occurring are irreversible. (C) 2011 Elsevier B.V. All rights reserved.

Molybdenum tetracarbonyl complexes of (aryloxy) lambda(3)-cyclotriphosphazanes; X-ray crystal structure of [Mo(CO)(4){EtNP(OC6H4Br-4)}(3)]

Treatment of the lambda(3)-cyclotriphosphazanes, cis-{EtNP(OR)}(3) [R = C6H4Br-4 (L-1) or C6H4Br-2 (L-2)] with [Mo(CO)(4)(NBD)] (NBD = norbornadiene) yields the mononuclear complexes [Mo(CO)(4)L-1] (1) and [Mo(CO)(4)L-2] (2). which have been characterised by IR, NMR (P-31 and H-1) and FAB mass spectral data. The structure of 1 has been confirmed by single crystal X-ray analysis. The structural and conformational changes brought about by complexation are discussed in terms of a bonding model based on "negative hyperconjugation". (C) 1998 Elsevier Science Ltd. All rights reserved.

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.

Explicit codes uniformly reducing repair bandwidth in distributed storage

A distributed storage setting is considered where a file of size B is to be stored across n storage nodes. A data collector should be able to reconstruct the entire data by downloading the symbols stored in any k nodes. When a node fails, it is replaced by a new node by downloading data from some of the existing nodes. The amount of download is termed as repair bandwidth. One way to implement such a system is to store one fragment of an (n, k) MDS code in each node, in which case the repair bandwidth is B. Since repair of a failed node consumes network bandwidth, codes reducing repair bandwidth are of great interest. Most of the recent work in this area focuses on reducing the repair bandwidth of a set of k nodes which store the data in uncoded form, while the reduction in the repair bandwidth of the remaining nodes is only marginal. In this paper, we present an explicit code which reduces the repair bandwidth for all the nodes to approximately B/2. To the best of our knowledge, this is the first explicit code which reduces the repair bandwidth of all the nodes for all feasible values of the system parameters.

The restriction mapping problem revisited

In computational molecular biology, the aim of restriction mapping is to locate the restriction sites of a given enzyme on a DNA molecule. Double digest and partial digest are two well-studied techniques for restriction mapping. While double digest is NP-complete, there is no known polynomial-time algorithm for partial digest. Another disadvantage of the above techniques is that there can be multiple solutions for reconstruction. In this paper, we study a simple technique called labeled partial digest for restriction mapping. We give a fast polynomial time (O(n(2) log n) worst-case) algorithm for finding all the n sites of a DNA molecule using this technique. An important advantage of the algorithm is the unique reconstruction of the DNA molecule from the digest. The technique is also robust in handling errors in fragment lengths which arises in the laboratory. We give a robust O(n(4)) worst-case algorithm that can provably tolerate an absolute error of O(Delta/n) (where Delta is the minimum inter-site distance), while giving a unique reconstruction. We test our theoretical results by simulating the performance of the algorithm on a real DNA molecule. Motivated by the similarity to the labeled partial digest problem, we address a related problem of interest-the de novo peptide sequencing problem (ACM-SIAM Symposium on Discrete Algorithms (SODA), 2000, pp. 389-398), which arises in the reconstruction of the peptide sequence of a protein molecule. We give a simple and efficient algorithm for the problem without using dynamic programming. The algorithm runs in time O(k log k), where k is the number of ions and is an improvement over the algorithm in Chen et al. (C) 2002 Elsevier Science (USA). All rights reserved.

Towards the concept of hydrodynamic cavitation control

A careful study of the existing literature available in the field of cavitation reveals the potential of ultrasonics as a tool for controlling and, if possible, eliminating certain types of hydrodynamic cavitation through the manipulation of nuclei size present in a flow. A glass venturi is taken to be an ideal device to study the cavitation phenomenon at its throat and its potential control. A piezoelectric transducer, driven at the crystal resonant frequency, is used to generate an acoustic pressure field and is termed an �ultrasonic nuclei manipulator (UNM)�. Electrolysis bubbles serve as artificial nuclei to produce travelling bubble cavitation at the venturi throat in the absence of a UNM but this cavitation is completely eliminated when a UNM is operative. This is made possible because the nuclei, which pass through the acoustic field first, cavitate, collapse violently and perhaps fragment and go into dissolution before reaching the venturi throat. Thus, the potential nuclei for travelling bubble cavitation at the venturi throat seem to be systematically destroyed through acoustic cavitation near the UNM. From the solution to the bubble dynamics equation, it has been shown that the potential energy of a bubble at its maximum radius due to an acoustic field is negligible compared to that for the hydrodynamic field. Hence, even though the control of hydrodynamic macro cavitation achieved in this way is at the expense of acoustic micro cavitation, it can still be considered to be a significant gain. These are some of the first results in this direction.

DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation

The origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephants imported in the 16th-18th centuries. Taxonomically, they have either been classified as a unique subspecies or placed under the Indian or Sumatran subspecies. If shown to be a unique indigenous population, this would extend the natural species range of the Asian elephant by 1300 km, and therefore Borneo elephants would have much greater conservation importance than if they were a feral population. We compared DNA of Borneo elephants to that of elephants from across the range of the Asian elephant, using a fragment of mitochondrial DNA, including part of the hypervariable d-loop, and five autosomal microsatellite loci. We find that Borneo's elephants are genetically distinct, with molecular divergence indicative of a Pleistocene colonisation of Borneo and subsequent isolation. We reject the hypothesis that Borneo's elephants were introduced. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionary significant unit. Thus, interbreeding Borneo elephants with those from other populations would be contraindicated in ex situ conservation, and their genetic distinctiveness makes them one of the highest priority populations for Asian elephant conservation.

Theoretical Studies on the Structure and Bonding of Metallacyclocumulenes, -cyclopentynes, and -cycloallenes

In this paper, we compare the electronic structure of the hafnacycloallene complex Cp(2)HfC(4)Rr'(2)R `' (5Hf), which was previously described by Erker et al., with those of the titanium, zirconium, and hafnium complexes Cp(2)M(eta(4)-RHC(4)HR) (3M; i.e. metallacyclopent-2,3,4-trienes, metallacyclocumulenes) and Cp(2)M(eta(2)-R(2)C(4)R(2)) (4M; i.e. 1-metallacyclopent-3-ynes) using density functional theory (BP86/LANL2DZ) calculations. Moreover, the eta(3)-phenylallenyl zirconocene complex 7Zr, which was synthesized by Wojcicki et al., is included for the comparison. These calculations and extended Huckel calculations show that the bonding in complex 5Hf is remarkably similar to that of complexes 4M and 7Zr. An analysis of the structural parameters and bonding reveals that the unique interaction of the internal carbon atoms along with the terminal carbon atoms with the bent-metallocene moiety is the reason for the unusual stability of these metallacycles. The molecular orbital analysis further suggests that complex 5Hf can react with another metal fragment to give the bimetallic complexes 9 and 10. The electronic structures of complexes 3M, 4M, 5Hf, and 7Zr have been comparatively studied to get a general understanding of the bonding in these metallacycles.