Identification and organization of genes for diutan polysaccharide synthesis from <Emphasis Type="Italic">Sphingomonas</Emphasis> sp. ATCC 53159

A cluster of genes for diutan polysaccharide synthesis was isolated from a library of Sphingomonas sp. ATCC 53159 genomic DNA by complementation of glucosyl-isoprenylphosphate transferase-deficient mutants of Sphingomonas elodea ATCC 31461 (producing gellan) and Xanthomonas campestris (producing xanthan). The synthesis of polysaccharide in these strains shares a common first step, transfer of glucose-1-phosphate from UDP-glucose to the isoprenylphosphate lipid. The cluster of 24 genes was compared to genes for biosynthesis of gellan, and S-88 sphingan from Sphingomonas sp. ATCC 31554. Diutan, gellan and S-88 sphingan have a common four-sugar backbone but different side chains, one rhamnose for S-88 sphingan, a two-rhamnose side chain for diutan and no side chain for gellan. The genes for biosynthesis of diutan, gellan and S-88 sphingan were similar in general organization but differed in location of some genes, in particular, dpsG (putative polymerase), dpsR (putative lyase) and dpsS (putative repeat unit transporter). An unidentified reading frame urf31, present in the gene clusters for diutan and S-88 sphingan but not gellan, had similarity to glycosyl transferase group 2 proteins, and was detrimental when cloned in Sphingomonas elodea producing gellan that lacks a side chain, but not in Sphingomonas ATCC 31554 producing S-88 sphingan with a rhamnose side chain. Gene urf31 could possibly encode a side-chain rhamnosyl transferase. Another gene urf31.4 was unique to the diutan gene cluster. A plasmid containing 20 of the 24 genes resulted in a slight increase in the amount of diutan produced, but a significant increase in the rheological properties of diutan.     

Conformational preferences of heterochiral peptides. Crystal structures of heterochiral peptides Boc-(D) Val-(D) Ala-Leu-Ala-OMe and Boc-Val-Ala-Leu-(D) Ala-OMe--enhanced stability of beta-sheet through C-H...O hydrogen bonds

The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P2(1),2(1),2(1), with a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)A. V = 5,884 (3) A3, Z = 8, R = 0.086. VALa crystallises in space group P2(1) with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) A, beta = 95.84 (8) degrees , V = 3,040(4) A3, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in antiparallel beta-sheet arrangement in both the structures. Several of the Calpha hydrogens are in hydrogen bonding contact with the carbonyl oxygen in the adjacent strand. An analysis of the observed conformational feature of D-chiral amino acid residues in oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of CSD has been carried out. This shows that all the residues except D-isoleucine prefer both extended and alphaL conformation though the frequence of occurence may not be equal. In addition to this, D-leucine, valine, proline and phenylalanine have assumed alphaR conformations in solid state. D-leucine has a strong preference for helical conformation in linear peptides whereas they prefer an extended conformation in cyclic peptides.     

Structural modification and aggregation of mucin by chromium(III) complexes

Metal ions binding to proteins regulate the functions of proteins and may also lead to structural changes. In this communication we demonstrate the interaction and subsequent conformational changes induced in pig gastric mucin (PGM) upon binding to certain chromium(III) complexes like, [Cr(salen)(H(2)O)(2)](ClO(4)) (1), [Cr(en)(3)]Cl(3) (2) and [Cr(EDTA)(H(2)O)]Na (3) which vary in charge and ionic character. Complexes 1 and 3 have been shown to interact coordinately with PGM whereas complex 2 binds through electrostatic interaction and hydrogen bonding. Steady state fluorescence experiment reveals that at lower concentration of complex 2 there is partial quenching of the tyrosine emission, whereas at higher concentration of the complex the emission intensity is enhanced. On the other hand with complexes 1 and 3 a decrease in fluorescence intensity was observed. PGM viscosity was found to decrease in the presence of complex 1 and 3 due to the formation of flexible fibres through coordinate interaction. Complex 2 was found to facilitate metal induced intertangling of PGM fibres which tends to stabilize the interaction and leads to sol-gel transition with subsequent increase in viscosity. A significant change in CD spectrum of PGM was observed in the presence of complex 2, where random coil spectrum became typical of a alpha-helical structure with 80% alpha helix content. In the case of complexes 1 and 3 only minor changes in the amplitude of the spectrum were observed. Histochemical analysis supports the contention that complex 2 favors the oligomerisation of PGM and leads to the formation of aggregated mass of macromolecules.     

Conformational Preferences of Heterochiral Peptides. Crystal Structures of Heterochiral Peptides Boc-(D) Val-(D) Ala-Leu-Ala-OMe and Boc-Val-Ala-Leu-(D) Ala-OMe-Enhanced Stability of β-sheet Through C-H…O Hydrogen Bonds

Abstract

The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P2₁2₁2₁ with a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)Å, V = 5884 (3) ų, Z = 8, R = 0.086. VALa crystallises in space group P2₁ with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) Å, β = 95.84 (8)°, V = 3040(4) ų, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in antiparallel β-sheet arrangement in both the structures. Several of the C^α hydrogens are in hydrogen bonding contact with the carbonyl oxygen in the adjacent strand.

An analysis of the observed conformational feature of D-chiral amino acid residues in oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of CSD has been carried out. This shows that all the residues except D-isoleucine prefer both extended and α_L conformation though the frequence of occurence may not be equal. In addition to this, D-leucine, valine, proline and phenylalanine have assumed α_R conformations in solid state. D-leucine has a strong preference for helical conformation in linear peptides whereas they prefer an extended conformation in cyclic peptides.     

Design,synthesis and biological evaluation of 2-(3,4-dimethoxyphenyl)-6 (1,2,3,6-tetrahydropyridin-4-yl)imidazo[1,2-a]pyridine analogues as antiproliferative agents

Two series of forty five novel 2-(3,4-dimethoxyphenyl)-6-(1,2,3,6-tetrahydropyridin-4-yl) imidazo[1,2-a]pyridine analogues (IPA 1–22, IPS 1–22 and IP-NH) have been designed, synthesized and structures confirmed by ¹H NMR, ¹³C NMR, mass spectrometry. Furthermore, single crystal was developed for IPS-13. All the final derived conjugates were evaluated for their in vitro antiproliferative activity against a panel of diverse cancer cell lines viz., A549 (lung cancer), HeLa (cervical cancer), B16F10 (melanoma) and found to show potent anticancer activity on the tested cell lines. Many of them showed the IC₅₀ values in the range 2.0–20.0 µM. The most active compounds (IPA 5,6,8,9,12,16,17,19 and IPS 7,8,9,22) from IPA and IPS series were screened to determine their cytotoxicity on HEK-293 (human embryonic kidney) normal cell line and were found to be nontoxic to normal human cells. The molecular interactions of the derivatised conjugates were also supported by molecular docking simulations. These derivatives may serve as lead structures for development of novel potential anticancer drug candidates.     

Effective seed harvesting strategies for the ex situ genetic diversity conservation of rare tropical tree populations

Tropical rain forests harbor a high diversity of tree species, a large portion of which are considered rare and threatened by anthropogenic factors such as land-use change. Addressing the global need for ex situ rescue populations of such species, we investigated whether certain methods of wild-source seed collection harvest greater amounts of genetic variation from the source population while minimizing the costs expended. We used an individual-based computer program (NEWGARDEN) to conduct simulation trials examining which aspects of seed procurement provided the most cost-effective methods for maximal rare allele capture for single isolated populations of rare tropical tree species. Aspects examined included the geometric pattern of harvesting, location of seed collections within the spatial distribution of the population (central vs. peripheral), geometric partitioning of sampling regions (contiguous vs. subdivided), gene dispersal distance, linear travelling costs, and ratio of seeds collected to plants sampled. Results demonstrated that ratio of seeds collected to plants sampled had the highest effect on genetic diversity harvested relative to sampling location or geometric pattern of collection, explaining 82 and 79% of the variance in alleles harvested, respectively. Collecting from subdivided peripheral sampling regions and populations having long distance gene dispersal led to increases of up to 39 and 51% in the amount of genetic variation conserved respectively. These results suggest that ex situ conservation efforts for rare tropical trees can benefit by collecting fewer seeds from each of a larger number of trees, sampling from peripheral subdivided regions of the population rather than in a contiguous centrally located one under the transect or nearest neighbor strategies, and adjusting harvesting based on the dispersal biology of the source population. This study underscores the need for more information regarding the dispersal characteristics of the target species and demonstrates the value of predictive modeling for planning seed collection projects.     

The quality of reporting of RCTs used within a postoperative pain management meta-analysis, using the CONSORT statement

Background

Randomized controlled trials (RCTs) are routinely used in systematic reviews and meta-analyses that help inform healthcare and policy decision making. The proper reporting of RCTs is important because it acts as a proxy for health care providers and researchers to appraise the quality of the methodology, conduct and analysis of an RCT. The aims of this study are to analyse the overall quality of reporting in 23 RCTs that were used in a meta-analysis by assessing 3 key methodological items, and to determine factors associated with high quality of reporting. It is hypothesized that studies with larger sample sizes, that have funding reported, that are published in journals with a higher impact factor and that are in journals that have adopted or endorsed the CONSORT statement will be associated with better overall quality of reporting and reporting of key methodological items.

Methods

We systematically reviewed RCTs used within an anesthesiology related post-operative pain management meta-analysis. We included all of the 23 RCTs used, all of which were parallel design that addressed the use of femoral nerve block in improving outcomes after total knee arthroplasty. Data abstraction was done independently by two reviewers. The two main outcomes were: 1) 15 point overall quality of reporting score (OQRS) based on the Consolidated Standards for Reporting Trials (CONSORT) and 2) 3 point key methodological item score (KMIS) based on allocation concealment, blinding and intention-to-treat analysis.

Results

Twenty-three RCTs were included. The median OQRS was 9.0 (Interquartile Range?=?3). A multivariable regression analysis did not show any significant association between OQRS or KMIS and our four predictor variables hypothesized to improve reporting. The direction and magnitude of our results when compared to similar studies suggest that the sample size and impact factor are associated with improved key methodological item reporting.

Conclusions

The quality of reporting of RCTs used within an anesthesia related meta-analysis is poor to moderate. The information gained from this study should be used by journals to register the urgency for RCTs to be clear and transparent in reporting to help make literature accessible and comparable.     

p50 (NF-κB1) is an effector protein in the cytotoxic response to DNA methylation damage

The functional significance of the signaling pathway induced by O(6)-methylguanine (O(6)-MeG) lesions is poorly understood. Here, we identify the p50 subunit of NF-κB as a central target in the response to O(6)-MeG and demonstrate that p50 is required for S(N)1-methylator-induced cytotoxicity. In response to S(N)1-methylation, p50 facilitates the inhibition of NF-κB-regulated antiapoptotic gene expression. Inhibition of NF-κB activity is noted to be an S phase-specific phenomenon that requires the formation of O(6)-MeG:T mismatches. Chk1 associates with p50 following S(N)1-methylation, and phosphorylation of p50 by Chk1 results in the inhibition of NF-κB DNA binding. Expression of an unphosphorylatable p50 mutant blocks inhibition of NF-κB-regulated antiapoptotic gene expression and attenuates S(N)1-methylator-induced cytotoxicity. While O(6)-MeG:T-induced, p50-dependent signaling is not sufficient to induce cell death, this pathway sensitizes cells to the cytotoxic effects of DNA breaks.     

Role of Rubia cordifolia Linn. in radiation protection

The radioprotective potential of alcoholic extract of root of R. cordifolia, was studied by survival, hemopoietic cell protection and micronucleus assay. The LD50 value for the alcoholic root extract was found to be 1200 mg/kg body weight at 72 hr post irradiation. A significant radiation protection (67%) as assessed by increased animal survival was observed when R. cordifolia (RC) extract was administered intraperitoneally, 90 min. before the radiation exposure. Besides, the extract also inhibited radiation induced lipid peroxidation measured by the inhibition of thiobarbituric acid reactive substance (TBARS). The RC extract at a selected dose of 460 mg/kg body weight was effective in protecting the radiation induced suppression of endogenous colony forming units in spleen. A significant inhibition of radiation (2 Gy) induced micronuclei formation was observed when RC extract was administered 90 min prior to irradiation. Thus, it appears that the alcoholic root extract of R. cordifolia provides significant protection against radiation induced lipid peroxidation, hemopoietic injury and genotoxicity. The mechanism of action of RC extract appears to be through its anti-oxidant, metal chelation and anti-inflammatory property.     

Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with cytosine,cytidine, and cytidine diphosphate

The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to interact with purine bases, adenine and guanine of RNA/DNA. We report here the binding and structural studies of MbRIP1 with a pyrimidine base, cytosine; cytosine containing nucleoside, cytidine; and cytosine containing nucleotide, cytidine diphosphate. All three compounds bound to MbRIP1 at the active site with dissociation constants of 10^?4 M–10^?7 M. As reported earlier, in the structure of native MbRIP1, there are 10 water molecules in the substrate binding site. Upon binding of cytosine to MbRIP1, four water molecules were dislodged from the substrate binding site while five water molecules were dislodged when cytidine bound to MbRIP1. Seven water molecules were dislocated when cytidine diphosphate bound to MbRIP1. This showed that cytidine diphosphate occupied a larger space in the substrate binding site enhancing the buried surface area thus making it a relatively better inhibitor of MbRIP1 as compared to cytosine and cytidine. The key residues involved in the recognition of cytosine, cytidine and cytidine diphosphate were Ile71, Glu85, Tyr111 and Arg163. The orientation of cytosine in the cleft is different from that of adenine or guanine indicating a notable difference in the modes of binding of purine and pyrimidine bases. Since adenine containing nucleosides/nucleotides are suitable substrates, the cytosine containing nucleosides/nucleotides may act as inhibitors.