Optical resolution by preferential crystallization of 4-methylpiperidinium hydrogen (RS)-phenylsuccinate

Gibbs energy of racemate formation, binary melting point diagram, and ternary solubility diagram suggested that 4-piperidinium hydrogen (RS)-phenylsuccinate [(RS)-4-MP salt] exists in a conglomerate. Appropriate conditions were explored on the basis of free energy of critical nucleation in a supersaturated solution to resolve efficiently (RS)-4-MP salt by preferential crystallization. Successive preferential crystallization of (RS)-4-MP salt in ethanol at 20°C gave (R)- and (S)-4-MP salts of 90–94% optical purities. Optically pure (R)- and (S)-phenylsuccinic acids were obtained by recrystallization of the (R)- and (S)-4-MP salts, followed by treatment of the salts purified with hydrochloric acid. © 1994 Wiley-Liss, Inc.     

In vitro interaction between calf thymus DNA and Escherichia coli LPS in the presence of divalent cation Ca2+

With increasing addition of Escherichia coli LPS to calf thymus DNA, both dissolved in CaCl2, absorption maxima of DNA at 260 nm decreased gradually with the appearance of isosbastic points at both ends of spectra, which implied some binding between DNA and LPS. Hill plot of absorbance data showed that the binding interaction was positive cooperative in nature. For any fixed concentration of DNA and LPS, extent of interaction increased as concentration of CaCl2 was raised from 1.0 to 100 mM, signifying the electrostatic nature of the interaction, mediated through Ca2+ ion. Stepwise addition of EDTA, a chelating agent for divalent cations, to DNA-LPS bound complex gradually reversed the spectral shift with increase in absorbance at 260 nm, which implied opening up of the complex, that is, reversible nature of the interaction. Circular dichroism spectral changes of DNA by the addition of LPS indicated partial transition of DNA from B to A form. Isothermal titration calorimetric (ITC) study showed that the DNA-LPS binding was an exothermic and enthalpy-driven phenomenon. Moreover, in the presence of 100 mM CaCl2, binding constant of the interaction was found to be 2.6 x 10(4) M(-1) and 3.1 x 10(4) M(-1) from the analysis of Hill plot and ITC result, respectively. DNA-melting study showed that the LPS binding had increased the melting temperature of DNA, indicating more stabilization of DNA double helix. The binding of LPS to DNA made the complex resistant to digestion with endonucleases EcoRI and DNase I.     

Purification, characterization and application of a novel extracellular agarase from a marine Bacillus megaterium

A marine, gram positive, aerobic, spore forming, and non flagellated bacterium which degrades low melting point (LMP) — agarose was isolated from the west coast of India and identified as Bacillus megaterium based on its morphological, biochemical, and molecular characterization. This bacterium produced clear haloes or zone of clearance on agar containing plates which was a clear indication of its agarolytic property. The extracellular agarase thus obtained was purified 8.8 and 78 fold from the culture supernatant by ammonium sulfate precipitation and gel filtration, respectively. Molecular mass by gel filtration and SDS-PAGE gave values of 15 and 12 kDa, respectively. The optimum temperature and pH for maximum agarase activity were 40°C and 6.6. The activity of agarase was drastically reduced by addition of metal ions in the assay system. This agarase, gave a K _m and V _max value of 4 mg/mL and 2.75 μmol/min/mg. The isolation of protoplast from agarophyte like Gelidiella acerosa using indegenous agarase is reported for the first time.     

Depositional sequences in the Kimmeridgian of the Vocontian Basin (France) controlled by carbonate export from shallow-water platforms

Detailed sedimentological analyses and sequential and cyclostratigraphic interpretations in the Kimmeridgian of the Swiss Jura and the Vocontian Basin lead to a high-resolution correlation from the platform to the basin where the biostratigraphy is well established. Several orders of depositional sequences are defined. Their duration is estimated from the time frame given in the sequence-chronostratigraphic chart of Hardenbol et al. (1998). It is suggested that an elementary sequence formed in tune with the 20 ky precession cycle. Small-scale and medium-scale sequences correspond to the 100 and 400 ky eccentricity cycles, respectively. The platform-to-basin correlation shows that the composition of the hemipelagic and pelagic deposits depends to a large part on cyclical variations of carbonate production in shallow-marine environments and subsequent export to the basin. The distribution of thick versus thin marl-limestone alternations and carbonate-dominated versus marl-dominated intervals observed in the basinal sections is explained by the superposition of high- and low-frequency sea-level changes that controlled the carbonate productivity on the platform and the export potential of carbonate mud to the basin.     

Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design

Glutamine synthetase (GS) catalyzes the ligation of glutamate and ammonia to form glutamine, with concomitant hydrolysis of ATP. In mammals, the activity eliminates cytotoxic ammonia, at the same time converting neurotoxic glutamate to harmless glutamine; there are a number of links between changes in GS activity and neurodegenerative disorders, such as Alzheimer's disease. In plants, because of its importance in the assimilation and re-assimilation of ammonia, the enzyme is a target of some herbicides. GS is also a central component of bacterial nitrogen metabolism and a potential drug target. Previous studies had investigated the structures of bacterial and plant GSs. In the present publication, we report the first structures of mammalian GSs. The apo form of the canine enzyme was solved by molecular replacement and refined at a resolution of 3 Å. Two structures of human glutamine synthetase represent complexes with: a) phosphate, ADP, and manganese, and b) a phosphorylated form of the inhibitor methionine sulfoximine, ADP and manganese; these structures were refined to resolutions of 2.05 Å and 2.6 Å, respectively. Loop movements near the active site generate more closed forms of the eukaryotic enzymes when substrates are bound; the largest changes are associated with the binding of the nucleotide. Comparisons with earlier structures provide a basis for the design of drugs that are specifically directed at either human or bacterial enzymes. The site of binding the amino acid substrate is highly conserved in bacterial and eukaryotic GSs, whereas the nucleotide binding site varies to a much larger degree. Thus, the latter site offers the best target for specific drug design. Differences between mammalian and plant enzymes are much more subtle, suggesting that herbicides targeting GS must be designed with caution.     

High-resolution Mapping and Analysis of the Resistance Locus <Emphasis Type="Italic">Rpi-abpt</Emphasis> Against <Emphasis Type="Italic">Phytophthora infestans</Emphasis> in Potato

Introduction of more durable resistance against Phytophthora infestans causing late blight into the cultivated potato is of importance for sustainable agriculture. We identified a new monogenically inherited resistance locus that is localized on chromosome 4. The resistance is derived from an ABPT clone, which is originally a complex quadruple hybrid in which Solanum acaule, S. bulbocastanum, S. phureja and S. tuberosum were involved. Resistance data of the original resistant accessions of the wild species and analysis of mobility of AFLP markers linked to the resistance locus suggest that the resistance locus is originating from S. bulbocastanum. A population of 1383 genotypes was screened with two AFLP markers flanking the Rpi-abpt locus and 98 recombinants were identified. An accurate high-resolution map was constructed and the Rpi-abpt locus was localized in a 0.5 cM interval. One AFLP marker was found to co-segregate with the Rpi-abpt locus. Its DNA sequence was highly similar with sequences found on a tomato BAC containing several resistance gene analogues on chromosome 4 and its translated protein sequence appeared to be homologous to several disease resistance related proteins. The results indicated that the Rpi-abpt gene is a member of an R gene cluster.     

Rapid detection and differentiation of the major mycoplasma contaminants in cell cultures using real-time PCR with SYBR Green I and melting curve analysis

A quantitative real-time polymerase chain reaction (PCR) procedure followed by melting curve analysis, using the green fluorescence dye SYBR Green I, was developed for rapid detection and differentiation of mycoplasma contaminants in cell cultures. This method showed that the detection of the target sequence was linear over a range from 10(4) to 10 colony-forming units (CFU) of the mycoplasma cells. Analysis of the melting temperature of the PCR products allowed differentiation of the major mycoplasma contaminants. These results demonstrate that the protocol described in the present study can decrease the time to obtain reproducible results by simultaneous detection and differentiation of the Mycoplasma species contaminating cell cultures.     

Modulation of chromatin organization by RH-3, a preparation of Hippophae rhamnoides,a possible role in radioprotection

The present study was aimed to understand the mode of action of alcoholic extract of whole berries of Hippophae rhamnoides (RH-3) which has already been reported to render more than 80% protection against radiation induced mortality in mice. Direct and indirect antioxidant action (free radical scavenging and metal chelating potential) were assayed using 2-deoxy ribose degradation and 2,2-bipiridyl assays. Effect of RH-3 on radiation and chemical oxidant mediated DNA damage was evaluated using single cell gel electrophoresis (Comet assay) and alkaline halo assay. Ability of RH-3 to bind with calf thymus DNA was assayed through change in melting temperature (Tm) while toxicity was assayed in thymocytes by trypan blue exclusion.RH-3 inhibited 2-deoxy ribose degradation in a dose dependent manner (IC 50 500 g/ml). 2,2-bipiridyl assay revealed the inability of RH-3 to chelate Fe²⁺ ions. RH-3 inhibited radiation and tertiary butyl hydroperoxide induced DNA strand breaks in a dose dependent manner and at concentrations of 100 and 120 g/ml the length of comet tail was considerably reduced and became almost similar to that of untreated control. RH-3 at a concentration of 120 g/ml or more induced a strong compaction of chromatin as was evident from lack of tail and appearance of intensely stained circular bodies. This made the nuclei resistant even to a radiation dose of 1000 Gy. The compaction of chromatin was not reversed even by relaxation buffer indicating that salt concentration had no role in RH-3 induced chromatin compaction. Alkaline halo assay also corroborated the results of comet assay. Lower DNA-RH-3 concentrations (1:0.5 and 1:1) induced a shift of Tm towards left by 2 and 5°C respectively; however higher concentrations (1:8 and 1:16) shifted the Tm towards right increasing it by 10 and 21°C correspondingly.RH-3, evinced only a mild free radical scavenging activity at concentrations used in the present study, therefore its ability to protect DNA could mainly be attributed to direct modulation of chromatin organization. Further work to unravel these facts would be necessary.     

Enhancing the Stability of Oligonucleotide Duplexes. The Effect of Adding 1-(2"-Deoxy-β-D-ribofuranosyl)-5-nitroindole

We studied the properties of DNA duplexes containing 5-nitroindole (N) in one of the chains. We synthesized 8-membered oligos with N at the 5" or at the 3" end: 5"-d(NXGACCGTC)-3" or 5"-d(GACCGTCXN)-3", where X is one of the four natural bases, making all four kinds of oligos with and without N. We also prepared 11-membered oligos complementary to the above octanucleotides: 5"-d(TGACGGTCYZT)-3" and 5"-d(TZYGACGGTCT)-3", where Y and Z are A, G, C, or T. The stability of duplexes obtained with these oligos was assessed by melting, and the thermodynamic parameters H, S, and T _m were calculated. Comparison of the melting curves for modified and nonmodified duplexes demonstrated that the presence of N at the 5" end of one chain raises the T _m by 6.6° on average; if N is at the 3" end of the same chain, the T _m increases by about 3°.