Crystal structure of the alpha, beta, gamma-tridentate manganese complex of adenosine 5'-triphosphate cocrystallized with 2,2'-dipyridylamine

The 1:1:1 complex of Mn2+, ATP, and 2,2'-dipyridylamine (DPA) crystallizes as Mn-(HATP)2.Mn(H2O)6.(HDPA)2.12H2O in the orthorhombic space group C222(1) with unit cell dimensions a = 10.234 (3) A, b = 22.699 (3) A, and c = 31.351 (4) A. The structure was solved by the multisolution technique and refined by the least-squares method to a final R index of 0.072 using 3516 intensities. The structure is composed of two ATP molecules sharing a common manganese atom. The metal exhibits alpha, beta, gamma coordination to the triphosphate chains of two dyad-related ATP molecules, resulting in a hexacoordinated Mn2+ ion surrounded by six phosphate groups. The metal to oxygen distances are 2.205 (6), 2.156 (4), and 2.144 (5) A for the alpha-, beta-, and gamma-phosphate groups, respectively. No metal-base interactions are observed. There is a second hexaaqua-coordinated Mn2+ ion that is also located on a dyad axis. The hydrated manganese ions sandwich the phosphate-coordinated manganese ions in the crystal with a metal-metal distance of 5.322 A. The ATP molecule is protonated on the N(1) site of the adenine base and exhibits the anti conformation (chi = 66.0 degrees). The ribofuranose ring is in the 2/3 T conformation with pseudorotation parameters P = 179 (1) degrees and tau m = 34.1 (6) degrees. The adenine bases form hydrogen-bonded self-pairs across a crystallographic dyad axis and stack with both DPA molecules to form a column along the dyad. The structure of the metal-ATP complex provides information about the possible metal coordination, conformation, and environment of the nucleoside triphosphate substrate in the enzyme.     

Molecular recognition in the minor groove of the DNA helix. Studies on the synthesis of oligonucleotides and polynucleotides containing 3-deaza-2''-deoxyadenosine. Interaction of the oligonucleotides with the restriction endonuclease EcoRV.

An improved procedure for the preparation of 3-deaza-2'-deoxyadenosine (d3CA) is described which is suitable for the synthesis of gram quantities of this analogue. Using phosphoramidite chemistry d3CA has been incorporated into the Eco RV restiction endonuclease recognition sequence (underlined) present in the self-complementary dodecamer d(GACGATATCGTC). The modified oligonucleotides have been thoroughly characterised by nucleoside composition analysis, circular dichroism and thermal melting studies. Studies with Eco RV show that incorporation of d3CA into either the central or outer dA-dT base-pair results in a substantial reduction in the rate of cleavage. The two-step conversion of d3CA to 3-deaza-2'-deoxyadenosine-5'-O-triphosphate (d3CATP) via the 5'-O-tosylate is also described. d3CATP is not a substrate in the poly[d(AT)].poly[d(AT)] primed polymerisation for either E. coli DNA polymerase I or Micrococcus luteus DNA polymerase. In a more detailed kinetic analysis d3CATP was shown to be a competitive inhibitor of E. coli DNA polymerase I with respect to dATP.     

Seasonal variation in freezability of buffalo semen

Fifty-six buffalo semen ejaculates of mass activity greater than plus three on a five-point scale (28 each in summer and winter seasons) were frozen in Tris yolk glycerol (TY-G) extender with four hours equilibration time. Motility of semen was checked after first extension (initial motility), after equilibration time, 15 minutes after freezing, and 30 days after freezing. Motility increased during winter season. Significant differences (P<0.01) in motility after freezing were observed between summer and winter seasons.     

The Binding of Indole-3-acetic Acid and 3-Methyleneoxindole to Plant Macromolecules

Homogenates of pea (Pisum sativum L., var. Alaska) seedlings exposed to ¹⁴C-indole-3-acetic acid or ¹⁴C-3-methyleneoxindole, an oxidation product of indole-3-acetic acid, were extracted with phenol. In both cases 90% of the bound radioactivity was found associated with the protein fraction and 10% with the water-soluble, ethanol-insoluble fraction. The binding of radioactivity from ¹⁴C-indole-3-acetic acid is greatly reduced by the addition of unlabeled 3-methyleneoxindole as well as by chlorogenic acid, an inhibitor of the oxidation of indole-3-acetic acid to 3-methyleneoxindole. Chlorogenic acid does not inhibit the binding of ¹⁴C-3-methyleneoxindole. The labeled protein and water-soluble, ethanol-insoluble fractions of the phenol extract were treated with an excess of 2-mercaptoethanol. Independently of whether the seedlings had been exposed to ¹⁴C-indole-3-acetic acid or ¹⁴C-3-methyleneoxindole, the radioactivity was recovered from both fractions in the form of a 2-mercaptoethanol-3-methyleneoxindole adduct. These findings indicate that 3-methyleneoxindole is an intermediate in the binding of indole-3-acetic acid to macromolecules.     

Computer-assisted motility assessment of spermatozoa from fresh and frozen-thawed semen of the bull, boar and goat

Generally, both subjective and computer-assisted (HTM-2000 motility analyzer) assessment of sperm motility in fresh and in frozen-thawed semen of bulls, boars and bucks yields comparable results. However, the use of a motility analyzer renders consistently more accurate estimates, especially when that motility is vigorous as in fresh bull semen.     

Role of sulfhydryl groups in band 3 in the inhibition of phosphate transport across erythrocyte membrane in visceral leishmaniasis

Membrane destabilization in erythrocytes plays an important role in the premature hemolysis and development of anemia during visceral leishmaniasis (VL). Marked degradation of the anion channel protein band 3 is likely to allow modulation of anion flux across the red cell membrane in infected animals. The present study describes the effect of structural modification of band 3 on phosphate transport in VL using (31)P NMR. The result showed progressive decrease in the rate and extent of phosphate transport during the post-infection period. Interdependence between the intracellular ionic levels seems to be a determining factor in the regulation of anion transport across the erythrocyte membrane in control and infected conditions. Infection-induced alteration in band 3 made the active sites of transport more susceptible to binding with amino reactive agents. Inhibition of transport by oxidation of band 3 and subsequent reversal by reduction using dithiothreitol suggests the contribution of sulfhydryl group in the regulation of anion exchange across the membrane. Quantitation of sulfhydryl groups in the anion channel protein showed the inhibition to be closely related to the decrease of sulfhydryl groups in the infected hamsters. Downregulation of phosphate transport during leishmanial infection may be ascribed to the sulfhydryl modification of band 3 resulting in the impaired functioning of this protein under the diseased condition.     

Comprehensive metabolic fingerprinting of Withania somnifera leaf and root extracts

Profiling of metabolites is a rapidly expanding area of research for resolving metabolic pathways. Metabolic fingerprinting in medicinally important plants is critical to establishing the quality of herbal medicines. In the present study, metabolic profiling of crude extracts of leaf and root of Withania somnifera (Ashwagandha), an important medicinal plant of Indian system of medicine (ISM) was carried out using NMR and chromatographic (HPLC and GC-MS) techniques. A total of 62 major and minor primary and secondary metabolites from leaves and 48 from roots were unambiguously identified. Twenty-nine of these were common to the two tissues. These included fatty acids, organic acids, amino acids, sugars and sterol based compounds. Eleven bioactive sterol-lactone molecules were also identified. Twenty-seven of the identified metabolites were quantified. Highly significant qualitative and quantitative differences were noticed between the leaf and root tissues, particularly with respect to the secondary metabolites.     

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl.html) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. While automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO), the preferred submission tool for individual submitters is Webin (WWW). Through all stages, dataflow is monitored by EBI biologists communicating with the sequencing groups. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI). Database releases are produced quarterly and are distributed on CD-ROM. Network services allow access to the most up-to-date data collection via Internet and World Wide Web interface. EBI's Sequence Retrieval System (SRS) is a Network Browser for Databanks in Molecular Biology, integrating and linking the main nucleotide and protein databases, plus many specialised databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, Blast etc) are available for external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.     

Optimization of factors for efficient recovery of transgenic peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.)

De-embryonated cotyledon explants of peanut were co-cultivated under different conditions with Agrobacterium tumefaciens harbouring pIG121hm plasmid carrying intron-containing β-glucuronidase as a reporter while hygromycin phosphotransferase and neomycin phosphotransferase as selectable marker genes. Co-cultivation duration and temperature, various antioxidants and their concentrations, bacterial strains and explant characteristics (incised and non-incised) were examined either alone or in combinations for optimization of transient expression of the reporter gene. Up to 81% transformation was recorded when non-incised explants were co-cultivated with strain EHA101 for 5 days at 21°C on shoot induction medium containing 100 mg/L l-cysteine. Addition of the optimized concentration of augmentin (200 mg/L) along with cefotaxime (200 mg/L) to the shoot induction medium not only effectively eliminated bacterial growth, but also facilitated high frequency of shoot induction. The 40 mg/L hygromycin concentration prevented complete shoot regeneration of non-transgenic explants thus considered for the regeneration of transgenics. Resistant shoots were successfully transferred to soil either by grafting or in vitro rooting. Survival rate of the grafted shoots was nearly 100% in glass-house conditions. The optimized protocol took around 3 months to generate healthy plants. Polymerase chain reaction, Southern blot hybridization, histochemical tests, segregation and hygromycin-leaf assays of selected transgenic plants showed integration of the transgene into peanut genome. No chimeras were noticed during the study.     

High level expression of a functionally active cholera toxin B: rabies glycoprotein fusion protein in tobacco seeds

A synthetic DNA construct containing cholera toxin B subunit, genetically fused to the surface glycoprotein of rabies virus was expressed in tobacco plants from a seed specific (legumin) promoter. Seed specific expression was monitored by real-time PCR, GM1-ELISA and Western blot analyses. The fusion protein accumulated in tobacco seeds at up to 1.22% of the total seed protein. It was functionally active in binding to the GM1-ganglioside receptors, suggesting its assembly into pentamers in seeds of the transgenic plants. Immunoblot analysis confirmed that the ~80.6 kDa monomeric fusion polypeptide was expressed in tobacco seeds and accumulated as a ~403 kDa pentamer. Evaluation of its immunoprotective ability against rabies and cholera is to be examined.