Stereochemistry of Internucleotide Bond Formation by the H-Phosphonate Method. 1. Synthesis and 31P Nmr Analysis of 16 Diribonulceoside (3′-5′)-H-Phosphonates and the Corresponding Phosphorothioates

Sixteen diribonucleoside (3′-5′)-H-phosphonates were synthesized via condensation of the protected ribonucleoside 3′-H-phosphonates with nucleosides, and the influence of a nucleoside sequence on the observed stereoselectivity was analyzed. ₃₁P NMR spectroscopy was used to evaluate a relationship between chemical shift and absolute configuration at the phosphorous center of the H-phosphonate diesters as well as of the corresponding phosphorothioate diesters. Although for the most cases such correlation was found, there was however several exceptions to the rule where the relative positions of resonances arising from R _P and S _P diastereomers were reversed.     

Synthesis of Oligoribonucleotides by the H-Phosphonate Approach Using Base Labile 2′-O-Protecting Groups. V. Recent Progress in Development of the Method

Abstract

A simple and inexpensive method for the preparation of oligoribonucleotides using N-isopropoxyacety(phenoxyacetyl)-2′-O-(2-chlorobenzoyl)-5′-O-dimethoxytritylnucleoside H-phosphonate building blocks has been developed.     

Acid Base Disorders—The Clinical Use of the Astrup Method of Determining pH. pCO2 and Base Excess

The Astrup method for determination of arterial pH, pCO₂, and “base excess” provides a simple and accurate means for quantitation of acid-base disorders. The “base excess” value, a measure of metabolic acidosis or alkalosis, gives the clinician a valuable tool with which to estimate electrolyte replacement. The pCO₂ is a measure of respiratory acidosis or alkalosis. The pH is used as a measure of the adequacy of compensation. Several representative cases illustrate the use and interpretation of the test.     

Synthesis of Oligodeoxynucleotides Containing the C-Nucleoside and 2′- Deoxy-2′-Fluoro-ara-Nucleoside Moieties by the H-Phosphonate Method.1,2

Abstract

A module type, computer-controlled, multipurpose synthesizer displaying a novel device for the transport of liquids, was constructed and used in the synthesis of oligomers containing some C-nucleosides and 2′-deoxy-2′-fluoro-ara-nucleoside moieties. H-Phosphonate method was applied in terms of a further adjustment of construction features of the synthesizer versus chemistry of the process. Results of preliminary studies on the effects of the modified nucleosides on the stability of duplexes showed a clear tendency of destabilization of duplexes in the case of C-nucleosides while fluorinated nucleosides in most cases stabilize the formed duplexes.     

Role of Fungal Mycelium in the Formation of Carbonate Concretions in Growing Media—An Investigation by SEM and Synchrotron-Based X-Ray Tomographic Microscopy

Soil fungi can facilitate calcification. Mushroom Morchella sp . mycelium induced the formation of carbonate concretions on the surface of an organic-based growing media amended with sand and ground limestone. According to SEM observation and X-ray-tomographic microscopy a dense mycelial network induced calcification. The CaCO₃ content of concretions (?: 0.3–1.5 cm) was found to be at 30%. Microsparitic calcite cemented the pores between the sand grains forming a dense clogging microstructure. Besides water uptake by the mycelium, a high evaporation rate and a decrease in pCO₂ contributed to the formation of the concretions. Fungal mycelium in the concretions is surrounded by voids indicating that at the surface of the mycelium, calcification is counteracted most probably by the release of organic acids.     

Catalysis and Selectivity in Prebiotic Synthesis: Initiation of the Formation of Oligo(U)s on Montmorillonite Clay by Adenosine-5′-methylphosphate

Adenosine-5′-methylphosphate (MepA) initiates the oligomerization of the 5′-phosphorimidazolide of uridine (ImpU) in the presence of montmorillonite clay. Longer oligomers form because the 5′-phosphate is blocked with a methyl group that prevents the formation of cyclic- and pyrophosphate-containing compounds. The MepA initiates 69–84% of the 5–9 charge oligomers, respectively. The montmorillonite catalyst also provides selectivity in the oligomerization reactions so that the main reaction pathway is MepA → MepA³′pU → MepA³′pU²′pU → MepA³′pU²′pU³′pU. MepA did not enhance the oligomerization of ImpA. The relative rates of the reactions were determined from an investigation of the products in competitive reactions. Selectivity was observed in the reaction of ImpU with equimolar amounts of MepA³′pU and MepA²′pU where the relative reaction rates are 10.3:1, respectively. In the reaction of ImpA with MepA³′pA and MepA²′pA the ImpA reacts 5.2 times faster with MepA³′pA. In the competitive reaction of ImpU and ImpA with MepA³′pA and MepA³′pU the elongation proceeds on MepA³′pA 5.6 times more rapidly than with MepA³′pU. There is no correlation between the extent of binding to the montmorillonite and reaction rates in the formation of longer oligomers. The formation of more than two sequential 2′,5′-linkages in the oligomer chain proceeds more slowly than the addition to a single 2′,5′-link or a 3′,5′-link and either chain termination or elongation by a 3′,5′-linage occurs. The central role that catalysis may have had in the prebiotic formation of biopolymers is discussed. Note added in proof: There are errors in the high resolution mass spectral data given in Section 4.2.1. The high resolution mass spectrum found for the cyclic dimer of UpUp (C-UpUp) was 657.02260. C₁₈H₂₁N₄O₁₆P₂Na₂ requires 657.02232. The high resolution mass spectrum found for the cyclic dimer of ApAp (C-ApAp) was 725.05850. C₂₀H₂₂N₁₀O₁₂P₂Na₃ requires 725.05839.     

Role of mitochondria in apoptosis induced by the 2‐5A system and mechanisms involved

The 2‐5A system (2-5OAS/RNaseL) is composed of the 2′,5′oligoadenylate synthetase 1 (2-5OAS1) and 2-5A-dependent RNase (RNaseL), enzymes that play a key role in antiviral defence mechanisms. Activation of the 2-5A system by double stranded RNA (dsRNA) induces degradation of ribosomal RNAs and apoptosis in mammalian cells. To obtain further information into the molecular mechanisms by which RNaseL induces apoptosis, we expressed human RNaseL and 2-5OAS in HeLa cells using recombinant vaccinia viruses as vectors and we analysed in detail different biochemical markers of apoptosis. In this expression virus-cell system the activation of RNaseL, as index of rRNA degradation, is an upstream event of apoptosis induction. RNaseL induces apoptosis in a caspase-dependent manner (caspases 8, 9 and 2). At the beginning of apoptosis RNaseL and 2-5OAS are localized in the mitochondria and cytosol fractions, while at the onset of apoptosis both enzymes are largely in mitochondria. The 2-5A system induces the release of Cytochrome c from mitochondria to cytosol in a caspase dependent manner. The onset of apoptosis elicits the disruption of mitochondrial membrane potential (ΔΦm), as well as the generation of reactive oxygen species (ROS). Moreover, the activation of RNaseL induces morphological alterations in the mitochondria. Apoptosis induced by the 2-5A system involves mitochondrial proteins, such as the human anti-apoptotic protein Bcl-2, which blocks both the apoptosis and the change of ΔΦm induced by the activation of RNaseL. These findings provide new insights into the molecular mechanisms of apoptosis induction by the 2-5A system, demonstrating the importance of mitochondria in 2-5OAS/RNaseL-induced apoptosis.     

Biosynthesis of l-Sorbose and l-Psicose Based on C—C Bond Formation Catalyzed by Aldolases in an Engineered Corynebacterium glutamicum Strain

The property of loose stereochemical control at aldol products from aldolases helped to synthesize multiple polyhydroxylated compounds with nonnatural stereoconfiguration. In this study, we discovered for the first time that some fructose 1,6-diphosphate aldolases (FruA) and tagatose 1,6-diphosphate (TagA) aldolases lost their strict stereoselectivity when using l-glyceraldehyde and synthesized not only l-sorbose but also a high proportion of l-psicose. Among the aldolases tested, TagA from Bacillus licheniformis (BGatY) showed the highest enzyme activity with l-glyceraldehyde. Subsequently, a “one-pot” reaction based on BGatY and fructose-1-phosphatase (YqaB) generated 378 mg/liter l-psicose and 199 mg/liter l-sorbose from dihydroxyacetone-phosphate (DHAP) and l-glyceraldehyde. Because of the high cost and instability of DHAP, a microbial fermentation strategy was used further to produce l-sorbose/l-psicose from glucose and l-glyceraldehyde, in which DHAP was obtained from glucose through the glycolytic pathway, and some recombination pathways based on FruA or TagA and YqaB were constructed in Escherichia coli and Corynebacterium glutamicum strains. After evaluation of different host cells and combinations of FruA or TagA with YqaB and optimization of gene expression, recombinant C. glutamicum strain WT(pXFTY) was selected and produced 2.53 g/liter total ketoses, with a yield of 0.50 g/g l-glyceraldehyde. Moreover, deletion of gene cgl0331, encoding the Zn-dependent alcohol dehydrogenase in C. glutamicum, was confirmed for the first time to significantly decrease conversion of l-glyceraldehyde to glycerol and to increase yield of target products. Finally, fed-batch culture of strain SY14(pXFTY) produced 3.5 g/liter l-sorbose and 2.3 g/liter l-psicose, with a yield of 0.61 g/g l-glyceraldehyde. This microbial fermentation strategy also could be applied to efficiently synthesize other l-sugars.     

Study on Reactivity and Protection of the α-Hydroxyphosphonate Moiety in 5′-Nucleotide Analogues: Formation of the 3′-O-P-C(OH)-C4′ Internucleotide Linkage

Abstract

The recently described epimeric nucleosidyl-5′-C-phosphonates (α-hydroxyphosphonates) represent novel nucleotide analogues that can be incorporated into chimeric oligonucleotides by the phosphotriester condensation method. In order to prepare suitable protected monomer(s) we have studied condensation reaction between protected 2′-deoxythymidine and 2′-deoxythymidinyl-5′-C-phosphonate, both as model compounds, in dependence on the nature of the 5′-hydroxyl protecting group. We have found that the O-acetyl group is unstable in the presence of TPSCl or MSNT used as condensing agents for activation of the phosphorus moiety. This instability negatively influences the scope of the condensation process. On the other hand, introduction of the O-methoxycarbonyl group gave excellent results. The O-methoxycarbonyl group does not participate in the condensation process, and its quantitative introduction into the nucleotide analogues is accomplished using a novel acylating agent, methoxycarbonyl tetrazole.     

The Role of Zinc in Thrombosis and Pulmonary Embolism in the Course of Antiphospholipid Syndrome (APS)—Short Review

Antiphospholipid antibodies may occur in the course of various diseases, but its presence is not necessarily associated with clinical symptoms. Zinc has multiple biological roles. For example, it stabilizes the cell’s membrane and regulates its functions by influencing the synthesis of phospholipids and its distribution. The present review focuses on the possible associations between zinc and antiphospholipid antibodies and with the symptoms of antiphospholipid syndrome.     

The Structure of Bacteriophage φCb5 Reveals a Role of the RNA Genome and Metal Ions in Particle Stability and Assembly

The structure of the Leviviridae bacteriophage φCb5 virus-like particle has been determined at 2.9 Å resolution and the structure of the native bacteriophage φCb5 at 3.6 Å. The structures of the coat protein shell appear to be identical, while differences are found in the organization of the density corresponding to the RNA. The capsid is built of coat protein dimers and in shape corresponds to a truncated icosahedron with T = 3 quasi-symmetry. The capsid is stabilized by four calcium ions per icosahedral asymmetric unit. One is located at the symmetry axis relating the quasi-3-fold related subunits and is part of an elaborate network of hydrogen bonds stabilizing the interface. The remaining calcium ions stabilize the contacts within the coat protein dimer. The stability of the φCb5 particles decreases when calcium ions are chelated with EDTA. In contrast to other leviviruses, φCb5 particles are destabilized in solution with elevated salt concentration. The model of the φCb5 capsid provides an explanation of the salt-induced destabilization of φCb5, since hydrogen bonds, salt bridges and calcium ions have important roles in the intersubunit interactions.Electron density of three putative RNA nucleotides per icosahedral asymmetric unit has been observed in the φCb5 structure. The nucleotides mediate contacts between the two subunits forming a dimer and a third subunit in another dimer. We suggest a model for φCb5 capsid assembly in which addition of coat protein dimers to the forming capsid is facilitated by interaction with the RNA genome. The φCb5 structure is the first example in the levivirus family that provides insight into the mechanism by which the genome-coat protein interaction may accelerate the capsid assembly and increase capsid stability.     

The Role of DNA–DNA Hybridization and 16S rRNA Gene Sequencing in Solving Taxonomic Problems by the Example of the Order Haloanaerobiales

In this review, the validity of evolutionary conclusions inferred from the quantitative estimates of the similarity between bacterial genes is evaluated using the order Halonanaerobiales as an example. The haloanaerobic phenotype is briefly characterized, as are some specific features that allow the order Haloanaerobiales to serve as a reference taxon. Phylogenetic analysis provides a set of standard quantitative criteria for ranking bacterial taxa from species to families. Recommendations for the use of these standard criteria are given.     

5-HT metabolism in the intestinal wall of the rat—II. The nerves plexuses—interactions between 5-HT containing cells

The presence of serotonin (5-HT) in dissected intestinal muscular wall of the caecum was demonstrated by the determination of endogenous level of the amine by both spectrofluorimetric and radioenzymatic assays. Biosynthesis of [³H]5-HT from [³H]tryptophan in in vitro conditions revealed the presence of tryptophan hydroxylase in these muscular layers and therefore strongly suggest the presence of serotoninergic neurons. Following dissection of the mucosa from the muscular layers containing the nerve plexuses, endogenous 5-HT and 5-hydroxyindol acetic acid levels as well as amounts of [³H]5-HT synthesized from [³H]tryptophan were always higher than those found in intact fragments of the caecum. These results are discussed in terms of metabolic processes involved in the regulation between the two 5-HT containing compartments.     

Cooperative Interactions of the Oligodeoxyribonucleotides on the Complementary Template. The Influence of Chemical Groups and Mismatched Nucleotides at the 5′- and 3′-ends of Oligonucleotides on the Parameters of Cooperativity

Abstract

Parameters of cooperative interactions of two or three oligodeoxyribonucleotides or their derivatives bound with the adjacent sites of the complementary template were measured using method of “complementary addressed modification titration” (CAMT). Complementary template (target) were modified with the reactive oligonucleotide derivatives (reagents) bearing covalently attached alkylating 4-[N-(2-chloroethyl)-N-methylaminojbenzylamino- group (C1RCH₂NH)- at 5′-terminal phosphate. The targets had only one binding site for the reagent and either no (T10), or one (T'22 and T22) or two sites (T26) for the oligonucleotides (effectors) cooperatively bound with the adjacent sites on the template. Both unmodified oligonucleotides E₁, E₂ and their derivatives E₁ ^phn, E₂ ^phn bearing N- (2-hydroxyethyl)-phenazinium residues Phn- both at 5′- and 3′- ends covalently linked via ethylenediamine linker were used as effectors. Effectors E₁ and E₂ (E₁ ^Phn and E₂ ^Phn) bind, respectively, upstream or downstream from the reagent. Hexameric (X6) or octameric (X8 or X8^m) reagents were used for the target modification. The reagent X8^m formed one TT-mismatch with the target at the end opposite to location of the reactive moiety. The cooperativity parameter values characterizing the mutual interactions between the reagents X6, X8, X8^m and effectors E₁, E₂, E₁ ^phn, E₂ ^Phn have been found as the ratio of the association constants of the reagents in the presence of effectors. The association constants were calculated from the dependencies of the target modification extent on initial concentrations of the reagents. The use of T26 existing both in linear and hairpin conformations permitted us to estimate additionally the role of indirect cooperativity originating from the induction of the target conformational change by the effectors. The following conclusions were done from the quantitative results. The efficiency of direct cooperativity is independent on the length of oligonucleotide for the same nature of the contact. The cooperativity parameter increases by factor about 3 in the presence of Phn-group covalently attached to oligonucleotides and located at the junctions. The presence of either alkylating group CIRCH₂NH- or TT-mismatch at the junctions eliminates cooperative interaction between the bases. In the same time sufficiently effective cooperative interaction takes place in the case of simultaneous presence of both Phn- and either CIRCH₂NH- group or TT-mismatch at the junction.     

The clastogenic effect of 5-methoxypsoralen plus UV-A in human lymphocytes in vitro and its modification by the anticlastogen β-aminoethylisothiouronium

Summary The treatment of human lymphocytes in vitro with 5-methoxypsoralen (5-MOP) plus UV-A induces a dose-dependent increase in the SCE rate and in structural chromosome aberrations. We carried out tests to see whether the clastogenic effect of 5-MOP plus UV-A could be reduced by the anticlastogen -aminoethylisothiouronium (AET). The occurrence of a protective effect proved to be dependent upon the conditions of treatment. When AET was present over a long period of time (22h) in cultures with 5-MOP, the number of breaks was reduced compared with such cultures without AET (reduction factor 0.5–0.6). On the other hand, a short period of action by AET (1.5 h) in the presence of 5-MOP produced no reduction of breaks. Posttreatment with AET (20 h) yielded an obvious protective effect (reduction factor 0.2–0.4). The possible mechanisms of the protective effect of AET are discussed.     

H4-isozyme of lactate dehydrogenase in the solution of sodium chloride—4. inhibition by oxalate and oxamate

• 1.1. The inhibition of H4-isozyme of lactate dehydrogenase (H4-LDH) by oxalate and oxamate was studied in 0.5 M sodium chloride. At 20 C. oxalate inhibition was a mixed type and at 40 C, the inhibition was uncompetitive.
• 2.2. Oxamate inhibition was shown as two different types. The inhibition was non-competitive at low pyruvate concentrations and competitive at high pyruvate concentrations. Inhibition type did not differ as temperature changed.
• 3.3. The inhibition mechanism is proposed on the basis of quaternary enzyme complex with two kinds of pyruvate as reported previously. The distribution of ternary and quaternary enzyme complexes may determine the inhibition type.

     

The regulation of the cortico-melanotrophic cell activity in aves—I. Evaluation and selection of in vitro systems for testing ACTH-releasing substances in the duck pituitary

• 1.1. In order to evaluate cortico-melanotrophic cell activity in the duck pituitary. we have adapted a mammalian ACTH radioimmunoassay (RIA) for the estimation of duck ACTH released from duck pituitary tissue in vitro.
• 2.2. The in vitro systems tested for the assay of corticotrophin-releasing substances in the duck were: incubation of pituitary pieces, incubation of collagenase and trypsm dispersed cells. and perfusion of collagenase dispersed cells.
• 3.3. The perfusion of duck pituitary dispersed cells proved to be the most suitable for evaluating cortico-melanotropic cell activity. Dose-response curves were obtained using ACTH response to varying dilutions of duck median eminence extract with an index of precision λ of 0.04 (plus or minus 3% of the regression coefficient, within 95% confidence limits).
• 4.4. Less than a hundredth dilution of a duck median eminence extract could be effectively detected in our system.