Computer search of calcium binding sites in a gene data bank: use of learning techniques to build an expert system

Using a learning set of 28 sequences able to bind calcium (each sequence is 12 residues long), we have built two filters by learning on this set. The first filter uses a pattern-matching technique and the second one takes into account the environment of amino-acids. These two filters have been used to find new calcium-binding proteins in a data bank. The results are discussed.     

Deoxyribonucleic acid homologies among 96 strains of ammonia-oxidizing bacteria

DNA of 96 strains of the genera Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosolobus, and Nitrosovibrio was isolated and analysed spectrophotometrically. Percentages of guanine plus cytosine (G+C) content, genome sizes, and DNA-DNA homologies were determined. The results indicated the presence of eight Nitrosomonas species, three or four Nitrosococcus species, five Nitrosospira species, and two species of both Nitrosolobus and Nitrosovibrio. DNA homologies between strains of a separate species ranged from 56–100%. Average homologies between strains of different species were 33% in Nitrosococcus, 36% in Nitrosomonas, 37% in Nitrosolobus, 40% in Nitrosospira, and 42% in Nitrosovibrio. Average homologies between species of different genera were 33% and thus not significantly above the background value of 30% detected between DNA of ammonia-oxidizing bacteria and Escherichia coli. Genome sizes ranged from 1.90–2.74×10⁹ dalton in Nitrosomonas, 2.09–2.37×10⁹ dalton in Nitrosococcus, 1.87–2.15×10⁹ dalton in Nitrosospira, 1.92–2.10×10⁹ dalton in Nitrosolobus, and 1.91–2.15×10⁹ dalton in Nitrosovibrio. Differences in genome sizes were in accordance with DNA homologies.     

Cloning and expression of the Listeria monocytogenes haemolysin in Escherichia coli

Abstract Listeriolysin, an SH-activated haemolysin probably involved in Listeria pathogenicity, has been cloned into the cosmid vector pHC79 and was expressed in Escherichia coli HB101 cells. Chromosomal DNA of Listeria monocytogenes serovar 1/2 was partially digested with Mbo I and ligated to the Bam HI cleaved cosmid. From 2000 recombinant clones examined, 12 (0.6%) produced haemolysin in solid and liquid media. All of them contained chromosome fragments of Listeria of about 40 kb. The cloning of the listeriolysin determinant will lead to a better understanding of the basis of Listeria pathogenicity.     

A new species of the lichen genusDiploschistes from Australia

Diploschistes hensseniae Lumbsch & Elix is described as new to science. It is characterized by its terricolous habitat, perithecioid closed ascomata, relatively small spores, cylindrical asci, and the presence of diploschistesic and orsellinic acids in addition to lecanoric acid. It occurs on soil in arid regions of Australia.     

Stoichiometric binding of diacylglycerol to the phorbol ester receptor

The major phorbol ester receptor is the Ca++-activated, phospholipid-dependent protein kinase C. Diacylglycerol stimulates protein kinase C in a fashion similar to the phorbol esters. Likewise, it inhibits phorbol ester binding competitively. Both results suggest that diacylglycerol is the/an endogenous phorbol ester analogue. Alternatively, the diacylglycerol might simply be acting to modify the phospholipid environment of the protein. If diacylglycerol were indeed functioning as an analogue, it should interact with the receptor stoichiometrically. This interaction can be quantitated by measuring the perturbation in apparent diacylglycerol binding affinity as a function of the ratio of diacylglycerol to receptor. We report here that 1,2-dioleoylglycerol interacts with the receptor with the predicted stoichiometry.     

The trajectory of a stiff rod in a curved potential energy trough

The equilibrium trajectory of the axis of a rod subject to an externally imposed curved potential energy trough tends to conform to the shape of the curved trough, but also tends to be straight because of elastic resistance to bending. The actual path of the axis is a balance between the two extremes. We consider a potential energy trough centered along a circular arc of radiusR. For a rod of small length compared toR, we show that the axis at equilibrium forms an arc of a circle of radius greater thanR. The value of the radius of the axial path depends on the relative values of the Hooke’s Law bending constant for the rod and the depth and width of the trough. Motivation for the calculation is provided by nucleosomal DNA, which conforms to the surface of a roughtly cylindrical histone core at physiological ionic strength, but is observed to unwind into a partially extended conformation at very low ionic strength. We suggest that the rigidity to bending of short DNA segments becomes sufficiently great at low ionic strength to overcome attractive interactions with the histone surface. Alternately, of course, if during the cell cycle mutually attractive forces between DNA and histone core are weakened at constant ionic strength, the same type of unfolding would be expected to occur as the strength of the DNA-histone contacts drops below the level required to overcome elastic resistance to bending of the DNA rod.     

Estimation of the size of freshwater ciliate populations by a sub-sampling technique

A technique is described for the estimation of the size of ciliate populations based on replicated counts. Sample drops were taken by automatic pipettes of different volume from activated sludge and from a small oligotrophic stream. Specific aims were: 1) the estimation of the number of species; 2) the estimation of the number of individual in each species; 3) the selection of a suitable sub-sample size and number of replicates. For each volume the cumulative increase in species taken in successive sub-samples was determined. For each species the minimum permissible sub-sample volume and the number of replicates required for an allowable error of 10% and 25% were determined. Lastly, the relationship between the mean number of individuals counted for each species and the relative coefficient of variation was visualized.     

Reactions of sugar nitro-alkenes with acetoacetic esters

3,4,5,6,7-Penta-O-acetyl-1,2-dideoxy-1-nitro-d-gluco-hept-1-enitol reacts with methyl acetoacetate in an unusual Michael reaction, giving the normal adduct (6), and a bicyclic derivative (9) that arises from quasi-dimerization of the former when a high concentration of the base is used. Acetylation of compound 9 gives the hydroxylamine O-acetate (10).From the reactions of 3,4,5,6,7-penta-O-acetyl-1,2-dideoxy-1-nitro-d-galacto-hept-1-enitol with ethyl and tert-butyl acetoacetate, the normal adducts (7 and 8) were isolated. The structures of compounds 6 to 10 were established on the basis of their spectral properties (u.v., i.r., mass, and ¹H- and ¹³C-n.m.r.)     

Amplification of lymph node cell tube leukocyte adherence inhibition (LAI) reactivity by leukocyte adherence inhibition factor (LAIF)

This investigation examines the immunologic basis for specific antigen-induced tube leukocyte adherence inhibition (LAI) reactivity of draining lymph node cells (LNC) from dogs with canine transmissible venereal sarcoma (CTVS). CTVS regressor LNC, macrophage-depleted LNC, and enriched T lymphocyte fractions, but not enriched B lymphocyte fractions, were specifically reactive to CTVS antigen extract in direct tube LAI. In addition, regressor LNC amplified tube LAI responses by generating supernatants with leukocyte adherence inhibition factor (LAIF) activity for normal dog indicator LNC and enriched peripheral blood mononuclear cells (PBMC) in an indirect tube LAI assay. However, macrophage-depleted LNC and enriched T lymphocyte fractions failed to generate supernatants with LAIF activity, suggesting that macrophage accessory cells play a central role in the amplification of tube LAI. Interestingly, CTVS regressor peripheral blood leukocytes (PBL) and PBMC, which were specifically reactive in direct tube LAI, also failed to generate supernatants with LAIF activity. These findings demonstrate a distinction between LAIF-mediated amplification and direct tube LAI reactivity, and suggest that leukocyte populations with differing cellular proportions and from different immunologic compartments may participate in tube LAI via different mechanisms.