Enlarged Similarity of Nucleic Acid Sequences

The concept of nucleic acid sequence base alternations is presented.The number of base alterations for the sequences of differentlength is established. The definition of "enlarged similarity"of nucleic acids sequences on the basis of sequence base alterationsis introduced. Mutual information between sequences is usedas a quantitative measure of enlarged similarity for two comparedsequences. The method of mutual information calculation is developedconsidering the correlation of bases in compared sequences.The definitions of correlated similarity and evolution similaritybetween compared sequences are given. Results of the use ofenlarged similarity approach for DNA sequences analysis arediscussed.     

Models for relating pH measurements in water and calcium chloride for a wide range of pH,soil types and depths

Soil pH is commonly measured in water (pHw) or 0.01 M CaCl₂ (pH_Ca). The need to convert between these methods has led to the publication of linear, quadratic and cubic polynomial relationships for limited suites of soils. Concerns over the applicability of such relationships when mapping a wide range of soils and pH led to the establishment of a database of pH_W and pH_Ca values on each of 7894 samples from soil survey and field experimental sites in Queensland. The relationship between pH_W and pH_Ca across all soils was investigated and preliminary results examining the effect of soil depth and soil type on the relationship are presented.For all soils and depths, a linear regression accounted for 93.2% of the variation but did not predict pH_Ca well at very high or low pH_W values. The inclusion of second and third powers of pH_W accounted for significantly more of the variation (R²=0.94) in pH_Ca and the resultant curve matched the data better at high and low pH.Analysis of surface, sub-surface and subsoil groupings did not reveal any appreciable differences in the relationship between pH_W and pH_Ca attributable to depth. In contrast, differences in the relationship were evident between soil types. Generally, the mildly leached soils had linear relationships, while the weathered soils were distinctly curvilinear at low pH.     

Visualization of Antipsychotic Drug Binding to Living Mesolimbic Neurons Reveals D2 Receptor, Acidotropic, and Lipophilic Components

Abstract: To examine the binding of antipsychotic drugs to living neurons, we applied fluoroprobe derivatives of the D2 antagonist spiperone to mesolimbic system neurons in postnatal culture. We found that rhodamine- N -( p -aminophenethyl)spiperone (rhodamine-NAPS) stereospecifically labeled the plasma membranes of 38 ± 6% of ventral tegmental area neurons, 22 ± 7% of which were dopaminergic, and 50 ± 6% of medium-sized putatively GABAergic nucleus accumbens neurons, with a time constant of ∼8 min. In contrast, the BODIPY derivative of NAPS rapidly labeled intracellular sites in all neurons in a punctate pattern, consistent with acidotropic uptake. Native antipsychotics also show acidotropic uptake, which we visualized by their displacement of the fluorescent weak base vital dye acridine orange from acidic intracellular compartments. We found that acidotropic uptake correlated best with the partition coefficients of the drugs. With a time constant of 23 min, rhodamine-NAPS labeled all neurons in a pattern suggestive of lipophilic solvation. Thus, initially rhodamine-NAPS makes possible visualization of D2 receptors on living neurons; however, acidotropic uptake and lipophilic solvation obscure receptor labeling and may account for time-dependent factors in the action of antipsychotic drugs, as well as affect their use as radioreceptor ligands.     

Dynamics and distribution of microphytobenthic chlorophyll-a in the Western Scheldt estuary (SW Netherlands)

The temporal dynamics and spatial distribution of microphytobenthic chlorophyll-a in the layer 0–1 cm were determined in the Western Scheldt estuary over the period 1991–1992. Connections between the annually averaged benthic chlorophyll-a and station elevation and sediment composition (as a measure of the hydrodynamic energy caused by currents and waves) were also examined.Microphytobenthic chlorophyll-a showed one main peak in early summer and a smaller peak in autumn. The mean chlorophyll-a concentration of 113 mg Chl-a m^–2 in the upper centimeter is of the same order of magnitude as in other estuarine areas. The average annual primary production of the microphytobenthos has been estimated at 136 g C m^–2 y^–1 The primary production of sediment inhabiting microalgae is at least 17% of the total primary production in the estuary.Considerable differences in annually averaged chlorophyll-a emerges between the stations. These differences are related mainly to the interaction between station elevation and clay content of the sediment.     

Theoretical Study of the TiO2 and MgO Surface Acidity and the Adsorption of Acids and Bases

We present ab-initio periodic Hartree–Fock calculations (crystal program) of small molecules on TiO₂ and MgO. The adsorption of the molecules may be molecular or dissociative. This depends on their acid and basic properties in the gas phase. For the molecular adsorption, the molecules are adsorbed as bases on Ti(+IV) sites, the adsorption energies correlate with the proton affinities. The dissociations on the surface correlate with the gas phase cleavages: thus, the dissociation of MeOH leads to a preferential basic cleavage (the fragment HO– is adsorbed on a Ti⁺⁴ ion and the fragment Me⁺ is adsorbed on a O²– ion of the oxide). The opposite result is obtained with MeSH. Another important factor is the adsorbate–adsorbate interaction: favorable cases are a sequence of H-bonds for the hydroxyl groups resulting from the water dissociation and the mode of adsorption for the ammonium ions. Lateral interactions also force the adsorbed CO₂ molecules to bend over the surface so that their mutual orientation resembles the geometry of the CO₂ dimer. With respect to water adsorption, MgO appears to be a basic oxide. As experimentally observed, NH₃ adsorbs preferentially on TiO₂ and CO₂ on MgO. However, this difference of reactivity should not be expressed in terms of acid vs. basic behaviour but in terms of hard and soft acidity. The MgO surface is a 'soft' acidic surface that reacts preferentially with the soft base, CO₂.     

Metal-modified nucleobase pairs involving 7,9-dimethylguanine: trans-a2PtII analogues (a = NH3 or CH3NH2) of Watson-Crick GC and homo GG pairs

 The analogy between H-bonded nucleobase pairs and their metalated analogues is extended to the hemiprotonated pair of 7,9-dimethylguanine (7,9-DimeG) and the Watson-Crick and reversed Watson-Crick pair between 7,9-dimethylguaninium (7,9-DimeGH⁺) and 1-methylcytosine (1-MeC). The crystal structure analyses of two model compounds, trans–[Pt(CH₃NH₂)₂(7,9-DimeG-N1)₂](NO₃)₂ (1) and trans–[Pt(NH₃)₂(1-MeC-N3)(7, 9-DimeG-N1)](PF₆)₂· 2.5 H₂O (3a) are reported. Pt binding is through N1 of 7,9-DimeG and N3 of 1-MeC. In solution, 3a exists in a mixture with Watson-Crick and reversed Watson-Crick arrangements of the two bases, depending on solvent, concentration and anions. Received: 16 October 1996 / Accepted: 27 January 1997     

Larval habitat preference of the endemic Hawaiian midge,Telmatogeton torrenticola Terry (Telmatogetoninae)

Telmatogeton torrenticola Terry is a large endemic chironomid (lastinstar >20 mm) commonly found in high gradient Hawaiian streams on smoothrock surfaces with torrential, shallow flow and in the splash zones ofwaterfalls. We have quantified benthic water flow in larval habitat in a 50m segment of Kinihapai Stream, Maui using a thermistor-based microcurrentmeter. Under base flow conditions at sites suitable for larval attachment,depth was measured and bottom water velocity measurements were made 2 mmabove populations. Larval densities ranged from 386.9–1178m^–2, habitat bottom water velocities from 13.4–64.2 cms^–1, and water depths from 1.5–50 cm. Bottom velocitiesof sites with zero larvae ranged from 20.8–21.8 cm s^–1with depths from 50 to >160 cm. Larval densities were greatest inareas with high bottom water velocities and shallow depths. Stepwisemultiple regression analyses showed that density could be confidentlypredicted best by Froude number (r=0.81; p=0.008). In the absence of Froudenumber as a regression term, the best variable to predict larval density wasbottom velocity ratio: relative depth ratio (r=0.75; p=0.019). In addition,the torrential habitat of the larvae was always characterized by aperiphyton community that appeared to be the primary food resource for thelarvae. These data suggest that torrential flows over appropriate substratesare important factors regulating habitat availability for T. torrenticolaand that reduced discharge (e.g. affected by water diversions) couldsignificantly reduce the amount of available habitat for this organism andother flow sensitive stream fauna.     

Superoxide dismutase mimetic activity of a cyclic tetrameric Schiff base N-coordinated Cu(II) complex

A pulse radiolytic study using the cyclic tetrameric Schiff base N-coordinated copper complex Cu(TAAB)²⁺ has been performed. The reaction of the Cu(TAAB)²⁺ complex with superoxide revealed pseudo first-order characteristics with the rate constant of k ₂ = (2.9 ± 0.5) × 10⁸ mol^–1 s^–1 dm³. The complex survive presence of competing serum albumin in physiological concentrations. The complex stability constant K = 1.15 × 10¹⁸ (log K = 18.06) is two orders of magnitude higher than that of Cu(II)-serum albumin (log K = 16.2). Transient changes of the stability during the oxidation/reduction process and in the presence of 600 /mol l^–1 albumin did not affect significantly either the electronic absorption of the complex or its catalytic activity.     

Purification of restriction endonuclease XcyI from Xanthomonas cyanopsidis

A new Type II restriction endonuclease XcyI, purified from Xanthomonas cyanopsidis 13D5, is an isoschizomer of SmaI and XmaI that cleaves at the nucleotide sequence 5'-C decreases CCGGG-3' of double-stranded DNA. The single restriction activity present in this strain permits rapid purification of 8000 units of cleavage activity from 10 g of freshly harvested cells. The resulting XcyI preparation is free of contaminating nuclease activities that interfere with in vitro manipulation of DNA.