An acid precipitation technique: A strip assay for the large-scale DNA polymerase activity screening

A new format of a very rapid, low-cost and high-productive analysis based on the acid precipitation of radiolabeled DNA was developed. By contrast to the conventional processing of a large number of GF/C discs, the method employs one GF/C strip containing samples on individual teeth. The strip assay was validated by comparison with the glass fiber disk technique; the efficiency was demonstrated by screening E. coli superproducers and fractions obtained at the steps of Bst DNA polymerase, Large Fragment purification by the protocol we developed. The principle proposed allows simultaneous assaying many samples for the activity of different polymerases.     

Hybrid Reverse Monte Carlo and electron phase contrast image simulations of amorphous silicon with and without paracrystals

Atomic networks of as-implanted and relaxed amorphous silicon solids were simulated using a Hybrid Reverse Monte Carlo algorithm constrained by high-resolution electron diffraction data. No significant structural distinction was observed between the two forms of amorphous silicon. A nanometer-sized crystallite was inserted into the as-implanted structure, to model medium-range order due to paracrystals, and the atomic network was energetically relaxed whilst maintaining consistency with experiment. Experimental pair–pair correlations were then simulated using a stochastic generalised Debye sum of fourth order. The idealised pair–pair correlation calculations were not able to readily distinguish between models with and without paracrystals. On the other hand, wave mechanical simulations surprisingly showed that paracrystals could be experimentally imaged using phase contrast transmission electron microscopy and/or nanoscale electron diffraction on a contemporary aberration-corrected microscope.     

Structural basis of hierarchical multiple substates of a protein. I: Introduction

A computer experiment of protein dynamics is carried out, which consists of two steps: (1) A Monte Carlo simulation of thermal fluctuations in the native state of a globular protein, bovine pancreatic trypsin inhibitor; and (2) a simulation of the quick freezing of fluctuating conformations into energy minima by minimization of the energy of a number of conformations sampled in the Monte Carlo simulation. From the analysis of results of the computer experiment is obtained the following picture of protein dynamics: multiple energy minima exist in the native state, and they are distributed in clusters in the conformational space. The dynamics has a hierarchical structure which has at least two levels. In the first level, dynamics is restricted within one of the clusters of minima. In the second, transitions occur among the clusters. Local parts of a protein molecule, side chains and local main chain segments, can take multiple locally stable conformations in the native state. Many minima result from combinations of these multiple local conformations. The hierarchical structure in the dynamics comes from interactions among the local parts. Protein molecules have two types of flexibility, each associated with elastic and plastic deformations, respectively.     

Counting viableAzotobacter chroococcum in vertisols

Methods for preparing soil suspensions for countingAzotobacter chroococcum in vertisols by soil dilution and plating were investigated. Mechanical methods to promote disaggregation of soil and Azotobacter microcolonies by shaking soil suspensions with glass beads (10% w/v) or coarse sand (1–2 mm fraction) increased soil dispersion and Azotobacter colony counts. Chemical methods for disaggregation were unsatis-factory. The non-ionic detergent Agral (0.004, 0.02, 0.1, 0.5 and 2.5% w/v) had no significant effect on soil dispersion and Azotobacter count. Both sodium pyrophosphate (0.03, 0.1, 0.3 and 0.9% w/v) and sodium metaphosphate as Calgon (0.022, 0.066, 0.2, 0.6 and 1.8% w/v) increased soil dispersion but were toxic to Azotobacter. Increasing time of shaking soil: distilled water suspensions increased deflocculation of the clay and Azotobacter counts to a maximum after 6–23 hours shaking. Comparable results were obtained within 30–60 minutes of shaking with coarse sand, but shaking with coarse sand beyond 2 hours reduced counts through mechanical damage to cells. Counts from suspensions in physiological saline (0.75% NaCl) and in distilled water were similar. Counts from suspensions in Jensen's mineral base shaken for <3 hrs were lower than from distilled water due to flocculation fo the soil by^Ca2+ ions, but were higher on extended shaking up to 23 hours due to better cell protection. Shaking soil suspensions in distilled water with 10% w/v coarse sand for 30 minutes is recommended when counting Azotobacter in vertisols.     

Spontaneous generation of selectable variation in the brain

Selection models of behavior presuppose selectable variation, diversity in the brain that is stable over time. Diversity can arise spontaneously through the mutual interactions of cell assemblies, which are postulated to align or disalign their neighbors into processing modes conforming to or opposite from their own. These processes are similar to magnetization and crystallization. If aligning and disaligning influences are distributed at random, a state resembling a spin glass can arise, where processing modes are highly varied in space but stable in time. If disalignment occurs regularly at the points of a two-dimensional lattice, and elsewhere the interactions are aligning, a pattern emerges with properties remarkably similar to visual orientation columns. These patterns are maintained dynamically, and emerge statistically without detailed genetic specification.Special issue dedicated to Dr. Eugene Roberts.     

Seasonal changes in ionoregulatory variables of the glass eel Anguilla anguilla following estuarine entry: comparison with resident elvers

In the present study, glass eels Anguilla anguilla in the Minho River estuary (41·5° N, 8·5° W) decreased in size (standard length, L _S and mass, M ) from the beginning (autumn) to the end of the sampling season (summer). On the other hand elvers increased in L _S and M from spring to summer and were significantly larger than glass eels in paired comparisons. Branchial Na⁺/K⁺-ATPase and vacuolar (V-type) proton ATPase ( in vitro activities), two important ion transporting pumps, did not show significant seasonal changes in either glass eels or elvers although in glass eels Na⁺/K⁺-ATPase (activity) expression was significantly higher than in elvers. In a single month comparison Na⁺/K⁺-ATPase branchial mRNA expression was also higher in glass eels as was the protein level expression of both Na⁺/K⁺-ATPase and NKCC (Na⁺:K⁺:2Cl⁻ co-transporter). Immunofluorescence microscopy indicated apical CFTR Cl⁻ channel labelling in Na⁺/K⁺-ATPase positive chloride cell in glass eels which was absent in elvers. Whole body sodium concentration and percentage water did not show significant seasonal differences in either glass eels or elvers although there were significant differences between these two groups during some months.     

Alteration of a Submarine Basaltic Glass under Environmental Conditions Conducive for Microorganisms: Growth Patterns of the Microbial Community and Mechanism of Palagonite Formation

In basaltic glass from the southern Mid-Atlantic-Ridge conducive environmental conditions for biogenic weathering resulted in excellent preserved microbial morphologies on glass surfaces. The distinct glass interface and open spaces between palagonite sheet and glass indicate a dissolution-reprecipitation mechanism of glass alteration potentially supported by microorganisms. On internal fracture surfaces, branching channels with widths at 20–30 μm containing longish structures with targeted dissolution of the glass by growing tips were observed. Alteration resulted in enrichment of Fe, Ti, P, and K in palagonite in amorphous mineral forms.     

Thermoluminescence dosimetric attributes of Yb3+-doped BaO–ZnO–LiF–B2O3 glass material after Er3+ co-doping

Motivated by our previous study on Sm³⁺ ions as thermoluminescence (TL) sensitizers to the BaO–ZnO–LiF–B₂O₃–Yb₂O₃ glass system, in the current study we examined the effect of Er³⁺ ion co-doping on the TL characteristics of this glass system. The 4f–4f electronic transitions of the Er³⁺ and Yb³⁺ ions were confirmed via the optical absorption spectrum. Notably, the use of Yb³⁺–Er³⁺ ions failed to improve the TL intensity, sensitivity, and trap density. However, they enabled the glass system to function as an activator–quencher system. The linearity range and effective atomic number remained unaffected after co-doping. In addition, the problem of anomalous fading caused a remnant signal of just 58% after a week of storage of the Yb³⁺ monodoped glass. This was resolved by the optimum co-doping of Er³⁺ ions to achieve an 89% signal. The co-doping of Er³⁺ ions to the BaO–ZnO–LiF–B₂O₃–Yb₂O₃ glass system regulated its thermal stability and therefore supplemented its potential for radiation monitoring in food processing and retrospective dosimetry.