Diversification and selection mechanisms for the production of protein repertoires: lessons from the immune system

The physiological mechanism for producing antigen-specific antibodies is based on a two-phase neo-Darwinian process: the first phase consists of diversity generation (formation of the repertoire), and the second phase is antigen-mediated selection. In this article, we consider how the natural immunoglobulin gene-diversification processes can be exploited both in vivo and in vitro in order to allow the generation of novel antibody (and heterologous protein) repertoires.     

Structural determination of spin label immobilization and orientation: a Monte Carlo minimization approach

Electron paramagnetic resonance (EPR) is often used in the study of the orientation and dynamics of proteins. However, there are two major obstacles in the interpretation of EPR signals: (a) most spin labels are not fully immobilized by the protein, hence it is difficult to distinguish the mobility of the label with respect to the protein from the reorientation of the protein itself; (b) even in cases where the label is fully immobilized its orientation with respect to the protein is not known, which prevents interpretation of probe reorientation in terms of protein reorientation. We have developed a computational strategy for determining whether or not a spin label is immobilized and, if immobilized, predicting its conformation within the protein. The method uses a Monte Carlo minimization algorithm to search the conformational space of labels within known atomic level structures of proteins. To validate the method a series of spin labels of varying size and geometry were docked to sites on the myosin head catalytic and regulatory domains. The predicted immobilization and conformation compared well with the experimentally determined mobility and orientation of the label. Thus, probes can now be targeted to report on various modes of molecular dynamics: immobilized probes to report on protein backbone and domain dynamics or floppy probes to report on the extent of steric restriction experienced by the side chain.     

Mit der Deutung chemischer Analysen von Konserven und Marmeladen

Ohne Zusammenfassung     

Literatur

Analytical and Bioanalytical Chemistry -     

SOME EFFECTS OF LIGHT ON LEAF GROWTH IN PISUM SATIVUM AND TROPAEOLUM MAJUS

Abstract— The effect of wave-length of light on leaf expansion in Tropaeolum majus 'Double Orange Gleam' and Pisurn sativum 'Meteor' has been studied. In both species leaf growth is strongly promoted by light.
Increasing the daily duration of exposure to light increased leaf expansion in Tropueolum in both blue and red wave-bands over a range of light intensities. In Pisum a similar effect of ail increase in duration of irradiation was found over the whole range of intensities used for blue light but only at the highest intensity for red light: at the two lower intensities in red an increase in duration of the light treatment beyond 1 hr did not increase leaf expansion.
In both species a period of 4 hr of blue followed by 4 hr of red promoted leaf growth more than 4 hr of red followed by 4 hr of blue. The effect of a 4 hr period of red light was largely prevented when it was followed by far-red; the effect of 4 hr of blue light, on the other hand, was not affected by subsequent exposure to far-red.
It is concluded that leaf growth in Pisum and Tropaeolum is dependent not only on the 'low-energy' red/far-red reversible reaction but also on one or more 'high-enerFy' photo-reactions.     

Tissue distribution and metabolism of the putative cancer chemopreventive agent 3′,4′,5′‐trimethoxyflavonol (TMFol) in mice

3′,4′,5′‐Trimethoxyflavonol (TMFol) is a synthetic flavonol with preclinical cancer chemopreventive properties. The hypothesis was tested that, in mice, p.o. administration of TMFol results in measureable levels of the parent in target tissues. A single oral dose (240 mg/kg) was administered to mice (n = 4 per time point) with time points ranging from 5 to 1440 min. TMFol and its metabolites were identified and quantitated in all tissues by high‐performance liquid chromatography (HPLC). Plasma levels of TMFol were at the limit of quantification or below, although metabolites were identified. Peak levels of TMFol in the gastrointestinal tract and the prostate averaged 1671 ± 265 µg/g (5.3 µmol/g) and 6.0 ± 1.6 µg/g (18.4 nmol/g), and occurred 20 and 360 min post‐dose, respectively. The area under the tissue concentration–time curve (AUC) for TMFol was greater than those of the metabolites, indicating that TMFol is relatively metabolically stable. Micromolar TMFol levels are easily achieved in the prostate and gastrointestinal tract, suggesting that TMFol might exert chemopreventive efficacy at these tissue sites. Further investigations are warranted to elucidate the potential chemopreventive potency of TMFol. Copyright © 2012 John Wiley & Sons, Ltd.     

On the theory of slowing down gracefully

We discuss the transport of a tracer particle through the Bose?CEinstein condensate of a Bose gas. The particle interacts with the atoms in the Bose gas through two-body interactions. In the limiting regime where the particle is very heavy and the Bose gas is very dense, but very weakly interacting (??mean-field limit??), the dynamics of this system corresponds to classical Hamiltonian dynamics. We show that, in this limit, the particle is decelerated by emission of gapless modes into the condensate (Cerenkov radiation). For an ideal gas, the particle eventually comes to rest. In an interacting Bose gas, the particle is decelerated until its speed equals the propagation speed of the Goldstone modes of the condensate. This is a model of ??Hamiltonian friction??. It is also of interest in connection with the phenomenon of ??decoherence?? in quantum mechanics. This note is based on work we have carried out in collaboration with D Egli, I M Sigal and A Soffer.