Kinetic aspects of the DNA helix—Cruciform transition

A kinetic model for the helix-cruciform transition is presented, mean lifetimes for the cruciform states are calculated and shown to be inconsistent with the notion of metastability.     

Thiamine repression and pyruvate decarboxylase autoregulation independently control the expression of the Saccharomyces cerevisiae PDC5 gene.

The Saccharomyces cerevisiae gene PDC5 encodes the minor isoform of pyruvate decarboxylase (Pdc). In this work we show that expression of PDC5 but not that of PDC1, which encodes the major isoform, is repressed by thiamine. Hence, under thiamine limitation both PDC1 and PDC5 are expressed. PDC5 also becomes strongly expressed in a pdc1delta mutant. Two-dimensional gel electrophoresis of whole protein extracts shows that thiamine limitation stimulates the production of THI gene products and of Pdc5p. Deletion of PDC1 only stimulates production of Pdc5p. We conclude that the stimulation of PDC5 expression in a pdc1delta mutant is not due to a response to thiamine limitation.     

A new approach for applying residual dipolar couplings as restraints in structure elucidation

Residual dipolar couplings are useful global structural restraints. The dipolar couplings define the orientation of a vector with respect to the alignment tensor. Although the size of the alignment tensor can be derived from the distribution of the experimental dipolar couplings, its orientation with respect to the coordinate system of the molecule is unknown at the beginning of structure determination. This causes convergence problems in the simulated annealing process. We therefore propose a protocol that translates dipolar couplings into intervector projection angles, which are independent of the orientation of the alignment tensor with respect to the molecule. These restraints can be used during the whole simulated annealing protocol.     

The rationale behind a vaccine based on multiple HIV antigens

The viral diversity of HIV-1 is likely to require a vaccine strategy that induces broad cellular and humoral anti-HIV-1 immunity. Our strategy is based on multiple HIV-1 DNA immunogens together with adjuvant recombinant granulocyte-macrophage stimulating factor. This article describes pre-clinical and clinical work preceding the initiation of clinical HIV-1 phase I/II trials.     

Statistical exploration of variation in quantitative two-dimensional gel electrophoresis data

Two-dimensional gel electrophoresis is a major technique in global analysis at the protein level. This paper presents an examination of spot volume data from three gel sets with radioactively labeled yeast Saccharomyces cerevisiae proteins. A strong variance versus mean dependence in data was found to be stabilized by applying a shifted logarithmic transformation. However, transformed data showed a remaining substantial variance heterogeneity for different proteins. Furthermore, examination of studentized residuals revealed that transformed data were approximately normally distributed and that there were spatial correlations among the measurement errors in the gel.     

Comparison of the proteomes of three yeast wild type strains: CEN.PK2, FY1679 and W303

Yeast deletion strains created during gene function analysis projects very often show drastic phenotypic differences depending on the genetic background used. These results indicate the existence of important molecular differences between the CEN.PK2, FY1679 and W303 wild type strains. To characterise these differences we have compared the protein expression levels between CEN.PK2, FY1679 and W303 strains using twodimensional gel electrophoresis and identified selected proteins by mass spectrometric analysis. We have found that FY1679 and W303 strains are more similar to each other than to the CEN.PK2 strain. This study identifies 62 proteins that are differentially expressed between the strains and provides a valuable source of data for the interpretation of yeast mutant phenotypes observed in CEN.PK2, FY1679 and W303 strains.     

An improved gas distribution system for anaerobic screening of multiple microbial cultures

A cultivation set-up for multiple cultures has been designed that can be used for anaerobic screening for quantitative changes in growth rate or other analyses, e.g. protein composition of different strains. The developed gas distribution system provides a reproducible level of anaerobicity in 30 cultivation flasks and resembles the open system of a high-performance bioreactor in that it ensures cultivation at atmospheric pressure and avoids supersaturation of carbon dioxide. The system is cheap and user-friendly and allows rapid screenings of many strains simultaneously.