Pharmacogenetics - five decades of therapeutic lessons from genetic diversity

Physicians have long been aware of the subtle differences in the responses of patients to medication. The recognition that a part of this variation is inherited, and therefore predictable, created the field of pharmacogenetics fifty years ago. Knowing the gene variants that cause differences among patients has the potential to allow 'personalized' drug therapy and to avoid therapeutic failure and serious side effects.     

Effects of natural and chemically synthesized furanones on quorum sensing in <Emphasis Type="Italic">Chromobacterium violaceum</Emphasis>

Background  

Cell to cell signaling systems in Gram-negative bacteria rely on small diffusible molecules such as the N-acylhomoserine lactones (AHL). These compounds are involved in the production of antibiotics, exoenzymes, virulence factors and biofilm formation. They belong to the class of furanone derivatives which are frequently found in nature as pheromones, flavor compounds or secondary metabolites. To obtain more information on the relation between molecular structure and quorum sensing, we tested a variety of natural and chemically synthesized furanones for their ability to interfere with the quorum sensing mechanism using a quantitative bioassay with Chromobacterium violaceum CV026 for antagonistic and agonistic action. We were looking at the following questions:     

The circadian clock as a molecular calendar

There are two dominant environmental oscillators shaping the living conditions of our world: the day-night cycle and the succession of the seasons. Organisms have adapted to these by evolving internal clocks to anticipate these variations. An orchestra of finely tuned peripheral clocks slaved to the master pacemaker of the suprachiasmatic nuclei (SCN) synchronizes the body to the daily 24h cycle. However, this circadian clockwork closely interacts with the seasonal time-teller.

Recent experiments indeed show that photoperiod—the dominant Zeitgeber of the circannual clock—might be deciphered by the organism using the tools of the circadian clock itself. From the SCN, the photoperiodic signal is transferred to the pineal where it is decoded as a varying secretion of melatonin.

Different models have been proposed to explain the mechanism by which the circadian clock measures day-length. Recent work using mutant mice suggests a set of two molecular oscillators tracking dusk and dawn, respectively, thereby translating day-length to the body. However, not every aspect of photoperiodism is covered by this theory and major adjustments will need to be made to establish a widely acceptable uniform model of circadian/circannual timekeeping.     

Control of GT repeat stability in Schizosaccharomyces pombe by mismatch repair factors

The mismatch repair (MMR) system ensures genome integrity by removing mispaired and unpaired bases that originate during replication. A major source of mutational changes is strand slippage in repetitive DNA sequences without concomitant repair. We established a genetic assay that allows measuring the stability of GT repeats in the ade6 gene of Schizosaccharomyces pombe. In repair-proficient strains most of the repeat variations were insertions, with addition of two nucleotides being the most frequent event. GT repeats were highly destabilized in strains defective in msh2 or pms1. In these backgrounds, mainly 2-bp insertions and 2-bp deletions occurred. Surprisingly, essentially the same high mutation rate was found with mutants defective in msh6. In contrast, a defect in swi4 (a homologue of Msh3) caused only slight effects, and instability was not further increased in msh6 swi4 double mutants. Also inactivation of exo1, which encodes an exonuclease that has an MMR-dependent function in repair of base-base mismatches, caused only slightly increased repeat instability. We conclude that Msh2, Msh6, and Pms1 have an important role in preventing tract length variations in dinucleotide repeats. Exo1 and Swi4 have a minor function, which is at least partially independent of MMR.     

Structure-based chimeric enzymes as an alternative to directed enzyme evolution: phytase as a test case

Thermostability is a key feature for commercially attractive variants of the fungal enzyme phytase. In an initial set of experiments, we restored ionic interactions and hydrogen bonds on the surface of Aspergillus terreus phytase, which are present in the homologous but more thermostable enzyme from A. niger. Since these mutations turned out to be neutral, we replaced-in the same region and based on the crystal structure of A. niger phytase-entire secondary structure elements. The replacement of one alpha-helix on the surface of A. terreus phytase by the corresponding stretch of A. niger phytase resulted in an enzyme with improved thermostability and unaltered enzymatic activity. Surprisingly, the thermostability of this hybrid protein was very similar to that of A. niger phytase, although the fusion protein contained only a 31 amino acid stretch of the more stable parent enzyme. This report provides evidence that structure-based chimeric enzymes can be used to exploit the evolutionary information within a sequence alignment. We propose this method as an alternative to directed enzyme evolution if due to expression constraints the screening of large mutant populations is not feasible.     

Resistance and resilience of ecosystem metabolism in a flood-prone river system

1. Gross primary production (GPP) and ecosystem respiration (ER) were analysed for 18 months in two reaches of the River Thur, a prealpine river in Switzerland. The upper reach at 655 m above sea level (a.s.l.) is bedrock constrained, has a high slope (0.60%) and a catchment area of 126 km2. The lower reach at 370 m a.s.l. has a more extensive hyporheic zone, a lower slope (0.17%) and a catchment of 1696 km2.
2. In both reaches, temporal patterns of stream metabolism reflected the occurrence of bed-moving spates. Average reductions of GPP and ER by spates were 53 and 24% in the upper reach, and 37 and 14% in the lower reach, respectively. The greater resistance of ER than GPP in both reaches shifted the ecosystem metabolism towards heterotrophy (decrease of the ratio of GPP to ER (P/R)) following spates.
3. Recovery of GPP was significantly faster in the lower reach and exhibited distinct seasonal variation (positive correlation with incident light). The differences in stability (both resistance and resilience) between reaches reflected differences in geomorphic settings and disturbance regime.
4. Stepwise regression analysis was used to explore the potential influence of season, disturbance and prevailing environmental conditions on stream metabolism in each reach. Time since spate plus temperature explained 73 and 86% of variation in ER and GPP, respectively, in the upper reach and 55% of variation in ER in the lower reach. Season plus prevailing environmental conditions explained 67% of variation in GPP in the lower reach.
5. To test how the perception of stability may change with increasing scale of observation, the disturbance regimes of 12 sites were compared with the disturbance regime of the entire Thur catchment. The analysis suggests that stream metabolism at the catchment scale is far more resistant to high flow events than at the reach scale.     

Analysis of the Drosophila maternal effect mutant MAT(3)1 by pole cell transplantation experiments

Summary Pole cell transplantations were used to construct germ line mosaics of the Drosophila melanogaster maternal effect mutant mat(3)1. The mutant is of particular interest since the development of embryos derived from homozygous mat(3)1 females is arrested at the pole cell stage. Such embryos form exclusively pole cells and no blastoderm cells. By means of germ line mosaics we could demonstrate the primary target tissue of mutant gene expression. For normal development the mat(3)1 ⁺gene has to be expressed in the germ line. Pole cells formed in defective embryos derived from homozygous mutant mothers were transplanted into normal recipient embryos to test their developmental potential. Heterozygous mat(3)1 pole cells were found to form fertile gametes in both sexes whereas homozygous mat(3)1 pole cells form fertile gametes only in males. The lack of progeny derived from homozygous mat(3)1 donor pole cells in recipient females further demonstrates the germ line autonomy of the mat(3)1 mutation. Pole cells from defective embryos that are transplanted into normal hosts colonize the gonads with the same frequency as donor pole cells derived from normal embryos. This indicates that mat(3)1 derived pole cells are normal with respect to their function as germ cells and that the mat(3)1 mutant might therefore offer a convenient source for the mass isolation of functional pole cells.     

Benign Obstetric History in Women with Sickle-cell Anaemia Associated with α-Thalassaemia

Two Ghanaian women with sickle-cell anaemia and α-thalassaemia were found to have an unusually benign obstetric history. In addition to two factors present which are known to moderate the clinical course of sickle-cell anaemia, good socioeconomic status and a relatively high Hb F level, it is suggested that α-thalassaemia may act among other things by lowering the haemoglobin concentration in the red cells and thereby lowering their tendency to sickle in vivo.