Clincial pharmacogenetics and potential application in personalized medicine

The current `fixed-dosage strategy' approach to medicine, means there is much inter-individual variation in drug response. Pharmacogenetics is the study of how inter-individual variations in the DNA sequence of specific genes affect drug responses. This article will highlight current  pharmacogenetic knowledge on important drug metabolizing enzymes, drug transporters and drug targets to understand interindividual variability in drug clearance and responses in clinical practice and potential use in  personalized medicine. Polymorphisms in the cytochrome P450 (CYP) family may have had the most impact on the fate of pharmaceutical drugs. CYP2D6, CYP2C19 and CYP2C9 gene polymorphisms and gene duplications account for the most frequent variations in phase I metabolism of drugs since nearly 80% of drugs in use today are metabolised by these enzymes. Approximately 5% of Europeans and 1% of Asians lack CYP2D6 activity, and these  individuals are known as poor metabolizers. CYP2C9 is another clinically significant drug metabolising enzyme that demonstrates genetic variants. Studies into CYP2C9 polymorphism have highlighted the importance of the CYP2C9*2 and CYP2C9*3 alleles. Extensive polymorphism also occurs in a majority of Phase II drug metabolizing enzymes. One of the most important polymorphisms is thiopurine S-methyl transferases (TPMT) that catalyzes the S-methylation of thiopurine drugs. With respect to drug transport  polymorphism, the most extensively studied drug transporter is  P-glycoprotein (P-gp/MDR1), but the current data on the clinical impact is limited. Polymorphisms in drug transporters may change drug's distribution, excretion and response. Recent advances in molecular research have revealed many of the genes that encode drug targets demonstrate genetic polymorphism. These variations, in many cases, have altered the targets sensitivity to the specific drug molecule and thus have a profound effect on drug efficacy and toxicity. For example, the β2-adrenoreceptor, which is encoded by the ADRB2 gene, illustrates a clinically significant genetic variation in drug targets. The variable number tandem repeat polymorphisms in serotonin transporter (SERT/SLC6A4) gene are associated with response to antidepressants. The distribution of the common variant alleles of genes that encode drug metabolizing enzymes, drug transporters and drug targets has been found to vary among different populations. The promise of pharmacogenetics lies in its potential to identify the right drug at the right dose for the right individual. Drugs with a narrow therapeutic index are thought to benefit more from pharmacogenetic studies. For example, warfarin serves as a good practical example of how pharmacogenetics can be utilized prior to commencement of therapy in order to achieve maximum efficacy and minimum toxicity. As such, pharmacogenetics has the potential to achieve optimal quality use of medicines, and to improve the efficacy and safety of both prospective and licensed drugs.

Substrate specificity, regulation, and polymorphism of human cytochrome P450 2B6

CYP2B6 is mainly expressed in the liver that has been thought historically to play an insignificant role in human drug metabolism. However, increased interest in this enzyme has been stimulated by the discovery of polymorphic and ethnic differences in CYP2B6 expression, identification of additional substrates for CYP2B6, and evidence for co-regulation with CYP3A4. This paper updates our knowledge about the structure, function, regulation and polymorphism of CYP2B6. CYP2B6 can metabolise approximately 8% of clinically used drugs (n > 60), including cyclophosphamide, ifosfamide, tamoxifen, ketamine, artemisinin, nevirapine, efavirenz, bupropion, sibutramine, and propofol. CYP2B6 is one of the CYP enzymes that bioactivate several procarcinogens and toxicants. This enzyme also metabolizes arachidonic acid, lauric acid, 17beta-estradiol, estrone, ethinylestradiol, and testosterone. Typical substrates of CYP2B6 are non-planar molecules, neutral or weakly basic, highly lipophilic with one or two hydrogen-bond acceptors. The crystal structure of CYP2B6 has not been resolved, while several pharmacophore and homology models of human CYP2B6 have been reported. Human CYP2B6 is closely regulated by constitutive androstane receptor (CAR/NR1I3) which can activate CYP2B6 expression upon ligand binding. Pregnane X receptor and glucocorticoid receptor also play a role in the regulation of CYP2B6. Induction of CYP2B6 may partially explain some clinical drug interactions observed. For example, coadministered carbamazepine decreases the systemic exposure of bupropion. There is a wide interindividual variability in the expression and activity of CYP2B6. Such a large variability is probably due to effects of genetic polymorphisms and exposure to drugs that are inducers or inhibitors of CYP2B6. To date, at least 28 allelic variants and some subvariants of CYP2B6 (*1B through *29) have been described and some of them have been shown to have important functional impact on drug clearance and drug response. For example, the efavirenz plasma levels in African-American subjects with the CYP2B6 homozygous 516T/T genotype are approximately 3-fold higher than individuals carrying the homozygous G/G genotype. The CYP2B6 516T/T genotype is associated with 1.7-fold greater plasma levels of nevirapine in HIV-infected patients. Smokers with the 1459C>T (R487C) variant of CYP2B6 may be more vulnerable to abstinence symptoms and relapse following treatment with bupropion as a smoking cessation agent. Further studies in the structure, function, regulation and polymorphism of CYP2B6 are warranted.

Variability of soil chemistry following irrigation with recycled municipal effluent: a Great Western vineyard case study

In areas of Australia where viticultural operations have been limited by lack of an acceptable irrigation water source, considerable expansion has occurred through the use of recycled wastewater. Despite this rapid expansion, little is known of the potential impacts of the water’s chemical constituents on soil properties, or the long-term sustainability of the vineyards using the water. In order to establish the impacts of drip irrigated recycled wastewater on a vineyard in Great Western, Australia, a study comparing the soils from the vineyard inter-row and row area was undertaken. Chemical and physical properties of the soil with varying distances from the drip emitter were also investigated. During the irrigation season, significant differences between the inter-row and row area were found for several chemical parameters including pH(1:5soil/water) (P<0.001), electrical conductivity (EC1:5) (P<0.001), water-soluble sodium (WS Na+) (P<0.001), and water-soluble chloride (WS Cl-) (P<0.001). This paper will discuss differences observed between soil properties of the inter-row and vine row area, as well as the spatial distribution of solutes under the drip emitter.

Seasonal variability in whale encounters in the Western Antarctic Peninsula

Cetacean sighting surveys were conducted as part of nine multidisciplinary research cruises over late summer, autumn and winter of 2 years (2001–2003) during the Southern Ocean Global Ocean Ecosystems (SO GLOBEC) program. Sea-ice cover differed markedly between years, with apparent effects on cetacean distribution. No ice was present until late June in 2001, while the previous winter sea ice never fully retreated (>30% cover) during the 2002 or 2003 summer, thus increasing the proportion of thicker and more complex ice, including multi-year floes. Humpback (237 sightings; 537 individuals) and minke (103 sightings: 267 individuals) whales were the most commonly detected species. Data from seven comparable cruises were used to identify habitat for minke and humpback whales over five geographically distinct spatial divisions in the study area. In all years, both species were predominantly found in near coastal habitat, particularly in the fjords where complex habitat likely concentrated prey. In 2002 and 2003 the presence of sea ice provided additional feeding habitat, and the numbers of minkes (in winter) and humpbacks (late summer and autumn) in the area doubled compared with 2001. Humpbacks in particular were concentrated at the ice boundaries during late summer and autumn, while minke numbers increased in the winter that followed and occupied ice-covered areas along the entire shelf edge. Important resource sites for these species are mainly located in near-coastal areas and are used in all years, but when ice margins exist and intersect with resource sites they attract much larger numbers of animals due to the dynamics between sea ice and prey.

Do dietary changes of Australasian gannets (Morus serrator) reflect variability in pelagic fish stocks?

The relationship between changes in the diet of Australasian gannets (Morus serrator) and commercial fisheries landings was investigated. The contribution of pilchard (Sardinops sagax) to the diet of gannets was significantly related to the commercial catch of that species, suggesting that changes in the relative proportion of pilchard in the diet of gannets may be a useful index of pilchard abundance and availability. Equivalent relationships, however, were not found for other common prey species in the gannet diet. It is considered that the abundance of important prey items in the gannet diet, such as pilchards, and commercial landings are proportional to stock abundance. The implications of this relationship for fisheries management are examined.

Intraspecific phenotypic variability in the black-eared miner (Manorina melanotis); human-facilitated introgression and the consequences for an endangered taxon

Prior to this study the circumscription of the endangered black-eared miner (Manorina melanotis) and the common yellow-throated miner (Manorina flavigula) has been clouded by the existence of hybrid individuals. We examined the intra- and inter-specific phenotypic variation of the two taxa. All available museum specimens (n=138) and a sample of live individuals (n=83) were examined. Cluster analysis revealed a continuum of phenotypic traits now exists between the two taxa. However, further analysis revealed the black-eared miner and yellow-throated miner were separable on phenotypic characters prior to extensive modification of mallee habitat after 1950, suggesting the black-eared miner should be afforded full species status [contrary to Schodde and Mason, 1999. (Schodde, R., Mason, I.J., 1999. The Directory of Australian Birds: Passerines. CSIRO Wildlife and Ecology, Canberra]. Our study highlights the need to carefully examine, not only intraspecific phenoptyic variation within a taxon, but to also consider how such variation may be affected by hybridisation facilitated by human disturbance of habitat.

Periodic variability in cetacean strandings: links to large-scale climate events

Cetacean strandings elicit much community and scientific interest, but few quantitative analyses have successfully identified environmental correlates to these phenomena. Data spanning 1920–2002, involving a total of 639 stranding events and 39 taxa groups from southeast Australia, were found to demonstrate a clear 11–13- year periodicity in the number of events through time. These data positively correlated with the regional persistence of both zonal (westerly) and meridional (southerly) winds, reflecting general long-term and large-scale shifts in sea-level pressure gradients. Periods of persistent zonal and meridional winds result in colder and presumably nutrient-rich waters being driven closer to southern Australia, resulting in increased biological activity in the water column during the spring months. These observations suggest that large-scale climatic events provide a powerful distal influence on the propensity for whales to strand in this region. These patterns provide a powerful quantitative framework for testing hypotheses regarding environmental links to strandings and provide managers with a potential predictive tool to prepare for years of peak stranding activity.

Distribution of an alien aquatic snail in relation to flow variability, human activities and water quality

1. Disturbance and anthropogenic land use changes are usually considered to be key factors facilitating biological invasions. However, specific comparisons of invasion success between sites affected to different degrees by these factors are rare.

2. In this study we related the large-scale distribution of the invading New Zealand mud snail (Potamopyrgus antipodarum) in southern Victorian streams, Australia, to anthropogenic land use, flow variability, water quality and distance from the site to the sea along the stream channel.

3. The presence of P. antipodarum was positively related to an index of flow-driven disturbance, the coefficient of variability of mean daily flows for the year prior to the study.

4. Furthermore, we found that the invader was more likely to occur at sites with multiple land uses in the catchment, in the forms of grazing, forestry and anthropogenic developments (e.g. towns and dams), compared with sites with low-impact activities in the catchment. However, this relationship was confounded by a higher likelihood of finding this snail in lowland sites close to the sea.

5. We conclude that P. antipodarum could potentially be found worldwide at sites with similar ecological characteristics. We hypothesise that its success as an invader may be related to an ability to quickly re-colonise denuded areas and that population abundances may respond to increased food resources. Disturbances could facilitate this invader by creating spaces for colonisation (e.g. a possible consequence of floods) or changing resource levels (e.g. increased nutrient levels in streams with intense human land use in their catchments).

The effect of clamping sequence on dimensional variability in sheet metal assembly

Finite element (FE) modelling techniques have become a popular tool for exploring welding and clamping sequence dependence in sheet metal assemblies. In the current paper, the dimensional variability associated with different assembly clamping sequences is investigated with a FE contact modelling approach implemented in the commercial code Abaqus. A simplified channel section assembly consisting of a top hat and bottom plate is the case study investigated. Expected variation modes of bow and twist were used to simulate key variability sources in the main structural component under investigation; the top hat of the channel section. It was found that final assembly variability can change considerably depending on clamp sequence selection. It was also found that different clamp sequences can control particular modes of variation better than others, and that there is not one particular clamping sequence that is the best for containing all variation modes. An adaptable assembly process is therefore suggested, where given the shape of input components the best available clamping sequence is selected. Comparison of the performance of the proposed adaptable clamping sequence to traditional fixed clamping sequences shows improvements for the dimensional control of variability in non-rigid components. While introducing such a method in production would require inspection of each component being assembled and investigation of the alternative clamping sequences, given access to fast and detailed dimensional inspection technology such as optical coordinate measuring machines (OCMM's), the approach shows promise for future application.

Effect of dietary omega-3 fatty acid deficiency on heart rate variability in hooded rats

Introduction: Recent reports in adult humans suggest that heart rate variability is modulated by the concentration of omega-3 polyunsaturated fatty acids (PUFA) contained in blood cell membranes. Material and methods: Hurst analysis of ECG data was conducted on 12 male adult hooded (Long-Evans) rats, representing the 3rd generation to be fed diets that were either deficient in, or supplemented with, omega-3 PUFA. ECG data were obtained from surface electrodes and 4000 beats were analyzed for each animal. Results: Dietary manipulation, despite leading to large changes in tissue omega- 3 PUFA levels, did not significantly affect the complexity of heart rate dynamics, with Hurst exponent (H) values of 0.15±0.02 and 0.12±0.03, for animals fed omega- 3 fatty acid-adequate and -deficient diets, respectively. Mean heart rate was also unaffected by the diets. A power calculation revealed that about one hundred animals per group would have been required to avoid a type II error. Conclusions: According to this model of dietary PUFA manipulation, omega-3 fatty acids are unlikely to exert a large effect on the autonomic functions that control heart rate variability. Prospective studies into the effect of omega-3 fatty acids on HRV should consider the need for large sample size as estimated by the results contained in this report.

Multivariate modelling of variability in sheet metal forming

The inherent variability in incoming material and process conditions in sheet metal forming makes quality control and the maintenance of consistency extremely difficult. A single FEM simulation is successful at predicting the formability for a given system, however lacks the ability to capture the variability in an actual production process due to the numerical deterministic nature. This paper investigates a probabilistic analytical model where the variation of five input parameters and their relationship to the sensitivity of springback in a stamping process is examined. A range of sheet tensions are investigated, simulating different operating windows in an attempt to highlight robust regions where the distribution of springback is small. A series of FEM simulations were also performed, to compare with the findings from the analytical model using AutoForm Sigma v4.04 and to validate the analytical model assumptions.

Results show that an increase in sheet tension not only decreases springback, but more importantly reduces the sensitivity of the process to variation. A relative sensitivity analysis has been performed where the most influential parameters and the changes in sensitivity at various sheet tensions have been investigated. Variation in the material parameters, yield stress and n-value were the most influential causes of springback variation, when compared to process input parameters such as friction, which had a small effect. The probabilistic model presented allows manufacturers to develop a more comprehensive assessment of the success of their forming processes by capturing the effects of inherent variation.

Implications of accuracy, sensitivity, and variability of body size estimations to disordered eating

The current study was conducted to investigate the relationships between body size estimations and disordered eating symptomatology. The method of constant stimuli was used to derive three measures of self-perceived body size in 93 women: (1) accuracy of body size estimations (body image distortion); (2) sensitivity in discriminating body size within blocks of trials (body image sensitivity); and (3) variability in making body size estimations between blocks of trials (body image variability). Participants also completed measures of disordered eating. Although body image distortion correlated with dietary restraint and eating concern, body image variability accounted for additional variance in these variables, as well as variance in binge eating. The relationships involving body image variability were found to be mediated by body dissatisfaction and internalization of the thin ideal. Together, these results are consistent with the proposition that body image variability is a significant factor in disordered eating.