Identification of 167 polymorphisms in 88 genes from candidate neurodegeneration pathways

Effect of Aging on Mitochondrial Energetics in the Human Atria

Energy production in myocardial cells occurs mainly in the mitochondrion. Although alterations in mitochondrial functions in the senescent heart have been documented, the molecular bases for the aging-associated decline in energy metabolism in the human heart are not fully understood. In this study, we examined transcription profiles of genes coding for mitochondrial proteins in atrial tissue from aged (≥65 years old) and comorbidities-matched adult (<65 years old) patients with preserved left ventricular function. We also correlated changes in functional activity of mitochondrial oxidative phosphorylation (OXPHOS) complexes with gene expression changes. There was significant alteration in the expression of 10% (101/1,008) of genes coding for mitochondrial proteins, with 86% downregulated (87/101). Forty-nine percent of the altered genes were confined to mitochondrial energetic pathways. These changes were associated with a significant decrease in respiratory capacity of mitochondria oxidizing glutamate and malate and functional activity of complex I activity that correlated with the downregulation of NDUFA6, NDUFA9, NDUFB5, NDUFB8, and NDUFS2 genes coding for NADH dehydrogenase subunits. Thus, aging is associated with a decline in activity of OXPHOS within the broader transcriptional downregulation of genes regulating mitochondrial energetics, providing a substrate for reduced energetic efficiency in the senescent human atria.

Transcriptome assembly and identification of genes and SNPs associated with growth traits in largemouth bass (Micropterus salmoides)

Growth is one of the most crucial economic traits of all aquaculture species, but the molecular mechanisms involved in growth of largemouth bass (Micropterus salmoides) are poorly understood. The objective of this study was to screen growth-related genes of M. salmoides by RNA sequencing and identify growth-related single-nucleotide polymorphism (SNP) markers through a growth association study. The muscle transcriptomes of fast- and slow-growing largemouth bass were obtained using the RNA-Seq technique. A total of 54,058,178 and 54,742,444 qualified Illumina read pairs were obtained for the fast-growing and slow-growing groups, respectively, giving rise to 4,865,236,020 and 4,926,819,960 total clean bases, respectively. Gene expression profiling showed that 3,530 unigenes were differentially expressed between the fast-growing and slow-growing phenotypes (false discovery rate ≤0.001, the absolute value of log₂ (fold change) ≥1), including 1,441 up-regulated and 2,889 down-regulated unigenes in the fast-growing largemouth bass. Analysis of these genes revealed that several signalling pathways, including the growth hormone-insulin-like growth factor 1 axis and signalling pathway, the glycolysis pathway, and the myostatin/transforming growth factor beta signalling pathway, as well as heat shock protein, cytoskeleton, and myofibril component genes might be associated with muscle growth. From these genes, 10 genes with putative SNPs were selected, and 17 SNPs were genotyped successfully. Marker-trait analysis in 340 individuals of Youlu No. 1 largemouth bass revealed three SNPs associated with growth in key genes (phosphoenolpyruvate carboxykinase 1, FOXO3b, and heat shock protein beta-1). This research provides information about key genes and SNPs related to growth, providing new clues to understanding the molecular basis of largemouth bass growth.

Gene sequence analysis and screening of feature genes in spinal cord injury

The aim of the present study was to screen for feature genes associated with spinal cord injury (SCI), in order to identify the underlying pathogenic mechanisms. Differentially expressed genes were screened for using pre‑processing data. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed to analyze and identify the genes involved in pathways associated with SCI. Subsequently, Gene Ontology enrichment analysis and Uniprot tissue analysis were used to screen out genes specifically expressed in spinal cord tissue. In addition, a protein‑protein interaction network was used to demonstrate possible associations among SCI‑associated feature genes. Finally, a link was identified between feature genes and SCI by analyzing protein domains in coding areas of the three feature genes. The cytochrome c oxidase subunit Va, adenosine triphosphate (ATP) synthase, H+ transporting, mitochondrial F1 complex, α subunit 1 and cardiac muscle and mitochondrial β‑F1‑ATPase may be downregulated in SCI, resulting in destruction of the mitochondrial electron transport chain and membrane‑bound enzyme complexes/ion transporters, thus, affecting the normal function of nerves. The three screened feature genes have the potential to become candidate target molecules to monitor, diagnose and treat SCI and may be beneficial for the early diagnosis and therapeutic control of the condition.

Gene-environmental interactions and organophosphate toxicity

Organophosphates (OPs) are an important class of insecticides that in the UK have been widely used for treating sheep for ectoparasites as well as in other sectors of the farming industry. Health problems associated with acute OP toxicity are well defined but, ill-health induced by chronic exposures to OPs remains controversial. A substantial number of sheep farmers complain of chronic ill-health which they attribute to repeated exposure to OPs. If OPs were associated with chronic ill-health then individuals with specific defects in OP metabolism might be expected to be at greater risk of ill-health following exposure. To examine such a hypothesis, the characterisation of both OP exposure and those pathways which lead to the formation and removal of the active OP metabolites becomes important. A wide range of OPs have previously been used to treat sheep but currently the only OP licenced for treating sheep is diazinon. Immediately after treatment, farmers' urines contain detectable levels of OP metabolites but few farmers have a significant decrease in plasma cholinesterase activity. Diazinon, like chlorpyrifos, is an organothiophosphate which is metabolised, particularly by cytochrome p450s, to the corresponding active oxon form. CYP metabolism also leads to the inactivation of the parent compound and the relative balance of inactivation and activation can depend upon the specific OP and the CYP isoform. OP oxons are inactivated by serum paraoxonase (PON1) and mice lacking PON1 activity are susceptible to oxon and parent OP induced toxicity. PON1 polymorphisms at positions 192 (R form with arginine at 192 and Q with glutamine) and 55 (L form with a leucine and a M form with methionine) influence paroxonase activity. The effect of the Q192R polymorphism is substrate specific with reports indicating that diazoxon is metabolised less by the R isoform. In a study of sheep farmers within the UK, the R allele was associated with an increased risk of self-reported chronic ill-health, a result consistent with the hypothesis that this ill-health may have been caused by OPs. Studies in other populations exposed to pesticides also show associations between ill-health and PON1 Q192R polymorphisms but not consistently so. This is not surprisingly given that exposure is often poorly characterised. In vivo models also suggest that PON1 genotypes may have little influence on susceptibility at low doses of the parent OP. Hence further work is required not only to better characterise OP exposure in humans populations but also to identify those populations susceptible to OP toxicity.

Nitration of the mitochondrial complex I subunit NDUFB8 elicits RIP1- and RIP3-mediated necrosis

Nitric oxide (NO) and other reactive nitrogen species target multiple sites in the mitochondria to influence cellular bioenergetics and survival. Kinetic imaging studies revealed that NO from either activated macrophages or donor compounds rapidly diffuses to the mitochondria, causing a dose-dependent progressive increase in NO-dependent DAF fluorescence, which corresponded to mitochondrial membrane potential loss and initiated alterations in cellular bioenergetics that ultimately led to necrotic cell death. Cellular dysfunction is mediated by an elevated 3-nitrotyrosine signature of the mitochondrial complex I subunit NDUFB8, which is vital for normal mitochondrial function as evidenced by selective knockdown via siRNA. Overexpression of mitochondrial superoxide dismutase substantially decreased NDUFB8 nitration and restored mitochondrial homeostasis. Further, treatment of cells with either necrostatin-1 or siRNA knockdown of RIP1 and RIP3 prevented NO-mediated necrosis. This work demonstrates that the interaction between NO and mitochondrially derived superoxide alters mitochondrial bioenergetics and cell function, thus providing a molecular mechanism for reactive oxygen and nitrogen species-mediated alterations in mitochondrial homeostasis.

Searching for alleles associated with complicated outcomes after burn injury

Sepsis is a serious and growing health problem among patients admitted to intensive care units. When accompanied by organ failure, sepsis carries a 30-50% case-fatality rate. Although our understanding of burn pathophysiology has grown in recent years, we are still unable to identify accurately patients who are at increased risk for infectious complications and death. Genetic predisposition is likely to explain a portion of this variation. Understanding which genes and allelic variants contribute to disease risk would increase our ability to predict who is at increased risk and intervene accordingly, as well as identify molecular targets for novel and individualized therapies. Several obstacles exist to identification of which specific alleles and loci contribute to patient risk, including achievement of sufficient statistical power, population admixture and epistatic interaction among multiple genes and environmental factors. Although increasing sample size will resolve most, if not all, of these issues, slow patient accrual often makes this solution impractical for a single institution within a reasonable timeframe. This situation is complicated by the fact that traditional analysis methods perform poorly in the face of data sparseness. Identification of risk factors for severe sepsis and death after burn injury will likely require collaborative patient enrollment as well as development of advanced analytical methodologies. While overcoming these obstacles may prove difficult, the effort is warranted, as the ultimate benefit to patients is considerable.

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions

BACKGROUND

A promising application of the huge amounts of genetic data currently available lies in developing a better understanding of complex diseases, such as cancer. Analysis of publicly available databases can help identify potential candidates for genes or mutations specifically related to the cancer phenotype. In spite of their huge potential to affect gene function, no systematic attention has been paid so far to the changes that occur in untranslated regions of mRNA.

RESULTS

In this study, we used Expressed Sequence Tag (EST) databases as a source for cancer-related sequence polymorphism discovery at the whole-genome level. Using a novel computational procedure, we focused on the identification of untranslated region (UTR)-localized non-coding Single Nucleotide Polymorphisms (UTR-SNPs) significantly associated with the tumoral state. To explore possible relationships between genetic mutation and phenotypic variation, bioinformatic tools were used to predict the potential impact of cancer-associated UTR-SNPs on mRNA secondary structure and UTR regulatory elements. We provide a comprehensive and unbiased description of cancer-associated UTR-SNPs that may be useful to define genotypic markers or to propose polymorphisms that can act to alter gene expression levels. Our results suggest that a fraction of cancer-associated UTR-SNPs may have functional consequences on mRNA stability and/or expression.

CONCLUSION

We have undertaken a comprehensive effort to identify cancer-associated polymorphisms in untranslated regions of mRNA and to characterize putative functional UTR-SNPs. Alteration of translational control can change the expression of genes in tumor cells, causing an increase or decrease in the concentration of specific proteins. Through the description of testable candidates and the experimental validation of a number of UTR-SNPs discovered on the secreted protein acidic and rich in cysteine (SPARC) gene, this report illustrates the utility of a cross-talk between in silico transcriptomics and cancer genetics.

Polymorphisms in manganese superoxide dismutase and catalase genes: functional study in Hong Kong Chinese asthma patients

BACKGROUND

Reactive oxygen species may contribute to the pathogenesis of asthma. Functional genetic polymorphisms of antioxidant enzymes, superoxide dismutase (SOD) and catalase are good candidates for asthma susceptibility.

OBJECTIVE

To investigate the association of the manganese-containing form of SOD (MnSOD) gene at amino acid position 16 (Val16Ala) and catalase gene in the promoter at A-21T and C-262T polymorphisms and asthma in a Hong Kong Chinese population.

METHODS

The association study was conducted in a case-control design in asthma patients (n=251) and healthy controls (n=316) by genotyping. The functional significance was assessed by determining erythrocyte SOD and catalase activity.

RESULTS

The Val allele of MnSOD at Val16Ala and the A allele of catalase gene at A-21T were not different between patients and controls, while the C allele of catalase gene at C-262T was found to be significantly different between patients and controls (P=0.033). The less frequent variant of catalase gene (-262T) was found to be protective from the development of asthma in a Hong Kong Chinese non-smoking population (adjusted odds ratio=0.35, 0.15-0.85; P=0.017). Asthma patients had elevated erythrocyte SOD and catalase activities in comparison with healthy controls (P<0.01). However, their activities were not associated with different genotypes within healthy controls or asthma patients.

CONCLUSION

This is the first report showing that SOD and catalase functional activities are not associated with their respective genetic polymorphisms but related to the presence of asthma in a Hong Kong Chinese population.

GSTT1 and GSTM1 allelic polymorphisms in head and neck cancer patients from Italian Lazio Region

BACKGROUND

The association between head and neck squamous cell carcinoma (HNSCC) and allelic variants of glutathione S-transferase M1 (GSTM1) and -T1 (GSTT1) is currently controversial. The present study investigates the prevalences of GSTT1 and GSTM1 polymorphism in a cohort of 100 head and neck cancer patients, 100 healthy donors and 200 controls with non-neoplastic head and neck diseases from Italian Lazio Region.

METHODS

The patients with benign head and neck pathologies, as well as the healthy donors were matched for age, sex, cigarette smoke (yes/no) and alcohol consumption (yes/no). Molecular definition of GSTT1 and GSTM1 genotype has been performed by means of allele-specific PCR technique.

RESULTS

A significant association between head and neck cancer and GSTM1 null genotype was observed both considering benign disease controls (p=0.001, OR=2.613; 95% C.I.=1.48-4.62), and healthy donors (p=0.0003, OR=3.35; 95% C.I. 1.69-6.67) while no significant association was found with GSTT1 null genotype (p>or=0.14). No interactive association was observed when combining the different genotypes of the two polymorphisms. These results were confirmed after correction for daily number of cigarettes and period of tobacco exposure.

CONCLUSIONS

The present study confirms a role for genetic alterations of GSTM1 detoxifying enzyme as a risk factor for the development of HNSCC in patients from the Italian Lazio Region, independently of age, sex and other confounding variables.

Genetic Factors in Outcome After Traumatic Brain Injury

It is becoming increasingly clear that genetic factors modify outcome after traumatic brain injury (TBI). The best known example of this is the association between the apolipoprotein E4 allele (APOE epsilon4) and poorer outcomes. However, our knowledge of the many other genes that might influence outcome is still in its infancy. This article will review the basic principles underlying recent advances in genetics, and then describe the current state of knowledge regarding the impact of genetic factors on TBI outcome. We conclude that although genetic advances have implications for prognosis, their biggest contribution will be to elucidate the pathophysiology of TBI, potentially leading to new treatments.

Polymorphism of human mu class glutathione transferases

OBJECTIVES AND METHODS

A combined database mining approach was used to detect polymorphisms in the mu class glutathione-S-transferase (GST) genes. Although a large number of potential polymorphisms were detected in the five genes that comprise the Mu class GSTs using sequence alignment programs and by searching single nucleotide polymorphism databases, the majority were not validated or detected in three major ethnic populations (African, Southern Chinese and Australian European).

RESULTS

Two new polymorphisms were detected and characterized in the GSTM3 gene. A rare pG147W substitution was detected only in the Southern Chinese subjects. A more common pV224I substitution was found in each of the ethnic groups studied, and significant differences in allele frequencies were observed between each group. These two polymorphisms can combine to form four distinct haplotypes (GSTM3A [p.G147;V224], GSTM3C [p.G147;I224], GSTM3D [p.W147;V224], GSTM3E [p.W147;I224]). The four isoforms were expressed in Escherichia coli and characterized enzymatically with several substrates including 1-chloro-2,4-dinitrobenzene (CDNB), cumene hydroperoxide and t-nonenal. GSTM3-3 containing the variant p.W147 residue tended to show diminished specific activity and catalytic efficiency with CDNB. In contrast, GSTM3-3 containing the variant p.I224 residue tended to show increased specific activity and catalytic efficiency with CDNB. Interactions between the different p.147 and p.224 residues were also observed, with the GSTM3C isoform exhibiting the greatest activity with each substrate, and GSTM3E the lowest.

CONCLUSION

These functional polymorphisms may play a significant role in modulating the ability of GSTM3-3 to metabolize substrates such as the chemotherapeutic agent 1,3-bis(2-chloroethyl)-1-nitrosourea.

Paraoxonase and superoxide dismutase gene polymorphisms and noise-induced hearing loss

BACKGROUND

Noise-induced cochlear epithelium damage can cause hearing loss in industrial workers. In experimental systems, noise induces the release of free radicals and may damage the cochlear sensorial epithelium. Therefore, genes involved in regulating the reactive oxygen species manganese-superoxide dismutase (SOD2) and the antioxidant paraoxonase (PON) could influence cochlea vulnerability to noise. We evaluated whether susceptibility to noise-induced hearing loss (NIHL) is associated with SOD2, PON1, and PON2 polymorphisms in workers exposed to prolonged loud noise.

METHODS

We enrolled 94 male workers from an aircraft factory in the study. The SOD2 gene was screened by denaturing reversed-phase HPLC, and the PON1 (Q192R and M55L) and PON2 (S311C) polymorphisms were analyzed by PCR amplification followed by digestion with restriction endonucleases.

RESULTS

Three known (A16V, IVS3-23T/G, and IVS3-60T/G) and two new SOD2 polymorphisms (IVS1+ 8A/G and IVS3+107T/A) were identified. Regression analysis showed that PON2 (SC+CC) [odds ratio (OR) = 5.01; 95% confidence interval (CI), 1.11-22.54], SOD2 IVS3-23T/G and IVS3-60T/G (OR = 5.09; 95% CI, 1.27-20.47), age (OR = 1.22; 95% CI, 1.09-1.36), and smoking (OR = 49.49; 95% CI, 5.09-480.66) were associated with NIHL. No association was detected for PON1 (QQ+RR) and PON1 (LL) genotypes.

CONCLUSIONS

Our data suggest that SOD2 and PON2 polymorphisms, by exerting variable local tissue antioxidant roles, could predispose to NIHL. However, caution should be exercised in interpreting these data given the small sample size and the difficulty in matching cases to controls regarding the overwhelming risk factor, i.e., smoking at least 10 cigarettes/day.

Host genetic polymorphisms in human immunodeficiency virus-related neurologic disease

The objective of this study was to determine whether host genetic polymorphisms influence the risk of developing human immunodeficiency virus (HIV) encephalitis and vacuolar myelopathy. Allelic association studies were carried out with common polymorphisms in candidate genes that are postulated to play a role in the pathogenesis of HIV-related neurologic complications. The authors studied brains and spinal cords from 270 patients who died of acquired immunodeficiency syndrome (AIDS) from 1989 to 1996. All had complete gross and microscopic pathologic evaluations, and the presence of microglial nodules, multinucleated giant cells, myelin pallor, and vacuolar myelopathy was assessed by an experienced neuropathologist who was blinded to the genotype. DNA was extracted from frozen brain samples, and determination of the presence of the APOE4, TNF-2, IL-1B*2, ILIRN*2 polymorphisms was determined by polymerase chain reaction (PCR) and restricted fragment length polymorphism (RFLP) mapping. The authors did not detect a consistent association between inheritance of candidate polymorphic alleles and the pathologic findings of HIV encephalitis or vacuolar myelopathy. Allelic association studies with candidate genes are powerful techniques that have the potential to contribute to understanding the pathophysiology of HIV-related neurodegeneration. This preliminary study, although including a substantial number of patients, was not sufficiently powered to exclude a modest but clinically significant effects. Future studies will require much larger sample sizes and technical advances to allow screening at larger number of candidate loci.

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Relationship of tobacco smoking with GSTM1 gene polymorphism in laringeal cancer

This paper aimed to analyze the association of polymorphism of GSTM1 0/0 genotype with laryngeal cancer along a hospital based case-control study. Polymorphisms of GSTM1 0/0 of samples from 36 patients with laryngeal cancer and 35 healthy controls were detected by PCR method. The reaction used as GSTM1 primers, using the sequence sense: 5'-CTGCCCTACTTGGATTGATGGG-3' and antisense: 5'-TGGATTGTAGCAGATCATGC-3'. N Acetyl transferase 1 (NAT1) gene using the primers sense: 5'-TAAAAGTAAAATGATTTGCTTTCG-3' and antisense: 5'- GCTTTCTAGCATAAATCACCAA-3' was used as internal positive control. Two sided 2 and multivariation analysis were used to analyse the results. The proportions of GSTM1 deleted genotype in cases and controls were 47.2% and 54.3%, respectively. There was significant increment of GSTM 0/0 genotype frequency in moderate smokers group of patients compared to control (P=0.033, OR= 4.78, 95% CI = 1.30-7.13). We conclude that GSTM1 deleted genotype may be a genetic susceptibility marker for laryngeal cancer whose exposed to low doses carcinogens. The absence of this enzyme seems to have a role in the development of laryngeal cancer, in which the mechanism still needs further investigation.

Detection and characterization of a novel functional polymorphism in the GSTT1 gene

A novel functional polymorphism in the GSTT1 gene associated with the non-conjugator phenotype has been identified. Sequencing of GSTT1 cDNA revealed a single nucleotide substitution, 310A>C, that altered the amino acid residue 104 from threonine to proline (T104P). Modelling studies of GSTT1 have suggested that residue 104 is located in the middle of alpha-helix 4. Introduction of an alpha-helix-disrupting proline most likely distorts the conformation of the protein. Individuals that lacked GSTT1 activity and carried the variant allele, tentatively denoted GSTT1*B, had no detectable GSTT1 immunoreactive protein. An allele-specific polymerase chain reaction method was developed to determine the frequency of the GSTT1*B allele. In 497 ethnic Swedes, the frequency of the active GSTT1*A allele was 0.65 [95% confidence interval (CI) 0.62-0.68] whereas the frequencies of the non-functional alleles GSTT1*O and the novel GSTT1*B allele were 0.34 (CI 0.31-0.37) and 0.01 (CI 0.01-0.02), respectively. In 100 Swedish Saamis, the GSTT1*B allele appeared to be slightly more common with a frequency of 0.03 (CI 0.01-0.07). The GSTT1 enzyme activity was measured in erythrocytes using methyl chloride as substrate. Individuals with the GSTT1*A/*A genotype had a two-fold higher GSTT1 activity compared to individuals with the GSTT1*A/*B genotype and subjects with the GSTT1*O/*B genotype totally lacked GSTT1 activity, indicating a strict gene-dose effect. By combining the analyses for the novel single nucleotide polymorphism with analyses for the deletion polymorphism, the accuracy in predicting all three GSTT1 conjugator phenotypes was improved from 96% to 99%.

Evaluation of multiple presenilin 2 SNPs for association with early-onset sporadic Alzheimer disease

The presenilin genes encode proteins that modify, mediate, or perform similar functions to gamma-secretase, the enzyme responsible for converting amyloid beta precursor protein (APP) into beta-amyloid. Mutations in the presenilin genes cause an increased production of Abeta42, the aberrant form of beta-amyloid found in the neural plaques of Alzheimer disease patients. Previously reported association studies of presenilin 2 (PSEN2) polymorphisms with early-onset Alzheimer disease (EOAD) have produced contradictory results. In an effort to resolve these differences, we tested eight single nucleotide polymorphisms in and around the 3' region of the PSEN2 gene for association with EOAD. An initial set of Scottish EOAD cases (n = 121) and controls (n = 152) was screened using the genotyping method dynamic allele-specific hybridization (DASH). No significant differences were seen between allele or genotype frequencies of cases and controls. However, when conditioned on the risk allele (epsilon 4) APOE, three polymorphisms showed allelic association with a P value below 0.05. These same polymorphisms were in near 100% linkage disequilibrium with each other (P < 5 x 10(-5)), and in each, one of the homozygous genotypes was absent in controls but present in the cases. Replication in an independent set of Scottish EOAD cases (n = 84) and controls (n = 173) did not confirm this finding. From this study we find no evidence to suggest that variations in the PSEN2 gene pose as major risk factors for sporadic EOAD.

Sequence variation in genes and genomic DNA: methods for large-scale analysis

The large-scale typing of sequence variation in genes and genomic DNA presents new challenges for which it is not clear that current technologies are sufficiently sensitive, robust, or scalable. This review surveys the current platform technologies: separation-based approaches, which include mass spectrometry; homogeneous assays; and solid-phase/array-based assays. We assess techniques for discovering and typing variation on a large scale, especially that of single-nucleotide polymorphisms. The in-depth focus is the DNA chip/array platform, and some of the published large-scale studies are closely examined. The problem of large-scale amplification is addressed, and emerging technologies for present and future needs are indicated.

Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily

The glutathione transferases (GSTs; also known as glutathione S-transferases) are major phase II detoxification enzymes found mainly in the cytosol. In addition to their role in catalysing the conjugation of electrophilic substrates to glutathione (GSH), these enzymes also carry out a range of other functions. They have peroxidase and isomerase activities, they can inhibit the Jun N-terminal kinase (thus protecting cells against H(2)O(2)-induced cell death), and they are able to bind non-catalytically a wide range of endogenous and exogenous ligands. Cytosolic GSTs of mammals have been particularly well characterized, and were originally classified into Alpha, Mu, Pi and Theta classes on the basis of a combination of criteria such as substrate/inhibitor specificity, primary and tertiary structure similarities and immunological identity. Non-mammalian GSTs have been much less well characterized, but have provided a disproportionately large number of three-dimensional structures, thus extending our structure-function knowledge of the superfamily as a whole. Moreover, several novel classes identified in non-mammalian species have been subsequently identified in mammals, sometimes carrying out functions not previously associated with GSTs. These studies have revealed that the GSTs comprise a widespread and highly versatile superfamily which show similarities to non-GST stress-related proteins. Independent classification systems have arisen for groups of organisms such as plants and insects. This review surveys the classification of GSTs in non-mammalian sources, such as bacteria, fungi, plants, insects and helminths, and attempts to relate them to the more mainstream classification system for mammalian enzymes. The implications of this classification with regard to the evolution of GSTs are discussed.

Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles of the head kidney

Analysis of expressed sequence tags (ESTs) is an efficient approach for gene discovery, expression profiling, and development of resources useful for functional genomics studies. As part of the transcriptome analysis in channel catfish (Ictalurus punctatus), we have conducted EST analysis using a cDNA library made from the head kidney. We analysed 2228 EST clones. Orthologues were established for 1495 (67.1%) clones representing 748 genes, of which 545 (36.5%) clones were singletons. The remaining 733 (32.9%) clones represent unknown gene clones, for which the number of genes has not yet been determined.

Pharmacogenomics: unlocking the human genome for better drug therapy

There is great heterogeneity in the way humans respond to medications, often requiring empirical strategies to find the appropriate drug therapy for each patient (the "art" of medicine). Over the past 50 years, there has been great progress in understanding the molecular basis of drug action and in elucidating genetic determinants of disease pathogenesis and drug response. Pharmacogenomics is the burgeoning field of investigation that aims to further elucidate the inherited nature of interindividual differences in drug disposition and effects, with the ultimate goal of providing a stronger scientific basis for selecting the optimal drug therapy and dosages for each patient. These genetic insights should also lead to mechanism-based approaches to the discovery and development of new medications. This review highlights the current status of work in this field and addresses strategies that hold promise for future advances in pharmacogenomics.

Oxidative stress, human genetic variation, and disease

Oxidative stress has been implicated in numerous pathophysiological conditions and also aging. The tools for studying oxidative stress are now expanding as a result of the human genome effort and, in particular, expanding knowledge on human genetic variation. A few genetic variants, mostly in the form of single nucleotide polymorphisms of relevance to oxidative stress are already studied by a molecular epidemiologic approach. A review of the current knowledge on variant human genes that are directly implicated in human protection against oxidative stress is presented.

Bioinformatic and experimental tools for identification of single-nucleotide polymorphisms in genes with a potential role for the development of the insulin resistance syndrome

OBJECTIVES

Genes with a possible role for the development of the insulin resistance syndrome (IRS) were scanned for novel single-nucleotide polymorphisms (SNPs) using bioinformatics.

METHODS

GenBank mRNA sequences were compared to the human EST database using gapped BLAST, software that is available on the internet. Mismatches between the search and the EST sequences indicated potential SNPs. Thirty-two SNPs in 13 genes were randomly chosen for experimental verification. PCR and direct sequencing were used to determine the 'true' SNPs. A random sample of 30 Swedish men with slightly elevated diastolic blood pressure (85-94 mmHg) obtained from a population-based study was selected for the sequencing. After completion of these stages, the potential SNPs were checked against the large and rapidly expanding SNP databases HGBASE and NCBI.

RESULTS

EST searches of 146 genes revealed 106 potential SNPs in 44 genes. Experimental analysis of 32 of these potential SNPs verified two SNPs; endothelin receptor A 1471 G/C (3' UTR) and PAI-1 Trp514Arg from a T/C exchange. These two SNPs were also identified in the NCBI and HGBASE databases together with two polymorphisms that were not experimentally identified in our homogeneous Swedish population. Overall, the HGBASE and NCBI databases contained entries of 22% (23 out of 106) of the SNPs identified through our EST searches.

CONCLUSIONS

In the search for genetic variations causing complex diseases like IRS in homogeneous populations (such as the Swedish one used here), important information can be obtained through bioinformatic searches of human genome databases and experimental verification.

Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation

We recently introduced a generic single nucleotide polymorphism (SNP) genotyping method, termed DASH (dynamic allele-specific hybridization), which entails dynamic tracking of probe (oligonucleotide) to target (PCR product) hybridization as reaction temperature is steadily increased. The reliability of DASH and optimal design rules have not been previously reported. We have now evaluated crudely designed DASH assays (sequences unmodified from genomic DNA) for 89 randomly selected and confirmed SNPs. Accurate genotype assignment was achieved for 89% of these worst-case-scenario assays. Failures were determined to be caused by secondary structures in the target molecule, which could be reliably predicted from thermodynamic theory. Improved design rules were thereby established, and these were tested by redesigning six of the failed DASH assays. This involved reengineering PCR primers to eliminate amplified target sequence secondary structures. This sophisticated design strategy led to complete functional recovery of all six assays, implying that SNPs in most if not all sequence contexts can be effectively scored by DASH. Subsequent empirical support for this inference has been evidenced by approximately 30 failure-free DASH assay designs implemented across a range of ongoing genotyping programs. Structured follow-on studies employed standardized assay conditions, and revealed that assay reproducibility (733 duplicated genotypes, six different assays) was as high as 100%, with an assay accuracy (1200 genotypes, three different assays) that exceeded 99.9%. No post-PCR assay failures were encountered. These findings, along with intrinsic low cost and high flexibility, validate DASH as an effective procedure for SNP genotyping.

Phenotype determination of a common Pro-Leu polymorphism in human glutathione peroxidase 1

Oxidative stress has been implicated in human illness such as cardiovascular and neurodegenerative disease. The genetic mechanisms involved are only poorly understood. Here we describe the determination of the allelic frequency and phenotype of a common polymorphism in Se-dependent glutathione peroxidase 1 (GPX1) in Finnish/Swedish populations. A proline/leucine variant occurs at position 197 close to the C-terminus of the protein. The more common allele encoding the Pro variant is present at 59% in a Finnish/Swedish population (n = 66) and at 73% in a Swedish population (n = 315). The genotypes encoding Pro/Pro, Pro/Leu, and Leu/Leu are distributed according to the Hardy-Weinberg relationship. The Swedish population consisted of 101 stroke cases and 214 controls. No significant association between allele frequency and risk to suffer from stroke was evident. Erythrocyte GPX activity was determined in the Finnish/Swedish population and no significant differences were obtained between the genotypes. It can be concluded that the Pro/Leu genetic variation does not appear to compromise the defense against oxidative stress in red blood cells nor to be associated with stroke.

The future of genetic analysis of neurological disorders

Molecular genetic analysis has allowed the elucidation of the etiology of many single-gene, neurodegenerative syndromes. However, as yet, it has had little direct impact on our understanding of the etiology in cases with more complex modes of inheritance. With the completion of the sequence of the human genome, it should be possible to start to attack these more complex problems. In this article, we review the genetic methods that may be used to dissect the etiologies of these diseases and outline what types of clinical samples will be needed for this quest.