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Novel approaches to plant drug discovery based on high throughput pharmacological screening and genetic manipulation.

Plants are potentially important for novel therapeutic drug leads, but the slowness of conventional methods for investigation of plants limits enthusiasm in the pharmaceutical industry. To overcome some of the drawbacks, we have applied high throughput pharmacological screening (HTPS) to crude plant extracts. Using a "differential smart screen", (DSS) the spectrum of activity contained in a crude extract is measured at several closely related receptor subtypes. This spectrum is then compared to that of known compounds. A unique spectrum suggests that the extract merits further investigation. Evaluation of species and environmental libraries of whole plants has demonstrated the value of this approach for rapid prioritization of plants for investigation. In addition, genomic and genetic manipulation of plants and plant cell cultures can increase the value of DSS. For example, the whole genomic potential of a plant species for biodiversity can be accessed by using gain of function mutations to generate a "functional genomics library" of mutant clonal cultures, and the bioactivity of these cultures tested by DSS. Clones that overproduce activity differing from the wild-type plant can be identified in this way. This "Natural Products Genomics" (NPG) strategy is limited by the massive numbers of clonal cultures that are required to cover all possible gain-of-function mutations. The rapidity and efficiency of this process can be improved by using transgenic plants expressing appropriate mammalian proteins. These may be designed to make the plant cell resemble a human cell for a specific form of toxicity. Now, "unnatural selection" of resistant mutant clones can be used to provide a sub-population potentially enriched in useful compounds. Alternatively, transgenic plant cells can be used for "in situ screening" in which a mammalian receptor protein, linked to a reporter construct, such as green fluorescent protein, is expressed. Clonal cultures that produce ligands for this receptor can now be rapidly identified visually in an ultra-HTPS. Overall, our aim is to use pharmacological screening, together with functional genomic approaches, to make plant drug discovery competitive with combinatorial chemistry.

Drug Evaluation, Preclinical↗

Rapid diagnosis of triploidy of maternal origin using fluorescent PCR and DNA fragment analysis in the third trimester of pregnancy.

OBJECTIVES: Triploidy is a common cause of spontaneous abortion in the very early stages of pregnancy. It is very rare for a prenatal diagnostic center to discover triploidy in the third trimester of pregnancy. A pregnant woman in the third trimester was referred to our genetic counselling clinic because of abnormal ultrasound findings. We planned to test for the most common chromosomal abnormalities. METHODS: We performed ultrasound examination, chorionic villus sampling, karyotyping and fluorescent-polymerase chain reaction (F-PCR) and fragment analysis. RESULTS: We diagnosed a 69,XXX karyotype fetus in the 31st week of gestation, based on a short tandem repeat (STR) pattern typical for triploidy, which was confirmed by karyotyping. The comparison of the fetal and parental STR patterns showed maternal origin of the extra haploid chromosome set. CONCLUSIONS: STR analysis of fluorescent-PCR and DNA fragment analysis is a rapid and reliable alternative to karyotyping for detection of certain aneuploidies. The method is also suitable for the determination of the origin of the extra chromosome set.

Abortion, Eugenic↗

Molecular genetic advances in fragile X syndrome.

The fragile X syndrome is recognized as the most common heritable condition resulting in mental retardation. The disabilities are substantial, and therefore early detection is mandatory to assist with reproductive counseling of families in which the fragile X syndrome has occurred. Highly accurate, direct DNA diagnostic testing can now be performed to diagnose the fragile X syndrome without the involvement of individual family members, as was the situation with the use of DNA linkage analysis. Such testing is rapidly becoming a standard diagnostic tool for screening of individuals with suspected fragile X syndrome, of potential unaffected carriers, and of patients with undefined mental retardation. Fragile X testing should be considered for all children with developmental delay of unknown cause. Autistic children will occasionally be found to have mutations in FMR-1. Detection of affected individuals will allow early intervention for these individuals and will assist families with their reproductive decisions (including prevention) in subsequent offspring. An understanding of the molecular genetics of fragile X syndrome has resulted in the resolution of the Sherman paradox and is the first molecular characterization of a chromosomal fragile site, a finding that almost certainly will be important in understanding the cause of chromosomal rearrangements involving fragile sites. In addition, molecular details of the fragile X mutations have yielded insight into "heritable unstable elements," of which the fragile X chromosome is one of the first characterized examples. Thus a similar molecular mechanism involving a trinucleotide repeat may explain the genetics of myotonic dystrophy and spinal-bulbar muscular atrophy (Kennedy disease); it seems reasonable to assume that other genetic diseases also may result from disruption of genes by inherited unstable elements.

DNA↗

Cosegregation of porcine malignant hyperthermia and a probable causal mutation in the skeletal muscle ryanodine receptor gene in backcross families.

A study of the inheritance of malignant hyperthermia (MH) in the British Landrace breed revealed the same substitution of T for C at nucleotide 1843 in the ryanodine receptor (RYR1) gene that was previously shown to be correlated with MG in five Canadian swine breeds. Cosegregation of the mutation with MH in 338 informative meioses led to a lod score of 101.75 for linkage at Omax = 0.0. The substitution was also associated with a HinPI- BanII+ RsaI- haplotype in this breed, as in the five breeds tested earlier, suggesting its origin in a common founder animal. DNA-based detection of the MH status in 376 MH-susceptible heterozygous (N/n) and homozygous (n/n) pigs was shown to be accurate, eliminating the 5% diagnostic error that is associated with the halothane challenge test and flanking marker haplotyping procedures in current diagnostic use. These results strongly support the view that the substitution of T for C at nucleotide 1843 is the causative mutation in porcine MH and demonstrate the feasibility of rapid, accurate, noninvasive, large-scale testing for porcine MH status using DNA-based tests for the mutation.

Animals↗

Genetic evidence for the role of GDP-mannose in plant ascorbic acid (vitamin C) biosynthesis.

Vitamin C (L-ascorbic acid; AsA) acts as a potent antioxidant and cellular reductant in plants and animals. AsA has long been known to have many critical physiological roles in plants, yet its biosynthesis is only currently being defined. A pathway for AsA biosynthesis that features GDP-mannose and L-galactose has recently been proposed for plants. We have isolated a collection of AsA-deficient mutants of Arabidopsis thaliana that are valuable tools for testing of an AsA biosynthetic pathway. The best-characterized of these mutants (vtc1) contains approximately 25% of wild-type AsA and is defective in AsA biosynthesis. By using a combination of biochemical, molecular, and genetic techniques, we have demonstrated that the VTC1 locus encodes a GDP-mannose pyrophosphorylase (mannose-1-P guanyltransferase). This enzyme provides GDP-mannose, which is used for cell wall carbohydrate biosynthesis and protein glycosylation as well as for AsA biosynthesis. In addition to genetically defining the first locus involved in AsA biosynthesis, this work highlights the power of using traditional mutagenesis techniques coupled with the Arabidopsis Genome Initiative to rapidly clone physiologically important genes.

Amino Acid Sequence↗

Rapid and repeated evolution of increased competitive ability in a global invader.

Rapid adaptive evolution can increase the competitive ability of invasive species in their non-native ranges. However, whether this increase is a general response and what drives it remain uncertain because the evidence is largely based on studies with limited sampling, inadequate consideration of population co-ancestry, and oversimplified estimates of competitive ability. We conduct a large-scale glasshouse experiment testing the effects of competition and drought on 100 native and 165 non-native populations of Erigeron canadensis, all genotyped to account for co-ancestry. Plants from non-native populations are significantly more competitive against other species than the conspecifics from native populations under both mesic and dry conditions. Genetic clustering indicates that the rapid evolution of competitive ability occurs independently in two out of four clusters in the non-native range. This advantage is present only during interspecific interactions and is absent during intraspecific competition. Repeated evolution of increased competitive ability suggests that adaptation following introduction can reshape species interactions and promote invasion success, even under future drought conditions, highlighting the importance of rapid evolution in determining the ecological impacts of invasive plants.

Biological Evolution↗

The use of genetic markers for personal identification and the analysis of family relationships.

In 1984 a family of hypervariable sequences was discovered in human DNA which when used as DNA probes provided a sufficiently informative sampling of an individual's DNA as to uniquely identify each person (except for genetically identical twins). Termed a DNA 'fingerprint', the DNA pattern revealed by the probes said nothing about characteristics of age, sex, height, or colour but immediately met a long-unanswered need for certain definition in the establishment of identity and family relationships. DNA tests are now a key tool in forensic investigations and are rapidly gaining acceptance in courts around the world. DNA tests are also replacing conventional serology for the resolution of paternity disputes. The definition provided by the DNA tests was possibly most urgently sought by immigration families in the UK who were separated by an inability to prove their family ties. The interest from the public has been overwhelming and Cellmark Diagnostics have already completed tests on over 15,000 individuals in the UK since opening in June 1987. Media coverage has been extensive, and continues to view DNA tests as beneficial; this, coupled with its commercial potential, suggests that DNA technology is here to stay.

Consanguinity↗

Polyadenylation polymorphism in the acetyltransferase 1 gene (NAT1) increases risk of colorectal cancer.

Exposure to carcinogens present in the diet, cigarette smoke, or the environment may be associated with increased risk of colorectal cancer. Aromatic amines (aryl- and heterocyclic) are a class of carcinogens that are important in these exposures. These compounds can be N- or O-acetylated by the NAT1 or NAT2 enzymes, resulting in activation or in some cases detoxification. Recent studies have shown that both NAT2 and NAT1 genes exhibit variation in human populations and that rapid acetylation by the NAT2 enzyme may be a risk factor for colorectal cancer. In this study we have analyzed for genetic polymorphism in both NAT1 and NAT2 in a group of 202 colorectal cancer patients and 112 control subjects from Staffordshire, England. We find significantly increased risk (odds ratio, 1.9; 95% confidence interval, 1.2-3.2; P = 0.009) associated with the NAT1*10 allele of NAT1, an allele that contains a variant polyadenylation signal. Individuals with higher stage tumors (Duke's C) were more likely to inherit this variant allele (odds ratio, 2.5; 95% confidence interval, 1.3-4.7; P = 0.005). In contrast, rapid acetylation genotypes of NAT2 were not a significant risk factor in this English population. However, we found that the risk associated with the NAT1 variant allele (NAT1*10) was most apparent among NAT2 rapid acetylators (odds ratio, 2.8; 95% confidence interval, 1.4-5.7; P = 0.003), suggesting a possible gene-gene interaction between NAT1 and NAT2 (test for interaction; P = 0.12). This is the first study to test for cancer risk associated with the NAT1 gene, and these positive findings suggest that NAT1 alleles may be important genetic determinents of colorectal cancer risk.

Adenocarcinoma↗

Quintuplex PCR-amplification of microsatellites.

We tested the potential usefulness of quintuplex PCR-amplification of STRs (D16S537, D8S320, FGA, D11S554 and THO1) for paternity testing, first by constructing 20 false family trios, each with a non-biological father, to estimate the actual exclusion rate, and next by a retrospective study of 20 paternity cases which had been previously tested by RFLP analysis and typing of conventional genetic markers. The five STR loci have a combined average exclusion power of 99.8%. The forensic efficiency values for four of the five STRs were based on typing of a Japanese population of 300 individuals. The observed rate of exclusion was in close agreement with the expected rate for the Japanese population. In 12 of the 20 cases, paternity was not excludable by any of the loci. The probability of paternity calculated for the alleged father was > 99% in the inclusion cases. In the remaining 8 cases, paternity was excluded by at least 2 of the STR loci. The results of STR typing agreed with the data from RFLP analysis and conventional genetic typing. Taking advantage of five STRs sharing AA in the tetranucleotide repeats (AAAG or AATG), we detected PCR products simultaneously with a digoxigenin-labeled (AAAG)6 oligonucleotide probe after sequencing-gel electrophoresis. The quintuplex PCR-amplification of STRs is a rapid and efficient method for paternity testing and individual identification.

Base Sequence↗

Rapid and efficient resolution of parentage by amplification of short tandem repeats.

Short tandem repeat (STR) loci are highly informative polymorphic loci that are gaining popularity for identity testing. We have conducted parentage testing by using nine STR loci on 50 paternity trios that had been previously tested using VNTR loci. These nine unlinked STR loci are amplified in three multiplex reactions and, when examined for genetic informativeness, provide a combined average power of exclusion of 99.73% (Caucasian data). The informative value of the selected loci is based on extensive STR typing of four racial/ethnic populations. In 37 of the 50 cases, paternity could not be excluded by any of the loci. In the remaining 13 cases, paternity was excluded by at least two of the STR markers. The probability of paternity calculated for the alleged father of each matching trio was > 99% in 36 of the 37 inclusion cases. All data agreed with the results reported using VNTR loci and conventional Southern technology. Our studies validate the use of DNA typing with STR loci for parentage testing, thus providing an accurate, highly sensitive, and rapid assay.

Alleles↗

A rapid PCR-based test for the endogenous viral element ev3 of chickens.

A short fragment of chicken genomic DNA encompassing the insertion site of the endogenous avian leucosis viral element ev3 was isolated using the inverse polymerase chain reaction (inverse PCR) technique. The nucleotide sequence of the unoccupied site was used to design PCR primers that can be used to unambiguously determine the genetic status of any chicken, with respect to ev3. Screening of a small number of individuals from exotic breeds of chickens suggested that the frequency of ev3 is highly variable. The ev3 integration site shows a high degree of sequence homology with the macrophage-specific tyrosine kinase gene, bmk, in mice.

Animals↗

Genetic diagnosis of factor V Leiden using heteroduplex technology.

A new genetic test has been developed for detection of the mutation known as factor V Leiden. The test employs heteroduplex technology and comprises a single PCR reaction followed immediately by PCR product analysis. It therefore represents the minimum practical route from blood/tissue sample to genetic result. A cohort of 100 patients with a history of thrombosis have been screened using both the new heteroduplex test and a previously described PCR-restriction endonuclease test. Results gave 100% correlation: normals 75 (75%), heterozygotes 24 (24%) and homozygotes 1 (1%). The heteroduplex test has been shown to give straightforward diagnosis in three different analytical systems: standard polyacrylamide gel electrophoresis (PAGE), mini-gel PAGE and capillary electrophoresis. The latter system is semiautomated, therefore rapid through-put of large sample numbers is now possible.

Factor V↗

Monitoring standards for molecular genetic testing in the United Kingdom, the Netherlands, and Ireland.

Molecular genetic techniques have entered many areas of clinical practice. Public expectations from this technology are understandably high. To maintain confidence in this technology, laboratories must implement the highest standards of quality assurance (QA). External quality assessment (EQA) is recognized as an essential component of QA. The United Kingdom National External Quality Assessment Service (UKNEQAS) for Molecular Genetics, first set up in 1991, is currently the longest provider of EQA to molecular genetic testing laboratories in the UK, The Netherlands, and Ireland. Errors in the scheme are sporadic events. However, evidence from this and other EQA schemes suggests that a residual error rate persists, which should be taken into account in clinical practice. This EQA scheme has evolved from the respective scientific bodies of the constituent countries and retains a strong emphasis on collective peer review. It is essential that the steps taken to ensure quality in this rapidly expanding field are clear and transparent to participants and public alike. We describe the procedures developed and the governance imposed to monitor and improve analytical and reporting standards in participant laboratories and we compare our experiences with those of equivalent EQA services in the United States.

Cytogenetic Analysis↗

Characterization of a cosmid library from flow-sorted chromosomes 11.

A cosmid library specific for human chromosome 11 has been constructed from flow-sorted chromosomes. The flow-purified chromosomes were prepared from the hamster/human hybrid line J1 which contains chromosome 11 as the only human chromosome. Individual clones were sampled in 187 microtitre plates, resulting in a total of 17,952 colonies. Hybridization analysis revealed that 83.7% of these clones were of human and 10.4% of hamster origin. The average insert size was estimated at 33.6 kb, and only 2.4% of insert fragments appear to be rearranged. This should result in 494,487 kb of cloned human DNA representing 3.5 chromosome 11 equivalents. We have prepared high-density nylon membranes of the arrayed library containing 1,536 single colonies per filter. We have demonstrated the usefulness of the library in the molecular genetic analysis of human chromosome 11 by testing for the presence of possibly polymorphic simple repeat motifs, by identifying cosmids that contain inserts from the telomeric ends of chromosome 11 and by assessing the potential of the library for rapid chromosome walking.

Animals↗

Diagnosing Friedreich's ataxia.

Clinical diagnosis is still of the utmost importance and following our review of cases diagnosed using the strict criteria, 100% were homozygous for the expansion. However, now that there is a relatively simple direct genetic test, the diagnosis can be considered in more unusual cases. Genetic testing has been shown to be of value in establishing the correct diagnosis and in directing the appropriate screening tests, including cardiological assessment and blood sugar estimation. Perhaps the most interesting development following identification of the gene is the rapid progress in our understanding of the protein. If, as seems likely, it turns out to be a mitochondrial protein involved in iron transport, it gives cause for hope of effective treatment.

Adolescent↗

[The human genome project as a scientific background of preventive medicine].

Conspicuous achievements in the Human Genome Project have already found spectacular implementation in both basic research and practice. The Human Genome Diversity, Functional Genomics, and numerous Social Programmes are under way and they are rapidly expanding the scientific area induced by the Human Genome Project. Its practical implication is mainly confined to molecular medicine and to its quickly growing area Predictive (Preventive) Medicine. The paper briefly considers the existing concepts of molecular genetic tests of "predisposition" genes, including such groups as "environmental" genes and "trigger"-genes to detect subjects highly susceptible to different common multifactorial diseases and the expediency for testing the genes whose mutations cause diseases showing their manifestations at the late stage. Evidence is provided for that there is a progressive increase in population, family, and personal predisposition gene DNA databanks. There is need for close interaction between researchers and all strata of society, including the clergy, governments, political parties, etc. in order to optimize perception of scientific achievements of modern genetics and their effective used for the welfare of mankind.

DNA↗

Inactivation of imprinted genes induced by cellular stress and tumorigenesis.

Cellular proliferation under stressful conditions may result in permanent genetic and epigenetic changes. Using primary mouse embryonic fibroblasts, we have completed a screening test to identify gene expression changes triggered when cells proliferate under stress. In this manner, we have discovered a novel phenomenon that consists of the rapid and coordinated silencing of genes subject to imprinting, including Cdkn1c, Igf2, H19, Ndn1, Grb10, and Meg3. This generalized silencing of imprinted genes is independent of the stress-responsive tumor suppressors p53, p19(Arf), and p16(Ink4a), and it is also independent of the oxidative culture conditions and the stress response known as "mouse embryonic fibroblast senescence". In the case of Cdkn1c and H19, their silencing is associated with unscheduled de novo methylation of the normally expressed allele at their corresponding CpG island promoters, thus resulting in biallelic methylation. Finally, we provide evidence for frequent de novo methylation of Cdkn1c in a variety of murine cancer types. Altogether, our data support the concept that silencing of imprinted genes, including methylation of Cdkn1c, constitutes an epigenetic signature of cellular stress and tumorigenesis.

Animals↗

Clinical evaluation and emergency management of inborn errors of metabolism presenting in the newborn.

Close to 500 biochemically diverse genetic metabolic disorders have been identified. Despite their diversity, these diseases share a number of features. First, the majority of patients with an inborn error present clinically with one of five general phenotypes; acute encephalopathy, progressive encephalopathy, primary muscle disease, primary liver disease or primary renal disease. Encephalopathy is by far the most common clinical manifestation of inborn errors of metabolism, and may be acute, intermittent, chronic (progressive), or even non-progressive. Although the five major phenotypes are a useful clinical guide, other clinical presentations of course occur, and some are virtually specific to a single disease or group of disorders. Second, almost all inborn errors are recessive in inheritance, and most of these conditions map to one of the 22 autosomes. Third, specific and effective treatment of inborn errors is often made possible by our understanding of their biochemical bases. Because inborn errors are genetic diseases, families with affected children can be made aware of the risk of recurrence, through genetic counselling. In many instances, presymptomatic treatment of affected relatives, carrier testing, and prenatal diagnosis can be offered. The types of inborn errors and their mode of presentation in the newborn are discussed, along with a schema permitting their rapid diagnosis. The principles of emergency and long term management are also discussed, with particular emphasis on those disorders that present in the newborn period with an acute encephalopathy, the so-called "small molecule" disorders.

Acute Disease↗