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Standardization of PCR amplification for fragile X trinucleotide repeat measurements.

To provide the clinical diagnostics community with accurate protocols and measurements for the detection of genetic disorders, we have established a quantitative measurement program for trinucleotide repeats associated with human disease. In this study, we have focused on the triplet repeat associated with fragile X syndrome. Five cell lines obtained from the Coriell Cell Repository were analyzed after polymerase chain reaction (PCR) amplification and size separation. These cell lines were reported to contain CGG repeat elements (ranging from 29 to 110 repeats). Our initial measurements focused on measurement variability: (a) between slab-PAGE and capillary (CE) separation systems (b) interlane variability (slab-PAGE) (c) intergel variability, and (d) variability associated with amplification. Samples were run in triplicate for all measurements, and the analysis performed using Gene Scan analysis software. The repeat sizes were verified by DNA sequence analyzes. The standard deviations for interlane measurements in slab-gels ranged from 0.05 to 0.35. There was also little variation in size measurements performed on different gels and among PCR amplifications. The CGG repeat measurements performed by capillary electrophoresis were more precise, with standard deviations ranging from 0.02 to 0.29. The slab-PAGE and CE size measurements were in agreement except for the pre-mutation alleles, which yielded significantly smaller sizes by CE.

Alleles↗

Cardiovascular risk in the Asia-Pacific region from a nutrition and metabolic point of view: abdominal obesity.

The level of obesity within the Pacific Islands is extremely high and so is the prevalence of weight-related morbidity and mortality. In contrast, the level of obesity, as defined by the standard WHO classification, remains relatively low in most Asian countries, yet rates of obesity-related disease, such as diabetes and cardiovascular disease are increasing rapidly. Many Asian races appear to be susceptible to the development of excessive abdominal fatness, even at low levels of body mass index (BMI). In addition, the health consequences of weight gain appear to occur at much lower levels of BMI and are more intense than in those of European origin. The exact reasons for these ethnic variations in the development of coronary heart disease (CHD) remain unclear. It is likely that genetic differences contribute to this variation in CHD risk, but different dietary and physical activity patterns may also play a role. The advent of modernisation has resulted in marked changes in the level of physical activity and the food supply available throughout the Asia-Pacific region. There has been a shift towards higher intakes of fats (particularly animal fats and vegetable oils) and sugars. Urbanisation and occupational restructuring have reduced daily physical activity levels. As a result, the population mean BMI and consequent illness is increasing in many countries within the region. Recent studies have shown that infants who were undernourished in utero and then born small have a greater risk of developing abdominal obesity and related morbidity as adults. As undernutrition coexists with overnutrition throughout the Asia-Pacific, focusing efforts to improve nutrition during pregnancy will need to be combined with programs to prevent weight gain in adults if CHD and other chronic diseases are to be effectively tackled in the region.

Abdomen↗

Marker-assisted screening of resistance to fire blight, powdery mildew, and apple scab in local apple varieties from Uzbekistan.

Apple (Malus domestica Borkh.) is one of the most economically important fruit crops worldwide; however, its production is severely constrained by major diseases, including fire blight, powdery mildew, and apple scab. Breeding disease-resistant cultivars represents a sustainable alternative to chemical control, particularly through the effective utilization of local germplasm resources from Central Asia. This study aimed to evaluate the presence and distribution of resistance-associated alleles in local apple varieties from Uzbekistan using polymorphic DNA markers. A collection of local apple accessions was screened to identify markers linked to resistance against fire blight, powdery mildew, and apple scab. The analysis revealed substantial genetic variation in resistance gene combinations among the studied varieties. The fire blight-associated marker AE10-375 was detected in 79.8% of the accessions. For powdery mildew resistance, 75.2% of the varieties carried resistance alleles corresponding to both Pl1 and Pl2 genes. Screening for apple scab resistance demonstrated that Vfa2, Vfa1, and Rvi6 were the most prevalent genes, with Vfa2 detected in 95.4% of the accessions. Regional analysis indicated that accessions from Karakalpakstan exhibited the highest proportion of genotypes harboring markers associated with resistance to multiple diseases. Six local varieties-Atlas olma, Turkish, Xuboni, Krasniy jeleznyak, Shoyi olma, and Besh barmoq-were identified as carrying resistance-associated markers for all three diseases. These findings demonstrate that local apple germplasm from Uzbekistan represents a valuable genetic resource for resistance to economically important diseases. The identified genotypes provide promising donor material for breeding programs aimed at developing cultivars with durable, broad-spectrum resistance while reducing reliance on chemical control strategies.

Malus↗

Analytical evaluation of the Bio-Rad variant II automated HbA(1C) analyzer.

OBJECTIVES: To evaluate the analytical performance of the Bio-Rad Variant II HbA(1C) analyzer (a completely automated system for the quantification of glycohemoglobin [HbA(1C)] in blood). DESIGN AND METHODS: The analytical parameters of precision, linearity and analytical range were assessed and HbA(1C) results from the Variant II were compared to HbA(1C) results from the Bio-Rad Variant (a method certified by the National Glycohemoglobin Standardization Program). The effect of a variety of hemoglobin variants on HbA(1C) obtained on the system was investigated. RESULTS: Total imprecision was less than 5% and the results compared well with those from an established method. The method has a wide analytical range with no carryover between specimens. CONCLUSION: The HbA(1C) method on the Variant II gives acceptable analytical performance.

Automation↗

Molecular genetics and role in infection of environmentally regulated lipopolysaccharide expression.

Lipopolysaccharides (LPSs) from different Gram-negative bacteria are structurally distinct. Even closely related serovars of single bacterial species may possess different LPS molecules. Further variability may then be superimposed on this ground-state structural diversity as a result of variable expression of other LPS structures. This variable expression is due in some cases to high-frequency, reversible, random "on-off" switching of genes required for biosynthesis of particular LPS structures. In other cases differential expression of LPS biosynthesis genes may be part of a programmed response to environmental stimuli, which may occur as adaptations by pathogenic bacteria to changing environments within the host during the course of infection.

Antigenic Variation↗

Biological and cultural sources of familial resemblance in plasma lipids: a comparison between North America and Israel--the Lipid Research Clinics Program.

Heterogeneity in determinants of familial resemblance of lipid and lipoprotein levels between populations in North America and Israel was investigated using path analysis. A common protocol, identical measurement techniques, and the same statistical procedures were used in the two samples. Both genetic (h2) and cultural (c2) determinants of inheritance were significant for all lipid variables in the two studies. Genetic and cultural heritability of total cholesterol (h2 = 0.61, c2 = 0.02), low-density lipoprotein cholesterol (h2 = 0.59, c2 = 0.02), and high-density lipoprotein cholesterol (h2 = 0.55, c2 = 0.06) did not differ significantly between North America and Israel, while there was a significant difference for triglyceride (h2 = 0.41, c2 = 0.07 in North America; h2 = 0.61, c2 = 0.05 in Israel). Secondary parameters of the path model describing intrafamilial environmental relationships differed between the two countries. In particular, there was a higher correlation between marital environments in Israel for all traits except triglyceride, and a larger effect of father's environment on offspring's environment in Israel for all traits. Within both populations, variation of plasma lipids and lipoproteins was mostly explained by genetic factors and random unmeasured environmental factors. The contribution of common family environment was found to be small, though statistically significant. This is probably due to homogeneity of the distribution of familial environmental determinants within both countries.

Cholesterol↗

Mitochondrial DNA Diversity in Three Populations of the Giant Tiger Shrimp Penaeus monodon.

: Mitochondrial DNA restriction fragment length polymorphism (mtDNA-RFLP) was utilized for determination of genetic variation and population structure in Penaeus monodon collected from Satun (the Andaman Sea) and Surat and Trat (the Gulf of Thailand). Twenty-eight composite haplotypes were generated from 52 restriction profiles of P. monodon mtDNA digested with 11 restriction endonucleases. The size of the entire P. monodon mitochondrial genome was estimated to be 15.913 +/- 0.177 kb. The average haplotype diversity in P. monodon was 0.864, whereas the mean nucleotide diversity within populations was 2.51%, 2.22%, and 1.91% for Satun, Trat, and Surat, respectively. Geographic heterogeneity analysis indicated population differentiation between P. monodon from the Andaman Sea and P. monodon from the Gulf of Thailand (p <.0001). On the basis of the high genetic diversity level of P. monodon in Thailand, the Satun and Trat P. monodon populations from the west and east of the pennisula were selected to be founder stocks in our selective breeding program.

Journal Article↗

GeneTRACE-reconstruction of gene content of ancestral species.

While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GENETRACE, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the method was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree.

Algorithms↗

Dried blood spots collected on filter paper: an international resource for the diagnosis and genetic characterization of human immunodeficiency virus type-1.

The collection of dried blood spots (DBS) on filter paper provides a powerful approach for the development of large-scale, population-based screening programs. DBS methods are particularly valuable in developing countries and isolated rural regions where resources are limited. Large numbers of field specimens can be economically collected and shipped to centralized reference laboratories for genetic and (or) serological analysis. Alternatively, the dried blood can be stored and used as an archival resource to rapidly establish the frequency and distribution of newly recognized mutations, confirm patient identity or track the origins and emergence of newly identified pathogens. In this report, we describe how PCR-based technologies are beginning to interface with international screening programmes for the diagnosis and genetic characterization of human immunodeficiency virus type 1 (HIV-1). In particular, we review recent progress using DBS specimens to resolve the HIV-1 infection status of neonates, monitor the genetic evolution of HIV-1 during early infancy and establish a sentinel surveillance system for the systematic monitoring of HIV-1 genetic variation in Asia.

AIDS Serodiagnosis↗

Complete typing of the HLA region in families. III. Analysis of responses in the primed lymphocyte test (PLT).

LCA, a rapid and efficient computer method to allocate blastogenic responses to positive and negative clusters, is described. The method involves the selection of a partition level for an ordered array of values, such that the resulting two clusters have minimal "within-cluster" variances. Individuals to whom the program assigned the same two HLA-D antigens were MLC-identical (cluster 0) in 50% of the cases. This proportion was lower for HLA-D-identical pairs that typed for Dw4 and/or Dw7, indicating that these antigens are less well defined than the rest. PLTs were less efficient than HTCs in HLA-D typing due to the induction of extra (non-HLA-D determined) responses in the higher cluster.

Computers↗

Gene regulation and host adaptation mechanisms in Candida albicans.

The yeast Candida albicans is a harmless member of the normal microflora on the mucosal surfaces of most healthy persons, but it can cause severe opportunistic infections in immunosuppressed patients. To become a successful human commensal and pathogen, C. albicans has evolved host adaptation mechanisms on different levels. The regulated expression of virulence and other genes in response to environmental signals allows an optimal adaptation to new host niches during the course of an infection. In addition, C. albicans is able to switch between different cell types in a reversible and apparently random fashion. Phenotypic switching involves the coordinated regulation of phase-specific genes, and the resulting generation of selected, pre-programmed cell types may represent an additional strategy to adapt to certain host environments. Finally, C. albicans produces genetically altered variants at a high rate. This microevolution ensures survival when the pathogen encounters new adverse conditions, as exemplified by the development of stable drug-resistant variants under the selection pressure caused by antimycotic therapy. Thus, rather than the possession of single dominant virulence factors, it is its remarkable versatility that makes C. albicans the most important fungal pathogen of humans.

Adaptation, Physiological↗

Telomere DNA sequences and the concept of ontogenetic reserve cells.

Dynamics of telomere sequences are considered in normal and immortalized cells. Immortalized cells are suggested to be derived mainly from a special subpopulation of ontogenetic reserve cells. Their epigenetic program consists of autoregeneration during external stimulus for genome reorganization and corresponding appearance of genetic variants of cells. It is suggested that cells surviving the crisis stage contain a special signal sequence integrated into telomere DNA. Its elimination during shortening of DNA telomere sequences in dividing ontogenetic reserve cells is a signal for the cooperative transition of chromatin into a new steady state that corresponds to the epigenotype of immortalized cells. Localization of telomere DNA sequences in intrachromosomal "hot spots" reflects phylogenetic rearrangement of the genome.

Animals↗

Molecular Action and Clinical Relevance of Aromatase Inhibitors.

BREAST CANCER: HIGH PREVALENCE AND RISING INCIDENCE: Breast cancer is the most common form of cancer among women in Europe, North and South America and Australasia; approximately 1 in 10 women in Western countries will develop breast cancer during their lifetime. It is estimated that the disease will affect five million women worldwide over the next decade, and the incidence of breast cancer is increasing on average by about 1% per year in industrialized countries and at a greater rate in developing countries. COMPLEX ETIOLOGY: Although the specific etiology of breast cancer remains unknown, a number of factors are recognized which increase a woman's risk of developing the disease. Genetic predisposition, or family history of breast cancer, is known to be responsible for 5% of all cases. However, the variation in incidence throughout populations, and changes relating to population migration and adoption of altered lifestyles, all point to the critical importance of nongenetic determinants. Such factors include early menarche, late menopause, late age at birth of first child or nulliparity, a history of benign breast disease, and diet. There is also evidence that hormones play a major role in the etiology of breast cancer, with the risk of developing malignancies related to the cumulative exposure of the breast to estrogen and progesterone, which stimulate the growth of tumor cells. TREATMENT FOR EARLY BREAST CANCER: SURGERY -/+ ADJUVANT THERAPY: At the time of diagnosis, approximately 50% of patients will be diagnosed with early breast cancer. This proportion is increasing as a consequence of the introduction of early detection programs. Surgery remains the primary treatment for early breast cancer, and the frequency of radical mastectomy has been replaced by breast conserving surgery. After surgery, other therapeutic modalities such as radiation, chemotherapy or endocrine therapy may be given in the adjuvant setting. Surgical cure rates vary for patients with early breast cancer; the US figure is approximately 40%, and there are no definitive means to predict those who will be cured and those who will have recurrent disease. As a result, following primary surgical treatment, adjuvant therapy is usually recommended to destroy any remaining cancer cells at the primary site, to control micrometastases and to prolong disease-free survival, with the ultimate aim of providing an overall survival benefit. Upon disease recurrence in the remaining 60% of patients, endocrine therapy and chemotherapy represent the two general classes of treatment. One of the principle decisions to be taken in advanced breast cancer is which therapy to select in order to maximize patient benefit. The choice is largely dependent upon prognostic factors and whether the patient is pre- or postmenopausal. ENDOCRINE THERAPY OR CHEMOTHERAPY IN ADVANCED BREAST CANCER: Unlike chemotherapy, endocrine therapy is not cytotoxic and is therefore better tolerated by the patient. A recent study comparing therapy for prognostically different groups showed that patients benefiting most from the use of sequential endocrine agents are those regarded as low risk. The preferred sequence of treatment has been suggested to be tamoxifen followed by selective aromatase inhibitor and then a progestin. ENDOCRINES AND ENZYMES OFFER NEW TREATMENTS FOR ADVANCED BREAST CANCER: ESTROGEN-DRIVEN BREAST CANCER: Since 1896, when Sir George Beatson demonstrated that ovariectomy induced regression of mammary tumors in women, the aim of endocrine breast cancer therapy has been to selectively deprive the body of estrogen. Ovariectomy accomplished this by removing the gland that is the predominant source of estrogens in premenopausal women. Since the avoidance of such surgery is preferable, emphasis is devoted to the pharmacological inhibitors of estrogen production. ENDOCRINE PATHWAY REVEALS "ACHILLES' HEEL": Like other steroid hormones, the two circulating estrogens-estrone and estradiol-are produced from cholesterol. Inhibiting the enzymes that are involved at earlier steps in the branching pathway of steroidogenesis could have an undesirable impact on the production of other physiologically important hormones such as aldosterone and cortisol. Since aromatase catalyzes the last step in estrogen production, it makes an ideal target for the development of selective and potent inhibitors (Fig. 1). STRUCTURE OF AROMATASE REVEALS SECRETS OF SELECTIVE INHIBITION: Aromatase is a cytochrome P450 enzyme, with both an iron-containing and a steroid-binding site. The substrate, androstenedione, sits in the enzyme's steroid-binding site, that site which otherwise catalyzes the formation of estrogen. From this structural relationship, there are, therefore, two reasonable ways to inhibit aromatase: * by occupying the steroid-binding site of the enzyme with a compound such as formestane (Lentaron&reg;), or * by binding the iron with nitrogen-containing compounds such as aminoglutethimide (Orimeten&reg;), the oldest aromatase inhibitor. AROMATASE INHIBITORS: STEROIDAL AND NON-STEROIDAL: Formestane (Lentaron&reg;) is the only commercially available steroidal compound which inhibits aromatase and must be administered parenterally. Other new aromatase inhibitors such as fadrozole (Afema&reg;) and letrozole (Femara&reg;) are orally active nitrogen-containing compounds that bind the heme iron of aromatase. AMINOGLUTETHIMIDE VERSUS LETROZOLE: OLD VERSUS NEW: Although aminoglutethimide has long been used to treat advanced breast cancer, its aromatase inhibition is not selective. Consequently, aminoglutethimide also binds to and thereby inhibits several other cytochrome P450 enzymes in the steroidogenesis pathway. An ideal aromatase inhibitor would fit the catalytic site of aromatase optimally and would thus interact only with aromatase. The affinity of letrozole (Femara&reg;) for the heme group of aromatase makes it a selective and potent inhibitor (Fig. 2). In fact, studies show that Femara&reg; has little effect on the other adrenal steroids, and is the most selective aromatase inhibitor available today.

Journal Article↗

Use of the G8 probe in predicting risk of Huntington disease.

Discovery of the linkage between the G8 probe and the gene for Huntington disease (HD) in families of varying ethnic origin, age-of-onset characteristics, and neurological symptomatology, makes it possible to use the G8 marker for presymptomatic testing of at-risk individuals. Risk estimates for such situations were calculated, using the program LIPED, with different G8 haplotype frequencies, different age-of-onset distributions, and varying amounts of family information. In the presence of untyped relatives, the resulting risk estimates can be extremely sensitive to G8 haplotype frequencies, and the higher risk was seen in individuals carrying rare haplotypes. Including haplotype information on distant relatives can also lead to greater variation in risk estimates. Changing the age-of-onset distribution had only a minimal effect on estimated risks; the largest effect was seen when informative at-risk sibs of the consultand were in their forties.

Adult↗

PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change.

BACKGROUND: Phylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic change represented by a tree and are commonly compared with other measures of mutation to investigate the substitutional processes or the goodness of fit of a tree to the raw data. Up until now no universal tool has been available for calculating patristic distances and correlating them with other genetic distance measures. RESULTS: PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs. CONCLUSION: The software overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses. It is available at http://biojanus.anu.edu.au/programs/ and requires the Java runtime environment.

Decision Trees↗

SPA: a probabilistic algorithm for spliced alignment.

Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approach to cDNA-to-genome alignment. Gene structures are assigned prior probabilities based on the lengths of their introns and exons, and based on the sequences at their splice boundaries. A likelihood model for sequencing errors takes into account the rates at which misincorporation, as well as insertions and deletions of different lengths, occurs during sequencing. The parameters of both the prior and likelihood model can be automatically estimated from a set of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implemented our method in a fast cDNA-to-genome alignment program, SPA, and applied it to the FANTOM3 dataset of over 100,000 full-length mouse cDNAs and a dataset of over 20,000 full-length human cDNAs. Comparison with the results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular, the quality of the SPA alignments near splice boundaries and SPA's mapping of the 5' and 3' ends of the cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variations. Finally, our splice boundary analysis on the human dataset suggests the existence of a novel non-canonical splice site that we also find in the mouse dataset. The SPA software package is available at http://www.biozentrum.unibas.ch/personal/nimwegen/cgi-bin/spa.cgi.

Algorithms↗

Differentiation of Mycoplasma gallisepticum strains using amplified fragment length polymorphism and other DNA-based typing methods.

Amplified fragment length polymorphism (AFLP) was used to type 34 strains of Mycoplasma gallisepticum (MG) including vaccine strains ts-11, 6/85, and F. Using AFLP, a total of 10 groups, with 30 distinguishable AFLP typing profiles, were generated in the analysis. The AFLP method was able to identify and differentiate both MG field strains from recent outbreaks and those that were epidemiologically related. The AFLP procedure will provide assistance in identifying the sources of mycoplasma infections. Vaccine strains were also differentiated from other field strains, which will be useful in the evaluation of vaccination programs. The AFLP discrimination potential was compared to other molecular typing techniques such as gene-targeted typing by DNA sequence analysis of the MG cytadhesin-like protein encoding gene, mgc2, and random amplified polymorphic DNA assay on the same MG isolates. The three assays correlated well with one another, with AFLP analysis having a much higher discriminatory power and reproducibility.

Bacterial Proteins↗

Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population.

Molecular forensic methods are being increasingly used to help enforce wildlife conservation laws. Using multilocus genotyping, illegal translocation of an animal can be demonstrated by excluding all potential source populations as an individual's population of origin. Here, we illustrate how this approach can be applied to a large continuous population by defining the population genetic structure and excluding suspect animals from each identified cluster. We aimed to test the hypothesis that recreational hunters had illegally introduced a group of red deer into a hunting area in Luxembourg. Reference samples were collected over a large area in order to test the possibility that the suspect individuals might be recent immigrants. Due to isolation-by-distance relationships in the data set, inferring the number of genetic clusters using Bayesian methods was not straightforward. Biologically meaningful clusters were only obtained by simultaneously analysing spatial and genetic information using the program baps 4.1. We inferred the presence of three genetic clusters in the study region. Using partial Mantel tests, we detected barriers to gene flow other than distance, probably created by a combination of urban areas, motorways and a river valley used for viticulture. The four focal animals could be excluded with a high certainty from the three genetic subpopulations and it was therefore likely that they had been released illegally.

Animal Migration↗