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Telomeres and telomerase in the fetal origins of cardiovascular disease: a review.

Telomeres are noncoding functional DNA repeat sequences at the ends of chromosomes that decrease in length by a predictable amount at each cell division. When the telomeres become critically short, the cell is no longer able to replicate and enters cellular senescence. Recent work has shown that within individuals, telomere length tracks with cardiovascular health and aging and is also affected by growth variation, both prenatally and postnatally. Therefore telomere length can be a marker of both growth history (cell division) and tissue function (senescence). Relationships between early growth and later health have emerged as a research focus in the epidemiology of chronic diseases of aging, such as heart disease and diabetes. The "fetal origins" literature has demonstrated that hormonal and nutritional aspects of the intrauterine environment not only affect fetal growth but also can permanently alter the metabolic program of the individual. Smaller infants tend to have a higher risk of developing cardiovascular disease. Much less attention has been paid to possible genetic links between the processes of early growth and later disease. Our aim in this review is to summarize evidence for one such genetic mechanism, telomere attrition, that may underlie the fetal origins of cardiovascular disease and to discuss this mechanism in light of the evolution of senescence.

Aging↗

[The use of biotechnology in animal breeding].

Biotechnological techniques are extensively used in dairy breeding programs. Thus, artificial insemination and embryo transfer (and associated techniques) constitute an integral part of modern breeding programs. In pig breeding, embryo transfer is mostly restricted to special problem areas because of its high costs. Currently this technique is used for the exchange of genetic material on an international level, for the creation of specific pathogene free herds, and in connection with cryoconservation for the setup of embryobanks in the context of the preservation of genetic resources.

Animals↗

Genetic control of dormancy in a Triumph/Morex cross in barley.

Seed dormancy in barley ( Hordeum vulgare L.) is one of the most important parameters affecting malting. Seed dormancy is quantitatively inherited and variously influenced by the environment. The objectives of the present study were to determine the genome location and effects of quantitative trait loci (QTLs) involved in the expression of seed dormancy in a barley cross between two varieties derived from different germplasm pools. Using a doubled-haploid population of 107 lines of the cross between the malting types Triumph (two-row, dormant) and Morex (six-row, non-dormant), seed dormancy phenotypic data sets from five environments and a 147-marker linkage map were developed in order to perform QTL analyses with simple interval mapping and simplified composite interval mapping procedures. Two different types of variables were considered for seed dormancy characterization: (1) level of dormancy induced during seed development, which was indirectly measured as germination percentage at 3 days and 7 days, GP3 and GP7 respectively; (2) rate of dormancy release in the course of a period after seed harvest (after-ripening). Different mechanisms of genetic control were detected for these two types of dormancy-related traits. A major and consistent dormancy QTL near the centromere on chromosome 7(5H) was associated with the establishment of dormancy during seed development and accounted for 52% and 33% of the variability for GP3 and GP7, respectively. Two other QTLs located in the vicinity of the vrs1 locus on chromosome 2(2H) and near the long arm telomere on chromosome 7(5H) explained 9% and 19% of variation, respectively, for the rate of dormancy release during after-ripening. Likewise, seed dormancy was assessed in an F(2) population derived from the cross between two dormant types of distinct germplasm groups, Triumph (European, two-row, malt) and Steptoe (North American, six-row, feed), which showed similar but not identical genetic control for dormancy. Interestingly, there is remarkable dormancy QTL conservation in both regions on chromosome 7(5H) identified in this study and among other barley mapping populations. These widely conserved QTLs show potential as targets for selection of a moderate level of seed dormancy in breeding programs.

Chromosome Mapping↗

Analysis of synonymous codon usage bias in Chlamydia.

Chlamydiae are obligate intracellular bacterial pathogens that cause ocular and sexually transmitted diseases, and are associated with cardiovascular diseases. The analysis of codon usage may improve our understanding of the evolution and pathogenesis of Chlamydia and allow reengineering of target genes to improve their expression for gene therapy. Here, we analyzed the codon usage of C. muridarum, C. trachomatis (here indicating biovar trachoma and LGV), C. pneumoniae, and C. psittaci using the codon usage database and the CUSP (Create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite). The results show that the four genomes have similar codon usage patterns, with a strong bias towards the codons with A and T at the third codon position. Compared with Homo sapiens, the four chlamydial species show discordant seven or eight preferred codons. The ENC (effective number of codons used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia is constrained by the G+C content, while translational selection and gene length exert relatively weaker influences. Moreover, mutational pressure appears to be the major determinant of the codon usage variation among the chlamydial genes. In addition, we compared the codon preferences of C. trachomatis with those of E. coli, yeast, adenovirus and Homo sapiens. There are 23 codons showing distinct usage differences between C. trachomatis and E. coli, 24 between C. trachomatis and adenovirus, 21 between C. trachomatis and Homo sapiens, but only six codons between C. trachomatis and yeast. Therefore, the yeast system may be more suitable for the expression of chlamydial genes. Finally, we compared the codon preferences of C. trachomatis with those of six eukaryotes, eight prokaryotes and 23 viruses. There is a strong positive correlation between the differences in coding GC content and the variations in codon bias (r=0.905, P<0.001). We conclude that the variation of codon bias between C. trachomatis and other organisms is much less influenced by phylogenetic lineage and primarily determined by the extent of disparities in GC content.

Animals↗

Retrospective evaluation of the influence of the interleukin-1 genotype on radiographic bone levels in treated periodontal patients over 10 years.

BACKGROUND: A difference in genetic susceptibility to plaque accumulation has been advocated to explain different responses to periodontal therapy. The purpose of this study is to assess the role of the interleukin-1 (IL-1) polymorphism on the rate of bone and tooth loss in non-smoking periodontally treated patients during maintenance. METHODS: Sixty consecutive non-smoking patients (mean age 46.8 +/- 5.0) with moderate to severe periodontitis, treated and maintained for over 10 years were selected. At baseline (T0), radiographic evaluation (cemento-enamel junction [CEJ]-root apex, CEJ-bottom of defect mesial and distal, CEJ-bone crest mesial and distal, crown-root ratio) was performed. All patients received scaling and root planing; 36 patients then underwent surgical therapy. Subsequently, all patients were enrolled in a periodontal maintenance program with recall visits every 3.4 +/- 1.0 months for at least 10 years. At the latest recall visit (T2) the same radiographic measurements evaluated at baseline were taken and a DNA sample for IL-1 genetic susceptibility testing was collected and sent for analysis. RESULTS: Twenty-three of the 60 patients (38.3%) were IL-1 genotype positive. A total of 52 teeth (3.3%) out of 1,566 were lost due to periodontitis between T0 and T2; 28 of 957 (2.9%) in the IL-1 genotype negative group and 24 of 609 (3.9%) in IL-1 genotype positive group. The mean variation in bone defect level (DeltaBD) averaged -0.04 mm in IL-1 genotype negative patients and 0.01 mm in IL-1 genotype positive patients. The mean variation in bone crest level (DeltaBC) averaged -0.24 mm in IL-1 genotype negative patients and -0.28 mm in IL-1 genotype positive patients. However, a few patients showed significant differences in response to therapy based on initial bone levels and genotype. IL-1 negative patients who showed minimal initial bone loss responded to the therapy better than the IL-1 positive patients. IL-1 positive patients with severe initial bone loss showed a better response to the therapy than IL-1 negative patients. CONCLUSIONS: On average, there were no significant differences related to IL-1 genotype in tooth loss after 10 years in a non-smoking, well-maintained periodontal population. On an individual patient basis, the IL-1 genotype, in combination with the initial bone level, seems useful at the beginning of therapy for predicting bone level variation.

Adult↗

BoLA class I allele diversity and polymorphism in a herd of cattle.

Major histocompatibility complex class I genes are among the most polymorphic genes characterized. The high level of polymorphism is essential for generating host immune responses. In humans, three distinct genomic loci encode human leukocyte antigen (HLA) class I genes, allowing individuals to express up to six different HLA class I molecules. In cattle, the number of distinct genomic loci are currently at least six, and the number of different bovine leukocyte antigens (BoLA) class I molecules that are expressed in individual animals are variable. The extent of allele variation within the cattle population is unknown. In this study, the number and variety of BoLA class I sequences expressed by 36 individuals were determined from full-length BoLA class I cDNA clones. Twenty distinct BoLA class I alleles were identified, with only four being previously reported. The number of expressed BoLA class I alleles in individual animals ranged between one and four, with none of the animals having an identical complement of BoLA class I molecules. Variation existed in the number of BoLA class I alleles expressed as well as the composition of expressed alleles, however, several BoLA class I alleles were found in multiple individual animals. Polymorphic amino acid sites were analyzed for positive and negative selection using the ADAPTSITE program. In the antigen recognition sites (ARS), there were eight positions that were predicted to be under positive selection and three positions that were predicted to be under negative selection from 62 positions. In contrast, for non-antigen recognition sites (non-ARS), there were three positions that were predicted to be under positive selection and 20 that were predicted to be under negative selection from 278, indicating that positive selection of amino acids occurs at a greater frequency within the antigen recognition sites.

Alleles↗

Identification of quantitative trait loci and epistatic interactions for plant height and heading date in rice.

Appropriate heading date and plant height are prerequisites for attaining the desired yield level in rice breeding programs. In this study, we analyzed the genetic bases of heading date and plant height at both single- locus and two-locus levels, using a population of 240 F(2:3) families derived from a cross between two elite rice lines. Measurements for the traits were obtained over 2 years in replicated field trials. A linkage map was constructed with 151 polymorphic marker loci, based on which interval mapping was performed using Mapmaker/QTL. The analyses detected six QTLs for plant height and six QTLs for heading date; collectively the QTLs for heading date accounted for a much greater amount of phenotypic variation than did the QTLs for plant height. Two-way analyses of variance, with all possible two-locus combinations, detected large numbers (from 101 to 257) of significant digenic interactions in the 2 years for both traits involving markers distributed in the entire genome; 22 and 39 were simultaneously detected in both years for plant height and heading date, respectively. Each of the interactions individually accounted for only a very small portion of the phenotypic variation. The majority of the significant interactions involved marker loci that did not detect significant effects by single-locus analyses, and many of the QTLs detected by single-locus analyses were involved in epistatic interactions. The results clearly demonstrated the importance of epistatic interactions in the genetic bases of heading date and plant height.

Journal Article↗

Reproducibility of anthropometric and body composition measurements: the HERITAGE Family Study.

OBJECTIVE: To determine the reproducibility of anthropometric and body composition measures using the HERITAGE Family Study protocol. DESIGN: Anthropometric and body composition measures were obtained on three separate days within a 3-wk period at each of the four HERITAGE Clinical Centers. SUBJECTS: Sixty men and women representative of the HERITAGE subject population, 15 from each of four Clinical Centers. MEASUREMENTS: Anthropometric measures included eight skinfolds, three girths and one length; and body composition measures included stature, mass, hydrostatic weight, residual volume, and body density, from which relative fat, fat mass and fat-free mass were estimated. RESULTS: Reproducibility as determined by technical error, coefficient of variation, and intraclass correlations was very high for the total sample. For example, intraclass correlations for the total sample generally ranged from 0.95-0.99 for the anthropometric measures, and from 0.97-1.00 for the body composition measures. The results across Clinical Centers were in close agreement with each other and with the pooled data. CONCLUSIONS: The reproducibility of anthropometric and body composition measures using the HERITAGE Family Study protocol is sufficiently high that it should be possible to detect small changes in any of these measures and to determine the genetic basis of these changes consequent to a 20 wk endurance training program.

Adult↗

Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data.

Inference of haplotypes is important for many genetic approaches, including the process of assigning a phenotype to a genetic region. Usually, the population frequencies of haplotypes, as well as the diplotype configuration of each subject, are estimated from a set of genotypes of the subjects in a sample from the population. We have developed an algorithm to infer haplotype frequencies and the combination of haplotype copies in each pool by using pooled DNA data. The input data are the genotypes in pooled DNA samples, each of which contains the quantitative genotype data from one to six subjects. The algorithm infers by the maximum-likelihood method both frequencies of the haplotypes in the population and the combination of haplotype copies in each pool by an expectation-maximization algorithm. The algorithm was implemented in the computer program LDPooled. We also used the bootstrap method to calculate the standard errors of the estimated haplotype frequencies. Using this program, we analyzed the published genotype data for the SAA (n=156), MTHFR (n=80), and NAT2 (n=116) genes, as well as the smoothelin gene (n=102). Our study has shown that the frequencies of major (frequency >0.1 in a population) haplotypes can be inferred rather accurately from the pooled DNA data by the maximum-likelihood method, although with some limitations. The estimated D and D' values had large variations except when the /D/ values were >0.1. The estimated linkage-disequilibrium measure rho2 for 36 linked loci of the smoothelin gene when one- and two-subject pool protocols were used suggested that the gross pattern of the distribution of the measure can be reproduced using the two-subject pool data.

Algorithms↗

Animal breeding and conservation genetics.

Conservation genetics in an animal breeding context relates both to questions of preservation of rare and endangered breeds or populations, and to utilization with planned genetic change to improve viability, productivity, and efficiency of production. In the developed world, preservation is the primary issue, and various organizations exist which are committed to the preservation of rare and endangered breeds. In the developing world, breeds as such often are not defined or recognized, but many local populations exist that are adapted to and integrated into existing production systems. The genotypes of at least some of these populations could well also be crucial for future production systems, but many are threatened, primarily by crossbreeding with breeds introduced from the developed world. However, not all can be conserved, and priorities will have to be set for preservation, for development (breeding programs) and for evaluation for future programs. Some priorities will be set for pragmatic reasons, but the primary rational reason must be that a breed is in some way genetically unique, and makes a substantial contribution to the genetic diversity of the species. Thus, measures of genetic distance are essential to quantify the degree of genetic differentiation among populations, but such measures must be based on a large sample of loci. Although this has been emphasized many times, it still seems not to be adequately appreciated, and the effect of using a limited sample of loci is illustrated with an example from swamp buffalo populations. Comparative estimates of distances based on electrophoretic variation and direct DNA variation (both mitochondrial and genomic) are needed as a basis for future work on conservation of the global domestic animal diversity. Finally, studies of feral populations and wild relatives of domestic animals will provide a link between natural populations and domestic animal populations, and bring together these two areas, which to now have been largely separate.

Animals↗

Efficacy of gene testing for von Hippel-Lindau disease.

OBJECTIVE: To determine the efficacy of genetic testing of individuals presenting with features possibly indicative of von Hippel-Lindau (VHL) disease, regardless of other relevant family and clinical details. SETTING AND PARTICIPANTS: Between September 1994 and December 1997, 16 unrelated individuals were referred to Genetic Services of Western Australia by local clinicians and by similar genetic services in other States, for VHL gene mutation analysis because of clinical manifestations suggestive of the diagnosis. METHODS: The subjects were investigated by screening for mutations in the polymerase chain reaction products of the three VHL gene exons using single-stranded conformational polymorphism analysis (SSCP). If no mutations were detected the exons were sequenced, and if no variations were found DNA was examined by Southern analysis for germinal rearrangements. RESULTS: Mutations in the VHL gene were detected in eight of 16 individuals (50%), including 3 individuals with no family history suggestive of VHL disease. Five mutations were detected by SSCP, two by gene sequencing and one by Southern analysis. Each mutation occurred only in a single family and three had not been previously reported. CONCLUSION: Genetic screening of individuals presenting with clinical features suggestive of VHL facilitates confirmation of the diagnosis, accurate genetic counselling and surveillance of at-risk family members. The necessity for costly and time-consuming screening programs can be reduced and screening directed at those carrying the mutation. Our low stringency criteria are justified for screening for VHL mutations.

Genetic Testing↗

[Molecular AFLP-marking of genotypes of pepper (Capsicum annuum) cultivars].

The results of AFLP study of 14 Capsicum annuum cultivars are presented. Notwithstanding the known low genomic variation of large-fruited sweet pepper, AFLP analysis proved to be suitable for detecting polymorphism and genotyping pepper cultivars. Nine primer pairs were selected to allow identification of the cultivars under study. Among-cultivar polymorphism detectable with these primers was estimated at 16.5%. A characteristic AFLP pattern was obtained for each cultivar. Several cultivar-specific fragments were revealed for seven cultivars. On the basis of the AFLP data, genetic distances between cultivars were computed and a tree was constructed by means of hierarchic cluster analysis (UPGMA) with the Jacquard coefficient. It was assumed that this information is useful in breeding programs involving the cultivars examined.

Capsicum↗

[Conservation efficiency of local chicken breeds in different farms as revealed by microsatellite markers].

Twenty-eight microsatellite markers were used to analyze the conservation efficiency of two local chicken breeds (Dagu Chicken and Beijing Fatty Chicken) in different farms. Genotypes were detected in 125 samples. The genetic variations among and within the populations were calculated by the number of alleles, gene frequency, genetic heterozygosity (H), PIC, F-statistics, Nei's genetic distance and UPGMA. High polymorphism was found in the four populations, and H and PIC values of each population were more than 0. 5. All loci detected in the study showed polymorphism and the number of alleles ranged from 2 to 22 in total population. Most of these loci were at Hardy-Weinberg equilibrium except two loci (LE110194, MCW0032). The four conservation farms for the two breeds were shown to have retained substantial biodiversity, indicating that the conservation programs are efficient. However, differences between the farms of the same breeds were observed.

Animals↗

Identification of the transcription initiation site of the asexually expressed rRNA genes of the malaria parasite Plasmodium berghei.

The start site of the A-type ribosomal RNA transcription units of the rodent malaria parasite, Plasmodium berghei, has been identified. The two A-type units cannot be distinguished within the transcription unit, yet exist as single copies on different chromosomes. Gene transcription initiates 820 bp upstream of the A-type small subunit (SSU) ribosomal gene and two major processing sites were mapped 610 and 611 nucleotides upstream of the SSU in the external transcribed spacer region. Surprisingly the nucleotide sequence of the DNA region containing the putative ribosomal promoter lacked repetitive DNA sequences typical of ribosomal promoters. This region was further analysed by computer using programs designed to reveal sequence-dependent structural features. Comparison of DNA curvature, duplex stability and pattern of twist angle variation revealed a striking degree of conservation between the ribosomal promoters from Plasmodium and other eukaryotes.

Animals↗

Synthetic DNA-based genetic markers reveal intra- and inter-species DNA sequence variability in the Bubalus bubalis and related genomes.

A series of synthetic oligonucleotide probes were developed as markers for genetic analysis and molecular systematics of Bubalus bubalis and other eutherian mammals. A very high level of heterozygosity (approximately 95%) was observed in the bubaline genome, with an overall band-sharing probability of 2.08 x 10(-11) using (TGG)6 and Hinf I probe-enzyme combination. Breed affiliation studies on different buffalo breeds, viz. Toda, Surti, Mehsana, and Murrah, revealed that the semiwild Toda breed belonged to a distinct group. The desired genotypes in each successive generation in an actual breeding program were also identified by employing a DNA fingerprinting approach using these markers. Estimation of genetic distances by calculating the mean allelic frequencies at (CA)n, (TGG)n, and (GGAT)n repeat loci between buffalo and other related animals such as horse (order Perisodactyla), rabbits (order Lagomorpha, (pigs, cattle, goat, and sheep (order Artiodactyla) revealed that with respect to the genetic distance coefficient (GDC), goat (caprine) was closer to buffalo (GDC = 0.0005) than sheep (ovine) (GDC = 0.0007). The genetic distance between horse and buffalo was calculated to be 0.4085, indicating that compared to other animals, horse was distantly related to buffalo. The understanding of overall allelic variations and breed affiliation of the bubaline genome will contribute to the propagation and conservation of the desired germ plasm and better management of this species.

Alleles↗

Molecular epidemiology, pathogenesis and prevention of gastric cancer.

Cancer of the stomach is one of the most commonly diagnosed malignancies and remains an important cause of mortality world wide. This type of cancer is not uniformly distributed among populations but shows a marked variation in both incidence and mortality. Although gastric cancer is declining in many parts of the world, the reasons for this decline are not well understood and its etiology remains unclear. Several factors are suspected to play a role in gastric carcinogenesis, including the effects of diet, exogenous chemicals, intragastric synthesis of carcinogens, genetic factors, infectious agents and pathological conditions in the stomach (such as gastritis). A new look at the results of epidemiological and experimental studies is important for the establishment of strategies for control. Since cancer of the stomach has a very poor prognosis in its more advanced stages, such a control program must have its main focus on primary prevention. This review describes our knowledge about cancer of the stomach regarding epidemiology, pathogenesis and prevention.

Asia↗

The Second International Collaborative Study on Comparative Mutagenesis re-visited: analysis by multi-variate statistical methods.

Computerized data analysis methods were applied to a selected subset of the results generated by the International Program on Chemical Safety Collaborative Study on In Vitro Assays. The rationale of this study was the analysis of test performances and the comparison with the conclusions of a similar analysis previously performed on the results of the First International Study. The multi-variate data analysis techniques used in the present work proved to be particularly suitable for looking at the complex field of comparative mutagenesis in a logical and systematic fashion, and generated a clear classification of the assays on the basis of their experimental performances. This classification proved not to be consistent with the traditional categories that group tests according to genetic end-point and phylogenetic position, and afforded classes of assays distinct for their sensitivity and specificity in respect to carcinogens. In particular, two systems (Saccharomyces cerevisiae XV185-14C mutation and Syrian Hamster Embryo cells transformation assays) on the basis of the published results, seemed to show a considerable sensitivity in predicting carcinogenicity, although they do not show high specificity.

Animals↗

International training programs in reproductive sciences for conservation of Latin American felids.

Survival of the ten non-domestic felid species endemic to Latin America is imperiled by habitat loss, poaching and poor captive management. Over the past 10 years, conservation of these felids has been the primary focus of a reproductive research and training program conducted in Brazil, Mexico, and the USA. The objectives of this program were to: (1) provide intensive training in reproductive sciences to Latin American scientists, (2) conduct collaborative studies investigating basic and applied reproduction in endangered felids, and (3) establish a highly-trained scientific cohort to conduct independent conservation-based research. Four formal training courses, consisting of didactic lectures and hands-on instruction in research techniques, including semen collection, sperm cryopreservation and laparoscopic artificial insemination (AI), were taught in Brazil and Mexico between 1995 and 1998. Several of these scientists received further training in conducting fecal hormone analysis in the USA, and a number of research studies, many in collaboration with American scientists, were initiated in Latin American felids. Research findings have characterized basal reproductive traits in several felid species, including ocelots, margay, tigrinas and jaguars, and established that Latin American felids exhibit only minimal seasonal variation in most reproductive traits. Other studies have explored the impact of acute and chronic stressors on adrenocortical activity and demonstrated the importance of environmental enrichment in captivity, especially in small felids. Additional research has examined ovarian and immunological responsiveness of Latin American felids to exogenous gonadotropins and assessed the impact of nutrition on sperm production and oocyte quality. Applied reproductive studies have investigated sperm cryopreservation in both captive and wild felid populations and demonstrated the production of viable offspring in ocelots and tigrinas following laparoscopic AI. Ongoing studies are investigating the potential of in vitro fertilization (IVF), embryo cryopreservation and embryo transfer for genetic management of ocelots and tigrinas. To date, over 75 Brazilian ocelot and 50 tigrina IVF embryos have been cryopreserved and two pregnancies have been established in ocelots following transfer of frozen-thawed embryos. Findings from these studies are helping to improve husbandry, population management, and breeding of Latin American felids in captivity. Continued advances in assisted reproduction eventually may provide an alternative route for exchanging genetic material among Latin American felid populations. Most importantly, this collaborative program has been essential for building scientific capacity, within Brazil and Mexico, in establishing a core group of highly-trained reproductive biologists that will continue applying their new knowledge and skills to the conservation of Latin American felids.

Animals↗