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PubMedDate not supplied

Phenylketonuria (PKU): screening and management.

OBJECTIVE: To provide health care providers, patients, and the general public with a responsible assessment of currently available data regarding screening for, and management of. phenylketonuria (PKU). PARTICIPANTS: A non-Federal, non-advocate, 14-member panel representing the fields of pediatrics, genetics, human development, public policy, nursing, molecular physiology, and including patient representatives. In addition, 19 experts in pediatrics, medical genetics, psychology, pediatric neurology, biochemical and molecular genetics, and gene therapy presented data to the panel and to a conference audience of more than 300. EVIDENCE: The literature was searched using MEDLINE and an extensive bibliography of references was provided to the panel. Experts prepared abstracts with relevant citations from the literature. Scientific evidence was given precedence over clinical anecdotal experience. CONSENSUS PROCESS: The panel, answering predefined questions, developed their conclusions based on the scientific evidence presented in open forum and the scientific literature. The panel composed a draft statement that was read in its entirety and circulated to the experts and the audience for comment. Thereafter, the panel resolved conflicting recommendations and released a revised statement at the end of the conference. The panel finalized the revisions within a few weeks after the conference. The draft statement was made available on the World Wide Web immediately following its release at the conference and was updated with the panel's final revisions. CONCLUSIONS: Genetic testing for PKU has been in place for almost 40 years and has been very successful in the prevention of severe mental retardation in thousands of children and adults. Metabolic control is necessary across the lifespan of individuals with PKU. A comprehensive, multidisciplinary, integrated system is required for the delivery of care to individuals with PKU. Greatly needed are consistency and coordination among screening, treatment, data collection, and patient support programs. There should be equal access to culturally sensitive, age-appropriate treatment programs. Ethically sound, specific policies for storage, ownership, and use in future studies of archived samples remaining from PKU testing should be established. Research into the pathophysiology of PKU and relationship to genetic, neural, and behavioral variation is strongly encouraged. Uniform policies need to be established to remove from the individual and the family financial barriers to the acquisition of medical foods and modified low-protein foods, as well as to provide access to support services required to maintain metabolic control in individuals with PKU. Research on nondietary alternatives to treatment of PKU is strongly encouraged. To achieve optimal statistical power, as well as cross-cultural applicability, it will be beneficial to use data acquired via national and international collaboration.

Cost-Benefit Analysis↗
PubMed2002

Community outreach: a call for community action.

For a variety of reasons, end-stage renal disease disproportionately affects minority populations. Factors such as socioeconomic status, cultural differences, and genetic variations, are all involved. In addition, there are often real and perceived barriers for these patient groups in fully accessing the healthcare system. Thus, there is a real need for the development of specific outreach programs that target these high-risk communities. In developing such programs, it is important to realize that there is not a homogeneous 'ethnic community', but rather, like any large demographic grouping, a diverse population. These differing communities will all have different requirements and needs and, thus, outreach programs need to be wide-ranging and adapted for individual, local communities, to ensure that all target audiences are reached. The core aims for these outreach programs must be raising disease awareness and education among minority patients. To achieve this goal, a wide range of organizations need to be actively involved, including national and--importantly--local, community-based patient organizations, and hospital management corporations, as well as local radio and television companies to advertise the outreach initiatives. However, any outreach campaign will need to be combined with policy changes and further research into kidney disease among minority groups if real improvements in outcomes are to be achieved.

Community-Institutional Relations↗
PubMed2002

Codon and rate variation models in molecular phylogeny.

This article generalizes previous models for codon substitution and rate variation in molecular phylogeny. Particular attention is paid to (1) reversibility, (2) acceptance and rejection of proposed codon changes, (3) varying rates of evolution among codon sites, and (4) the interaction of these sites in determining evolutionary rates. To accommodate spatial variation in rates, Markov random fields rather than Markov chains are introduced. Because these innovations complicate maximum likelihood estimation in phylogeny reconstruction, it is necessary to formulate new algorithms for the evaluation of the likelihood and its derivatives with respect to the underlying kinetic, acceptance, and spatial parameters. To derive the most from maximum likelihood analysis of sequence data, it is useful to compute posterior probabilities assigning residues to internal nodes and evolutionary rate classes to codon sites. It is also helpful to search through tree space in a way that respects accepted phylogenetic relationships. Our phylogeny program LINNAEUS implements algorithms realizing these goals. Readers may consult our companion article in this issue for several examples.

Algorithms↗
PubMed2000

Major histocompatibility complex variation in the Arabian oryx.

In the 1960s, the Arabian oryx was one of the most endangered species in the world, extinct in the wild and surviving in only a few captive herds. The present day population of over 2000 descends from a small number of founders and may have restricted genetic variation for important adaptive genes. We have examined the amount of genetic variation for a class II gene in the major histocompatibility complex thought to be the most important genetic basis for pathogen resistance in vertebrates. We found three very divergent alleles, which on average, differed by 24 nucleotides and 15 amino acids in the 236-bp fragment we examined. Using single-strand conformation polymorphism, we found that in a sample of 57 animals, the alleles were in Hardy-Weinberg proportions, although one allele was found only in four heterozygous individuals. The average heterozygosity for the 22 amino acid positions involved in antigen binding was 0.165, three times as high as that for the 56 amino acids not involved with antigen binding. Because the three alleles have such divergent sequences, it is likely that they may recognize peptides from quite different pathogens. As a result, maintenance of these variants should be considered as a goal in the captive breeding program of the Arabian oryx.

Adaptation, Physiological↗
PubMed2003

[Variation and evolution of meiosis].

Meiosis arose in the evolution of primitive unicellular organisms as a part of sexual process. One type of meiosis, the so-called classical type, predominates in all kingdoms of eukaryotes. Meiosis is controlled by hundreds of genes, both shared with mitosis and specifically meiotic ones. In a wide range of taxa, which in some cases include kingdoms, meiotic genes and features obey Vavilov's law of homologous variation series. Synaptonemal complexes (SCs) temporarily binding homologous chromosomes at prophase I, ensure precise and equal crossing over and interference. SC proteins have 60-80% homology within the class of mammals but differ from the corresponding proteins in fungi and plants. Thus, nonhomologous SC proteins perform similar functions in different taxa. Some recombination enzymes in fungi and insects have common epitopes. The molecular mechanism of recombination is inherited by eukaryotes from prokaryotes and operates in special compartments: SC recombination nodules. Chiasmata, i.e., physical crossovers of nonsister chromatids, are preserved in bivalents until metaphase I due to local cohesion of sister chromatids in the remaining SC fragments. Owing to chiasmata, homologous chromosomes participate in meiosis I in pairs rather than individually, which, along with unipolarity of kinetochores (only in meiosis 1), ensures segregation of homologous chromosomes. The appearance of SC and chiasmata played a key role in the evolution of unicellular organisms since it promoted the development of a progressive type of meiosis. Some lower eukaryotes retain primitive meiosis types. These primitive modes of meiosis also occur in the sex of some insects that is heterozygous for sex chromosomes. I suggest an explanation for these cases. Mutations at meiotic genes impair meiosis; however, due to the preservation of archaic meiotic genes in the genotype, bypass metabolic pathways arise, which provide partial rescue of the traits damaged by mutations. Individual blocks of genetic program of meiotic regulation have probably evolved independently.

Animals↗
PubMed1995

Evidence of molecular heterogeneity for generalised glycogenosis between and within breeds of cattle.

Northern analyses revealed normal levels of acidic alpha-glucosidase mRNA in cultured fibroblasts from a Shorthorn calf affected with glycogenosis but a gross deficiency in an affected Brahman calf. Analyses of acidic alpha-glucosidase activity, relative to that of other lysosomal enzymes, in blood mononuclear cells revealed greater variation within and between Brahman herds than Shorthorn herds. A Msp1 restriction fragment length polymorphism associated with glycogenosis in Brahmans was not found in Shorthorns. These results are considered in relation to molecular heterogeneity for AAG deficiency in cattle and its implications for disease control programs.

Animals↗
PubMed2006

Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent.

Wild barley shows a large morphological and phenotypic variation, which is associated with ecogeographical factors and correlates with genotypic differences. Diversity of defense related genes and their expression in wild barley has been recognized and has led to attempts to exploit genes from H. spontaneum in breeding programs. The aim of this study was to determine the variation in the accumulation of hordatines, which are Hordeum-specific preformed secondary metabolites with strong and broad antimicrobial activity in vitro, in 50 accessions of H. spontaneum from different habitats in Israel. Differences in the accumulation of hordatines in the seedling stage were significant between different H. spontaneum genotypes from different regional locations and micro-sites. Variation in the hordatine accumulation within genotypes was between 9% and 45%, between genotypes from the same location between 13% and 38%, and between genotypes from different locations up to 121%. Principal component analysis showed that water related factors explain 39%, temperature related factors explain 33% and edaphic factors account for 11% of the observed variation between the populations of H. spontaneum. Genetic analysis of the tested accessions with LP-PCR primers that are specific for genes involved in the biosynthetic pathway of hordatines showed tight correlations between hordatine abundance and genetic diversity of these markers. Multiple regression analyses indicated associations between genetic diversity of genes directly involved in hordatine biosynthesis, ecogeographical factors and the accumulation of hordatines.

Agmatine↗
PubMed2004

Population genetic structure of a colonising, triploid weed, Hieracium lepidulum.

Understanding the breeding system and population genetic structure of invasive weed species is important for biocontrol, and contributes to our understanding of the evolutionary processes associated with invasions. Hieracium lepidulum is an invasive weed in New Zealand, colonising a diverse range of habitats including native Nothofagus forest, pine plantations, scrubland and tussock grassland. It is competing with native subalpine and alpine grassland and herbfield vegetation. H. lepidulum is a triploid, diplosporous apomict, so theoretically all seed is clonal, and there is limited potential for the creation of variation through recombination. We used intersimple sequence repeats (ISSRs) to determine the population genetic structure of New Zealand populations of H. lepidulum. ISSR analysis of five populations from two regions in the South Island demonstrated high intrapopulation genotypic diversity, and high interpopulation genetic structuring; PhiST = 0.54 over all five populations. No private alleles were found in any of the five populations, and allelic differentiation was correlated to geographic distance. Cladistic compatibility analysis indicated that both recombination and mutation were important in the creation of genotypic diversity. Our data will contribute to any biocontrol program developed for H. lepidulum. It will also be a baseline data set for future comparisons of genetic structure during the course of H. lepidulum invasions.

Alleles↗
PubMed2000

LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis.

SUMMARY: LIAN is a program to test the null hypothesis of linkage equilibrium for multilocus data. LIAN incorporates both a Monte Carlo method as well as a novel algebraic method to carry out the hypothesis test. The program further returns the genetic diversity of the sample and the pairwise distances between its members.

Chromosome Mapping↗
PubMed1999

The role of interindividual variation in human carcinogenesis.

The process of chemical carcinogenesis is a complex multistage process initiated by DNA damage in growth control genes. Carcinogens enter the body from a variety of sources, but most require metabolic activation before they can damage DNA. There are multiple protective processes that include detoxification and conjugation, DNA repair and programmed cell death. Most of these functions exhibit wide interindividual variation in the population and thus are thought to affect cancer risk. The role of gene-environment interactions is being explored, and current data indicate that genetic susceptibilities can modify carcinogen exposures from the diet and tobacco smoking, although much more data exist for the latter. This review addresses the relationships of human carcinogenesis to these interindividual differences of phase I, phase II and DNA repair enzymes.

Carcinogens↗
PubMed2002

Genetic relationships of American alligator populations distributed across different ecological and geographic scales.

Although much work has been conducted on coastal populations of the American alligator (Alligator mississippiensis), less is known about the population dynamics and genetic structure of populations of alligators confined to inland habitats. DNA microsatellite loci, derived from the American alligator, were used to investigate patterns of genetic variation within and between populations of alligators distributed at coastal and inland localities in Texas. These data were used to evaluate the genetic discreteness of different alligator stocks relative to their basic ecology at these sites. Observed mean heterozygosities across seven loci for both coastal and inland populations ranged from 0.50-0.61, with both inland and coastal populations revealing similar patterns of variation. Measures of F(st) revealed significant population differentiation among all populations; however, analyses of molecular variance (AMOVAs) failed to demonstrate any apparent geographic pattern relative to the population differentiation indicated by F(st) values. Each population contained unique alleles for at least one locus. Additionally, assignment tests based on the distribution of genotypes placed 76% of individuals to their source population. These genetic data suggest considerable subdivision among alligator populations, possibly influenced by demographic and life history differences as well as barriers to dispersal. These results have clear implications for management. Rather than managing alligators in Texas as a single panmictic population, translocation programs and harvest quotas should consider the ecological and genetic distinctiveness of local alligator populations.

Alligators and Crocodiles↗
PubMed2004

Genetic constraints on floral evolution in a sexually dimorphic plant revealed by artificial selection.

Sexual dimorphism is one of the most widespread and recognizable patterns of phenotypic variation in the biotic world. Sexual dimorphism in floral display is striking in the dioecious plant Silene latifolia, with males making many, small flowers compared to females. We investigated this dimorphism via artificial selection on two populations to determine whether genetic variation exists within populations for flower size and the extent of the between-sex correlation, whether a flower size and number trade-off exists within each sex, and whether pollen and ovule production vary with flower size. We selected for decreased flower size (calyx width) in females and increased flower size in males and measured the response to selection in size and correlated responses in flower dry mass, flower number, and pollen or ovule number per flower. Four bouts of selection in each of two selection programs were performed, for a total of three selection lines to decrease size, three to increase it, and two control lines. Flower size always significantly responded to selection and we always found a significant correlated response in the sex not under selection. Selection decreased but did not eliminate the sexual dimorphism in flower dry mass and number. A negative relationship between flower size and number within each sex was revealed. Whereas ovule number showed a significant correlated response to selection on flower size, pollen number did not. Our results indicate that although substantial additive genetic variation for flower size exists, the high between-sex genetic correlation would likely constrain flower size from becoming more sexually dimorphic. Furthermore, floral display within each sex is constrained by a flower size and number trade-off. Given this trade-off and lack of variation in pollen production with flower size, we suggest that sexual dimorphism evolved via sexual selection to increase flower number in males but not females.

Biological Evolution↗
PubMed1998

Livestock variation of linked microsatellite markers in diverse swine breeds.

A panel of nine framework microsatellites (MS) linked to the Calcium Release Channel (CRC) locus on swine chromosome 6 (SSC6) was developed from the consensus genetic map. MS were screened across groups of unrelated animals from Yorkshire, Hampshire, Duroc, Landrace and Meishan swine breeds. Unique MS alleles for Yorkshire, Duroc, Landrace and Meishan breeds, and statistically significant (P < .05) associations between breeds and allele frequencies were found for each MS. Although breed marker heterozygosities ranged from 0.0 (S0035 in Duroc) to 0.92 (S0087 in Meishan), Correspondence Analysis identified MS alleles uniquely associated with either the Meishan breed, western breeds or alleles common to all breeds. Furthermore, an overall marker heterozygosity of < 0.70 demonstrates the need for multiple MS panels to accommodate reduced within-breed differences for identification of quantitative trait loci (QTL), marker assisted selection (MAS) programs or parental identification in commercial breeds.

Alleles↗
PubMed1999

Genetic recombination of poliovirus in vitro and in vivo: temperature-dependent alteration of crossover sites.

Genetic recombination that occurs with high frequency during poliovirus genome replication is a process whose molecular mechanism is poorly understood. Studies of genetic recombination in a cell-free system in vitro and in infected tissue culture cells in vivo have led to the unexpected observation that temperature strongly influences the loci at which cross-over between the two recombining RNA strands occurs. Specifically, cross-over between two genetically marked RNA strands in vitro and in vivo at 34 degrees C occurred over a wide range of the genome. In contrast, recombination in vivo at 37 and 40 degrees C yielded cross-over patterns that had shifted dramatically to a region encoding nonstructural proteins. Preferential selection of recombinants at 37 and 40 degrees C was ruled out by analyses of the growth kinetics of the recombinants. During the studies of recombination in the cell-free system we found that there is a direct correlation between the ability of a poliovirus RNA molecule to replicate in the cell-free system and its capacity to complement de novo virus synthesis programmed by another viral RNA.

Binding Sites↗
PubMed2006

Microbial community structure during oxygen-stimulated bioremediation in phenol-contaminated groundwater.

This research explored the changes in genetic diversity and spatial distribution of microbial communities in association with the changes in phenol concentration during a bioremediation process. Results using the traditional plate count method indicated an increase of average bacteria densities in groundwater from 10(4) to 10(7)CFUml(-1) initially to 10(7) to 10(9)CFUml(-1) after remediation. The diversity and stability of phenol-degrading bacterial communities were investigated by using single-strand-conformation polymorphism (SSCP) genetic profile analysis of 16S rDNA fragments amplified from groundwater samples. The molecular data showed a high degree of genetic similarity between communities from certain monitoring wells during the early phases of remediation, probably due to similar initial physical conditions among wells. Molecular signatures of several cultivated phenol-degrading bacterial strains could be seen in most groundwater profiles throughout the study period, suggesting that these strains were indigenous to the study site. It was also observed that the species diversity of these microbial communities increased as the phenol levels in the groundwater decreased during the 9-month study period, and recovered to the pre-treatment levels after the remediation program was completed.

Bacteria↗
PubMedDate not supplied

Genetic diversity in Hemileia vastatrix based on RAPD markers.

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs.

Basidiomycota↗
PubMed2026

Large-scale admixture mapping in the All of Us Research Program improves the characterization of cross-population phenotypic differences.

Admixed individuals have been understudied in medical research largely due to their complex genetic ancestries. However, the consideration of admixture can identify ancestry-enriched genetic associations, delineating genetic underpinnings of cross-population phenotypic variation. Here, we performed admixture mapping in individuals with inferred admixture from African and European populations (N&#x2009;=&#x2009;48,921). Across 22 traits, we identified 71 ancestry-trait associations, including loci where ancestral haplotypes explained phenotypic variation yet were missed by single-variant association testing due to their stricter multiple testing burden. One such locus where inferred local AFR ancestries are associated with increased hemoglobin A1c (HbA1c) was 12q14.3, highlighting its potential role in explaining differences between populations. Together, our results expand upon the phenotypic differences between populations and characterize loci where genetic ancestries play a critical role in the architecture of disease.

Humans↗
PubMed2000

Angiotensin-converting enzyme ID polymorphism and fitness phenotype in the HERITAGE Family Study.

It has been suggested that genetic variation in the angiotensin-converting enzyme (ACE) gene is associated with physical performance. We studied the association between the ACE insertion (I)/deletion (D) polymorphism and several fitness phenotypes measured before and after 20 wk of a standardized endurance training program in sedentary Caucasian (n = 476) and black (n = 248) subjects. Phenotypes measured were oxygen uptake (VO(2)), work rate, heart rate, minute ventilation, tidal volume, and blood lactate levels during maximal and submaximal [50 W and at 60 and 80% of maximal VO(2) (VO(2 max))] exercise and stroke volume and cardiac output during submaximal exercise (50 W and at 60% VO(2 max)). The ACE ID polymorphism was typed with the three-primer PCR method. Out of 216 association tests performed on 54 phenotypes in 4 groups of participants, only 11 showed significant (P values from 0.042 to 0. 0001) associations with the ACE ID polymorphism. In contrast to previous claims, in Caucasian offspring, the DD homozygotes showed a 14-38% greater increase with training in VO(2 max), VO(2) at 80% of VO(2 max), and all work rate phenotypes and a 36% greater decrease in heart rate at 50 W than did the II homozygotes. No associations were evident in Caucasian parents or black parents or offspring. Thus these data do not support the hypothesis that the ACE ID polymorphism plays a major role in cardiorespiratory endurance.

Adult↗