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At least 163 records · Page 9Linked to original sources
PubMed1998

The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7-9 and comparison with those in the other eight genetic groups.

We have proposed that hepatitis C virus should be classified into eleven genetic groups (types) which further divide into more than 80 genotypes (subtypes). However, only eight genetic groups (1-6, 10 and 11) have been defined on the basis of the full-length sequence. Hence, the entire nucleotide sequences of three HCV isolates in genetic groups 7-9 have now been determined. Phylogenetic analysis over the full-length sequences of these three isolates, along with 30 more in the other eight genetic groups, indicated that genetic groups 6-9 and 11 have bifurcated from a common branch and groups 3 and 10 from another. In the former branch groups 7 and 11, and groups 8 and 9, are closely related. Consequently, HCV can be classified into either eleven (1-11) or six groups (1; 2; 3 and 10; 4; 5; 6-9 and 11), allowing a clear separation of group and genotype similarity within the NS5b region or a subregion of 1093 nt. When pairwise comparison of 1093 nt in the NS5b sequence was performed on 106 HCV isolates of 36 genotypes in eleven genetic groups, they were classified into either eleven (1-11) or six (1; 2; 3 and 10; 4; 5; 6-9 and 11) genetic groups. However, group and genotype similarities were not clearly separable in either classification. The overlapping range was smaller using the classification into eleven genetic groups as compared to six genetic groups (2.7 vs 4-7%). These results indicate that HCV might not have evolved in the two-tiered fashion, at least in a strict sense.

Base Sequence↗
PubMed2003

[Genetic co-adaptability among structural genes under the condition of genetic disequilibrium].

With the technology of PAGE,the genetic polymorphism of blood protein and enzyme was investigated,and genetic co-adaptability among structural genes was studied in three goat populations(147 goats) including Chaidamu goat(CS), Chaidamu Cashmere goat(CRS) and Liaoning Cashmere goat(LRS) in Qinghai Province, China. The results were showed that the genetic disequilibrium of 10 locus combinations was found among 45 locus combinations in the three goat populations,and these genetic disequilibria were caused only by the difference of genetic co-adaptability among genes,because there didn't exist the linkage disequilibrium among non-allelic genes. The genetic disequilibrium including the difference of genetic co-adaptability between non-allelic genes was only found at Tf-P(A-3) locus combinations in LRS population,the other ones were all caused by the genetic disequilibrium at a single locus. The difference of genetic co-adaptability of LAP-EsD locus combinations could be messaged among different populations.

English Abstract↗
PubMed2005

Genetic progress in multistage dairy cattle breeding schemes using genetic markers.

The aim of this paper was to explore general characteristics of multistage breeding schemes and to evaluate multistage dairy cattle breeding schemes that use information on quantitative trait loci (QTL). Evaluation was either for additional genetic response or for reduction in number of progeny-tested bulls while maintaining the same response. The reduction in response in multistage breeding schemes relative to comparable single-stage breeding schemes (i.e., with the same overall selection intensity and the same amount of information in the final stage of selection) depended on the overall selection intensity, the selection intensity in the various stages of the breeding scheme, and the ratio of the accuracies of selection in the various stages of the breeding scheme. When overall selection intensity was constant, reduction in response increased with increasing selection intensity in the first stage. The decrease in response was highest in schemes with lower overall selection intensity. Reduction in response was limited in schemes with low to average emphasis on first-stage selection, especially if the accuracy of selection in the first stage was relatively high compared with the accuracy in the final stage. Closed nucleus breeding schemes in dairy cattle that use information on QTL were evaluated by deterministic simulation. In the base scheme, the selection index consisted of pedigree information and own performance (dams), or pedigree information and performance of 100 daughters (sires). In alternative breeding schemes, information on a QTL was accounted for by simulating an additional index trait. The fraction of the variance explained by the QTL determined the correlation between the additional index trait and the breeding goal trait. Response in progeny test schemes relative to a base breeding scheme without QTL information ranged from +4.5% (QTL explaining 5% of the additive genetic variance) to +21.2% (QTL explaining 50% of the additive genetic variance). A QTL explaining 5% of the additive genetic variance allowed a 35% reduction in the number of progeny tested bulls, while maintaining genetic response at the level of the base scheme. Genetic progress was up to 31.3% higher for schemes with increased embryo production and selection of embryos based on QTL information. The challenge for breeding organizations is to find the optimum breeding program with regard to additional genetic progress and additional (or reduced) cost.

Animals↗
PubMed2006

Genetic disorders among Palestinian Arabs. 4: Genetic clinics in the community.

Genetic disorders are frequent in the Arab population of Israel, mainly because of the preference for consanguineous marriages. Many of the inherited diseases are present with a high frequency only in a limited region or a single village. It is therefore not surprising that, in each of the villages, a different distribution of genetic diseases is found; thus, a detailed knowledge of the genetic disorders present in each village is of utmost importance for genetic counseling. As a direct consequence of these observations two community genetics clinics were opened as a pilot project to study their impact on the population to be served. The use of a computer database allowed for easier and more accurate genetic counseling. There were almost 1,500 visits in the 4-year period since the introduction of the services. During the years an increase in the mean number of consultations per clinic as well as a change in the type of referrals was observed. There was an increasing proportion of clinics that were made at a time in which genetic counseling allow for primary prevention. The presence of a genetic counselor in the village clinic allows for better and closer contacts with the family physician.

Arabs↗
PubMed2000

Surrogate genetics: the use of bacterial hybrids as a genetic tool.

Experimental dissection of bacterial genomes requires a well-developed set of genetic tools, but many bacteria lack the essential tools required for genetic analysis. Recombination of a region of chromosomal DNA from poorly characterized donor bacteria with the chromosome of a suitable surrogate host creates a genetically malleable hybrid, providing a short-cut for the detailed genetic analysis of the substituted genes. However, recombination between closely related but nonidentical DNA sequences ("homeologous recombination") is strongly inhibited, posing a powerful barrier to gene exchange between bacteria and a major impediment to the construction of genetic hybrids. By taking advantage of mutS and recD mutant recipients, it is possible to effectively overcome the recombination barrier, allowing construction of genetic hybrids in a related surrogate host. Once stably recombined into the recipient chromosome, the donor DNA can be studied with all the genetic tools available in the surrogate host. In addition to facilitating standard genetic analysis, use of a surrogate host can provide novel approaches to study the physiological roles of unique genes from poorly characterized bacteria.

Bacteria↗
PubMed2005

Genetic diversity and genetic structure of an endangered species, Trillium tschonoskii.

The genetic diversity and genetic structure of Trillium tschonoskii (Maxim) were investigated using amplified fragment length polymorphism markers. Eight primer combinations were carried out on 105 different individuals sampled from seven populations. Of the 619 discernible DNA fragments generated, 169 (27.3%) were polymorphic. The percentage of polymorphic bands within populations ranged from 4.52 to 10.50. Genetic diversity (H(E)) within populations ranged from 0.0130 to 0.0379, averaging 0.0536 at the species level. Genetic differentiation among populations was detected based on Nei's genetic diversity analysis (53.03%) and analysis of molecular variance (AMOVA) (52.43%). AMOVA indicated significant genetic differentiation among populations (52.43% of the variance) and within populations (47.57% of the variance) (p < 0.0002). Gene flow was low (0.4429) among populations. Species breeding system and limited gene flow among populations are plausible reasons for the high genetic differentiation observed for this species. We propose an appropriate strategy for conserving the genetic resources of T. tschonoskii in China.

China↗
PubMed2006

Seascape genetics: a coupled oceanographic-genetic model predicts population structure of Caribbean corals.

Population genetics is a powerful tool for measuring important larval connections between marine populations [1-4]. Similarly, oceanographic models based on environmental data can simulate particle movements in ocean currents and make quantitative estimates of larval connections between populations possible [5-9]. However, these two powerful approaches have remained disconnected because no general models currently provide a means of directly comparing dispersal predictions with empirical genetic data (except, see [10]). In addition, previous genetic models have considered relatively simple dispersal scenarios that are often unrealistic for marine larvae [11-15], and recent landscape genetic models have yet to be applied in a marine context [16-20]. We have developed a genetic model that uses connectivity estimates from oceanographic models to predict genetic patterns resulting from larval dispersal in a Caribbean coral. We then compare the predictions to empirical data for threatened staghorn corals. Our coupled oceanographic-genetic model predicts many of the patterns observed in this and other empirical datasets; such patterns include the isolation of the Bahamas and an east-west divergence near Puerto Rico [3, 21-23]. This new approach provides both a valuable tool for predicting genetic structure in marine populations and a means of explicitly testing these predictions with empirical data.

Animals↗
PubMed2000

Perception of genetic risk among genetic counselors.

A mailed survey of female prenatal genetic counselors, obstetric nurses, and high school biology teachers was conducted to determine if these groups hold different attitudes toward genetic risk and to investigate the extent to which any differences result from the effect of different professional experiences. In this study, the participants were 166 genetic counselors, 116 obstetric nurses, and 78 biology teachers (n=360). Survey participants completed a written questionnaire designed to assess their numeric estimate of the empiric risk for birth defects/genetic problems, their subjective perception of this risk, and their personal use of prenatal diagnosis. Genetic counselors were found to be less likely than the other groups to consider the frequency of birth defects/genetic problems as rare and were 10 times more likely than nurses and 8 times more likely than teachers to have had prenatal diagnosis. Furthermore, more than half of the prenatal diagnosis procedures had by genetic counselors were not medically indicated. These results suggest that genetic counselors have an increased perception of genetic risks relative to nurses or teachers. Possible explanations for this funding are discussed, and the potential role of discordant risk perception in creating biases in genetic counseling process is explored.

Attitude↗
PubMed2006

DISCERN-Genetics: quality criteria for information on genetic testing.

Information currently available to the public is inadequate to support those deciding to consent to a genetic test. As genetic knowledge continues to evolve, more people will be forced to consider the complex issues raised by genetic testing. We developed and tested criteria to guide the production and appraisal of information resources produced for the public on genetic testing. Lay people with and without experience of a genetic condition, and providers and producers of health information appraised and listed the criteria they used to rate the quality of a sample of information on cystic fibrosis, Down's syndrome, familial breast cancer, familial colon cancer, haemochromatosis, Huntington's disease, sickle cell disease, and thalassaemia. These genetic conditions represent different populations, disease pathways, and treatment decisions. The information medium could be written, electronic, CD, audio or video. The quality criteria were tested iteratively (using the weighted kappa statistic) for the level of agreement between users applying successive drafts of the criteria to different samples of information. The final set of criteria consisted of 19 questions plus an overall quality rating. Chance corrected agreement (weighted kappa) among the appraisers for the overall quality rating was 0.61 (0.60-0.62). The criteria cover the scope of the information resources, information on the condition, the test procedure and results, decision making, and the reliability of the information. The DISCERN-Genetics criteria will guide the production and appraisal of information produced for the public, and will facilitate the involvement of the public in decisions around genetic screening and testing.

Female↗
PubMed2003

Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout.

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.

Animals↗
PubMed2003

Population genetic analysis of white shrimp, Litopenaeus setiferus, using microsatellite genetic markers.

The white shrimp (Litopenaeus setiferus) is a commercially and recreationally valuable species, yet little is known of its population structure or genetic diversity. White shrimp are distributed along the Atlantic coast of the United States and from the west coast of Florida to the Bay of Campeche, Mexico. In this study, shrimp were collected from North Carolina, South Carolina (four separate collections were taken from 1995 to 1999), Georgia, the Atlantic and Gulf coasts of Florida, Louisiana, Texas and Mexico. DNA was isolated from these individuals, and genetic variation was assessed at six microsatellite loci. These loci were, for the most part, highly polymorphic with an average expected heterozygosity of 0.68. Deviations from Hardy-Weinberg proportions were observed over all samples, but experimental results suggested the presence of null alleles, which confounded a biological interpretation of this result. Pairwise tests of the similarity of allele frequency distributions and distance measure analyses showed broad-scale genetic homogeneity superimposed over occasional indications of random geographical and temporal differentiation. FST and RST estimates over all loci and samples were 0.002 or less and indicated little population structure. Weak but significant genetic differentiation was evident only between pooled western Atlantic and pooled Gulf of Mexico samples. Within the Gulf of Mexico or within the western Atlantic, the large-scale genetic homogeneity observed may be a consequence of genetic mixing resulting from pelagic larvae and adult migrations, while the random local genetic differentiation may be a result of genetic sampling or experimental sampling error. The weak differentiation between shrimp from the Gulf of Mexico and the western Atlantic can be explained by a relatively recent separation of these two populations and/or small amounts of ongoing gene flow.

Animals↗
PubMed2006

Use of genetically modified viruses and genetically engineered virus-vector vaccines: environmental effects.

Despite major therapeutic advances, infectious diseases remain highly problematic. Recent advancements in technology in producing DNA-based vaccines, together with the growing knowledge of the immune system, have provided new insights into the identification of the epitopes needed to target the development of highly targeted vaccines. Genetically modified (GM) viruses and genetically engineered virus-vector vaccines possess significant unpredictability and a number of inherent harmful potential hazards. For all these vaccines, safety assessment concerning unintended and unwanted side effects with regard to targeted vaccinees has always been the main focus. Important questions concerning effects on nontargeted individuals within the same species or other species remain unknown. Horizontal transfer of genes, though lacking supportive experimental or epidemiological investigations, is well established. New hybrid virus progenies resulting from genetic recombination between genetically engineered vaccine viruses and their naturally occurring relatives may possess totally unpredictable characteristics with regard to host preferences and disease-causing potentials. Furthermore, when genetically modified or engineered virus particles break down in the environment, their nuclei acids are released. Appropriate risk management is the key to minimizing any potential risks to humans and environment resulting from the use of these GM vaccines. There is inadequate knowledge to define either the probability of unintended events or the consequences of genetic modifications. The objective of this article is to highlight the limitations in environmental risk assessment and raise awareness of the potential risks involving the use of genetically modified viruses and genetically engineered virus-vector vaccines.

Environmental Pollution↗
PubMed1998

Linkage of the MHC to familial multiple sclerosis suggests genetic heterogeneity. The Multiple Sclerosis Genetics Group.

Multiple sclerosis (MS) is a demyelinating autoimmune disease of the central nervous system. While its etiology is not well understood, genetic factors are clearly involved. Until recently, most genetic studies in MS have been association studies using the case-control design testing specific candidate genes and studying only sporadic cases. The only consistently replicated finding has been an association with the HLA-DR2 allele within the major histocompatibility complex (MHC) on chromosome 6. Using the genetic linkage design, however, evidence for and against linkage of the MHC to MS has been found, fostering suggestions that sporadic and familial MS have different etiologies. Most recently, two of four genomic screens demonstrated linkage to the MHC, although specific allelic associations were not tested. Here, a dataset of 98 multiplex families was studied to test for an association to the HLA-DR2 allele in familial MS and to determine if genetic linkage to the MHC was due solely to such an association. Three highly polymorphic markers (HLA-DR, D6S273 and TNFbeta) in the MHC demonstrated strong genetic linkage (parametric lod scores of 4.60, 2.20 and 1.24, respectively) and a specific association with the HLA-DR2 allele was confirmed (TDT; P < 0.001). Stratifying the results by HLA-DR2 status showed that the linkage results were limited to families segregating HLA-DR2 alleles. These results demonstrate that genetic linkage to the MHC can be explained by the HLA-DR2 allelic association. They also indicate that sporadic and familial MS share a common genetic susceptibility. In addition, preliminary calculations suggest that the MHC explains between 17 and 62% of the genetic etiology of MS. This heterogeneity is also supported by the minority of families showing no linkage or association with loci within the MHC.

Alleles↗
PubMed2006

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.

BACKGROUND: The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. RESULTS: The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. CONCLUSION: Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

Computational Biology↗
PubMed2003

Discovering and addressing the client's lay construct of genetic disease: an important aspect of genetic healthcare?

Genetic health care includes provision of information about (a) the cause of the condition, (b) recurrence risks, and (c) options for avoiding or treating the disease. This specialized aspect of health care may be offered by appropriately trained nurses, doctors or genetic counselors, but for brevity in this article the term "genetic counselor" will be used to describe any health professional providing such care. The accepted definitions of genetic counseling emphasize the transfer of information from the counselor to the client, to facilitate the client in making informed decisions (Ad Hoc Committee on Genetic Counseling, American Society of Human Genetics, 1975; Harper, 1998). However, it is important to recognize that both clients and counselors bring to the process of genetic counseling their own knowledge, values, and beliefs (Hallowell & Richards, 1997). The information provided during the genetic counseling process may not be novel to the client, and will be received against a background of the client's previous knowledge about the condition.

Adolescent↗
PubMed2002

Estimates of parameters between direct and maternal genetic effects for weaning weight and direct genetic effects for carcass traits in crossbred cattle.

Estimates of heritabilities and genetic correlations were obtained for weaning weight records of 23,681 crossbred steers and heifers and carcass records from 4,094 crossbred steers using animal models. Carcass traits included hot carcass weight; retail product percentage; fat percentage; bone percentage; ribeye area; adjusted fat thickness; marbling score, Warner-Bratzler shear force and kidney, pelvic and heart fat percentage. Weaning weight was modeled with fixed effects of age of dam, sex, breed combination, and birth year, with calendar birth day as a covariate and random direct and maternal genetic and maternal permanent environmental effects. The models for carcass traits included fixed effects of age of dam, line, and birth year, with covariates for weaning and slaughter ages and random direct and maternal effects. Direct and maternal heritabilities for weaning weight were 0.4 +/- 0.02 and 0.19 +/- 0.02, respectively. The estimate of direct-maternal genetic correlation for weaning weight was negative (-0.18 +/- 0.08). Heritabilities for carcass traits of steers were moderate to high (0.34 to 0.60). Estimates of genetic correlations between direct genetic effects for weaning weight and carcass traits were small except with hot carcass weight (0.70), ribeye area (0.29), and adjusted fat thickness (0.26). The largest estimates of genetic correlations between maternal genetic effects for weaning weight and direct genetic effects for carcass traits were found for hot carcass weight (0.61), retail product percentage (-0.33), fat percentage (0.33), ribeye area (0.29), marbling score (0.28) and adjusted fat thickness (0.25), indicating that maternal effects for weaning weight may be correlated with genotype for propensity to fatten in steers.

Adipose Tissue↗
PubMed2000

[Genetic diagnosis for cancer--tumorigenesis and genetic alterations].

During malignant transformation, cancer cells acquire multiple genetic alterations that override the normal mechanisms controlling cellular proliferation. In brief, cancer is a disease of genetic abnormalities caused by hereditary and/or environmental factors. Genetic diagnosis for cancer can be divided into four categories: 1) pre-symptomatic diagnosis, 2) existence diagnosis, 3) property diagnosis-prognosis diagnosis and 4) genetic test for gene therapy. 1) For hereditary cancer families, pre-symptomatic diagnosis is available. Individuals with multiple cancers can be diagnosed by microsatellite instability(MSI) test using resected cancer tissues and by genotyping of mismatch repair enzymes. If the genotype abnormality is detected, the propositus can obtain early diagnosis and prevention of cancer, and genetic services of their siblings. 2) Using PCR technology, occult tumor cells can be detected from blood and other biological body fluids, as targets of chimeric transcripts and tissue-specific expressions. 3) Molecular properties of cancer cells are investigated for grading malignancy and therapeutic sensitivities. Using the molecular properties, prognosis of the patient can be estimated. 4) Following the genetic test results, the specific and superior gene therapy can be applied individually. Post-therapeutic monitoring is also available only by genetic test. After the genome project, the significance of single nucleotide polymorphisms(SNPs) related with cancer will be established, then tailor-made therapy and/or prevention will be applicable to individuals. The ultimate goal of genetic diagnosis would be the final priority to the phenotypic diagnosis.

Genetic Counseling↗
PubMed1997

Selection of homogeneous populations for genetic study: the Portugal genetics of psychosis project.

Molecular genetic studies of psychiatric disorders must face the possibility that despite the significant contribution of genetic factors to the expression of syndromes like schizophrenia, these syndromes may be a heterogeneous collection of genetic and non-genetic illnesses. These illnesses may be etiologically distinct from each other and still share many clinical features in common. Linkage studies of families with multiple affected members tend to favor the selection of genetic forms of a syndrome but can still represent a heterogeneous set of different genetic illnesses. To limit the potential genetic heterogeneity of a study sample, we selected a population that was geographically isolated and was historically relatively genetically homogeneous. We then assessed the relative level of homogeneity utilizing a surname analysis of the population of the Azores, mainland Portugal, rural USA, and urban USA. The average number of families with the same last name corrected for population size in the Azores is 30.88, in Coimbra it is 21.42, compared to 1.13 in a rural American population and 0.38 in an urban American population. The results of this analysis indicate that the Azores have the highest degree of homogeneity, and mainland Portugal has a high degree of homogeneity.

Azores↗