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Results for “Genetic characterization”

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PubMed1979

Genetic characterization of the new morphological and UV-sensitive mutants in Coprinus cinereus. I. A UV-sensitive mutation rad 1 associated with elevated frequencies of mitotic and meiotic recombination.

Studies on the effect of an UV-sensitive mutation, rad 1, in meiotic and mitotic recombination in Coprinus indicated that, in homozygous condition, rad 1 increased the spontaneous meiotic recombination by 50% and UV-induced mitotic intergenic recombination by about 5-fold. The homozygous rad 1 diploid was shown to be much more sensitive to the recombinogenic effects of polyfunctional than than of mono- or non-functional alkylating agents.

Agaricales↗

PubMed1997

Genetic characterization of vif, vpr, and vpu sequences from long-term survivors of human immunodeficiency virus type 1 infection.

The identification of HIV-1-infected individuals who remain asymptomatic despite prolonged infection presents a unique opportunity to understand virologic and host factors involved in the pathogenesis of AIDS. We have previously identified 10 long-term survivors (LTS) who are clinically healthy and immunologically normal despite 13 to 15 years of HIV-1 infection. In this study, we examined three accessory genes of HIV-1, vif, vpr, and vpu, in these LTS. A total of 52 vif, 54 vpr, and 55 vpu nucleotide sequences were obtained from the peripheral blood mononuclear cells of these patients. Analysis of these sequences revealed no gross deletions or insertions. Most of the clones were full-length with an intact open reading frame. Phylogenetic analyses of the vif, vpr, and vpu sequences from the LTS suggested that the HIV-1 strains found in the study subjects are not significantly different from those found in patients with AIDS and that the viruses in the LTS are unlikely to share a common genetic origin. Furthermore, a similar degree of overall genetic diversity between viruses from the LTS and AIDS patients suggests that there is unlikely a significant correlation between the degree of genetic diversity and the rate of disease development. Factors other than genetic divergence, such as viral load and phenotype, are likely to impact more on disease status.

Adult↗

PubMed1999

Genetic characterization of the hemagglutinin of two strains of influenza B virus co-circulated in Taiwan.

Two isolates of influenza B virus were obtained in the spring of 1997. One strain, B/Taiwan/21706/97, was isolated from a patient who had acute tonsillitis. The other, B/Taiwan/3143/97, was isolated from a patient who was diagnosed with meningoencephalitis. This implies that the influenza B viruses not only cause respiratory symptoms but may also cause inflammation of the nervous system. Sequence analysis of the hemagglutinin (HA) gene, HA1 domain, indicated that there were remarkable amino acid changes in the strain B/Taiwan/3143/97 compared to B/Victoria/2/87, B/Yamagata/16/88, and B/Taiwan/7/88. The changes in the positions 116, 200, 238, 242, and 271 were correlated with receptor binding. Furthermore, a potential glycosylation site at position 233 was lost. In total, 30 amino acid changes were noted at positions ranging from 116 to 295. These changes may affect the antigenicity of the virus. Phylogenetic analyses also showed that the B/Taiwan/3143/97 was located in an independent lineage, when compared to the reference strains belonging to B/Victoria/2/87 and B/Yamagata/16/88 lineages. This supports the hypothesis that influenza B viruses with distinct genetic characteristic were co-circulated in Taiwan.

Base Sequence↗

PubMed2006

Differences between Lactococcus garvieae isolated from the genus Seriola in Japan and those isolated from other animals (trout, terrestrial animals from Europe) with regard to pathogenicity, phage susceptibility and genetic characterization.

AIMS: To clarify the epidemiological relationship between Lactococcus garvieae isolates from the Seriola in Japan and isolates from other animals. METHODS AND RESULTS: A total of 32 isolates obtained from aquatic (the genus Seriola and trout) and terrestrial animals (cow, pig, cat, dog and horse) was used to evaluate its pathogenicity to yellowtail and mouse, phenotype (KG+ and KG-), its susceptibility to three bacteriophages and the pattern of pulsed field gel electrophoresis (PFGE). Lactococcus garvieae isolated from Seriola showed strong pathogenicity to yellowtail, while isolates from trout showed weak pathogenicity and those obtained from terrestrial animals showed no distinct pathogenicity. Only, the isolates from the genus Seriola in Japan showed susceptibility to the bacteriophages. The results of PFGE pattern indicate that the isolates obtained from the Seriola predict homogeneity, while there is no similarity among the isolates obtained from different animals. CONCLUSION: This experiment indicates that L. garvieae isolated from Seriola in Japan appears to be very different from the isolates obtained from other animals, and the isolates prevalent among the genus Seriola in Japan might be homogeneous. SIGNIFICANCE AND IMPACT OF THE STUDY: This study suggests that a particular genetic group that has specially adapted and acquired virulence toward yellowtail were prevalent among the genus Seriola in Japan.

Animals↗

PubMed2004

Genetic characterization of the Indian cattle breeds, Ongole and Deoni (Bos indicus), using microsatellite markers - a preliminary study.

BACKGROUND: Molecular characterization of cattle breeds is important for the prevention of germplasm erosion by cross breeding. The Indian zebu cattle have their significant role in evolution of present day cattle breeds and development of some of the exotic breeds. Microsatellites are the best available molecular tools for characterization of cattle breeds. The present study was carried out to characterize two Indian cattle breeds, Ongole and Deoni, using microsatellite markers. RESULTS: Using 5 di- and 5 tri-nucleotide repeat loci, 17 Ongole and 13 Deoni unrelated individuals were studied. Of the ten loci, eight revealed polymorphism in both the breeds. The di-nucleotide repeat loci were found to be more polymorphic (100%) than tri-nucleotide repeat loci (60%). A total of 39 polymorphic alleles were obtained at 4.5 alleles per locus in Ongole and 4.1 in Deoni. The average expected heterozygosity was 0.46 (+/-0.1) and 0.50 (+/-0.1) in Ongole and Deoni breeds, respectively. The PIC values of the polymorphic loci ranged from 0.15 to 0.79 in Ongole and 0.13 to 0.80 in Deoni breeds. Six Ongole specific and three Deoni specific alleles were identified. The two breeds showed a moderate genetic relationship between themselves with a FST value of 0.117 (P = 0.01). CONCLUSIONS: This preliminary study shows that microsatellite markers are useful in distinguishing the two zebu breeds namely, Ongole and Deoni. Further studies of other zebu breeds using many microsatellite loci with larger sample sizes can reveal the genetic relationships of Indian breeds.

Animals↗

PubMed1998

Genetic characterization of the malaria parasite Plasmodium falciparum in the transmission from the host to the vector.

The present study followed a Plasmodium falciparum population through its life-cycle at the level of individual hosts and vectors. The aim was to determine to what extent genotypes of the parasite that were found in the host were transmitted to the vector. Mosquitoes were collected that had fed on people sleeping under mosquito nets with holes. Genes determining 2 highly polymorphic merozoite surface proteins, MSP-1 and MSP-2, were used to characterize the parasite by PCR at different stages of the life-cycle. The parasite genotypes found in the host were compared to the genotypes of the oocyst stages after transmission to the mosquitoes. The results show that there was no significant correlation in the rate of oocyst-positive mosquitoes and the presence of parasites in the blood samples. For MSP-1, most of the parasites characterized in the human blood by PCR fragment size were also found afterwards in the oocyst-stage (22 of 29; MSP-2: 17 of 36). This study indicates that there is no selective transmission of distinct genotypes to the vector. In addition, the frequencies of the allelic families of both genes are similar in the blood samples and in the oocysts for the whole population.

Adolescent↗

PubMed1991

Heat shock in Bacillus subtilis: genetic characterization of a mutant.

Bacillus subtilis strain BUL786, a transposon-generated mutant, lacks a 97 kD protein following heat shock and has unique protein secretion properties. In this study, transduction analysis demonstrated that the properties of high temperature protease secretion, heat shock protein distribution, and loss of the 97 kD heat shock protein were all transferred as a single trait to recipient bacteria. The high temperature-specific protease released by this mutant into the supernatant was also shown to be produced during heat shock by the parental cells, but is retained intracellularly.

Bacillus subtilis↗

PubMed2003

Genetic characterization of new Dobrava hantavirus isolate from Greece.

The first complete genome sequence of Dobrava hantavirus isolated from yellow-necked mouse Apodemus flavicollis trapped in the northeastern Greece is described. The S, M, and L segments of the Greek isolate of Dobrava virus are 1673, 3635, and 6532 nucleotides (nt) long, respectively, and encode the nucleocapsid (N) protein of 429 amino acids (aa), glycoprotein precursor of 1135 aa, and the L protein of 2151 aa. N protein contains three cysteine residues conserved in all known hantaviruses, as well as structural domains responsible for the RNA binding and presumable interaction with the apoptosis enhancer Daxx. All cysteine residues and glycosylation sites that are conserved among G1G2 sequences of all hantaviruses species were also found in the Greek isolate. The L protein contains all the polymerase motifs and structural domains found in other hantavirus polymerases. Comparison of the Greek isolate of Dobrava virus with other hantaviruses showed the highest level of sequence homology with Dobrava virus isolate from Slovenia. Other hantaviruses carried by Murinae rodents (Saaremaa, Hantaan, Seoul, and Thailand viruses) were more divergent and hantaviruses carried by Arvicolinae or Sigmodontinae rodents showed the highest genetic diversity with the Greek isolate of Dobrava. The results of phylogenetic analyses confirmed these observations and showed a monophily of all the Dobrava virus strains that, in turn, shared more ancient ancestors first with Saaremaa virus and then with other Murinae-borne hantaviruses.

Amino Acid Sequence↗

PubMed2001

Maturity-onset diabetes of the young: from clinical description to molecular genetic characterization.

Maturity-onset diabetes of the young is a heterogeneous group of autosomal dominantly inherited, young-onset beta-cell disorders. At least two consecutive generations are affected with a family member diagnosed before 25 years of age. Diabetes is caused either by mutations in the glucokinase gene (glucokinase MODY) or by mutations in transcription factors (transcription factor MODY). Glucokinase maturity-onset diabetes of the young is a mild, non-progressive hyperglycaemia caused by a resetting of the pancreatic glucose sensor. It is treated with diet, and complications are rare. Pregnancies affected by glucokinase mutations have specific management strategies and prognosis. Transcription factor maturity-onset diabetes of the young, caused by mutations in the hepatocyte nuclear factor genes HNF-1alpha, HNF-4alpha and HNF-1beta, and in insulin promoter factor-1 results in a progressive beta-cell defect with increasing treatment requirements and diabetic complications. Cystic renal disease is a prominent feature of HNF-1beta mutations. Further maturity-onset diabetes of the young genes remain to be identified. MODY is part of the differential diagnosis of diabetes presenting in the first to third decades of life. Diagnostic molecular genetic testing is available for the more common genes involved.

Adult↗

PubMed1978

Genetic characterization of hydroxyurea-resistance in Chinese hamster ovary cells.

Hydroxyurea is an excellent selective agent for obtaining drug-resistant mutants. At a frequency of approximately 1 X 10(-5) it was possible to select, in a single step, colonies that exhibited significant resistance to the cytotoxic effects of the drug. These hydroxyurea-resistant cell lines maintained their resistant phenotype after extensive cultivation in the absence of the drug. Reconstruction experiments indicated that the expression of hydroxyurea-resistance and the frequency of drug-resistant colonies was independent of cell densities up to 5 X 10(5) cells per 100-mm selection plate. Luria-Delbrück fluctuation analyses indicated that the appearance of hydroxyurea-resistant cells in wild type populations occurred spontaneously and at a rate of 4.8 X 10(-6) per cell per generation in the presence of 0.33 mM drug. Studies with the mutagen, ethyl methane sulfonate indicated that it was capable of increasing the frequency of hydroxyurea-resistant cells by a factor of approximately 10. Also, cell-cell hybridization experiments showed that hydroxyurea-resistance behaves as a dominant or codominant trait and that hydroxyurea-resistance was a useful new genetic marker for selection of somatic cell hybrids. Furthermore, similar to many other drug-resistant cell lines hydroxyurea-resistant cells were found to exhibit an altered sensitivity to a number of non-selective agents (guanazole, N-carbamoyloxyurea, formamidoxime, and hydroxyurethane). Except for guanazole these compounds are structurally very similar to hydroxyurea and may be expected to have similar modes of action. The results presented in this paper support the view that hydroxyurea-resistance is expressed as a normal genetic trait and is a useful genetic marker for somatic cell genetic studies.

Animals↗

PubMed2005

Genetic characterization of Chromobacterium isolates from black water environments in the Brazilian Amazon.

AIMS: To isolate and to characterize the diversity of Chromobacterium violaceum from the Brazilian Amazon region. METHODS AND RESULTS: Twenty-two isolates were obtained from the waters and banks of the river Negro, in the Brazilian Amazon. All isolates were able to grow in vitro at 44 degrees C and pH 4.0, but were adversely affected by temperatures below 15 degrees C, and unable to survive at 4 degrees C, properties that may be related to the adaptation to the ecosystem. The isolates were joined at a final level of similarity of only 13% in the rep-PCR analysis. The analysis of 16S rRNA genes resulted in three main groups clustered at a final level of similarity of 97% and only three isolates were clustered with the type strain. Similar data were obtained for the 23S rRNA gene. CONCLUSIONS: A high level of genetic diversity was verified with indications that the Brazilian isolates would fit into at least two new clusters besides C. violaceum species. SIGNIFICANCE AND IMPACT OF THE STUDY: The results show remarkable bacterial adaptability and genetic diversity of C. violaceum in the Amazon region.

Brazil↗

PubMed1995

Molecular genetic characterization and prenatal diagnosis in a family with Hunter disease.

Hunter disease, Mucopolysaccharidosis type II, is an X-linked recessive lysosomal storage disorder caused by a deficiency in iduronate sulfatase activity. We studied at molecular level a Neapolitan family with the disease. We report, in patient, the delta 139 mutation on the third exon of the gene, on female family members, the DNA analysis that allowed to assess or exclude their carrier status and on fetal DNA from a pregnancy of patient's mother, a prenatal diagnosis that resulted negative.

Base Sequence↗

PubMed1988

Genetic characterization and origin of Tunisian Berbers.

Blood samples from 120 Tunisian Berbers of Gallala village were typed for Gm and Km immunoglobulin allotypes, alpha-1-antitrypsin variants and AB0 blood groups. The results were compared with those of other Berber groups. The combined data, considered in the light of sociological, historical and paleontological data, support the hypothesis that the Berbers are native to North Africa and their ancestors, the first modern man (Homo sapiens) of North Africa, were the founders of the European populations. The ancestors of the Berbers could have been an intermediate population between H. sapiens from Europe and from South Africa.

ABO Blood-Group System↗

PubMed2005

Immunophenotypic and genetic characterization of a CD8 positive mantle cell lymphoma in a patient with concomitant Mycosis fungoides.

Mantle cell lymphoma (MCL) is immunophenotypically characterized by cell surface co-expression of CD19, CD20, CD5, IgM and FMC7. However, the concomitant presence of other antigens distinctive of a particular leukocyte subset, e.g. T-lymphocytes, is an exceptional finding in MCL. Here, the first case of a blastic MCL in leukaemic phase with aberrant expression of the T-cell associated antigen CD8 occurring in a patient with concomitant Mycosis fungoides is described. Comprehensive immunophenotypic analysis showed that the MCL cells expressed the typical B-lymphocytic markers, were CD5 and CD8 positive, but did not express other T-cell proteins, such as CD2, CD3, CD4, CD7, TCRalphabeta and TCRgammadelta. The MCL cells expressed both CD8alpha and CD8beta chains indicating cell surface presence of CD8alphabeta heterodimers. Intriguingly, expression of the cytotoxic enzymes perforin and granzyme A was detected by RT-PCR. Cytogenetic and molecular genetic analysis of the lymphoma cells confirmed cyclin D1 overexpression secondary to the t(11;14)(q13;32) chromosomal translocation. Furthermore, trisomy 11, trisomy 14 and extra copies of t(11;14) translocated chromosomes were detected in sub clones of the analyzed MCL cells. Clinically, an aggressive course of disease including cerebral lymphoma involvement was noted in the reported patient. Hence, systematic studies addressing the incidence, biology and clinical behavior of this form of MCL seem to be justified in future.

Antigens, CD↗

PubMed1998

Genetic characterization of RRS1, a recessive locus in Arabidopsis thaliana that confers resistance to the bacterial soilborne pathogen Ralstonia solanacearum.

The soilborne, vascular pathogen Ralstonia solanacearum, the causative agent of bacterial wilt, was shown to infect a range of Arabidopsis thaliana accessions. The pathogen was capable of infecting the Col-5 accession in an hrp-dependent manner, following root inoculation. Elevated bacterial population levels were found in leaves of Col-5, 4 to 5 days after root inoculation by the GMI1000 strain. Bacteria were found predominantly in the xylem vessels and spread systematically throughout the plant. The Nd-1 accession of A. thaliana was resistant to the GMI1000 strain of R. solanacearum. Bacterial concentrations detected in leaves of Nd-1, inoculated with an hrp+ strain of R. solanacearum, were only slightly higher than those detected in the susceptible accession, Col-5, following inoculation with a strain whose hrp gene cluster was deleted. Leaf inoculation of the GMI1000 strain on the resistant accession Nd-1 induced the formation of lesions in the older leaves of the rosette whereas the same strain of R. solanacearum provoked complete wilting of Col-5. Resistance to strain GMI1000 of R. solanacearum segregated as a simply inherited recessive trait in a genetic cross between Col-5 and Nd-1. F9 recombinant inbred lines generated between these two accessions were used to map a locus, RRS1, that was the major determinant of resistance between restriction fragment length polymorphism markers mi83 and mi61 on chromosome V. This region of the A. thaliana genome is known to contain many other pathogen recognition capabilities.

Arabidopsis↗

PubMed1990

Molecular and genetic characterization of a radiation-induced structural rearrangement in mouse chromosome 2 causing mutations at the limb deformity and agouti loci.

Molecular characterization of mutations in the mouse, particularly those involving agent-induced major structural alterations, is proving to be useful for correlating the structure and expression of individual genes with their function in the whole organism. Here we present the characterization of a radiation-induced mutation that simultaneously generated distinct alleles of both the limb deformity (ld) and agouti (a) loci, two developmentally important regions of chromosome 2 normally separated by 20 centimorgans. Cytogenetic analysis revealed that an interstitial segment of chromosome 17 (17B- 17C; or, possibly, 17A2-17B) had been translocated into the distal end of chromosome 2, resulting in a smaller-than-normal chromosome 17 (designated 17del) and a larger form of chromosome 2 (designated 2(17). Additionally, a large interstitial segment of the 2(17) chromosome, immediately adjacent and proximal to the insertion site, did not match bands 2E4-2H1 at corresponding positions on a normal chromosome 2. Molecular analysis detected a DNA rearrangement in which a portion of the ld locus was joined to sequences normally tightly linked to the a locus. This result, along with the genetic and cytogenetic data, suggests that the alleles of ld and a in this radiation-induced mutation, designated ldIn2 and ajIn2, were associated with DNA breaks caused by an inversion of an interstitial segment in the 2(17) chromosome.

Abnormalities, Radiation-Induced↗

PubMed2004

Genetic characterization of very virulent infectious bursal disease viruses from Latin America.

Very virulent infectious bursal disease viruses (vvIBDVs) were detected in phenol inactivated bursal samples obtained from Brazil, the Dominican Republic, and Venezuela. After nucleotide sequence analysis of the hypervariable region of VP2 gene, the vvIBDVs from Brazil and Venezuela exhibited all of the 14 nucleotide changes that are conserved in the European UK-661 and most other vvIBDV strains. However, the vvIBDV from the Dominican Republic presented 11 nucleotide changes that are conserved in vvIBDV strains. After phylogenetic analysis, the Latin American strains were found to be related to other vvIBDV strains from Europe, Asia, and Africa. However, Brazilian and Dominican vvIBDVs clustered in two separate subgroups, while the vvIBDVs from Venezuela were closely related to other strains from other parts of the world. By deduced amino acid sequence, the three conserved amino acid residues in vvIBDV strains (222 Ala, 256 Ile, and 294 Ile) were confirmed in the Latin American viruses, and one amino acid change (300 Ala) was unique to all vvIBDVs from the Dominican Republic. The occurrence of this change in the Dominican vvIBDVs may have an impact in their antigenic makeup. Results of this study indicate that the vvIBDVs detected in Latin America are genetically similar to IBDV strains from other parts of the world. However, vvIBDVs from Venezuela were more similar to the vvIBDV strains from Europe and Asia. Of all the samples analyzed, vvIBDVs from Brazil and the Dominican Republic exhibited more genetic changes. These changes may have emerged as a result of the different management practices and environmental conditions present in each particular geographic area.

Amino Acid Sequence↗

PubMed1999

Molecular genetic characterization of both components of a dedifferentiated chondrosarcoma, with implications for its histogenesis.

Dedifferentiated chondrosarcoma is defined as a high-grade, anaplastic sarcoma adjacent to a low-grade malignant cartilage-forming tumour. Controversy remains as to whether the anaplastic and cartilaginous components are derived from a common precursor cell, or whether they represent separate genotypic lineages (collision tumour). Both components of a case of dedifferentiated chondrosarcoma were therefore separately investigated by loss of heterozygosity (LOH) analysis, comparative genomic hybridization (CGH), DNA flow cytometry, and p53 analysis. Both showed p53 overexpression and an identical somatic 6 bp deletion in exon 7 of p53. Combination of the CGH and LOH results revealed that both components had lost the same copy of chromosome 13. These results provide compelling evidence in this case for a common origin, instead of the 'collision tumour' theory. Certain genotypic alterations were not shared. The anaplastic component showed severe aneuploidy, LOH at additional loci, and amplification and deletion of several chromosome parts. In contrast, the cartilaginous component had lost chromosomes 5, 22, 17p and part of 16p and revealed an amplification of 17q. The LOH and CGH results further demonstrated that the two components had lost a different copy of chromosome 4. Thus, a substantial number of genetic alterations have occurred after the diversion of the two components, indicating that the separation of the two clones, derived from a single precursor, was a relatively early event in the histogenesis of this case of dedifferentiated chondrosarcoma.

Autoradiography↗