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PubMed2005

Phytochemical analysis and genetic characterization of six Hypericum species from Serbia.

The secondary metabolite contents and genetic profiles of six Hypericum species (H. barbatum Jacq., H. hirsutum L., H. linarioides Bosse, H. maculatum Crantz, H. rumeliacum Boiss. and H. tetrapterum Fries), collected from different locations in Serbia, have been analyzed. Methanol extracts of the aerial parts of the plants were obtained by accelerated solvent extraction (ASE) at 40 degrees C and 100 bar, and analyzed for five pharmacologically important standard constituents (hyperoside, quercitrin, pseudohypericin, hyperforin and hypericin) by LC-MS/MS. The highest content of hypericin and pseudohypericin was observed in the H. barbatum extract, while the highest content of hyperforin and quercitrin was found in the H. tetrapterum extract and the highest content of hyperoside in the H. maculatum extract. A literature survey shows that the above six Hypericum species, with the exception of H. maculatum, have not been previously genetically profiled. In order to correlate the chemical constituents of the species under investigation with their genetic factors, genetic profiling of these species was undertaken using the random amplification of polymorphic DNA (RAPD) and single sequence repeat (SSR) profiles of the above selected plants. Among the 52 random primers used for the initial screening, only 10 yielded polymorphic RAPD profiles. A total of 111 polymorphic markers were generated using these primers. The SSR analysis shows that 8 out of the 10 primers used were polymorphic. The correlation among the species under investigation using the two genetic markers was performed using Jaccuard's coefficients of similarity and a high correlation (r=0.99) was obtained. The main conclusion from the above data is that there exists a stronger correlation for secondary metabolite contents with RAPD data than with SSR data among the six Hypericum species from Serbia.

Chromatography, Liquid↗
PubMed1996

Genetic characterization of Mycobacterium avium isolates recovered from humans and animals in Australia.

Genetic relationships amongst 115 mainly Australian isolates of Mycobacterium avium were assessed using multilocus enzyme electrophoresis (MEE). The isolates were divided into 58 electrophoretic types (ETs), with a mean genetic diversity of 0.29. Isolates from humans were closely related to but distinct from those cultured from birds, whilst some porcine isolates belonged to the same ETs as certain human isolates. Pulsed field gel electrophoresis (PFGE) was used to differentiate related isolates, and those from birds and some from other animals, including pigs, were distinguished from the human isolates. The results of MEE and PFGE suggested that certain strains of M. avium may be transmitted between birds and pigs, but there was no clear evidence of transmission to humans. The serovar of the M. avium isolates was not obviously related to their ET assignment or their PFGE type.

Animals↗
PubMed1994

Genetic characterization of American and Western Samoans.

The Samoan islands were politically separated into American Samoa and Western Samoa in the early 1900s. Economic modernization is far more extensive in American Samoa. However, the Samoan archipelago has maintained a remarkable degree of sociocultural homogeneity, including intermarriage. The sociocultural exchanges presumably led to genetic homogeneity between the two Samoas. Detailed genetic comparisons and characterizations of Samoans are scanty, however. As part of a multidisciplinary study of modernization and cardiovascular risk factors in adults, we analyzed nine hypervariable nuclear DNA (HVR) and four serum protein polymorphisms in the two Samoan groups. The average heterozygosities at both DNA and serum protein loci are comparable in the two groups. As expected, the HVR loci reveal a high degree of variability (heterozygosity 30-87%) compared with the serum protein loci (heterozygosity 1-52%). A large proportion of alleles at the HVR loci, ranging from 50% to 100%, are shared between American and Western Samoa. With the exceptions of the D1S80 locus in American Samoa and the D13S118 locus in Western Samoa, the genotype distributions at all loci conform to their respective Hardy-Weinberg expectations. Sporadic occurrence of the F13B*2 allele at the F13B locus in Samoans indicates a low level of European admixture because this allele is unique to Europeans. The calculated zero values of kinship coefficients and standard genetic distances indicate minimal population differentiation between the two Samoan groups.

Alleles↗
PubMed2002

Genetic characterization of the paraimmunoblastic variant of small lymphocytic lymphoma/chronic lymphocytic leukemia: A case report and review of the literature.

Paraimmunoblastic variant of small lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL) is characterized by a diffuse proliferation of cells, called paraimmunoblasts, normally located on the pseudoproliferation centers. Patients usually present with multiple lymphadenopathies and a rapid and aggressive progression of the disease. We report a case with paraimmunoblastic variant of SLL/CLL genetically well-characterized by conventional cytogenetics, comparative genomic hybridization (CGH), IgH/BCL-1, IgH/BCL-2, and p53 fluorescent in situ hybridization (FISH) probes and polymerase chain reaction (PCR) for detection of IgH/BCL-2 translocation. A complex karyotype was found, with p53 deletion confirmed by CGH and FISH; however, no translocations involving either BCL-2 or BCL-1 and the immunoglobulin heavy chain gene were identified. A literature review shows only 20 previously reported cases, 6 of which involve genetic studies.

Aged↗
PubMed2004

[Molecular and genetic characterization of Changos descendants living in Paposo Cove].

BACKGROUND: There are geographic and ethno historic evidences that relate Paposo cove, located 150 km south of the city of Antofagasta, with old fishermen-collector populations known as Changos, that lived in that zone in the XVII and XVIII centuries. AIM: To perform a genetic and molecular characterization of current Paposo inhabitants, through mitochondrial DNA polymorphism analysis and molecular analysis of classical ABO and Duffy blood groups. MATERIAL AND METHODS: Forty unrelated individuals were studied. The presence of restriction polymorphisms that define A, B, C, and D Amerindian founder mitochondrial haplogroups was studied and molecular determination of classical blood groups were done by PCR. RESULTS: One individual had A haplogroup (2.5%), 19 had B haplogroup (47.5%), six had C haplogroup (15%) and 11 had D haplogrotup (27.5%). Three subjects (7.5%) did not have any of these haplogroups. Among ABO blood groups, the frequency of O101 allele was 0.39, that of allele O201 was 0.53 and that of A allele was 0.08. Duffy blood group frequencies were 0.58 for FY*A and 0.42 for FY*B. FY null allele was not found. CONCLUSIONS: The frequency distribution of Amerindian mitochondrial haplogroups in Paposo inhabitants suggest that these individuals are related with Aymara and Atacameño Amerindians that can be considered culturally and geographically close populations. This proposal is supported by the results of the molecular determination of classical blood groups. Our findings in Paposo cove may represent the distribution of these markers in Chango Indians, of whom there is limited physical evidence and that became extinct near 1890.

ABO Blood-Group System↗
PubMed2003

Genetic characterization of environmental isolates of the Cryptococcus neoformans species complex from Brazil.

The genetic affiliation of a large number of isolates of the Cryptococcus neoformans species complex from environmental sources in Brazil has been investigated using amplified fragment length polymorphism (AFLP). The strains of C. neoformans isolated from a single tree, as well as from neighbouring trees, showed high similarity values (> 95%) of their AFLP patterns, thus suggesting considerable genetic homogeneity. The majority of isolates of C. neoformans belonged to AFLP genotype 1, and had serotype A and mating type alpha (= C. neoformans var. grubii). Three isolates belonged to AFLP genotype 2, with serotype D and mating type alpha (= C. neoformans var. neoformans). One isolate, obtained from a building in Rio de Janeiro inhabited by pigeons, belonged to the AD hybrid AFLP genotype 3. All isolates from trees of C. neoformans var. gattii (= C. gattii) belonged to AFLP genotype 6, and their banding patterns showed relatively low genetic homogeneity with a similarity value of about 76%. Isolates of this genotype occupy an environmental niche in the Americas, and they may cause disease in non-AIDS and AIDS patients as well.

Air Microbiology↗
PubMed1997

Genetic characterization of an oral treponeme isolated from human subgingival plaque.

We examined the genetic characteristics of a human oral treponeme isolated from subgingival plaque of a patient with periodontal disease that could not be assigned to any of the previously described oral Treponema species. The guanine-plus-cytosine content of its DNA was 51 mole%. The levels of DNA-DNA relatedness of the organism to other Treponema species, including Treponema denticola, Treponema vincentii, Treponema socranskii, Treponema pallidum and Treponema phagedenis, were less than 30%. This study clearly demonstrated that the isolated treponeme could be completely distinct from the established oral Treponema species genetically. Also, the study indicated remarkable genetic heterogeneity among human oral Treponema species.

Cytosine↗
PubMed2006

Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.

BACKGROUND: Breast cancer in men is an infrequent occurrence, accounting for approximately 1% of all breast tumors with an incidence of about 1:100,000. The relative rarity of male breast cancer (MBC) limits our understanding of the epidemiologic, genetic and clinical features of this tumor. METHODS: From 1997 to 2003, 10 MBC patients were referred to our Institute for genetic counselling and BRCA1/2 testing. Here we report on the genetic and phenotypic characterization of 10 families with MBC from the North East of Italy. In particular, we wished to assess the occurrence of specific cancer types in relatives of MBC probands in families with and without BRCA2 predisposing mutations. Moreover, families with recurrent BRCA2 mutations were also characterized by haplotype analysis using 5 BRCA2-linked dinucleotide repeat markers and 8 intragenic BRCA2 polymorphisms. RESULTS: Two pathogenic mutations in the BRCA2 gene were observed: the 9106C>T (Q2960X) and the IVS16-2A>G (splicing) mutations, each in 2 cases. A BRCA1 mutation of uncertain significance 4590C>G (P1491A) was also observed. In families with BRCA2 mutations, female breast cancer was more frequent in the first and second-degree relatives compared to the families with wild type BRCA1/2 (31.9% vs. 8.0% p = 0.001). Reconstruction of the chromosome phasing in three families and the analysis of three isolated cases with the IVS16-2A>G BRCA2 mutation identified the same haplotype associated with MBC, supporting the possibility that this founder mutation previously detected in Slovenian families is also present in the North East of our Country. Moreover, analysis of one family with the 9106C>T BRCA2 mutation allowed the identification of common haplotypes for both microsatellite and intragenic polymorphisms segregating with the mutation. Three isolated cases with the same mutation shared the same intragenic polymorphisms and three 5' microsatellite markers, but showed a different haplotype for 3' markers, which were common to all three cases. CONCLUSION: The 9106C>T and the IVS16-2A>G mutations constitute recurrent BRCA2 mutations in MBC cases from the North-East of Italy and may be associated with a founder effect. Knowledge of these two recurrent BRCA2 mutations predisposing to MBC may facilitate the analyses aimed at the identification of mutation carriers in our geographic area.

Adult↗
PubMed2000

Enzyme-activity mutants in Mus musculus. I. Phenotypic description and genetic characterization of ethylnitrosourea-induced mutations.

The specific activity of erythrocyte enzymes was measured to detect gene mutations in F(1)-offspring of male mice treatment with different doses (80, 160, or 250 mg/kg body weight) of ethylnitrosourea (ENU). Altogether 13,230 offspring were screened for 10 enzyme activities. Mutants with reduced activity as well as mutants with enhanced activity were found. Of the 36 independently observed mutations, 20 were homozygous lethal. Genetic and biochemical characterizations were routinely performed. These mutants provide insight into the mechanism of ENU mutagenesis and can serve as models for structure-function studies of the corresponding enzymes.

Animals↗
PubMedDate not supplied

Genetic characterization of Dirofilaria repens and D. immitis by electrophoretic analysis of gene-enzyme systems.

A multilocus genetic analysis based on protein electrophoresis was carried out on 39 adult specimens of Dirofilaria repens and 31 of D. immitis. Seventeen enzymatic loci provided reliable electrophoretic patterns which were compared in the two species. All loci except one were monomorphic. Fixed alternative allozymes were found at 13 loci while only 3 loci shared apparently the same allozyme in the two species. The polymorphic locus, Pgm, also showed alternative allozymes. This remarkably high genetic divergence, which presumably reflects a very old speciation process, allows an easy characterization of D. repens and D. immitis and supports their classification in the subgenera Nochtiella and Dirofilaria, respectively.

Animals↗
PubMed1993

Genetic characterization of the vaccinia virus DNA polymerase: cytosine arabinoside resistance requires a variable lesion conferring phosphonoacetate resistance in conjunction with an invariant mutation localized to the 3'-5' exonuclease domain.

In this report, we describe the isolation, molecular genetic mapping, and phenotypic characterization of vaccinia virus mutants resistant to cytosine arabinoside (araC) and phosphonoacetic acid (PAA). At 37 degrees C, 8 microM araC was found to prevent macroscopic plaque formation by wild-type virus and to cause a 10(4)-fold reduction in viral yield. Mutants resistant to 8 microM araC were selected by serial passage of a chemically mutagenized viral stock in the presence of drug. Because recovery of mutants required that initial passages be performed under less stringent selective conditions, and because plaque-purified isolates were found to be cross-resistant to 200 micrograms of PAA per ml, it seemed likely that resistance to araC required more than one genetic lesion. This hypothesis was confirmed by genetic and physical mapping of the responsible mutations. PAAr was accorded by the acquisition of one of three G-A transitions in the DNA polymerase gene which individually alter cysteine 356 to tyrosine, glycine 372 to aspartic acid, or glycine 380 to serine. AraCr was found to require one of these substitutions plus an additional T-C transition within codon 171 of the DNA polymerase gene, a change which replaces the wild-type phenylalanine with serine. Congenic viral stocks carrying one of the three PAAr lesions, either alone or in conjunction with the upstream araCr lesion, in an otherwise wild-type background were generated. The PAAr mutations conferred nearly complete resistance to PAA, a slight degree of resistance to araC, hypersensitivity to aphidicolin, and decreased spontaneous mutation frequency. Addition of the mutation at codon 171 significantly augmented araC resistance and aphidicolin hypersensitivity but caused no further change in mutation frequency. Several lines of evidence suggest that the PAAr mutations primarily affect the deoxynucleoside triphosphate-binding site, whereas the codon 171 mutation, lying within a conserved motif associated with 3'-5' exonuclease function, is postulated to affect the proofreading exonuclease of the DNA polymerase.

Animals↗
PubMed1999

Genetic characterization of an epidemic of Plasmodium falciparum malaria among Yanomami Amerindians.

Malaria parasites are genetically diverse at all levels of endemicity. In contrast, the merozoite surface protein (MSP) alleles in samples from 2 isolated populations of Yanomami Amerindians during an epidemic of Plasmodium falciparum were identical. The nonvariable restriction fragment length polymorphism patterns further suggested that the sequential outbreak comprised only a single P. falciparum genotype. By examination of serial samples from single human infections, the MSP characteristics were found to remain constant throughout the course of infection. An apparent clonal population structure of parasites seemed to cause outbreaks in small isolated villages. The use of standard molecular epidemiologic methods to measure genetic diversity in malaria revealed the occurrence of a genetically monomorphic population of P. falciparum within a human community.

Animals↗
PubMed1994

Genetic characterization of pathogenic Saccharomyces cerevisiae isolates.

Saccharomyces cerevisiae isolates from human patients have been genetically analyzed. Some of the characteristics of these isolates are very different from laboratory and industrial strains of S. cerevisiae and, for this reason, stringent genetic tests have been used to confirm their identity as S. cerevisiae. Most of these clinical isolates are able to grow at 42 degrees, a temperature that completely inhibits the growth of most other S. cerevisiae strains. This property can be considered a virulence trait and may help explain the presence of these isolates in human hosts. The ability to grow at 42 degrees is shown to be polygenic with primarily additive effects between loci. S. cerevisiae will be a useful model for the evolution and genetic analysis of fungal virulence and the study of polygenic traits.

Crosses, Genetic↗
PubMed1991

Biochemical and genetic characterization of autoagglutinating phenotypes of Aeromonas species associated with invasive and noninvasive disease.

The genetic characteristics and biochemical and structural properties of a number of autoagglutinating (AA) strains of Aeromonas associated with invasive and noninvasive disease in humans and infections in animals and from environmental sources were investigated. Of 27 strains analyzed by multilocus enzyme typing and DNA hybridization studies, 25 (93%) were confirmed to belong to either hybridization group 1 (phenospecies and genospecies Aeromonas hydrophila) or 8 (phenospecies Aeromonas sobria; genospecies Aeromonas veronii). Further analysis of 19 of these strains indicated that four major groups could be identified on the basis of serologic and surface characteristics, protein and lipopolysaccharide composition, and virulence properties; these groupings held true regardless of the site of isolation or disease process involved. The major AA+ group identified was serogroup O:11, whose strains possessed an S layer, were resistant to the bactericidal activity of normal serum, and were pathogenic in mice. The results suggest a set of useful phenotypic and structural markers for identification of specific subsets of mesophilic Aeromonas involved in a wide range of infections in the animal kingdom.

Aeromonas↗
PubMed2001

Genetic characterization of the rotaviruses associated with a nursery outbreak.

G1P[6] rotaviruses were demonstrated previously to be associated with the neonatal nursery outbreak of gastroenteritis in Changhua Christian Hospital that is located in the central region of Taiwan, from September 1994 to May 1995. Meanwhile, rotaviruses were detected in children hospitalized for acute gastroenteritis. Our study characterizes the rotaviruses associated with the nursery outbreak by using genetic approaches. Nucleotide sequence analysis revealed that the VP7 genes of the nursery rotaviruses were distinct from those of the strains circulating in the community. The G1P[6] rotaviruses recovered from the nursery were closely related to another neonatal G1P[6] strain from the northern region of Taiwan in both the VP4 and VP7 genes. The VP4 genes of these nursery strains differed from those of the P[6] human reference strains 1076, M37, RV3, and ST3. Apparently, these nursery rotaviruses were distinct from the strains circulating in the community and seemed to be a variant when compared with P[6] strains reported previously.

Amino Acid Sequence↗
PubMed1995

Primary genetic characterization of HIV-1 isolates from WHO-sponsored vaccine evaluation sites by the RNase-A mismatch method.

We have analyzed by the RNase-A mismatch method 35 isolates from four WHO-sponsored vaccine evaluation sites as a secondary laboratory of the WHO Network for HIV Isolation and Characterization. The application of an estimator for the establishment of genetic distances based on the RNase-A digestion patterns in combination with the phylogenetic analysis has allowed us to construct a tree with five well defined groups of viruses. Because the clustering with known reference strains, samples from Brazil could be grouped as subtype B and the majority of those from Thailand were subtype E. Some of the samples from Uganda were classified as subtype D. Isolates from Rwanda and some from Uganda were identified as subtype A viruses. These results coincide with data obtained by heteroduplex mobility assay and nucleotide sequencing in env regions. The RNase-A mismatch method combined with phylogenetic analysis permitted the primary genetic classification of 33 of 35 samples from the WHO Network.

AIDS Vaccines↗
PubMed2000

Streptococcus thermophilus cell wall-anchored proteinase: release, purification, and biochemical and genetic characterization.

Streptococcus thermophilus CNRZ 385 expresses a cell envelope proteinase (PrtS), which is characterized in the present work, both at the biochemical and genetic levels. Since PrtS is resistant to most classical methods of extraction from the cell envelopes, we developed a three-step process based on loosening of the cell wall by cultivation of the cells in the presence of glycine (20 mM), mechanical disruption (with alumina powder), and enzymatic treatment (lysozyme). The pure enzyme is a serine proteinase highly activated by Ca(2+) ions. Its activity was optimal at 37 degrees C and pH 7.5 with acetyl-Ala-Ala-Pro-Phe-paranitroanilide as substrate. The study of the hydrolysis of the chromogenic and casein substrates indicated that PrtS presented an intermediate specificity between the most divergent types of cell envelope proteinases from lactococci, known as the PI and PIII types. This result was confirmed by the sequence determination of the regions involved in substrate specificity, which were a mix between those of PI and PIII types, and also had unique residues. Sequence analysis of the PrtS encoding gene revealed that PrtS is a member of the subtilase family. It is a multidomain protein which is maturated and tightly anchored to the cell wall via a mechanism involving an LPXTG motif. PrtS bears similarities to cell envelope proteinases from pyogenic streptococci (C5a peptidase and cell surface proteinase) and lactic acid bacteria (PrtP, PrtH, and PrtB). The highest homologies were found with streptococcal proteinases which lack, as PrtS, one domain (the B domain) present in cell envelope proteinases from all other lactic acid bacteria.

Amino Acid Sequence↗