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Barbara Pertl - One of the best experts on this subject based on the ideXlab platform.

  • detection of maternal dna in umbilical cord plasma by fluorescent pcr amplification of short Tandem Repeat Sequences
    Annals of the New York Academy of Sciences, 2006
    Co-Authors: Margit Bauer, Irmgard Orescovic, Wolfgang Schoell, Diana W Bianchi, Barbara Pertl
    Abstract:

    : Recently, maternal DNA was detected in umbilical cord blood using PCR amplification of minisatellite Sequences. The presence of maternal DNA was demonstrated in 1% to 100% of umbilical cord blood samples. The objective of this study was to determine the frequency of cord blood contamination by maternal genetic material. We used fluorescent PCR amplification of highly polymorphic short Tandem Repeat (STR) markers to detect maternal DNA in umbilical cord plasma.

  • detection of maternal deoxyribonucleic acid in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of short Tandem Repeat Sequences
    American Journal of Obstetrics and Gynecology, 2002
    Co-Authors: Margit Bauer, Irmgard Orescovic, Wolfgang Schoell, Diana W Bianchi, Barbara Pertl
    Abstract:

    Abstract Objective: Umbilical cord blood is a source of hematopoietic stem cells for transplantation. Although the first clinical applications have been encouraging, concern has been raised about contamination of umbilical blood by maternal cells, which might constitute a theoretical risk of graft-versus-host disease. The aim of this study was to assess the frequency of maternal deoxyribonucleic acid (DNA) contamination in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of highly polymorphic short Tandem Repeat DNA markers. Study Design: Fifty-seven mother/child pairs were tested for the presence of maternal DNA Sequences in cord plasma. After delivery, cord blood samples were collected via gravity. Maternal specific alleles were detected by using polymerase chain reaction amplification of 9 highly polymorphic short Tandem Repeat markers (D21S11, D21S1411, D21S1412, D18S386, D18S535, MBP-A, MBP-B, D13S631, and D13S634). Results: All 57 mother-child pairs were informative for the identification of uniquely maternal alleles in at least 2 of 9 different short Tandem Repeat markers used per case. Uniquely maternal DNA Sequences were found in 43 of 57 (75%) cord plasma samples. Conclusion: The results of our study demonstrate that maternal DNA is present in the majority of umbilical cord blood plasma samples. The technique described herein might have application in the screening of umbilical cord blood samples for the presence of contaminating maternal genetic material. (Am J Obstet Gynecol 2002;186:117-20.)

  • diagnosis of trisomy 21 in fetal nucleated erythrocytes from maternal blood by use of short Tandem Repeat Sequences
    Clinical Chemistry, 2001
    Co-Authors: Osamu Samura, Barbara Pertl, Satoshi Sohda, Kirby L Johnson, Steven J Ralston, Laurent Dellibovi, Diana W Bianchi
    Abstract:

    Background: The purpose of this study was to determine whether aneuploid fetal nucleated erythrocytes (NRBCs) could be detected in maternal blood through the use of fluorescent PCR amplification with polymorphic short Tandem Repeat (STR) markers as an alternative or complementary method to analysis by fluorescent in situ hybridization (FISH). Methods: Peripheral blood samples were obtained from women who had just undergone termination of pregnancy because of fetal trisomy 21 (three cases, 47,XY,+21; four cases, 47,XX,+21). Candidate fetal cells were isolated by flow-sorting by antibodies to the γ chain of fetal hemoglobin and Hoechst 33342. FISH analysis was performed by the use of chromosome-specific probes for X, Y, and 21. Fetal NRBCs, as defined by the presence of γ staining, characteristic morphology, and three chromosome 21 signals, along with maternal leukocytes, defined as γ negative and two chromosome 21 signals, were micromanipulated separately and subjected to fluorescent PCR amplification of chromosome 21 STR markers (D21S11, D21S1411, and/or D21S1412). Results: In five of seven cases analyzed, fetal NRBCs were aneuploid, as determined by the presence of triallelic or diallelic peaks of chromosome 21 Sequences when compared with Sequences from the maternal leukocytes. Conclusions: Fluorescent PCR amplification of STRs can detect fetal aneuploidy and may be useful in the setting of poor hybridization efficiency with FISH analysis. These results suggest that combined fetal aneuploidy and single-gene diagnoses by the use of DNA microarrays may be feasible in the near future.

Diana W Bianchi - One of the best experts on this subject based on the ideXlab platform.

  • detection of maternal dna in umbilical cord plasma by fluorescent pcr amplification of short Tandem Repeat Sequences
    Annals of the New York Academy of Sciences, 2006
    Co-Authors: Margit Bauer, Irmgard Orescovic, Wolfgang Schoell, Diana W Bianchi, Barbara Pertl
    Abstract:

    : Recently, maternal DNA was detected in umbilical cord blood using PCR amplification of minisatellite Sequences. The presence of maternal DNA was demonstrated in 1% to 100% of umbilical cord blood samples. The objective of this study was to determine the frequency of cord blood contamination by maternal genetic material. We used fluorescent PCR amplification of highly polymorphic short Tandem Repeat (STR) markers to detect maternal DNA in umbilical cord plasma.

  • detection of maternal deoxyribonucleic acid in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of short Tandem Repeat Sequences
    American Journal of Obstetrics and Gynecology, 2002
    Co-Authors: Margit Bauer, Irmgard Orescovic, Wolfgang Schoell, Diana W Bianchi, Barbara Pertl
    Abstract:

    Abstract Objective: Umbilical cord blood is a source of hematopoietic stem cells for transplantation. Although the first clinical applications have been encouraging, concern has been raised about contamination of umbilical blood by maternal cells, which might constitute a theoretical risk of graft-versus-host disease. The aim of this study was to assess the frequency of maternal deoxyribonucleic acid (DNA) contamination in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of highly polymorphic short Tandem Repeat DNA markers. Study Design: Fifty-seven mother/child pairs were tested for the presence of maternal DNA Sequences in cord plasma. After delivery, cord blood samples were collected via gravity. Maternal specific alleles were detected by using polymerase chain reaction amplification of 9 highly polymorphic short Tandem Repeat markers (D21S11, D21S1411, D21S1412, D18S386, D18S535, MBP-A, MBP-B, D13S631, and D13S634). Results: All 57 mother-child pairs were informative for the identification of uniquely maternal alleles in at least 2 of 9 different short Tandem Repeat markers used per case. Uniquely maternal DNA Sequences were found in 43 of 57 (75%) cord plasma samples. Conclusion: The results of our study demonstrate that maternal DNA is present in the majority of umbilical cord blood plasma samples. The technique described herein might have application in the screening of umbilical cord blood samples for the presence of contaminating maternal genetic material. (Am J Obstet Gynecol 2002;186:117-20.)

  • diagnosis of trisomy 21 in fetal nucleated erythrocytes from maternal blood by use of short Tandem Repeat Sequences
    Clinical Chemistry, 2001
    Co-Authors: Osamu Samura, Barbara Pertl, Satoshi Sohda, Kirby L Johnson, Steven J Ralston, Laurent Dellibovi, Diana W Bianchi
    Abstract:

    Background: The purpose of this study was to determine whether aneuploid fetal nucleated erythrocytes (NRBCs) could be detected in maternal blood through the use of fluorescent PCR amplification with polymorphic short Tandem Repeat (STR) markers as an alternative or complementary method to analysis by fluorescent in situ hybridization (FISH). Methods: Peripheral blood samples were obtained from women who had just undergone termination of pregnancy because of fetal trisomy 21 (three cases, 47,XY,+21; four cases, 47,XX,+21). Candidate fetal cells were isolated by flow-sorting by antibodies to the γ chain of fetal hemoglobin and Hoechst 33342. FISH analysis was performed by the use of chromosome-specific probes for X, Y, and 21. Fetal NRBCs, as defined by the presence of γ staining, characteristic morphology, and three chromosome 21 signals, along with maternal leukocytes, defined as γ negative and two chromosome 21 signals, were micromanipulated separately and subjected to fluorescent PCR amplification of chromosome 21 STR markers (D21S11, D21S1411, and/or D21S1412). Results: In five of seven cases analyzed, fetal NRBCs were aneuploid, as determined by the presence of triallelic or diallelic peaks of chromosome 21 Sequences when compared with Sequences from the maternal leukocytes. Conclusions: Fluorescent PCR amplification of STRs can detect fetal aneuploidy and may be useful in the setting of poor hybridization efficiency with FISH analysis. These results suggest that combined fetal aneuploidy and single-gene diagnoses by the use of DNA microarrays may be feasible in the near future.

Margit Bauer - One of the best experts on this subject based on the ideXlab platform.

  • detection of maternal dna in umbilical cord plasma by fluorescent pcr amplification of short Tandem Repeat Sequences
    Annals of the New York Academy of Sciences, 2006
    Co-Authors: Margit Bauer, Irmgard Orescovic, Wolfgang Schoell, Diana W Bianchi, Barbara Pertl
    Abstract:

    : Recently, maternal DNA was detected in umbilical cord blood using PCR amplification of minisatellite Sequences. The presence of maternal DNA was demonstrated in 1% to 100% of umbilical cord blood samples. The objective of this study was to determine the frequency of cord blood contamination by maternal genetic material. We used fluorescent PCR amplification of highly polymorphic short Tandem Repeat (STR) markers to detect maternal DNA in umbilical cord plasma.

  • detection of maternal deoxyribonucleic acid in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of short Tandem Repeat Sequences
    American Journal of Obstetrics and Gynecology, 2002
    Co-Authors: Margit Bauer, Irmgard Orescovic, Wolfgang Schoell, Diana W Bianchi, Barbara Pertl
    Abstract:

    Abstract Objective: Umbilical cord blood is a source of hematopoietic stem cells for transplantation. Although the first clinical applications have been encouraging, concern has been raised about contamination of umbilical blood by maternal cells, which might constitute a theoretical risk of graft-versus-host disease. The aim of this study was to assess the frequency of maternal deoxyribonucleic acid (DNA) contamination in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of highly polymorphic short Tandem Repeat DNA markers. Study Design: Fifty-seven mother/child pairs were tested for the presence of maternal DNA Sequences in cord plasma. After delivery, cord blood samples were collected via gravity. Maternal specific alleles were detected by using polymerase chain reaction amplification of 9 highly polymorphic short Tandem Repeat markers (D21S11, D21S1411, D21S1412, D18S386, D18S535, MBP-A, MBP-B, D13S631, and D13S634). Results: All 57 mother-child pairs were informative for the identification of uniquely maternal alleles in at least 2 of 9 different short Tandem Repeat markers used per case. Uniquely maternal DNA Sequences were found in 43 of 57 (75%) cord plasma samples. Conclusion: The results of our study demonstrate that maternal DNA is present in the majority of umbilical cord blood plasma samples. The technique described herein might have application in the screening of umbilical cord blood samples for the presence of contaminating maternal genetic material. (Am J Obstet Gynecol 2002;186:117-20.)

John M. Archibald - One of the best experts on this subject based on the ideXlab platform.

  • Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements
    BMC Genomics, 2018
    Co-Authors: Jong Im Kim, Hwan Su Yoon, Woongghi Shin, John M. Archibald
    Abstract:

    Background Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. Results To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas , Cryptomonas , Hemiselmis , Proteomonas , Rhodomonas , Storeatula and Teleaulax . The mitochondrial genomes were similar in terms of their general architecture, gene content and presence of a large Repeat region. However, gene order was poorly conserved. Characteristic features of cryptophyte mtDNAs included large syntenic clusters resembling α-proteobacterial operons that encode bacteria-like rRNAs, tRNAs, and ribosomal protein genes. The cryptophyte mitochondrial genomes retain almost all genes found in many other eukaryotes including the nad , sdh , cox , cob , and atp genes, with the exception of sdh 2 and atp 3. In addition, gene cluster analysis showed that cryptophytes possess a gene order closely resembling the jakobid flagellates Jakoba and Reclinomonas . Interestingly, the cox 1 gene of R. salina , T. amphioxeia , and Storeatula species was found to contain group II introns encoding a reverse transcriptase protein, as did the cob gene of Storeatula species CCMP1868. Conclusions These newly sequenced genomes increase the breadth of data available from algae and will aid in the identification of general trends in mitochondrial genome evolution. While most of the genomes were highly conserved, extensive gene arrangements have shuffled gene order, perhaps due to genome rearrangements associated with hairpin-containing mobile genetic elements, tRNAs with palindromic Sequences, and Tandem Repeat Sequences. The cox 1 and cob gene Sequences suggest that introns have recently been acquired during cryptophyte evolution. Comparison of phylogenetic trees based on plastid and mitochondrial genome data sets underscore the different evolutionary histories of the host and endosymbiont components of present-day cryptophytes.

  • Retrotransposons and Tandem Repeat Sequences in the Nuclear Genomes of Cryptomonad Algae
    2015
    Co-Authors: Sharen Bowman, John M. Archibald
    Abstract:

    Abstract. The cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endo-symbiont. The endosymbiont nuclear genome, or nucleomorph, of the cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of 1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the crypto-monad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fo-smid clone libraries from two distantly related cryp-tomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corre

  • Retrotransposons and Tandem Repeat Sequences in the Nuclear Genomes of Cryptomonad Algae
    Journal of Molecular Evolution, 2007
    Co-Authors: Hameed Khan, Catherine Kozera, Bruce A. Curtis, Jillian Tarrant Bussey, Stan Theophilou, Sharen Bowman, John M. Archibald
    Abstract:

    The cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endosymbiont. The endosymbiont nuclear genome, or nucleomorph, of the cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of ∼1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the cryptomonad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fosmid clone libraries from two distantly related cryptomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corresponding to ∼150 and ∼235 kb of sequence, respectively. Very few of the random end Sequences determined in this study show similarity to known genes in other eukaryotes, underscoring the considerable evolutionary distance between the cryptomonads and other eukaryotes whose nuclear genomes have been completely sequenced. Using a combination of fosmid clone end-sequencing, Southern hybridizations, and PCR, we demonstrate that Ty3-gypsy long-terminal Repeat (LTR) retrotransposons and Tandem Repeat Sequences are a prominent feature of the nuclear genomes of both organisms. The complete sequence of a 30.9-kb genomic fragment from R. salina was found to contain a full-length Ty3-gypsy element with near-identical LTRs and a chromodomain, a protein module suggested to mediate the site-specific integration of the retrotransposon. The discovery of chromodomain-containing retroelements in cryptomonads further expands the known distribution of the so-called chromoviruses across the tree of eukaryotes.

Huangxian Ju - One of the best experts on this subject based on the ideXlab platform.

  • cascade signal amplification strategy for subattomolar protein detection by rolling circle amplification and quantum dots tagging
    Analytical Chemistry, 2010
    Co-Authors: Wei Cheng, Lin Ding, Huangxian Ju
    Abstract:

    A cascade signal amplification strategy was proposed for detection of protein target at ultralow concentration by combining the rolling circle amplification (RCA) technique with oligonucleotide functionalized quantum dots (QDs), multiplex binding of the biotin−strepavidin system, and anodic stripping voltammetric detection. The RCA product containing Tandem-Repeat Sequences could serve as excellent template for periodic assembly of QDs, which presented per protein recognition event to numerous quantum dot tags for electrochemical readout. Both the RCA and the multiplex binding system showed remarkable amplification efficiency, very little nonspecific adsorption, and low background signal. Using human vascular endothelial growth factor as a model protein, the designed strategy could quantitatively detect protein down to 16 molecules in a 100 μL sample with a linear calibration range from 1 aM to 1 pM and was amenable to quantification of protein target in complex biological matrixes. The proposed cascade s...