Analysis of ancient bone DNA: techniques and applications

1991 ◽  
Vol 333 (1268) ◽  
pp. 399-407 ◽  
Keyword(s):  
Polymerase Chain Reaction ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Genetic Information ◽  
Chain Reaction ◽  
Base Pairs ◽  
Dna Recovery ◽  
Human Femur ◽  
Ancient Bone ◽  
Polymerase Chain

The analysis of DNA from ancient bone has numerous applications in archaeology and molecular evolution. Significant amounts of genetic information can be recovered from ancient bone: mitochondrial DNA sequences of 800 base pairs have been amplified from a 750-year-old human femur by using the polymerase chain reaction. DNA recovery varies considerably between bone samples and is not dependent on the age of the specimen. We present the results of a study on a small number of bones from a mediaeval and a 17th-century cemetery in Abingdon showing the relation between gross preservation, microscopic preservation and DNA recovery.

scholarly journals Barcode DNA Edelweis (Anaphalis javanica) Berdasarkan Gen matK

Jurnal MIPA ◽  
2015 ◽  
Vol 4 (2) ◽  
pp. 131
Author(s):  
Muzakir Rahalus ◽  
Maureen Kumaunang ◽  
Audy Wuntu ◽  
Julius Pontoh
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Living Organism ◽  
Chain Reaction ◽  
Base Pairs ◽  
Barcode Dna ◽  
Reverse Primer ◽  
Total Dna ◽  
Polymerase Chain

DNA barcode merupakan metode identifikasi organisme hidup dengan menggunakan urutan DNA pendek (± 500 pasang basa). Tujuan dari penelitian ini adalah memperoleh barcode DNA Edelweis dan menganalisis kemiripan gen matK Edelweis (Anaphalis javanica) dengan kerabat terdekatnya. Isolasi DNA total Edelweis berhasil dilakukan dengan menggunakan  manual prosedur dari InnuPrep Plant DNA Kit yang dimodifikasi. Gen matK parsial telah diisolasi dengan metode Polymerase Chain Reaction (PCR) menggunakan Primer forward matK-1RKIM-f dan Primer Reverse matK-3FKIM-r. Hasil analisis sekuens menghasilkan barcode DNA edelweis berukuran 843 bp. Hasil analisis kemiripan menunjukkan tingkat kekerabatan terdekat dengan A. margaritaceae yaitu 99.86% pada BOLD System dan 100 % pada NCBI.DNA barcode is a method to identify living organism by using several short sequences of DNA (± 500 base pairs). The purpose of this study was to obtain a DNA barcode and analyze the similarity of matK genes of edelweis (Anaphalis javanica) with its closest relatives. Isolation of total DNA of edelweis has been succesfully done by using modified manual procedures of InnuPrep Plant Kit. matK partial gene has been isolated by the method of Polymerase Chain Reaction (PCR) using forward primer MATK-1RKIM-f and reverse primer MATK-3FKIM-r. Analysis of DNA sequences of edelweis confirmed its DNA barcode size was 843 bp. Furthermore, A. javanica showed similarity 99.86% in BOLD system and 100% in NCBI with A. margaritaceae.

Comparison of mitochondrial DNA sequences of seven morphospecies of black flies (Diptera: Simuliidae)

Genome ◽  
1991 ◽  
Vol 34 (2) ◽  
pp. 306-311 ◽  
Author(s):  
Bai Xiong ◽  
Thomas D. Kocher
Keyword(s):  
Polymerase Chain Reaction ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Polytene Chromosomes ◽  
Universal Primers ◽  
Homologous Region ◽  
Black Flies ◽  
Chain Reaction ◽  
Nucleotide Substitutions ◽  
Polymerase Chain

Universal primers constructed from the 16S ribosomal RNA gene in the Drosophila yakuba mitochondrial genome were successfully used to amplify, via the polymerase chain reaction, the homologous region of mitochondrial DNA from seven black fly morphospecies. Amplification was achieved from single larval salivary glands and from single adults preserved in Carnoy's fixative (ethanol – acetic acid, 3:1), allowing DNA sequences and polytene chromosome banding pattern data to be gathered from the same individuals. Nucleotide sequences of the amplified DNA segment (347 base pairs) were obtained from all the species examined. As in Drosophila, the nucleotide base composition of the sequenced segment from black flies had a high adenine (A) and thymine (T) content (A + T on average comprised 77% of all nucleotides.). Nucleotide differences among the seven species were observed at 59 positions (55 nucleotide substitutions and 4 deletions). There were more transversion differences than transition differences both among and within genera; the proportion of transversions was higher between genera than within genera. Most transversion differences were A ↔ T type, comprising 79% of all transversion differences and 50% of all sequence differences. Phylogenetic inference based strictly on transversion differences confirmed traditional generic and tribal groupings, i.e., Prosimulium fuscum (Syme &Davies) is close to Prosimulium magnum (Dyar &Shannon); Simulium decorum (Walker), Simulium venustum s.l. (Say), and Simulium vittatum s.l. (Zetterstedt) are close to each other; Stegopterna mutata (Malloch) and Cnephia dacotensis (Dyar &Shannon), which belong to the tribe Cnephiini, are grouped together.Key words: polymerase chain reaction, mitochondrial DNA, polytene chromosomes, phylogeny, black flies.

Identification of Bovine-Specific DNA in Feedstuffs

2001 ◽  
Vol 64 (1) ◽  
pp. 117-119 ◽  
Author(s):  
PAVEL KRČMÁŘ ◽  
EVA RENČOVÁ
Keyword(s):  
Polymerase Chain Reaction ◽  
Mitochondrial Dna ◽  
Czech Republic ◽  
Dna Sequences ◽  
Fish Meal ◽  
Spongiform Encephalopathy ◽  
Vertebrate Species ◽  
Chain Reaction ◽  
The Czech Republic ◽  
Polymerase Chain

Considering the menace of transmission of bovine spongiform encephalopathy, feed components intended for cattle nutrition must be checked for the presence of bovine-derived materials. We have been using a method based on polymerase chain reaction for the identification of bovine-specific mitochondrial DNA sequences for this purpose. The specificity of the primers for polymerase chain reaction has been tested using samples of DNA of other vertebrate species, which may also be present in rendering plant products. The method allows the detection in concentrate mixtures of 0.125% of bovine-derived material. Bovine DNA at concentrations corresponding to less than 0.5% of bovine-derived material was detected in 3 of the 30 samples of concentrate mixtures collected from distributors' stores all over the Czech Republic. All 44 samples of fish meal collected from the same sources were free of bovine-derived material.

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

Using a Polymerase Chain Reaction as a Complementary Test to Improve the Detection of Dermatophyte Fungus in Nails

2014 ◽  
Vol 104 (3) ◽  
pp. 233-237 ◽  
Author(s):  
María José Iglesias Sánchez ◽  
Ana María Pérez Pico ◽  
Félix Marcos Tejedor ◽  
María Jesús Iglesias Sánchez ◽  
Raquel Mayordomo Acevedo
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Classical Method ◽  
Clinical Manifestations ◽  
Culture Method ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Traditional Procedure ◽  
Polymerase Chain

Background Dermatomycoses are a group of pathologic abnormalities frequently seen in clinical practice, and their prevalence has increased in recent decades. Diagnostic confirmation of mycotic infection in nails is essential because there are several pathologic conditions with similar clinical manifestations. The classical method for confirming the presence of fungus in nail is microbiological culture and the identification of morphological structures by microscopy. Methods We devised a nested polymerase chain reaction (PCR) that amplifies specific DNA sequences of dermatophyte fungus that is notably faster than the 3 to 4 weeks that the traditional procedure takes. We compared this new technique and the conventional plate culture method in 225 nail samples. The results were subjected to statistical analysis. Results We found concordance in 78.2% of the samples analyzed by the two methods and increased sensitivity when simultaneously using the two methods to analyze clinical samples. Now we can confirm the presence of dermatophyte fungus in most of the positive samples in just 24 hours, and we have to wait for the result of culture only in negative PCR cases. Conclusions Although this PCR cannot, at present, substitute for the traditional culture method in the detection of dermatophyte infection of the nails, it can be used as a complementary technique because its main advantage lies in the significant reduction of time used for diagnosis, in addition to higher sensitivity.

scholarly journals Accuracy of quantitative polymerase chain reaction in samples of frozen and paraffin-embedded healthy skin for the diagnosis of canine visceral leishmaniasis

2017 ◽  
Vol 69 (6) ◽  
pp. 1443-1450 ◽  
Author(s):  
M.P. Campos ◽  
M.F. Madeira ◽  
D.A. Silva ◽  
M.S. Solcà ◽  
O.M. Espíndola ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Healthy Skin ◽  
Sample Collection ◽  
Chain Reaction ◽  
Dna Recovery ◽  
Ffpe Samples ◽  
Fresh Frozen ◽  
Polymerase Chain ◽  
Commercial Kits

ABSTRACT The purpose of the present work was to evaluate the accuracy of quantitative polymerase chain reaction (qPCR) performed on samples of fresh frozen tissue (FT) and formalin-fixed, paraffin-embedded (FFPE) healthy skin. This is a validation study conducted with samples from 46 dogs from an endemic area in Brazil. After sample collection, DNA extractions were conducted using commercial kits and qPCR was oriented to kinetoplast DNA (kDNA) targets of the Leishmania infantum species. The results obtained for the FFPE samples showed 63.6% sensitivity and 77.1% specificity, whereas those obtained for the FT samples showed 100% and 48.6%, respectively. Poor agreement was observed for the results of the qPCR technique with FT and FFPE samples. Our results suggest freezing as the most suitable conservation method for the formation of sample databases considering DNA recovery

Polymerase chain reaction based mapping of rye involving repeated DNA sequences

Genome ◽  
1992 ◽  
Vol 35 (4) ◽  
pp. 621-626 ◽  
Author(s):  
Peter M. Rogowsky ◽  
Ken W. Shepherd ◽  
Peter Langridge
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Chromosome 1 ◽  
Repeated Dna ◽  
Chain Reaction ◽  
Pcr Marker ◽  
Banding Patterns ◽  
Repeated Dna Sequences ◽  
Cereal Rye ◽  
Polymerase Chain

A novel type of polymerase chain reaction (PCR) marker was developed for the mapping of cereal rye (Secale cereale). Primer pairs were synthesized targeting the insertion sites of three individual copies of the R173 family of rye specific repeated DNA sequences. While one primer was derived from a sequence within the respective R173 element, the second primer corresponded to a flanking region. The complex banding patterns obtained in rye allowed not only the mapping of the three R173 elements to certain chromosome regions of 1RS (the short arm of rye chromosome 1) but also the mapping of an additional 3–10 easily identifiable bands per primer pair to other rye chromosomes. Linkage mapping of a polymorphic 1R band derived from three rye cultivars demonstrated the presence of nonallelic, dominant markers in two independent crosses. Because of the high copy number of the R173 family (15 000 copies per diploid rye genome), its dispersion over the entire length of all chromosomes and the high number of markers obtained per primer pair, PCR markers based on the R173 family provide an almost unlimited source for well-spaced markers in rye mapping.Key words: polymerase chain reaction, mapping, repetitive DNA sequences, wheat, rye.

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