Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

Science ◽  
2005 ◽  
Vol 311 (5759) ◽  
pp. 392-394 ◽  
Author(s):  
Hendrik N. Poinar ◽  
Carsten Schwarz ◽  
Ji Qi ◽  
Beth Shapiro ◽  
Ross D. E. MacPhee ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Large Scale ◽  
Loxodonta Africana ◽  
Chain Reaction ◽  
Base Pairs ◽  
Mammuthus Primigenius ◽  
Sequence Identity ◽  
Polymerase Chain ◽  
Woolly Mammoth

We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.

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.

DNA sequence of the androgen receptor in prostatic tumor cell lines and tissue specimens assessed by means of the polymerase chain reaction

The Prostate ◽  
1993 ◽  
Vol 22 (1) ◽  
pp. 11-22 ◽  
Author(s):  
Zoran Culig ◽  
Helmut Klocker ◽  
Johannes Eberle ◽  
Felizia Kaspar ◽  
Alfred Hobisch ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Androgen Receptor ◽  
Tumor Cell ◽  
Dna Sequence ◽  
Cell Lines ◽  
Tumor Cell Lines ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Prostatic Tumor ◽  
Tissue Specimens

Polymerase Chain Reaction Assay for Detection of Escherichia coli O157:H7 and Escherichia coli O157:H−

2002 ◽  
Vol 65 (1) ◽  
pp. 5-11 ◽  
Author(s):  
TAKAHISA MIYAMOTO ◽  
NATSUKO ICHIOKA ◽  
CHIE SASAKI ◽  
HIROSHI KOBAYASHI ◽  
KEN-ICHI HONJOH ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Escherichia Coli O157 ◽  
Chain Reaction ◽  
Pcr Assay ◽  
E Coli ◽  
Pcr Product ◽  
Genomic Dnas ◽  
Polymerase Chain

The DNA band patterns generated by polymerase chain reaction (PCR) using the du2 primer and template DNAs from various strains of Escherichia coli and non–E. coli bacteria were compared. Among three to five prominent bands produced, the three bands at about 1.8, 2.7, and 5.0 kb were detected in all of the E. coli O157 strains tested. Some nonpathogenic E. coli and all pathogenic E. coli except E. coli O157 showed bands at 1.8 and 5.0 kb. It seems that the band at 2.7 kb is specific to E. coli O157. Sequence analysis of the 2.7-kb PCR product revealed the presence of a DNA sequence specific to E. coli O157:H− and E. coli O157:H7. Since the DNA sequence from base 15 to base 1008 of the PCR product seems to be specific to E. coli O157, a PCR assay was carried out with various bacterial genomic DNAs and O157-FHC1 and O157-FHC2 primers that amplified the region between base 23 and base 994 of the 2.7-kb PCR product. A single band at 970 bp was clearly detected in all of the strains of E. coli O157:H− and E. coli O157:H7 tested. However, no band was amplified from template DNAs from other bacteria, including both nonpathogenic and pathogenic E. coli except E. coli O157. All raw meats inoculated with E. coli O157:H7 at 3 × 100 to 3.5 × 102 CFU/25 g were positive both for our PCR assay after cultivation in mEC-N broth at 42°C for 18 h and for the conventional cultural method.

Specific detection of mousepox virus by polymerase chain reaction

1997 ◽  
Vol 31 (3) ◽  
pp. 201-205 ◽  
Author(s):  
Heinrich Neubauer ◽  
Martin Pfeffer ◽  
Hermann Meyer
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapid Identification ◽  
Mouse Lung ◽  
Chain Reaction ◽  
Base Pairs ◽  
Viral Origin ◽  
Body Protein ◽  
Polymerase Chain ◽  
Mouse Lung Tissue ◽  
Type Inclusion

Polymerase chain reaction was applied to the rapid identification and detection of mousepox virus. This was accomplished by selection of primers targeting the A-type inclusion body protein gene. By investigating 20 strains belonging to five different species of the genus Orthopoxvirus, amplification was achieved only with the seven mousepox virus strains examined. The size of the resulting DNA fragment accounted for 116 base pairs and contained a recognition site for the restriction enzyme HindII, thus confirming its viral origin. Amplification of mousepox virus specific sequences was also possible from infected mouse lung tissue and serum.

Detection of Intraspecific.DNA Sequence Variation in the Mitochondrial Cytochrome b Gene of Atlantic Cod (Gadus morhua) by the Polymerase Chain Reaction

1991 ◽  
Vol 48 (1) ◽  
pp. 48-52 ◽  
Author(s):  
Steven M. Carr ◽  
H. Dawn Marshall
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Cytochrome B ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Mitochondrial Cytochrome ◽  
Chain Reaction ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene ◽  
Polymerase Chain

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for 55 Atlantic cod (Gadus morhua) from Norway and from 10 locations within the Northern Cod complex and adjacent stocks off Newfoundland. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Eleven variable nucleotide positions within a 298 base region defined 12 genotypes. Genotype proportions differed significantly between Newfoundland and Norwegian populations: the majority genotype among Newfoundland populations was present in a minority of Norwegian cod. Newfoundland cod showed less genotypic diversity than those from the eastern Atlantic: nine genotypes were found among all 10 Newfoundland populations, as compared with seven genotypes within the single Norwegian population. An exception was an overwintering, inshore Newfoundland population that showed four genotypes among five fish. As in other vertebrates, third position synonymous transitions predominate over other types of nucleotide changes. However, two amino acid replacement substitutions occur among cod, and the ratio of purine transitions to pyrimidine transitions is significantly higher than in other species. The existence of DNA sequence polymorphism permits the various hypotheses of the distribution and differentiation of Newfoundland cod stocks to be tested, and points to the utility of PCR technology in fishery genetics.

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