X-Nico

16 unusual facts about DNA sequencing


DNA sequencing

Allan Maxam and Walter Gilbert published a DNA sequencing method in 1977 based on chemical modification of DNA and subsequent cleavage at specific bases.

Emulsion PCR is used in the methods developed by Marguilis et al. (commercialized by 454 Life Sciences), Shendure and Porreca et al. (also known as "Polony sequencing") and SOLiD sequencing, (developed by Agencourt, later Applied Biosystems, now Life Technologies).

Escherichia coli O104:H4

Analysis of genomic sequences obtained by BGI Shenzhen show that the O104:H4 outbreak strain is an enteroaggregative E. coli (EAEC or EAggEC) type that has acquired Shiga toxin genes, presumably by horizontal gene transfer.

Gerald M. Rubin

Gerald Mayer Rubin (born 1950) is an American biologist, notable for pioneering the use of transposable P elements in genetics, and for leading the public project to sequence the Drosophila melanogaster genome.

History of plant systematics

In the 1990s DNA technology saw immense progress, resulting in unprecedented accumulation of DNA sequence data from various genes present in compartments of plant cells.

Hoatzin

However, using mt and nDNA sequences of increased length, Sorenson et al. in 2003 noted that all three previous DNA studies were apparently flawed due to errors in methodology, small sample size, and sequencing errors; their study strongly suggested against a close relationship between the Hoatzin and cuckoos or turacos.

Joint Genome Institute

The U.S. Department of Energy Joint Genome Institute (DOE JGI), located in Walnut Creek, California, was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL).

Lafora disease

Currently the preferred method of certain diagnosis is DNA sequencing.

Massimiliano Di Ventra

Di Ventra's research interests are in the theory of electronic and transport properties of nanoscale systems, non-equilibrium statistical mechanics, DNA sequencing/polymer dynamics in nanopores, and memory effects in nanostructures for applications in unconventional computing and biophysics.

Metagonimiasis

Recent studies analyzing the DNA of the three agents causing metagonimiasis found that DNA sequencing supports M. yokagawai and M. takahashii be placed in the same clade, and phylogenic tree analysis supports their genetic similarity.

Phylogeography

Advances in both laboratory methods (e.g. capillary DNA sequencing technology) that allowed easier sequencing DNA and computational methods that make better use of the data (e.g. employing coalescent theory) have helped improve phylogeographic inference.

Populus sect. Tacamahaca

It was announced on 15 September 2006 in the journal Science that P. trichocarpa became the first tree species to have its entire genome sequenced.

Saiphos equalis

In a recent study of coastal Saiphos equalis populations, mitochondrial nucleotide sequences (ND2 and cytochrome b) were used to organize the relationships among the various populations.

Stewart Blusson

The prize will go to the person or group that can develop a quick (100 people in 10 days) and inexpensive way to sequence a human genome.

Variant Call Format

The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project.

Xyloplax medusiformis

DNA sequencing was done on Xyloplax medusiformis and on a range of about twenty other varied species of echinoderm.


Exon trapping

The technique has largely been supplanted by the approach of sequencing cDNA generated from mRNA and then using bioinformatics tools such as NCBI's BLAST server to determine the source of the sequence, thereby identifying the appropriate exon-intron splice sites.

Genomic Standards Consortium

Established in September 2005, this international community includes representatives from a range of major sequencing and bioinformatics centres (including NCBI, EMBL, DDBJ, JCVI, JGI, EBI, Sanger, FIG) and research institutions.

Horse genome

In 2012, researchers at the University of Copenhagen used NEXTGEN sequencing to sequence four modern domesticated horses of different breeds, a Przewalski's horse, and a donkey, comparing these to DNA from three fossil horses dated between 13,000 and 50,000 years ago.

Luidia

This has been shown to take place both in the field and in laboratory cultures and has been studied by molecular analysis of sequences of mitochondrial tRNA to identify the taxa involved.

Maxam–Gilbert sequencing

Maxam–Gilbert sequencing is a method of DNA sequencing developed by Allan Maxam and Walter Gilbert in 1976–1977.

New Forest pony

DNA sequencing revealed that the affected foal was homozygous for a missense mutation in the gene encoding CLCN1, a protein which regulates the excitability of the skeletal muscle.

Sequencing by ligation

Sequencing by ligation is a DNA sequencing method that uses the enzyme DNA ligase to identify the nucleotide present at a given position in a DNA sequence.