Category Archives: Transhuman News

Finding the Telltale Genome
Whenever a cell divides, its genetic code is copied into the new cell. But sometimes an imperfect copy is made, and the result is called a mutation. Most of the time, this does nothing; sometimes...

By: World Science Festival

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Finding the Telltale Genome - Video

14.01.2015 - (idw) Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Genome of the Escherichia coli type strain finally sequenced DNA includes potentially pathogenic segments The colon bacillus Escherichia coli is one of the best studied model organisms in the life sciences. However, the reference organism for this species, its so-called type strain, has been overlooked in microbial genomics until now. In the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, the DNA of type strain DSM 30083T has now been sequenced and compared to that of close relatives of the strain. This study not only allows an entirely new view of the numerous E. coli strains that play relevant roles in medicine and biotechnology, including the EHEC pathogen and Shigella, but they also yielded a generally applicable method for determining the subspecies of any bacterial species. The research was conducted at the Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany, and at the Joint Genome Institute, Walnut Creek, CA, USA.

The colon bacterium Escherichia (E.) coli to microbiologists and biotechnologists is like a pet bacterium and looks back on an exciting history. Initially described as "Bacterium coli commune" by bacteriologist Theodor Escherich in 1886, its original isolate was lost at the beginning of the 1920s. It was not until 1941 that it was isolated again, this time by Fritz Kaufmann at the State Serum Institute in Copenhagen, Denmark, who also deposited it in in several collections of microbial strains and provided a scientific description. Today, E. coli is likely the best understood microorganism in the world and serves as an important indicator for the quality of drinking and recreational waters.

"It seems strange that the number one, the type strain of a bacterium that has entire scientific conferences dedicated to it as a model organism, had not been fully sequenced until now", said Christine Rohde, Head of the E. coli strain collection at DSMZ, Braunschweig, Germany. "Initially, scientists primarily sequenced the genomes of pathogenic strains of E. coli, or of genetically modified strains of biotechnological relevance. In addition, physicians and hygienists in their daily practice use serotypes that are quickly determined by antibody tests in order to differentiate between different strains of E. coli. As Markus Gker, a bioinformatics scientist at DSMZ added: Complete bacterial genomes are of fundamental importance for diagnostics in humans, for biotechnology, and for the search for antimicrobial agents. Today, this is truer than ever, as some strains of E. coli have developed into dangerous pathogens such as EHEC or EAHEC. The E. coli type strain was sequenced as part of the GEBA project that focuses on type strains exhibiting an unusual physiology or occupying a key place in the phylogenetic tree. This is the only microorganism in the project that was included based on its importance as a model organism.

A genome with pathogenic potential

There are major physiological and genomic differences between the E. coli type strain and the harmless laboratory strain K-12. Due to its serotype, the type strain had been grouped into the biological containment level 2, and its genome sequence now confirmed its pathogenic potential, said Jrn Petersen, an expert of plasmid biology at the DSMZ. Unlike laboratory strain K-12, the E. coli type strain harbors an additional circular plasmid of 131,289 base pairs in its genome of 5,038,133 base pairs; this plasmid exhibits a sequence identity of 99% with plasmids from pathogenic E. coli isolates. These strains cause, e.g., colibacillosis in poultry and meningitis in newborns, with the horizontally transferable plasmid being responsible for their virulence, explained Petersen.

Sophisticated computer-aided phylogenetic analysis

Thanks to the complete genome sequence of the E. coli type strain, the Braunschweig scientists were able to examine whether the huge number of previously sequenced isolates of E. coli actually belong to the same species, using modern taxonomic techniques in the process. To this end, we analyzed more than 250 strains of E. coli and also verified their published taxonomic classification in subgroups, the 'phylotypes'. This bioinformatics-based analysis was performed with the state-of-the-art GGDC method. This technique is analogous to classical DNA-DNA hybridization in the laboratory, but yields significantly more exact results," as Markus Gker explained.

Original article:

Meier-Kolthoff JP et al. (2014). Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 9: 2 http://www.standardsingenomics.com/content/pdf/1944-3277-9-2.pdf

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The Number One of Enterobacteria Deciphered

The genetic sequencing of cats has now officially taken off

The first cat genome sequence from an Abyssinian named Cinnamon was reported in 2007. Credit:Valerius Geng via Wikimedia Commons

Cats may have beaten dogs on the Internet but felines have been a rare breed in genetics labs compared with their canine counterparts. Now, at last, cats are clawing their way into genomics.

At a meeting this week in San Diego, California, a close-knit group of geneticists unveiled the first results from an effort to sequence the genomes of 99 domestic cats. The work will benefit both humans and felines, the researchers say, by mapping the mutations underlying conditions that afflict the two species, such as kidney disease.

Its a great time to be in cat genomics, says William Murphy, a geneticist at Texas A&M University in College Station who is involved in the effort. Plummeting costs for DNA sequencing now make it possible to do genomics cheaply and cat genomics, long under-funded compared with similar efforts in dogs, is benefiting, he says. Were finally at the point where we can do all sorts of things we wanted to do 5 or 10years ago.

The first cat genome sequence from an Abyssinian named Cinnamon was reported in 2007. But the sequence contained significant gaps and errors, which slowed efforts to map genes. A high-quality version of Cinnamons genome was not publisheduntil late 2014. Domestic dogs, meanwhile, have become a darling of geneticists: their full genomewas reported in 2005, and the sequence has been continually improved. Hundreds of genes underlying canine diseases and traits are estimated to have been discovered, compared with as few as a dozen for cats.

The discrepancy can be traced back to the early 2000s. After the completion of the human, mouse and rat genomes, the US National Institutes of Health organized a commission to decide on their next target; the dog genome was selected for high-quality sequencing, whereas cats were put on hold.

That got some cat geneticists backs up. The truth is there were more powerful people interested in dogs, says Stephen OBrien, director of the Theodosius Dobzhansky Center for Genome Bioinformatics in StPetersburg, Russia, who led the initial cat-sequencing efforts.

But canine researchers were able to make a compelling case. Pet dogs suffer from many of the same conditions as humans, from narcolepsy to arthritis. And the intensely inbred nature of dog breeds made it relatively easy to identify disease-causing genes: because there is little genetic variation within any particular breed, the genes that cause disease in affected individuals stand out.

Dogs had other advantages, too. The existence of kennel clubs, which maintain breed standards and are full of enthusiastic pet owners and veterinary surgeons, helped dog geneticists to recruit subjects for study. Given the resources they had, they were discovering new genetic diseases in breeds almost daily, says Niels Pedersen, a veterinary scientist at the University of California, Davis.

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Cats Claw Their Way into Genomics