Category Archives: Genome

The Cat: evolution, domestication and Genome 10k
A public lecture by Dr Stephen J O #39;Brien at the UCD Earth Institute, University College Dublin, Ireland. Dr O #39;Brien is a world leading molecular biologist an...

By: UCD - University College Dublin

Go here to see the original:
The Cat: evolution, domestication and Genome 10k - Video

April Flowers for redOrbit.com Your Universe Online

A team of scientists from Harvard and Yale have recorded the entire genome of the bacteria E. coli, and in a dramatic demonstration of the potential of rewriting an organisms genetic code, they have improved the bacteriums ability to resist viruses.

This is the first time the genetic code has been fundamentally changed, according to Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale. Creating an organism with a new genetic code has allowed us to expand the scope of biological function in a number of powerful ways.

Creating this genomically recoded organism raises the possibility that future researchers might be able to retool nature and create potent new proteins to accomplish a wide variety of purposes from combating disease to generating new classes of materials. The findings from this groundbreaking study, which changes the rules of biology, were published in Science.

Isaacs and co-author George Church of Harvard Medical School led this research, which is a product of years of studies in the emerging field of synthetic biology, which seeks to re-design natural biological systems for useful purposes.

Encoded by DNAs instructional manual and made up of 20 amino acids, proteins carry out various important functional roles in the cell. A full set of 64 triplet combinations of the four nucleic acids that comprise the backbone of DNA encode amino acids. Triplets are sets of three nucleotides, called codons, and they are the genetic alphabet of life.

For this study, the research team examined the possibility of expanding upon natures handywork by substituting different codons or letters throughout the genome and then reintroducing entirely new letters to create amino acids not found in nature. This landmark study represents the first time that the genetic code has been completely changed across an organisms genome.

The research team first swapped all 321 instances of a specific codon, or genetic three-letter word, in E. coli for a supposedly identical word. Then they recoded the original word with a new meaning and new amino acid to eliminate its natural stop sign that terminates protein production. This novel genome allowed the bacteria to resist viral infection by limiting the production of natural proteins that viruses use to infect cells. They then converted the stop codon into one that encodes new amino acids, inserted it into the genome in a sort of plug and play fashion.

The results set the stage for using the recoded E. coli as a living foundry, capable of biomanufacturing new classes of exotic proteins and polymers. The recoded molecules could be the foundation for a new generation of materials, nanostructures, therapeutics, and drug delivery vehicles, Isaacs said.

Since the genetic code is universal, it raises the prospect of recoding genomes of other organisms, Isaacs said. This has tremendous implications in the biotechnology industry and could open entirely new avenues of research and applications.

The rest is here:
Plug And Play Synthetic Biology - Rewriting An Entire Genome

Harnessing the power of genome sequencing could have a "really tremendous impact" on cancer testing and treatment, says Nazneen Rahman of the Institute of Cancer Research and the Royal Marsden Hospital.

Speaking at Wired 2013 in London, Rahman who is a geneticist and doctor specialising in disease gene discovery, cancer predisposition and clinical genomics explains that she wants to make genome evangelists of us all. We should sit up and take notice, because she says we all have the ability to develop cancer -- "cancer has no respect for age or gender, race or ethnicity, wealth or class".

"Our genomes are both beautifully simple and unfeasibly complex," she says. They consist of the three billion letters of code, inside which are stored the instructions for how our cells divide. Looking for a mutation in the code has up until now involved combing laboriously through it.

A new process though, means you can break up the code into millions of fragments and read them all at once. Rahman describes this as "an all-bets-are-off, anything-is-possible kind of change" that has vastly changed the potential of what scientists are able to do in all areas of medicine.

To discover the mutations that have caused cancer in people, doctors used to have to look down the microscope, but now they can just look at the genome and trace the path of the mutating code. Similarly, chemotherapy used to tackle all fast-dividing cells, but we can now make a specific targeted drug that only tackle the mutating cells.

The same tactic can be used to identify mutations that are passed down through generations which means lots of people in the same family are affected by the same cancer. Using the old process for combing through genetic code for hereditary mutations was so time-consuming and difficult that it's very expensive, and therefore only available to the super rich. If we adapt the new changed in genome technologies though, says Rahman, we can make genome testing an affordable possibility for everyone.

In looking for mutations, one of the challenges is that our genomes are littered with mutations -- some of which are dangerous, some of which aren't -- but misinterpretations rather than helping people, can end up doing harm. To avoid this, more people will need to be sequenced, because the more data you put into a system, the better interpretations you get out of it. "This is an area where big data is going to be a big help," she says.

In order to have a way that doctors can routinely use these tests, we need to make sure tests are accurate, but also that people are educated about sequencing and have confidence in the process. This is why we all need to be genome evangelists, but, she adds "we do have to be cautious evangelists -- if that's not a contradiction in terms."

Read more from Wired 2013's incredible spread speakers, thinkers, innovators and thought-leaders in our Wired 2013 hub.

See the rest here:
Nazneen Rahman on why she wants to make genome evangelists of us all

Youve heard of decoding the genomethe monumental scientific project to learn the blueprint of a human being by reading the DNA book of life, letter by letter. Over the past few years, scientists have been making quiet progress on a less-publicized effort to recode the genome, by developing powerful tools that will allow them to edit or completely rewrite it on a massive scale.

When trying to understand why thats important, the powerful book of life metaphor unravels a little bitafter all, what would be valuable about taking a finished work of Shakespeare and swapping in synonyms or completely new words at various spots in the text? Its hardly likely to enrich the experience of reading a classic play.

To understand why it matters, one has to think about DNA more like an engineer trying to build new things. The four letters of DNA are strung together in three letter words, each of which makes an amino acidcompounds that cells combine to make proteins. Swapping out letters or words therefore means that scientists can create whole new organisms that manufacture novel kinds of proteins that might have industrial or biomedical uses.

Its expanding the chemical repertoire, said Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale University. By making these fundamental changes to the code, you can create organisms that are safer,... more useful for the biotechnology industry, and organisms with alternate genetic codes are actually resistant to viruses.

On Thursday in the journal Science, Isaacs and George Church, a biologist at Harvard Medical School, reported in a pair of papers on new efforts to advance a technique developed a few years ago that enables massive editing of the genome.

In one paper, the researchers were able to replace several hundred instances of a particular sequence of three letters in E. coli with a different sequence that essentially instructed cells to create the same proteins. That meant the bacteria could still function. Then, they inserted a novel sequence, creating a bacteria that could create a protein not found in nature. They were able to show that these changes also made the bacteria resistant to viral infections.

In a second paper, the researchers were able to show the scope of genetic words they could tweak, not limiting themselves to a single sequence of three letters.

There have been a number of methods pioneered over the past few years to edit the genomes of organisms, giving biologists a large tool kit. Isaacs and Church used a technique that makes targeted changes to DNA and also takes advantage of the process of evolution to select the strains of altered bacteria that are most viable.

There are different ways to skin the cat, Isaacs said. Its pretty exciting right nowwere suddenly in the past few years seeing this influx of new types of technologies that are allowing us to perform unprecedented changes to genomes, and thats really exciting and powerful.

See the rest here:
Re-coding the genome

In an advance that could help battle disease and create new biotech materials, researchers at Yale and Harvard universities have fundamentally changed an organism's genome for the first time.

The researchers developed a new genome for an e.coli bacterium by replacing one kind of codon a sequence of three nucleotides that regulates amino acids with another kind of codon. Scientists have previously replaced genes, but this is the first time that such changes have been across the an organism's genome, the complex blueprint of life.

The study is published in Friday's issue of the journal Science.

By recoding the genome, researchers say, the bacteria will be able to produce proteins that don't occur in nature, creating the possibility of new drugs and biotechnology materials.

For instance, the researchers say it could lead to the use of virus-resistant organisms in the biotech industry. Viruses use the proteins produced by the host organism, such as a bacteria, to infect cells, but doing this requires that the virus and host have the same genetic sequences. If the organism contains a new genetic code, the virus is rendered powerless because it can no longer properly produce proteins.

"By changing the code, we're establishing the fundamental proof of principle that they can be resistant to viruses," said the paper's co-senior author, Farren Isaacs, assistant professor of molecular, cellular and developmental biology at Yale. George Church, professor of genetics at Harvard Medical School, is the study's other senior author.

By using organisms with recoded genomes, Isaacs said, biotech companies could stave off the kind of havoc that a single viral infection can cause. For instance, Genzyme, a Massachusetts-based biotech company that shut down for three months and suffered up to $1 billion in damages after a viral contamination.

"If you could use a genetically recoded organism, it could mean a striking decrease in the rate of viral infections," Isaacs said.

The research could also potentially allay fears about genetically modified organisms, he said, because the recoded organisms would be unable to infect natural organisms in the wild.

Brenton Graveley, professor of genetics and developmental biology at the UConn Health Center, said the research could have "profound possibilities" for synthetic biology the field of creating new organisms through genetic manipulation.

Read the original post:
Yale, Harvard Scientists Change An Organism's Entire Genome

Breast Cancer Genome Guided Therapy Study (BEAUTY)
Breast Cancer Genome Guided Therapy Study (BEAUTY), Dr. Lyndsay Harris, Director of the UH Breast Cancer Program, discusses research of genome sequencing to ...

By: Charlie Dara

Read more:
Breast Cancer Genome Guided Therapy Study (BEAUTY) - Video

#39;smORFs #39;: Functional Little Genome Gems Confront Evolution
http://www.icr.org/article/7730/ Based on their 3-D shape, the researchers claimed that the human smORF proteins evolved from fly smORFs over a span of 550 m...

By: Dave Flang

Continue reading here:
'smORFs': Functional Little Genome Gems Confront Evolution - Video

PUBLIC RELEASE DATE:

17-Oct-2013

Contact: David Cameron david_cameron@hms.harvard.edu 617-432-0441 Harvard Medical School

In two parallel projects, researchers have created new genomes inside the bacterium E. coli in ways that test the limits of genetic reprogramming and open new possibilities for increasing flexibility, productivity and safety in biotechnology.

In one project, researchers created a novel genomethe first-ever entirely genomically recoded organismby replacing all 321 instances of a specific "genetic three-letter word," called a codon, throughout the organism's entire genome with a word of supposedly identical meaning. The researchers then reintroduced a reprogramed version of the original word (with a new meaning, a new amino acid) into the bacteria, expanding the bacterium's vocabulary and allowing it to produce proteins that do not normally occur in nature.

In the second project, the researchers removed every occurrence of 13 different codons across 42 separate E. coli genes, using a different organism for each gene, and replaced them with other codons of the same function. When they were done, 24 percent of the DNA across the 42 targeted genes had been changed, yet the proteins the genes produced remained identical to those produced by the original genes.

"The first project is saying that we can take one codon, completely remove it from the genome, then successfully reassign its function," said Marc Lajoie, a Harvard Medical School graduate student in the lab of George Church. "For the second project we asked, 'OK, we've changed this one codon, how many others can we change?'"

Of the 13 codons chosen for the project, all could be changed.

"That leaves open the possibility that we could potentially replace any or all of those 13 codons throughout the entire genome," Lajoie said.

The results of these two projects appear today in Science. The work was led by Church, Robert Winthrop Professor of Genetics at Harvard Medical School and founding core faculty member at the Wyss Institute for Biologically Inspired Engineering. Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale School of Medicine, is co-senior author on the first study.

See the article here:
Researchers advance toward engineering 'wildly new genome'

PUBLIC RELEASE DATE:

17-Oct-2013

Contact: Bill Hathaway william.hathaway@yale.edu 203-432-1322 Yale University

Scientists from Yale and Harvard have recoded the entire genome of an organism and improved a bacterium's ability to resist viruses, a dramatic demonstration of the potential of rewriting an organism's genetic code.

"This is the first time the genetic code has been fundamentally changed," said Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale and co-senior author of the research published Oct. 18 in the journal Science. "Creating an organism with a new genetic code has allowed us to expand the scope of biological function in a number of powerful ways."

The creation of a genomically recoded organism raises the possibility that researchers might be able to retool nature and create potent new forms of proteins to accomplish a myriad purposes from combating disease to generating new classes of materials.

The research headed by Isaacs and co-author George Church of Harvard Medical School is a product of years of studies in the emerging field of synthetic biology, which seeks to re-design natural biological systems for useful purposes.

In this case, the researchers changed fundamental rules of biology.

Proteins, which are encoded by DNA's instructional manual and are made up of 20 amino acids, carry out many important functional roles in the cell. Amino acids are encoded by the full set of 64 triplet combinations of the four nucleic acids that comprise the backbone of DNA. These triplets (sets of three nucleotides) are called codons and are the genetic alphabet of life.

Isaacs, Jesse Rinehart of Yale,,and the Harvard researchers explored whether they could expand upon nature's handywork by substituting different codons or letters throughout the genome and then reintroducing entirely new letters to create amino acids not found in nature. This work marks the first time that the genetic code has been completely changed across an organism's genome.

Read the original here:
Researchers rewrite an entire genome -- and add a healthy twist

QIAGEN N.V. ( QGEN ) announced the Empowered Genome Community, a noble initiative meant to help people who have had their genomes sequenced through efforts such as the Harvard's Personal Genome Project (PGP) and Understand Your Genome (UYG) program.

At a time, when the medical community needs more innovative and technologically advanced devised ways and means, to cater to the challenging needs of the healthcare industry, the Empowered Genome Community of QIAGEN brings a new leash of hope for the common people as well as researchers.

The first-of-its-kind in the bio science industry, this community intends to help those who have had their genomes sequenced, share, explore and interpret data among themselves as well as with researchers. This is made possible through QIAGEN's secure online genome interpretation application, Ingenuity Variant Analysis. It is a powerful HIPAA-compliant cloud-based solution that can compare and interpret human genomes to help researchers understand diseases and other phenotypes.

The core of this interpretation resource is the Ingenuity Knowledge Base, the leading expert-curated knowledge resource for next generation biology.

To showcase the utility of the Empowered Genome Community, QIAGEN released an open collaborative analysis of myopia in 111 people whose genomes were sequenced through Harvard's PGP. QIAGEN scientists implemented Variant Analysis to compare the whole genomes of 111 PGP participants surveyed for eye diseases.

The study revealed that 46 genes were enriched with rare, potentially functionally relevant variants in people with myopia, but not those without the condition. Further filtering using Variant Analysis and significant insights from Ingenuity Knowledge Base showed that 17 of these genes demonstrate characteristics related to eyes found in people or mice, or directly interact with such genes.

The company is soon planning to invite an open collaboration till Jan 31, 2014, to build a pool of data on human genomes that will help to strengthen its expertise on myopia physiology, epidemiology, and filtering strategies. Substantial contributions recognized by joint authorship on any resulting publication will also be welcome.

QIAGEN believes the Empowered Genome Community has the potential to contribute meaningfully to the study of genomes. This revolutionary knowledge platform can go a long way in the bioscience industry enabling researchers and scientists to spark new insights from its data and findings.

The Empowered Genome Community also carries forward the noble mission taken up by public sequencing efforts like the PGP, aiding better understanding of important phenotypes like eyesight.

QGEN currently carries a Zacks Rank #2 (Buy). Other stocks that are worth a look include Actelion Ltd. ( ALIOF ), Alexion Pharmaceuticals, Inc. ( ALXN ), each carrying a Zacks Rank #1 (Strong Buy), and Agenus Inc. ( AGEN ) carrying a Zacks Rank #2 (Buy).

More:
QIAGEN Aids Genome Sequencing Study - Analyst Blog