Daily Archives: October 3, 2012

Sequencing, splicing and expressing DNA may seem to be the quintessence of cutting-edge scienceindeed DNA manipulation has revolutionized fields such as biofuels, chemicals and medicine. But in fact, the actual process can still be tedious and labor-intensive, something Lawrence Berkeley National Laboratory (Berkeley Lab) scientist Nathan Hillson learned the hard way.

After struggling for two days to design a protocol to put together a genetic circuit with 10 pieces of DNAusing a spreadsheet as his primary toolhe was dismayed to discover that an outside company could have done the whole thing, including parts and labor, for lower cost than him ordering the oligonucleotides himself. "I learned two things: one, I never wanted to go through that process again, and two, it's extremely important to do the cost-effectiveness calculation," said Hillson, a biochemist who also directs the synthetic biology program at the Berkeley Lab-led Joint BioEnergy Institute (JBEI). "So that was the genesis of the j5 software. This is the perfect thing to teach a computer to do."

The j5 software package, which has attracted users from more than 250 institutions worldwide since it was made available last year, is now the basis for the latest startup to emerge from JBEI, a Department of Energy research center established in 2007 to pursue breakthroughs in the production of cellulosic biofuels. By building on j5 and adding modules for commercial users, TeselaGen Biotechnology, founded by Hillson and two partners, says it will significantly reduce the time and cost involved with DNA synthesis and cloning, a multibillion-dollar market.

"It's like AutoCAD for biology," said TeselaGen co-founder and CEO Mike Fero. "Modern cloning is a computational problem. We are the missing informatic piece to making modern scarless DNA assembly methods a reality for the majority of biologists. Otherwise it's a small cadre of people who can do it."

Recombinant DNA assemblies are critical tools in a number of scientific pursuits: for understanding how cells are altered in diseases such as cancer, for building better antibiotics, for converting plant biomass to biofuels and for basic scientific understanding of cellular pathways. Standard cloning techniques have been in use for 40 years and are still the industry standard.

"Our biggest competition is traditional cloning, or inertia," said Fero, who was a particle physicist for 10 years before pursuing a career in biotech. "We have to make it so easy people will happily switch to the newer methods."

TeselaGen licensed j5 from Berkeley Lab, the lead institutional partner of JBEI, and currently has more than 100 scientists and engineers from large industrial and pharmaceutical companies in private beta.

"We are so pleased with the startup of TeselaGen, based on a deceptively simple idea but clearly providing a solution to a very difficult problem," said Cheryl Fragiadakis, director of technology transfer at Berkeley Lab. "It is a great example as well of a company coming out of our JBEI activities.The Lab's Tech Transfer encourages and supports entrepreneurial ventures, providing education and networking for our scientists, as a great way to get technologies out for the benefit of society."

The cloud-based software not only designs DNA construction protocols, it will compare methods to determine the one that is most cost-effective, weighing, for example, if it is cheaper to outsource a portion of the DNA construction.The more complex the task, the more time and money the program can save. The greatest savings are with combinatorial libraries, collections of hundreds to millions of related DNA assemblies, each with a different combination of genes or parts that perform similar functions in different organisms.

For example, simple construction of a metabolic pathway that takes two and a half weeks and costs $1,400 using traditional cloning can be cut down to two weeks and less than half the cost with j5. A more complex task of constructing a combinatorial protein library (with 243 constructs) would drop from $122,000 and 11 months with traditional cloning to under $30,000 and 1.5 months with j5. The same task using direct DNA synthesis would cost $538,000 and take 2.3 months.

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DNA construction technology makes genetic engineering cheaper, faster

October 3, 2012 Updated Oct 3, 2012 at 2:52 PM EDT

Miami County, Ind. (Indianas NewsCenter) DNA evidence plays a key role in helping authorities make an arrest in a 20-year-old murder case.

The Miami County Prosecutors Office announced Wednesday Timothy J. Jimerson of Biloxi, Mississippi was arrested in connection to the cold case murder of Toni Spicer, who was found murdered in her mobile home in the southern part of Miami County, all thanks to DNA evidence collected 20 years ago.

Prosecutor Bruce Embrey says that due to the very detailed and thorough crime scene investigation performed by Sgt. Dean Marks and State Trooper Gary Boyles in 1992, police agencies at any time could help in the murder investigation.

The evidence collected from the scene was sent off for DNA examination and cataloging, awaiting a DNA hit so that a suspects name could be issued. But it wasnt until recently that a DNA match was found.

Since a DNA match in most cases isnt enough to identify a suspect, the help of the Biloxi, Mississippi Police Department was enlisted and after extensive investigation Jimerson was arrested and is now awaiting extradition back to Peru.

Copyright 2012 A Granite Broadcasting Station. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

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DNA Helps Locate Cold Case Murder Suspect

DNA found on the gun allegedly used to murder a Dartmouth taxi driver matches that of Chaze Lamar Thompson, a Halifax jury was told Tuesday.

Michelle Fisher, an expert in forensic DNA analysis, testified that theres a one-in-79-million chance that DNA swabbed from the grip of the gun belongs to a black Canadian other than Thompson.

The 22-year-old Thompson is on trial in Nova Scotia Supreme Court for first-degree murder in the death of Sergei Kostin, a driver for Bobs Taxi.

Thompson, of Dartmouth, is accused of shooting Kostin in the head from the back seat of his cab on Johnson Road in Cherry Brook on the afternoon of Jan. 17, 2009.

Kostins burned-out cab was discovered three days later, parked in woods at the end of Downey Road in North Preston.

His body was found that April 1 under the roots of a fallen tree along Upper Governor Street in North Preston.

Wayne McAvoy, Thompsons first cousin, led police to the body and was given immunity from prosecution after agreeing to testify for the Crown.

McAvoy said a gun found by police at Thompsons sisters apartment in Dartmouth in February 2009 was the murder weapon.

Part of the gun was in a couch and part was by a refrigerator.

Fisher testified Tuesday that of five swabs taken from the gun, only one was suitable for a meaningful comparison. The swab was from both sides of the guns grip.

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DNA on gun matches Thompson’s, expert testifies at trial

LOS ANGELES (AP) -- A nationally known professional tennis referee charged with the coffee-cup killing of her husband gave police a DNA sample Wednesday after dropping her opposition to the procedure.

Lois Ann Goodman, 70, who is charged with beating her husband to death with the cup last April, was accompanied by about 25 supporters, including friends and relatives, when she appeared briefly in court for a pretrial hearing.

A judge scheduled Goodman's next hearing for Nov. 8.

In the meantime, defense attorneys say they have a huge amount of evidence and court documents provided by prosecutors to review before a trial is scheduled. They also demanded to see original notes taken at Goodman's home by police officers who initially ruled the case an accidental death. In addition, they are seeking notes and recordings from coroner's investigators and the mortician who examined the body.

Goodman was arrested in August just before she was to referee at match at the U.S. Open.

Her attorneys say her 80-year-old husband was the victim of a freak accident.

Authorities initially believed Alan Goodman fell down stairs at home while she was away but later decided it was homicide. Prosecutors now believe he was struck 10 times on the head and stabbed with the broken cup.

The couple was married nearly 50 years with three grown children.

Defense attorneys Alison Triessl and Robert Sheahen told reporters that they anticipate surprise revelations in the case after all of the discovery materials are reviewed. They had opposed having Goodman provide a DNA sample but relented after losing an appeal on the issue.

''No DNA sample is going to prove anything,'' said Sheahen. ''Proving that her DNA is in her own home is ridiculous.''

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Woman charged in husband's death gives DNA sample

Scanning the DNA of sick infants using a new speed-reading method can diagnose rare genetic disorders in two days instead of weeks, according to research that brings gene mapping a step closer to everyday hospital use.

Researchers at Childrens Mercy Hospitals and Clinics in Kansas City, Missouri, created software that takes raw data from DNA scanning machines and combs though hundreds of genetic disorders to spot disease-causing mutations. The system provided likely diagnoses for three of four sick babies in about two days, results published in Science Translational Medicine found.

The new method has the potential to make genome sequencing practical for neonatal intensive care units, enabling doctors to diagnose mysterious genetic diseases more quickly, said Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Childrens Mercy and a study senior author. Fast diagnoses of sick babies could lead to life-extending treatments sooner in some or help avoid futile, costly therapies in others.

This is the biggest breakthrough in this technology for clinical applications we have seen in a few years, said David Dimmock, a geneticist at the Medical College of Wisconsin and Childrens Hospital of Wisconsin in Milwaukee, who wasnt involved in the study. The ability to sequence and interpret a genome in less than week is huge.

Dimmock said researchers at his institution were working on a similar fast genome interpretation system, but hadnt published the results yet. They beat us to the punch, he said.

There are about 3,500 known genetic diseases of which 500 have treatments, Kingsmore said. Many of these genetic illnesses hit young kids. Roughly 20 percent of infant deaths are caused by genetic conditions, according to the study released today.

The Childrens Mercy Hospital system was made possible in part by a new sequencing machine developed by San Diego-based Illumina Inc. (ILMN) that can decode an entire DNA sequence of a person in one day. This generates a colossal volume of raw data that must be analyzed by expert genetic researchers, a process that previously has taken weeks or months.

Heres where the system devised by Childrens Mercy researchers comes into play. Kingsmore and his team devised smart software that allows treating doctors to enter in a sick babys symptoms. The software then matches these reported symptoms to known genetic diseases that have similar symptoms, and scans through the babys genome results for likely harmful mutations in relevant genes.

We think this is going to transform the world of neonatology, Kingsmore said during a conference call with reporters. Until now, this was just not possible to get whole genome scan results quickly enough to help sick newborns in intensive care units, he said. Babies either died or else got better and were discharged home before the results of a gene test were returned.

For cases in which treatments are available, spotting the cause of a disease sooner may allow treatments to be started before it is too late, he said. Kingsmore estimated the total cost of the test to be about $13,500.

Read more from the original source:
Inherited Diseases Found Sooner in Newborns With DNA Scan