Featured Research

from universities, journals, and other organizations

Human Genome Sequence Yields New Tool For Microbe-Hunting; Dana-Farber Scientists To Search For Infectious Causes Of Chronic Diseases

Date:
January 15, 2002
Source:
Dana-Farber Cancer Institute
Summary:
Scientists say they have developed a powerful method for detecting foreign bacteria and viruses in human tissue samples, even if the organisms haven't previously been encountered.

BOSTON - Scientists say they have developed a powerful method for detecting foreign bacteria and viruses in human tissue samples, even if the organisms haven't previously been encountered.

Related Articles


The microbe-hunting method relies on DNA sequence data compiled in the nearly completed Human Genome Project over the past 10 years. Dana-Farber Cancer Institute researchers already are preparing to use the technique to investigate the causes of mysterious chronic diseases like rheumatoid arthritis, Type I diabetes, atherosclerosis, lupus, multiple sclerosis, and several types of cancer. Undetected, possibly novel infectious agents have been suggested as possible causes of these and other illnesses.

"The technique is good for investigating all these chronic diseases of unknown origin," said Matthew Meyerson, MD, PhD, senior author of a report that will be published online by the journal Nature Genetics on Jan. 14. It will appear in print in the journal's February issue. Another potential use of the method is identifying emerging infectious diseases: examples are HIV and Ebola virus, which were unknown when they first showed up in recent decades.

Microbiologists have traditionally identified pathogens (disease-causing organisms) by growing them in a laboratory dish from a sample of infected tissue. But not all pathogens can be cultured this way. Molecular tools do exist and have been used to identify some new disease organisms, but they have major limitations, said Meyerson.

Meyerson, who trained as a pathologist, has a longstanding interest in diseases whose causes remain unknown or have been wrongly linked to other factors. For example, he noted that doctors used to blame stress and diet for stomach and duodenal ulcers, which only in recent years have been shown to be caused by a bacterial infection. Infections may be involved in a long list of inflammatory and autoimmune diseases, he said, and cancers including lymphomas, bladder cancer and some lung cancers.

The technique is called "computational subtraction" because the actual matching of DNA sequences is carried out with computers after the sample has been analyzed. "The potential power of sequence-based computation subtraction lies in its ability to identify new nonhuman sequences in a comprehensive and unbiased manner," the authors write in their report.

"It is made possible by the sequencing of the human genome," said Meyerson, because scientists can now call up on a computer nearly the entire "instruction book" of humans - the sequence of some 3 billion chemical "letters" that make up all the 30,000 or so human genes.

Starting with a sample of human tissue from someone with a disease, the scientists would determine the sequence of a portion of the DNA its cells contain. Using a powerful computer program called MEGABLAST, scientists can then match the sample's DNA to the sequence of DNA in the entire human genome.

"So if you sequence the DNA and compare your sequences to the human genome, you eliminate anything that matches," says Meyerson. "What's left is the DNA of the infectious agent."

Meyerson and his colleagues tested 3.2 million "expressed sequence tags," or ESTs, segments of genes collected from many humans including those with diseases, They compared these EST sequences against the sequences of the human genome itself, which should contain exclusively human DNA. They found that about 2 percent of the EST sequences didn't match to human sequences. Some of these sequences are non-human, and turned out to be contaminating or infecting viruses, bacteria and fungi.

Among this leftover DNA, Meyerson's team found DNA from such organisms as the hepatitis B and C viruses, human papillomavirus, cytomegalovirus, Kaposi's sarcoma herpesvirus, and Epstein-Barr virus.

To test whether the subtraction method worked on a sample in which the infecting agent was known, the investigators tried it in a human tissue sample known to contain a specific type of human papillomavirus (which causes cervical cancer). The technique worked as expected, highlighting the papillomavirus in the "leftover" DNA.

At times, the method likely will pinpoint an unfamiliar nonhuman DNA sequence in diseased human tissue, said Meyerson. It may be a novel microbe, and investigators will have to use other tools, like making antibodies to the protein the DNA sequence makes, to identify it.

The other authors are Griffin Weber and Jay Shendure, MD-PhD students at Harvard Medical School; David Tanenbaum, PhD, of Dana-Farber; and George Church, PhD, of Harvard Medical School.

Dana-Farber Cancer Institute (www.dana-farber.org) is a principal teaching affiliate of the Harvard Medical School and is among the leading cancer research and care centers in the United States. It is a founding member of the Dana-Farber/Harvard Cancer Center (DF/HCC), a designated comprehensive cancer center by the National Cancer Institute.


Story Source:

The above story is based on materials provided by Dana-Farber Cancer Institute. Note: Materials may be edited for content and length.


Cite This Page:

Dana-Farber Cancer Institute. "Human Genome Sequence Yields New Tool For Microbe-Hunting; Dana-Farber Scientists To Search For Infectious Causes Of Chronic Diseases." ScienceDaily. ScienceDaily, 15 January 2002. <www.sciencedaily.com/releases/2002/01/020115075730.htm>.
Dana-Farber Cancer Institute. (2002, January 15). Human Genome Sequence Yields New Tool For Microbe-Hunting; Dana-Farber Scientists To Search For Infectious Causes Of Chronic Diseases. ScienceDaily. Retrieved October 25, 2014 from www.sciencedaily.com/releases/2002/01/020115075730.htm
Dana-Farber Cancer Institute. "Human Genome Sequence Yields New Tool For Microbe-Hunting; Dana-Farber Scientists To Search For Infectious Causes Of Chronic Diseases." ScienceDaily. www.sciencedaily.com/releases/2002/01/020115075730.htm (accessed October 25, 2014).

Share This



More Health & Medicine News

Saturday, October 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Texas Nurse Nina Pham Cured of Ebola

Texas Nurse Nina Pham Cured of Ebola

AFP (Oct. 25, 2014) — An American nurse who contracted Ebola while caring for a Liberian patient in Texas has been declared free of the virus and will leave the hospital. Duration: 01:01 Video provided by AFP
Powered by NewsLook.com
IKEA Desk Converts From Standing to Sitting With One Button

IKEA Desk Converts From Standing to Sitting With One Button

Buzz60 (Oct. 24, 2014) — IKEA is out with a new convertible desk that can convert from a sitting desk to a standing one with just the push of a button. Jen Markham explains. Video provided by Buzz60
Powered by NewsLook.com
Ebola Protective Suits Being Made in China

Ebola Protective Suits Being Made in China

AFP (Oct. 24, 2014) — A factory in China is busy making Ebola protective suits for healthcare workers and others fighting the spread of the virus. Duration: 00:38 Video provided by AFP
Powered by NewsLook.com
WHO: Millions of Ebola Vaccine Doses by 2015

WHO: Millions of Ebola Vaccine Doses by 2015

AP (Oct. 24, 2014) — The World Health Organization said on Friday that millions of doses of two experimental Ebola vaccines could be ready for use in 2015 and five more experimental vaccines would start being tested in March. (Oct. 24) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:

Strange & Offbeat Stories

 

Health & Medicine

Mind & Brain

Living & Well

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:  

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile iPhone Android Web
Follow Facebook Twitter Google+
Subscribe RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins