India science blog

Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma

2006-10-09T06:57:00.000-07:00

Background

RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological variation in expression have not been explored sufficiently to define the true extent of usability and limitations of such amplification techniques.

Results

We show that expression ratios are occasionally distorted by amplification using the Affymetrix small sample protocol version 2 due to a disproportional shift in intensity across biological samples. This occurs when a shift in one sample cannot be reflected in the other sample because the intensity would lie outside the dynamic range of the scanner. Interestingly, such distortions most commonly result in smaller ratios with the consequence of reducing the statistical significance of the ratios. This becomes more critical for less pronounced ratios where the evidence for differential expression is not strong. Indeed, statistical analysis by limma suggests that up to 87% of the genes with the largest and therefore most significant ratios (p<10e-20) in the unamplified group have a p-value below 10e-20 in the amplified group. On the other hand, only 69% of the more moderate ratios (10e-20
Conclusions

We conclude that microarray analysis of amplified samples performs best at detecting differences in gene expression, when these are large and when limma statistics are used.

Source: BMC Genomics

Cured meats may reduce lung function

2006-09-03T07:49:00.000-07:00

People who eat large amounts of cured meats have about a 3% reduction in lung function compared to those who never consume these foods, a new study shows. Such a difference may have a noticeable effect in a person with a lung disease, such as bronchitis, the researchers say.

Sorce: NewScientist

Bird flu research must be shared faster

2006-09-03T03:20:00.000-07:00

It gives a new meaning to the phrase "publish or perish". Scientists have not been sharing information about bird flu fast enough, say experts. While the World Health Organization keeps a database of viral sequences, access has been restricted, and other researchers have hoarded data for fear of rivals publishing it without giving them credit.

Source: NewScientist

Spacecraft strikes Moon with intense flash

2006-09-03T03:18:00.000-07:00

The SMART-1 lunar probe crashed into the Moon right on cue on Sunday morning. Mission controllers at the European Space Agency lost contact with the probe at 0542 GMT, indicating that it had struck close to the planned landing site on the lunar “Lake of Excellence”.

Source: NewScientist

Hubble takes first image of solar eclipse on Uranus

2006-09-02T08:55:00.000-07:00

A tiny moon has been caught floating in front of Uranus for the first time, the Hubble Space Telescope reveals. The moon's shadow can also be seen on the planet's cloud tops, creating a solar eclipse on Uranus itself.

Read more

Scientists temper fears on global warming

2006-09-02T08:53:00.000-07:00

SYDNEY, Sept. 1 (UPI) -- World scientists have revised their doomsday scenario on climate change caused by global warming, the Weekend Australian reported.

Read more

Aussie study links asthma to smoking

2006-09-02T08:52:00.000-07:00

HOBART, Australia, Sept. 2 (UPI) -- Australian scientists who spent nearly 40 years on a research program say asthma in adults can be the result of maternal smoking.

Read more

Wheel of Life: Bacteria provide horsepower for tiny motor

2006-09-02T06:54:00.000-07:00

For millennia, people have hitched beasts to plows to exploit the animals' strength and energy. In a modern variant of that practice, scientists have chemically harnessed bacteria to a micromotor so that they can make the device's rotor slowly turn.

Read more

Engineering a Cure: Genetically modified cells fight cancer

2006-09-02T06:53:00.000-07:00

By inserting a gene into normal immune cells isolated from melanoma patients, scientists have turned the cells into cancer fighters. This new technique represents the first use of gene therapy to treat cancer, the researchers say.

Read more

Gene therapy breakthrough against skin cancer

2006-09-01T11:15:00.000-07:00

mmune cells removed from melanoma sufferers and genetically engineered to better recognise cancer can fight the disease when reintroduced into the patients.

Source: NewScientist

Gene-altered flies testify to global warming

2006-09-01T11:14:00.000-07:00

Populations of fruit flies on three separate continents have independently evolved identical gene changes within just two decades, apparently to cope with global warming.

Source: NewScientist

Scientist-astronaut Sends T-cells Into Space

2006-09-01T11:10:00.000-07:00

A former astronaut and researcher at the San Francisco VA Medical Center will be traveling to the Cosmodrome space-launch site at Baikonur, Kazakhstan, this Saturday, Sept. 2, 2006, to prepare a crucial experiment designed to demonstrate how human immune response is suppressed in the weightless environment of space.

More

New Method Of Gene Therapy Offers Hope For Treatment Of Melanoma, Other Common Cancers

2006-09-01T11:07:00.000-07:00

A team of researchers at the National Cancer Institute (NCI), part of the National Institutes of Health, has demonstrated sustained regression of advanced melanoma in a study of 17 patients by genetically engineering patients' own white blood cells to recognize and attack cancer cells. The study appears in the online edition of the journal Science on August 31, 2006*.

More

Nature to modify stem cell study report

2006-09-01T11:06:00.000-07:00

LONDON, Sept. 1 (UPI) -- The British journal Nature plans changes to an article that described a method of creating embryonic stem cells without destroying the embryos.

Nature officials say the move is intended to clear up any confusion over an article last week that said a research team in Massachusetts succeeded in developing a process for growing stem cells while sparing the embryos, the Chicago Tribune reports.

Read more

FDA rejects French heart drug

2006-09-01T11:01:00.000-07:00

WASHINGTON, Sept. 1 (UPI) -- The U.S. Food and Drug Administration has rejected a heart drug which a French company hoped would become a blockbuster medication.

The rejection of Multaq, designed to correct irregular heartbeat, came in a "nonapprovable letter" to manufacturer Sanofi-Adventis, the Wall Street Journal reports.

Read more

New cancer treatment hopeful

2006-09-01T10:59:00.000-07:00

BETHESDA, Md., Sept. 1 (UPI) -- The U.S. National Institutes of Health says using the body's immune system to attack cancerous tumors has brought limited success.

The new treatment is being tried to see if it can replace surgery, chemotherapy or radiation, reports CNN.

Read more

Tiny Shock Absorbers Help Bacteria Stick Around Inside The Body

2006-09-01T10:57:00.000-07:00

Bacteria have hair-like protrusions with a sticky protein on the tip that lets them cling to surfaces. The coiled, bungee cord-like structure of the protrusions helps the bacteria hang on tightly, even under rough fluid flow inside the body, researchers report in the journal PLoS Biology.

Read more

New Solar System? Twelve planets and counting (Updated)

2006-09-01T10:50:00.000-07:00

Pluto aficionados, rejoice! Pluto is a planet. So are the giant asteroid Ceres, Pluto's moon Charon, and a large outer-solar system object called 2003 UB313. The solar system has 12 planets instead of the familiar 9, according to a proposal that the General Assembly of the International Astronomical Union (IAU) will vote on next week in Prague, Czech Republic.

Read more

Risky Legacy: African DNA linked to prostate cancer

2006-09-01T10:46:00.000-07:00

The high rate of prostate cancer among African American men may result in large part from a newly identified stretch of DNA passed down from their African ancestors.

Read More

High Mortality Due to Multidrug-resistant Tuberculosis among HIV Positive Patients in South Africa

2006-08-31T10:19:00.000-07:00

Tuberculosis (TB) is a second epidemic that co-exists with the HIV/AIDS epidemic in much of the developing world, and is responsible for considerable morbidity and mortality, especially among people coinfected with both TB and HIV.

At the XVI International AIDS Conference in Toronto, several presentations focused on HIV/TB coinfection. Kevin De Cock, MD, director of the World Health Organization HIV/AIDS Department, called for TB management to be prioritized "at the head of AIDS management."

In recent years there has been a growing awareness of the problem of multidrug-resistant (MDR) TB, which is resistant to the commonly used first-line therapies, as well as the emergence of extensively drug-resistant (XDR) TB, which is resistant to all first-line and most second-line drugs. The Centers for Disease Control and Prevention have documented about 350 cases of XDR TB worldwide.

In a late-breaker presentation at the conference, researchers from South Africa and the U.S. reported on a cross-sectional study to determine the extent and consequences of MDR TB among patients in a rural district in KwaZulu-Natal, South Africa. In this district, antiretroviral therapy has significantly reduced the rate of death among people with HIV/AIDS. Of the remaining deaths, however, more than two-thirds are due to MRD TB.

The researchers performed sputum cultures and drug susceptibility tests on individuals with known or suspected TB at a rural district hospital between January 2005 and March 2006. Spoligotyping (a PCR method that simultaneously detects and determines the type of TB) was performed on isolates resistant to all tested TB drugs (isoniazid, rifampin, ethambutol, streptomycin, ciprofloxacin, and kanamycin).

Results

Between January 2005 and March 2006, sputum collected from 1540 individuals revealed that 544 patients (35%) were culture-positive for Mycobacterium tuberculosis.
Of these, 221 (41%) had MDR TB resistant to isoniazid and rifampicin.
53 patients (24% of MDR isolates, 10% of all positive cultures) had XDR TB, with resistance to all first-line and second-line drugs tested.
Spoligotyping revealed that nearly 90% of XDR TB patients were infected with a genetically similar TB strain (26 out of 30 isolates).
52 of 53 XDR TB patients (98%) died during follow-up; the median survival time after sputum collection was just 16 days (range 11-136).
All 47 XDR TB patients with known HIV status were HIV positive, and many had AIDS.
51% of patients had not been previously treated for TB, indicating that they did not develop resistance due to suboptimal prior therapy.
36% had no history of prior hospitalization, suggesting that XDR TB was transmitted in the community outside of a hospital setting.

Conclusion

"Increased surveillance in rural South Africa revealed a markedly greater MDR TB prevalence than previously recognized, with evidence of recent nosocomial and community transmission of XDR TB in HIV coinfected patients," the researchers concluded. "The convergence of the TB/HIV epidemic with MDR and XDR TB in resource-poor settings is a deadly threat to gains in survival achieved by TB [directly-observed therapy] and antiretroviral therapy."

Reference
N R Gandhi, A Mol, R Pawinski, and others. High Prevalence and Mortality from Extensively-Drug Resistant (XDR) TB in TB/HIV Coinfected Patients in Rural South Africa. August 13-18, 2006. XVI International AIDS Conference. Toronto, August 13-18, 2006. Abstract THLB0210.

How low will we go? Check out Yahoo! Messengers low PC-to-Phone call rates.

Sterilisation 'may not kill CJD'

2006-08-24T07:16:00.000-07:00

Edinburgh University found every instrument they tested was contaminated with enough protein residue to pose a potential infection risk.

Brazil embryo registry worries scientists

2006-08-24T07:12:00.000-07:00

RIO DE JANEIRO, Brazil - Brazilian scientists are worried about how they will be able to comply with a government requirement to identify the many thousands of frozen embryos stored for in-vitro fertilization in clinics around the country.

U.S. firm creates human stem cells without destroying embryos

2006-08-24T07:05:00.000-07:00

LOS ANGELES, Aug. 23 (Xinhua) -- Scientists with the Advanced Cell Technology, Inc. announced on Wednesday that they have successfully generated human embryonic stem cell lines with an approach that does not harm embryos.

Curbing AIDS epidemic means treating TB

2006-08-22T10:38:00.000-07:00

A huge and growing tuberculosis (TB) epidemic threatens to crush the world's efforts to fight AIDS, health officials, scientists and activists warned at the XVI International AIDS Conference in Toronto, Canada, this Wednesday.

TB, 'Achilles Heel' of HIV/AIDS Treatment

2006-08-22T10:34:00.000-07:00

At the 16^th International AIDS Conference, experts warned that tuberculosis may undermine much of the progress that’s been made with anti-retroviral drugs. They say urgent action is needed to prevent the deaths of 250,000 people living with HIV/AIDS every year. Anti-retroviral drugs now have a 10-year history of prolonging the lives of those living with HIV/AIDS. But while those drugs keep HIV at bay, patients may succumb rather quickly to TB infection. In fact, TB is being called the Achilles heal of HIV treatment. VOA English to Africa reporter Joe De Capua spoke with experts and people living with HIV/AIDS about treatments.