Category Archives: Science

Yogurts Used to Combat Superbugs

Dieticians at Addenbrooke’s have said evidence suggested the yoghurt might cut the risk of contracting C.diff. Caroline Heyes, dietetic services manager at Addenbrooke’s hospital, said: “Probiotic yoghurts may play a role in preventing C.difficile infection so we have been running a pilot on three of the care of the elderly wards for six months.
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“We can’t say for sure how much of that benefit is down to the yoghurt and how much they are down to a whole range of infection control procedures that the hospital has in place such as the deep cleaning programme, the bare-below-the-elbow programme, and the increased isolation procedures,” Ms Heyes said.

Bacteria and Efficient Food Digestion

Gut Bacteria May Cause And Fight Disease, Obesity

“We’re all sterile until we’re born,” says Glenn Gibson, a microbiologist at the University of Reading in Britain. “We haven’t got anything in us right up until the time we come into this big, bad, dirty world.”

But as soon as we pass out of the birth canal, when we are fetched by a doctor’s hands, placed in a hospital crib, put on our mother’s breast, when we drag a thumb across a blanket and stick that thumb in our mouths, when we swallow our first soft food, we are invaded by all sorts of bacteria. Once inside, they multiply – until the bacteria inside us outnumber our human cells.
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University of Chicago immunologist Alexander Chervonsky, with collaborators from Yale University, recently reported that doses of the right stomach bacteria can stop the development of type 1 diabetes in lab mice. “By changing who is living in our guts, we can prevent type 1 diabetes,” he told The Wall Street Journal.

The bottom line: We now have two sets of genes to think about – the ones we got from our parents and the ones of organisms living inside us. Our parents’ genes we can’t change, but the other set? Now that is one of the newest and most exciting fields in cell biology.

Follow link with related podcast: Gut bacteria may cause and fight, disease, obesity. This whole area of the ecosystem within us and our health I find fascinating. And I fall for confirmation bias on things like becoming inefficient at converting food to energy as a way reduce obesity.

You could have two people sitting down to a bowl of cheerios, they could each eat the same number of cheerios but because of a difference in their gut bacteria one will get more calories than the other.

They then gave an example of the difference being 95 calories versus 99 calories. Hardly seems huge but it would add up. Still that is a less amazing difference than I was expecting.

Trieste Science Prize Winners 2008

Beatriz Barbuy, an eminent Brazilian astrophysicist who has made a major contribution to the study of the evolution of the chemical composition of stars, and Roddam Narasimha, an internationally renowned Indian engineer and physicist whose work in fluid dynamics has increased our understanding of turbulence, have been awarded the 2008 Trieste Science Prize.
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Barbuy’s research has shed light on the formation of the Milky Way through studies of its oldest components. She was the first to demonstrate that metal-poor stars in the galactic halo (the faint sphere surrounding the galactic disk) have an overabundance of oxygen, relative to iron. This indicates that the halo was chemically enriched by ‘supernova’ explosions of massive first-generation stars, which may have been 500 times the size of the sun.

Hydrogen and helium were the only elements produced in abundance during the formation of the first generation of stars. All of the heavier elements, which astronomers call ‘metals’, were subsequently produced by stars through nuclear fusion. At the end of a star’s life, some of these elements were recycled into the stellar medium, from which the next generation of stars (with greater ‘metallicity’) was born.
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Narasimha’s contributions have extended to aircraft design, monsoon predictions and the prospects of using wind energy in rural India. He has also conducted important work on shock wave structure and turbulent shear flows. He is best known for his research on the transitions between laminar and turbulent flows. ‘Laminar flow’ is the smooth movement of fluid (for example, air or water) in parallel layers or paths (streamlines). Turbulence is the chaotic movement of fluid.

A search for the hidden order in chaos has been a fundamental motif of Narasimha’s work. His path-breaking research includes examinations of the ways in which chaos can arise from ordered motion and the structure and memory of fully turbulent flows.

The prize is awarded to outstanding scientists living and working in the developing world. Winners share a US$100,000 cash award.

Science, Engineering and Math Fellowships

I work at the American Society for Engineering Education as an Information Technology Program Manager (this blog is not affiliated with ASEE). A large portion of the computer applications I work on are related to the science and engineering fellowships we administer. The fellowship applications are all open now (for certain fields the NSF application deadline is next week). Those fellowships include:

National Science Foundation Graduate Research Fellowship has the earliest deadline, starting November 3rd for some while some fields are as late as November 12th. The fellowship provides support for 3 years (a yearly stipend of $30,000 plus educational expense) to approximately 1,000 students and is open to most science, engineering and math fields.
National Defense Science and Engineering Graduate Fellowship applications are accepted until January 5th, 2009. 200 students receive $31,000 for 3 years plus educational expenses.
Science, Mathematics And Research for Transformation Scholarship for Service Program is another Department of Defense fellowship with a deadline of December 15th, 2008. This program offers awards to 200 science and engineering undergraduate and graduate students with awards between $25,000 and $41,000 a year as well as education expenses, health insurance, internships and employment placement after graduation.
NASA Aeronautics Scholarship offers 20 two-year undergraduate scholarships and 5 two-year graduate scholarships to students in Aeronautics and related fields. The deadline is January 16th, 2009.

Other scholarships and fellowships (these are not managed by ASEE): Gates Millennium Scholars Program (January 12th deadline) – NASA Graduate Student Researchers (February 1st) – Goldwater Science Scholarships (January 30th)

Atlantic Hurricane Season 2008

photo of hurricane evacuation sign

Here is a nice post on weather and understanding data – Atlantic Hurricane Season 2008

A well-accepted metric which convolves storm frequency, intensity, and duration is called accumulate cyclone energy (ACE) and is calculated very simply: take the maximum sustained winds reported by the NHC every 6-hours for all storms (> 34 knots), square this value, and sum over the entire lifetime, then divide by 10,000. In 2007, even though there were also 15 storms, the ACE was only 72 compared to 132 for 2008 with the same number of named storms. This is partially because the storms in 2008 were much longer lived especially Bertha.
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When encapsulated in the recent active period in North Atlantic activity (1995-2007), 2008 experienced normal or expected activity as measured by ACE. In terms of a long-term climatology, either the last 30 or 65 years, 2008 is clearly an above average year.

Data can’t lie but mistaken assumptions can lead you to form mistaken impressions. If you believe the number of named storms = hurricane activity and then are surprised that in fact there was many more days of hurricane activity it is not because the data lied but because you didn’t understand what the data represented.

76 Nobel Laureates in Science Endorse Obama

76 Nobel Laureates in Science Endorse Obama!. This is the largest number of Nobel laureates to endorse anything according to that post. Letter:

An Open Letter to the American People

This year’s presidential election is among the most significant in our nation’s history. The country urgently needs a visionary leader who can ensure the future of our traditional strengths in science and technology and who can harness those strengths to address many of our greatest problems: energy, disease, climate change, security, and economic competitiveness.

We are convinced that Senator Barack Obama is such a leader, and we urge you to join us in supporting him.

During the administration of George W. Bush, vital parts of our country’s scientific enterprise have been
damaged by stagnant or declining federal support. The government’s scientific advisory process has been distorted by political considerations. As a result, our once dominant position in the scientific world has been shaken and our prosperity has been placed at risk. We have lost time critical for the development of new ways to provide energy, treat disease, reverse climate change, strengthen our security, and improve our economy.

We have watched Senator Obama’s approach to these issues with admiration. We especially applaud his emphasis during the campaign on the power of science and technology to enhance our nation’s
competitiveness. In particular, we support the measures he plans to take – through new initiatives in
education and training, expanded research funding, an unbiased process for obtaining scientific advice, and an appropriate balance of basic and applied research – to meet the nation’s and the world’s most urgent needs.

Senator Obama understands that Presidential leadership and federal investments in science and technology are crucial elements in successful governance of the world’s leading country. We hope you will join us as we work together to ensure his election in November.

Signed,

Alexei Arikosov, Physics, 2003
Peter Agre, Chemistry, 2003
Sidney Altman, Chemistry, 1989
Philip W. Anderson, Physics, 1977
Richard Axel, Medicine, 2004
David Baltimore, Medicine, 1975
Baruj Benacerraf, Medicine, 1980
Paul Berg, Chemistry, 1980
J. Michael Bishop, Medicine, 1989
N. Bloembergen, Physics, 1981
Michael S. Brown, Medicine, 1985
Linda B. Buck, Medicine, 2004 Continue reading →

Common Cold Alters the Activity of Genes

Scientists Come Closer to Unlocking Secrets of Common Cold

Canadian and U.S. researchers have found that the human rhinovirus, long blamed for causing the common cold, doesn’t actually cause those annoying sniffles, sneezes, and coughs.

Instead, the ubiquitous virus alters the activity of genes in the body, which then results in the misery that afflicts most people every year or so, according to a study in the first November issue of the American Journal of Respiratory and Critical Care Medicine.
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Human rhinovirus (HRV) causes some 30 percent to 50 percent of common colds and can also worsen more serious conditions, such as asthma.
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A “microarray analysis” of DNA showed no genetic changes eight hours after infection. But, after two days, about 6,500 genes had been affected, either with heightened activity or dampened activity.

The genes most affected by the presence of the virus were ones that make antiviral proteins and pro-inflammatory chemicals that contribute to airway inflammation, the researchers said.

Read: Learning How Viruses Evade the Immune System – Gene Carnival – Black Raspberries Alter Hundreds of Genes Slowing Cancer – Study Finds No Measurable Benefit to Flu Shots

Plants can Signal Microbial Friends for Help

When under attack, plants can signal microbial friends for help

Researchers at the University of Delaware have discovered that when the leaf of a plant is under attack by a pathogen, it can send out an S.O.S. to the roots for help, and the roots will respond by secreting an acid that brings beneficial bacteria to the rescue.
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In a series of laboratory experiments, the scientists infected the leaves of the small flowering plant Arabidopsis thaliana with a pathogenic bacterium, Pseudomonas syringae. Within a few days, the leaves of the infected plants began yellowing and showing other symptoms of disease.

However, the infected plants whose roots had been inoculated with the beneficial microbe Bacillus subtilis were perfectly healthy. Farmers often add B. subtilis to the soil to boost plant immunity. It forms a protective biofilm around plant roots and also has antimicrobial properties, according to Bais.

Using molecular biological tools, the scientists detected the transmission of a long-distance signal, a “call for help,” from the leaves to the roots in the plants that had Bacillus in the soil. The roots responded by secreting a carbon-rich chemical–malic acid.

All plants biosynthesize malic acid, Bais explains, but only under specific conditions and for a specific purpose–in this case, the chemical was actively secreted to attract Bacillus. Magnified images of the roots and leaves showed the ratcheted-up defense response provided by the beneficial microorganisms.
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“Plants can’t move from where they are, so the only way they can accrue good neighbors is through chemistry,” Bais notes.

Silk E.coli Sensors

“Edible Optics” Could Make Food Safer

Scientists at Tufts University’s School of Engineering have demonstrated for the first time that it is possible to design such “living” optical elements that could enable an entirely new class of sensors. These sensors would combine sophisticated nanoscale optics with biological readout functions, be biocompatible and biodegradable, and be manufactured and stored at room temperatures without use of toxic chemicals. The Tufts team used fibers from silkworms to develop the platform devices.
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The possibility of integrating optical readout and biological function in a single biocompatible device unconstrained by these limitations is tantalizing. Silk optics has captured the interest of the Defense Department, which has funded and been instrumental in enabling rapid progress on the topic. The Defense Advanced Research Projects Agency (DARPA) awarded Tufts a research contract in 2007 and is funding Tufts and others on groundbreaking projects that could someday result in biodegradable optical sensing communications technology.
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To form the devices, Tufts scientists boiled cocoons of the Bombyx mori silkworm in a water solution and extracted the glue-like sericin proteins. The purified silk protein solution was ultimately poured onto negative molds of ruled and holographic diffraction gratings with spacing as fine as 3600 grooves/mm.
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The Tufts team embedded three very different biological agents in the silk solution: a protein (hemoglobin), an enzyme (horseradish peroxidase) and an organic pH indicator (phenol red). In the hardened silk optical element, all three agents maintained their activity for long periods when simply stored on a shelf. “We have optical devices embedded with enzymes that are still active after almost a year of storage at room temperature.

The Rush to Save Timbuktu’s Crumbling Manuscripts

Fabled Timbuktu, once the site of the world’s southernmost Islamic university, harbors thousands upon thousands of long-forgotten manuscripts. A dozen academic instutions from around the world are now working frantically to save and evaluate the crumbling documents.
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The Ahmed Baba Library alone contains more than 20,000 manuscripts, including works on herbal medicine and mathematics, yellowed volumes of poetry, music and Islamic law. Some are adorned with gilded letters, while others are written in the language of the Tuareg tribes. The contents remain a mystery.

Manuscript hunters are now scouring the environs of Timbuktu, descending into dark, clay basements and climbing up into attics. Twenty-four family-owned collections have already been discovered in the area. Most of the works stem from the late Middle Ages, when Timbuktu was an important crossroads for caravans.
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Archaeologists have shown that an incredible system of underground canals up to 20,000 kilometers (12,422 miles) long once existed at Wadi al-Hayat in Libya. Thanks to such hydraulic marvels, the desert blossomed and crops sprouted in the fields of the Tuareg.