Tag Archives: Science

Bacteria In Cave Isolated for 4 Million Years Highly Resistant to Many Antibiotics

PLoS published an interesting open access research paper on bacteria and their resistance to antibiotics. I am surprised how widespread and strong the antibiotic resistance was is the isolated bacteria that were studied. It raises more interesting questions about the important area of antibiotics.

The lead researcher on this study, Gerry Wright, previously published on antibiotic properties of bacteria found in soil.

Abstract of Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

Antibiotic resistance is a global challenge that impacts all pharmaceutically used antibiotics. The origin of the genes associated with this resistance is of significant importance to our understanding of the evolution and dissemination of antibiotic resistance in pathogens. A growing body of evidence implicates environmental organisms as reservoirs of these resistance genes; however, the role of anthropogenic use of antibiotics in the emergence of these genes is controversial.

We report a screen of a sample of the culturable microbiome of Lechuguilla Cave, New Mexico, in a region of the cave that has been isolated for over 4 million years. We report that, like surface microbes, these bacteria were highly resistant to antibiotics; some strains were resistant to 14 different commercially available antibiotics. Resistance was detected to a wide range of structurally different antibiotics including daptomycin, an antibiotic of last resort in the treatment of drug resistant Gram-positive pathogens.

Enzyme-mediated mechanisms of resistance were also discovered for natural and semi-synthetic macrolide antibiotics via glycosylation and through a kinase-mediated phosphorylation mechanism. Sequencing of the genome of one of the resistant bacteria identified a macrolide kinase encoding gene and characterization of its product revealed it to be related to a known family of kinases circulating in modern drug resistant pathogens. The implications of this study are significant to our understanding of the prevalence of resistance, even in microbiomes isolated from human use of antibiotics. This supports a growing understanding that antibiotic resistance is natural, ancient, and hard wired in the microbial pangenome.

Baboons Learn to Recognize Hundreds of Words

The (Monkey) Business Of Recognizing Words by Jon Hamilton

[Jonathan Grainger, researcher, Aix-Marseille University] says a baboon named Dan learned more than 300 words. “Dan’s our star baboon,” he says. “He’s a high-performing individual, basically. He does well in most tasks.”

But here’s the amazing thing: Dan and the other baboons also learned to tell whether a string of letters they’d never seen before was an English word. That’s something first-graders learn to do when they start reading, but scientists had assumed that children were simply sounding out the letters to decide whether they make sense.

Of course, the baboons couldn’t do this because they’re not learning to read a language they already speak. They had to rely on a part of the brain that can tell whether objects fit a known pattern.
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Michael Platt, who directs the Duke Institute for Brain Sciences, says he was surprised by what the baboons were able to do.

“I was really looking for holes to poke in this study, but it was very difficult to find any because it was really beautifully done,” he says. “And I think the linchpin here was that the baboons, once they had learned the rule, could generalize to new words that they had not seen before.”

Platt says when you think about it, the finding makes sense, given what’s known about human and animal brains. “Brains are always looking for patterns,” he says. “They are always looking to make some statistical pattern analysis of the features and events that are in the environment. And this would just be one of those.”

Platt says that’s a big departure from the idea that reading is a direct extension of spoken language.

One questions I have, is why the experiment done in France tested wether the Baboons could recognize English words?

Flavonoids Reduce Instances of Parkinson’s Disease in Men

Men who eat flavonoid-rich foods such as berries, tea, apples and red wine significantly reduce their risk of developing Parkinson’s disease, according to new research by Harvard University and the University of East Anglia.

The findings add to the growing body of evidence that regular consumption of some flavonoids can have a marked effect on human health. Recent studies have shown that these compounds can offer protection against a wide range of diseases including heart disease, hypertension, some cancers and dementia.

This latest study is the first study in humans to show that flavonoids can protect neurons against diseases of the brain such as Parkinson’s.

Around 130,000 men and women took part in the research. More than 800 had developed Parkinson’s disease within 20 years of follow-up. After a detailed analysis of their diets and adjusting for age and lifestyle, male participants who ate the most flavonoids were shown to be 40 per cent less likely to develop the disease than those who ate the least. No similar link was found for total flavonoid intake in women.

“These exciting findings provide further confirmation that regular consumption of flavonoids can have potential health benefits,” said Prof Aedin Cassidy of the Department of Nutrition, Norwich Medical School at UEA.

“This is the first study in humans to look at the associations between the range of flavonoids in the diet and the risk of developing Parkinson’s disease and our findings suggest that a sub-class of flavonoids called anthocyanins may have neuroprotective effects.”

Prof Gao said: “Interestingly, anthocyanins and berry fruits, which are rich in anthocyanins, seem to be associated with a lower risk of Parkinson’s disease in pooled analyses. Participants who consumed one or more portions of berry fruits each week were around 25 per cent less likely to develop Parkinson’s disease, relative to those who did not eat berry fruits. Given the other potential health effects of berry fruits, such as lowering risk of hypertension as reported in our previous studies, it is good to regularly add these fruits to your diet.”

Flavonoids are a group of naturally occurring, bioactive compounds found in many plant-based foods and drinks. In this study the main protective effect was from higher intake of anthocyanins, which are present in berries and other fruits and vegetables including aubergines, blackcurrants and blackberries. Those who consumed the most anthocyanins had a 24% reduction in risk of developing Parkinson’s disease.

The findings must now be confirmed by other large epidemiological studies and clinical trials.

Parkinson’s disease is a progresssive neurological condition affecting one in 500 people. There are few effective drug therapies available.

The result is far from conclusive and even if the result were confirmed the 24% reduction is hardly huge. But since berries are yummy there seem little reason to not tilt toward more berries in your diet.

Citizen Science

Citizen science enters a new era

Another online program, Phylo, is advancing scientists’ knowledge of genetics by making a game out of DNA matching. If areas of genetic sequence are roughly similar between species, it suggests strongly that they could have an important function. Finding them has been beyond the scope of computer algorithms. But earlier this month, researchers published a study where gamers outsmarted the best computers – they made the best possible DNA sequence match between up to eight species at a time.

The potential for regular people contributing to science is great. This has a long history. For most of human history science was done by non-scientists since there were no scientists. Calling is science might be a stretch but to me it was (passing on what health cures worked for various sicknesses, how to use various tools, how to grow crops…). As scientists came into being they were primarily unprofessional – that is they practiced science but were doing so as a hobby, they were not paid and had no requirements to get a PhD or anything.

Today regular people help by collecting data (counting birds, documenting plant growth [time of year], migration data, weather data…) sharing knowledge with scientists who ask, sharing their computer to be used to analyze data, analyzing data (for example, in astronomy hobbyists often make new discoveries) and the latest way people help is through games (that essentially tap human brainpower to analyze data – such as Foldit, which I have posted about previously).

I like the contributions people can make to science but I think the biggest value is the scientific understanding people gain while participating. As Neil Degrasse Tyson says the scientifically literate see a different world.

Cornell University provides an online tool to find opporunities participate in scientific research.

And we shouldn’t forget the amazing science done by students like those honored with Intel Talent Search, though the work those winning the awards do I would lump with science by “real scientists” (I believe now most of those who win are working on projects with university scientists).

Is Dirt Healthier Than Broccoli?

That dirt I ate as a kid is maybe why I have been relatively healthy. Ok, probably that hasn’t been the most important factor. But it may be that some dirt and germs (kids licking their dirty hands and the ice cream melts on it, etc.) is actually more important for their long term health than finishing off the broccoli (of course, a healthy diet requires eating a bunch of vegetables, more than most kids eat).

The hygiene hypothesis has become a popular explanation for the boom in asthma, allergies and other health problems. Boiled down to one sentence the hypothesis is that exposure to germs early in life creates a healthy immune system and too little exposure results in a hypersensitive immune system (that is not as effective and leads to things like allergies).

A recent closed science paper, Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function, found mice exposed to more germs early on where healthier:

Exposure to microbes during early childhood is associated with protection from immune-mediated diseases such as inflammatory bowel disease (IBD) and asthma. Here, we show that, in germ-free (GF) mice, invariant natural killer T (iNKT) cells accumulate in the colonic lamina propria and lung, resulting in increased morbidity in models of IBD and allergic asthma compared to specific pathogen-free (SPF) mice. This was associated with increased intestinal and pulmonary expression of the chemokine ligand CXCL16, which was associated with increased mucosal iNKT cells. Colonization of neonatal—but not adult—GF mice with a conventional microbiota protected the animals from mucosal iNKT accumulation and related pathology. These results indicate that age-sensitive contact with commensal microbes is critical for establishing mucosal iNKT cell tolerance to later environmental exposures.

The microscopic battles waged in our bodies every day and over our lifetimes are amazing.

Lean Science: Using Cheap Robots to Aid Research

Fun video showing how scientists use Lego Mindstorm robots to aid research into creating artificial bones. Lego Mindstorm robots are useful at a very reasonable price.

The webcast also includes this practical quote from Michelle Oyen, lecturer in the Department of Engineering at Cambridge University: “without your bones you would be a pile of goo lying on the floor.”

The thinking discussed in the webcast echos the lean manufacturing principles discussed in the Curious Cat Management Improvement Blog: finding good solutions to aid people in doing their jobs. The type of custom solutions they discuss here are great.

This type of use of technology is great. One of the problems we often see with technology solutions though is when they are imposed on the workplace in a way that doesn’t aid people. There is a big difference between what Toyota does (using robots to make people’s jobs easier) and what others do in trying to copy Toyota (using robots to eliminate jobs). Lean manufacturing stressed the importance of using brainpower people bring to work every day. You want to use technology to enable people. These scientists understand that. Unfortunately many managers don’t.

Photosynthesis: Science Explained

Another very good webcast on a science topic from Crash Course. It is packed with info, thankfully you can pause and rewind as much as you need. Well normally you can, YouTube decided to not let me do that just now 🙁

Â£50m Package to Attract Scientists and Boost Welsh Economy

‘Star scientists’ Â£50m package to boost Welsh economy

First Minister Carwyn Jones said the fund would be used to encourage leading professors to move to Wales to work and boost research and the economy. It will pay for specialist equipment, top-up salaries to the level outstanding academics would expect and will fund members of their teams.
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our network plans will enable us to attract more talent to Wales to help drive this figure up and in due course create more high quality business and research jobs in Wales.” The strategy sets out three key areas to boost research and businesses – the life sciences and health; low carbon, energy and environment; and advanced engineering and materials.

The Welsh government said it wanted to see more industry-academic partnerships like SPECIFIC led by Swansea University with Tata Steel UK. The Â£20m project aims to turn homes and businesses into self-generating “power stations” by developing a special coating for ordinary building materials, such as steel and glass, that traps and stores solar energy.

The USA dominated the practice of attracting leading scientists a few decades ago. In the last decade or two Europe stepped up and was able to attract global talent. Lately Asia (Singapore, Korea, China…) has been spending to attract leading scientists. I believe Asia will continue to do so and the benefits of doing so will pay off handsomely for Asia (at the expense of Europe and the USA).

Intel Science Talent Search 2012 Awardees

Nithin Tumma, whose research could lead to less toxic and more effective breast cancer treatments, received the top award of $100,000 at the Intel Science Talent Search 2012, a program of Society for Science & the Public. Other finalists from across the U.S. took home additional awards totaling $530,000.

The Intel Science Talent Search, the nation’s oldest and most prestigious pre-college science and math competition, recognizes 40 high school seniors who are poised to be the next leaders in innovation and help solve some of the world’s greatest challenges.

Nithin Tumma, 17, of Fort Gratiot, Mich., won the top award of $100,000 from the Intel Foundation for his research, which could lead to more direct, targeted, effective and less toxic breast cancer treatments. He analyzed the molecular mechanisms in cancer cells and found that by inhibiting certain proteins, we may be able to slow the growth of cancer cells and decrease their malignancy. Nithin is first in his class, a varsity tennis player and a volunteer for the Port Huron Museum, where he started a restoration effort for historical and cultural landmarks.

Second place honors and $75,000 went to Andrey Sushko, 17, of Richland, Wash., for his development of a tiny motor, only 7 mm (almost 1/4 inch) in diameter, which uses the surface tension of water to turn its shaft. Born in Russia, Andrey worked from home to create his miniature motor, which could pave the way for other micro-robotic devices. Andrey, a long-time builder of small boats, recently filed for a Guinness World Record for the smallest radio-controlled sailing yacht.

Third place honors and $50,000 went to Mimi Yen, 17, of Brooklyn, N.Y., for her study of evolution and genetics, which focuses on microscopic worms, specifically looking at their sex habits and hermaphrodite tendencies. Mimi believes that through research such as hers, we may better understand the genes that contribute to behavioral variations in humans. Mimi was born in Honduras and is fluent in Cantonese. She plays French horn and volunteers to prepare and deliver meals to people with serious illnesses.

These finalists join the ranks of other notable Science Talent Search alumni who over the past 70 years have gone on to win seven Nobel Prizes, two Fields Medals, four National Medals of Science, 11 MacArthur Foundation Fellowships and even an Academy Award for Best Actress.

“We invest in America’s future when we recognize the innovative achievements of our nation’s brightest young minds,” said Intel President and CEO Paul Otellini. “Hands-on experience with math and science, such as that required of Intel Science Talent Search finalists, encourages young people to think critically, solve problems and understand the world around them. Rather than simply memorizing facts and formulas, or repeating experiments with known outcomes, this competition engages students in an exciting way and provides a deeper level of understanding in such important but challenging subjects.”

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The Information: A History, a Theory, a Flood by James Gleick

James Gleick is a great science writer. I remember first reading his book, Chaos, which I loved. He continues to write engaging and entertaining books on science. His 2011 release The Information: A History, a Theory, a Flood, is now available in paperback.

From the invention of scripts and alphabets to the long-misunderstood talking drums of Africa, Gleick tells the story of information technologies that changed the very nature of human consciousness. Gleick provides portraits of the key figures contributing to the inexorable development of our modern understanding of information: Charles Babbage, the idiosyncratic inventor of the first great mechanical computer; Ada Byron, the brilliant and doomed daughter of the poet, who became the first true programmer; pivotal figures like Samuel Morse and Alan Turing; and Claude Shannon, the creator of information theory itself.

And now the information age arrives. The Information is the story of how we got here and where we are heading.