Tag Archives: Research

One Scientists 20 Year Effort to Defeat Dengue Fever

As I have said many times scientific breakthroughs often follow many years of effort. Here is a great example of a scientist putting in great work for years and it looks like it is about to payoff for hundreds of millions of people.

A Scientist’s 20-Year Quest To Defeat Dengue Fever

Now as I said, Scott’s been pushing this idea of using Wolbachia to control dengue for decades, for a most of that time without any success. I asked Scott what it takes to stick with something for that long.

“I think being obsessive,” he replied. “Being maybe a little ill in that regard. And it’s just that I seem to have focused my obsession onto Wolbachia instead of on to postage stamps or model trains.”

And even though his obsession has brought him to the point where he’s shown he can get his Wolbachia-infected mosquitoes to spread in the wild, that’s not the success he’s ultimately after. “Success for me is having a significant impact on dengue disease in communities,” he says.

To do that, he’ll have to release his mosquitoes in a place where there’s a lot of dengue, and then see if that brings down the number of cases of the disease in humans. Those studies are being planned now.

The stakes are high. By some estimates, more than a billion people around the world are at risk for getting dengue. Even if it doesn’t kill you, I’m told a case of dengue can make you feel so bad, wish you were dead.
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But Scott says it’s not yet time to celebrate.

“We’ve got some good preliminary data, and we’re on the path. And it’s looking good. But you know I am a realist. It could fall over at any day,” says Scott.

Modeling Weight Loss Over the Long Term

Researchers at the National Institutes of Health have created a mathematical model of what happens when people of varying weights, diets and exercise habits try to change their weight. The findings challenge the commonly held belief that eating 3,500 fewer calories, or burning them off exercising, will result in a pound of weight loss.

Instead, the researchers’ computer simulations indicate that this assumption overestimates weight loss because it fails to account for how metabolism changes. The computer simulations show how these metabolic changes can significantly differ among people.

However, the computer simulation of metabolism is meant as a research tool and not as a weight-loss guide for the public. The computer program can run simulations for changes in calories or exercise that would never be recommended for healthy weight loss. The researchers hope to use the knowledge gained from developing the model and from clinical trials in people to refine the tool for everyone.

“This research helps us understand why one person may lose weight faster or slower than another, even when they eat the same diet and do the same exercise,” said Kevin Hall, Ph.D., an obesity researcher and physicist at the NIH’s National Institute of Diabetes and Digestive and Kidney Diseases. “Our computer simulations can then be used to help design personalized weight management programs to address individual needs and goals.”

The online simulation tool based on the model enables researchers to accurately predict how body weight will change and how long it will likely take to reach weight goals based on a starting weight and estimated physical activity. The tool simulates how factors such as diet and exercise can alter metabolism over time and thereby lead to changes of weight and body fat.

The team found that people’s bodies adapt slowly to changes in dietary intake. They also found heavier people can expect greater weight change with the same change in diet, though reaching a stable body weight will take them longer than people with less fat.

The model also points to a potential simplified method to approximate weight loss in an average overweight person. An adult who has a body mass index (a measure of a person’s weight in relation to his or her height) between 25 and 29.9 is considered overweight. One example: For every pound you want to lose, permanently cut 10 calories from your current intake per day. At that rate, it will take about one year to achieve half of the total weight loss, and almost all of the weight loss will have occurred by three years. This calculation shows how long it takes to achieve a weight-loss goal for a single permanent change of diet or exercise.

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Majority of Clinical Trials Don’t Provide Meaningful Evidence

The largest comprehensive analysis of ClinicalTrials.gov finds that clinical trials are falling short of producing high-quality evidence needed to guide medical decision-making.

The analysis, published today in the Journal of the American Medical Association, found the majority of clinical trials is small, and there are significant differences among methodical approaches, including randomizing, blinding and the use of data monitoring committees.

This is a critical issue as medical studies continue to leave quite a bit to be desired. Even more importantly the failure to systemically study and share evidence of effectiveness once treatments are authorized leaves a great deal to be desired. On top of leaving quite a bit to be desired, the consequences are serious. If we make mistakes for example in how we date fossils it matters but it is unlikely to cause people their lives or health. Failure to adequately manage and analyze health care experiments may very well cost people their health or lives.

“Our analysis raises questions about the best methods for generating evidence, as well as the capacity of the clinical trials enterprise to supply sufficient amounts of high quality evidence to ensure confidence in guideline recommendations,” said Robert Califf, MD, first author of the paper, vice chancellor for clinical research at Duke University Medical Center, and director of the Duke Translational Medicine Institute.

The analysis was conducted by the Clinical Trials Transformation Initiative (CTTI), a public-private partnership founded by the Food and Drug Administration (FDA) and Duke. It extends the usability of the data in ClinicalTrials.gov for research by placing the data through September 27, 2010 into a database structured to facilitate aggregate analysis.

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How do Plants Grow Into the Sunlight?

Plants are extremely competitive in gaining access to sunlight. A plant’s primary weapon in this fight is the ability to grow towards the light, getting just the amount it needs and shadowing its competition. Now, scientists have determined precisely how leaves tell stems to grow when a plant is caught in a shady place.

Hole in the Wall trail, Olympic National Park, Washington, USA by John Hunter

The researchers discovered that a protein known as phytochrome interacting factor 7 (PIF7) serves as the key messenger between a plant’s cellular light sensors and the production of auxins, hormones that stimulate stem growth.

“We knew how leaves sensed light and that auxins drove growth, but we didn’t understand the pathway that connected these two fundamental systems,” says Joanne Chory, professor and director of the Salk’s Plant Biology Laboratory and a Howard Hughes Medical Institute investigator (HHMI provides huge amounts of funding for scientific research). “Now that we know PIF7 is the relay, we have a new tool to develop crops that optimize field space and thus produce more food or feedstock for biofuels and biorenewable chemicals.”

Plants gather intelligence about their light situation—including whether they are surrounded by other light-thieving plants—through photosensitive molecules in their leaves. These sensors determine whether a plant is in full sunlight or in the shade of other plants, based on the wavelength of red light striking the leaves. This is pretty cool; I love to learn about the brilliant strategies that have evolved.

If a sun-loving plant, such as thale cress (Arabidopsis thaliana), the species Chory studies, finds itself in a shady place, the sensors will tell cells in the stem to elongate, causing the plant to grow upwards towards sunlight.

When a plant remains in the shade for a prolonged period, however, it may flower early and produce fewer seeds in a last ditch effort to help its offspring spread to sunnier real estate. In agriculture, this response, known as shade avoidance syndrome, results in loss of crop yield due to closely planted rows of plants that block each other’s light.

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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?

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.

Thorium Nuclear Reactors

Kirk Sorensen is founder of Flibe Energy and is an advocate for nuclear energy based on thorium and liquid-fluoride fuels and author of Energy From Thorium blog.

He also taught nuclear engineering at Tennessee Technological University as a guest lecturer. He is active in nonprofit advocacy organizations such as the Thorium Energy Alliance and the International Thorium Energy Organization. He is married and has four small children.

See another video with him on why the thorium molten-salt reactor wasn’t developed (from a Google tech talk).

Bacteriophages Enter Bacteria Using an Iron Tipped Spike

Bacteria-Killing Viruses Wield an Iron Spike

Forget needles in haystacks. Try finding the tip of a needle in a virus. Scientists have long known that a group of viruses called bacteriophages have a knack for infiltrating bacteria and that some begin their attack with a protein spike. But the tip of this spike is so small that no one knew what it was made of or exactly how it worked. Now a team of researchers has found a single iron atom at the head of the spike, a discovery that suggests phages enter bacteria in a different way than surmised.

Wherever there are bacteria you will find bacteriophages; digestive tracts, contaminated water, and feces are usually a good start. These viruses begin their dirty work by drilling into the outer membrane of bacteria. Once completely through all of a bug’s defenses, the phages inject their DNA, which essentially turns the bacterium into phage-producing factories. Eventually, the microbes become filled with so many viruses that they burst, releasing a new horde of phages into the environment.

Bacteriophages are amazing. It is so interesting to learn about amazingly creative solutions that have evolved over time. Real-life science is not easy to match with fiction that springs from our imaginations.