Category Archives: Research

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?

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.

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.

How Bee Hives Make Decisions

The Secret Life of Bees by Carl Zimmer

The decision-making power of honeybees is a prime example of what scientists call swarm intelligence. Clouds of locusts, schools of fish, flocks of birds and colonies of termites display it as well. And in the field of swarm intelligence, Seeley is a towering figure. For 40 years he has come up with experiments that have allowed him to decipher the rules honeybees use for their collective decision-making. “No one has reached the level of experimentation and ingenuity of Tom Seeley,” says Edward O. Wilson of Harvard University.
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Enthusiasm translates into attention. An enthusiastic scout will inspire more bees to go check out her site. And when the second-wave scouts return, they persuade more scouts to investigate the better site.

The second principle is flexibility. Once a scout finds a site, she travels back and forth from site to hive. Each time she returns, she dances to win over other scouts. But the number of dance repetitions declines, until she stops dancing altogether. Seeley and his colleagues found that honeybees that visit good sites keep dancing for more trips than honeybees from mediocre ones.

This decaying dance allows a swarm to avoid getting stuck in a bad decision. Even when a mediocre site has attracted a lot of scouts, a single scout returning from a better one can cause the hive to change its collective mind.
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“Bees are to hives as neurons are to brains,” says Jeffrey Schall, a neuroscientist at Vanderbilt University. Neurons use some of the same tricks honeybees use to come to decisions. A single visual neuron is like a single scout. It reports about a tiny patch of what we see, just as a scout dances for a single site. Different neurons may give us conflicting ideas about what we’re actually seeing, but we have to quickly choose between the alternatives. That red blob seen from the corner of your eye may be a stop sign, or it may be a car barreling down the street.

To make the right choice, our neurons hold a competition, and different coalitions recruit more neurons to their interpretation of reality, much as scouts recruit more bees

Very cool stuff.