Category Archives: Life Science

How Lysozyme Protein in Our Tear-Drops Kill Bacteria

A disease-fighting protein in our teardrops has been tethered to a tiny transistor, enabling UC Irvine scientists to discover exactly how it destroys dangerous bacteria. The research could prove critical to long-term work aimed at diagnosing cancers and other illnesses in their very early stages.

Ever since Nobel laureate Alexander Fleming found that human tears contain antiseptic proteins called lysozymes about a century ago, scientists have tried to solve the mystery of how they could relentlessly wipe out far larger bacteria. It turns out that lysozymes have jaws that latch on and chomp through rows of cell walls like someone hungrily devouring an ear of corn.

“Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them,” said molecular biologist and chemistry professor Gregory Weiss, who co-led the project with associate professor of physics & astronomy Philip Collins.

The researchers decoded the protein’s behavior by building one of the world’s smallest transistors – 25 times smaller than similar circuitry in laptop computers or smartphones. Individual lysozymes were glued to the live wire, and their eating activities were monitored.

“Our circuits are molecule-sized microphones,” Collins said. “It’s just like a stethoscope listening to your heart, except we’re listening to a single molecule of protein.”

It took years for the UCI scientists to assemble the transistor and attach single-molecule teardrop proteins. The scientists hope the same novel technology can be used to detect cancerous molecules. It could take a decade to figure out but would be well worth it, said Weiss, who lost his father to lung cancer.

“If we can detect single molecules associated with cancer, then that means we’d be able to detect it very, very early,” Weiss said. “That would be very exciting, because we know that if we treat cancer early, it will be much more successful, patients will be cured much faster, and costs will be much less.”

The project was sponsored by the National Cancer Institute and the National Science Foundation. Co-authors of the Science paper are Yongki Choi, Issa Moody, Patrick Sims, Steven Hunt, Brad Corso and Israel Perez.

Study of the Colony Collapse Disorder Continues as Bee Colonies Continue to Disappear

I can understand why people get complacent. We have a pretty remarkable run of science and technology finding solutions for whatever peril we face.

Also, quite often, future risks are over-blown. Then, people get habituated to reading ominous predictions, followed by a future doesn’t seem to reach those dramatic predictions. But this is a risky pattern to just expect – that no matter what we will figure out some way to avoid the consequences.

Risks actually do come true. The obvious result of overfishing, just as predicted, has resulted in collapses of fish populations over and over creating great hardship for those who had fallen victim to that prediction. If people don’t vaccinate themselves (and their kids) we will have ever increasing numbers of deaths and sickness. If we fail to use anti-biotics is a long term sustainable way, our actions will result in many deaths.

I am not sure why we find it so easy to ignore the evidence of bad consequences but we do. Partially I would imagine that as problems begin to be manifest countermeasures take affect. So in the fishing example, many people leave that line of work and so the numbers in the industry after a collapse, who are suffering in the present, are reduced. Still I find it odd how easily we ignore the risks in the future.

I do understand if there are short term benefits to ignoring the risks (or pretending they don’t exist): so you have fisherman that don’t want to take steps in advance to avoid collapse. Or you have industries and politicians that want to pretend ignoring global warming is a strategy to avoid the consequences. Or you have parents that say, well today we don’t have many risks of sicknesses people get vaccinated against (yes, because people have been vaccinated – if you stop vaccinating your children they we get to experience the avoidable pain and suffering).

I have been following the honeybee colony collapse disorder for several years (see the end of the posts for links to posts from 2006 – 2010, like this one The Study of Bee Colony Collapses Continues from 2007). It is a great example of the scientific inquiry process. It is messy and confusing and full of studies that have trouble finding what the actually causes are or what solutions will work.

There are occasionally mentions of how devestating things could get if the trend continues. In fact stories that seem so devestating that they just don’t seem real. surely either that won’t happen or if it started to some countermeasure would be found to deal with the problem and avoid the most severe consequences. That is basially how I have felt about it. But that is not because of some scientific understanding but just a feeling that hey that couldn’t really happen. Well that isn’t exactly solid evidence that it can’t.

Honeybee problem nearing a ‘critical point’

In addition to continued reports of CCD — a still somewhat mysterious phenomenon in which entire bee colonies literally disappear, alien-abduction style, leaving not even their dead bodies behind — bee populations are suffering poor health in general, and experiencing shorter life spans and diminished vitality. And while parasites, pathogens, and habitat loss can deal blows to bee health, research increasingly points to pesticides as the primary culprit.
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farmers use these chemicals to protect their crops from destructive insects, but in so doing, they harm other insects essential to their crops’ production — a catch-22 that Hackenberg said speaks to the fact that “we have become a nation driven by the chemical industry.” In addition to beekeeping, he owns two farms, and even when crop analysts recommend spraying pesticides on his crops to kill an aphid population, for example, he knows that “if I spray, I’m going to kill all the beneficial insects.” But most farmers, lacking Hackenberg’s awareness of bee populations, follow the advice of the crop adviser — who, these days, is likely to be paid by the chemical industry, rather than by a state university or another independent entity.

I believe this is the latest advise of the Unites States Department of Agriculture (though their web site doesn’t make it nearly as obvious as it should that this is in fact the current advice – the document seems to indicate it is but if someone were to say no, that is outdated, it wouldn’t be hard to believe)

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Healthy Diet, Healthy Living, Healthy Weight

Living and eating healthily is tricky but not entirely confusing. The whole area of eating healthy food and what is a healthy weight is one where the scientific inquiry process and the complexity of scientific research on what is healthy for us is clear. Scientists study various issues and learn things but creating simple rules has proven difficult. Different studies seem to show benefits of contradictory advice, advice once seen as wise is now seen as wrong…

This is an area I am far from knowledgable about. Still I try to pay some attention as I like being healthy. Being sick is the quickest way to appreciate how great it is to be healthy. From various things I have skimmed it seems there is more evidence from several studies about how difficult it is to lose weight. Our bodies seem to work against our efforts.

And this, it seems to me, makes the problem of increasing childhood and teen obesity even more important to deal with as soon as issues arise.

It seems to me the most important thing to take from this, is the importance of maintaining a healthy weight: since you can’t just easily make up for a bad year of weight gain. I am not sure why I haven’t seen this note in most of what I have read – I suspect it is our reluctance to make value judgements about what is healthy. The problem I see with that is, the best advice we have is confusing enough without people with more knowledge being reluctant to state their best advice given the current knowledge. That doesn’t mean the suggestions are right, but at least they are educated guesses.

I try to eat relatively healthily. Which for me means taking steps to increase the amount of vegetables I eat (especially greens and some fiber) and decrease the amount of sweets and heavily processed food I eat (I still eat way too much heavily processed food). And I try to exercise as it seems to have many benefits including helping make up for some weaknesses in your diet (like eating too many calories and too many “empty calories). In my opinion (which on this topic may well not be worth much) eating a bit more stuff that really isn’t so good for you and exercising more is an easier tradeoff than trying to eat perfectly and do the minimum amount of exercise needed to stay healthy.

I also eat yogurt – I like it and the beneficial benefits of some bacteria seems likely. I heard recently something that surprised me which is that the beneficial bacteria remain for close to 2 weeks. I figured they would be gone in a couple days. I only heard that from one source (I can’t remember now but some seemingly knowledgable source – scientist researching the area), so it might not be accurate but it was interesting.

Here is an example of one of these health studies. They find that a low protein diet resulted in a loss of “lean weight” (muscle…) and more fat than a comparable diet with more protein. The same weight with a higher percentage of fat is not a good thing for human health. Thus the message is that a lower protein diet has this risk that must be considered (and therefor higher protein diets may well be wise). Of course things get much more complicated than that when we actually try to live by a diet.

Effect of Dietary Protein Content on Weight Gain, Energy Expenditure, and Body Composition During Overeating

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Memory is Stored by Turning on Genes in Neurons (to Alter Connection Between Neurons)

I find these kind of stories so interesting. I really have so little understanding of genes. I knew memory had something to do with altering connections between neurons. I had no idea that required turning on many genes in those neurons. Life really is amazing.

Neuroscientists identify a master controller of memory

When you experience a new event, your brain encodes a memory of it by altering the connections between neurons. This requires turning on many genes in those neurons.
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Lin and her colleagues found that Npas4 turns on a series of other genes that modify the brain’s internal wiring by adjusting the strength of synapses, or connections between neurons. “This is a gene that can connect from experience to the eventual changing of the circuit,” says [Yingxi] Lin

So far, the researchers have identified only a few of the genes regulated by Npas4, but they suspect there could be hundreds more. Npas4 is a transcription factor, meaning it controls the copying of other genes into messenger RNA — the genetic material that carries protein-building instructions from the nucleus to the rest of the cell. The MIT experiments showed that Npas4 binds to the activation sites of specific genes and directs an enzyme called RNA polymerase II to start copying them.

“Npas4 is providing this instructive signal,” Ramamoorthi says. “It’s telling the polymerase to land at certain genes, and without it, the polymerase doesn’t know where to go. It’s just floating around in the nucleus.”

When the researchers knocked out the gene for Npas4, they found that mice could not remember their fearful conditioning. They also found that this effect could be produced by knocking out the gene just in the CA3 region of the hippocampus. Knocking it out in other parts of the hippocampus, however, had no effect.

One of the things I aim to do in 2012 is read a few more books on biology and genes. I find it incredible what are genes actually are doing to allow us to live our lives. And I am also very ignorant on the whole area. So hopefully I can have some fun next year learning about it.

Can Just A Few Minute of Exercise a Day Prevent Diabetes?

That just 1 minute of exercise a day could help prevent diabetes seems to good to be true. But research at the University of Bath indicates it might be true. I am a bit of a soft touch for seeing the benefits of exercise. And I also love health care that focuses on achieving healthy lives instead of what most of the spending focuses on: treating illness.

Performing short cycle sprints three times a week could be enough to prevent and possibly treat Type 2 diabetes researchers at the University of Bath believe.

Volunteers were asked to perform two 20-second cycle sprints, three times per week (but really this works out to under 10 minutes of total time including warm up). After six weeks researchers saw a 28% improvement in their insulin function. Type 2 diabetes occurs when blood sugar levels build up to dangerously high levels due to reduced insulin function, often caused by a sedentary lifestyle. The condition can cause life-threatening complications to the heart, kidneys, eyes and limbs, and has huge costs (monetarily and to people’s lives).

Regular exercise can help keep blood sugar levels low but busy lifestyles and lack of motivation mean 66% of the population is not getting the recommended five 30-minute sessions of moderate exercise a week.

Dr Niels Vollaard who is leading the study, said: “Our muscles have sugar stores, called glycogen, for use during exercise. To restock these after exercise the muscle needs to take up sugar from the blood. In inactive people there is less need for the muscles to do this, which can lead to poor sensitivity to insulin, high blood sugar levels, and eventually type 2 diabetes… We already knew that very intense sprint training can improve insulin sensitivity but we wanted to see if the exercise sessions could be made easier and shorter.”

In the study the resistance on the exercise bikes could be rapidly increased so volunteers were able to briefly exercise at much higher intensities than they would otherwise be able to achieve. With an undemanding warm-up and cool-down the total time of each session was only 10 minutes.

This type of study is very helpful in identifying solutions that will allow more people to lead healthy lives and save our economies large amount of money. Medical studies can’t be accepted on face value. They are often not confirmed by future studies and therefore it is unwise to rely on the results of 1 study. The results provide interesting information but need to be confirmed (and in the area of studies on human health this has been shown to be problematic – are health is quite a tricky area to study).

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Rats Show Empathy-driven Behavior

Rats free trapped companions, even when given choice of chocolate instead

The experiments, designed by psychology graduate student and first author Inbal Ben-Ami Bartal with co-authors Decety and Peggy Mason, placed two rats that normally share a cage into a special test arena. One rat was held in a restrainer device — a closed tube with a door that can be nudged open from the outside. The second rat roamed free in the cage around the restrainer, able to see and hear the trapped cagemate but not required to take action.

The researchers observed that the free rat acted more agitated when its cagemate was restrained, compared to its activity when the rat was placed in a cage with an empty restrainer. This response offered evidence of an “emotional contagion,” a frequently observed phenomenon in humans and animals in which a subject shares in the fear, distress or even pain suffered by another subject.

While emotional contagion is the simplest form of empathy, the rats’ subsequent actions clearly comprised active helping behavior, a far more complex expression of empathy. After several daily restraint sessions, the free rat learned how to open the restrainer door and free its cagemate. Though slow to act at first, once the rat discovered the ability to free its companion, it would take action almost immediately upon placement in the test arena.

“We are not training these rats in any way,” Bartal said. “These rats are learning because they are motivated by something internal. We’re not showing them how to open the door, they don’t get any previous exposure on opening the door, and it’s hard to open the door. But they keep trying and trying, and it eventually works.”

To control for motivations other than empathy that would lead the rat to free its companion, the researchers conducted further experiments. When a stuffed toy rat was placed in the restrainer, the free rat did not open the door. When opening the restrainer door released his companion into a separate compartment, the free rat continued to nudge open the door, ruling out the reward of social interaction as motivation. The experiments left behavior motivated by empathy as the simplest explanation for the rats’ behavior.

“There was no other reason to take this action, except to terminate the distress of the trapped rats,” Bartal said. “In the rat model world, seeing the same behavior repeated over and over basically means that this action is rewarding to the rat.”

As a test of the power of this reward, another experiment was designed to give the free rats a choice: free their companion or feast on chocolate. Two restrainers were placed in the cage with the rat, one containing the cagemate, another containing a pile of chocolate chips. Though the free rat had the option of eating all the chocolate before freeing its companion, the rat was equally likely to open the restrainer containing the cagemate before opening the chocolate container.

“That was very compelling,” said Mason, Professor in Neurobiology. “It said to us that essentially helping their cagemate is on a par with chocolate. He can hog the entire chocolate stash if he wanted to, and he does not. We were shocked.”

Now that this model of empathic behavior has been established, the researchers are carrying out additional experiments. Because not every rat learned to open the door and free its companion, studies can compare these individuals to look for the biological source of these behavioral differences. Early results suggested that females were more likely to become door openers than males, perhaps reflecting the important role of empathy in motherhood and providing another avenue for study…

Interesting study. My guess is this is the kind of thing those that don’t like science would deride. I believe in the value of science. I believe in the value of learning. I believe that such experiments are what drives science forward. I believe if you want your economy to benefit from investing in science you should be encouraging hundreds and thousands of such experiments. Funding for this study was provided by The National Science Foundation (NSF), and others.

I am thankful that more and more countries are willing to invest in science, especially since the USA is showing an increasing anti-science attitude. I would rather the USA continue to believe in the value of science and other countries looked to increase investments. But, it is much better that other countries increase their interest in science, and willingness to invest in science, to more than make up for the USA’s decisions to reduce the appreciation for science than for the world to just lose do to a decrease in investments in science.

Nature Uses Stem Cells from Fetus to Repair Health of Mother

Science shows us so many amazing things. Scientists have learned mice use stem cells from the fetus to repair damage to the mother in the event of things like heart attacks. And there is evidence people do the same thing. Very cool. Nature beat us to the idea of using stem cells to treat health problems.

Helpful Mouse Fetuses Naturally Send Stem Cells to Mom to Fix Her Damaged Heart

When the scientists examined the female mice’s heart tissue two weeks after the heart attacks, they found lots of glowing green tissue—cells that came from the fetus—in the mom’s heart. Mice who had heart attacks had eight times as many cells from the fetus in their hearts as mice who hadn’t had a heart attack did, meaning the high volume of fetal cells was a response to the heart attack.

What’s more, the embryo’s stem cells had differentiated into various types of heart tissue, including cardiomyocytes, the rhythmically contracting muscle cells that produce a heartbeat.
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The hearts of two women who suffered from severe heart weakness were later found to contain cells derived from the cells of a male fetus years after they gave birth to their sons.

The same thing seems to hold true for other organs. When pregnant women have damage in other organs, including the brain, lung, and liver, earlier studies have shown, fetal cells show up there, too.

It makes sense for a fetus to try and aid the mother but it is amazing the evolution found such solutions. Given how many challenges the fetus creates for the mother giving some benefits can help increase the odds of a health birth.

Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle Age

Family living conditions in childhood are associated with significant effects in DNA that persist well into middle age, according to new research by Canadian and British scientists.

The team, based at McGill University in Montreal, University of British Columbia in Vancouver and the UCL Institute of Child Health in London looked for gene methylation associated with social and economic factors in early life. They found clear differences in gene methylation between those brought up in families with very high and very low standards of living. More than twice as many methylation differences were associated with the combined effect of the wealth, housing conditions and occupation of parents (that is, early upbringing) than were associated with the current socio-economic circumstances in adulthood. (1252 differences as opposed to 545).

I find Epigenetics to be a very interesting area. My basic understanding as I grew up was that you inherited your genes. But epigenetics explores how your genes change over time. This has been a very active area of research recently. Your DNA remains the same during your life. But the way those genes are expressed changes.

I don’t know of any research supporting the idea I mention in this example, but, to explain the concept in a simple way: you may carry genes in your DNA for processing food in different ways. If you have very limited diet the way your body reacts could be to express genes that specialize in maximizing the acquisition of nutrition from food. And it could be that your body sets these expressions based on your conditions when young; if later, your diet changes you may have set those genes to be expressed in a certain way. Again this is an example to try and explain the concept, not something where I know of research that supports evidence for this example.

The findings by these universities, were unfortunately published in a closed way. Universities should not support the closing of scientific knowledge. Several universities, that support open science, require open publication of scientific research. It is unfortunate some universities continue to support closed science.

The research could provide major evidence as to why the health disadvantages known to be associated with low socio-economic position can remain for life, despite later improvement in living conditions. The study set out to explore the way early life conditions might become ‘biologically-embedded’ and so continue to influence health, for better or worse, throughout life. The scientists decided to look at DNA methylation, a so-called epigenetic modification that is linked to enduring changes in gene activity and hence potential health risks. (Broadly, methylation of a gene at a significant point in the DNA reduces the activity of the gene.)

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Bacteria Living Inside Animals Cells

Interesting discussion on the bacteria living inside our cells. For example, many plants have bacteria that get inside the root system and then help fix nitrogen for the plant. Some sea slugs take the chloroplasts from algae they eat and incorporate it themselves, allowing them to get energy from light (photosynthesis): they become photosynthetic slugs.

Adults need science education more than kids do is also a good segment. And I agree strongly that we (as individuals and society) lose a great deal when we fail to help people enjoy learning about science during their whole lives.

I also like the usability of this widget above, where it lets you include the internal links easily into a video.

Molecule Found in Sharks Kills Many Viruses that are Deadly to People

photo of 3 dogfish sharks
Shark Molecule Kills Human Viruses, Too

“Sharks are remarkably resistant to viruses,” study researcher Michael Zasloff, of the Georgetown University Medical Center, told LiveScience. Zasloff discovered the molecule, squalamine, in 1993 in the dogfish shark, a small- to medium-size shark found in the Atlantic, Pacific, and Indian Oceans.

“It looked like no other compound that had been described in any animal or plant before. It was something completely unique,” Zasloff said. The compound is a potent antibacterial and has shown efficacy in treating human cancers and an eye condition known as macular degeneration, which causes blindness.
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By studying the compound’s structure and how it works in the human body, Zasloff thought it might have some antiviral properties. He saw that the molecule works by sticking to the cell membranes of the liver and blood vessels. While there, it kicks off other proteins, some of which are essential for viruses to enter and survive in the cell.

The researchers decided to test the compound on several different live viruses that infect liver cells, including hepatitis B, dengue virus and yellow fever. They saw high efficacy across the board.
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Zasloff hopes to start human trials in the next few years.
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Marc Maresca, a researcher at Paul CÃ©zanne University in Aix-en-Provence, France, who wasn’t involved in the study, agreed that the concentrations used were quite high, possibly in toxic ranges for some cells, but in an email to LiveScience Meresca also called the study “very exciting.”