Tag Archives: Research

Raising Interest in Science

An article was published last month on artofthestem.com that was titled “Five Reasons Why Your Child Won’t Be a Scientist.”  As a science nerd myself and someone always interested in raising excitement about science (hence this blog), I thought it would be useful to reflect on the reasons given in this article (which by the way, I agree with wholeheartedly).

The article begins by talking about the decrease in interest in STEM subjects (science, technology, engineering and math).  Recent research has found that students are  uninterested in STEM subjects despite the increase in STEM jobs available.

So why don’t students like science?  What makes them turn away from science and other STEM topics?  And why do some of us actually enjoy learning about science?  The article proposes five reasons that children find it hard to get excited about science.  I’ll add my thoughts to each of their reasons.

1. We have instilled the phrase “I’m not good at math or science” into a new generation.

As the article goes on to explain after its first point, many students who do study science grow up in a household where science discussion is prevalent.  This is, in fact, the case for me.  My father is a chemist, and I remember seeing his science books and articles all around the house.  I’m positive that knowing he would have an answer to a science question took the fear out of science for me.  I always had an in-house expert to go to in case of confusion.

So what if kids don’t have an in-house scientist?  I think it’s important, then, for parents to be willing to learn science with their kids as the article suggests.  This was the case for me with my mother.  While she didn’t have a science background, she was always willing to make a baking soda volcano, look up a topic in our encyclopedia with me or come cheer me on at the science fair.  Between my dad’s knowledge and my mom’s support and encouragement, science was never a scary topic for me.

2. Science is taught in a way that is opposite to what it truly is.

This statement, while sad, is usually very true.  Throughout science classes, students are taught to memorize and write down everything the teacher is saying so that they can later memorize it.  This creates an environment in which students learn what they have to learn and then probably forget it once they are tested on it.  Not only does this not encourage scientific learning, but it also doesn’t allow students to practice the scientific process.  Where is the questioning?  Where is the formation of a hypothesis? Where is the testing of a hypothesis?  So little of true science exploration is memorization.  Instead, let kids experiment and learn through that experimentation.

3. Science has lost the “cool factor” and kids have no “science heroes.”

When I was growing up, I thought Bill Nye the Science Guy was one of the greatest shows on television.  He was funny and he knew stuff!  Even in the song that opened his show he said, “Science is cool.”  So why don’t kids think it is?  With so much emphasis on rock stars and celebrities, scientists get lost in the shuffle.  We have to make it a point to explain how cool scientists are – after all, without scientists we wouldn’t have mp3 players, vaccines or even pasteurized milk.  Maybe kids need a reminder of how many cool things scientists have in fact created!

4. We don’t focus on current issues in the discipline.

The world of science, especially today, is changing at an incredibly high speed.  New discoveries and improvements on those discoveries are published every day.  Yet students are reading about science out of the same textbooks year after year.  It students can’t see science as new and changing, why would they want to study it?  Let’s focus on new findings and recent discoveries that actually affect the students and the world around them!

5. Good grades in science will not make you a scientist.

I know about this point firsthand.  Throughout high school, and even college, I did decently well in my science classes.  However, the rote memorization that allowed me to do well on science exams did little to help me at the bench as I did scientific research.  The amount of creative thinking and troubleshooting required at a science bench is not taught in science classes.  Nor is the ability to work with others toward a common discovery or the need to ask endless questions and form countless hypotheses.  These are the talents that allow scientists to succeed, yet they are not taught in classes.  If they had been, I might still be working at the bench.  I, however, much prefer reading and writing about science to actually doing it, so as a science research dropout maybe you shouldn’t listen to me anyway!

Regardless of my meandering thoughts on the topic, the truth is that we need to get kids interested in STEM topics again.  We need to encourage the next Einstein sitting in a science class right now and wondering when recess is.

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How Fireflies Help Us Understand Cancer

I’m back with the promised follow-up to the firefly post.  But before I get to fireflies and luciferase, I have to start with cancer cells and metabolism.  So how are fireflies and cancer cells related?  I promise it will all come together in the end.

Normal cells in our bodies respond to signals around them to decide whether to grow or not.  The signals that the cells respond to are called growth factors.  Cells will take up food and nutrients from their environment only when instructed to do so by the growth factors.  In this way, excess growth and cell division is avoided.

Cancer cells, however, are able to ignore these signals and grow uncontrolled due to mutations in their genes.  These mutations can lead to abnormal uptake of food that then leads to cancer cell growth.

In 1924, Otto Warburg observed that cancer cells take up glucose, a main food source, differently than normal cells.  In addition to taking up an abundance of glucose, cancer cells turned the glucose into lactate.  While normal cells can do this, they do so when oxygen levels are low.  Warburg found that cancer cells, however, convert glucose to lactate even when there is plenty of oxygen – a process called aerobic glycolysis.  This altered metabolism seen in cancer cells became known as “the Warburg effect.”

Tumor cells produce lactate even when oxygen is present

While the underlying cause of the Warburg effect is still being studied, the altered metabolism has been utilized for tumor imaging.  Glucose labeled with a marker can be visualized with a PET (positron emission tomography) scan, a common imaging procedure.  Because cancer cells take up more glucose than normal cells, the labeled glucose will be most abundant in cancer cells, highlighting these cells in the resulting PET image.  In this way, doctors can pinpoint areas of tumor cells.

Tumor visualized by PET scan

In a recent paper from Radiotherapy and Oncology, researchers from Switzerland looked further into the altered metabolism of cancer cells.  They aimed to observe changes in cancer cell metabolism upon treatment of the tumor with common therapies.

So, what does this have to do with fireflies?  We’re getting there.

Using tumors harvested from mice, the researchers made very thin slices of the tumor tissue.  They then measured levels of metabolites, glucose and lactate, in the slices using specific assays – bioluminescent assays.  Through an enzymatic reaction, the metabolites in the tumor slices were turned into light so that the amount of light produced indicated the amount of metabolite present in the tumor tissue.

The enzyme that catalyzed these light-producing reactions?  Luciferase, of course!

After measuring the amount of light produced from each tumor slice using a high-tech camera, the scientists could compare the levels of metabolites in different tumors.  They found that tumors that were treated with cancer therapeutics (called patupilone and IR) had lower levels of lactate and higher levels of glucose as compared to untreated tumors.  Decreased lactate levels suggested that less glucose was being converted to lactate.  Likewise, increased glucose in the tumor slice suggested that less glucose was being consumed by the cells (and, in turn, made into lactate).  In short, the altered metabolite levels in the treated tumors suggested that those cancer cells were reverting back to a more normal metabolism.

Modified from original manuscript

The measurement of altered metabolite levels in tumor slices upon treatment could be extremely useful in the therapeutics field.  By monitoring changes in cell metabolism in tumors, doctors could predict early in treatment if a therapy was going to be beneficial for a patient.  Active monitoring of cancer cell responses to a given therapy could greatly improve cancer patients’ treatment courses.

I think the firefly would be proud to know that its enzyme is working to improve the health of cancer patients, don’t you?

Proud firefly?

Fireflies and Science – An Enlightening Combination

Because they seem unusually abundant this summer (and in anticipation of an upcoming post), I thought I’d talk about fireflies today – fireflies and their role in scientific research.

Close-up

 There are over 2,000 species of fireflies, and they are named such due to the bioluminescence they produce to attract mates and deter predators.  The bioluminescent reaction is clearly seen on a hot summer night, especially in tropical and temperate climates.  Many people have fond memories of catching fireflies as children, gathering them in a jar with holes poked in the lid and enjoying the soft glow – a bioluminescent nightlight.

Firefly in jar (Sounds like the title of an ode)

 So what is bioluminescence?  Bioluminescence is the production of light by a living thing (bios = living, lumen = light).  This type of luminescence is a natural example of chemiluminescence – energy released as light through a chemical reaction.  It is seen in a variety of organisms including anglerfish, fungi and glowworm beetles (which are distinct from the firefly larvae that are also sometimes called glowworms).

While, as kids, we loved the blinking lights of the fireflies, few of us probably understood how the yellow-green glow was actually created.  It is indeed a chemical reaction.

Fireflies produce two compounds that make their light show possible.  One is called luciferin and the other is luciferase.  Luciferin is a pigment that reacts with oxygen to create the light we see.  Luciferase is a catalyst in this reaction meaning that it speeds up the reaction without being used up itself.  Other components within the firefly including magnesium and ATP, an energy source, fuel the reaction.

The energy resulting from the chemical reaction is released as heatless green, yellow, or reddish light (wavelengths between 510 to 670 nanometers for the light spectrum enthusiasts out there).

Light spectrum

It is this light that we see twinkling around us on hot summer nights.  In fact, scientists think the fireflies can control the pattern and speed of “twinkling” by controlling how much oxygen (a component of the reaction) they have in their bodies.

So what does this have to with scientists and research?  It turns out that the luciferase produced by fireflies can be a powerful research tool.  Organisms can be made to glow by engineering them to express the luciferase gene.  The plant below expresses luciferase, and when watered with a luciferin-containing mixture, it glows brightly.

Glowing tobacco plant

 Probably the most common use of luciferase in labs, and one that I found helpful in my own research, is as a reporter for what is happening within the DNA of a cell.  The luciferase gene can be engineered into a cell so that it is expressed only when a specific promoter – a segment of DNA that drives gene expression – is active.

So, if I wanted to know if a chosen promoter was active, I would create a stretch of DNA in which my promoter in question would lead to creation of luciferase when active.  Then, by adding luciferin to the mix, the presence or absence of light would tell me if luciferase was expressed and if my promoter was active.

Active promoter –> luciferase expression + luciferin = light (as in a firefly)

Inactive promoter –> no luciferase expression + luciferin = no light

Using this “equation” then, scientists can determine if a stretch of DNA is active merely my measuring whether light is produced.  This is one way in which firefly luciferase helps scientists do their work.

So the next time you catch a firefly, thank it for its contribution to science.  And then let it go so it can scare away predators, attract a mate and entertain kids of all ages with its bioluminescent backside.

A glowing backside

A New Breed of Pet

Specific puppy hybrids are high-cost designer pets.  Puggles and labradoodles are carefully bred to create desired characteristics such as less shedding or more docile personalities.

But research on a new breed may change the way people think about pets.  The new designer pet?  Foxes.

Research at the Institute of Cytology and Genetics in Siberia is breeding foxes to have the same docile characteristics as our favorite lapdogs.  This is the latest version of animals being bred for domestication.  The goal at that outset of the project, over 50 years ago, was to recreate the domestication of wolves into dogs.

With each generation of fox pups, researchers tested the responses of the foxes to humans – are they approachable, can they be pet, do they wag their tails?  Amazingly, instead of taking thousands of years, it took only a few years.

Just the second generation was approachable, the fourth generation allowed themselves to be pet, and by the sixth generation, the kits followed humans around and licked them – actions practically indistinguishable from that of pet dogs.

Even more interestingly than the domestication (at least to this biologist) were the physical changes that accompanied it.  Within 15 generations of the specially bred foxes, they acquired floppy ears, spotted coats, and curly and shorter tails.  These characteristics (called a domestication phenotype) are seen in many species of domesticated animals including dogs, pigs, and chickens.

These changes seen in many domesticated animals suggest that there is a set of genes that are shared by all animals capable of domestication.  The researchers in Siberia are currently searching for those genes.  However, the genes responsible for tameness are proving difficult to find.

And how do the genes affect docility and domestication?  No one knows yet, but one theory is that the genes control chemical signals in the brain that affect attitude.  These chemical changes may then have downstream effects on the physical appearance of the animals.

So, do you want a tame fox?  A company in Siberia will sell you one.  For the low, low price of just $6, 950 (transportation and paperwork included).  The youngest that foxes can be adoped is 3 ½ months old.  And I have to admit, they’re pretty cute…

 A domesticated fox pup

The company claims that caring for the foxes is much like caring for dogs.  They can live inside or outside and can benefit from having a crate.  They can eat dog food and can even be trained to use a litter box.  They should be walked and brushed regularly.

And apparently they’re rather playful.

So, if you’re up for it, you have $7,000 lying around, and you need something a little more interesting than a plain old dog, look into getting your very own pet fox!  Oh, and as for that genetic research – maybe it’ll lead us to the next domesticated pet.  Any bets on what it’ll be?

For more information, see the recent article in National Geographic, March 2011.  Want to buy your own fox?  Visit http://www.sibfox.com/

Causes of Alzheimer’s Disease

The causes of Alzheimer’s disease are still in question, and the changes that take place in the brain are constantly being studied.  There are several theories about the causes underlying Alzheimer’s disease including:

1. The brain doesn’t make enough acetylcholine, a neurotransmitter.

2. Beta amyloid, shortened forms of a protein, join together to form plaques in the brain.

3. Myelin, an insulating material that surrounds neurons, breaks down.

4. Tau tangles form in the brain.

Let’s discuss that last theory, the tau theory, in more depth.  The tau protein interacts with and stabilizes microtubules, the scaffolding structure of cells.  It is found mostly in neurons.  Two different changes in the tau protein can affect its ability to function normally – isoforms and phosphorylation.

Different isoforms of the tau protein can be present in cells.  Isoforms of tau are different versions of the protein.  They are made when the gene from which the protein is created is cut in various places creating different sequences.  These isoforms have variable structures with different attributes.  Some of the isoforms of tau are more likely to form tangles than others.

The tau protein can also be changed after the protein is made through a process called phosphorylation.  Phosphorylation adds a phosphate group to the tau protein.  If several phosphate groups are added to the protein, tau can self-assemble into the tangles that are characteristic of Alzheimer’s patients.

Tau protein aggregates into filaments (left).  The filaments form tau tangles (right).

Tau tangles can lead to disintegration of microtubules in neurons.  This can then result in malfunctions in the communication between neurons leading to cell death and cognitive impairment seen in Alzheimer’s patients.

Listen Up…or Down or to the Side

We hear sounds around us every day, and usually we are able to find the direction from which the sounds come.  When hiking, a few notes of a bird’s song can lead us to locate the bird.  When walking down the street, someone calling our name causes us to turn in the direction of the caller.  How do we locate the source of a sound?

Let’s do a little experiment…  First, find a friend to help you.  As you sit in a chair with your eyes closed, have your friend shake a set of keys one of three places – above your head, at eye level, or near the ground.  After each shake, guess the location of the keys.  I bet you guessed correctly.  Now, push on the back of your ears, just above the lobes.  Push hard enough that you distort the shape of the ear canal but don’t completely block sound from reaching the ear.  Have your friend shake the keys in various locations again.  Did you guess correctly?  If you didn’t fare as well on the second part of the experiment, there is a good reason.

How do we hear and interpret the sounds coming into the ears?   It’s a question that Donata Oertel, professor and interim director of the Department of Physiology at the University of Wisconsin-Madison, has spent her career studying.  I sat down with Oertel in an attempt to understand this sense that many of us take for granted every day.

Oertel explains that when we hear sounds, we receive two important pieces of information – where the source of the sound is and what that sound means.  But the ear itself does not carry out these functions.

“From the signals that come from the ear, the brain has to extract the information it needs,” explains Oertel, “It turns out these are quite complicated computations.”

Our ears are far apart from each other on our heads for good reason.  When sounds come from the side, they will reach the near ear a little bit earlier than they reach the far ear.  If the sound is at a high frequency, it will also be louder in the near ear.

“These time and intensity differences sensed by the ear give our brains the cues to compute the location of the source of a sound in the horizontal plane,” says Oertel.  “But that process doesn’t help us determine where the sound is coming from in the vertical plane.”

Oertel explains that to locate a sound in the vertical plane, the asymmetry of our ears is important.  Our ears are asymmetrical, both top to bottom and front to back.  As sounds coming from various locations impinge on the ear at different angles, they interact with the ear differently and give the brain spectral cues.  The cues change as the elevation of the sound source changes, and we can then locate the source in the vertical plane.

Being able to hear a sound and locate the source is a great skill, but once a sound is heard, the brain must work to interpret it.  The question of how this happens was a new concept when Oertel began working in the auditory system, a field dominated by engineers in the late 1970s.

“Engineers described, where as I wanted to ask.  I wanted to ask why it was that these brain circuits were doing what they were doing,” says Oertel.

To find answers to the “why” questions, Oertel and her lab study the brains of mice.  Electrophysiological recordings can be taken from the part of the brain where the auditory nerves terminate, giving Oertel and her colleagues information about the neurons and how they are processing auditory messages.

Oertel’s hard work and knowledge of the brain have led to a number of interesting findings, including a circuit in the auditory pathway of the brain which Oertel believes functions to suppress echoes.  Sounds come directly from a source to our ears, but they also bounce off walls around us.  To accurately hear the sound and locate its source, we must suppress the echoes.

“I think one part of that ability comes from a brain circuit which receives a first excitation and then inhibits further signals,” explains Oertel.  “In this way, we can use the first signal but ignore the subsequent signals to accurately process the sound.”

So the next time you are walking through a crowd of people or trying to spot a bird you hear, stop and appreciate your ability to determine the direction from which sounds are coming.  And when a friend calls your name from through the crowd, be grateful you can pinpoint that person without calling for a search party.

Imaging Brain Changes in Alzheimer’s Disease

Alzheimer’s research aims to decrease some of the uncertainty surrounding causes, diagnosis, and treatment of the disease.  Many researchers believe that an important aspect of treatment will involve identifying the disease early and treating those early changes in the brain.

Beta-amyloid plaques are aggregates found in the brain of Alzheimer’s patients. Historically, these plaques were only identifiable upon autopsy.

A beta-amyloid plaque

Recently, better techniques for imaging these plaques have been developed.  As techniques improve, more information about the effects of the development of the disease on the brain can be gathered.

In a recent paper in Brain: A Journal of Neurology (published online February 9th), Gael Chetelat and colleagues use imaging techniques to more fully recognize early brain changes in Alzheimer’s progression and how those changes relate to memory decline.  Using magnetic resonance imaging (MRI), the researchers image and recognize a portion of the brain called grey matter.  They also use positron emission tomography (PET) to visualize a tracer that marks beta-amyloid deposits.  They aim to relate the breakdown of brain matter and the location of beta-amyloid plaques to the degree of memory loss in patients in the pre-dementia stage of Alzheimer’s disease.

The researchers find that memory performance of patients in the pre-dementia stage relates to two changes in the brain.  The first change is increased beta-amyloid deposition, specifically in the temporal neocortex.  The temporal neocortex is part of the outer layer of the brain located on either side, and it plays a critical role in visual processing, storage of language, and memory.

Labeling of temporal beta-amyloid deposition (left) and location of reduced grey matter in the hippocampus (right)

The second change in the brain is a decrease in grey matter in the hippocampus.  The hippocampus is located inside the brain structure with mirror-image halves in the right and left sides of the brain, and it is important in navigation and long-term memory.  The authors suggest that these insults to the brain structure should be considered separately as researchers look for possible targets of therapies.

The prospect of imaging specific changes in brain structure is exciting.  If these changes can be related to future Alzheimer’s progression or other forms of memory loss (which the authors caution cannot be done from their study), early identification of these insults may allow time for intervention and treatment that can slow or stop memory loss.  Knowledge of the specific locations of the insults as well as improvements in the techniques available to image the brain will be invaluable advances in the fight against dementia and Alzheimer’s.

Beta-amyloid photo here.  MRI photos from Chetelat study here.