All posts by Leah Burrows

Hi, I'm Leah Burrows, the Senior Research Communications Specialist in the Office of Communications. I cover undergraduate, graduate and faculty research for BrandeisNOW and Brandeis Magazine.

DNA’s Wild West: Bounty hunters and outlaws vie for control of your genes

We like to think of evolution as a fine-tuning process, one that whittles away genetic redundancies in pursuit of that elusive goal first articulated by Victorian intellectual Herbert Spencer: becoming “the fittest” species. The only problem is, we are not fine-tuned machines. Our bodies are chock-full of parts that either don’t work anymore (talking to you, appendix) or are so buggy that our biology has Macgyvered a way to make it work.

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Take our DNA. No, seriously, take our DNA. It’s mostly garbage anyways. Fifty percent of our genome is comprised of genetic parasites, called transposable elements or transposons, that usually lie dormant. When they are allowed to move around the genome, they can wreak havoc on our genes. These bundles of rogue DNA sequences, nicknamed jumping genes, can hop into an essential gene and interrupt it, leading to a variety of mutations that cause conditions like infertility.

Barbara_McClintock_(1902-1992)
Barbara McClintock

The woman who discovered transposons, Barbara McClintock, won the Nobel Prize in Physiology or Medicine, and is the only woman to receive an unshared Nobel in that category.

Our reproductive cells, called germ cells, are particularly sensitive to transposons, so they rely on a system called the PIWI pathway to keep the transposons in check. Scientists have long wondered how the pathway works and why, despite its checks and balances, do transposons still make up such a large portion of our genome. Understanding the system would help scientists demystify human infertility and other diseases that result when transposons run amok.

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Lau Lab: Reazur Rahman, Yuliya Sytnikova, Nelson Lau, Gung-wei Chirn and Josef Clark

Brandeis biology professor Nelson Lau and his lab recently published two studies on the PIWI pathway, short for P-element Induced Wimpy testis. When the pathway is blocked in fruit flies, it results in small, infertile testes and ovaries.

The pathway’s main weapons against transposons are PIWI proteins and small RNA molecules called piRNAs.

Think of PIWI proteins as transposon bounty hunters and piRNAs as the wanted posters that provide vital information about the outlaw DNA.  But the piRNAs don’t offer a complete picture. “Germ cells do something very weird by shredding that wanted poster into a lot of small pieces,” Lau says. “Instead of carrying the whole poster, piRNAs carry what might look like part of a nose, half of an eye or a sliver of a lip.”

PIWI proteins are bounty hunters, like Boba Fett
PIWI proteins are bounty hunters, like Boba Fett

Just as a shredded wanted poster could match many faces, those small piRNAs could match many good genes, so how do PIWI proteins track down and silence transposons without silencing good genes in the process?

In a study published in RNA, Lau and his team, led by graduate student Josef Clark and former technician Christina Post, observed that PIWI proteins are careful. The proteins waited until they had a good composite picture from enough piRNAs before they clamped down on the transposon.

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The little red and blue dots are a swarm of PIWI proteins and piRNAs attacking a transposon (purple) coming out of our DNA.

But that doesn’t mean the system is flawless. Far from it, Lau’s team discovered.

In a second study published in Genome Research, Lau and postdocs Yuliya Sytnikova, Reazur Rahman and bioinformatician Gung-wei Chirn observed new transposable elements in the fruit fly cells moving to different areas of the genome, affecting nearby genes. “We all knew that the PIWI pathway was continuously active, so the conventional wisdom was that it was doing a decent job keeping these transposons under wraps,” Lau says. “We stood corrected.”

It turns out transposons are not so easily subdued. Many slipped past the PIWI system, landing on new genome spots and impacting surrounding genes. Some transposons could even make disguises — long non-coding RNAs that Lau thinks are meant to trick the PIWI proteins.

This may explain why transposons continue to make up such a large part of our genome, Lau says. “The PIWI pathway works just well enough to allow our germ cells to develop, but not well enough to keep all of the transposons fully redacted,” he says.

This may seem an ineffective way to protect our genome — our body’s most important artifact — but there may be a method in PIWI’s madness. After all, transposons have evolved with every member of the animal kingdom, from sponges to humans — there must be some reason they’re tolerated.

Perhaps, Lau says, a bit of genetic mischief, in the right places, is good. It ensures genetic variation and diversity, which is important for a species to reproduce and evolve.

Like so much of our biology, it’s not pretty but it is effective — for the most part.

Wandering the stars with the Brandeis Astronomy Club

The Brandeis Astronomy club, led by Isaac Steinberg, meets several times a month to observe and photograph the cosmos. Here are a few of their snapshots:

Jupiter has the shortest day of all the planets in the solar system. It turns on its axis once every 9 hours and 55 minutes, spinning so quickly that the planet  is slightly flat, giving it an oblate shape.

Jupiter has the shortest day of all the planets in our solar system. It turns on its axis once every 9 hours and 55 minutes, spinning so quickly that the planet is slightly flat, giving it an oblate shape.

The moon is rotating in synchrony with the earth, known as tidal locking. As a result we can only see the nearside of the moon from earth, which is a bit more than half of the moon given oscillation in its orbit.

The moon is rotating in synchrony with the earth, known as tidal locking. As a result we can only see the near side of the moon from Earth.

The Andromeda Galaxy  is the nearest spiral galaxy to the Milky Way, which is also spiral galaxy. It has an approximate trillion stars to our puny 300 billion. This image was composed of 8 long exposure photos, which were then merged to pull out detail and remove noise.

The Andromeda Galaxy is the nearest spiral galaxy to the Milky Way, which is also a spiral galaxy. It has an approximate trillion stars to our puny 300 billion. This image was composed of 8 long exposure photos, which were then merged to pull out detail and remove noise.

The Albireo star system in the center is in the constellation Cygnus. The larger of the double star is a binary star system composed of two stars that orbit each other. The larger star appears yellow and the smaller one blue when resolved with a telescope.

The Albireo star system (center) is in the constellation Cygnus. The larger of the double star is a binary star system composed of two stars that orbit each other. The larger star appears yellow and the smaller one blue when resolved with a telescope.

Saturn, the sixth planet from the sun and the second largest in the solar system, is comprised mostly of helium.

Saturn, the sixth planet from the sun and the second largest in the solar system, is mostly helium.

Vega is the fifth brightest star in the night sky and 25 lightyears away. It is found in the constellation Lyra.

Vega is the fifth brightest star in the night sky and 25 light years away. It is found in the constellation Lyra.

To find alien life, look for the weird

Life is a lot like Supreme Court Justice Potter Stewart’s famous definition of pornography — hard to define, but you know it when you see it. At least, that’s what scientists hope when they search the cosmos for life, or the remnants of life. But how do scientists know what to look for on planets where life could have evolved under drastically different circumstances than it did here on Earth? Would they really know it when they saw it?

There would be chemical clues, says Judith Herzfeld, professor of biophysical chemistry. Even if an organism itself didn’t look like any we’ve seen before, its appearance and its impact on its environment would be distinct from that of lifeless material, she says.

There’s a famous experiment that shows how life can change the surrounding environment. About 60 years ago, University of Chicago chemists Stanley Miller and Harold Urey built an apparatus that recreated pre-life conditions on the Earth’s surface. The experiment combined water and the gases in Earth’s primitive atmosphere — hydrogen, water vapor, methane and ammonia — with an electric spark to simulate lightning.  In the experiment the simple molecules were electrically stimulated to produce more complex molecules, like amino acids and sugars that we closely identify with life.

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courtesy/ wikipedia

“Life has a remarkable tendency to throw things out of whack,” says Herzfeld, who won a NASA grant a few years ago to study a curious aspect of the Urey-Miller experiment.

In the original experiment, hydrogen cyanide and some amorphous gunk that could be precursors to biological polymers, chains of molecules, were also produced. Chemists suspected a relationship between the two, as hydrogen cyanide — a deadly gas, formerly used in gas chambers — is known to spontaneously form polymers. Herzfeld and graduate student Irena Mamajanov studied the structure of these polymers and discovered three forms that were nothing like scientists had imagined.

But what does this have to do with finding life on other planets?

First, it means that life can emerge from unlikely places. Second, how life changed Earth’s environment can provide clues for finding life on other planets. Before life, our atmosphere (well, it wasn’t really ours then) was composed primarily of methane, ammonia, hydrogen and water vapor. Once life took hold, the new organisms consumed methane and caused oxygen and carbon dioxide to accumulate.

“What would really point to life is if the balance of the chemistry somewhere doesn’t make sense with all the ordinary factors on the planet, like overall composition, temperature or radiation,” Herzfeld says.  “We are looking for something distinctive.”

Of course, whatever life on other planets looks like, it will likely need water, Herzfeld says.

“It’s hard to imagine life without water because it’s just such an unusual molecule,” she says. “Liquid water buffers temperature really well, it has a way of helping proteins fold and cell membranes form, it readily dissolves ions. Each water molecule can participate in hydrogen bonds with four neighbors, so it can do pretty amazing stuff.”

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NASA’s Maven — Mars Atmosphere and Volatile EvolutioN — is investigating the upper reaches of Mars’ atmosphere to see how much of its ancient water was lost to space. Credit: NASA

So, what are the chances of finding a planet with liquid water and chemistry that doesn’t make a lot of sense?

“The universe is a big place,” Herzfeld says. “There’s a good chance there is something really interesting out there. If we find it, we’ll probably argue about what it means for a while. But, then again, we argue about what is life on Earth, too.”

To learn how Brandeis alumna Valerie Scott is developing devices to chemically analyze soil and rock samples on celestial bodies, perhaps to find life, check out our profile on BrandeisNow.

 

 

Sickly sweet: How HIV uses sugar against us

It’s National Chemistry Week and this year’s theme is the chemistry of candy. What do all candies have in common? Sugar. Lots and lots of sugar.

But when it comes to chemistry, what is sugar — besides delicious?

Sugar is the sweet name we give to strands of carbohydrates built with carbon, hydrogen and oxygen. The sugar we know and love most is sucrose, a carbohydrate strand composed of two simple sugars, glucose and fructose. These simple sugars are energy sources, absorbed directly into the blood stream during digestion — and the main culprits in a sugar high.

But sugars do more than give us a buzz, excess pounds and cavities. Complex sugars, called oligosaccharides, are a vital part of our cellular landscape, coordinating cell-to-cell interactions and stabilizing protein structures. Our immune system uses sugar in signaling structures. Sugars and lipids combine to differentiate blood types.

We are chock full of sugar — making it the perfect camouflage for a deadly virus.

In 2012, 1.6 million people died of AIDS-related illnesses worldwide. There are treatments but still no cure or vaccine for HIV, in part because of the arsenal of weapons the virus deploys to infiltrate and destroy the immune system. Sugar is one of those lethal weapons.

HIV H9 T Cell
HIV H9 T Cell

One particular HIV protein, called gp120, is covered in sugars, allowing it to slip through our immune defenses just like any other harmless protein. Now, Brandeis researchers are turning that sugary weapon against HIV, researching a vaccine that can target gp120.

Some immune systems are better than others at fighting HIV; they have broadly neutralizing antibodies, such as 2G12, which bind to gp120 and block it from being able to infect cells.

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Carbohydrate found on gp120

Isaac Krauss, assistant professor of chemistry, and his lab are researching an HIV vaccine that would boost 2G12 antibodies by designing clusters of carbohydrates that closely mimic the sugars on the outside of gp120. By using a technique of directed evolution, Krauss and his team have created several antigenic mimics, meaning they bind well with the 2G12 antibodies. Their next step is to test whether they are immunogenic, meaning if they can elicit an immune response.

If successful, these harmless mimics would spur the production of 2G12 antibodies, which would be able to identify the actual HIV virus and neutralize it.

And that would be very sweet.

 

Special thanks to graduate student Jenn Bailey, who sweetly contributed to this story. 

What happens when good genes get lost?

Scientifically speaking, there is no bad DNA, though we like to blame it for unruly hair, klutziness or poor gardening skills. There is, however, junk DNA.

Heterochromatin are tight bundles of DNA that often contain the genes our cells want to keep quiet, either because they are not needed or they are repetitive. Heterochromatic genes are silenced by a muzzle-like protein while the gene cells we want expressed, called euchromatin, are activated.

Sometimes, an important gene — a gene we want activated — gets mistakenly embedded in junk DNA. Scientists have long wondered how those genes get activated. Now, Brandeis University researchers may have solved that mystery.

Michael Marr, associate professor of biology, published a paper in the journal Molecular and Cellular Biology this summer with John Lis of Cornell University, Jessica Treisman of the NYU School of Medicine and former Brandeis research associate Sharon Marr, now at the Massachusetts General Hospital.

Hp1 Med26
Polytene chromosome stains

Transcription of DNA into RNA is an insanely complicated process that is still not entirely understood. In the 1990s, Roger Kornberg, a professor of structural biology at Stanford University, discovered a huge, multiprotein complex he called Mediator, which helps activate transcription. Kornberg won the Nobel Prize for his discovery.

Mediator, which is present in every eukaryotic organism from yeast to humans, is composed of dozens of subunits. However, some of the subunits are found only in animal cells. One of these subunits, Med26, has long been thought to be a marker for active, euchromatin genes.

Yet Marr and his colleagues discovered Med26 in heterochromatin — the first time the subunit has been observed among inactive genes. Either Med26 is moonlighting in an entirely new role, says Marr, or it is there tracking down lost genes and activating them.

“It looks as though Med26 is tethered to the silencer and maybe activates essential genes that got lost in the junk pile,” Marr says.

Marr and his team studied Med26 in Drosophila, the first time the subunit has been studied in an intact animal model. The team discovered that while cells and organs can develop without Med26, the organism as a whole dies if the subunit is removed.

“Med26 is essential for multicellular life and is involved in both active and silent genes,” Marr says. “Exactly how is the next big question.”

The Science of Stressing People Out

Ever had that dream where you’re about to take a test or perform in a play or go to a job interview and you are completely, woefully unprepared?

Many of us have that classic nightmare when we’re stressed out. But, for the scientists who study the effect of stress on the body, recreating those unnerving situations in real life is an important part of their research, however sadistic it may sound.

Psychology professor Nicolas Rohleder and his team of graduate and undergraduate researchers use so-called stress tests to study interleukin-6 (IL-6), an inflammatory agent linked to stress and a known contributor to heart disease, diabetes and cancer.

The science of stressing people out has, thankfully, evolved over the years from early tests in which participants were asked to stick their hands in buckets of ice or forced to watch videos of bloody surgeries, to more humane procedures today.

Although stress and its impact on the body have been studied since Austrian-Canadian endocrinologist Hans Selye’s experiments in the 1930s, stress tests weren’t standardized until the 1990s, when Clemens Kirschbaum of the Technische Universität in Germany came up with the Trier Social Stress Test (TSST).

Instead of using ghoulish or physically shocking methods to measure stress response, the TSST is designed to trigger a stress response to a social threat.

Considered the gold standard of stress tests, it has been used around the world in thousands of studies. Rohleder’s lab alone has put more than 1,200 people through the test. Though Rohleder can’t reveal everything in the TSST — it would ruin the stress for participants — he can share the basics.

First, researchers invite participants to sit in a comfy chair in a quiet room to draw blood to establish a baseline. Of course, needles themselves are stressors for some, so researchers attempt to make the experience as relaxing as possible.

Next, participants are introduced to a team of researchers and asked to perform two different kinds of tasks. The first requires interacting with the researchers and the second requires solving a problem. Two researchers observe and time participants performing the tasks.

Credit:  John Coetzee
Credit: John Coetzee

I know problem-solving tasks can be stressful — math certainly stresses me out. But what’s so scary about a social interaction, you might ask. Think about a time you went on a first date, or to a party where you didn’t know many people. Think about your first day of orientation at Brandeis. How did you feel? Were your palms sweaty? Was your heart beating a little faster?

As social creatures, humans need social interactions to survive, says Rohleder. But people who perform poorly in social situations risk being isolated or cast out of the group. Evolutionarily speaking, their genetic longevity may be in danger (though there are exceptions to the rule).

Obviously, researchers can’t expose subjects to life-threatening stressors, but luckily, social stressors provide the next best measure. The risk of social isolation triggers many of the same biological responses as physical threats, and the sympathetic nervous system kicks into gear, cortisol levels spike, and secondary stress systems, such as the inflammatory agent IL-6, activate.

Most of the time, by the end of the TSST, participants’ heart rates are up,  they might be sweating; their adrenalin might be pumping. The test usually stresses researchers out, too, Rohleder says, since they are also in a difficult social situation.

After the test, researchers take another blood sample to measure the biochemical changes in the body caused by stress. Participants can then leave — probably to calm down over a stiff drink.

Future stress test might include social media stressors, like Twitter trolls or nasty Facebook posts but we likely won’t see that in the lab until more people start seeing it in their dreams.

To read about Rohleder’s current research, check out our story on BrandeisNow.

Dogic Lab gets Science cover

On Sept. 5, the Dogic lab’s active matter research was featured on the cover of the journal Science.  Dogic, with a team from Technical University of Munich (TU Munich), Leiden University in the Netherlands, and Syracuse University, created a Frankenstein-like synthetic sac,  stitched together from different kinds of biomolecules, that can move and change shape on its own. It’s called an active nematic vesicle and it could be the first step towards building artificial cells.

So you want to work in a lab? Abby Knecht ’15 offers some advice

Dear freshmen,

You probably learned about RNA transcription in high school but have you ever seen it in action? I spent my summer watching, in real time, as small sections of DNA were converted into RNA for gene expression.

I work in a biochemistry lab at Brandeis that studies transcription under special fluorescent microscopes that allow us to observe single molecules interacting. It’s an incredible feeling to be able to see and study something that is so fundamental for life itself but hidden from our everyday view.

Working in a lab is unlike any science course you’ve taken so far. Science is about puzzles.  It’s about looking at the world, asking questions and finding ways to uncover the answers to those questions. But as one answer is found, more questions invariably pop up and the process continues.

Some of you may find this uncertainty frustrating, and long for the hard facts of lectures. Others may find that you enjoy discovering new things — things no one else has seen and are glad that memorization is not required. Others (like myself) may find that you like science in all its forms and enjoy both.

Whatever group you fall into, you won’t know until you try working in a lab.

Working in a lab is the best way to see how science is really done. You’re on the frontier of discovery. Unlike high school, where lab results are often spoon-fed to you, no one knows what the results will be: that’s why you’re doing the experiment.

Brandeis is a great place for undergraduate research. There are a lot of research labs and undergraduates have a chance to step up and perform their own research. I recommend anyone even remotely interested in science to try working in a lab.

If you want more help applying for labs or deciding whether or not to try it, I advise talking to Hiatt, our on-campus career center, your adviser, or the undergraduate department representative (UDR) in your field of interest.

Good luck!

Abby Knecht is a senior studying Biological Physics at Brandeis University.  She works in the Gelles lab researching the effects of negatively supercoiled DNA on the mechanism of transcription initiation.  When she is not in the lab or studying for one of her many science classes, she is either reading, drawing, or hanging out with friends. 

Making the Case for Cool Science

In 1888, an Austrian botanist dissected a carrot and today, we have LCD TVs. That’s the thing about science, you never know where it will lead.

That botanist was Friedrich Reinitzer, and he observed cholesterol extracted from a carrot that behaved both like a liquid and a solid. It was the first observation of a liquid crystal. Over the next century, it spawned a new field of research and countless technologies.

Would Reinitzer’s research be funded today?

With funding down and competition up, researchers have to fight for every dollar. Even fundamental researchers — the scientists who explore the basic building blocks of life and matter — are often asked to predict how their research could be applied.

At Brandeis, researchers build the foundations for curing disease, developing clean energy and understanding the cosmos. The research goal may be identifying how a particular protein operates in the disease process, or which chemicals won’t act like greenhouse gases in the atmosphere. But we also celebrate research that explores an unknown frontier without knowing where it will lead.

Physicists Zvonimir Dogic and Michael Hagan are doing just that.

Recently, their research into two-dimensional physics was featured in Nature, one of the most respected journals in science. The paper was also authored by Brandeis University graduate students Prerna Sharma and Andrew Ward. Knowing just how their research will be applied is decades down the road. But that doesn’t diminish the cool factor; indeed maybe it heightens it.

In the three-dimensional world, oil and water separate when combined. The smaller droplets of oil merge with larger ones, eventually forming one continuous layer that floats on water.

It’s a basic principle in physics.

But in the two-dimensional world, things work very differently.

Take our cell membranes, a two-dimensional liquid world. Liquid lipid “rafts” float on the surface of membranes, carrying proteins and regulating transport in and out of the cell.

If the lipid rafts behaved like liquid in the three-dimensional world, the individual rafts would coalesce into one larger raft.

But, as the researchers observed, the 2-D world has its own operating system.

To get an inside peek at this microscopic world, Dogic and Hagan needed to scale up, big time. They used long rod-like viruses to create a colloidal membrane — a membrane made up of thousands of smaller particles — like our cell membranes except much, much larger.

To build the lipid rafts, they used shorter rod-like viruses.

When the team put the shorter and longer viruses together, something unexpected happened: instead of separating like oil and water, the short rods self-assembled into smaller droplets of equal size and shape.

And they held that size and shape. Even when the sample started out with different sized droplets, they all equalized.

Even when the team split a droplet, it returned to its original size a few hours later.

Dogic and Hagan discovered droplets don’t coalesce because they actively repel each other, like magnets flipped on one side. A droplet’s chirality — the way its component rods twist in space — creates a distortion in the membrane, which its fellow droplets want to avoid. The effect is long-range, with the droplets avoiding each other as far as 10 diameters away.

The droplets constantly exchange and rearrange their rods to maintain the same size.

In the 3-D world this just doesn’t happen, but our rules don’t apply to the 2-D world.

Dogic and Hagan also discovered that by tweaking the parameters of the droplets — their chirality, for example — they can assemble into different shapes, like long, polymer-like strings or horseshoes.

So what does this all mean?

It means we’re just beginning to lift the curtain on the two-dimensional world. Sure, Dogic and Hagan can speculate about applications like self-healing fabrics or new drug delivery systems, but right now, it’s just cool science. No, it’s fundamental science. And that’s cool.