Category Archives: Research

#TheDress Effect: What you see isn’t necessarily what’s there

Last week, a poorly lit picture of a dress sparked one of the fiercest — and perhaps most meaningless — debates in Internet history: Was it white and gold or blue and black? Now that the dust has settled, and the definitive answer established it’s blue and black, it’s time to move onto a more important question: Why did people see the dress differently? ReAction asked biology professor Stephen Van Hooser to break down the science of the dress.

We tend to think we are able to understand the world perfectly through our eyes. In reality, our visual system makes best guesses with limited information. Take, for example, the fact that the world is three-dimensional but the images on our retina are two-dimensional. Our visual system has to make guesses as to the locations of objects based on this two-dimensional image.

Visual illusions force us to confront the fact that the brain still makes guesses, or especially when the visual system doesn’t have all the information its needs.

Consider the “Cornsweet effect” (Purves et al., 1999). If we look at the following scene, we perceive that the gray patch above the white rectangle has the same luminance as the gray patch below the white rectangle.

Cornsweet Effect
Cornsweet Effect

However, if we fill in the white rectangle with a rounded contour and transition in luminance, our perception changes. We believe the light source must be coming from above, and that it is shining more directly on the upper surface than the lower surface. Yet, because the amount of light that hits our retina from the upper surface and lower surface is the same, we assume that the upper surface is inherently darker than the lower surface. That is, we imagine that if we were to shine a light directly on the two surfaces, the upper surface would appear darker than the lower one.


Our perception is influenced by assumptions that our visual system makes about the light source and reflectance of the materials.

This is what is going on in “the dress,” except that our uncertainty is in the chromatic nature of the illuminating light. Is the illuminating light daylight, which contains a broad range of component colors ranging from blue to red? Or is it an artificial light source, which usually contains much higher percentages of green, yellow and red light?

TheDressAn object that looks white when illuminated by daylight will reflect more yellow light when it is illuminated by a yellowish light source, simply because of the color of the light that’s being shone on it. However, if we know that the light source is yellow-dominated, and we have some objects in the room that allow us to guess that the light source is yellow-dominated, then our brain will “correct” the raw data it is receiving and we will still perceive the object as white.

Now let’s consider an object that looks blue when illuminated by daylight. When it is illuminated by a yellowish light source, it will still reflect the weak blue light that is present in the yellowish light source, and it will also reflect some weak yellow light simply because the object is getting hit with a lot of yellow light. That is, in terms of “raw data,” our eyes will collect light more broadly across the spectrum — blues, greens, yellows and reds. If we have cues that tell us that the light source is yellow-dominated, we will still see the object as blue.

If we see a blue object illuminated by yellow-dominated light but for some reason our brain thinks that it is actually illuminated by daylight, our brains will perceive the object as white.

The dress illusion is strong because the light source is ambiguous. Some people might imagine that the dress is being illuminated by daylight, and they will perceive the material as white. Others may think it is under strong artificial illumination, and the material will appear blue.

From moment to moment, our impression can change, but we always have a single impression.

It looks pink to me.

This story was written by Stephen Van Hooser.

Update:  Rosa Lafer-Sousa at MIT has combined the dress image with images from Beau Lotto that evoke strong sensations of yellow-dominated or blue-dominated illuminating light. Separately zoom in on both images. See if you can see the dress as blue or white in the different figures!

Want renewable energy? There’s an enzyme for that.

It’s all about those enzymes.

Enzymes are nature’s magicians. They perform incredibly complicated feats of chemistry in milliseconds. They change light and food into energy, carbon dioxide into oxygen, one cell into two. They are responsible for catalyzing — speeding up — every biological process. If researchers could replicate the power, speed and efficiency of nature’s enzymes, it could mean true renewable energy, not to mention new drugs and greener industrial materials.

There has been some progress in engineering enzymes — think ethanol and other biofuel fuels — but enzymes designed in a lab still can’t compete with those evolved in nature. This is partly because researchers haven’t had a clear, step-by-step understanding of how enzymes do their magic.

Now, we do.

For the first time, Brandeis University researchers have observed and recorded each step of how the enzyme adenylate kinase (ADK), catalyzes the transfer of energy in our cells. Dorothee Kern, professor of biochemistry and Howard Hughes Medical Institute Investigator, published the findings in a recent issue of Nature Structural and Molecular Biology.

Adenylate kinase
Adenylate kinase

ADK plays an important role in cellular energy homeostasis, maintaining the right nucleotide (chemical energy storage molecules) levels in cells. Kern and her team, which included professor Michael Hagan, outlined the minimum five-step process of catalysis, during which the sophisticated ADK enzyme binds the target nucleotides, closes around them, catalyzes the chemical reaction, reopens and releases the final product. The whole process takes milliseconds with the enzyme. Without it, it would take about 8,000 years for this process to happen naturally.

The team also observed what each part of the enzyme does during the process — revealing an efficient team of players, including magnesium, each responsible for multiple parts of catalysis.

“We found that you really can’t get much more efficient than ADK,” Kern says. “It really is an amazing accelerator.”

Kern’s work is a first step to designing better, faster, stronger enzymes but there is still a long way to go.

“The first step is seeing how it works in nature,” Kern says. “Then, we can figure out how to make it better.”

This work was supported by the Howard Hughes Medical Institute, the Office of Basic Energy Sciences, Catalysis Science Program, Department of Energy and the National Institutes of Health.

Evolution may hold the key to rational drug design

This is the story of Abl and Src — two nearly identical protein kinases whose evolution may hold the key to unlocking new, highly specific cancer drugs.

Abl and Src are bad guys — oncogenes with a predilection to cause cancer in humans, mainly chronic myeloid leukemia (CML) and colon cancer. These two proteins are separated by 146 amino acids, and one big difference — Abl is susceptible to the cancer drug Gleevec, while Src is not.


From left, Src and Abl proteins
From left, Src and Abl proteins

Dorothee Kern, professor of biochemistry and Howard Hughes Medical Institute investigator, unraveled the journey of these two proteins over one billion years of evolution, pinpointing the exact evolutionary shifts that caused Gleevec to bind well with one and poorly with the other. This new approach to researching enzymes and their binding sites may have a major impact on the development of rational drugs to fight cancer.

Dorothee Kern
Dorothee Kern

The findings were published in the journal Science and coauthored by Doug Theobald, professor of biochemistry, with Christopher Wilson, Roman Agafonov, Marc Hoemberger, Steffen Kutter, Jackson Halpin, Vanessa Buosi, Adelajda Zorba, Renee Otten and David Waterman.

When Gleevec hit the market in 2001, it was hailed as the magic bullet against cancer.

That’s because most cancer drugs fight a scorched-earth campaign — killing as many healthy cells as cancerous ones. But Gleevec is specifically attracted only to Abl, the enzyme in cancerous cells responsible for growth and reproduction. Gleevec binds with Abl, deactivating it and stopping the spread of cancer in its tracks.


Developing more drugs to work like Gleevec — known as rational drug design —could create therapies that target specific enzymes in many types of cancer. Unfortunately, scientists haven’t known why Gleevec is so picky, binding with Abl but not with its close cousin Src.

To solve this puzzle, Kern and her team turned back the evolutionary clock one billion years to find Abl and Src’s common ancestor, a primitive protein in yeast they dubbed ANC-AS. They mapped out the family tree, searching for changes in amino acids and molecular mechanisms.

“Src and Abl differ by 146 amino acids and we were looking for the handful that dictate Gleevec specificity,” says Kern. “It was like finding a needle in a haystack and could only be done by our evolutionary approach.”

As ANC-AS evolved in more complex organisms, it began to specialize and branch into proteins with different regulation, roles and catalysis processes — creating Abl and Src. By following this progression, while testing the proteins’ affinity to Gleevec along the way, Kern and her team were able to whittle down the different amino acids from 146 to 15 responsible for Gleevec specificity.

These 15 amino acids play a role in Abl’s conformational equilibrium — a process in which the protein transitions between two structures. The main difference between Abl and Src, when it comes to binding with Gleevec, is the relative times the proteins spend in each configuration, resulting in a major difference in their binding energies.

By understanding how and why Gleveec works on Abl — and doesn’t work on Src — researchers have a jumping off point to design other drugs with a high affinity and specificity, and a strong binding on cancerous proteins.

“Understanding the molecular basis for Gleevec specificity is opened the door wider to designing good drugs,” says Kern. “Our results pave the way for a different approach to rational drug design.”

This research was supported by HHMI, the Office of Basic Energy Science, the U.S. Department of Energy Catalysis Science Program and grants from the National Institutes of Health.

Why all-nighters don’t work

Want to ace that test tomorrow? Here’s a tip: Put down the coffee and hit the sack.

Scientists have long known that sleep, memory and learning are deeply connected. Most animals, from flies to humans, have trouble remembering when sleep deprived, and studies have shown that sleep is critical in converting short-term into long-term memory, a process known as memory consolidation.

But just how that process works has remained a mystery.

The question is, does the mechanism that promotes sleep also consolidate memory, or do two distinct processes work together? In other words, is memory consolidated during sleep because the brain is quiet, allowing memory neurons to go to work, or are memory neurons actually putting us to sleep?

h6F72EF3EIn a recent paper in the journal eLife, graduate students Paula Haynes and Bethany Christmann in the Griffith Lab make a case for the latter.

Haynes and Christmann focused their research on dorsal paired medial (DPM) neurons, well-known memory consolidators in Drosophila. They observed, for the first time, that when DPM neurons are activated, the flies slept more; when deactivated, the flies kept buzzing.

These memory consolidators inhibit wakefulness as they start converting short-term to long-term memory. All this takes place in a section of the Drosophila brain called the mushroom body, similar to the hippocampus, where our memories are stored. As it turns out, the parts of the mushroom body responsible for memory and learning also help keep the Drosophila awake.

“It’s almost as if that section of the mushroom body were saying ‘hey, stay awake and learn this,’” says Christmann. “Then, after a while, the DPM neurons start signaling to suppress that section, as if to say ‘you’re going to need sleep if you want to remember this later.’”

Understanding how sleep and memory are connected in a simple system, like Drosophila, can help scientists unravel the secrets of the human brain.

“Knowing that sleep and memory overlap in the fly brain can allow researchers to narrow their search in humans,” Christmann says. “Eventually, it could help us figure out how sleep or memory is affected when things go wrong, as in the case of insomnia or memory disorders.”

To learn more about this and other fly research, check out Christmann’s blog, Fly on the Wall. 

This research was funded by the National Institute of Health


An Overwhelming Sense of Discovery

Jose Vargas ’15 is a time traveler.

As an undergraduate researcher in professor John Wardle’s lab, Vargas studies quasars, the brightest and most remote objects in the universe, clocking in at 10 to 12 billion light years away, meaning Vargas is looking 10 to 12 billion years in the past.

Quasars form when supermassive black holes — billions of times the mass of the Sun — feed on nearby material. The matter forms an accretion disk around the black hole, heating up to millions of degrees and blasting out radiation and powerful jets of particles, traveling at nearly light speed — like the universe’s largest particle colliders.

Astrophysicists believe that quasars may be an important step in the birth of galaxies.

We asked Vargas to describe what it’s like to see into the past. Here is what he said:

Big news for little cilia

Dust mite

Take a deep breath. You just inhaled dust, dirt, pollen, bacteria and probably more than a few of these dust mites — but don’t worry, your cilia are on it.

Cilia, the cell’s tails and antennae, are among the most important biological structures. They line our windpipe and sweep away all the junk we inhale; they help us see, smell and reproduce. When a mutation disrupts the function or structure of cilia, the effects on the human body are devastating and sometimes lethal.

The challenge in diagnosing, studying and treating these genetic disorders, called ciliopathies, is the small size of cilia — about 500-times thinner than a piece of paper. It’s been difficult to examine them in molecular detail until now.

Professor Daniela Nicastro and postdoctoral fellow Jianfeng Lin have captured the highest-resolution images of human cilia ever, using a new approach developed jointly with Lawrence Ostrowski and Michael Knowles from the University of North Carolina School of Medicine. They reported on the approach in a recent issue of Nature Communications.

A 3-D reconstruction of cilia, courtesy of the Nicastro Lab

About 20 different ciliopathies have been identified so far, including primary ciliary dyskinesia (PCD) and polycystic kidney disease (PKD), two of the most common ciliopathies. They are typically diagnosed through genetic screening and examination of a patient’s cilia under a conventional electron microscope.

The problem is, conventional electron microscopy is not powerful enough to detect all anomalies in the cilia, even when genetic mutations are present. As a result, the cause of ciliary malfunctions can be elusive and patients with ciliopathies can be misdiagnosed or undiagnosed.

Nicastro and her team developed an approach that includes an advanced imaging technique that entails rapidly freezing human samples to preserve their native structure, imaging them with transmission electron microscopy, and turning those images into 3D models. This cutting-edge imaging was in part made possible by the advanced instrumentation in the Louise Mashal Gabbay Cellular Visualization Facility at Brandeis. It is the first time this approach has been used on human cilia and patient samples.

We have a new window into the structure and defects in human cilia, says Nicastro.

“For so long, researchers haven’t been able to see the small defects in human cilia,” Nicastro says. “Now, we can fill in the pieces of the puzzle.”

The hunt for dark matter (and other fun physics in 2015)

There may not be an equation to prove it — but 2015 promises to be a big year for Brandeis physics.


In 2015, the Large Hadron Collider at CERN — the world’s largest science experiment — will reboot after two years of upgrades, with double the energy of its first run. The Brandeis High Energy Physics Group will be in the thick of it, exploring the newly discovered Higgs boson and hunting for supersymmetry, dark matter and extra dimensions.

With its National Science Foundation Grant renewed for six years at $12 million, The Brandeis Bioinspired Soft Materials Research Science and Engineering Center (MRSEC) will enter a new phase in 2015. Led by physicist Seth Fraden, the interdisciplinary group will continue its groundbreaking research into active biological matter and membranes materials, paving the way for soft robotics, novel drug delivery systems and artificial cells.

Over the next year, the Brandeis Astrophysics Group will continue its exploration of the cosmos, peering deep into the cores of galaxies and quasars, while Brandeis theorists continue to unravel the mysteries of quantum entanglement and gravity.

Expect new ideas and directions in undergraduate education as well, says professor Jané Kondev, physics department chair. In 2014, Kondev received a $1 million grant from The Howard Hughes Medical Institute to bolster interdisciplinary undergraduate research at Brandeis.

In 2015, physics professor Zvonimir Dogic and biology professor Melissa Kosinski-Colllins will begin collaborating on a new first-year lab course for premeds and life-science students, focusing on the physics of living systems.

Whether you’re interested in dark matter or active matter, 2015 promises to be an exciting year. Stay tuned!

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.


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

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.

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.

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.

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.”

maven_mars_sunrise copy
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.