Category Archives: Faculty

Focus on Faculty: Isaac Krauss wins Strage Award

Isaac Krauss, assistant professor of chemistry, will receive the 15th Annual Alberta Gotthardt and Henry Strage Award for Aspiring Young Science Faculty.

Isaac Krauss, photo by Mike Lovett
Isaac Krauss, photo by Mike Lovett

“Isaac has been recognized as one of the up and coming scientists in the field of chemical glycobiology,” says professor John F. Wardle, head of the Division of Science and chair of the Strage Award Selection Committee.

The Strage Award is presented annually to a distinguished junior faculty member in the Life Sciences.  Alberta Gotthardt ‘56 and Henry Strage of London, England, created the award for researchers who have not yet received tenure but have made outstanding scientific contributions in the early stages of their independent research programs.

Previous winners include chemistry professor Christine Thomas and physics professor Michael Hagan.

Krauss and his lab are researching possible HIV vaccines, using directed evolution to create antigenic mimics of the virus.

His work has been highlighted in Chemical & Engineering News  and reviewed in Nature Chemical Biology and Current Opinion in Chemical Biology. He received the 2013 National Science Foundation CAREER Award and the 2012 Thieme Chemistry Journal Award.

The award will be presented on Wednesday, April 15 in Gerstenzang 123 at 2:00 PM. Krauss will deliver a lecture entitled: “Glycocluster Evolution: Combining Organic Synthesis and Directed Evolution to Design Carbohydrate Cluster HIV Vaccine Candidates.”

Watch the video to learn more about Isaac Krauss’ work.

Guest post: We need a super agenda to tackle superbugs

This article was written by Moaven Razavi, Senior Research Associate in the Schneider Institutes for Health Policy at the Heller School of Brandeis University.  It was originally published on Heller News

Drug resistant infections are turning into the biggest challenge that modern health systems will face in the near future. Statistics and estimates are breathtaking: by 2050, such infections are estimated to kill 10 million people per year. To put it in context, this is higher than the current global burden of cancer.

Today, there are 700,000 cases of drug resistant infections annually— and this is not just a problem for developing nations. In Europe and the U.S., these infections are already killing more than 50,000 people each year. If our response remains status quo, we would see the death toll rise more than 10 times by 2050, and the economic cost would spiral to $100 trillion.

The true gravity of the threat is being seriously examined in Europe. In July 2014, British Prime Minister David Cameron warned that we are in danger of being “cast back into the dark ages of medicine” if we fail to act, and announced an internationally focused review to address the problem. The taskforce was charged with developing a package of actionable recommendations in response to antimicrobial resistance (AMR) by the summer of 2016.

In the United States, however, the reaction to the problem has been sporadic and limited in scope. In January 2015, Senators Orrin Hatch (R-Utah) and Michael Bennet (D-Colo.) reintroduced legislation to accelerate the approval of new antibiotics to address drug-resistant “superbugs.” The bill, known as the PATH Act, would allow the FDA to expedite approval processes for novel medications.

While the U.S. Senate bill is tied to the threat that AMR poses to U.S. troops returning from Iraq and Afghanistan, the biggest risk is to senior citizens due to two major factors: the need for more invasive surgeries such as major joint replacements and heart surgeries, and the weakened immune system due to aging. The elevated risk level due to AMR poses a serious challenge to solvency of the Medicare program.

Even though the threat to the Medicare population is looming, the extent of the problem is not well assessed. Globally, the reliable estimates are scarce, and there is considerable variation in the patterns of AMR. However, drug resistant infections are a problem that should concern every country regardless of geography or income. According to the European Centre for Disease Prevention and Control’s Antimicrobial Resistance Interactive Database, in 2013, 15 European countries saw more than 10 percent of their bloodstream Staphylococcus aureus infections caused by methicillin-resistant strains (MRSA), with several of these countries seeing resistance rates closer to 50 percent.

Recognizing the severity of this issue, I joined several of my colleagues from the Institute on Healthcare Systems in investigating just how severely AMR is threatening the Medicare population. The study, which was funded by GlaxoSmithKline Pharmaceuticals (GSK), focused on Staphylococcus aureus (S. aureus), which is by far the most dangerous superbug. We examined the incidence of S. aureus infections following 219,958 major surgical procedures for a representative 5 percent sample of Medicare beneficiaries from 2004 to 2007.

We found that 0.3 percent of these patients had S. aureus infections immediately following their surgical procedures, while 1.7 percent were hospitalized with S. aureus infections within 60 days and 2.3 percent were hospitalized with S. aureus infections within 180 days. S. aureus infections within 180 days were most prevalent following gastric or esophageal surgery, with 5.9 percent of patients affected, followed by hip surgery (2.3 percent), and coronary artery bypass graft surgery (1.9 percent).

Of patients hospitalized with a major infection during the first 180 days after surgery, 15 percent of those infections were due to S. aureus, 18 percent were other documented organisms, and no specific organism was reported in 67 percent. We also found that infections prolonged the length of hospitalization by 130 percent, and S. aureus infection was associated with a 42 percent excess risk of mortality.

Due to incomplete documentation of organisms in Medicare claims, these statistics may underestimate the true magnitude of S. aureus infection; nevertheless, this study found a higher rate of S. aureus infections than previous investigations.

I believe that tackling the superbug crisis requires a super-agenda—one that involves both public and private stakeholders who are informed by solid research in a timely manner. Such an agenda should not only include promotion of research and investment in new drugs and treatment modalities, but also prevention measures in all domains. The role of Medicare and commercial payers is also critical and can be incorporated through payment reforms, value based purchasing efforts, and introduction of relevant re-admission and complication quality indicators.

Moaven Razavi is the lead author of the study, Postoperative Staphylococcus aureus Infections in Medicare Beneficiaries, which was published in the November 2014 edition of PLoS ONE. Other researchers include Donald S. Shepard and William B. Stason from Heller, and Jose A. Suaya form GlaxoSmithKline. 

#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!

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.

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!

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.

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.