Decades ago, Rensselaer chemist James Ferris created long chains of RNA molecules in the lab using simple clay materials and basic organic molecules as a catalyst. The discovery helped launch a theory on how life on Earth may have arisen so many years ago – a theory that still stands strong today.

Many astrobiologists support the theory that life first arose as RNA-based instead of DNA-based. The theory, known widely as the RNA World Hypothesis, is a highly plausible pathway to life because RNA, like DNA, can store genetic information and catalyze many of the chemical reactions required to maintain cellular life. Though well supported, the theory still lacks some important pieces of evidence. Most critically, scientists are trying to prove what the actual process was that caused the giant leap from the proverbial “primordial soup” to the formation of RNA.

In Ferris’ well-known theory, a simply clay material likely to be found on the surface of Earth around the time of life’s formation called montmorillonite served as a catalyst for the formation of RNA. He supported this theory in the landmark paper in the journal Nature when he grew chains of RNA molecules as long as 50 molecules at near room temperature. It was an exceptional feat of chemistry that still resonates today.

This week, nearly 50 years after Ferris joined Rensselaer, several of his mentees, colleagues, and collaborators are coming together to honor his sustained legacy in origins of life research. The group is dedicating a session at this year’s Astrobiology Science Conference to Ferris and his work. The conference is the largest gathering of astrobiology scientists in the world.

And despite his long career and legacy in the field, Ferris and his long-time colleagues within his laboratory here at Rensselaer continue to regularly publish new research on the origins of life and the possibilities of the humble montmorillonite.

For example, Ferris and his research partners recently published new findings in both Biochemical and Biophysical Research Communications and Origin of Life and Evolution of Biospheres that further support the theory of montmorillonite as a sparkplug for life. They found that as the chains of RNA formed by montmorillonite grow longer in length, they also become more specifically organized.

One of the main issues with all existing theories on the origins of life has to do with the basic arrangement of our molecules. Molecules can either be chiral or achiral. Chiral objects are mirror images of one another. The most common example of chiral objects is human hands. As anyone who has only mismatched gloves can tell you, you can’t stack a left-handed glove on a right-handed glove and have them match up (those darn thumbs). Achiral molecules are exact copies of one another in their mirror image (think of two beach balls).

What in the world does this have to do with the origins of life? Well, life is homochiral. This means that life is comprised of molecules of the same chiral arrangement. So if two chiral molecules are mirror images of one another (right- and left-handed if you will); two homochiral molecules are exact copies of one another in the same right- or left-handed arrangement. In other words, the molecules that make up our proteins, RNA, DNA and other vital components are either right- or left-“handed”. And so, our RNA and DNA is made up of only right-handed molecules. Any significant deviations from this arrangement and we would no longer have the classic double helix structure. Try stacking a bunch of right-handed gloves on top of one another and then throwing in the occasional left-handed one. The structure would be wonky and unsound. More evidence is pointing to the fact that homochirality of our molecules proceeded life. Thus, any theory on the origins of life worth its salt must account for the jump from a jumble of mismatched molecules to a neat homochiral combination. So how on Earth or Mars or even Gliese 581-g did life become homochiral?

The problem with uncovering our homochiral roots is that the precursors to life are actually a little too easy to grow in the lab. Sort of creepy to think about, but the equipment and processes of the modern chemistry laboratory can make easy work of creating organic molecules. But, recreating homochiral molecules has been very hard for research to do in the lab without resorting to the use of harsh chemicals or processes that weren’t present on the early Earth and therefore aren’t likely natural pathways to life.

In their most recent studies of montmorillonite, Ferris and his team discovered that as chains of RNA were formed, the longer they grew the more homochiral they became. And it wasn’t a tiny increase. Homochirality increased from 64 to 97 percent. This means that something about the clay may be causing the molecules to sort themselves into the correct formation as they grow without harsh chemicals or high temperatures. The work continues to support the theory Ferris has long supported and provides an important framework of knowledge on the potential chemical origins of each of us.

Rensselaer President Shirley Ann Jackson and three of our leading scientists and engineers have just completed their “IdeasLab” presentation at the World Economic Forum out in Davos, Switzerland. They were invited there to talk about taking concepts from the university setting into commercial arenas. We thought we’d share a few photos. They also had the pleasure of spending time with Ecovative CEO and co-founder Eben Bayer, a Rensselaer alumnus, as he signed a new contract with Sealed Air Corp. Ecovative was incubated at Rensselaer.

At the IdeasLab, above, from left to right, Claire and Roland Schmitt Distinguished Professor of Computer Science Boleslaw Szymanski, President Jackson,  Robert W. Hunt Professor of Materials Science and Engineering Dick Siegel, National University of Singapore President and session moderator Chorh Chuan Tan, and Howard P. Isermann Professor of Chemical and Biological Engineering Jonathan Dordick.

Siegel, Szymanski, Dordick, and President Jackson at the IdeasLab.

Bayer (left) and President Jackson after the new Ecovative contract was signed, with William V. Hickey, President and CEO of Sealed Air.

The human immune system is a marvelous machine. Bacteria enter the body (perhaps through those nasty, chalky mints at the local diner that you simply could not resist diving in to). Above is a gross image of the mints’ effects as you see salmonella bacteria attacking human tissue. To fight the invasion, our white blood cells immediately get to work to attack the bacteria. If you are lucky, the bacteria are neutralized by the immune system and you can peel yourself off the bathroom floor and move on with your life, hopefully avoiding future contact with publicly shared jars of candy.

Scientists are discovering that plants also have a type of immune system that attacks bacteria and fungi. Instead of white blood cells, plants produce an abundance of things called flavonoids. And some very ingenious scientists here at Rensselaer are starting to ask the question, “If it works for plants, might it also work for humans?”

Why bother checking if flavonoids stop the spread of bacteria in humans? The answer is simple: society is running out of ways to kill bacteria. New methods to stop bacteria are becoming essential as the old methods – antibiotics like Z-pak, penicillin, amoxicillin, and the like – become less and less effective.

Despite being very simple organisms, bacteria have developed some exceptionally smart survival systems. As they and their brethren have been bombarded by decades by pills and sticky medicines, they have slowly adapted to survive the barrage. One of these adaptations actually allows bacteria to pump toxic compounds like antibiotics out of their systems before the drugs can leave lasting damage. And so, the antibiotics go in and the bacteria spit them right back out. To combat this, doctors need entirely new molecules to throw at the bacteria. When faced with a new molecule, the bacteria simply will not have the systems in place to combat it and they will be killed.

Of course there are a lot of different chemicals and compounds out there besides antibiotics that will kill bacteria on contact. But, drinking pool chlorine or injecting battery acid is not something I look forward to. I am guessing you are with me on at least this point. So, new drugs to combat bacteria also need to be safe for the very sensitive human system.

Flavonoids have long been praised for their health benefits (eat your kale), but little is understood about their antimicrobial effects. Mattheos Koffas who works in the Center for Biotechnology and Interdisciplinary Studies and a team of researchers at the State University of Buffalo and in the pharmaceutical industry are looking at how effective flavonoids might be in combating bacteria in the human system. The scientists recently published a paper in the journal PLoS One that shared some very promising results on the future uses of flavonoids in medicine.

What they found was that naturally occurring flavonoids in plants had strong antibacterial and antifungal properties. They were also safe to human cells. Koffas and the team then took the research an important step forward by designing non-natural flavonoids in the lab. These new molecules took all the best aspects of the natural flavonoids and essentially turned up the volume.

What they found was that these chemically-synthesized non-natural flavonoids were even more potent against bacteria and fungi. They also appeared safe for human use.

The research provides an important path forward for a new class of antimicrobial agents – flavonoids. Koffas plans to continue to study the potential of these new molecules.

One of the most amazing things about the world of matter is that regardless of how different two objects may appear, they can only be comprised of one or more of just 118 known elements.

So, as different as a horse and a jar of mayonnaise may appear on the surface, they are both made the same stuff (mostly carbon, hydrogen, and oxygen). But, for as strikingly diverse as the compilations of elements can appear, our standard visualization tool for those elements has remained essentially unchanged for the past fifty years.

Ahhh, the periodic table! You will recall its stodgy glory on your high school chemistry walls. This mainstay of chemistry with its simple arrangement of elements in rows (periods) and columns (groups). And because so many of you are science aficionados yourselves, you will likely also remember that the elements are arranged in order of their atomic number. Today, Michael Aldersley, a research associate in our New York Center for Astrobiology, has given the ol’ PT a makeover. Aldersley recently received a U.S. patent for his invention of a three-dimensional periodic table.

Aldersley has transformed the flat and floppy table into an interactive learning tool that literally leaps off the page. The new 3-D periodic table was created by Aldersley as a tool to teach school children about the elements in a new, more interactive way. The table is comprised of several different cardboard or paper sheets with a series of elements printed on them. The different sections break the elements into groups with similar properties (e.g. Earth metals). The students are then instructed on how to cut out the different groups and fold them into a 3-D structure.

The new table lets the student’s interact and play with the table, helping facilitate learning. It more clearly delineates the different groups of elements based on their origins or properties. It also looks a whole lot cooler. The completed 3-D periodic table invented by Aldersley looks sort of like a 3-D map of the RPI campus – the noble gases are the Low Center for Industrial Innovation, the rare earth elements are the Experimental Media and Performing Arts Center…

The complete patent information can be found here.

Aldersley is certainly no stranger to the elements. As a researcher in the astrobiology center he is helping to uncover the elemental starting points for life in outer space. For more on astrobiology at Rensselaer visit them here.

We are all familiar with those news articles that wax poetic about the health benefits of previously unhealthy fare such as red wine and chocolate. Believe it or not, there is actually some science behind the claims. One of things about these former vices that have given healthy eaters a new lease on life is the flavonoid.

Natural compounds found in plants, flavonoids are the molecules responsible for the vibrant and varied colors of flowers. They have also been widely studied to be a strong antioxidant, antiviral, antibacterial, antiobesity, and anticancer agent in humans. But, before you run out and stock up on merlot and milk chocolate, perhaps a better source could be found than something laced with sugar, calories, and alcohol?

One of newest members of the faculty, Mattheos Koffas, is working is his lab to help develop an easy to produce, affordable, and potent way to get your daily flavonoids. He recently published a paper in the journal Metabolic Engineering detailing a way to optimize the production of flavonoids from simple glucose.

A metabolic engineer, Koffas focuses his research on ways to use chemistry to mimic and optimize some important cells that occur in the natural world. Another example is the cell of yew tree bark. Why tree bark? This simple bark is the chemical basis for some of the most potent and widely used chemotherapy drugs in use today. Koffas is taking these cells and looking at the pathways that they use to fight cancer in the body. This information will also help him uncover ways to further increase their potency.

With flavonoids, Koffas and his colleagues use simple E. coli as a means to easily convert simple glucose into beneficial flavonoids. Their simplified process reduces the cost of producing flavonoids in the lab and decreases the productions steps currently required to manufacture flavonoids in factories. The photo above, shows the four steps of the process that results in the production of the main flavonoid precursor, naringenin.

The complex chemistry might not look as delicious as dark chocolate, but the research is an important step toward developing better and less expensive flavonoids supplements or drugs.

At the lab benches, in the board rooms of Fortune 500 companies, before the podium of advanced graduate courses, even within the White House. Today, more and more women are in these places of influence in science and engineering.

One of those successful scientists, Professor Linda McGown, took part in a virtual conference earlier this week on how to continue to foster and support women in science. Called “The Future We Create,” the conference gave 60 exceptional women in chemistry and related fields one minute each to provide some insight into what it means to be a woman in science today.

McGown, who is more formally known as the William Weightman Walker Professor of Chemistry and Chemical Biology at Rensselaer, provides an excellent example of what a woman dedicated to science can achieve. A fellow of AAAS, she studies a broad range of important topics within her lab from genomic DNA, to the origins of life, to nanotechnology.

During the virtual conference she joined former governors, journalists, leading chemists and other scientists, and business leaders to share insight on how to succeed in science. The 60-minute conversation discussed topics like leadership, preserving the pipeline of women in science, the creation of family-responsible policies in the work place, and mentorship.

Here is McGown’s insight from the talk:

Over the course of my 30 plus years in academia, I am constantly reminded of the importance of engaging in conversations with colleagues and students. It is incredibly enriching and productive to reach beyond your immediate area of expertise and discover different ways of identifying and framing the key scientific questions.

If you are teaching more than learning, then you stop growing as a scientist. The way to learn is not only through immersion in your field, but through connecting with other creative individuals who can lead your thoughts in new directions.

I find this is best achieved when research groups are smaller and less confining than traditional large, hierarchical groups that tend to look inward for expertise and ideas.

I hope that in the future, such smaller, interconnected groups will become the model for academic research.

Another participant was Mary Good. Good is an honorary member of our Board of Trustees and founding Dean of the Donaghey College of Engineering & Information Technology at the University of Arkansas at Little Rock. Good is a member of the National Academy of Engineering, a past president of the American Chemical Society as well as the AAAS and winner of the prestigious NSF Vannevar Bush Award. Good talks about the exciting and unexpected places a chemistry degree can take a young scientist. And she would know, having worked for four U.S. Presidents and held positions on the board of several top U.S. scientific companies.

To see all the insights go to http://www.futurewecreate.com/#. Good is Chapter 8 and McGown Chapter 10.

Some ingenous chemists here at RPI are combining chemistry with advanced computation to rapidly compare different protein bindings sites. Their results are both novel and beautiful, earning them the cover of the Dec. 28, 2009 issue of the journal Chemical Information and Modeling.

The interactions between different proteins in our bodies can spell the difference between health and illness. These chains of amino acids keep our cells from turning to jelly, keep our bodies metabolizing food, and regenerate a constant supply of new, healthy cells as old ones die. They are also increasingly being used in medications to correct protein dysfunctions within the body. With such a robust resume, you would think we would already know all there is to know about most of the major proteins in our bodies. But, alas, proteins are also among the most complex molecules in nature. They are constantly folding, resulting in a seemingly completely rearranged structure often within seconds.

Their shape-shifting ways can make it very difficult to predict what their function is at any given time. One of the most best way to figure out a protein’s function is to determine what it binds to. Following a chain of protein binding events gives scientists a road map of a specific function without our bodies. But again, proteins prove vexing as the binding sights on each protein surface are often very difficult to compare to each other because of all the folding and movement on the protein surface. How can anyone expect to find a matching binding site when the pesky polypeptides won’t sit still?!

Professor Curt Breneman and graduate students Sourav Das and Arshad Kokardekar’s article within the publication outlines a computational method that does not rely on the specific molecular composition of the binding sites to determine what the protein it is likely to bind to. As they note in the paper, these aspects of the protein can appear significantly different, but still be drawn to the same ligand (think of these as the glue that draws and hold proteins together at their similar binding sites). Instead, they look at the distribution of shapes as well as the chemical environment to map out of the structure of a binding site and then to quickly compare that to other binding sites. They tested out their new method and found it to be extremely powerful to picking binding sites with identical functions. Check out the image below. One of these binding sites is a lot like the other…

And for those of you who enjoy the bigger picture, these results are extremely important to scientists and doctors trying to develop new drugs using proteins. With more information on what these proteins will interact with in the body, researchers can limit some of the dangerous or uncomfortable side effects that have riddled many protein-based drug trails.

The research is all part of the work coming out of the Rensselaer Exploratory Center for Cheminformatics Research led by Breneman.

By now, all of us at RPI are very familiar with a tiny glycosaminoglycan named heparin. If not, bone up on your RPI research knowledge here, here, and here. But, for those who pay a little bit more attention, the sugar is synonymous with the Robert Linhardt lab. His life-saving work with the famous and infamous blood thinner has captured national attention. And while the big research results, such as his discovery of the first fully synthetic alternative to the current and potentially dangerous version scraped from the bowels of overseas livestock, usually draw all the attention, Linhardt and his colleagues are also still hard at work learning the basics about this very complex carbohydrate.

In a recent paper, Linhardt is among an international group who is splitting apart heparin in a variety of ways to understand how it can be broken down into its separate components. One method of breaking down heparin is with heparinases. In the paper the researchers looked specifically at a heparinase called heparin lyase 1.

Don’t be intimidated by the names. Here is a little cell bio tip. When any biochemical substance ends in the word “lyase” you need only think of the words “cuts up.” Now, put “cuts up” in front of the first word – “cuts up heparin” – and you know exactly what heparin lyase 1 does. Go impress your family during Thanksgiving dinner. “Hey Grandpa, did you know that heparin lyase depolymerizes heparin at the iduronic acid?” Or less scientifically accurate, ”Dad, would you like me break out the poultry lyase to carve that turkey?”

For the researchers, the big questions were what exactly does heparin lyases cut heparin up into and, more importantly, why. Their findings provide important details on the various structural components of the heparinase.

Why spend time studying the spliting of sugar? Well, when people around the world began to get sick from contaminated doses of heparin, researchers, including Linhardt, determined the cause of the illness by breaking down the contaminated heparin with heparinases.  When broken apart, the pieces of the broken puzzle no longer fit together to form true and safe heparin and the contaminant could then be quickly pinpointed. A little more respect for the lyases right?

Source: National Atomic Museum

Meet Simon. The 11,000 lb nuclear bomb was detonated amongst the sand and rocky crags of the Nevada desert the morning of April 25, 1953. Thirty-six hours later and 2,300 miles away, rain poured from the sky onto our humble city, Troy, NY. Forty-eight hours later the Geiger counters in the lab of Rensselaer chemistry professor Herbert Clark were crackling away at surprising levels. The counters closest to the outside wall picked up background radiation levels three times greater than the normal rate of 30 counts/min.

Clark and his students, intrigued by the sudden change, went to work outside. They gathered pavement, leaves, drinking water, and ground water around the city of Troy to test them for possible nuclear rainout. Autoradiographs (a image on x-ray film produced by the pattern of decay emissions for a substance) of the materials showed strong and even distribution of fission products on their surface. Nearby drinking water during the first day after the rainout showed levels of radioactivity 100 to 1000 times greater than natural radioactivity.

This Trojan fallout was documented by Clark in a 1954 volume of the journal Science. The historic article provides a striking look at the relationship between the detonation of nuclear weaponry and the strikingly fast and far ramifications. It was an area that Clark excelled and – as a scientist involved in the Manhattan Project - took extremely seriously. And while Clark did find fallout in Troy, NY more than a half century ago, he was also quick to point out that even though the increases were very apparent, they were never at hazardous levels. As a comparison, that 1,000-fold increase in the radioactivity of Troy drinking water resulted in levels around 1 micro microcurie per milliliter, while water near the actual Nevada detonations sites reached levels 87 times that amount.

Sadly, nuclear science lost a pioneer recently, which is how I came upon this exciting tidbit of Troy history. Herbert Clark passed away last month leaving behind not only his research, but a legacy of study on the powerful impacts of nuclear technology that lives on in the countless Rensselaer students that he taught during his 38 years on the faculty.

NASA

It has been proven. We are not alone in the universe. There are millions of life forms in outer space.

The problem is that we put them there and now we don’t really know how to control them.

Floating along with and inside our astronauts are literally little green men (well technically they are mostly asexual). They are microorganisms, including nasty things like staph.  And they don’t stop multiplying in microgravity. To the contrary, studies are now showing that they become more virulent.  And anywhere there are people, there is bacteria and when bacteria is let loose on say the International Space Station, mixed with a little water vapor from the calm breathing of an engineer on the job, they start to develop biofilms (a microbial metropolis if you will)…on EVERYTHING! These microorganisms are not fettered by mere gravity and can form on the top, bottom, or even inside objects in the microgravity of the Space Shuttle or Space Station or even the astronaut.

Professors Cynthia Collins, Jonathan Dordick, and Joel Plawsky are being tasked by NASA to start looking into these pesky and – in their defense – often beneficial organisms in space and how exactly their unfettered growth can be stopped.

In the spirit of interdisciplinary innovation, each researcher brings an important component to the biofilm-coated table. Collins’ research focuses on microbial communities – how they grow, what they are made of, how the individual organisms, communicate with each other. Dordick is the chemist in this equation and Plawsky the materials expert. Together they can grow, analyze, and stop the growth of a microbial colony using a mix of biology (to grow the microbes in the first place), chemistry (mixing enzymes that kill or stop the spread of the microbes), and materials science (to build the platform that the enzymes sit upon).

Their plan is to get a series of microbial communities and antimicrobial surfaces into space on an upcoming Shuttle mission. Currently, they are in the first stage of their research. They are simulating the effects of microgravity in small centrifuges within the Rensselaer labs and monitoring their growth and investigating various materials surfaces and enzymes for favorable antimicrobial tendencies. You will surely hear a lot more about their work should it make it on a mission. And Rensselaer will have yet another product of an RPI education in space (a few million actually).