picture of Mark

Mark A. Engelhardt, PhD

Samuel Lunenfeld Research Institute
Toronto, ON, Canada

engelhardt [at] mshri.on.ca

link to curriculum vitae

link for collaborators

Welcome to the home page of Mark A. Engelhardt, currently of Toronto, Ontario (at the centre of the map on the right.) I'm very happily married to Erin Engelhardt, and we have the joy of two wonderful daughters. thumbnail of a map of North America

I am currently a postdoctoral fellow at the Samuel Lunenfeld Research Institute in the labs of Tony Pawson and Mike Tyers, interested in using synthetic biology and invertebrate flatworms as avenues to understanding the working of biological systems. My studies use a combination of experimental and computational approaches.
thumbnail of a photo of flatworms

I completed my graduate studies in the labs of Dan Herschlag and Vijay Pande at Stanford University. If you are visiting here because you are interested in working with either group, please feel free to e-mail me (see the above address) with questions.
thumbnail of Stanford logo

I've had the great fortune to work on a variety of cool scientific projects, including:
• Discovering a new species! (These cute little guys seem to have my initials.) Engelhardt et al, JAM 90:237 This was part of some work I did with Richard Swannell to study the way that microorganisms degrade oil after oil spills. thumbnail picture of bacteria
• Studying prostacyclin (a molecule involved in why aspirin works the way it does, among other things) and how its interaction with its receptor on the outside of cells causes effects inside cells. I think this area of research, called "cell signalling," is really fascinating - on a large scale, it encompasses every interaction of every living thing with its environment. thumbnail image of prostacyclin
• Investigating the cooperativity of interactions within RNA structure! (The large RNA I studied folds into a compact structure with the help of mutually reinforcing interactions within the molecule.) Engelhardt et al, Biochemistry 39:2639 thumbnail picture of an RNA secondary structure
• Applying computational models to smaller RNA molecules to test our understanding of them, as well as learn new things about them on a level that is not accessible by experiment. Sorin et al, JMB 317:493 thumbnail picture of RNA loop folding
• Applying computational models to try to understand how a long highly charged polymer (i.e. RNA) interacts with clouds of metal ions to generate the long floppy polymer that can fold into useful structures and do all the jobs it does in your cells. The image on the right links to neat little video taken from one of these simulations. I have the great fortune of wonderful experimental collaborators for this work (noteably Yu Bai of the Herschlag lab), who make possible the comparison of my simulation results to empirical 'real world' tests. This is a work in progress and has not yet been published. movie showing ions around a helix

You may be thinking, "Well, I can understand how discovering a new form of life is cool, but what is RNA, and why do I care about it?"
• First off, check out the wikipedia entry on RNA for a fairly understandable explanation of what it is.
• Why should you care? RNA is the stuff of life! RNA acts as a go-between between DNA and pretty much everything that DNA does: all that genetic information you carry around uses RNA to get its message across (for this reason, much of the RNA in your cells is called 'messenger RNA'). Scientists have also shown that RNA can do other things (e.g. catalyze chemical reactions, leading the to 1989 nobel prize), and more recently that it does a whole LOT of things. For examples, check here (the function of the ribosome, the central player in the decoding of DNA, is conducted by RNA!) and here (RNA molecules can interact very specifically with molecules in cells to control metabolism!) and here (regulation of genes in the brain by very small RNAs!).
• Think about how studying molecular signalling is about studying the way that every living thing interacts with its environment. Similarly, the messages that RNA carries are a critical part of the way that every living thing interacts with its genome (the part of you that does not come from your environment).
• "Ok, RNA is important. Why study its structure?" Because, for large molecules, the way that they 'fold' (their 'structure') determines how parts of them are arranged with respect to other parts of the same molecules and other molecules in the cell, and, in the end, is what determines whether they can do their jobs.
• Last (and probably least), you can use pictures of RNA and cool free graphics utilities to generate neat sidebars like the one on the left.