Zombie Enzymes

Biomimetics is a field of engineering that seeks to learn new engineering design principles and technologies from nature. As an engineer or scientist, suppose you wanted to move on in your career, become a MAD scientist (generally self-employed, better pay, more time at home ...), and take over the world with a zombie army?

The technology isn't in use yet (by humans), but never fear. Nature is here. Biomimetics can serve you, be you mad scientist, disgruntled university student, or Halloween prankster. It's all in the enzymes.

A recent article in the New York Times Science section reviewed the current issue of the Journal of Experimental Biology. The whole issue is dedicated to parasites in nature that turn their hosts into zombies and force them into subservience.

Viruses - A Vector to Remember

Invisible killers. An unsanitary butcher in Indonesia shakes hands with a tourist who sneezes in the airport and contaminates a traveler to New York who exposes a taxi driver who dooms the city to mortality en masse. Is this your view of viruses? It certainly is the view of the average person on the street (who won't want to shake your hand after you broach the topic of viruses). Perhaps your first thought was of a computer virus and a blue screen error. Viruses are bad, right?

WRONG! Viruses can be extremely bio-awesome, if you give them a chance. They are a hot tool in biotech, and one that is under-appreciated.

Bioinformatics: Genome Assembly

Assembly-Solving Really Big Puzzles

One of the primary duties of a Bioinformacian is to combine little pieces of DNA into bigger pieces. When scientists sequence the genome of a species, it doesn't spit out of a machine in one magical lump. Sequencing machines (that read DNA sequences) produce lots of little sequences of DNA (strings of A's, T's, G's, or C's) 50-700 base pairs (bps) long. They spit out millions of them. The challenge of bioinformatics is to assemble those millions of short reads into the full sequence of the genome. Imagine shredding a textbook and putting the pieces back together. This process is called (no surprise here) Assembly, since we're assembling pieces of DNA into a larger sequence. This process really made a splash in 2003 when the human genome was sequenced ...

Bioinformatics: DNA = Bioinformation

CLC Bio

Rocket Science is for Kids (No offense to all the rocket scientists out there)

As we've discussed, informatics by itself is only about as cool sounding as cutting grass. But we're not talking about just any old informatics. We're talking about bio-informatics. In this case, the coolness factor increases by the number of bases stored in GenBank. You'll find out how many that is in a minute. For now, just know that bioinformatics is really cool and really, really important for modern biotechnology. So important in fact, that without it, biotech wouldn't exist. My job is to convince you that such is the case. We'll start by talking about DNA sequence. We'll talk about where it comes from and what it's used for. 

Battling Malaria with ... Baker's Yeast?

According to the World Health Organization (WHO), malaria killed an estimated 655,000 people, mostly children, in 2010.  Artemisinin is an effective antimalarial  drug recommended by the WHO to be used in combination therapies. Artemisinin-based treatments could prove to be a silver bullet for the malaria scourge affecting developing areas of the world. There's just one catch: artemisinin is derived from Artemisia annua (Wormwood), an herb. Artemisia farming depends on the weather. Artemisinin may be only a small, small part of the overall plant mass, meaning that a great deal of resources (water, land, etc) are needed to produce small amounts of the desired drug. Thus, the current method of artemisinin production is unpredictable and inefficient. Queue, genetic engineering.

Molecular Biology - The Portal to Biotechnology

Suppose a researcher wants a cell to produce a particular protein—say, Green Fluorescent Protein (GFP). Now that we understand the central dogma, the researcher's path is pretty straight forward. First, the researcher would need a copy of the gene, usually from an existing source, like jellyfish DNA. There are many ways to insert the gene into a cell, and more ways are being explored. Let's say for now that the researcher puts the GFP gene on a plasmid (a circular piece of DNA that is self-replicating in a cell). To cut-and-paste a piece of DNA, scientists use restriction enzymes, which are like molecular scissors. They recognize specific sequences of the DNA alphabet and sever double stranded DNA in predictable ways. DNA ligase is like the glue, that bonds strands back together. 

Setting up Shop: RNA to Proteins

Ribonucleic acid (RNA to its friends, including us) is a sibling to DNA. You may have noticed from the name that RNA is really just DNA without the "deoxy". Much of what has been said about DNA applies to RNA as well. RNA contains genetic instructions, is made up of an alphabet, can base pair with DNA or other RNA strands. However, there are some crucial differences. The alphabet is different—instead of T, RNA uses a U (for Uracil). While DNA is usually found as a double-stranded molecule, RNA is almost always single stranded.  You can think of RNA as a working copy of the DNA, a copy that is intended to be recycled after use. RNA is disposable, because it's main purpose is to serve as a template for protein machinery and protein machinery is a huge part of biotechnology.

Where it all begins - DNA

DNA, known to biochemistry geeks and molecular biologists as Deoxyribonucleic acid. 

DNA Stores Information

This is the information center of the cell. It contains instructions for the cell that describe how to reproduce, how to communicate, how to maintain itself, how to eat, how to sleep—put simply, what the inputs and outputs of the cell should be.  The DNA performs the same function in a cell that blueprints,  and managers play in  a factory. Blueprints determine how the machinery is put together, and managers  decide which machines and hardware to keep in the factory. DNA provides both functions by determining which proteins are created, and how those proteins are structured. 

Cellular Factories

Think of cells as tiny factories—imagine a chocolate factory—where there are inputs and outputs. 

In a chocolate factory, the inputs are cocoa beans, sugar, milk, maybe some nuts or fruit. Do we need to know the 40,000 character IUPAC name for cocoa to understand this? No! What are the outputs of a chocolate factory? Sweet, melt-in-your-mouth chocolate bars that can potentially be added to s'mores, which can then be input to your cells. The really interesting part of this process (overlooking the delicious chocolate output, of course) is the process inside the factory that turns raw inputs into a useful output. A lot of work went on inside the factory to make bitter cocoa beans into something worth eating. So it is with cells.

Biotechnology - the Alien World Inside

To understand biotechnology, it's best to start by understanding the "bio" part before moving on to the "technology".  

Building Blocks

As diverse as life on earth is, ranging from tiny bacteria to blue whales and aspen clonal colonies, there are simple organizational rules that tie everything together. Life is made up of building blocks that are shared by everything from ancient dinosaurs to paleontologists.

Don't Freak Out

We'll discuss what those building blocks are, so that the "technology" later on will make sense. If you're thinking "I hated third period biology precisely because I didn't get all that biochemistry mumbo jumbo!" don't bail on me now.