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Showing posts from 2010

Brief update: Testing my PCR thermocycler

The first tests gave me temperature readings that were off by 30 degrees C from what I'd expect from the thermocycler program I was running. Next up are some auxiliary tests to make sure my setup isn't producing errors. I strongly suspect it is. However, that'll have to wait until the current day job project thing is done, which is keeping me away from Vienna and thus my lab for five days a week. Lesigh.

Genetic engineering bits and pieces: Codon bias

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Random thing I learned today: One of the many details one has to pay attention to when genetically modifying an organism revolves around a thing called codon bias. What led me to this bit of information is part of a writing assignment for the course "Laboratory Fundamentals of Biological Engineering", taught at MIT. Here's part of the documentation for this course. The question was this:
"Would you expect the phage to tolerate p8 modifications that encode all Leucines with the CTA codon instead of the CTG codon? Would you expect the phage to tolerate these same modifications to p3?"
When the authors ask whether the phage would "tolerate" this or that modification, I assume they mean to ask whether the phage would still be active and reasonably effective after the modification. Leucine is an amino acid. p8 signifies the protein VIII of bacteriophage (a virus that infects bacteria) M13. Proteins, of course, are chains of amino acids. A codon is a triplet …

Testing my PCR thermocycler, Part I: Setup

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Way too long ago, I bought a used thermocycler on ebay. It's quite a monster, a Perkin Elmer Cetus, and I've been meaning to test it. I initially thought about testing it simply by running a PCR and seeing whether I get the expected results, but there are so many sources of error in this plan that I've discarded it. There are just so many things that can go wrong with a PCR, even if the thermocycler works perfectly - not least due to my very limited lab skills.
So instead, I'm going to measure the temperature of the heating block over a few cycles. There are even sources on the internet that document the temperature profiles of other thermocyclers, so I can use those as a reference. All in all, this approach does not only yield quantifiable results, but seems more attainable to me. Plus, this will (ideally) produce a setup that allows me to test other thermocyclers, too.
So. After some investigation of temperature sensors in general and in particular, I decided to use an…

Ghetto Sanger Sequencing, Part I

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Here are some ruminations about the first steps I'm taking towards a kind of Ghetto Sanger sequencing contraption:
Basically, what I'm trying to build is a setup that will automate some of the steps in Sanger sequencing. One of these steps involves automatically starting a gel electrophoresis, which includes placing the gel into the buffer-filled gel box, firing up the power source, monitoring the gel's progress, shutting down the power source in time and removing the gel from the gel box. One of the problems here is that gels are somewhat difficult to handle for something like a robotic arm. It's much like trying to transfer a slab of Jell-O into a water bath and then out again. So my idea was to use plastic slides with gel-filled channels. Let's call them gel slides for short. The material should be non-conductive, transparent, and withstand a certain a mount of heat. Here's a sketch of one, with 8 channels, 6 of them are sketched as being gel-filled:


Initially, …

The German Pirate Party Gender Debate: An outside view

Intro: I am not a member of the Pirate Party, nor of any other party. I briefly considered joining the PP, but changed my mind. I have not actively participated in said debate, and I've been following it casually rather than obsessively. Still, here's the impression it left me with:

The gender debate was a classic example of political conflict, where the participants hold very different beliefs, values and perceptions of what the world is like. What I expect from a good politician is that they can relate to their opponent on some level, accepting that just because someone doesn't agree with them doesn't necessarily mean they're wrong, hostile or just plain stupid. I expect them to understand that in a complex world, there are many valid experiences and many valid viewpoints, and that politics is about reaching an understanding between this multitude of positions.

What the Pirate Party (through many of its members, sympathizers and leading voices) exhibited, was prett…

Term confusion: Synthetic biology, Biohacking, DIYbio

There seems to be some confusion as to what these concepts mean and how they differ. I'll make an attempt at clarification and explain what these three terms - Synthetic biology, DIYbio, Biohacking - mean to me.


Synthetic biology (synbio): This is an academic field of study that moves the focus from biology as an activity of observation to one of manipulation. One motivation here is that of understanding by synthesis, much like a beginning electronics enthusiast would build a circuit from scratch to understand how the different components interact, what happens when you leave out one component, how the behaviour of the circuit changes when you use a different resistor etc.
Apart from this, one important idea in the synbio community seems to be that biotechnology should become a true engineering discipline, which requires standardization, abstraction, modularization, and componentization. This is the spirit behind BioBricks and the Registry of Standard Biological Parts.


DIYbio: Do-it-…

Gene Assembly in Ciliates - A glimpse into biological information processing

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When researching material for a term paper on biocomputing, I came across a fascinating group of critters called ciliates. Ciliates are unicellular organisms that process their genomic information in a peculiar and unique way, one that was fascinating to study for the computer scientist side of me. In ciliates, we find a very illustrative example of how biological systems use structure as information. Plus they use pointers and linked lists.

There they are. Some ciliates. [Image from http://www.liacs.nl/~rbrijder/views_gene_assembly/]
Ciliates, unlike other eukaryotes, have two different kinds of nuclei: macronuclei and micronuclei. A macronucleus is used in the everyday operation of the organism, for synthesizing the proteins it needs to survive. A micronucleus only comes into play during sexual reproduction (I'm stressing this because ciliates can also reproduce asexually). During sexual reproduction, two ciliates recombine their genetic material. The result is somewhat unusual: i…

Follow-up on "To GM or not to GM?"

In a previous post, I wrote about the controversy around a toxicity study of Monsanto crops. This post got a very valid comment, which I'd like to respond to here.

Paul wrote:
"de Vendomois' statistics are poor and not applicable to the Monsanto research data they used. The funding for their research was also funded in its entirity by Greenpeace. You have to ask yourself why Greenpeace/de Vendemois used the statistical approach they did knowing its flaws (as pointed out to them by the European Food Safety Authority in 2007). A cynic would suggest they conspired to use whatever method appeared to shed a negative light on GM crops. Would this collaboration have published truly independant research that showed no difference in toxicity between GM and Non-GM plants?
I'm no fan of multinational corporations profiting from our basic food needs, but the dodgy, deceitful and blindly prejudiced approaches used by NGOs such as Greenpeace as part of their scaremongering campaigns …

Google Xistence - a new approach to identity

It's a public secret: The world of social networks is about constructing identity. Let's be honest: Every one of us has probably tweeted about the cool club we've been to, or what airport we're currently stuck at, or that we're reading poems in some cool foreign language, to make our lives appear intriguing and cosmopolitan. Social networks are as much about constructing identities as anything else. They have enabled a construcivist approach to that elusive beast, identity, and Google Xistence is merely taking this a step further.

Inside rumours that shed a bit more light on how Google Xistence works have reported that there will be a host of preset identities to mix and match - start with a "Renaissance Man" baseline, then throw in some "World Citizen" and "Political Activist", and Xistence will generate status updates, photos, locations and more that fit this synthetic persona.

But who wants to be stuck with a static identity? This is …

To GM or not to GM? Another look at the data...

A recently circulated paper by Vendomois et al takes an independent look at data from food trials of genetically modified (GM) corn on rats. The data was originally obtained in studies conducted by Monsanto as part of the application for market approval of these GMOs. I'd like to highlight a few points here. But first, some introduction.

The original data stems from a trial where a population of rats was fed different kinds of GM corn over a period of 90 days. The GM crops in question were Monsanto's NK 603, MON 810 and MON 863.

NK 603 is one of the Roundup Ready crops. Roundup Ready crops are genetically engineered to withstand large doses of Monsanto's herbicide Roundup. The idea is that fields can be sprayed with Roundup, the genetically engineered Roundup Ready crops survive, and all the weeds around it die. Let it be mentioned here that this approach has drawbacks all its own, as weeds have started to develop a resistance to Roundup over the years, which led to ever in…