Dammit Jim!

It looks like Gravatar has added Identicons and MonsterIDs to their system. I’d been wondering when they would add something like this since it seems like such a simple and useful addition. I was thinking my plugins wouldn’t get much use now but it seems like they’ve gotten quite a few hits in the last few days. Not sure if that’s related to Gravatar or just random but I guess some people are still finding them useful.

So I guess I’ll keep maintaining the plugins since unfortunately Gravatar doesn’t really give you all the configuration possibilities of WP_Identicon or the hand drawn monsters of WP_MonsterID.

Speaking of hand drawn, Lemm, the kind illustrator that drew up the new monsters, has (re?)started No More Tangerines, a blog showing off some of her art. It’s pretty cool to see the progression her drawings go through.

I was doing a bit of background reading and came across an interesting paper about mutating normal bacteria into cancer-fighting bacteria. The paper centers around a single gene called inv (short for invasin) that can give an otherwise mild-mannered noninfectious bacteria the ability to invade cells.

Now this might seem like a pretty bad idea since there are probably enough infectious bacteria in the world already but this was only the first step of the research. Anderson and colleagues attached inv to a genetic switch (normally used for bacterial metabolism control) that turns on when arabinose (a type of sugar) is present. Unfortunately this switch was a little leaky. So even bacteria without arabinose were still infectious. Not ones to let that stop them, the researchers took out the ribosome (protein-making organelle) binding region of the gene, randomly mutated it and tested to find bacteria that were off by default but still able to turn on.

Once they got that working, they decided to attach a sensor to the infective gene. Bacteria often do things like switch metabolisms when they run out of oxygen. The researchers picked one of the bacteria genes that turns on when oxygen is low and replaced the arabinose switch from the previous bit with the oxygen sensing switch from this gene. Again the switch was leaky and they had to mutate it so it stayed off by default. Once that was done they had a bacteria that was only invasive in anaerobic environments. That’s pretty cool because tumors are often anaerobic (since they’re big lumps of fast growing dense tissue).

To go even further, the researchers tried to create bacteria that only turn on when there are many bacteria in one location. This will be useful because tumors often have higher concentrations of bacteria due to leaking nutrients and poor immune response. By creating a switch that only turns on when a bunch of bacteria are present, the bacteria can be further targeted to cancerous cells. To do this they used a gene from an ocean-dwelling bacteria that only turns on when many bacteria are present (the ocean bacteria uses the gene to detect when it has reached the light organ of squid). It seems odd that bacteria can communicate but it comes down to a simple mechanism made up of two genes. One gene encodes an enzyme that makes a chemical, called AI-1, that easily disperses in and out of the cell membrane. The second encodes a gene activator that is turned on by high concentrations of AI-1. When there are many bacteria, the environment becomes rich in AI-1 and the gene activator turns on even more production of AI-1 and gene activators. This positive feedback causes creates a sensitive switch that switches quickly from all off to all on when bacterial concentration crosses a certain level. By linking these genes to the infectious inv gene, the researchers created a bacteria that was only infectious when in high concentrations.

So now we have bacteria that might be able to selectively infect tumor cells. By combining this selective invasiveness with cell killing or immune response activating mechanisms, bacteria could become helpful tools for treating cancer (although there is still a pretty long way to go). The paper makes it look easy but that must have taken a good bit of work to get it all working so nicely. They ended up using DNA from three different bacteria species and many different bacterial systems. It’s always really cool to see how scientists can take DNA “parts” and combine them together to create new and useful functions and even edit the DNA directly when the parts don’t fit correctly.

I guess the next step in the research is to figure out how to get a bacteria to sense both an anaerobic and a high density environment. This might be a bit tricky since the two sensors would have to interact but I see some of the same researchers also have a paper on creating bacterial AND gates so I’ll have to give that one a read too.

Reference

Anderson, J., Clarke, E., Arkin, A., Voigt, C. (2006). Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria. Journal of Molecular Biology, 355(4), 619-627. DOI: 10.1016/j.jmb.2005.10.076

It looks like I’m the next host of the biology blog carnival Tangled Bank (if you’re not familiar see the last couple sessions for some good collections of biology reading). Pretty exciting since it’s my first hosting. Feel free to drop off any suggestions for stories in the comments here or email host@tangledbank.net (I think those end up coming to me somehow).

There’s a new stories about a “rare giant sea turtle” being caught and eaten in the Gaza Strip going around now. I dug up a video for it and it’s definitely a leatherback so I figured I’d throw in my two cents since I just posted about leatherback turtles.

Here’s the video. Sorry if there’s an advertisement in front of it. I’m not making anything from it but it was the only source I could find. They do show the turtle being killed so it’s not really fun to watch.

A few corrections to the video first, it’s not “thought” to be a leatherback. There’s no mistaking a leatherback for any other turtle. That’s a leatherback. The fisherman says it’s 600-700 kilograms. I’m never good at estimating weights but the biggest one weighed in Canada so far was just a bit above 600 kilograms and that one looks on the small side so probably less than 400 kilograms (still a big animal though).

I thought it was odd they were talking about eating the meat since I’d often heard that leatherback flesh is poisonous but I can’t find a good citation for that and there do seem to be substinence fisheries for them so I guess leatherbacks are either edible or only occasionally poisonous. Also, I’d heard of people eating the eggs for ‘viagra’ effects but never the blood or the whole ailing children thing. I’m not sure what conditions are like in Gaza but if they’re not killing the turtle for necessary food, it really seem like a shame to kill an endangered species for bogus penis enhancement.

Also the fisherman says the turtle ruined a bunch of fishing gear. This is actually a common problem with leatherbacks. They don’t seem to have a way to reverse directions. So if they run into a net or even a loose rope in the water, they can easily become entangled. This can often end badly when the loops get caught around their neck and choke them or the tide rises while the ropes hold them underwater (or people decide to drag the turtle ashore and drink its blood to improve their sex lives).

In more encouraging news, the Reuters article ends with this:

A smaller Leatherback was caught off the Gaza coast last month but the turtle was released after fishermen discovered it carried a tag classifying it as an endangered species.

Thanks to William F. Landell for pointing this story out in the comments.

I’m just finishing up a contract making maps of telemetry data from satellite tagged animals. Basically just finding daily positions and making a pretty map out of them. It’s taken me a little while to write the code for it and while I’m not sure a whole lot of other people will be able to use it, I thought it might help one or two people out if I posted it online. The boss ended up wanting that as part of the contract too so pretty good motivation.

It’s not completely automatic but if you want pretty hexmaps of animal positions and you’re reasonably proficient in R (with maybe a little knowledge of GMT), then this may save you a good bit of time (or least let you skip some of the stumbling blocks I ran into). There’s also a function to read the output from the Douglas Argos Filter which could be handy if you’re working with Douglas filtered data in R.

The project page is here. Feel free to leave any comments or suggestions below.