Tuesday, April 24, 2007

Google Tisp (beta)


Notice the "PhD" on the sewage dude.


Monday, April 23, 2007

My middle-school biology teacher died

I haven't seen him for almost nine years, but getting notice today still sent a shudder down my spine. Thanks to his enthusiasm I always enjoyed biology and he was probably the first who encouraged me to study a biological science subject.

Farewell Prof. Kydlicek, you've been a true friend.

Silent protest

A picture says more than a thousand words.


Friday, April 20, 2007

«The apple experiment» is finished

Since the little bugger wasn't moulding after a considerable time-span (5 months!), I eventually ate it last week in a peculiar hunger attack [1]. Luckily, I was smart enough to collect photographic evidence about my mission, as «some» folks have taken my alleged secretiveness as a serious affront.

About the culinary experience: admittedly, it was a little to sweet for my taste, but what do expect after somewhat more than 5 months of ripening?

[1] I can see the next Sun headline: «Poor student had to eat decaying apple! Authorities are shocked!»

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Wednesday, April 11, 2007

We just had a fire-alarm

... in my place. This is a pure procrastination blog entry. Thesis word count: 3300. Days until deadline: 12. Motivation: dependent on caffeine levels [1].

[1] That I'm writing about adenosine receptors is obviously a macabre joke. Well, at least I now know that it makes no sense to excessively drink small portions of coffee; gulping down a whole can is much more effective from a pharmacological point of view.

Update: It's now 2am and I managed to add amazing 500 words within the last two hours. Someday I'll have to work out the intricate relationship between the lack of daylight, excessive but concentrated caffeine consumption, and why my productivity increases by the factor ten when those criteria are met [2]. Good night, I'm going to listen to whatever story my matress is willing to tell me.

[2] Another hypothesis claims that it may have something to do with my roommate usually playing computer games during the day.

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Friday, April 06, 2007

GM crops: insect resistance

Insect pests of the corn borer or the cotton boll worm represent a major threat to maize and cotton farmers respectively. Both insect’s larvae feed on the inside of the plant and are therefore difficult to reach by sprayed insecticides.

European Corn Borer

The Gram-positive soil bacterium Bacillus thuringiensis has been long known to produce a range of crystal (Cry) proteins. These proteins - commonly known as Bt toxins – become cleaved in the insect’s midgut bind specifically to cell-surface receptors. The cells are lysed by pore formation via an oligomerisation step after recognition. Subsequently, larvae stop feeding and starve. Due to high specificity the Cry proteins are toxic to a very limited range of insects and are harmless to other organisms; no toxicity to mammals, birds and fish.

In the pre-GM era, Bt toxins were used as a biological alternative to chemical insecticides, however, the costly production prevented a major breakthrough. The introduction of Cry genes into plants circumvents this problem, and a Cry-protein content as low as 0.1% of the total cell protein suffices to protect cultivars from certain insect pests. Accordingly, Cry genes were engineered into cotton and maize, and found successful application in the US (29% of the maize, 41% of the upland cotton), Australia, China, India and the Philippines, known as Bt variants.

As an unexpected positive side effect, the grains of Bt maize contain lower amounts of mycotoxins such as aflatoxin and fumicosin, which are risk factors for liver carcinoma.

Another approach to achieve insect resistance is based on protease inhibitors, which are produced by some plants protecting against animals. The protease inhibitors disrupt digestive processes leading to starvation, enabling broad insect resistance. On the downside, protease inhibitors work on a variety of species and the plants needs to be cooked before consumption to inactivate the protease inhibitors. This may also have a lot of ramifications on the surrounding fauna when bred outdoors.

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Tuesday, April 03, 2007

The exasperating issue of GM plants

25-11-2016 - A little pre-script from a 10-year older Mike: Although I haven't done any deep research on the matter, there seem to be diverging opinions on the safety of glyphosate. The Roundup-resistant GM plants themselves are harmless though (unless of course they are an invasive species, which is a completely different ecological matter).

As I have reached my revision period, I might as well contribute to public education and write about some of the topics I tackled in this year's lectures. One of the most prominent and controversial issues in the modern era of genetic engineering revolves around genetically modified organisms, mainly plants.

The public debate is going nowhere, because protesters always have the loudest voices, usually only spreading their misinformed ideologies of general devastation and death. Yes, if we are not getting killed by an upcoming ice-age, volcano eruption or nuclear fallout triggered by a bunch of terrorists, plants are going to wipe us off the planet. Nature is cruel.

Now that we considered and ignored the general gobbledygook [1], we can face the facts. Genetically modified plants hardly differ from their «normal» pendants' genotype; meaning that they typically carry one to a couple of additional genes. The big advantage to conventional breading is the possibility to introduce specifically a single gene, which may be of any species as long as one can get a grasp on the cDNA and it can be expressed in plants.

The most frequent traits embrace herbicide tolerance, insect resistance, virus and fungal resistance, modified nutritional value and several other traits that exploit plants as bioreactors for the production of e.g. pharmaceuticals [2,3].

glyphosateA widely used herbicide is glyphosate that interferes with plants' shitimake pathway, which is responsible for the production of many aromatic metabolites, including some amino acids [4]. As animals don't have this pathway, glyphosate only exhibits low toxicity for animals; it is also cleared quite rapidly by soil bacteria. The herbicide has found extensive application in e.g. killing plants off rail tracks even in the pre-GM era. In GM plants tolerant to glyphosate, an additional EPSPS gene from the soil bacterium Agrobacterium tumefaciens has been introduced which isn't affected by the chemical. This allows selective growth of the GM crops, decreased the use of herbicides applied in tillage, improved the soil quality and therefore enabled crop rotations [5]. Other common herbicide traits include tolerance against bromoxynil and gluphosinate, whereby both approaches rely on the detoxication of the compounds by the transgene product.

Herbicide tolerance has been engineered into many crops and is by far the most successful GM trait. To show some figures: 81% of the USA's soybean crops in 2003 was glyphosate-tolerant [6], facilitating effective cost-cuts in herbicide expenditures (and therefore environmental burden) which easily amortise the additional technology costs for GM seeds.

More about GM later.

[1] Thanks Dr Colquhoun for that great word.
[2] I haven't heard anyone crying out that we abuse Escherichia coli for the production of insulin.
[3] This list is not supposed to be comprehensive in any way and only provides a rough outline.
[4] The exact target is EPSPS, 5-enolpyruvylshikimate-3-phosphate synthase.
[5] Normal herbicides are not cleared quickly enough from the soil and would kill crops different to the ones grown.
[6] Benbrook, CM. 2003. Impacts of Genetically Engineerd Crops on Pesticide Use in the United States: The First Eight Years. BioTech InFo Net Technical Paper Number 6.

My apologies for not providing all the references, but this is merely a blog, not a scientific journal.

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