It’s time to look around those blogs again. On offer this week: The Tree of Science, a perfect Western at the first attempt and how to kill someone using an IPod Nano. Read more »

Tuesday, I posted on Bt Corn as an example of a “good” genetically modified (GM) crop whose benefits vastly outweigh its risks, risks which are akin to the development of antibiotic resistance in the health sector. Here, I thought I’d mention Pharma Corn as an example of a “bad” GM crop, in my opinion at least.

The PLoS Biology article from last time touches on Pharma Corn as well, but only for a short summary. Check out the Journal for Agrobiotechnology Management and Economics (2005) for a more comprehensive article on Biopharming and the Food System.

For Pharma Corn, gene flow *is* a serious concern, and extensive measures are required to contain Pharma Corn. Just think of the consequences of hybridization between corn engineered to manufacture drugs and corn intended for human consumption. What happens if you inadvertantly consume a drug to which conflicts with your body’s chemistry or your correct prescriptions, just by eating an ear of corn.

But okay, the FDA is known for tight regulation of such things, and Pharma Corn doesn’t require much acreage, making containment easier. But look at the situation:

Given the potential risks and liabilities associated with accidental commingling with the food supply, and facing the daunting task of ensuring near-100% containment, the food and the biotech industries have taken a precautionary approach to pharmaceutical crops and support for risk-based regulations. The Prodigene incident case in 2002 illustrates the type of risks facing the food industry. In Nebraska, during the 2002 growing season, APHIS inspectors discovered “pharmaceutical” volunteer corn growing in a soybean field. The corn was from the previous year, when Prodigene had tested a pharmaceutical corn to produce a swine vaccine. As a result, both the harvested soybeans (500 bushels) and the entire soybean load of 500,000 bushels in local elevator were quarantined. In another accident in Iowa, the USDA forced Prodigene to burn 155 acres of conventional corn that may have cross-pollinated with some of the company’s pharmaceutical plants. In both cases, the infraction was viewed to come from Prodigene’s failure to adhere to permit protocols issued by APHIS. Prodigene was fined US$250,000 and required to pay approximately $3 million for the cleanup costs and disposal of contaminated corn and soybeans.

Clearly, “prodigious obstacles” summarizes the situation for Pharma Corn as a agricultural product of the future.

You are working late in the lab and you need to do a transformation, but sod it, you don’t have any antibiotic plates on hand. So you go on the hunt to see if there are any secret stashes anywhere in the lab (you can find secret stashes in every lab if you look hard enough).

And lo and behold, come across the ampicillin plates you poured 4 weeks ago then forgot about. But they are old, so how do you know if they will give adequate selection? Should you use them? Read more »

Last December, I posted a running question - What’s with Europe’s Opposition to GMOs? - and moved on to other topics. This week, I’d like to contrast “good” versus “bad” genetically modified crops. Beginning with the former, a prominent example of a “good” GM crop is Bt corn.

In 2003, PLoS Biology ran an article on Genetically Modified Corn that spent a good deal of time on Bt Corn. The highlights: Read more »

So, you see an ad for your dream job and, of course, decide to apply. But how do you make sure you get it?

Your chances of getting any given job are mainly influenced by two things; your technical abilities and how you come across in the job interview.

At short notice, you can’t do too much about your technical skills, apart from making sure you present them optimally in your CV/resume but you can do something about how you come across, and that can set you above the competition in the eyes of the interviewer.

One approach, according “job interview master” Vj Vijai is to use his tried and tested formula, which he describes briefly in the following short, entertaining video.

Let us know what you think of his ideas in the comments.

Photo: language translation

Here’s a list of blog posts worth passing along from the past couple of weeks, in the order I bookmarked them.
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cDNA (complementary DNA) is an extremely useful tool - gifted to molecular biologists by RNA viruses, which fortunately “invented” the reverse transcriptase enzyme that allows us to make the stuff.

RNA viruses use this mRNA dependent DNA polymerase to convert their single-stranded genome into double-stranded DNA for integration in their host’s genome. But in the lab, it can be harnessed to make cDNA copies from mRNA templates. That means that reverse transcriptase can be used synthesize a cDNA copy of every mRNA that is present in an mRNA extract, and that’s a pretty useful thing to be able to do.

Because from those cDNA copies you can do things like PCR amplify agene of interest, or make a cDNA library and probe it for a specific sequence or activity. There are several advantages to using cDNA as opposed to genomic DNA for doing this:

• No introns: Eukaryote genes commonly contain introns (non-coding sequences). These are removed after mRNA synthesis so cDNA contains no introns. This means that a cDNA copy of a gene can be isolated as a single, intron-free fragment. Prokaryotes don’t have introns so this is not a problem if you are working with bacterial genes.
• More template: There are multiple copies of mRNA for every copy in the genome, so means you will get more copies per cell of the sequence of interest.
• Less background sequence: Because only sequences that have been expressed as mRNA will be present in a cDNA prep, there is less background sequence compared to genomic DNA, which makes it less likely that your primers will bind non-specifically.

That’s the basics but for the rest of this article I’ll be focusing on a topic that might concern those of you who need to isolate genes with tissue-specific expression profiles. For this you need to synthesize cDNA from the entire mRNA complement of your tissue of choice then use this as a template to amplify your target gene.

But how do you choose the right tissue to isolate your cDNA from? I’ll tell you how. Get it wrong and you could have to re-think your strategy - I’ll tell you how to do that too. Read more »

It seems that everyone is throwing their hands up about gas/petrol prices these days. In the US, gas prices have now reached $4/gallon, while in the UK, they are hovering around a whopping $10/gallon.

But what’s all the fuss about? A lot of effort goes into producing gas - you have to find, extract, refine, transport, and of course, tax it (especially in the UK) none of which is cheap. So maybe gas consumers are getting value for money.

Well, compared to lab workers they certainly seem to be. For some of the liquids available for molecular/cell biology, some of which are much easier to produce than petrol, $4 or even $10/gallon is peanuts. Here are some examples to help keep things in perspective next time you are at the pump. Read more »

Did you know that it is more likely that the next graduate student you meet in the US is from one of two Chinese alma mater’s than from any other U.S. university, including UC Berkeley, Cornell University, and the University of Michigan, Ann Arbor? That’s a striking figure, the topic of a tiny comment in last week’s Science: Top Ph.D. Feeder Schools Are Now Chinese.

While I may not have known that statistic however, it’s not surprising, as any past or current graduate student will tell you. There are a lot of non-American’s in American grad schools. Props to those non-Americans - they worked hard and have earned it.
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In this week’s around the blogs - biorap, one-ton tomatoes and a PCR machine that fits into your pocket. Read more »