This week’s around the blogs focuses on lab life and impacts of science on society. That’s a big area to cover, but there are still only a handful of really noteworthy discussions in the last couple of weeks on the topic. Check ‘em out.
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Multi-tasking used to be my favourite way to get ahead.

During my PhD I saw others around me working extremely long hours in the lab and not really having much of a personal life and quite early on I made the decision that this was not for me.

Although I enjoy my work, having a good life outside the is also very important. Also, I found that if I worked very long hours then I tended to be far less efficient overall.

But, I still wanted to get through as many experiments as possible. So I also made the decision that my approach would be to work a regular 8 hour day and be as efficient as possible during that time. My basic recipe for an efficient working day was: Read more »

We have had a rush on time and money saving techniques on Bitesize Bio in the last few weeks. Ways to re-cycle electroporation cuvettes, reduce gel buffer costs, do fast restriction digests and re-cycle midiprep columns have all been suggested.

In this article I’ll add the possibility of using a microwave to sterilize or decontaminate growth media. From the outset I’d like to say that I am not too sure about this, but I’ll make the case and you can tell me what you think.

Normally, growth medium is sterilized or decontaminated using an autoclave. Autoclaves are generally expensive, energy-hungry beasts that (in my experience) break down a lot so I would be very happy to use them less if I could.

Decontamination using microwaves.

The case for using microwave ovens for decontamination of cultures or materials was made back in 1977 by Latimer and Matsen. They showed that 1-5 minutes in a conventional microwave was sufficient to decontaminate 5mL cultures or petri dishes of common clinical pathogens including E. coli, S. aureus and K. pneumoniae. B. subtilis spores proved a bit more subborn, requiring more than 10 minutes of microwaves to wipe them out.

Border and Rice-Spearman backed this up with a 1999 study that showed materials contaminated with various bacteria and yeast strains were completely decontaminated by one minute in the microwave (I guess their microwave was better). And in 2006, Silva et al, investigating the decontamination of dentures, showed that 6 minutes in the microwave sterilised S. aureus and C. albicans but only partially disinfected P. aeruginosa and B. subtilis.

Sterilisation using microwaves

A 2001 Biotechniques paper by Weiss and Galande showed that LB plates made from microwave-sterilised LB-agar were apparently sterile (control plates were no detectably contaminated by microorganisms), had a similar shelf-life to autoclaved plates and supported bacterial growth as normal. The plates were prepared from dry powders dissolved in distilled water and aliquoted into 50mL tubes.

This is a very fast way to make plates and has the added advantage that the antibiotics can be added in from the start as they are not destroyed by microwaves. Invitrogen have a product that takes advantage of this. ImMedia is LB medium provided as sachets of dried, weighed power containing all of the required media components (including antibiotics). It is designed so that you can just add the sachet contents to water, microwave and your media is ready. But Weiss and Galande’s method is just as good and much cheaper.

My view

My take-home from this is that microwaves are are reasonably good at decontamination but more stubborn microorganisms (e.g. the spore-forming B subtilis) are not effectively disinfected. So the method does not sound too reliable to me. Also, filling the lab with smelly fumes from contaminated stocks does not seem to be a good idea. For easy liquid culture decontamination I think I will stick with Virkon, and for solid media, autoclaving seems to be the only good option.

The microwave media prep method is certainly interesting. Weiss and Galande’s results seem to be pretty robust and I would consider this method for an emergency media prep - if I need to start an E. coli culture last thing at night and there’s no sterile media available. Although the decontamination results show that microwaves don’t kill everything, E. coli grows so quickly that for routine purposes, a low level of contamination by slower growing organisms can be tolerated.

But I would not use this method for anything other than routine cultures and certainly not for slow growing organisms. Maybe that’s just me being a typical scientist, reluctant to take on new methods as Liam suggested. The microwave method is also limited by the fact that only small volumes (50ml) can be sterilised so it is never going to replace the autoclave for batch media production.

That’s my view - what’s yours?

What is this thing called ‘Life?’ One popular game in the relevant area of philosophy is to provide robust counter examples, which reveal failures in operational definitions of life. Failed attempts include physiological, metabolic, biochemical, genetic and thermodynamic definitions of life, all of which face problems. For example, a metabolic definition finds it hard to exclude fire (which grows and reproduces via chemical reactions), a biochemical definition does not exclude enzymes (which are biologically functional but not living systems), while a thermodynamic definition does not exclude mineral crystals (which create and sustain local order and may reproduce).
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As per tradition, it’s time for the weekly roundup of informative blog posts outside of your regular Bite of Bio. This week, it’s striking that the posts to choose from have an extra supply of posts on the science, and light on the personal or social commentary that bloggers enjoy so much. So this week, we’re focusing on the science itself - visit the posts, and leave comments if you find them interesting.
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Staying in science - getting funding and getting peer reviewed - is tough.

That’s one of my main gripes with creationist simpletons who imply that scientists are uncritical of their peers, and that criticism is directed solely at those who refuse to take their claims at face value. They have no clue whatsoever what they’re talking about.

Every scientific claim, as it’s actually being formulated, must be paved with meticulous attention to detail. The scientist advancing some newly-considered possibility must endure a constant barrage of critiquing, on both the grant application and results publication stages.

It’s for a darn good reason - people, even scientists, are prone to error.
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If you have ever worked out the price of an electroporation cuvette you will realise that, at several dollars each, they are worth recycling.

Accounts on how amenable electroporation cuvettes are to recycling vary, but I find that as long as you treat them well it is possible to use single cuvette many times.

It’s the metal parts of the cuvette you need to worry about the most - you need to get them clean of DNA and cells and dry again quickly to prevent corrosion.

So the key is to wash and dry as soon as possible after transformation. Read more »

Today’s issue of the Biotechniques journal is well worth a read. The journal celebrates 25 years of existence with a series of retrospective articles covering developments in various fields over the same period.

Among the picks are:

Twenty-five years of quantitative PCR for gene expression analysis

Bacterial genetics: past achievements, present state of the field, and future challenges

Over the rainbow: 25 years of confocal imaging

Mass spectrometry: m/z 1983–2008

Kits and their unique role in molecular biology: a brief retrospective

Remember that access to Biotechniques is free, but registration is required.

Do you remember where you were 25 years ago?

I often wonder why it is that molecular biology researchers stubbornly refuse to change 40 year old methods that, while they work, are not as good as newer, faster and cheaper methods out there.

I suppose rational scientists often have irrational superstitions.

One example of an old method that could be improved is the growth media used for plasmid preparation.

The majority of us, throughout our university careers, have used either SOC, LB or TB, for recombinant plasmid propagation, typically in E. coli. LB or Luria-Bertani broth has been in use for almost 60 years or thereabouts, while SOC has certainly been in use for 2 decades.

But by adding in a few more ingredients or being more economical on others (especially yeast extract and tryptone) that you could get a higher plasmid yield, quicker and with less money. Read more »

Let’s see what’s been going on around the blogs, shall we?
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