Routine PCR? Let’s be honest, there’s no such thing. Even with the simplest PCR reaction things can go wrong, so you need to have a good checklist of ideas for troubleshooting and rectifying the problem. Today I have brainstormed all of the ways I can think of to approach problems with standard PCR reactions.

I’ve inevitably missed some things out so please chip in if you can think of anything else to add. I will add your ideas to the list to make it a resource we can all refer to. Read more »

As noted in the previous post on Model Organisms, Dictyostelium discoideum is a popular model for studying fundamental aspects of cell-cell communication and chemotaxis. This is a soil-living social amoeba grows as separate, independent cells that interact to form multicellular structures when challenged by adverse conditions such as starvation. Up to 100,000 cells signal each other by releasing the chemoattractant cAMP and aggregate together by chemotaxis to form a mound that is surrounded by an extracellular matrix. This mechanism for generating a multicellular organism differs radically from the early steps of metazoan embryogenesis. However, subsequent processes depend on cell-cell communication in both Dictyostelium and metazoans. Many of the underlying molecular and cellular processes appear to have arisen in primitive precursor cells and to have remained fundamentally unchanged throughout evolution. Basic processes of development such as differential cell sorting, pattern formation, stimulus-induced gene expression, and cell-type regulation are common to Dictyostelium and metazoans. Read more »

The term “model organism” is often used in research, to describe species that are extensively studied to understand particular biological phenomena. We say “model,” because there is usually the expectation that discoveries made in the organism model will be representative of related taxonomic groups. In particular, model organisms are widely used to explore potential causes and treatments for human disease when human experimentation would be unfeasible or unethical. For instance, a it may be difficult or impossible to visualize cellular processes in mammalian embryos; and the manipulation of human subjects is tightly regulated for obvious reasons. This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution.
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After years of loyalty, our relationship was becoming stale - things just weren’t the way they used to be. I was putting in more than I was getting back and complaining about it didn’t seem to help. I just got the same old answer thrown back at me… “it’s not our problem, it’s yours”.

Then things changed. I don’t know how it happened, it just did. We met on the internet and I immediately knew this could be the answer to my prayers. I said I just wanted my routine DNA-handling procedures to be uncomplicated, they said “the beauty of science is to make things simple”.

With shaking hands I pressed the e-mail “send” button - I had just ordered free samples of Zymo Research’s Zyppy plasmid miniprep, DNA clean-up and gel extraction kits. It felt so good. Would this be the start of something new and wonderful? The end of low quality DNA samples? The end of poor yields? I hoped so. Read more »

It’s Friday again, and time to recap some recent and relevant posts around the rest of the blogs:
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The late Francis Crick once said that “Trying to determine the structure of a protein by UV spectroscopy was like trying to determine the structure of a piano by listening to the sound it made while being dropped down a flight of stairs.”

But, if you thought that protein structure determination was the closest that biologists got to making music, you’d be wrong. It turns out that behind the veneer of the laboratory, biopop - a thriving underground biology music scene - is just waiting to burst onto your iPod (or other music player).

For your listening pleasure, I have scoured the internet to bring you 10 of the very best songs that biopop has to offer. From Unca John’s bluesy “Growth Hormone Hero” to Amy Hartnell’s karaoke classic “Form a phosphate-ester link (to carbon three)” to BioRad’s slick but shamelessly corporate “Scientists for Better PCR”, every taste is catered for.

Whether you love, hate or even make biopop, be sure to make your views or your favorite songs known here.

Here’s the biopop top 10. Enjoy:

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In Deserting the hungry?, a Nature essay argues today that “Monsanto and Syngenta are wrong to withdraw from an international assessment on agriculture.” The assessment, titled the International Assessment of Agricultural Science and Technology, is an ambitious, 4-year, US$10-million project that aims to do for hunger and poverty what the Intergovernmental Panel on Climate Change has done for another global challenge. Drafts of the assessment can be read here: http://www.agassessment.org/.

The goals of the assessment are of course are noteworthy and laudable. Very recently, Monsanto and Syngenta decided to quit the project, and no comments have been issued other than to say: Read more »

A while back I wrote a post on a T4 DNA polymerase dependent ligation independent cloning method. In the comments, Max asked if anyone had a protocol. Since there does not appear to be a simplified protocol available on the web, I thought I would post mine for reference.

It is adapted from a 2006 Organic & Biomolecular Chemistry article by Bonsor et al and although it works for me, I have to caution that I have not been using it for very long so improvements may be possible. If you have any suggestions on how the protocol can be changed or improved, let me know.

The protocol just deals with the bare bones of the digest, T4 DNA polymerase treatment, annealing and transformation. For information in designing the cloning site, see my original article, or the paper.

Here’s the protocol: Read more »

It’s no secret that science journalism is, with a few notable exceptions, very lackluster in general. It seems to a lot of biologists whom I speak to that cell and molecular biology, genetics, and related fields, are especially underrepresented in the press. Yesterday, Alex vented a bit on this, reflecting on the capacity for wonder in the fundamental features of life, and lamenting the public’s overall ignorance of this branch of science. The conversation in the comments looks to get a bit off-track, as it usually does: will creationists quote-mine Alex on his descriptions of cellular complexity, and adaptability vis-a-vis nature vs. nurture. I think though that the original topic, attention in the media, deserves far more discussion however.

Who are the voices that carry discussions of the subcellular world forth to the public? Astronomy and the biology of organisms have long captured the public’s interest, and geophysics has gained repute in the past decade as well. We have a handful of Nobel Laureates, such as Harold Varmus, trying to popularize subcellular biology, but where are the rockstars? (moonlighting musician scientists like Greg Graffin aside). Read more »

I shudder to think of the way I was taught about metabolic pathways as an undergrad. Lists of mysterious names connected by arrows - all to be memorized, with little reference to how the processes actually worked on a chemical basis.

Even worse - and perhaps embarrassingly for me - I was almost at the end of my first year as a biochemistry undergrad before I understood how functional proteins arose from DNA. Having already studied biology for 5 years I knew about the functions of some proteins, and I knew about transcription and translation as isolated processes, but the fact that proteins folded spontaneously and that they way they folded, and their consequent function, was dependent on their amino acid sequence had never been pointed out to me. Read more »