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This is the story of how one of the most famous and quirky naming conventions in biology came into being.
Calculating your fudge ratio can help you get your work done on time and get home before dark. Here’s how.
Biology researchers have a bad habit of doing accurate assays using semi-accurate tools. Here are some suggestions on how to sharpen up the accuracy of your assays.
You probably use and rely them more than any other tool in the lab, but just how accurate are your pipettes?
As far as your lab work is concerned, your lab book is the source of all knowledge. Making it easy to find things in there will help. Here’s how to do it.
Bioscientists are generally nature-lovers at heart, but the average bio lab is incredibly wasteful. Here are some ways to reduce your lab’s environmental impact.
An introduction to the Monash protein folding database, which contains protocols for refolding over 600 different proteins from inclusion bodies.
Could ligation independent cloning get any better? Well here is a technique that is sequence AND ligation independent.
Several peer-reviewed articles advocate using microwaves for sterilization, but would you trust microwave-sterilized growth medium?
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…
Cover letters are possibly the most important documents you will write in your career because they can open or close the door to your dream job. But, surprisingly, people often under-estimate their importance and assume that they are just the lesser companion to the CV/resume. Of course, that’s not the case. Your cover letter should…
You know those ridiculously priced and throw-away DNA mini, midi and maxi-prep columns? Well the good news is that you can actually re-use them if you are reasonably careful at regenerating them, with this simple and cheap method described in detail by Nagadenahalli B. Siddappa in Biotechniques in 2007. Apparently these columns can be reused…
All over the world, molecular biologists are tragically wasting hours of their life running DNA gels using tris-based conduction buffers like TBE or TAE. These buffers are known to overheat at high voltages, causing problems with gel integrity, sample denaturation and more. Because of this, molecular biologists are forced to keep the voltage of their…
Problems with DNA gel extraction can be a real show-stopper since this is such a routinely used procedure. But, even if you are having no particular problems, it’s always nice to try and pick up some information that might improve your technique just that little bit. Probably for these very reasons, Suzanne’s article 10 Tips…
For identifying positive clones from a plasmid cloning procedure, the routine of performing a mini-prep and then checking the putative clones by restriction digestion is most commonly used. Of course, if you need to screen a large number of clones, another option is a colony PCR to identify positives, followed by restriction digests to confirm….
Amid growing recognition that a successful scientific career requires skills beyond scientific acumen, institutions are racing to provide management training for newly minted principal investigators. Young scientists spend years conducting complicated experiments and crunching data, but when they are finally given the keys to their own lab, they suddenly face tasks they were never trained…
Only a handful of people ever become world experts in their field. The rest attain somewhere between a functional and world expert level of knowledge. So what makes the best better than the rest? Are they born with greater knowledge? Intelligence? Inner strength? Well, the latter is the more likely. Although some world experts are…
A while back, I wrote an article on 5 DNA ligation tips that could improve the efficiency of your cloning procedures. It proved to be quite a popular article so here are another 3 tips that might make your ligations even better! 1. Change ligase brand. All T4 DNA ligase preps are not equal. Many…
Relating to my recent comments on seminars, a beginning grad student or undergrad researcher might wonder why journal club is such a good thing. Or you might not be wondering, since the benefits are more or less the same: digesting, discussing, and analyzing research findings. But whether or not you realize the benefits of journal…
How can you avoid the perils of exposing DNA to UV light during the cloning procedure? Use an alternative DNA stain! Ethidium bromide is not your only option. In this article, we will compare the available DNA stains that can be used in electrophoresis to clarify the options available to you. Ethidium Bromide The classic…
I just got done reading Ernst Mayr’s The Growth of Biological Thought, which is on the history and philosophy of biology, from Aristotle to ~1980 (written in 1982). Of particular interest to me was the section on the Modern Synthesis, where the views on evolution of the geneticists and other experimental biologists were reconciled with…
This is a story that could strike fear into your heart if you use UV light to visualize DNA that you later intend to clone. Read on if you dare. A while back I was doing a project where I had to make a mutation library of a plasmid. There are a number of ways…
Whether you need to get your plasmid DNA to a lab on the other side of the world, or a few hundred miles down the road, it’s important to make sure your precious sample gets there, it is not degraded, and you don’t end up in jail. Here’s the Bitesize guide on how to send…
With the recent development of transparent Zebrafish, allowing scientists to directly view its internal organs, and observe processes like tumor metastasis and blood production after bone-marrow transplant, it seems appropriate to describe Zebrafish as a model organism.
Continuing with the recent theme on model organisms, there is the nematode (roundworm) Caenorhabditis elegans. This organisms is particularly useful owing to the fact that it has very defined development patterns involving fixed numbers of cells, and it can be rapidly assayed for abnormalities. Further, strains are cheap to breed and can be frozen. When…
Please read and pass this life-saving information on to your friends. A chemical that all of us use in the lab has turned out to be highly dangerous. It is an asphyxiant, can cause severe burns and is a contributor to the greenhouse effect. Medical organizations all over the world confirm it to be responsible…
Another popular model organism is the African Clawed Frog, Xenopus laevis, which is extremely useful for studying development and cellular physiology, owing to its particularly large and easy manipulable oocytes and embryo.
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…
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…
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…
Random mutagenesis is an incredibly powerful tool for altering the properties of enzymes. Discover 8 different approaches.
In the early 1950’s so many new enzymes were being discovered in the burgeoning field of biochemistry that enzyme nomenclature was in danger of getting out of hand. With no guidelines on how to name enzymes, researchers simply chose their own. Some enzymes were given names, like diaphorase or Zwischenferment, that conveyed nothing about the…
In any experimental procedure, getting the controls right can save you a lot of work when things go wrong by allowing you to troubleshoot the source of the problem. DNA ligation is no different. In this article, we explain how to set up a ligation reaction with a complete set of controls, and use them…
After all that hard work, you finally have your PhD. Now what? If your career choice is academic research, your first post-doc position beckons. The choice of where, and with whom, to take up a post-doc position is a very important one as it is at the post-doc stage where publications are required to move…
Wide eyed and wet behind the ears, the rookie researcher steps into the lab for the first time. Armed with several years’ knowledge mined from text books, lectures and undergrad labs he feels ready to take his place amongst the worldwide legions of scientists who battle daily in the pursuit of knowledge. Little does he…
For every half-way decent mentor or adviser that an aspiring scientist comes across, it sometimes seems as though there is another lurking, who is simply a jerk*. Let’s face it – scientists aren’t consistently “people-persons.” Maybe they had bad mentors, and inadvertently end up passing on the karma. Or maybe science just attracts a higher-than-average…
….statistics. The very word strikes fear into the heart of many a biologist (including me). In an article published earlier this year, Cumming and co-workers of La Trobe University, Melbourne gave a very useful rundown of common mistakes made when using statistical error bars in biology and suggested a number of rules that should be…
Ok, this week has been a bad week in the lab so far. A few weeks ago I wrote a post describing 15 reasons to be a scientist. Today I am in the mood to cross over to the dark side and give you 10 reasons NOT to be a scientist! Strangely I could only…
Spare a thought for your poor over-worked neurons. In the information age, they are bombarded with input from the moment they are dragged into consciousness by the radio alarm clock each morning then throughout the day by e-mail, Google searches, RSS feeds, mobile phones, newspapers, books, blogs and more. In the post genomic era, it’s…
As a freshman biology major in undergrad, I was introduced to molecular biology with the following description: Molecular biology represents the intersection of genetics, biochemistry and cell biology. Some people, it turns out, add microbiology and virology into the mix. So molecular biology is often used as a catch-all, to describe a wide breadth of…
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