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Run to red! It’s a mantra I learned when first using gel electrophoresis to separate DNA molecules. This can save you a lot of frustration and humiliation in the lab (stage right: a complaining scientist who swears the equipment is broken as a supervisor facepalms in embarrassment). But what about how does this jell-o like…
In the first part of this article (you can read it here), we looked at clipping and saturation in terms of microscope images, followed by a definition of Dynamic Range and an introduction to Bit Depth. Intrascene Dynamic Range The dynamic range which can be detected at the same time in the same field of…
Radioactive protein labeling is not as common as it used to be. With the advent of modern protein labeling techniques, such as fluorescence, radioactive labeling has largely fallen out of favor. However, radioactive protein labeling is still a very useful technique and is often superior to more modern labeling techniques. Radiolabeling can provide a snapshot…
With the current proliferation of new dyes and instruments that can detect many colors simultaneously, it seems like an entire rainbow is at your disposal for your flow cytometry experiments. And we know that when designing a polychromatic flow cytometry panel, more is often better – right? The more antigens you can detect, the more…
Here are five unfortunately easy ways to wreck a centrifuge, and how to make sure it never happens in the first place!
Everybody has to die at some point. But fortunately, the death of a cell does not mean the end of the organism, at least for us metazoans. Indeed, controlled cell death a.k.a apoptosis, or programmed cell death, is an integral part of the biology of all organisms, from nematodes on up. Apoptosis is central to…
We are pleased to announce that the famous maid of microbiology, dear old Aunt Yersinia, has agreed to start writing a microbiology and molecular biology advice column for Bitesize Bio. She will be free to answer your most pressing questions sent to: auntyersinia@bitesizebio.com By way of introduction, Aunt Yersinia is bestowing 8 spores of knowledge garnered…
Perfect your subcellular fractionation in the lab by understanding how these protocols work. Plus, discover the various kits for organelle separation.
Around and around the cell cycle goes, where it stops, nobody knows. Unless you have the right tools to analyze DNA content, that is. The DNA markers propidium iodide, Hoechst and DAPI are commonly used in flow cytometry to analyse a cell’s DNA content. Although they are simple to use, they do have disadvantages. Figure…
One of the most exciting aspects of being a biologist is getting opportunities to examine how and why living organisms behave the way they do. We have technology that enables us to obtain images at sub-cellular levels, and the skills to work directly with the micro-environments essential for the progression of life. However, at the…
A wide variety of enzymes are available for PCR and RT-PCR and the optimal choice depends on a range of factors specific to your experiment. Some of these factors will now be explored to help you to make the most suitable and cost effective choices when ordering. PCR Type and Other Factors to Consider First,…
Much of your success and happiness in grad school depends on an effective relationship with your mentor. Despite your best efforts, sometimes the first relationship doesn’t work out, and you need to switch mentors to succeed in your program. But how do you prepare to change mentors mid-PhD? Step 1: Write it all down Before…
Ever tried to turn the volume all the way up on a small radio or small stereo system? (Hopefully you have not tried it with earphones in!) Notice how, after some point, the sound didn’t get any louder- it just got more distorted? That’s because you’ve hit the ceiling of your machine’s dynamic range. It’s…
What if there was a way to take the power and speed of a flow cytometer and couple it with the resolution of a microscope? Imaging flow cytometry does just that! Flow cytometry is a very powerful tool for the complex characterization of cells and cell populations but flow cytometers can also be thought of…
People often joke about hiding from sales reps, but the fact of the matter is that valuable opportunities are lost when scientists disappear into thin air. Think twice before attempting your own vanishing act; a brief chat could reward you with amazing deals, introduce you to faster, better technology and keep you in the loop…
Grad school is a long, hard, long, time-consuming, and–wait for it–long process. A bad relationship with your primary mentor can make it worse, and may even drive you away from a science career. Unfortunately, you often can’t spot incompatibility until you’ve spent time with a mentor and lab. Even then, how do you tell the…
If you are struggling to optimise your Western blot protocol, one step to consider is the equilibration of your gel and membrane before transfer. Wondering what this step achieves and whether it’s necessary? You’re not alone! I did dozens of Westerns without ever bothering to equilibrate before I realised that it was having a big…
You are sitting in a seminar when you glimpse it: the figure that beats all other figures – a beautiful contour plot – and you realise that a similar figure is what you need to publish your paper in a high-ranking journal. You know the basics of flow cytometry, but admit you need a little…
What did we do before the internet? And where would we be without handy online molecular biology tools? Apparently in the ‘olden days’ doing a simple gene or protein alignment required programs that used dynamic programming algorithms such as the Needleman-Wunsch and Smith-Waterman algorithms. These required long processing times and the use of supercomputers or…
So you’re designing a new experiment that requires PCR quantification. You used to have only one method to choose from, but now you have two – Quantitative Real-Time PCR (qPCR) and Digital PCR (dPCR). Which one is right for your application? Both methods have good quantification, sensitivity and specificity for most applications. They are compatible…
Finding adequate sources of funding is the primary challenge of just about any startup company, and biotechnology is no different. In fact, the regulatory, scientific and logistical requirements of making a new drug or device could easily be the most challenging of any industry. In addition, the global recession of 2007-2009 (combined with austerity measures…
As you’ve probably kind of guessed from our previous articles Introducng R and the Basic R Tutorial, we think R programming language and R-studio are great tools for data analysis and figure production. And now we are about to prove it! So, you’ve collected some data and are pretty sure you know what statistical test…
Stimulation of cells/tissue with a given stimulus (e.g., a cytokine) is a common experimental setup in any cell biology lab. The cellular response to the external stimulus e.g., the activation/deactivation of intracellular signaling pathways and/or the secretion of proteins is often the research goal, and there are a number of different methods that you can use to analyze such…
Bitesize Bio has had a lot to say about RNA isolation, mainly because it is one of the most anxiety-producing requirements for molecular biology; especially when you are first starting out (although isolating proteins from complex samples like soil and stool is far more difficult, let me tell you. But that’s a future post.) We’ve…
If you want to visualize elastic fibers in your sample, you need to use Verhoeff-van Gieson stain. Find out more about this stain, including how to use it.
You spent the last few weeks tweaking your Co-immunoprecipitation conditions, testing different antibody/bead combinations, and sampling a panaply of solutions and FINALLY! You have your Co-immunoprecipitation (Co-IP) elution… Now what? Well, you have a few choices. It really all depends on what you need know about the proteins in your elution. Do you need to identify…
The flow cytometer that we have all grown to know and love may have only come into its own in the 1990’s, but who would have known that the first cell sorter was invented as early as the 1950’s? With the recent death of one of the key developers of fluorescence activated cell sorting (FACS),…
Freeze-thaw—you know it’s bad for your samples, don’t you? While working in the lab, you have most likely heard someone say ‘aliquot your protein/cells/DNA/RNA to avoid too many freeze-thaw cycles.’ But do you actually understand why? You probably thought that avoiding freeze-thaw cycles had something to do with damaging cell structure as well as proteins…
Resolve lab obstacles with creative solutions with these non-lab products that can actually be very useful in the lab environment.
The relationship you have with your supervisor during the course of your PhD is a critical one. Like all other personal or professional relationships it can range from being harmonious to disastrous. Choosing a supervisor you think will work well with you in the first place is important, however it can be difficult to foresee…
Every PCR battle is the same: Too little amplification of your target DNA versus too much amplification of off-target DNA. But you can win the PCR battle and amaze your co-workers by mastering the use of PCR additives. PCR additives usually work one of two ways: 1) By reducing secondary DNA structures and thus increasing…
Figures play a central role in science not just as a way of displaying results, although this is obviously important, but also as a way of getting across complicated theories and processes in a relatively simple and direct manner. I’m a firm believe in the power of putting ideas into diagrams and spent a considerable…
“A two photon microscope has higher sensitivity than a normal confocal microscope, because it uses two photos instead of one!” Yes, I can bear witness that this phrase has actually been uttered, and it was not by an undergraduate student. No exception to the rule The condensation of various levels of misunderstandings in this statement…
Ever had a blot so bad it looked like a Rorschach test? We have ten things that might be going wrong with your western blots and how to fix them.
DNA sequencing (PCR, Sanger or next-generation sequencing (NGS)) is a now familiar part of any molecular biology lab. But ‘RNA-seq’, the so-called “Cinderella of genetics”, is now becoming the belle of the ball, providing new insights into this most central molecule of the ‘central dogma’. The many flavors of RNA Whilst genomic DNA is the…
A variety of lab supplies can be purchased off the shelf in your neighborhood, which can save you time and money. Here is a grocery list of items that you can stock your lab with today!
If you remember from one of my previous articles (if not, you can read it here!), we introduced ‘fluorophores’. These are basically substances (natural or synthetic) which have the ability to absorb light at a low wavelength and re-emit at a higher wavelength. In other words- they fluoresce! In this article, I’ll introduce the three…
Buffers are often taken for granted, but they can make or break an experiment. In previous posts, we’ve talked about the wide ranges of buffers available for biological research and the characteristics of a “Good” buffer. Organic buffers are not inert! They can interact with your experimental molecule, or change pH due to changes in…
So you’ve performed a test such as an ANOVA and have found that there is statistical significance in your data (lucky you!), however you now want to know where that significance lies. When you are comparing multiple sets of data it might seem like a logical thought to simply perform an individual t-test between each…
As widely used as it is, isolating RNA remains one of the more finicky protocols. Just about anyone who has performed the technique has their own personal tips and tricks to successfully isolate intact RNA from their samples with consistency. Although RNA can be somewhat unpredictable since it is so labile, there are a few…
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