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PCR has become the tool of choice for molecular diagnostics and is now a staple platform in any laboratory setting. The versatility of this method has led to a myriad of spin-off techniques, including probe-based quantitative PCR (qPCR). This method effectively combines PCR amplification and detection into a single step to measure the specific amount…
Counterstaining can have a big impact on your histology result. This short guide will introduce you to some available counterstains providing you with a few more choices.
Achieving a good immunohistochemistry signal-to-noise ratio involves many factors, including a good blocking protocol. Read on to learn about blocking non-specific staining in IHC.
Plasmid mapping and DNA annotation software is pretty abundant these days. A quick Google search brings up dozens of hits – but how do you know which one to use? If you are like most molecular biologists, you probably use the same software your colleagues do—usually it is either the stuff that gets passed down…
Following on from the first part of the H and E 101 articles, here are the materials and recipes you’ll need for your own H and E workstation (assuming you don’t have access to a histology lab). Many of the chemicals listed below are toxic and/or harmful. Use PPE when handling/storing, follow SOP’s in your…
The Irish Famine (or ‘Great Potato Famine’ if you live outside the Emerald Isle) killed one million people and forced another million to leave the country between 1845 and 1852. It was caused by a blight on the country’s main food stock- the Irish ‘Lumper’ potato. Now, researchers have identified the genome of the blight…
In the previous article, I showed you how to interpret mean-squared displacement (MSD) and showed four easy things you can learn from an MSD graph at a quick glance. Now let’s turn from analyzing an MSD plot to making one. I am going to use the programming language R to generate simulated data and then…
Haematoxylin and Eosin staining is the most common staining in the modern (and old!) histology lab. This staining technique gives an overview of the structure of the tissue and can be used in pathological diagnosis. This article follows on from Nicola’s introduction, but we’ll take an in-depth look at the stains, chemistry and method to…
I was first introduced to Conrad Waddington’s epigenetic landscape when reading ‘The epigenetic revolution’, a fantastic introduction to epigenetics, and in my opinion, a must read for anyone who is looking for an entertaining and enjoyable introduction to this fascinating field. In his model, Waddington likens the process of cellular differentiation to a marble, which…
Stuff moves. It is useful to study how stuff moves, because motion analysis can tell us a lot about the object that is moving. For example, we can learn if an object’s motion is aimless, diffusive wandering, or directed towards some goal, free to explore the available environment, or restricted to a confined space. Studying…
Developing a career in the biological sciences can be a daunting venture. You must throw your heart and soul into your career and wait years before you know if you are going to be successful. For those of you who are feeling a bit lost, I have garnered some pearls of wisdom from post-doctoral scientists…
Unlike immortalized cells lines, primary cells can only be kept in cell culture for a finite period of time, if at all. Therefore, you often need to obtain primary cells directly from an animal source. After which, you may fix and image the primary cells in situ (as part of the whole organ), or you…
Isoelectric focusing electrophoresis (IEF) of proteins is nowhere near as popular as its cousin – sodium dodecyl sulphate-polyacrylamide gel electrophoresis aka SDS-PAGE. While in both methods the proteins are denatured, IEF is a gel-based electrophoretic separation of proteins using difference in their overall charges. The sodium dodecyl sulphate – SDS part of the usual gel…
Fixing suspension cells for imaging can be trickier than fixing adherent cells, as they can’t be cultured on a coverslip. Discover how you can stick them down with the help of centrifugation.
Here are our top 10 least favorite ways to ruin that larger-than-life-sized autoclave. Don’t try these—your lab manager won’t be pleased!
Wouldn’t it be great to put your nucleotide sequence into a program and get back a 3D-structure of your protein and a full description of its functions? In theory, because the protein 3D-structure is determined by the aminoacid sequence, given the right algorithm and a powerful enough computer, this should be simple. In practice, because…
You just can’t put raw tissue or cell samples on your slides and expect good histology results! Instead you must preserve or ‘fix’ your samples. Fixing ensures that your cell structures stay intact and that your antigens are immobilized. Ideally, fixation would also still permit unfettered access of your antibodies to your antigens. However, as…
According to the central dogma of molecular biology, DNA is transcribed into RNA, that is translated to proteins. Inconveniently, the vast majority of the genome contains sequences that do not actually code for proteins. So, this non-coding RNA (ncRNA) was dismissed as non-functional junk, letting researchers tick the box on their to-do lists and head off…
Most of us have had to write a lay summary or abstract at some point. How easy do you find this? In my experience, it is harder than you think! Whether for your thesis, graduate fellowship grant application, or even lab newsletter, writing about your research in plain English is a crucial skill. Communicating your…
The theory behind the idea of having shared microscopes is a good one, but, in reality, this can sometimes mean you have to put up with the dirty habits of your fellow scientists and researchers. And some of your lab mates turn out to be really mucky! Here’s my Top 10 of things which really…
The conventional sequence for getting a new job in science (or anywhere else) goes like this: 1) Apply for a job 2) Get an interview 3) Ace the interview 4) Pray that your references hold up. So if you had a bad relationship with your last boss, you’re in trouble. Because no matter how well…
Recently BsB author Yevgeniy Grigoryev shared a total RNA isolation protocol. The one I use is even simpler—no expensive Trizol, which is a mix of phenol and some salts, all that is required is some Tris, SDS and phenol/chloroform mix. I have never used this protocol on non-yeast cells but I am almost sure that…
It is the black death of cell culture. Scientists don’t dare utter its name and many a graduate student has fallen victim to its indiscriminate menace. These stealthy anarchists infiltrate quietly but deliberately until their numbers swell and then they attack in strength, overwhelming their victims before they can put up a fight! What is…
Have you ever emerged from the lab, bleary-eyed, blinking dazedly at the sun after spending hours hunched over a lab bench counting endless bacterial colonies or viral plaques? A necessary evil… I consider colony/plaque counting one of the necessary evils of working with microorganisms. Necessary because many experiments have an endpoint that requires determining the…
“Do we use a monolayer or 3-D cell culture for our experiments?” A simple, yet puzzling question asked by my group leader while I was working on a drug development project at the University of Abertay Dundee. How do you answer such a question? Just read on to find out! Monolayer vs spheroid One of…
The field of epigenetics is exploding and given the strong links between epigenetic state and disease, the need to study markers like DNA methylation in humans is very relevant. This article outlines some of the main factors you should be taking into account in your study of DNA methylation in human tissues. Here goes: Biological…
Did you know fixation can mask antigen sites in your sample? Discover how you can unmask them and get your signal back on track!
Whole genome sequencing (WGS) is becoming increasingly common. Doctors now routinely order it for patients with puzzling diseases. The NHS (National Health Service in the UK) has declared that it will sequence 100,000 genomes over the next few years. Increase WGS…increase ethical questions The direct-to-consumer company 23andme has been experimenting with whole exome sequencing (WES), and another company, DNA…
I met a final year PhD student once, who told me a sad story. His supervisor had a plausible idea that exercise reduces the chances of developing bowel cancer. To test the hypothesis, the student made a transgenic mouse with an increased incidence of bowel cancer and got the mice to run (or not run)…
To answer some of the more interesting research questions, you often need to get a good look at what’s going on inside the cell. Whether you’re running a Western blot or measuring enzyme activity, many assays require access to the materials (e.g. proteins, DNA, subcellular fragments) contained within the cell walls. There are several ways…
So now you’re convinced that R is the language for you, you’ve downloaded R-Studio (from https://www.rstudio.com/) and opened it, and. . .what the hell do you do now? Great question! I always find it easiest to learn by doing something, rather than just by seeing a list of possibilities, so here I’ll walk you through…
As part of my job ensuring plasmid quality at Addgene, I analyze 50-100 sequencing reactions a week. So I have developed some good habits that I wanted to pass on to you to make sure you are getting the most out of the data you get back from your sequencing runs. The most important of…
You’ve been told that maintaining a sterile environment in a tissue culture hood is vital to preventing contamination of cell cultures. But what exactly is meant by sterile? The definition of sterile is ‘completely clean, sanitized, and free of all forms of life’. Obviously you still want your cells and/or any other organisms you are…
Have you ever isolated a great little population of cells after days or months of trying, got truly excited about doing some immunofluorescence with them only to find out (at the very end) that all your cells washed away?! If this has happened to you, then look no further; we will introduce you to some…
Most ‘wet lab’ biologists do not have much computer programming experience, which can make downstream analysis of next generation sequencing results a bit daunting. After the sequencing platform spits out your data, what do you do with it? That’s where Galaxy comes in. What is Galaxy? Galaxy is a bioinformatics workflow management system, created by collaboration…
Working with large datasets can be very frustrating and time consuming. If only there were more tools out there to simplify things without needing to invest a PhD’s worth of time to learn how to use them! I am here to tell you that there is a solution, and a free one at that. If…
I was shocked recently at a seminar called “Writing with style” by the Manchester University writer-in-residence, Chris Simms. He opened by saying that he has never done a presentation using Powerpoint in his life. What? Surely biologists and PowerPoint presentations (PPT) go together like biologists and white lab coats. They teach you to make PPTs…
Unlike DNA, which can last for eons, RNA is a fragile and degradation-prone cousin. After working with RNA for a while, one becomes quite paranoid about handling RNA because even a single sneeze or drop of saliva can potentially affect your results. The reason is that there are enzymes called RNases that specifically target and…
In 1895, Alfred Nobel wrote in his Last Will and Testament that he wished the bulk of his sizable estate to “constitute a fund, the interest on which shall be annually distributed in the form of prizes to those who, during the preceding year, shall have conferred the greatest benefit to mankind.” Nobel made his…
A while back, I read an article on Bitesize Bio entitled “When Your Partner is NOT a Scientist” that piqued my interest…for the wrong reasons. And I discovered that I hold polar opposite views on balancing a marriage and an occupation as a scientist. So I was compelled to write this article, not to be…
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