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In the previous article on EC numbers, I explained how the Enzyme Commission names enzymes, and why it is so important. In this article I’d like to take you on a brief journey through the history of the Enzyme Commission. Like many histories in science (e.g. this!), it is fascinating and gives a useful perspective…
As a biologist you will no doubt have seen Enzyme Commission (EC) numbers. An EC number is group of four numbers separated by periods in papers discussing enzymes…something like this: EC 1.1.2.1. But do you know what these numbers mean? Or where they came from? Or why we use them? If not, I will aim…
So having read our article on how a cytometer works, surely the next question is ‘what’s the right flow cytometer for me?!’ Basic Components of Flow Cytometers We know that at their most basic level, cytometers are made up of 3 main components: So, what are the considerations when selecting a flow cytometer? What…
Have you ever wondered how the media can write (often cringingly inaccurately) about a recently published scientific paper? Attending the Standing up for Science media workshop organised by the Sense about Science charity shed a lot of light on this issue for me There are times when the media are hungry for any news, mostly…
Every research lab is full of equipment specially designed for specific technical and experimental requirements, unfortunately this means said equipment is often expensive. Thankfully there are simple and cheap everyday items which can help you with your experiments and generally make life a lot easier. 1) Perforated metal ladle – to fish out samples from…
Up until last year I had been working in scientific research for just over six years. The insecurity of a career in academia had always niggled at me. About eight months into a very stressful postdoc position that didn’t seem to be going anywhere, I felt my heart wasn’t in it anymore and a change…
Next-generation sequencing (NGS) really has taken the world by storm! In NGS, millions of short ‘read’s are sequenced in a short space of time, leaving you with vast amounts of data to analyze! For all NGS platforms, the input sample (i.e. your cell free DNA) must be cleaved into short sections or fragments prior to…
Reagents are expensive and are a significant cost to your lab. You know what to do to keep others from stealing your reagents. But contamination, improper storage and “lost” batches will all eat into your stock of reagents, bump up your consumables costs and waste your precious time. Unless you take steps to prevent them, that…
If you found our previous section on super resolution interesting, you may be curious for a more detailed explanation behind some of the techniques. Introduction to this counterintuitive method Of the super-resolution microscopy techniques, structured illumination microscopy (SIM) is arguably the most counterintuitive to grasp. Of course, that’s what makes it so much fun! To understand how…
With ever increasing demands on researchers to publish, sometimes it feels like the whole world and their dog are vying for authorship on your latest manuscript. Appropriate and fair representation of those that contributed to sample collection, lab experiments and preparation of the manuscript is essential but can often be complex. So in this article…
“Any sufficiently advanced technology is indistinguishable from magic.” – Arthur C. Clarke In the fast-moving field of next generation sequencing, standard practices are evolving rapidly. Today, more and more labs are using Solid Phase Reversible Immobilization (SPRI) beads instead of gel purification in the preparation of libraries for sequencing. A crucial step, not for the…
As biological catalysts, enzymes transform target substrates into products. Enzyme kinetics is the rate of that transformation. By understanding how an enzyme’s behavior is affected, you can figure out how it functions in physiology or fails to function in disease. Now it gets complicated… What Affects an Enzyme’s Kinetics? In the first place, most enzymes…
Following on from our previous article, here are some suggestions for an old microscope (should you happen not to destroy it!). 1. Museum piece Start your own mini scientific instruments museum. Before you know it, you be raking through the old skips and dumpsters at your institute looking for exhibits. 2. Teach kids Teach your…
You’ve added the final touches to your scientific manuscript / presentation / thesis. You’ve even run the spellchecker and grammar checker and everything seems perfect. There are no little green or red squiggles under the text. Now it’s ready to submit or present – or is it? What could be wrong? If you read my…
Few scientists in the training stage are lucky enough to have the perfect advisor (aka PhD supervisor PI, boss). The reality is that most scientific advisors receive little to no training on how to be good mentors. You may want to take a look at a companion post to this one called “Getting the Most…
Apart from lung cells, surprisingly few cells are ever exposed to 20% oxygen, which is one of the reasons it’s hard to get in vitro cell cultures to behave. Read more about whether 20% oxygen is always the best level for cell culture and why it became the standard amount to use.
Do you see what I see? Maybe not, if the microscope is wrecked in one of these ten ways when you… 1. Carry the microscope incorrectly. A death-grip on anything but the arm and the base almost guarantees that it will slip away, crashing onto the floor to break in pieces. You don’t want a microscope which…
The monthly meeting with your supervisor is approaching and you are getting nervous. What can you do to get the most out of it? For starters, let’s hope that you are actually having regular, one-to-one meeting with your lab head. If not, you have bigger problems than just preparing (look out for my upcoming article…
Did you ever encounter resistance from a mammalian cell line when trying to extract the contents? Probably not, because destroying cell membranes is easy. Cell walls, however, are a different story. They are rigid, protective layers that can be so strong that the organism gives up movement in favor of protection! Cell walls exist in…
You should never completely rely on your spellchecker or grammar checker when writing your scientific manuscript, thesis, or presentation. I’ll talk more about exactly why in my next article, but first let’s have a bit of fun to get you warmed up – this is Bitesize Bio after all. Over the years, I have lovingly…
For those of you who prepare your own DNA libraries, this article will cover the most critical aspects of library preparation to ensure a successful sequencing run. Previous Bite Size Bio articles have covered the basics of how 454 sequencing works, so give those a quick review if you are unfamiliar with the process. This video is also highly…
Do you know what your histology fixatives are really doing to your samples? Read on to learn what happens to tissue treated with two common fixatives.
Common lab reagents may appear innocuous, but don’t be fooled! Sometimes even the most-used lab chemicals are hazardous to your health. It is important to make sure you have an understanding of the dangers a reagent can present before you use it. Which common chemicals should you look out for? Here is a brief look…
What Does Oil Red O Stain? Oil Red O (‘ORO’) is used to demonstrate the presence of fat or lipids in fresh, frozen tissue sections. Introduced by French in 1926, ORO is a fat-soluble diazo dye, and is classified as one of the Sudan dyes which have been in use since the late 1800s. Like…
Want to detect iron in your samples? You need Prussian blue! Discover the incredible sensitivity of this stain and how to use it.
In my previous article on DNA gel extraction, I explained how most commercially available DNA gel extraction kits work. However, there was a time before our society was blessed with these convenient marvels of technology and scientists had to summon the gods of “Crush and Soak”. This method has been proven for millennia, as people…
Size Selection via Gel Electrophoresis Whether you are using NGS for whole genome sequencing, SNP variant analysis, HLA typing, HLA matching, or even transcriptome or miRNA analysis by RNA-seq, size selection is an extremely important consideration for optimum results. Precise size selection can increase sequencing efficiency, save money and improve genome assemblies, as well as…
Isolating pure DNA is key to many downstream applications for molecular biologists. Isolating large quantities of pure DNA used to be a laborious task. But thanks to commercially available kits, older methods have been streamlined to allow efficient recovery of pure DNA. In this article, I will talk about a method called DNA gel extraction,…
Following on from Part 1, we’ll now take a look at the actual use of geometric probability in stereology, as well as the advantages and disadvantages of this technique. As you’ll know from the introduction (here), stereology looks at the relativity between an object and its sections, while geometric probability allows a researcher to expand…
Check out our rundown of the key features of the most popular reference managers to work out which one will be best for you and your research.
The study of geometric probability in stereology may seem like a large, overwhelming area of focus but, don’t panic, it’s not! In fact, it is a very specific field that is likely to come easy to those that excel in mathematics or science (yes that means you). However, the concept is not one that most…
In Part 1, we looked at diffraction limits and how these can be overcome using Super-Resolution Microscopy techniques. We covered Single Molecule Localization Techniques, Structured Illumination Microscopy and Stimulated Emission Depletion. In this second part, we’ll take a look at Near-Field and Dual Objective Methods as well things to consider before buying a system. Near-field…
So you’ve isolated your DNA or RNA from your favorite sample. And now, if you are anything like me, the first thing you’ll do is scramble to check the quality and concentration of your extract. You have a few different options at your disposal to perform this crucial analysis, which will let you know whether…
Whenever you make up a solution or use a purchased reagent in the lab, you trust the work of a whole army of people and equipment. If any one of those links in the chain has a technical problem or makes a mistake, then your reagent might turn out to be faulty. And that can…
You’ve carefully collected your samples, extracted nucleic acids and made your first set of next-generation sequencing libraries. How are you going to know if the data you get back is any good and whether it will be worth the effort in learning how to do the analysis? Who is to blame? Fortunately, there are several…
If you already spend all day hanging out with other scientists, the last thing you might feel like doing is joining a professional scientific society. With today’s shrinking budgets, you might also start to question whether this line on your CV is worth the membership dues. However, joining societies has many career benefits in addition…
So you want to do meiotic spreads do you? Maybe it’s to check if meiosis is progressing the way it should, or even to look for sites of DNA damage. Whatever the case this technique can be a little tricky at first, but once you learn a few tricks it’s like riding a bicycle- so…
Ribonucleases (RNases). We’ve been giving them a hard time here lately. We’ve been talking about how they are the bane of the lives of researchers who work with RNA. And we’ve told you how to find their weaknesses and shown you a myriad of weapons that you can use to kick their RNase butts. But…
If you want a more efficient, cheaper way to do bacterial transformation, you are definitely going to like this article.
If you’re reading our Microscopy and Imaging Channel here on BitesizeBio, you might have heard about the new techniques which fall under the umbrella of ‘Super-Resolution Microscopy’. In her recent article, Cynthia introduced us to the limits of resolution and how this can be overcome. Question time You may have more questions; In this introduction…
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