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Do you need your protein in its native form, intact, with full functionality? Do you need to isolate organelles and nuclear fractions from the cytoplasm? Or do you need a slurry of everything in your cell or tissue? Whatever your experiment, you can maximize the amount of functional, detectable or active proteins by handling your…
Once you have been in the field of Flow Cytometry for a bit, the name Howard Shapiro will be familiar to you. However, for those who are new to Cytometry, you might not be aware of Dr Shapiro and his fabulous book ‘Practical Flow Cytometry’. Most Cytometrists have a paper copy of this bible of Flow…
With in vitro translation (IVT) you can produce protein in a tube. Cool sure, but would IVT be a good choice for your experiments? Not sure? Then read on. Here I will cover the strength and weaknesses of IVT. How In Vitro Translation works First things first, for IVT you need ribosomes. While theoretically possible,…
There are about as many protocols to prepare coverslips as there are ways to make tuna casserole. You can spend from 5 seconds to 2 days, depending on what your lab prefers. But in the end, what’s really needed? I’ve tried many protocols over the years and I’ve questioned some steps. Here I share my…
If you want to get the maximum yield and quality from your next-generation sequencing experiment then you are going to need to make sure each of the libraries you produce is carefully quantified ready for pooling and/or loading onto a flow cell. If the quantification goes wrong you’ll get a bad balance of samples within…
After designing a multicolor flow cytometry panel and securing the necessary cells and reagents, the process of optimization of the panel can begin. The first step in that optimization is titration of your antibodies. In this process, following a standard protocol to be used in the final analysis, you stain a known amount of cells with…
Loop-mediated Isothermal amplification (LAMP), is an emerging technology that allows DNA amplification at a constant temperature. The key to this principle is the use of a DNA polymerase that possesses strand displacement activity. As a result of this property there is no need for heat denaturation of double stranded DNA in order to allow primer…
One of the most annoying traits of “classical cloning” is an imperfect system of discriminating between the clones containing an empty vector and vector with insert after cloning. Even when your self-ligation control plate is empty, you can have a lot of colonies containing an empty vector on the “vector + insert” plate. Even the blue-white…
In my previous article ‘Choosing a scripting language for next gen sequencing: Python, Perl, and more’ I discussed several of the more common programming languages used for next generation sequencing and things to consider when picking which one to learn. But now that you know WHAT you want to learn, HOW do you go about…
You use your antibody frequently, maybe even every day. You rely on it for western blotting, immunohistochemistry, FACS, ELISA, and immunoprecipitation. You’d be lost without it. But how well do you really know your antibody? Are you sure that it detects what you believe it to detect? If you have the slightest doubt, or if you have…
Every protocol for single cell PCR can be broken down into two steps. In the first step, the cells are isolated by micromanipulation, laser capture microdissection, flow cytometry, or by direct micropipetting. Next, the genetic material is processed by PCR to amplify your sequence of interest. Here, we’ll go through the different options for isolating…
“The greater the power, the more dangerous the abuse.” – Edmund Burke “With great power comes great responsibility.” – Uncle Ben (quoting Voltaire) While it’s unlikely that either of these speakers performed multi-dimensional flow cytometry, it is important to remember these quotes in the context of developing and implementing a good polychromatic flow panel. More fluorochromes are…
It’s a familiar story – molecular biology meets protein science, they get closer and sparks fly. But how exactly does a proximity ligation assay (PLA) work and how do you make sure yours will have a happy ending? What PLA Does PLA allows you to detect individual proteins or individual protein interactor pairs without ectopic…
T cells can be problematic to characterise because they have a wide variety of subtypes and because of the technical difficulties of studying the membrane-bound T cell receptor, but there are situations where you want to be able to do this such as analysing the degree to which immunological memory has been induced to measuring…
“It is the weight, not numbers of experiments that is to be regarded.” Isaac Newton Read any flow cytometry protocol and somewhere near the beginning will state something to the effect of ‘Place 1 million cells into a tube.’ The question is, faced with that special sample for THE experiment, how do you count cells…
Bacterial cultures may be much easier to grow than mammalian cells, but if your yields are suboptimal there are plenty of parameters to play with. Here we list a few of the things you should consider to maximize your culture growth. Shaking speed Shaking is performed to allow aeration of your culture, which is of…
Chemical chaperones are necessary in protein experiments. From buffers to storage solutions, chemical chaperones silently make proteins happy and soluble. Read this article to appreciate the love that chemical chaperones bathe on your proteins and learn when to use them! A chemical chaperone is a molecule that promotes the favorable interaction of protein with water…
Large amounts of data? Check. Repetitive tasks? Check. If you work with next gen sequencing data, you have probably already realized it’s a good idea to learn a scripting language. But learning a programming language is a major endeavour, and with lots of languages available how do you decide which one to study? And once…
If you want to make molecules stick together you need to know about streptavidin/biotin. This article follows on from Mike’s article looking at ‘sandwich’ and ‘amplification’ methods of immunohistochemistry (IHC) and covers how streptavidin-biotin works in IHC, including protocols. Streptavidin-Biotin What is it? Avidin is a natural biotin-binding protein found in egg whites. Streptavidin is similar…
As Morrissey once sang “in the midst of life we are in death, etc.” A fact of life in the research Lab is that whenever we run an assay there will almost certainly be some cell death in our sample. This may be insignificant in some techniques but in others it can be problematical. Why…
Have you ever been shown how to use a microscope properly? Or do you just dive right onto the microscope with little or no training and scant knowledge of the basics, then twiddle knobs, snap photos and expect the publication-quality images to appear? If it’s the latter you are certainly not alone! If only there…
When I buy a new sweater, I love finding out that it goes with several pairs of pants, the scarf that’s an awkward color and the earrings I haven’t worn yet. PCR is like this sweater – it goes with almost everything and molecular biology is taking full advantage of this using it at every…
Making a Next Generation Sequencing (NGS) library can seem a bit daunting to the new user, as failures can be expensive. But don’t be put off, as NGS library preparation is relatively simple molecular biology, and can be very easy if you choose to use a commercial kit from one of the many suppliers. Take…
The biggest source of PCR contamination is aerosolized PCR products. How do you fix PCR contamination and avoid it in the future?
I often wonder why it is that molecular biology researchers stubbornly refuse to change 40-year old methods that, while work, are not as good as newer, faster and cheaper methods out there. I suppose rational scientists often have irrational superstitions. One example of an old method that could be improved is the growth media used…
Gene expression analysis plays a pivotal role in a wide range of studies, including biomedical analysis and diagnostics. Of all the methods available for gene expression analysis, quantitative real-time PCR (qRT-PCR) is the most rapid, sensitive, and accurate to measure mRNA, and its use in clinical diagnostics is rising steadily. RNA quality entails both purity and…
The Rise and Fall of the 454 Sequencer The GS20 454 sequencer, released in 2005, was the first next-generation DNA sequencer to hit the market, and its feats quickly dazzled the scientific community. As new sequencing platforms proliferated, however, many researchers opted for less expensive options and 454 market share fell. About a year ago,…
When you fix your tissue samples with paraformaldehyde (PFA) the proteins in your sample become covalently cross-linked. This is good to preserve the ‘architecture’ of your tissue sample. However, this cross-linking can become a problem when you carry out immunohistochemistry (IHC). Cross-linking can ‘mask’ or hide your antigens-of-interest and make them ‘invisible’ to your IHC…
The half-life of a protein is an important factor in many molecular biology studies. If your thesis has anything to do with proteins then your graduate advisory committee will ask about half-life, so start planning your 35S experiment today. To help you here is my overview of the major steps of 35S labeling complete with…
If you are bringing cells to a core to be sorted there are a few things you can do to optimise your sorting and will help the core staff. Here are a few hints: 1) Know the size of your cells Do you know the size of your cells? Not many people do and its one of…
Mercury burners are one of the most common light sources used in fluorescence microscopes, producing a wide spectrum of wavelengths making them a great light source for viewing your samples. But they do have their issues – one of which is their propensity to break or become damaged if not used and cared for correctly, which…
Today, PCR is as common a feature to the lab as pipettes and beakers. The majority of us regularly need to amplify our DNA or RNA samples, sometimes for an ‘everyday’ PCR run just to check if our primers actually work, or in a quantitative (q)PCR run, where we might be comparing the levels of…
Figuring out what’s what When studying cells and cell subsets (and cell sub-subsets, and so on!!) we need ways to identify and classify every single cell. This will allow us to individually analyse each population and, for example, help to discover their role in health and disease. A principal way we do this is by looking…
Do you need purified recombinant protein to test biological drugs? But you don’t have the time or facilities for cell culture and purification? Try using in vitro translation (IVT) instead! IVT is like your own miniature protein factory. And it is great for a wide range of molecular biology applications because IVT can be much…
SLIC, or sequence and ligase independent cloning, was developed by Li in 2007 and published in Nature Methods. What makes it a Nature Methods worthy protocol? Unlike other forms of cloning, SLIC does not require restriction enzymes or a ligase! Seriously! Don’t believe me? Why not have a go for yourself? I’ve detailed the main steps below to get you started. How it works To…
When you’re trying to solve a PCR problem, you’ll probably resort to a Google search at some point or another. Here’s a list of the Top 10 go-to websites to help solve your PCR problem.
You’ve nurtured your cells for weeks, perfected your experimental conditions, and nailed down all the controls. You’ve harvested your cells and gently lysed them, now you’re ready to look at the proteins. What’s one of the most common next step in protein analysis? A denaturing gel or SDS-Polyacrylamide Gel Electrophoresis! SDS-Polyacrylamide Gel Electrophoresis, or SDS-PAGE…
Do you suspect that your favourite protein is doing something really cool? But you cannot see it because your confocal microscope’s resolution is limited. Then Stimulated Emission Depletion (STED) microscopy is what you need! With the power to smash through the diffraction limit of confocal microscopy, STED opens up a whole new world of improved…
Oligonucleotides are those smallish bits of DNA or RNA that we rely so heavily on for many of our molecular biology experiments. In their naked form, they are single, inert strands of DNA or RNA bases. But if you dress them up, you can increase their functionality. Here are some of the common oligo wardrobe…
Want a PCR method that gives you high sensitivity and is cost-effective? Then you might want to try Mediator Probe PCR. This method gives you sensitivity and limit of detection comparable to that of dual-labeled hydrolysis probes without the high cost. We all know how expensive small batch probe synthesis orders can be, especially when…
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