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Do you work with plants? Are they genetically engineered? Do you know where and how? If not, you could experience problems. After all you do not want your transgenic gene cassette to disrupt genes that would affect your phenotype of interest. In this article I will tell you about Agrobacterium-mediated transformation – a widely used…
Like most other chromatographic techniques, thin layer chromatography (TLC) separates out individual compounds from a mixture depending upon the polarity of each compound. The solvent system travels up a silica plate by capillary action and passes over the sample that you spot onto the plate. As the solvent travels up, it moves the compounds present…
Having trouble with your cloning? It might be to do with the DNA gel extraction. Get our top 10 DNA gel extraction tips to help you out.
There are some wonderful toys in the lab that enable us to open up a whole new world in science. One of those is a rather pricey and an incredibly sensitive laser-based apparatus capable of counting and sorting cells, detecting biomarkers, and engineering proteins: the flow cytometer. By propelling cells through the path of the…
The Boom method, or Boom nucleic acid extraction method, is a solid phase extraction technique for isolating nucleic acids from a solution of biological matter. This is just a fancy way of saying you use this technique to expose and remove the nucleic acids from a cell. First developed by William R. Boom, the Boom…
Human bronchial epithelial cells (HBECs) are a challenge to culture. As highly specialised cells that exist in carefully ordered multi-layered structures, they are especially fickle and finding optimum conditions to keep them happy is tricky. The cultures are also extremely sensitive to tiny changes in routine or environment. However, there are certain basic principles that…
If you want to know what is going on in the brain of drosophila you can use neurobiology imaging techniques to get a global whole-brain perspective. However, such techniques are slow compared to the rapid nature of the neuronal electrical activity, which may be better studied using Drosophila electrophysiology. Lab techniques are often shrouded in…
What do you use if antibodies are too large for super resolution microscopy? Aptamers. These are small affinity reagents (~ 2 nm!) that interact with their target in the same way as an antibody, but without the hefty backbone attached.
Do you know about algae and their potential in today’s world? Do you know how to work with algae? Algae are becoming increasingly important in the research world.
While working as biologists, we often come across mixtures of compounds, and the first question that strikes our minds is ‘what are the components in this mixture?’ One might think of using chemical assays to find the presence of specific compounds. But that sounds painful, doesn’t it? Well, the good news is that thin layer…
Size selection is a critical step in NGS pipelines, but may be most challenging for studies of small RNAs. The concept behind size selection is simple: separate a sheared DNA or cDNA sample by fragment size, and then use the resulting sizes to remove unwanted fragments. This is a tried-and-true way to get rid of…
In the previous installment of this series on western blotting, we addressed potential sources of error when your final product is completely bare. But alternatively, what do you do when too much background is the problem? You may have beautiful bands of interest—but if there is a bunch of non-specific binding, your quantification and data…
In Part 1 of these articles, you’ll have learnt about common microscope light sources and how to replace and align these correctly. In this article, we will discuss the importance of Köhler illumination and how to set up the microscope to achieve optimal imaging results. What is Köhler illumination? Before discussing this technique, let us…
Do you want the best imaging experience each time you use a microscope? Well, this is a rhetorical question, as we all desire that these delicate optical instruments are clean, free from immersion oil and correctly aligned. From the routine checking of slides, capturing images for presentations and publications, to diagnosing diseases using point-of-care microscopes,…
It took scientists a little while to warm up to long-read sequencing, but now you couldn’t pry most of them away from their sequencers with a crowbar. Long reads — we’re talking 10,000 bases and more — provide a level of contiguity and completeness in genome assemblies that simply isn’t possible with short-read sequencers. They…
The age of sequencing is undoubtedly upon us. From improving cancer diagnostics to pinning down elephant poaching hotspots, DNA sequencing is revolutionizing the world around us from the ground up. The latest video from Thermo Fisher Scientific’s “Behind the Bench” blog, 10 moments in DNA sequencing gives fascinating insights into the amazing advances being made…
Of all the sample prep steps necessary for next generation sequencing, DNA size selection may have the greatest impact on quality of results. After all, ineffective sizing can waste sequencing capacity on low molecular weight material such as adapter-dimers or primer-dimers, while imprecise sizing can prevent bioinformaticians from producing accurate assemblies. High-quality size selection can…
Do you want to know more about the story behind some of today’s big developments in sequencing technology? Illumina recently started a video series called “Adventures in Genomics” that introduces the people working on methods and applications, making big waves in our understanding of science, biology, and medicine. The company’s most recent video covers single-cell…
Western Blotting is a long established method for which the protocol varies little from lab to lab. However, there are kits available and some tweaks that can be made to the protocols that may improve your results and reduce the time it takes you to execute this popular technique. Save Time by Co-Incubating the Primary…
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),…
As a protein biochemist and a Ph.D. student, I was given the task to express a eukaryotic protein in a bacterial system. And to say that I was having a hard time would be an understatement. It took me many PCRs, cloning and transformations to get to the right construct that would eventually express the desired…
Sometimes the biggest hurdle to mastering a new topic is mastering the vocabulary. To help you master optical fibers I put together this illustrated glossary of Optical Fiber Vocabulary. Read this along with my first article “Introduction to Optical Fibers” and you will be well on your way to mastering optical fibers. Acceptance Angle The…
Normal cells are unable to replicate past several rounds of proliferation (termed the Hayflick limit) as with each round of proliferation the telomeres shorten. When the telomeres reach a critically reduced length, DNA damage is triggered leading to cellular senescence. Therefore, if you tried to culture a primary cell population it would eventually die unless…
While they may not be as in demand as when they were the basis of sequencing projects, bacterial artificial chromosomes (BACs) are still used for a wide variety of projects. Based off of the F origin of replication, BAC vectors can stably maintain up to 300 kb of sequence in a single plasmid, lending themselves…
Murine bone marrow derived dendritic cells (BMDCs) are one of the easiest primary cell cultures to generate. The beauty lies in the fact that in the end you have a large quantity of robust DCs that can be matured and used to study a variety of DC functions and DC-T-cell interactions. But there are a…
Monoclonal antibodies: You’ve probably heard a lot about them. Unsurprisingly, you may have also used them in your research. These antibodies (mAbs) are classically produced by the hybridoma technology pioneered by Köhler and Milstein in 19751: A mouse is immunized with the substance against which you need to produce an antibody. The mouse spleen cells (consisting…
A new lab toy to make it big in the last 5–10 years is the Accuri C6 cytometer (now under the BD umbrella), a low-cost instrument in comparison to the big boys. Lightweight, with a small footprint and straightforward maintenance, it’s often the cytometer of choice. It may be suitable for those labs that require…
There is something undeniably special about embryonic stem cells (ESCs) and not just because they can produce every cell type in the adult body. In vivo, ESCs are a transitory state of early development, which has been captured indefinitely in vitro. Whether you are a hardened cell culture enthusiast or have just graduated from the…
If you’re new to next gen sequencing, figuring out what to do with your results can be a daunting process. Luckily, you’re not alone—plenty of people have been in your shoes, and there is tons of information about data analysis out there. Here are some free resources you can use to get up to speed…
I think we all have been through those my-PCR-product-didn’t-get-amplified days. Sometimes, playing around a bit more with the PCR conditions brings luck, or sometimes it doesn’t work at all. These days we have access to many different types of DNA polymerases, ultrapure and buffered nucleoside triphosphates, and other necessary starting materials in convenient concentrations; but…
So far in this series I have given you an overview of how STED works and how to design your STED experiments. In this final article, I will tell you how to do two color STED and go over some tips and tricks to acquire the best images from your sample. Dual Color STED Fluorophore…
While most may think standard Taq is the backbone of PCR, many other DNA polymerase options exist. The polymerase you use significantly impacts the efficacy of your PCR, specifically on the product yield, the purity of the product, and the faithfulness with which the starting product is transcribed. Sometimes, these matter less, and quick and…
Through our eyes, seeing is not always believing. Under different lighting conditions, we tend to see the same objects as having the same color. For example, an apple will appear red whether it is lit by daylight or candlelight and a white sheet of paper will be perceived as being white regardless of the light…
When you share an incubator with a number of people it can be very hard to keep a clean shop and months, or more, of work can be lost due to contamination. The two biggest sources of bugs in an incubator are: the water pan the containers being put in and out. Both of these…
In many biological experiments the question that a researcher wants to ask is – ‘do some or all of my cells express a particular protein?’ There are many ways of doing this, which you will be familiar with e.g. Western blotting, immunoprecipitation, microscopic examination of stained cells and even mass spectrometry. Using Flow Cytometry to…
Think of the very first time you looked at cells under a table-top microscope. Here’s what you would have done in that experiment: Step 1: Grow cells. Step 2: Plate cells on to a glass/quartz slide. Step 3: Insert the slide under a microscope and look. The protocol for performing single-cell microscopy has a similar…
The ELISA (enzyme-linked immunosorbent assay) is arguably one of the most important and versatile tools in the toolbox of molecular biologists, biochemists and diagnosticians across the world. Defined by its simplicity and speed, the assay is easy to learn and perform in as few as five steps. But with so few variables to manipulate, an…
Let’s say you work with a gene, and it has wonderful potential. Excitedly, you throw your gene into the cells and voila! It’s there. Great. Now what? Genes are powerful tools for directing cell activity, but thanks to that curiosity characteristic of scientists, we want to know more: We want to be able to confirm…
Protein expression is an art. There are many routes to optimize a protein expression protocol, such as using different expression systems (e.g. E. coli, yeast cells, insect cells) or changing the expression vector or culture media for the expression host. Fortunately, optimizing the parameters mentioned above often leads to improvements in your protein expression results. However, there is one other…
Everybody’s talking about them, tens of millions use them, but do you know anything about optical fibers/cables? Well you should. In this first (of many) articles I will cover the basics of optical fibers, what they look like and what they are made of. Optical Fiber Anatomy First thing first, the terms “optical fiber” and…
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