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Thousands upon thousands of genetic variants are now associated with every disease and trait you can possibly think of. Such traits range from cancers to blood pressure, intelligence, height, weight… and many more! This is largely because of the advent of genome-wide association studies (GWAS). However, the vast majority of genetic loci associated with these traits are…
It is never too late to take proactive measures to protect your research budget in the event of a funding lapse.
Techniques to study entire tissues, such as brain imaging microscopy, provide great insight into the biology of the whole tissue, rather than just individual cells. Taking this one step further is intravital microscopy (IVM); a newer approach for the imaging of living tissues and organs in live animals. A wide variety of organs can be…
ChIP-seq has proved amazing. Through these new techniques, we can obtain big datasets in a matter of days, making our lives in the lab easier and more efficient. ChiP-seq combines chromatin immunoprecipitation (ChIP) assays with whole genome sequencing. This makes it possible to understand where proteins bind to DNA and epigenetic modifications. Humans are not only their…
Every lab has a culture, a vibe of its own. Nowhere does the distinct character of the lab become most apparent than the way in which the lab chooses to pour agar plates. You may have heard or been told to pour plates at some point in your lab career. These “plates” could be called…
In recent years, three-dimensional (3D) scanning electron microscopy techniques have gained recognition in the biological sciences. In particular, array tomography, serial block face scanning electron microscopy (SBFSEM) and focused ion beam scanning electron microscopy (FIBSEM) (described in Three-Dimensional Scanning Electron Microscopy for Biology) have shown an increase in biological applications, elucidating ultrastructural details of cells…
During my first year as a graduate student, one of the earliest pieces of advice that I received from a senior student in the lab was to keep detailed protocols. In fact, she had a folder of her own protocols, all of them extremely detailed and riddled with notes. When she showed me how to…
Grab an overview of CRISPR technology from its roots as a bacterial defense system to how it can be utilized in health and research.
Surface plasmon resonance (SPR) offers highly efficient, label-free detection for quantifying biomolecular interactions in real-time. Two exciting SPR variants that have sprung up in recent years are SPR for cellular analysis and SPR-mass spectrometry (SPR-MS). SPR for cellular analysis allows you to study how cells attach to different substrates and each other, while SPR-mass spectrometry…
The mere mention of thesis writing causes many students to instantly reach for their panic button. I was no different. I was freaking out about the mere thought of all that writing. However, after successfully preparing and defending my thesis, I learned that the process is just that, a process. Below are 5 points I…
Good quality starting material is king for reverse transcription! Obtaining reliable results in any experiment requires good preparation. We often take reverse transcription for granted, and we don’t always consider that our qPCR might be performing poorly because of problems in that step. Since it’s quite often the reverse transcription reaction itself that causes fuss…
Cryosectioning is difficult when your tissues melt, fold, curl, wrinkle, tear, or crack. Learn how to troubleshoot these pesky cryosectioning problems.
As a researcher, it’s satisfying to manage your own projects and do the bench work yourself. After all, if you don’t have experience with a technique, you’re usually expected to figure it out (with or without direct supervision). In some situations, dealing with difficult molecular techniques is simply part of the job description. The scientific…
In this World of Microbes series, so far we’ve covered the importance of microbes in medicine including their use in vaccines, antibiotics, probiotics and protein production of antibodies for immunotherapy. Now we’ll diverge away from medicine and explore two other important fields where microbes are invaluable – food production and biofuel. Food Production When you…
If you ever worked in a biology or biochemistry laboratory, you probably already heard about ELISA. You may have even used it. But do you know what’s behind it? And how you can improve it? Let me guide you through the basics of ELISA, and introduce you to my favorite ELISA technique—AlphaLISA. First Things First… So,…
Part of the fun of science is the opportunity to conjure up hypotheses and ways in which to test them. Of course, being scientists, our ideas are highly thought out and logical. We aim to test the hypothesis which we think is the most likely explanation using the available supporting evidence. In addition, it is…
Tissue culture can sometimes seem like a black art. Too careful—your cells go down. Not careful enough—your cells go down. A butterfly flutters its wings in the middle of the Atlantic Ocean—your cells go down. It’s annoying, it’s frustrating, and there are times (and I’m speaking from personal experience here) that you’ll end up chucking…
Starting a PhD program is both an exciting time as well and a challenging one… One of the main things that keeps most PhD students up nights, is rethinking their steps in the lab during the day. Did I do that one thing I may not have? Is that one reagent back in the fridge?…
If you have sorted samples or phenotyped cells by surface expression of proteins, you’ve probably wondered how each cell is sorted or phenotyped in a flow cytometer? This question seems trivial, but in reality it took a while for engineers to figure it out. Before I get into today’s topic on “hydrodynamic focusing,” I’ll walk…
Viral vector production is a worthwhile skill that can be made even easier with a few tips and tricks. In general, transfection of multiple plasmids into a producer cell line results in infectious, non-replicative virus. However, it is important to ensure that your vector preparation is efficient, giving your experiments the best chance of success….
You might have come across protein glycosylation before. Somewhere in the recesses of your memory you might even recall reading something about the protein you’re studying being glycosylated, but what does this mean and how do you analyze it? Glycosylated proteins are molecules decorated with sugar groups as they pass through the ER and Golgi…
Keeping up to date with the scientific literature is a large part of the work-load of any researcher. Love it or loathe it, this means of sharing research findings with the larger scientific community is still the way in which most of us inform ourselves of the latest findings in our fields of research, or…
There are several methods you can use to see if your T cells are cytotoxic, but a chromium release assay using radioactive 51chromium (51Cr) is one of the oldest. It gives good results, and is great for labs that can’t afford or don’t have flow cytometry readily available. Here, I will outline a simple method…
Look out technical science writing, there’s an alternative voice in town. In the past decade, bloggers have taken to their keyboards and changed the voice of the internet. With their relaxed writing styles and ability to impart wisdom in a few short paragraphs, most of the online population consumes science blogs. Although scientists are often…
While the microscope is synonymous with biology, it is a child of physics and technology. When we learn about the microscope we learn physics—specifically, we learn about optics. Many great resources are available that explain the inner working of microscopy. And, like most things in physics, the inner working of microscopes comes down to a numbers…
Are you tired of staring at all of your sequence data? Want to know the easiest way to look at it? For complex genomics data, an appropriate visualization tool is a must have. The right genomics software will make it easy-peasy to get some results as well as test all those ideas you have. Since…
One of my favorite things about being a biochemist is to imagine everything at the molecular level—sometimes, in very corny ways. I envision the proteins I pipet and mix as dynamic characters in a molecular soap opera that intermingle with each other in complex ways. The biomolecular characters in my soap opera interact and react,…
Metabolomics may sound like a fictional character in the famous comic series “Asterix”, but it is very important in understanding systems biology and in clinical research against various diseases. Metabolomics is the last piece of a puzzle of omics applications following genomics, transcriptomics, and proteomics. It allows us to ask “What has happened and what…
There are those of us who began our careers literally in the dark. Yes, there was a time and not that long ago, that all figures had to be on film. Slide presentations were slides. Micrographs were, well, micrographs on film. Figure creation involved several steps: figures for publications had to be mocked up; then…
So, you’ve designed PCR primers to amplify your sequence of interest, and you’re ready to go. But unless you have a never-ending supply of template, polymerase, and a thermocycler with a gradient function—not to mention a hefty dose of time and patience—you probably don’t want to spend the next week finding the perfect conditions for…
Ever wanted to go to a conference, but don’t know what to expect, which one to go to, or how to even begin to ask your boss to let you attend a conference? Look no further! I have some suggestions on how to choose from the many great scientific conferences out there, how to get…
Multi-parameter data acquisition is key to the modern era of science research. I, for one, wish every single experiment that I design would give me the maximum amount of information. For example, in cell biology and immunology, we want to capture as much information (be it cytokines/hormones/chemokines) as possible about a given cell population. Of…
In Part I of AAV Production, I described how to produce crude (non-purified) AAV. In this article, I am going to tell you how to purify that crude prep. Virus purification is usually done by gradient ultracentrifugation. Two common methods involve gradients made from increasing concentrations of cesium chloride or iodixanol. A cesium chloride prep…
Working in a research lab is not a normal job. The hours are often unconventional and the tasks can run from exciting to mundane—it’s a world all of its own. Even so, your loyalty to your field and people is unmatched; there is a level of comradery you experience that is unlike any other. This…
If you study human disease, you will likely handle a pre-analytical sample or two (or hundreds). For example, you could handle whole blood, serum or plasma, tissue biopsies, urine, fecal samples, cerebrospinal fluid, or synovial fluid—to name a few. You will probably use these samples to look for specific metabolites, proteins, or nucleic acids that provide…
Today, about half of all therapeutic drug approvals by the US Food and Drug Administration (FDA) are for biological drugs. That number is expected to rise to 75 percent by 2025. When these biologics come off patent, the gates will open for a flood of biosimilar drugs (biopharmaceutical generics) that are designed to be much…
An anti-cancer drug or antibody drug conjugate (ADC) screening assay is the first step to establish the utility of a drug candidate in killing cancer cells. Nevertheless, these assays are time consuming and tedious. The purpose of this article is to make things easier when you are required to set up these in vitro screening…
Currently, there are more than 75 antibody drug conjugates (ADCs) in various stages of pre-clinical and clinical development. The combination of a targeted antibody coupled with a cytotoxic small-molecule drug (via a flexible linker) makes for a lethal and specific oncologic drug product. However, an ADC is a heterogeneous cocktail of molecules with a range…
When it comes to light sources for microscopy, there is really no such thing as the “best.” The type of light source you use depends on the system you are working with and the type of result that you want. Digital systems are usually designed to work with either a halogen or a LED light…
So, you’ve spent time planning your high-throughput sequencing experiment. You’ve chosen how many replicates to use, deliberated about sequencing depth, and kept everything RNase-free. Now you have many gigabytes of data available. What’s next? While the first step of RNA-Seq analysis is aligning your sequencing reads to a reference genome, first you need to get…
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