Immunohistochemistry: Getting The Stain You Want
Need a simple, error-proof protocol for using immunohistochemistry to stain your slides? Here’s a protocol to try – from dewaxing to mounting.
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Need a simple, error-proof protocol for using immunohistochemistry to stain your slides? Here’s a protocol to try – from dewaxing to mounting.
One of the many perks that we often experience as graduate students is the chance to work with a collaborating lab on a research project. A successful collaboration results in: I recently came back from a visit to one of my collaborator’s lab, and wanted to share the aspects that I felt were most important…
If you google “What’s hot in medicine,” you will see the word “gut microbiome” popping up in every corner of the webpage. Microbes keep your body functioning in balance – from digesting complex carbohydrates to fighting off foreign pathogens and educating your immune system. They have even been linked to maintaining brain function as well….
Flow cytometry remains unparalleled as a single-cell analysis technology. The ability to analyze 14 or more fluorescent parameters on a million cells or more allows for detailed understanding of complex biological processes. The Problem With Traditional Flow Cytometry One limitation of flow cytometry is the reliance on fluorescent tags. Even with careful panel design, loss…
How long has it been since you checked your lab freezer? Remember that plasmid you designed? How about that cell line you developed that now sits idly in the vapors of a liquid Nitrogen tank? And the novel peptide or enzyme from a few years ago that remains buried in permafrost? It’s time to revisit…
Mass Cytometry is a relatively new technology which has recently featured in many high-impact journals. You may have read about instruments including the CyTOF, CyTOF2, and more recently, the Helios. With these instruments becoming more widespread, you might find yourself asking, what is mass cytometry, and what can it do for you? The Basis: Conventional…
To isolate your protein, you are going to need to tag it with something that will allow you to fish it out of the bacterial protein soup. This is where transition metals can help you out!
Scientists today depend heavily on many molecular biology techniques to perform their research. For example, with the advent of next generation sequencing (NGS): scientists are able to look at very minute details, right down to individual genetic sequence variations. However, the increase in experimental complexity means that every extra step becomes more crucial than…
Nowadays, it is no longer absolutely true that applying for a PhD means that you are striving for an academic position in the future. Although a majority of graduate students are certainly still aiming for a career in academia, and will thus benefit from doing a postdoc or two, more and more graduates are pursuing…
Do you fear failure every time you do an experiment?Do you feel constantly stressed about obtaining poor results?Do you feel personally culpable when an experiment goes wrong?If you answered “yes” to any or all of these questions, you may be suffering from perfectionism. For a scientist, this is a particularly damaging trait that needs to…
Ion Torrent technology, when it was introduced in 2010, was one of several machines that promised to revolutionize genetics. These were benchtop machines that showed their prowess in quickly sequencing smaller exomes and other DNA samples (about 10-20 million bases per run, compared to Illumina HiSeq, which could read 250 billion bases in a run)….
Unless you are one of those rare breeds that do organization naturally, setting a system in place to archive your experiments takes practice and perseverance. It’s hard to imagine when you are doing an experiment for the 100th time that you will ever forget how to do it; but a year down the line, when…
So, you’re sitting there with your list of significant SNPs, thinking, “what do I do now”? Hopefully this article can point you in the right direction! So far, you will have extracted genomic DNA from your organism of interest, sourced the SNP chips required, and had the DNA run on these chips. The chips will…
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.
How do we decide whether our research is having an impact or not? Is there a way to quantify the effect or judge the quality of the articles? Read on to find out about the nuances behind “impact factor.”
A disruptive sequencing technology Every new generation, a new concept is born and can completely reshape the landscape of biomedical research. Nanopore sequencing technology, although still at its infancy, is beginning to look like a “game-changer.” It’s a revolutionary concept in sequencing in which strands of nucleic acids are fed through a tiny pore (nanopore)…
The resolution of any microscope is related to the numerical aperture of the lens and the wavelength of light used to form the image, and can be calculated using Abbe’s law. This, however, is the ideal situation – the best case scenario. In real life, resolution must be defined in terms of contrast, and there…
Finishing my third year of grad school, I can’t help but notice what a balancing act it has been- research and relaxation, finances and fun, beer and…not beer? I wanted to write this article to advise incoming first years and veteran grad students – even those mysterious 7th year students- on graduate school and the…
When choosing a model system for culturing tumor cells, we often think of the obvious tried and tested models. In vitro methods include cell lines that have been specifically selected to grow in culture flasks in incubators. While conveniently available, consistent and reproducible, cell lines are limited in that they may not represent the desired…
Deciding to start a family with your partner is one of the most exhilarating and frightening times you’ll likely ever experience, outside of welcoming the little F1 to the world that is. Your job should not be an inhibitory factor in making that decision. We all know that post-docs live in a purgatory of sorts:…
First of all let me say the technique of labeling tissues (immunohistochemistry, IHC), and cells (immunocytochemistry, ICC) is indeed immunoscience NOT alchemy, though at times it may certainly seem like alchemy! But to scientists inexperienced in this technique, who typically see the results of IHC/ICC experiments in the form of pretty pictures, it can certainly…
Statistics is one of the most hated subjects by biologists around the globe. In spite of its daily dose of abuse, knowledge of statistics can be a life-saver. Chi-square distribution and test is one of the most important and widely used probability distributions in inferential statistics for biology and life science students. It is generally…
Greetings, I’m a research student and I’m having a lot of trouble in finding the right antibodies for my study, because I need both monoclonal and polyclonal. And I need to start addressing some other international scientists. The problem is that I don’t know how to address the situation. If they indeed have antibodies that…
At a meeting recently, I asked two PhD molecular biologists about the last time they used a Southern blot. After nearly a minute of unrestrained laughter, they asked “Who on earth still does that?” “Maybe for a very, very specific use,” conjectured one of the scientists. When I asked the scientist who taught me the…
The more experienced hands in your lab know that molecular biology is rarely just a journey from A to B. As a result, I’ve constructed this short workflow as an introduction to genomic molecular techniques.
People would have said that a USB sequencer not much bigger than a memory stick which could sequence genomes in 50kb+ read-lengths was impossible “’Star Trek’ technology!” Now, that futuristic technology is here.
“It didn’t WORK!” The panic was tangible. Anyone who performs PCR on a regular basis is used to the ups and downs involved, but it occurred to me that this might be the first time in the student’s academic life where he had actually failed at something.
On the surface, it would seem easy enough to pick an enzyme (or an amount of enzyme) for an experiment. Just look at the concentration on the label, adjust accordingly, and you’re on your way. Alas, not with enzymes. The number of units used to measure enzymes is dizzying. However, it’s better now than it…
Genomic Science has come a long way since the early days of Sanger sequencing in the 1970’s. Today, there are jazzy new sequencing technologies that include fragment analysis, epigenetic sequencing, RNA/transcriptome sequencing and Next Generation Sequencing (NGS). Increasingly these technologies are becoming more accessible, but they still require highly specialized (read: expensive) equipment. Unless your…
Obtaining external funding for your project through an NIH grant is a coup at any career stage. However, obtaining one of these grants is much easier said than done. Here is some advice from someone who has been through it and lived to tell the tale.
As biochemists, we routinely run SDS-PAGE to analyze our proteins. Imagine the time and effort you are going to save when you can run every gel to perfection.
gif by Kronin Okay not talking about that kind of matrix. But the kind of matrix that is crucial for MALDI (Matrix-Assisted Laser Desorption Ionization). I talked briefly about MALDI in my last article, Imaging Mass Spectrometry: The New(ish) Kid on the Block. Now I want to tell you more about MALDI, specifically the matrix….
It doesn’t matter how excited you are about the research or how intriguing the biology is, if you cannot record it – and record it well – it won’t matter. Here I will tell you how to take the perfect electron micrograph.
In part I, I answered the question, “How do proteins in thermophiles survive under high temperatures?“ In this part, I’ll look look at how nucleic acids survive -thrive, even- in conditions that are too hot for most of us, but ideal for a number of organisms, including the one that gave us Taq polymerase and…
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…
The most comprehensive way to evaluate DNA concentration and purity is to use both UV spectrophotometeric measurements and agarose gel eletrophoresis. This quick reference guide gives an overview of the information that can be derived from both. UV spectrophotometric measurement of DNA concentration and purity DNA itself, and most of the common contaminants found in…
In real life, cells are instructed to commit suicide for the greater good of the organism. The programmed cell death (apoptosis) is important during development of a multi-cellular organism. A good example you will appreciate is the dis-appreance of the tail from a tadpole as it turns into a frog. On the reverse, the lack…
Need tips for surviving being the newbie of the lab, and what you can do to handle all the possible personality types you may encounter. Read on.
Interested in whether your protein uses oxygen to mediate reactions? Wondering if oxygen is keeping your enzyme from its duty? Then what you need as an anaerobic tent! These tips provide some basic knowledge to help you perform experiments using an anaerobic tent. What is an anaerobic tent? Most biologists who work in oxygen-free environments…
You have a new plasmid, now what do you do? You are excited to go further with your project. But before you can move on, you have to confirm the presence of your insert as well as the sequence and orientation of the insert. Is the insert the right size? Most people use restriction enzymes…

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