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The primers for your gene of interest have finally arrived in the mail, and you’re ready to figure out whether your favorite gene’s expression level is elevated in those precious tissue samples. Only one small last step before you can proceed. Primer validation. This is a standard procedure where you run PCR or qPCR on…
Studying DNA–protein interactions is an important aspect of molecular biology. Researches use a variety of methods to study these like the chromatin immunoprecipitation (ChIP) assay, electrophoretic mobility shift assay (EMSA), DNA pull down assay, luciferase reporter assay, filter binding assay, yeast one hybrid system, etc. Another interesting assay that helps investigate DNA–protein interactions is the…
Interest in the three-dimensional structure of chromatin has exploded over the past few years—and for good reason! We now know that DNA isn’t randomly piled into the nucleus like a bowl of spaghetti, but arranged in functional loops and domains, more like a city blueprint. This is particularly exciting to (epi)genomic scientists, because 3D chromatin…
Automated image analysis uses finely tuned software to extract data from digital images. Algorithms recognize specific shapes and patterns in the images and gather quantitative information that is then used for further data analysis. The pharmaceutical and biological research industries have benefitted greatly from this technology, which allows researchers to analyze hundreds—if not thousands—of samples…
Thinking about studying extracellular RNA and in particular microRNA? Read on for some great tips for extracting circulating microRNA.
As an undergraduate student, one of the first experiments I did was staining chromosomes in mitotically active onion root tip cells. The stains that are conventionally used for this purpose are acetocarmine or aceto-orcein (which smell like vinegar). However, the cost of these stains is quite high. Personally, I find safranin, which is another stain, more…
Kidney Modeling with Kidney Organoids Derived from Human Pluripotent Stem Cells Stem cells are a valuable tool for kidney disease modeling as well as experimental regenerative medicine and drug screening. There are more than twenty different cell types in the mature kidney, which adds to the complexity of the model, but also provides the opportunity…
Is ELISA giving you the blues? The frustrating kind, not the lovely kind you get while watching the enzyme substrate reaction! This age old assay has the perks of being quick and fairly simple to perform, but when conditions are not perfect, ELISAs can deliver less than optimal results, and fail to be consistent and…
Welcome back, fellow flow cytometry friend! I am sure that you are rocking your data acquisition at this point, having perfected your understanding of panel setup, fluorophore usage, and using the flow cytometer of your choice. However, with as many samples as you are running, it is possible that you may be experiencing a little…
My favorite reason for being a biologist is that I am endlessly amazed by how life adapts to various pressures on planet Earth. This especially holds true for endospores, one of nature’s most resilient means of surviving for thousands of years in non-ideal environmental conditions. In this article, we’ll explore some of the extreme environments…
The technology for DNA sequencing was developed back in 1977 thanks to Frederick Sanger. It took a bit longer before it was possible to sequence a complete genome. This is because we needed an appropriate mathematical model and massive computational power to assemble millions or billions of small reads to a larger complete genome. Today’s…
Ever since the invention of the first compound microscope by Zacharias Jansen in 1590, our understanding of the microscopic world has grown exponentially. Microscopes have evolved from mere assemblies of magnifying lenses to extremely powerful tools for visualization on the atomic scale. You can find a wealth of information on the workings of a microscope…
We all know the impact fluorescent proteins have had in advancing cell biology. Although fluorescent proteins have revolutionized the field, they aren’t perfect and like all things research, they have their limitations. If you’re looking for a genetic tool with superior fluorescent properties, or one that allows you to introduce a variety of labels into…
In part 1, ‘iPOND: Fishing for Proteins with DNA as Bait’ we went on a fishing expedition and learned how the iPOND technique can help us investigate the protein landscape of DNA synthesis. In this article, we will pit iPOND against a few other widely used techniques in order to answer the question: ‘Why should…
I’m a simple molecular biologist. It’s awesome how computational biologists use math to reduce and rebuild biological phenomenon. In my own way, I also like to reduce my observations to numbers. As a budding biochemist, I need to assemble and quantify the players in my pathway to truly understand it. In particular, I am interested…
Simple BLAST searching is pretty straightforward to many of us. Just plug in your sequence, select the species genome, and hit search! But have you ever wondered what it takes to run a BLAST query using these mammoth-sized (no pun intended!) sequence databases? BLAST searching can produce dozens, hundreds, or even thousands of candidate alignments….
Even though our knowledge about genomes grows daily, and in huge leaps, we sometimes need to remind ourselves that DNA was first isolated in 1869 and its molecular structure was only identified in 1953. The PCR reaction only hit the scientific community as recently as 1983! So even though we are growing fast, we are…
For all of you who have never heard of exosomes: You are missing out on a whole new paradigm in cell-to-cell communication. Exosomes are tiny extracellular vesicles that arise from fusion of the plasma membrane with specific endosomal compartments called multivesicular bodies. Most cells types make exosomes, and release them in order to communicate with…
A lot of people today are drawn to freelancing and want to become a freelance writer. There are great benefits when you work from home (like doing work in your pajamas) or wherever you feel most comfortable. The appeal is even greater when you count in that you make your own hours and you are…
What do water pipe slime, dental plaque, and persistent contact lens case contamination have in common? All are the result of biofilms! Biofilms are aggregates of microbes that adhere to surfaces using secreted matrices. Although relatively under explored, this fascinating phenomenon plays a critical role in some of the biggest challenges currently facing medicine, ranging…
There are two types of electron microscopy—transmission electron microscopy (TEM) and scanning electron microscopy (SEM). SEM creates fascinating 2D images by bouncing electrons off the surface of the sample. I highly recommend searching for SEM samples on Google images. There are a wide variety of applications for electron microscopy. While SEM images are aesthetically amazing,…
Every man, woman, and dog is doing quantitative real time reverse transcriptase PCR (qRT-rtPCR) these days. It’s a great method to measure your favorite transcript’s expression levels. One of the big plusses (like the Swiss flag!) of quantitative PCR in general is its high sensitivity. In principle, it can detect and quantify one molecule of…
Whether you work with human cell lines or microbes, their growth is governed by the same principles. I invite you to learn about something that lies at the base of any work with cell culture, whether cells have circular or linear chromosomes: the S-curve of the population growth. The length of each phase depends on…
Allele-specific expression can occur for various biological reasons, such as gene imprinting, or differential transcription caused by mutations, or single nucleotide polymorphisms (SNPs), or epigenetic alterations. Traditional end-point RT-PCR or qRT-PCR-based methods only detect overall levels of mRNA expression from a given gene rather than mRNA transcripts originating from individuals. If your project requires more…
No, iPOND is not a sleek electronic fishing device from Apple. However, if you thought about fishing, well, you’re not far off the mark. If you find yourself wondering which proteins are present at DNA during or after replication, iPOND is an elegant technique to help you find out. In this article, I will explain…
I have worked in flow cytometry for a number of years. I’m still annoyed that many myths and imprecisions are perpetrated and perpetuated. Here is my non-exhaustive list of cytometry-related beliefs that send flow cytometrists screaming from the room or at least, being English, make me tut sadly. Forward Scatter Equals Cell Size No No…
Yeasts, such as Saccharomyces cerevisiae, Schizosaccharomyces pombe and Pichia pastoris, are routinely used in biology research labs around the world. Yeasts are easy-to-culture, unicellular eukaryotes, and make excellent model organisms because of the similarity of their genes and proteins with those of their mammalian counterparts. Yeast cells are used to study gene function, protein interactions,…
You made it. You got into the grad school of your dreams! You worked hard, you spent hours working on your application, bravely navigated your way through the interview and you now are here. So, why do you feel like maybe you shouldn’t be? Why You Might Suffer From Impostor Syndrome The dreaded impostor syndrome:…
Immunolabeling is the tried-and-true immunochemistry method of getting the stain you want onto the molecular target you want. Whether that target is contained within a large region of tissue (immunohistochemistry) or inside a single cell (immunocytochemistry), the ability to accurately label large numbers of samples will simplify your workflow and help you to achieve excellent…
The first time I did a transformation was when I worked with site directed mutagenesis. I cloned a protein sequence into the p15TVL vector, created my mutants (but that’s another story), and was finally ready for the next step: transformation and expression of my desired protein. Little did I know that my enthusiasm would fall…
Enzymes are special among proteins. It is not enough to detect them. You need to know their activity level. If you have devoted a substantial part of your research to studying proteases, like I did, you’ll know how crucial it is to choose an appropriate enzyme assay. There’s a heap of lab techniques out there…
Imagine directly creating a mutation at (almost) any site in your target genome instead of screening thousands or millions of random mutants! The CRISPR/Cas9 system does just that. In its traditional form, this forward genetics approach takes 7 steps from start to mutated genome. However, there is a way to obtain your designer genome in…
Continuing from our first article on lasers for confocal microscopy, we will now discuss two specialized types of lasers: lasers for two-photon excitation and tunable, white light lasers. We will also discuss the applications of the two lasers. Lasers for Two-Photon Excitation The two-photon absorption phenomenon was first described for microscopy in 1931. Here, the…
Before we go any further, we have to get some things straightened out: RT-PCR versus qPCR versus RT-qPCR. Sooo confusing, amirite?? They all refer to specific molecular biology assays, but the names are unfortunately used interchangeably, which can be awfully confusing for just about anyone. So without further ado: Whew! I don’t know about you,…
I am sure many of you have been there. Everything is going smoothly, and your project seems to be working out perfectly. And then there is this one PCR. For some reason, it just won’t work. It is a black dot on your record. Even though I have a scientific mind, I have to be…
In its simplest form, a bacterial growth medium is designed to support the growth of bacteria. Depending on which bacteria you want to culture, you may have a range of different media to choose from, each containing a rather unique blend of sometimes surprising (and odd!) components! In this article, I will take you through…
Once upon a time, I thought reproducible research meant if someone else showed X in a paper, then I should be able to get X in my experiment. However, this actually refers to replication, an important but separate concept. Reproducible research is data analysis that starts with the raw data and arrives at the same…
When I first told a lab colleague I was going to be doing phage work in a lab that had otherwise only dealt with bacteria, I was met with expressions of awe, and then fear. Being that a bacteriophage is essentially a predator of bacteria, this reaction is legitimate for a bacteria-loving scientist. Also, we…
In the first part of this series, we discussed the differences between a color and a monochrome microscope camera and when one is advantageous over the other. We also touched on the subject of optimal camera resolution for a given imaging system. In this part, we will tackle a few additional camera specifications and how…
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