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Techniques

NGS Target Enrichment Strategies

Next-generation sequencing (NGS) has ushered in a new era of understanding of both the inner workings and the function of the genome. NGS allows researchers to look at traits—including diseases—that are linked to differences or mutations in an individual’s genes. Since only about 1% of the human genome constitutes genes that code for proteins, several…

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How to Feed Fruit Fly Larvae Small Molecules

Generally speaking, fruit flies are a great model system. Not only are they small, thus taking up very little space in the lab, but their adult lifespan is only 40-60 days, so you can track age-dependent changes without having to wait months and months. Fruit flies also display complex behaviors and more than 75% of…

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Cryofixation and Chemical Fixation for Electron Microscopy

Specimen preparation is the most important aspect of biological electron microscopy (EM), as it influences everything from the preservation of the sample itself to the kind of information that can be obtained. It is vital to define the questions you are asking of the sample before embarking on an electron microscopy project. This enables you…

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The EMSA – Teaching an Old Dog New Tricks

Probing Nucleic Acid-Protein Interactions with EMSA The electrophoretic mobility shift assay (EMSA) is a powerful technique for detecting specific-binding of nucleic acid-protein complexes. Over the past 30 years, EMSA has been the “go to assay” to investigate the qualitative interactions between nucleic acids (DNA or RNA) and nucleic-acid binding proteins. Through the use of radio-labeled…

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Emerging Model Microorganisms Take to the Stage

Estimates indicate that there may be up to 2 billion living species of organisms, each with conserved and unique biological mechanisms that are vital for survival. How do scientists understand them all? Enter model organisms. Model organisms, as the name implies, are living things which are used as representative models for understanding other organisms. They…

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Isolating Bacterial RNA from Blood

For many decades, the only way to detect sepsis – bacterial growth in blood – was isolating the bacteria and growing bacterial colonies on a special medium. This was done by first spinning down the blood, which brought the blood cells and bacteria into the pellet. The pellet was spread on a blood agar plate…

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Ultramicrotomy for Electron Microscopy

Ultramicrotomy is the process by which a sample is cut into very thin slices or “sections”, usually for imaging by transmission electron microscopy (TEM) or relatively new techniques using scanning electron microscopy (See Array tomography in three dimensional scanning electron microscopy for biology). This technique requires a bit of finesse, and this article will help…

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How (and Why) to Label Nucleic Acids

Have you ever wished you could snag individual strands of DNA or RNA with a lasso? Or look at them one by one, figuring out exactly where they are or what they are doing? Fortunately, there are techniques that exist to label nucleic acids for their visualization and purification! Nucleic acids can be labeled at…

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Gender Reveal: How to Determine the Gender of Drosophila Larvae

Drosophila melanogaster, otherwise known as the common fruit fly, is one of the oldest and most powerful model systems used in biology. Fruit flies are cheap to maintain, and have a shorter life cycle and higher fecundity than mammalian models. They also have extraordinary genetic tools with which to investigate many molecular and cellular questions.…

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The Beginner’s Guide to Reading Plasmid Maps

Very often plasmid maps, especially historical ones that are hand-drawn by a long-forgotten PhD student, are a puzzle. What are these arrows and boxes? Where do I start? Don’t worry, we have a crash course introduction into deciphering plasmid maps. Familiarizing Yourself with Your Plasmid of Interest Let’s start with a classic plasmid: pBR3221. It…

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Greenhouse Maintenance: Keeping Your (Green) Laboratory Clean

Cleaning the lab is one of the hardest jobs because it’s dull and repetitive. However, nobody in their sound scientific mind would argue that this can be avoided. Dust accumulates bugs, bacteriophages, and RNAses that can stray into your experiment and ruin it. Old boxes piling up is a fire hazard. Anybody who refuses to…

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An Introduction to Alexa Dyes

Long before “Alexa” was a household name, Alexa dyes were an established series of fluorescent dyes. The inventor Richard Paul Haugland named the dyes after his son Alex. Originally a trademark of Molecular Probes, the Alexa family is now a part of Thermo Fisher Scientific. Alexa dyes are frequently used as labels in fluorescence microscopy,…

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10 Tips on Mating Mice Successfully

Tiny, furry, spinning around a wheel – few creatures are as endearing as the lab mouse. Trying to obtain reproductive success with them, however, can leave you spinning your own wheels. Why is it that what works so well for the animal facility staff, or experienced technician, seems to be beyond your reach? After all,…

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How it Works: Storage Phosphor Screen

Radioactivity is still the most sensitive detection mechanism for many macromolecules and enzymatic activities. In graduate school, I performed countless radioactive kinase assays, watching the radioactive gamma 32P of ATP get transferred to my autophosphorylating receptor of interest, and then separating my protein from free hot ATP on a gel. The gel is dried, covered…

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3 Ways to Use Flow Cytometry for Your Activation Experiment

Studying immune cell activation allows scientists to understand the way the body mounts a response to a specific infection, autoimmune diseases, or cancer. This knowledge plays a direct role in developing more efficacious vaccines and therapies. When tasked with capturing information on immune cell activation, flow cytometry remains the gold standard due to its versatility,…

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The Rites of Passage: Subculturing Microorganisms

Anyone who has worked with microorganisms, be it bacteria or yeast, is familiar with subculturing – the act of transferring some cells from a previous culture to a fresh growth medium. You do it either to reset the growth phase of your culture or to increase the biomass for downstream experiments. But there’s more to…

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Generating RNA-seq Libraries from RNA

One of the most powerful methods of modern cellular biology is creating and analyzing RNA libraries via RNA-sequencing (RNA-seq). This technique, also called whole transcriptome shotgun sequencing, gives you a snapshot of the transcriptome in question, and can be used to examine alternatively spliced transcripts, post-transcriptional modifications, and changes in gene expression, amongst other applications.…

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