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Techniques

Laser in a droplet

When you hear about a laser, you likely imagine a medium-size apparatus with a light beam coming out of it, not a bacterium in a drop of liquid. Well, Turkish and British scientists went beyond ordinary imagination – they expressed a fluorescent protein in E.coli and suspended live bacteria in droplets. Illuminated droplets served as…

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The art of generating single cell clones

Making mutations in mammalian cell lines is becoming much easier, especially with advanced molecular engineering techniques such as CRISPR/Cas9, among others. However, after making a mutation, do you know if all of the cells contain the same mutation with the same expression profiles, and are therefore homogenous? If you have 100% transfection efficiency using a…

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Battle of the Methods: Whole Transcriptome Versus mRNA-seq

Maybe you want to examine the entire transcriptome or maybe you want to investigate changes in expression from your favorite gene. You could do whole transcriptome sequencing or mRNA-seq. But which one is right for your project? From budget considerations to sample collection, let’s briefly look at both to see which might be best for your…

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Optimal Conditions for Live-Cell Imaging

Live-cell imaging is the investigation of dynamic physiological processes in living cells using time-lapse imaging from milliseconds to hours. Live-cell imaging turns multiple snapshots to movies, which is in contrast to fixed-cell imaging that examines cellular activity at a time point. Typical applications of live-cell imaging that are used to study kinetic events include enzyme…

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Analyzing RNA-Seq Data

RNA-seq is based on next-generation sequencing (NGS) and allows for discovery, quantitation and profiling of RNA. The technique is quickly taking over a slightly older method of RNA microarrays to get a more complete picture of gene expression in a cell. Data generated by RNA-seq can illustrate variations in gene expression, identify single nucleotide polymorphisms…

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Breaking the Wall: How to Make Protoplasts

Non-mammalian cells, including bacteria, fungi, and plant cells, have a cell wall that maintains the shape of the cell. These cell walls are particularly strong, due to their composition as they contain polymers that create a rigid sphere around the vulnerable cytoplasm contained inside the plasma membrane. In bacteria, the cell wall includes several layers…

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Multiplex Ligation-dependent Probe Amplification (MLPA)

Multiplex ligation-dependent probe amplification (MLPA) is a molecular technique developed by MRC-Holland back in 2002. In a nutshell, MLPA is a sensitive technique that allows quantification of nucleic acid sequences, quickly and efficiently. It is performed in many laboratories worldwide, and can be applied to detect copy number changes (like deletions or duplications) of a…

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Thinking Outside the Box: Microscopy for Immunologists

When you think of an immunologist, you will likely imagine someone who studies the immune system… or maybe a person who speaks in a completely different language (CD? IL? The list goes on.). You may also think of a slew of assays that almost exclusively “belong” to immunologists, including ELISA, ELISpot, Flow Cytometry, chromium release…

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Kick-Start Your Gut Microbiome Study in Four Easy Steps

Today, the gut microbiome is garnering a large amount of media attention for its role in human health and disease. From influencing immune responses to impact our brain, the gut microbiome is an important and necessary aspect of our life. So much so, that current investigations in the gut microbiome are focusing on developing biomarkers for…

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Studying the Epigenome by Next Generation Sequencing

The epigenome has been in the research spotlight, and for good reason. Not only has it been associated with the developmental stages of an organism, but epigenetic alterations lead to disorders and have been linked to many human diseases. So, the question stands: what exactly is an epigenome? What Is the Epigenome? Simply put, the…

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RNA Strandedness: A Road Travelled In Both Directions

For most molecular biology purposes, DNA is thought of as a string of nucleotides running from 3’ to 5’, and the corresponding mRNA sequence is complementary to this DNA string. However, visualizing this quirky DNA structure for what it is – two antiparallel strands joined together – it quite important for many applications, such as…

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The Next Big Thing: Alternative Polyadenylation

What Is Alternative Polyadenylation? Processing of mRNA and its regulation plays a fundamental role in gene expression. As science progresses, alternative polyadenylation takes center stage in the undercurrents of gene expression. 1,2 Polyadenylation is part of the pre-mRNA maturation process and involves polyadenylation of the 3’ end of the emerging RNA.  This process happens to…

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The Importance of Non-coding RNAs

What Are Non-Coding RNAs? What was once considered “junk” may end up being the most important part of our genome. Non-coding RNA (ncRNA) is RNA that is transcribed from DNA but diverts from the “central dogma” because it does not code for proteins. NcRNAs are ubiquitous in eukaryotes: while 90 percent of eukaryotic genomes are…

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Will the Real NP-40 Please Stand Up? Chemical Nomenclature Woes.

One day, a colleague stopped by my workbench to ask which detergent would not break the nuclear membrane. Based on my previous experience using gentle detergents in lysis buffers, I replied, “NP-40”. However, we had two brands of NP-40. A closer look at the datasheets revealed that the chemical names were different even though they…

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