Quantcast

Techniques

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…

Read More

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…

Read More

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…

Read More

Protocols for Cloning Without Restriction Enzymes or Ligases

There are many cloning methods that do not require restriction enzymes or ligases. Read below to learn about how to achieve seamless cloning results via Topoisomerase cloning, SLIC, and Gibson. Method #1: Topoisomerase Technology Topoisomerase technology requires no special primers and no ligases – it is as easy as cloning comes. This technology is based…

Read More

Five Methods for Assessing Protein Purity and Quality

If you’ve ever worked with proteins in the lab, you probably know just how critical protein purity and quality are for downstream applications. In this article, we’ll review the multitude of problems that are encountered with ‘bad’ protein samples and how you can analyze the purity and integrity of your favorite protein prior to using…

Read More

An Introduction to Live Cell Imaging

The term live cell imaging collectively refers to the technologies used to capture images of cells in a living, active state, either as individual static pictures or as time-lapse series. Correspondingly, the applications of live cell imaging can be divided in two broad categories: image recording of cells in their natural, living state observing and…

Read More

Cloning Methods: 5 Different Ways to Assemble

Over the past few decades molecular biologists have developed procedures to simplify and standardize cloning processes, allowing vast arrays of artificial DNA structures to be more easily assembled. Are you familiar with all the cloning options out there? Let’s look at five different cloning methods you can use to get your construct. At the end…

Read More

Ligation Independent Cloning Primer Design

Ligation independent cloning (LIC) is an easy and effective method to ensure successful cloning, all without the need for ligation. As easy as the technique is, designing primers can be a bit tricky. In this article, we will present a quick overview on primer design for ligation independent cloning.

Read More

Using dbSNP and ClinVar to Classify Gene Variants

As we discussed previously, the gaps in our understanding of the human genome make variant classification an extremely difficult job. However, with each passing day our knowledge increases, and the tools to help us become increasingly more efficient. Let’s pick up where we left off in our first article about variants. After checking Ensemble to…

Read More

“Viable But Non-Culturable (VBNC)”: Zombies of the Bacterial World

Imagine that you want to test the efficiency of an antimicrobial treatment in inhibiting a certain bacterial pathogen. As part of the experiment, you expose the bacteria to the treatment and monitor the cultivability of the microorganism by counting the number of colony forming units (CFU) formed on culture media. If the microorganism is sensitive…

Read More

8 Tricks to Improve Your Negative Staining of Membrane Proteins

Negative staining of proteins is a versatile tool for structural biology. The sample preparation protocol is simple: the sample is embedded in a heavy metal stain that gives rise to increased specimen contrast. Thus, negative staining is a very convenient method to assess sample homogeneity, formation of macromolecular complexes, or quality of protein preparation. Conventional…

Read More

A Beginner’s Guide to Measuring Metabolism In Vivo

Have you ever seen a mouse chowing down on its dinner and wondered how it translates to energy? Well, that’s exactly what is keeping some scientists up at night, and luckily these questions are now becoming easier to answer in quite significant detail. Over the last couple of decades, several companies have developed ‘metabolic cages’.…

Read More

A Beginner’s Guide to Lentiviral Transduction

The use of viral delivery systems to transduce cells for gene and protein investigations has become prominent over the last 20 years. In particular, the use of lentiviral vectors permits stable expression of your gene of interest. This is all possible with a little bit of nucleic acid magic. Lentiviruses (a genus of retrovirus) express reverse…

Read More

ChIP-seq Workflows Run Best with Automated DNA Size Selection

Chromatin immunoprecipitation sequencing, better known as ChIP-seq, is a massively parallel approach for understanding the interactions between proteins and DNA. This is especially important for determining the activity of transcription factors, which is why it’s frequently used to learn about the complicated series of biological steps leading to cancer. It’s also key to many epigenetic…

Read More

Crash Course in Fourier Transform Infrared Spectroscopy

Fourier transform infrared spectroscopy (FTIR) is an extremely sensitive technique for measuring the absorption and intensity of electromagnetic radiation in the infrared region of the spectrum of either a solid, liquid or gas sample. You can use FTIR to: quantify unknown compounds identify unknown compounds study the detailed structured coordination of compounds How Does Fourier…

Read More

Old Reliable: Two-Step Allelic Exchange

Manipulating the genes of organisms is crucial for studying their functions. In times before genetic engineering, scientists would shoot bacteria with X-rays or expose them to destructive chemicals until spontaneous mutations would arise. Fortunately, current methods are more sophisticated and less torturous. Researchers now use more directed techniques to introduce mutations. There are several ways…

Read More