Quantcast

Techniques

Codon Optimization 101

The intriguing thing about protein expression is that the combination of transfer RNAs (tRNAs) that translate the 3 letter codon into an amino acid (aa) far exceeds the number of existing amino acids (aa). If you do the math correctly, the maximum number of unique combinations using the triplet code to code for the 4…

Read More

Microsoft Excel Can Help You Set Up Multi-Well Plates

When you are a newbie to qPCR or qRT-PCR, it is quite common to write everything down in your lab notebook and then tediously mark off reagents or samples as you add them. People typically start with a master mix for items you add to multiple samples such as (Mg2+, dNTPs, 10X PCR buffer, additives,…

Read More

Those Site-Specific Recombinases in Your Tool Kit

Most of us are aware of genetic engineering systems like Cre-Lox, TALENs, Zinc finger systems, and of course, CRISPR-Cas9.  These are all examples of CSSR- Conservative Site-Specific Recombination. We use these site specific recombinases routinely, but do we really know about them or what the future hold for these tools? It turns out that CSSR…

Read More

How to Genotype T-DNA Insertion Mutants in Arabidopsis

If you are a plant biologist and working with the model plant Arabidopsis thaliana, undoubtedly you are a great fan of The Arabidopsis Information Resource (TAIR).   You also probably order seeds/materials from the Arabidopsis Biological Resource Center (ABRC), or request them from fellow scientists. Of course, seeds are one of the basic materials you…

Read More

Intercalating Dyes or Fluorescent Probes For RT-qPCR?

The unique feature of real-time quantitative polymerase chain reaction (RT-qPCR) is that it associates the amplification of your target gene with a fluorescent signal in a quantifiable manner. Presently, there are numerous fluorescent tool kits/methods to consider when designing your RT-qPCR experiment. However, the two major categories to choose from are fluorescent intercalating dyes and…

Read More

Crash Course in Microbial Identification

Welcome to this crash course in microbial identification methods! Here, you will get an overview of the traditional and modern methods available for the identification of bacteria, yeast or filamentous fungi to the species level. Species level identification allows you to discriminate confidently between two species from the same genus, something that is often essential in the treatment of infectious…

Read More

Maxam-Gilbert Sequencing: What Was It, and Why It Isn’t Anymore

In the mid-1970s, two methods were developed for directly sequencing DNA: the Maxam-Gilbert sequencing (or chemical sequencing) method and the Sanger chain-termination method. Indeed, in 1980, both Walter Gilbert and Frederick Sanger were awarded The Nobel Prize in Chemistry for “their contributions concerning the determination of base sequences in nucleic acids”. Actually, each got a…

Read More

Applying Your MALDI Matrix Like a Boss

Matrix-assisted laser desorption/ionization (or simply, MALDI) is a type of mass spectrometry method. If you are new to mass spectrometry, check out our excellent primers, titled How Does Mass Spec Work and Get Out of Western Blot Hell: An intro to Mass Spec. Basically, however, mass spectrometry allows you to measure, sort, and quantify small…

Read More

Oligo Purification Methods: How, Why and for What?

Who amongst us hasn’t had the need for oligonucleotides in an experiment? It is a cornerstone in many procedures and techniques. Depending on the goal, it can be very hard to design just the right oligo for your experiment.  Oligos must have the right length; the right amount of C-G, T-A; they can’t form secondary…

Read More

An Introduction to Nanopore Sequencing

DNA sequencing is the most powerful method to reveal genetic variations at the molecular level, leading to a better understanding of our body in physiological settings, and pathological conditions. It is the beginning of the long road towards better diagnostics and personalized medicine. Even though there have been great advances in DNA sequencing technologies there…

Read More

Tips for Getting Your Neurons Firing… Consistently

Primary cultures of rodent (rat and mice) neurons are widely used for disease modeling and studying cellular mechanisms in neurobiology. If you are in this field and need help with protocols and batch-to-batch variability of your dissociated primary rodent neurons, read further below. Also consider watching several JoVE (Journal of Visualized Experiments) articles.1-24 These cover…

Read More

Guidelines for Efficient Cell Sorting – Part 1

Flow cytometry is a pervasive tool to characterize just about anything in cell biology. From quantifying the expression of surface antigens, to determining the physiological changes in cells and everything in between, flow cytometry is as indispensable to a cell biologist as a knife is to a surgeon. Cell sorting is pivotal in enabling researchers…

Read More

Brefeldin A v Monensin: How to Hunt for Proteins

As any good biologist knows, one of the easiest ways to determine if a cell is functionally active is the production and secretion of proteins in response to a stimulus. In many circumstances, the quantity of the secreted protein, and thus the level of cellular activation can be assessed by ELISA. However, if you are…

Read More

Using Synthetic DNA For Long Term Data Storage

The amount of data requiring long-term storage is growing and accelerating. Current long-term digital storage technology cannot keep up. Imagine roughly 2.5 QUINTILLION bytes of data being created everyday in this world1–2 as more computers and network infrastructure come online. For average users, a long-term storage solution is probably not an issue. However, organizations and…

Read More

Taking up the Challenges of In Vitro Monoclonal Antibody Production

Monoclonal antibodies are extensively used in research laboratories, diagnostic products and immunotherapy and have multiple advantages over polyclonal antibodies. They exhibit enhanced specificity to single epitopes, have little or no variability, and are easy to modify and customize as required. The History of Monoclonal Antibodies In 1984, Georges Köhler, César Milstein, and Niels Jerne received…

Read More

Seeing Your Way Clear: Corneal Stem Cells from Bench to Bedside

Welcome to the first Bitesize Bio article focused on the cornea. As you read this you are peering through at least one cornea—a thin layer of cells on the surface of the eye. The cornea is the eye’s first line of defense against harsh environmental assaults, such as dust, infectious microbes and errant mascara, all…

Read More