Couples Counselling for Zebrafish: How to Optimize Breeding Efficiency

Couples Counselling for Zebrafish: How to Optimize Breeding Efficiency

It’s Sunday morning, the sun has just begun to rise, and you find yourself on the way to the lab (again!), sipping hot coffee and melancholically thinking of your abandoned bed. But something is different this time. Today, the freezing-cold wind blowing from behind is not the only motivation pushing you to sacrifice another weekend in…

4 Important Considerations for Your Cell Lysis

4 Important Considerations for Your Cell Lysis

You’ve cultured your cells and completed your treatments, now it’s time to harvest them and proceed to the downstream effects. Cell lysis is the crucial stage that determines if your experiment has a chance of producing the data that you have been waiting for. Part of the starting biological material is inevitably lost on each…

Ten Tips for Pipetting the 384-Well Plate

Ten Tips for Pipetting the 384-Well Plate

I was so excited to start using 384-well plates for my assays. With so many wells, these plates are useful for testing many conditions in parallel, as required in ELISAs, siRNA library screens, and drug treatment dilutions. However, I quickly learned that pipetting in these plates is more complicated than I thought. This article contains…

The qRT-rtPCR Control You Should Be Doing, But Probably Aren’t

The qRT-rtPCR Control You Should Be Doing, But Probably Aren’t

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…

Why You Should Use Cas9 Ribonucleoprotein Transformation for CRISPR Genome Editing

Why You Should Use Cas9 Ribonucleoprotein Transformation for CRISPR Genome Editing

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…

Need a Few More Hours in the Day?  Here Are Some Timesaving Tips

Need a Few More Hours in the Day? Here Are Some Timesaving Tips

Are you constantly looking for ways to squeeze more lab hours out of the day? Here are some timesaving tips that can help. Figure out Where Your Time Goes Not sure where you are losing those valuable hours? Use a website like Toggl to help you keep track of your time. This will make it…

Small Particles (Things) Matter!- Introducing Nanoparticle PCR

Small Particles (Things) Matter!- Introducing Nanoparticle PCR

There are many different methods and protocols on making your PCR  run more efficiently. I recently came across an interesting PCR method called “nanoparticle” PCR. This method seems to attract a lot of attention, because it enhances a PCR  by a few orders of magnitude. More interestingly, while the enhancement effect has been reported in a…

Outsourcing Research:  Should Your Experiment Spend Some Time Away from You?

Outsourcing Research: Should Your Experiment Spend Some Time Away from You?

As a researcher, it’s satisfying to manage your own projects and do the bench work yourself. After all, if you don’t have experience with a technique, you’re usually expected to figure it out (with or without direct supervision). In some situations, dealing with difficult molecular techniques is simply part of the job description. The scientific…

Faster PCR Optimization

Faster PCR Optimization

So, you’ve designed PCR primers to amplify your sequence of interest, and you’re ready to go.  But unless you have a never-ending supply of template, polymerase, and a thermocycler with a gradient function—not to mention a hefty dose of time and patience—you probably don’t want to spend the next week finding the perfect conditions for…

How to Separate Nucleotides Using Ion-paired Reverse Phase HPLC

How to Separate Nucleotides Using Ion-paired Reverse Phase HPLC

If you work in the field of molecular biology, there is hardly a day that goes by that you don’t use nucleotides. But beyond the use of the four well-known deoxynucleotides in PCR, you can use nucleotides for several other applications. For example, kinases and phosphatases use nucleotides as substrates, and phosphotransferases transfer phosphate group…

Sonication – 7 Tips for Mastering the Art

Sonication – 7 Tips for Mastering the Art

Sonication is mostly used during preparation of protein extracts to help break apart the cell. Although most lysis buffers have buckets of detergent that lyse cell membranes, sonication just gives an extra hand in breaking everything apart. Sonication also breaks up, or shears, DNA in a sample—preventing if from interfering with further sample preparation. Have…

Common Mass Spectrometry Contaminants: I Messed It Up So You Don’t Have To!

Common Mass Spectrometry Contaminants: I Messed It Up So You Don’t Have To!

Through many trials, and lots of error, I learned that there are many considerations for mass spectrometry that might not be obvious to you as a molecular biologist. Common contaminants, even in small quantities, can mask important peaks in your mass spec data and have a huge impact on the final results.

The Messy World of Human Tissue Research

The Messy World of Human Tissue Research

In neuroscience and other biomedical research fields, animal models allow us to answer critical but otherwise impossible questions. Despite the value of these models, however, sometimes nothing can replace the real deal—human tissue. The limitations of human tissue research stem from the variability between subjects and the risk for covariates that influence your results. Which…

Open and Closed:  Two Ways to Grow Your Own Algae

Open and Closed: Two Ways to Grow Your Own Algae

In my last article, I talked about the basic protocols and experiments conducted in the process of converting algae into biofuel. Our ability to culture algae has efficiently improved over the years. Continuous improvisation in basic techniques has helped us to understand the growth limiting step of algae culture. In this article, I will discuss…

The Care and Keeping of Primary Murine B Cells

The Care and Keeping of Primary Murine B Cells

So you want to work with mouse B cells? Primary murine B cells are a difficult, yet fascinating system to work with and can help deepen your understanding of an immunological system. You can study many things with primary B cells, including: immune activation antibody production cell-cell interactions between immune cells and immune phenotype These…

E.coli Electroporation vs Chemical Transformation

E.coli Electroporation vs Chemical Transformation

This is the first in a three-part series on the transformation of E.coli. By the end of this, you should be an expert on E.coli transformation and on which strains to choose for different applications. If you’re already an expert, I hope it’ll be an enjoyable refresher for you. In either case, please comment below…

SPUD’s Your Bud When it Comes to Sensitive qPCR

SPUD’s Your Bud When it Comes to Sensitive qPCR

There’s piloting a brand new technique for the first time. Then, there’s jumping through hoops trying to get an established lab technique to work. The former, in contrast to the latter, is expected to be fraught with hardships. Yet troubleshooting an old lab technique that isn’t working anymore, is frustrating at a whole new level….

10 Tips for Consistent qPCR

10 Tips for Consistent qPCR

Quantitative PCR (qPCR) uses fluorescent dyes or probes to visualize the amplification of specific DNA sequences as it happens (i.e. in real time). The dyes or probes fluoresce when they bind to newly amplified DNA, and the amount of fluorescence emitted is proportional to the amount of DNA (or mRNA) present in the original sample. By detecting newly synthesized DNA…

How to Express Proteins Across Kingdoms:  Prokaryotes vs Eukaryotes

How to Express Proteins Across Kingdoms: Prokaryotes vs Eukaryotes

In the sci-fi novel Terminal World by Alistair Reynolds, a planet consists of zones with defined characteristics of matter interactions on a subatomic level. These conditions permit different levels of technology sophistication in various zones. For example, in the “Steamville zone” nothing more complicated than steam engines works – electronic schemes fuse irreversibly. Something like…

Immunoscience or Immunoalchemy?

Immunoscience or Immunoalchemy?

First of all let me say the technique of labeling tissues (immunohistochemistry, IHC), and cells (immunocytochemistry, ICC) is indeed immunoscience NOT alchemy, though at times it may certainly seem like alchemy! But to scientists inexperienced in this technique, who typically see the results of IHC/ICC experiments in the form of pretty pictures, it can certainly…

Long-Range PCR:  It’s About Choosing the Right Enzyme

Long-Range PCR: It’s About Choosing the Right Enzyme

The ability for DNA polymerase to copy a long stretch of DNA is becoming increasingly important. Why? It has to do with the advances in our sequencing technologies. Our next generation sequencing (NGS) technology requires the DNA polymerase to copy a long stretch of DNA (sometimes up to 50kb) as NGS is churning out genetic…

Where are My Bands? Troubleshooting a Signal-less Western

Where are My Bands? Troubleshooting a Signal-less Western

Western blotting uses electrophoresis and antibody-epitope affinity to give a semi-quantitative and (theoretically) clear measure of protein abundance. It’s a long procedure, filled with many steps—and even more room for error. Learning to troubleshoot certain problems is incredibly important for continued success with this technique. So what do you do when your final imaged product…

Non-specific Binding? Tips to Sharpen up Your Western Blot

Non-specific Binding? Tips to Sharpen up Your Western Blot

In the previous installment of this series on western blotting, we addressed potential sources of error when your final product is completely bare. But alternatively, what do you do when too much background is the problem? You may have beautiful bands of interest—but if there is a bunch of non-specific binding, your quantification and data…

Roadside Assistance: Fixing Your Broken-Down ELISA

Roadside Assistance: Fixing Your Broken-Down ELISA

The ELISA (enzyme-linked immunosorbent assay) is arguably one of the most important and versatile tools in the toolbox of molecular biologists, biochemists and diagnosticians across the world. Defined by its simplicity and speed, the assay is easy to learn and perform in as few as five steps. But with so few variables to manipulate, an…

Keeping On Top of Housekeeping Genes

Keeping On Top of Housekeeping Genes

Want to measure how much mRNA you have in a particular sample? Easy! Make some cDNA, add some fluorescent DNA-intercalating dye, pop it into a quantitative real-time PCR (qRT-PCR) machine and Bob’s your uncle! You have your result! Easy right…? Not so fast. As with any scientific assay, qRT-PCR requires some optimization. First, you need…

Importance of Antibody Titration in Flow cytometry

Importance of Antibody Titration in Flow cytometry

After designing a multicolor flow cytometry panel and securing the necessary cells and reagents, the process of optimization of the panel can begin. The first step in that optimization is titration of your antibodies. In this process, following a standard protocol to be used in the final analysis, you stain a known amount of cells with…

Get Great Yields by Optimizing Your Bacterial Cultures

Get Great Yields by Optimizing Your Bacterial Cultures

Bacterial cultures may be much easier to grow than mammalian cells, but if your yields are suboptimal there are plenty of parameters to play with. Here we list a few of the things you should consider to maximize your culture growth. Shaking speed Shaking is performed to allow aeration of your culture, which is of…