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Researchers have always been in search of model organisms that can be used to study and explore biological phenomena to make discoveries that can be extrapolated to more complex higher organisms like humans. Of the various model organisms developed and used, starting from the ubiquitous E. coli and S. cerevisiae to the humble D. melanogaster…
Hello, my name is Emilee and it’s been 5 months since I last yelled “That’s it, I quit graduate school!” It comes in waves, like the build-up of ripples at the beach followed by the crash against the shore’s rocks, or the slow and steady climb up a rail on a roller coaster followed by…
There are several methods for size-selecting DNA fragments prior to sequencing. How do you choose which is best? Here’s a look at various options, plus considerations to help you determine when to use each one. Manual Gels Virtually every student in a biology lab knows how to prepare and cut a manual gel—but their ubiquity…
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.
Selecting fluorophores can be a tricky business, but we’ve got you covered in this handy how-to guide.
In this article I will not talk about ‘wild’ proteases, which destroy cellular proteins in your lysates like wolves destroy sheep. Instead, I’ll be talking about the shepherd dog proteases—purified, tame and useful to digest proteins your research. In Protein Research and Crystallization Several programs can predict your protein domains. However, we wet biologists know…
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…
I’m an anxiety-ridden stress ball 90% of the time. Graduate school only amplifies my nervous energy, and it’s a struggle. However, recently, while I rushed to catch a bus, I had a life altering experience using a mental technique called “reframing” From “Flipping Out” to Flipping the Switch to “Cool” It rained heavily. I balanced…
Mass Spec is all about getting the perfect peaks. Without a good peak assigning the correct mass is impossible and you cannot make accurate identifications. Make sure you know how to adjust your MALDI-TOF instrument parameters to achieve your perfect peak. In our previous posts ‘How does Mass Spec Work’ and ‘Imaging Mass Spectrometry: the…
Academia or industry? Basic research or applied research? You are thinking of what to do next. What is right for you? Honestly, it is a never ending discussion. So what should you do? Here are some insider tips from a person who has worked in both biotech industries and universities. The Freedom to Manage your Own…
While many scientists are methodical and precise, some of us like to live on the edge. Read a protocol all the way through? No thanks, I’ll take my chances and guess what concentration of HCl I should use. Label my tubes with the correct content? Puh-lease – it’s much more exciting deducing which is which…
Fortunately for microscopy users, measuring intracellular fluorescence has been made relatively simple through an ImageJ plugin called the Cell Magic Wand. For those of you unfamiliar with ImageJ, it’s a popular image processing program that runs on Mac, Windows, and Linux. How to use ImageJ for measuring intracellular fluorescence First of all, to begin measuring…
An academic lab is a unique working environment. Lab members are expected to take responsibility for their own research projects and perform the work quickly and efficiently. However, unlike an industrial or corporate setting, there are often no clearly defined management structures. This means that when it comes to communal equipment, reagents and resources, individual…
When you think of microbes what comes to mind? Moldy bread, Penicillin and antibiotics? Vaccines? Fermented food, like yogurt and kombucha? And the latest Probiotics health craze? How about antibody production for immune therapy? Maybe not so much, but you should know that the use of microbes is wide and ever growing. Now researchers are finding…
Apoptosis, often called programmed cell death, is a carefully regulated process that is part of normal development and homeostasis. Apoptosis is morphologically and biochemically distinct from necrosis, which is conversely called accidental cell death. Dysregulation of apoptosis is implicated in disease states such as cancer, autoimmune disease and degenerative conditions. Apoptosis consists of an orderly…
A good scientist must see to believe… but if you just landed in the lab and things aren’t working, maybe it’s not you. We all love to try and save our hypothesis, but in this publish or perish climate, looking the other way during truth bending happens, and it happens a lot. Here are some…
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: These cells can be fickle to work with, but here are a few…
Without good planning and preparation, writing your thesis can be a nightmare. Here are some tips on how to make the process a whole lot easier.
Are you planning to do cellular immunology research? Then chances are you will be introduced to the flow cytometer – “a modern immunologist’s best friend.” This modern magic box is a highly versatile machine packed with cutting-edge fluidics and photonics (lasers). Combined with the monoclonal antibodies conjugated to fluorochromes capable of emitting light signals from a…
Put in the time now to optimize protein solubility so you don’t have to suffer later! With this in mind, here are some considerations and tips for selecting the optimal conditions for recombinant protein expression and purification.
If there is one profession that benefited from globalization, it is the medical writer. While the university research groups shrink and global biomedical companies fire their research stuff, medical writing companies are expanding, providing stable jobs with good salaries. The American Medical Writers Association (AMWA) reported in 2011 that the median salary of an experienced…
Has your supervisor asked you to do a polysome profile? Are you attempting them but running in to problems? This article will help explain what they are, the basics of the protocol and provide some helpful tips (including some things that I wish I had known when I first started out). Polysome Profiling: The Basics…
Photography has undergone great improvements in the last few decades. In times gone past, photographic film was used. Now most researchers use digital means to capture their images. But not all digital cameras are the same. For optimal results you need to know the different types of microscope cameras and how they work. Before the…
A sprinkling of Bis-tris is all it takes improve your protein gels considerably. If you can afford it!
It’s the hot new technique. With a single procedure, you can get information about all RNA transcripts at once! It sounds like a dream. While RNA sequencing (RNA-seq) has opened the door to exciting new questions, scientists interested in pursuing this technique should be aware of the roadblocks ahead of them. While RNA-seq can be…
Sometimes working with a liquid handling machine seems a bit like wrangling a wild mustang—I know what I want it to do, but the software doesn’t work that way. That’s particularly true when working with 96-well plates. So, sometimes you have to think “outside the box.” Don’t limit yourself to what the manufacturer intended (but…
Sometimes the wide view is the best so a good genome viewer is a must for every molecular biologist. We review three leading genome viewer packages to get you started..
Routine PCR? Let’s be honest, there’s no such thing. Even with the simplest PCR reaction things can go wrong, so you need to have a good checklist of ideas for PCR troubleshooting and rectifying the problem. Today I have brainstormed all of the ways I can think of to approach problems with standard PCR reactions….
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…
The whole TLC technique sounds easy to do, but it can be difficult and tricky during interpretation or give unexpected results, especially when working with biomolecules. For this reason, it is important to be familiar with troubleshooting thin layer chromatography. Some of the common problems faced during TLC and their solutions are listed below: Solvent…
Scientific research is a demanding and stressful career requiring lots of patience, dedication and hard work. Sadly the monetary benefits are not commensurate with the effort. Moreover, lack of opportunities, uncertainty, instability and the pressure to publish makes a traditional academic science career difficult. Inspiring (forcing?) many scientists and researchers to leave their traditional science…
When starting a long-term experiment, you need to take a lot of things into consideration (availability of cells, reagents, planning time points), but do you ever think about your antibodies? If you buy an antibody from a manufacturer, run out half way through the study, and buy the same antibody again, have you thought about…
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….
Need a simple, error-proof protocol for using immunohistochemistry to stain your slides? Here’s a protocol to try – from dewaxing to mounting.
One of the many perks that we often experience as graduate students is the chance to work with a collaborating lab on a research project. A successful collaboration results in: I recently came back from a visit to one of my collaborator’s lab, and wanted to share the aspects that I felt were most important…
If you google “What’s hot in medicine,” you will see the word “gut microbiome” popping up in every corner of the webpage. Microbes keep your body functioning in balance – from digesting complex carbohydrates to fighting off foreign pathogens and educating your immune system. They have even been linked to maintaining brain function as well….
Flow cytometry remains unparalleled as a single-cell analysis technology. The ability to analyze 14 or more fluorescent parameters on a million cells or more allows for detailed understanding of complex biological processes. The Problem With Traditional Flow Cytometry One limitation of flow cytometry is the reliance on fluorescent tags. Even with careful panel design, loss…
How long has it been since you checked your lab freezer? Remember that plasmid you designed? How about that cell line you developed that now sits idly in the vapors of a liquid Nitrogen tank? And the novel peptide or enzyme from a few years ago that remains buried in permafrost? It’s time to revisit…
Mass Cytometry is a relatively new technology which has recently featured in many high-impact journals. You may have read about instruments including the CyTOF, CyTOF2, and more recently, the Helios. With these instruments becoming more widespread, you might find yourself asking, what is mass cytometry, and what can it do for you? The Basis: Conventional…
To isolate your protein, you are going to need to tag it with something that will allow you to fish it out of the bacterial protein soup. This is where transition metals can help you out!
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