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The development of new drugs requires reliable and robust animal disease models. Since the cause of many diseases is still unknown, it is often difficult to identify adequate and predictive disease models. For example, researchers developing treatments for neuropsychiatric diseases such as Parkinson’s and Alzheimer’s face a particular challenge given the subjectivity of many of…
In my previous article I discussed steps you can implement to ensure that a sample is ready for cell sorting. But now it’s time to make sure the sort worked. Here are a few sorting checks and measures to ensure that all’s well that ends well. Post-sorting Checks and Measures Re-evaluate Your Catch Tubes Sorting…
The first thing one might notice when working with metallo-proteins is that they offer unique, colorful reactions. These colorful reactions are based not only on the metal, but the ligand, or coordinating molecules. Approximately 80% of proteins contain inorganic cofactors like iron (Fe) and copper (Cu) metals necessary to catalyze a reaction. Understanding how these…
The use of restriction enzymes to characterize DNA has been popular since the 1970s. Today, this “old school” technique is still one of the easiest and fastest ways to assess DNA sequences. Like most lab reagents, restriction enzymes can be fickle and you should bear a few things in mind when using them. Generally, sticky-ended enzymes have greater…
Mammalian cell culture techniques are not something you learn from a book, per se. And because of this, it is important to be properly trained, especially in sterile techniques. It is important to keep your cell lines from contamination and just as important to keep yourself safe. Nevertheless, people tend to do things a little…
From Alkaline phosphatase to Warthin-Starry, we take you through the various histology stains available.
Are you stressing about applying for grant funding early on in your career? Are you worrying about lack of preliminary data or lack of experience in your current field? Here are some tips that can help. Why Apply at an Early Stage of Your Career? All of your experiences build upon each other to strengthen…
Next generation sequencing opened the doors to our genome. It gives massive amounts of information in a week – whereas Sanger sequencing takes thrice as long, and causes lab lesions due to the abusive use of pipettes. Indeed, with minimal hands-on procedures we obtain a lot of data. But nothing in Science is ever easy….
Rapid genomic analysis offered by next generation sequencing (NGS) is ideal for personalized medicine approaches to clinical genetics, microbiological profiling, and diagnostic oncology. Many standard clinical samples are preserved as formalin-fixed, paraffin-embedded (FFPE) tissues, which presents obstacles for use in NGS analysis. FFPE tissue preservation has the benefit of keeping samples intact for histological examination…
Construction of high-quality sequencing libraries is pivotal to successful NGS, and DNA quality is one of the most critical aspects of library preparation. As this Nature Methods paper illustrates, DNA shearing involves appropriate and consistent fragment sizes for sensitive and accurate sequencing, and the fragments must be accurately analyzed prior to sequencing to measure molarity…
Bacteria are the workhorses of many molecular biology laboratories, and mastering the basic techniques to manipulate bacteria is an important stepping-stone towards achieving great results. When isolating DNA from bacteria, it is important to start with a single colony to ensure a homogenous population of bacteria in your culture. Isolating a single bacterial colony from…
When you work in a laboratory, preparing samples sets for many different experiments is a large part of the job. Keeping track of your samples can be tedious or even challenging if you don’t already have a good system in place. However, getting this right is a critical part of the experimental process. In this…
If you’ve ever been on the job market, you know how many job applications you can end up filling out and submitting. Sometimes the entire process takes months or even years to culminate in the right job offer! It can be overwhelming to keep track of what you applied for and when. This is especially…
According to Bill Nye, “Science rules!” – and I think most of us would agree. We are learning more and more about the world around us each day, as well as about ourselves. But is there a difference between a Science Fan, and a Scientist? Everyone has their own parameters, but below are some that…
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…
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,…
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…
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…
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…
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…
One of the biggest favors you can do for yourself as a postdoc is to get a personal postdoctoral fellowship. Your own funding covers your salary and (often) some research costs as well. As such, you will have a degree of independence that you would not have otherwise. Also, being able to show that you…
How time flies. One day you are giving your first presentation in front of your fellow students, seemingly the next you are listening to a presentation by your own student. And frankly, the talk is awful. It’s twice the time limit, the student weaves around the topic as a drunken sailor, and she acknowledges her…
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…
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…
For the longest time I just couldn’t decide between medical school and graduate school. I mean come on, being a physician would be great. I could save lives just like they do on TV! But on the other hand, being a biomedical scientist excited me just as much. You can’t tell me you’ve never dreamt…
Primary cultures of rodent (rat and mice) neurons are widely used for disease modeling and studying cellular mechanisms in neurobiology, using a variety of techniques including neurobiology imaging. 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…
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…
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…
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…
Pulling an over-nighter is a common theme for many of my college friends. I, however, like my sleep—particularly between midnight and 7 am. Therefore, I tend not to stay up late to study and avoided jobs that required me to work a night shift. Then, I went to grad school and had to put in…
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…
We use fluorescent in situ hybridization (FISH) techniques routinely to detect DNA or RNA sequences in tissues, but what about micro RNAs (miRNAs)? No worries, FISH is now optimized to meet the challenge. To help you get going with the method, here’s what you need to know. The first thing that comes to mind when…
Purchasing a microscope camera is one of the most daunting tasks you might have to undertake. Before you set out to buy that camera, carefully consider your applications. Things like sample brightness or the speed of the phenomenon you are trying to capture can dictate your choices. Also, this is the time to make peace…
When I first learned how to design scientific presentations, I kept hearing the same advice from well-intentioned mentors: “Make sure your presentation tells a story!” they’d say. I understood what they meant in principle, but I had difficulty implementing this advice in my own presentations. In this article, I’m going to share a simple way…
In a previous article, we took a quick journey through the wonderful world of microbes. Let’s take a step back now and have a closer look at the benefits of microbes. We will also look at reasons to avoid many of them. For example, the ‘plague’ which is caused by a particularly nasty bacteria called…
Interested in the detailed structure of your tissue? High-resolution imaging techniques, such as brain electron microscopy, provide an intricate view of your tissue. While it may be a rather complicated procedure with nasty chemicals, the advantages of epon embedding can make it the best choice for morphological studies. The hard blocks are excellent for structural…
Tissue embedding and sectioning is a backbone of many biological research labs. While commiserating with other grad students over tedious hours spent in the lab, you’re probably aware that there is more than one way to slice up a chunk of tissue. We’ve previously introduced what to consider when choosing a tissue embedding medium and…
There’s nothing better than relaxing at the end of a long week with a good movie. As scientists, we are drawn to analyze (and sometimes overanalyze) the accuracy of science movies and especially their portrayal of scientists. Being the movie aficionado that I am, I looked for movies that are not typically touted for their…
It often happens that you do everything right with a PCR. You have perfectly isolated template DNA, used sterile tubes and tips, used clean reagents, and said a quick prayer to the PCR Gods. And still, something unknown messes up your results. This unknown at work is generally a PCR inhibitor. Before you blame it…
Pop Quiz Time: You get a new bacterial strain from a culture collection, but you’re not quite sure what the genetic notation (i.e., all the letters and symbols) means. Do you: A. Cry? B. Ask around to see what your lab mates think? C. Cross your fingers that your friends at Bitesize Bio can help…
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