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In research, choosing a model system is like choosing a partner – you want it to be a perfect fit. If you are attempting to solve problems such as finding unknown proteins in known processes, investigating unknown functions of known proteins or correlating cell biology to a function for which you want a relatively simple…
Let’s face it: the nature of behavior itself is inherently variable, whether it’s the heterogeneous socializing behavior of humans at parties, the complex aggressive behavior of rodents when they perceive a threat, or the intricate courtship behavior of insects during their mating dances. Because of this variability, the struggles associated with trying to (successfully) reproduce…
How to Prevent False Results in Colony PCR Colony PCR saves time and reduces costs by eliminating the need for plasmid purification. However, confounding results abound — but only if you fail to anticipate them. This article outlines the major perpetrators of false results and how to prevent them. For a more general overview of…
What do DNA mini preps and protein immunoprecipitation experiments have in common? They start differently, but they end with the same, critical stage – elution. But what exactly is elution, and what is the point? The Terminology First, let’s start with some basic terminology: Elution – extracting one material from another by washing with a…
What is Isothermal Titration Calorimetry? Isothermal titration calorimetry (ITC) measures the heat generated (or absorbed) when one solution is titrated into another. Most commonly, a small molecule or peptide is titrated into a protein. If the molecule binds to the protein, heat is given off (or absorbed) with each injection, until the protein is saturated.1…
Nanopore is a relatively new sequencing platform and researchers are still trying to optimize the protocol for their own specific applications. In our lab, we work primarily with metagenomic samples and use the 1D sequencing kits. Over the past year, we have optimized this technique. To check the quality of the Nanopore library preparation we…
In the first article of this series, I introduced microscopic parasites that infect greenhouse plants. Initially, my goal for Part 2 was to list all the main types of infestations, but I quickly realized to do so would result in a textbook. Thus, this article will be about the most familiar and easy to identify…
If you look at the composition of peripheral blood, using hematology microscopy, you’ll see that it’s composed of multiple different cell types, including monocytes. It’s possible to isolate these different components to study and experiment on them directly. So, if you’ve done a few experiments and had fun with THP-1 cells, you can move on…
CRISPRa allows you to activate or overexpress genes in a more endogenous manner. Find out the steps to getting started.
As the vast majority of bacteria cannot be readily cultured in the laboratory [1], culture-dependent methods to investigate bacteria grossly underestimate the diversity of bacterial communities. To investigate unculturable bacteria without isolating them, culture-independent methods such as sequencing have been used. Unculturable bacteria can be identified by PCR amplification and sequencing of housekeeping genes such…
Cloning Strategies – a Whole Lot of Options to Choose Molecular cloning has come a long way from simple restriction digestion-ligation cloning strategies to a large number of highly efficient alternatives. Broadly classified, cloning techniques can be divided as sequence dependent and sequence independent strategies. Sequence-dependent strategies are based on restriction digestion-ligation techniques or site-specific…
In both the lab and field, it is important to know what species we are working with. While morphological data has always been a tried and true method of identifying species, DNA barcoding allows us to identify species when we don’t have that option (e.g. if we don’t have enough of a specimen to identify…
When developing an assay, whether it is for basic research or for use in diagnostics, you will often be asked about your assay’s sensitivity. This is perhaps one of the most important performance characteristics you can determine for an assay, and in regulated work, such as in vitro diagnostic (IVD) development and clinical diagnostics, it…
Level-up your troubleshooting ability by determining the success of failure of each stage of your CRISPR experiment.
Keeping a meticulous lab record of your experiments is a necessity. And it’s drilled into us to back up our computers, including backups stored in different locations to ensure vital records don’t get lost. But how do we protect the hard copy information in our lab books? You may not have given much thought previously…
What is the first image which comes to mind when you think about microalgae? Green scum that covers the surfaces of ponds? Unsightly stains on pavements and walls? Far from being a nuisance in ponds, lakes, drains and on surfaces, microalgae are fascinating microorganisms which are used to understand various biological processes. Microalgae have been…
Studying nucleic acid interactions with proteins can be accomplished using a rapid and efficient electrophoretic mobility shift assay (EMSA). This method is essentially an agarose gel electrophoresis technique that detects protein:nucleic acid interactions, as the mobility of the labeled nucleic acid will be retarded if bound to a protein (compared to unbound DNA). A lesser-known…
Reduced-representation genome sequencing has been one of the most important advances in the last several years for enabling massively parallel genotyping of organisms for which there is no reference-grade genome assembly. An implementation of the approach known as ddRAD-seq, first conceived in the Hoekstra lab at Harvard, has been widely adopted by the plant and…
Out with the Old… Well-based assays have been the standard for common laboratory experiments, such as fluorescence cytometry. A researcher places a small amount of sample into a well on a plate and assays it, which produces a single data point. However, this so-called single data point is actually an average of the measurements of…
Introduction Did you know that the idea of using genetic engineering to ameliorate certain human diseases was viewed as ‘science fiction’ only 10 short years ago? While cell mutagenesis studies and genetic knockout experiments were feasible before genetic engineering, they were not very reliable. Indeed, due to the random and imprecise nature of these older…
In theory, the greenhouse is a controlled laboratory environment where only the organisms you’ve introduced live. But in practice, just as other laboratory environments suffer from ‘unwelcomed guests’ (e.g. contamination and infestation), greenhouses are not always as sterile as you would like. To avoid any experimental issues, you have to be vigilant about these pesky…
Working late nights or weekends in the lab—we’ve all been there. Why isn’t your cell culture considerate enough to get to exponential phase during normal business hours, anyway? Maybe you just need utter peace and quiet while you pipette hundreds of wells worth of stinky beta-mercaptoethanol. Or perhaps you’re using your wealth of microbiology knowledge…
WGS technologies have seen significant progress since the completion of the Human Genome Project in 2003. First-generation Sanger Sequencers were limited by lengthy run times, high expenses, and throughputs that read only tens of kilobases per run. The arrival of second-generation sequencers in the mid-2000s brought about the plummeting of sequencing costs and run times,…
In whole genome sequencing (WGS) initiatives it is not enough to simply sequence the whole length of the genomic DNA sample just once. This is because genomes are usually very large. The human genome, for example, contains approximately 3 billion base pairs. Although sequencing accuracy for individual bases is very high, when you consider large…
Growing up in Australia, I remember a common phrase: ‘only in America’. Sometimes this was in reference to bizarre cultural events or phenomena but it was generally accepted that the USA was an extraordinary place, where everything was bigger, brighter, and more outrageous. America has fostered a culture of big ideas and innovation, partly because…
Next-generation sequencing (NGS) has ushered in a new era of understanding of both the inner workings and the function of the genome. NGS allows researchers to look at traits—including diseases—that are linked to differences or mutations in an individual’s genes. Since only about 1% of the human genome constitutes genes that code for proteins, several…
Have you ever wondered what it would be like if someone helped you step-by-step through your job search? A good recruiter does exactly that! Recruiters provide value to job-seekers by reviewing resumes, finding jobs that may be a good fit, and providing interview tips. But how does that process work? In this article we’ll cover…
Here we take you through 7 of the best science software apps that can save you time and money!
Does your laboratory resemble the nest of an overly enthusiastic laboratory rat that went on a scavenger hunt and squirrelled away all that it has found? Do you find yourself playing Jenga with stacks of Petri dishes and freezer boxes? Have you ever attempted to decipher the meaning of the mysterious string of numbers on…
Generally speaking, fruit flies are a great model system. Not only are they small, thus taking up very little space in the lab, but their adult lifespan is only 40-60 days, so you can track age-dependent changes without having to wait months and months. Fruit flies also display complex behaviors and more than 75% of…
Sample fixation for electron microscopy can be done using either chemical fixation or cryofixation. Discover the benefits and drawbacks of each of these methods.
Probing Nucleic Acid-Protein Interactions with EMSA The electrophoretic mobility shift assay (EMSA) is a powerful technique for detecting specific-binding of nucleic acid-protein complexes. Over the past 30 years, EMSA has been the “go to assay” to investigate the qualitative interactions between nucleic acids (DNA or RNA) and nucleic-acid binding proteins. Through the use of radio-labeled…
Alveolar epithelial cells (AECs) are one of the major types of lung cells that can be used to analyze the response of lung epithelia to external agents. AECs from mouse lungs can thus be utilized as an in vitro model of diseases. AECs are indispensable for studying lung development, injury, and repair. People working on…
Estimates indicate that there may be up to 2 billion living species of organisms, each with conserved and unique biological mechanisms that are vital for survival. How do scientists understand them all? Enter model organisms. Model organisms, as the name implies, are living things which are used as representative models for understanding other organisms. They…
For many decades, the only way to detect sepsis – bacterial growth in blood – was isolating the bacteria and growing bacterial colonies on a special medium. This was done by first spinning down the blood, which brought the blood cells and bacteria into the pellet. The pellet was spread on a blood agar plate…
Ultramicrotomy is the process by which a sample is cut into very thin slices or “sections”, usually for imaging by transmission electron microscopy (TEM) or relatively new techniques using scanning electron microscopy (See Array tomography in three-dimensional scanning electron microscopy for biology). This technique requires a bit of finesse, and this article will help you…
Have you ever been looking through a box of slides and found something that you want to image or look at later, or even show to one of your colleagues or supervisor? Finding that exact spot on the slide at a later date can prove to be difficult- using a marker pen on the coverslip…
Have you ever wished you could snag individual strands of DNA or RNA with a lasso? Or look at them one by one, figuring out exactly where they are or what they are doing? Fortunately, there are techniques that exist to label nucleic acids for their visualization and purification! Nucleic acids can be labeled at…
Drosophila melanogaster, otherwise known as the common fruit fly, is one of the oldest and most powerful model systems used in biology. Fruit flies are cheap to maintain, and have a shorter life cycle and higher fecundity than mammalian models. They also have extraordinary genetic tools with which to investigate many molecular and cellular questions….
Cleaning the lab is one of the hardest jobs because it’s dull and repetitive. However, nobody in their sound scientific mind would argue that this can be avoided. Dust accumulates bugs, bacteriophages, and RNAses that can stray into your experiment and ruin it. Old boxes piling up is a fire hazard. Anybody who refuses to…
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