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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…
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…
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…
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…
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…
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…
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…
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…
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…
Tiny, furry, spinning around a wheel—few creatures are as endearing as the lab mouse. Trying to obtain reproductive success with them, however, can leave you spinning your own wheels. Why is it that what works so well for the animal facility staff, or experienced technician, seems to be beyond your reach? After all, mice have…
Anyone who has worked with microorganisms, be it bacteria or yeast, is familiar with subculturing – the act of transferring some cells from a previous culture to a fresh growth medium. You do it either to reset the growth phase of your culture or to increase the biomass for downstream experiments. But there’s more to…
Russell and Burch first described the ‘3Rs’ concept in 1959. It acknowledges that animals are a valuable resource through which great discoveries can be made, but it is up to you to use them ethically and judiciously. The ultimate benefit is that people and animals will be able to live longer, happier, healthier lives! So…
Making mutations in mammalian cell lines is becoming much easier, especially with advanced molecular engineering techniques such as CRISPR/Cas9, among others. However, after making a mutation, do you know if all of the cells contain the same mutation with the same expression profiles, and are therefore homogenous? If you have 100% transfection efficiency using a…
When you think about culturing bacteria or fungi in large quantities, you likely envision flasks shaking or maybe bioreactors filled to the brim with liquid media. But did you know that many bacteria and fungi can grow on solid carriers without being submerged in liquid? Enter solid state fermentation (SSF). In this article, I’ll introduce…
A lot of research experiments require the use of a eukaryotic host as opposed to E. coli due to its greater conformity and suitability in expressing eukaryotic proteins. This is the reason why yeast cells have gained importance as cloning and expression hosts. For protein expression studies to hybrid screens, many applications require insertion and…
Non-mammalian cells, including bacteria, fungi, and plant cells, have a cell wall that maintains the shape of the cell. These cell walls are particularly strong, due to their composition as they contain polymers that create a rigid sphere around the vulnerable cytoplasm contained inside the plasma membrane. In bacteria, the cell wall includes several layers…
Imagine that you want to test the efficiency of an antimicrobial treatment in inhibiting a certain bacterial pathogen. As part of the experiment, you expose the bacteria to the treatment and monitor the cultivability of the microorganism by counting the number of colony forming units (CFU) formed on culture media. If the microorganism is sensitive…
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…
Just like you need to clean up your room from time to time, your cells also need to do a bit of housekeeping. Your cells accomplish this through a process called autophagy. Autophagy mainly serves two roles. The first is to remove damaging materials, such as misfolded proteins, dysfunctional organelles, and foreign invaders. The second…
Because of the ease of performing controlled crosses, maize (or corn (Zea mays)), has been a staple of plant genetics research for decades. Barbara McClintock herself chose maize as her research organism for her Nobel Prize winning work. If you are looking to get involved but aren’t sure how to get good yields in the…
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…
If you have ever had a home garden, you are probably familiar with the fact that adding a little fertilizer to a plant can really do wonders. This can also be the case in a lab greenhouse! The difference is that instead of adding a bit of the “blue stuff,” we try to be a…
Kidney Modeling with Kidney Organoids Derived from Human Pluripotent Stem Cells Stem cells are a valuable tool for kidney disease modeling as well as experimental regenerative medicine and drug screening. There are more than twenty different cell types in the mature kidney, which adds to the complexity of the model, but also provides the opportunity…
My favorite reason for being a biologist is that I am endlessly amazed by how life adapts to various pressures on planet Earth. This especially holds true for endospores, one of nature’s most resilient means of surviving for thousands of years in non-ideal environmental conditions. In this article, we’ll explore some of the extreme environments…
For all of you who have never heard of exosomes: You are missing out on a whole new paradigm in cell-to-cell communication. Exosomes are tiny extracellular vesicles that arise from fusion of the plasma membrane with specific endosomal compartments called multivesicular bodies. Most cells types make exosomes, and release them in order to communicate with…
What do water pipe slime, dental plaque, and persistent contact lens case contamination have in common? All are the result of biofilms! Biofilms are aggregates of microbes that adhere to surfaces using secreted matrices. Although relatively under explored, this fascinating phenomenon plays a critical role in some of the biggest challenges currently facing medicine, ranging…
Whether you work with human cell lines or microbes, their growth is governed by the same principles. I invite you to learn about something that lies at the base of any work with cell culture, whether cells have circular or linear chromosomes: the S-curve of the population growth. The length of each phase depends on…
Yeasts, such as Saccharomyces cerevisiae, Schizosaccharomyces pombe and Pichia pastoris, are routinely used in biology research labs around the world. Yeasts are easy-to-culture, unicellular eukaryotes, and make excellent model organisms because of the similarity of their genes and proteins with those of their mammalian counterparts. Yeast cells are used to study gene function, protein interactions,…
In its simplest form, a bacterial growth medium is designed to support the growth of bacteria. Depending on which bacteria you want to culture, you may have a range of different media to choose from, each containing a rather unique blend of sometimes surprising (and odd!) components! In this article, I will take you through…
When I first told a lab colleague I was going to be doing phage work in a lab that had otherwise only dealt with bacteria, I was met with expressions of awe, and then fear. Being that a bacteriophage is essentially a predator of bacteria, this reaction is legitimate for a bacteria-loving scientist. Also, we…
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…
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…
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…
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…
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…
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…
The Cre-loxP recombination system is routinely used for the generation of mouse knockouts. In part 1 of this mini-series, I introduced the concept and applications of Cre-loxP. As with any other technology or research tool, it has limitations and pitfalls that need to be considered while planning experiments or interpreting results. This article will take…
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