Cells and Model Organisms
A Bug Ate My Experiment, Part 2
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…
Read MoreIsolating Monocytes from Whole Blood: A Step-by-Step Guide
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…
Read MoreCulturing the Unculturable: Working with Difficult Bacteria
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…
Read MoreHow to Transform Microalgae
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…
Read MoreAssays: Wellular to Cellular
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…
Read MoreAn Invisible Bug Ate My Experiment: What to Do about Greenhouse Infestation
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…
Read MoreHow to Feed Fruit Fly Larvae Small Molecules
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…
Read MoreMastering the Art of Isolating Pure Alveolar Epithelial Cells
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…
Read MoreEmerging Model Microorganisms Take to the Stage
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…
Read MoreGender Reveal: How to Determine the Gender of Drosophila Larvae
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.…
Read MoreGreenhouse Maintenance: Keeping Your (Green) Laboratory Clean
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…
Read More10 Tips on Mating Mice Successfully
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…
Read MoreThe Rites of Passage: Subculturing Microorganisms
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…
Read MoreReduce, Reuse, Refine Your Animal Model Resources with the ‘3Rs’
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…
Read MoreThe art of generating single cell clones
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…
Read MoreHow to Eliminate 99% of the Water from Your Culture, or Solid State Fermentation
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…
Read MoreHow to Fool-“Proof” Your Experiment: An Introduction to Yeast Plasmids
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…
Read MoreBreaking the Wall: How to Make Protoplasts
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…
Read More“Viable But Non-Culturable (VBNC)”: Zombies of the Bacterial World
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…
Read MoreCouples 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…
Read MoreThe Correct Way To Quantify Cellular Autophagy
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…
Read MoreHow to Grow Corn in a Greenhouse
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…
Read More4 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…
Read MoreEpidemiology: The Underdog of Disease Studies
As bench scientists, we deal primarily with the tangible aspects of biology. The mechanisms and pathways that we try to understand not only allow for us to delve more into how the world works, but can also shed light on disease. However, there is a subject that while distant from traditional bench work, is equally…
Read MoreAn Introduction to Fertilizers in Plant Research
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…
Read MoreKidney Organoids in a Dish
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…
Read MoreMeet Nature’s Oldest Doomsday Preppers: Endospores
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…
Read MoreA Beginner’s Guide to Exosome Isolation
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…
Read MoreThe Amazing World of Biofilms
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…
Read MoreWhy Isn’t My Culture Growing? The S-Curve Explained
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…
Read MoreGuide to Making and Storing Competent Yeast Cells
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,…
Read MoreAlphabet Soup for Bacteria!
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…
Read MoreHandling Your Bacteriophage in a Sea of Bacteriologists
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…
Read MoreHow to Manage Greenhouse Pests
In my last article I introduced what it takes to work in a greenhouse. While for the most part it is a pretty simple work environment, there is one aspect that warrants a more in-depth discussion: greenhouse pests. It doesn’t matter if the pest is an insect, virus, or bacteria, it can very quickly bring…
Read MoreThe Trouble with Disease Models: Case Study in Diabetes
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…
Read MoreThe Nitty Gritty’s of Cell Culture Techniques
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…
Read MoreHow to Properly Streak a Single Bacterial Colony
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…
Read MoreHow to Genotype T-DNA Insertion Mutants in Arabidopsis
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…
Read MoreTips for Getting Your Neurons Firing… Consistently
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…
Read MoreSeeing Your Way Clear: Corneal Stem Cells from Bench to Bedside
Welcome to the first Bitesize Bio article focused on the cornea. As you read this you are peering through at least one cornea—a thin layer of cells on the surface of the eye. The cornea is the eye’s first line of defense against harsh environmental assaults, such as dust, infectious microbes and errant mascara, all…
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