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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…
Negative staining of proteins is a versatile tool for structural biology. The sample preparation protocol is simple: the sample is embedded in a heavy metal stain that gives rise to increased specimen contrast. Thus, negative staining is a very convenient method to assess sample homogeneity, formation of macromolecular complexes, or quality of protein preparation. Conventional…
Have you ever seen a mouse chowing down on its dinner and wondered how it translates to energy? Well, that’s exactly what is keeping some scientists up at night, and luckily these questions are now becoming easier to answer in quite significant detail. Over the last couple of decades, several companies have developed ‘metabolic cages’….
The use of viral delivery systems to transduce cells for gene and protein investigations has become prominent over the last 20 years. In particular, the use of lentiviral vectors permits stable expression of your gene of interest. This is all possible with a little bit of nucleic acid magic. Lentiviruses (a genus of retrovirus) express reverse…
Chromatin immunoprecipitation sequencing, better known as ChIP-seq, is a massively parallel approach for understanding the interactions between proteins and DNA. This is especially important for determining the activity of transcription factors, which is why it’s frequently used to learn about the complicated series of biological steps leading to cancer. It’s also key to many epigenetic…
Pipetting all day? Scrolling and scrolling through Excel columns trying to make sense of your data? Spending hours at the microscope because your boss wants Nature-worthy pictures? It’s not uncommon that performing lab work forces you into unhealthy postures, and after a day at work your spine begs for mercy. How Your Posture Suffers on…
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…
Fourier transform infrared spectroscopy (FTIR) is an extremely sensitive technique for measuring the absorption and intensity of electromagnetic radiation in the infrared region of the spectrum of either a solid, liquid or gas sample. You can use FTIR to: How Does Fourier Transform Infrared Spectroscopy Work? Briefly, FTIR measures how well a sample can absorb…
Manipulating the genes of organisms is crucial for studying their functions. In times before genetic engineering, scientists would shoot bacteria with X-rays or expose them to destructive chemicals until spontaneous mutations would arise. Fortunately, current methods are more sophisticated and less torturous. Researchers now use more directed techniques to introduce mutations. There are several ways…
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…
Universities are often organized by faculties, colleges, schools, and/or departments. So, as an academic, you often work closely with colleagues studying similar subject areas. A common interest, however, often transcends the boundaries of this organizational structure. Enter scientific special interest groups. What Are Scientific Special Interest Groups? Scientific special interest groups are member-led initiatives within…
Transitioning from a PhD in Biotechnology to the industry of my choice (scientific communication and marketing) involved an intense period of application and rejection. Every time I got a rejection letter, I feared that the industry probably did not want fresh graduates like me, that they wanted someone with years of experience. These were moments…
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 may have heard about a breakthrough cancer therapy that engineers patient’s immune cells to fight their cancer using chimeric antigen receptor (CAR)-T cells. If you don’t live in the world of immunology, you may not know what a CAR is, or what it is used for. Here you’ll find a brief guide to CARs,…
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…
There are many examples of the impact of physician-scientists on translational research. Dr Barry Marshall swallowed a steaming culture of Helicobacter pylori which eventually resulted in antibiotics curing peptic ulcer disease. However, the process of training these individuals is as effortless as training fish to ride bicycles. Our journeys into the laboratory have been equally…
What Is Optical Mapping and How Is It Used? Synchronisation of the contraction of heart muscle is essential for the efficient pumping of blood through the circulatory system. Cardiac contraction is controlled by the regulated spread of electrical impulses from cell-to-cell within the heart. In pathological conditions, these electrical impulses can become disordered and lead…
RNAscope is a new method of quantitative RNA in situ-hybridization that has taken laboratories by storm. Learn advantages over traditional techniques and how RNAscope works in this introduction article.
The decreasing costs in genomic sequencing over the past decade have inspired researchers to apply shotgun next-generation sequencing to entire microbial communities. While the reads generated typically cannot be assembled cleanly into individual genomes, there is often enough information produced to identify most microbes present in the population. However, this approach lacks sufficient resolution to…
Researchers have relied on immunodetection techniques such as Western blotting, flow cytometry and Enzyme-Linked Immunosorbent Assay (ELISA) for years, but immuno-PCR is a relatively new method. By merging an ELISA with the Polymerase Chain Reaction (PCR), immuno-PCR provides extremely high levels of assay sensitivity. ELISA An ELISA is an assay in which a molecule is…
Isolating RNA from either Drosophila larvae or adult heads can seem a bit daunting, primarily due to the presence of the cuticle. The cuticle is a protective exoskeleton comprised of insoluble collagens, cuticlins, glycoproteins, and lipids. While it may take some force to remove the cuticle, you can do this easily and without compromising your…
There is something about kinases that resemble ghosts. Their effects reveal their presence, but they can be difficult to catch. With a low abundance of hundreds or even tens of molecules per cell, they are difficult to detect using conventional methods such as Western blotting or mass spectrometry (MS). However, you will need to detect…
Since our early steps in Science we have been told that every cell in our body has the exact same genetic information (minus one or two alterations). Therefore, the great variety of cells in our body comes from gene expression – each cell must express one set of genes and repress another set to function…
So you’ve discovered the Holy Grail all life scientists in your field are searching for – congratulations! The dollar signs start appearing and you realize that there is a huge scope for commercializing your research. But before you can actually collect the rewards, you need to have been thinking tactically about how to protect your…
In any application that uses antibodies for signal detection (e.g., Western blotting, ELISA, immunohistochemistry, or FACS), there are two approaches to antibody labeling: direct and indirect labeling. Standard Western blotting uses indirect labeling because you use a primary antibody to detect the target antigen, followed by a secondary antibody to which a detection molecule is…
Excellent research takes time and effort, and a publication is your chance to showcase your hard work. While your main motivation might be to share and discuss your results, your methodology section is key to the reproducibility of your work, acting as a foundation for other researchers to repeat and build upon your findings. In…
As scientists, we are trained to design an experiment with the bigger picture in mind; the ultimate goals being to publish quality data and demonstrate scientific rigor. However, sometimes you need to focus on the little things, such as perfecting control and experimental samples, incubation times, and ordering reagents to truly ensure that you obtain…
Proteins in the cell are in a constant flux governed by events including synthesis and degradation. In an effort to make cells more efficient by reducing the unnecessary protein load, most proteins in the cell have a specifically defined half-life. Another reason why cells have evolved to degrade proteins is to ensure timely removal of…
I was so excited to start using 384-well plates for my assays. With so many wells, these plates are useful for testing many conditions in parallel, as required in ELISAs, siRNA library screens, and drug treatment dilutions. However, I quickly learned that pipetting in these plates is more complicated than I thought. This article contains…
Obtaining your doctorate is one of the toughest academic and professional tasks that you can take on. The stats on future employment in academic science careers are horrifying at worst or misleading at best. At the same time, many argue that we need more scientists with a PhD.1,2 With these statistics, it might be time to…
Whether your experiment relies upon a reference-based genome assembly or mapping reads to a reference genome to identify variants, you need to choose a human reference genome assembly. But wait! You go to the FTP site of NCBI’s refseq and click on the Homo sapiens folder. There you are presented with two choices. Which one…
Picture it: 6:00 pm on a Friday night. You have one or more experiments running. Maybe you’re doing a western blot, or following a staining protocol for an immunohistochemistry experiment, or just labeling tubes. But rather than working on active experiments, you’re helplessly searching through the lab drawer for that one pair of forceps, that…
Target capture through PCR has been a mainstay in genomics for years, but scientists working on especially repetitive, poorly characterized, or rapidly evolving regions continue to struggle to fish out those stretches of DNA for further study. However, whole genome sequencing, the only other alternative for these regions, can force researchers to pay for much…
If you have any training in genetics, chances are that during the course of your education you ran into those funny little sequences called microsatellites. These are repeated tandem motifs 1-6 nucleotides long, scattered all over our genomes. These used to be called “junk DNA,” because researchers thought that the repeats served no purpose. Nowadays,…
Pipettes are not just fancy handlebars for your tips, they are essential for precisely measuring and dispensing liquids. These standard ‘tools of your trade’ enable you to accurately repeat experiments, validate results, make important comparisons between projects and eventually publish that outstanding paper. But there are a few pipette pitfalls. And they don’t just trap…
As a newly-minted PhD, I began my postdoc with wild fellowship dreams. I set a schedule, applying to 1-2 fellowships a month. Research experience and broader impacts were a breeze. Research strategy and specific aims, with help from my new PI, solidified quickly. For weeks, however, my “training potential” document remained empty. At first, I…
If you have studied cellular movement or cell division, you have encountered Rho in the literature, because it regulates both processes. And the list of roles for Rho in the cell continues to grow! The prominence of Rho in the biology of non-diseased and diseased cells has caused researchers to continually optimize the Rho pull-down…
The cells I work with are special — they’re stem cells. This means that when it comes to deciding their ultimate fate, they’re still sitting on the fence. This ability is great for identifying pathways of cellular development and differentiation. It also serves research into tissue regeneration and human disease. But how can we make…
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…
If you compare a biologist with a cook and the lab with the kitchen, the pipette will be analogous to the most important cooking tool – the knife. But while the knife’s design has remained more or less the same since man moved from stone to metal some five to twelve thousand years ago, laboratory…
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