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Retroviral transduction is becoming a popular choice for gene delivery into mammalian cells and has multiple advantages over other techniques. If you decide to start work on this useful technique, here is how you can go about it: Step 0: Obtain permission First and foremost, do you have the permission, authorization, and training to work…
Need tips for surviving being the newbie of the lab, and what you can do to handle all the possible personality types you may encounter. Read on.
The concepts of brightness and contrast are so general, and the issues related to them so many, that it may seem strange to have a single brief article with such a title. Indeed, when we speak about brightness, we can think about the brightness of the light source, the aperture and magnification of the lens,…
In the last years, the need for using statistical testing in bioscience has grown exponentially and so has the development of statistical software. It is now common that everyone is using some sort of stats in their basic research. Among the skillful biostatisticians, R is the most popular software for data analysis, but not all…
If you’re hoping to reel in a positive interaction between a protein and an RNA sequence, try to catch a winner with a yeast three-hybrid assay. What is yeast three-hybrid (Y3H)? The Y3H system is based on the same principle as a yeast two-hybrid– namely, that the DNA binding domain and the transcription activation domain…
Flow Cytometry is a great way of seeing how many of your cells express a particular marker and how much of it is there. We do this by measuring fluorescence, but, as with all measuring systems, there will be signal that we are always trying to measure the above the noise. The signal that we…
Finishing my third year of grad school, I can’t help but notice what a balancing act it has been- research and relaxation, finances and fun, beer and…not beer? I wanted to write this article to advise incoming first years and veteran grad students – even those mysterious 7th year students- on graduate school and the…
When choosing a model system for culturing tumor cells, we often think of the obvious tried and tested models. In vitro methods include cell lines that have been specifically selected to grow in culture flasks in incubators. While conveniently available, consistent and reproducible, cell lines are limited in that they may not represent the desired…
So you have a gene or protein that you think may be involved in migration or invasion and the next step is to embark on migration assays. These assays are useful for testing fundamental migratory processes, such as embryonic development, immune response, metastasis and angiogenesis. For a long time these have been an invaluable mainstay…
A PhD, like any worthy endeavor in life, requires hard work, patience and perseverance. It also involves challenges that will make you doubt your choice to pursuit an advanced degree in the first place. It is inevitable that a series of failed experiments or that one paper rejection will bring you down and temporarily make…
Western blotting uses electrophoresis and antibody-epitope affinity to give a semi-quantitative and (theoretically) clear measure of protein abundance. It’s a long procedure, filled with many steps—and even more room for error. Learning to troubleshoot certain problems is incredibly important for continued success with this technique. So what do you do when your final imaged product…
Flow cytometry is a fluorescence-based technology, as is fluorescence microscopy and confocal microscopy. Fluorescence is fundamental to how a cytometer gathers data, but I am often surprised, as a core manager, at how little new users know about the process of fluorescence. So, this is where I always start the training process. Let’s get physical…
Imagine trying to build a house without power tools: It’s completely doable – after all, people did it that way for centuries – but it’ll take you a lot longer and has limits. Similar to this, modern day biology now has its own set of “power tools.” So while you could do biology the old-fashioned…
Some tissues are tricky to work with. This truth was lost on me in the early years of grad school because I worked with liver samples. If you’re extracting RNA from liver samples, you’re likely not losing sleep over your massive RNA yields. But for the folks doing RNA extractions with less willing donors, such…
Let’s face it, at least once in your lab life you are going to need a favor. You may need to go on vacation, you may be sick or you may just be a little overwhelmed at the bench. At least once, you will need to ask for a little help and someone will surely…
When restrictions come in the form of paperwork and approvals, we detest them. Whereas, when the restrictions come in the form of enzymes, we love them, don’t we? Restriction enzymes play a key role in biotechnology research. Read ahead for six useful facts about restriction enzymes. 1. Restriction enzymes are helpful to bacteria Restriction enzymes…
If you do cell culture you will inevitably need to count your cells. Counting cells can be tedious, but it is important to do accurately. Your assessed quantity of living cells will affect all your downstream applications. In this article I will not only cover how to manually count your cells and how to do…
You had been happily measuring your DNA samples with your NanoDrop for a while, until… you noticed that your results are not reproducible *gulp*.
Read on – here are 10 points that will help you troubleshoot the issue.
You open the incubator in the morning and to your dismay there are a hundred glorious colonies… on your vector-only control plate. While there are a number of potential causes, I’ll highlight a few of the more likely culprits and their solutions.
When we are doing a double labelling, it makes good sense to choose two fluorophores with spectra widely spaced apart to avoid mixing. Why combine GFP with Rhodamine, when you can combine it with Texas Red?
Welcome to the last article in this series! Last, but by no means least, we will look at the importance of plant miRNAs and how they differ from their animal counterparts. When/How Were Plant miRNAs Discovered? Plant miRNAs were first described in 2002, a decade after the seminal miRNA study in the nematode C. elegans…
People would have said that a USB sequencer not much bigger than a memory stick which could sequence genomes in 50kb+ read-lengths was impossible “’Star Trek’ technology!” Now, that futuristic technology is here.
When it comes to data analysis and interpretation, you need to be very clear about the meaning of a given p value and be aware of all its intrinsic limitations.
We have to rely on artificial systems to test our hypotheses and often have to come up with original set-ups to investigate specific problems. One of these creative inventions is the use of supported lipid bilayers.
I’ve noticed that there exists some ambiguity about the different terms relating to homology. I’ll try to break them down here, with significant help from Genome Biology.
After countless immunos with free-floating sections – troubleshooting, testing antibodies, and finally doing the actual experiments – I felt like an expert on immunohistochemistry. I knew everything there is to know, right? Well, of course not – it does not work like this in science! For my next project, I would need to perform immunohistochemistry…
Predicting how proteins will fold in vivo is a Holy Grail of proteomics and theoretical chemistry. Current hopes are that this can be achieved by designing an in silico platform that can predict protein folding, either de novo (a.k.a. from scratch) or using known proteins as a guide. What would we need to do, why…
If you want to know what is going on in the brain of drosophila you can use neurobiology imaging techniques to get a global whole-brain perspective. However, such techniques are slow compared to the rapid nature of the neuronal electrical activity, which may be better studied using Drosophila electrophysiology. Lab techniques are often shrouded in…
While it is true that there are some useful websites like SNPedia, or NCBI that can help you find rs codes for genetic variants, sometimes you need that info coming straight from the oven – particularly when you want to look at atypic SNPs or substitutions that have not been validated. So, in this post I…
Lab work, as we are all aware, comes with many pressures: one of which is productivity. You want to generate as much quality data as possible to meet publication deadlines or perhaps the elusive thesis. Sometimes it may feel like hours spent in the lab don’t match the amount of data produced: for some this…
As a dual-degree MD/PhD student I spent two years in the medical school doing classroom learning, now I’m in the lab trying to get a PhD, and then in a few years I’ll return for the last two years of medical school and work in the hospital. In this process, I’ve heard a lot about…
PhDs have been known for their nightmarish effects on students’ psychological wellbeing, to the point that the acronym PhD has also been dubbed ‘Permanent Head Damage’, ‘Philosophically Disturbed’ or ‘Please Help. Desperate’. Doing a PhD is an emotionally exhausting experience rather than being physically challenging. Here are some tips on how to survive the PhD…
As a protein biochemist where bacteria were mere workhorses, imagine my surprise when I began work in a bonafide micro lab! I discovered that bacteria could be much fussier than my good ol’ cloning and expression friends E. coli DH5ɑ or BL21. One broth would not do for all, some even required blood! No, no,…
So it’s time to write up your thesis. By now, you probably consider yourself an expert on your topic or you hate the sight of it (or both!). Either way, hundreds of typewritten pages are all that stands between you and graduation/freedom. One of your first requirements will be to review the current knowledge on…
A cover letter is a letter written to accompany a job application, a grant application, project reports, manuscripts, etc. that explains the purpose of your writing and incorporates certain key points of your application. It plays a decisive role in accomplishing the task it’s been written for, which is why it is so important to…
We have already looked into the different types of viral expression systems and when you might use one over another in my previous article. But why would you use viral transduction over similar techniques like plasmids? Just a reminder: Transfection is a lab technique where nucleic acids or proteins may be introduced into cells. When…
One of the key characteristics of cytotoxic cells (i.e. CD8+ T cells, natural killer cells) is the presence of pre-formed cytoplasmic lysosomal granules. These structures house perforin and granzyme; two molecules that are essential for the lysis of target cells. Upon effector cell activation, granules are polarized toward the target cell and the contents are…
The gap year I intended to take between my Master’s degree and hypothetical Ph.D. is now going into its 4th year. Here’s why I’m not worried. These days it seems like undergraduates are proceeding en masse to graduate programs shortly after completing their senior year of college. An abundance of undergraduate research opportunities and poor…
Producing lentiviral or retroviral vectors is theoretically fairly straightforward. However, anyone new to viral vector work is usually confronted with vast amounts of confusing information. It seems that anyone who has ever made a lentivirus has their own protocols and is adamant that their method is the best one to follow. In reality, there are…
BLAST is the most popular bioinformatics online tool. But in order to properly use it, you have to understand that is not just a search query against a database but something far more complicated, and the information you get back far more…precious!
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