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For many students, a PhD project is the first opportunity to really sink your teeth into your very own research project over a long period of time. This initial period is exciting but can also be a little daunting. Where do you begin? How do you actually design your first experiments? I mean, what are…
The enemy of my enemy is my friend –Ancient Sanskrit proverb Luna, 20 July 1969. Neil Armstrong set his foot in another world for the first and only time in human history. But this is not a story about space exploration; it is a story about the vehicle they used to do it—the Lunar Module…
A few years ago, when I was working for a biotechnology company, I got a special letter in the mail. The NIH asked me to be an ad-hoc grant reviewer for small business grants. Although I drew these lessons from the NIH grant review process, they can probably be applied to many granting agencies. If…
Speed up your SDS-PAGE with our time-saving tips and tricks!
Phosphorylation Equals Cell Signaling! How do cells communicate and respond to their environmental cues? This question has been on the hot list for scientists ever since the discovery of the cell. Cells use signaling cascades based on biochemical reactions to deliver or receive messages. How cool is that? The major secret of cell signaling was…
How do you pick which antibody you should use in your assay? If you’re starting a new assay and need an antibody for the job, then selecting a new antibody from the plethora available could be high up on your to-do list.
Restriction cloning, at its core, is quite simple. You simply cut the target vector and insert with the same enzymes, clean digested vector and insert up, ligate the two together, transform the ligated vector and insert into bacteria, and then screen. While getting each of the steps correct can be a bit of a hassle,…
Have you ever needed to work in a cold room for a long period of time? For example, if you need to dialyze or purify a protein of interest that is temperature sensitive, working in a 4°C cold room might be the only way to accomplish the work. Well, you are in luck. I dislike…
An essential step in mouse breeding is genotyping them to determine the genotype of every mouse in the litter. It is also useful to differentiate between various groups of experimental mice if any confusion arises. When genotyping, you will be hunting for the specific gene that you want your mice to have or a genetic…
The scientific method naturally includes the so-called “trial and error” approach. And you can think of your PhD experience in the same way. My PhD experience is a long story, and I’ve made a lot of mistakes. Therefore, I’ll share some of my trials and errors in earning a PhD to help you avoid the…
Scanning electron microscopy (SEM) is a powerful technique, traditionally used for imaging the surface of cells, tissues and whole multicellular organisms (see An Introduction to Electron Microscopy for Biologists)(Fig. 1). While the resultant images appear to be three dimensional (3D), they actually contain no depth information. However, there are several SEM techniques that can obtain…
Sometimes only a small subset of a cell population will show apoptotic features making flow cytometry an excellent way to identify and quantify them. A previous Bitesize Bio article showed how flow cytometry can detect apoptotic hallmarks. More than 30 different dyes can be used to detect apoptosis. It is also true to say that…
Writing manuscripts is an integral part of research. And being listed as an author on a published article is the most cherished dream of a research scholar/ graduate student. However, what about the corresponding author role? During your Ph.D tenure, you will be encouraged to compile your data and write manuscripts based on your results….
Cloning, purifying, and expressing modified genetic material is routinely done in microbes such as Escherichia coli (E.coli). Relatives of this molecular biology workhorse normally live in the intestinal track of humans. The particular E. coli strain (K-12) that scientists use all over the world was isolated from the feces of a diphtheria patient in 1922.1…
Every biochemist is familiar with proteases. More often than not, proteases cause a lot of anxiety. To this end, a lot of research has been done in developing techniques to prevent the activity of proteases. But some of these proteases can be the good guys too! For example, you can use them to separate your…
All scientists should be involved in some aspect of outreach. There. I said it. I know, I know. This goes completely against why most scientists pursued their careers in the first place: to dedicate their lives to discovery, and to do so alone. With minimal human interaction, especially with non-scientists. Why You Should Reach Out…
If you’ve ever had backache from sitting at the microscope or biosafety cabinet, these tips may be useful for you!
If you type on a keyboard, pipette, or do anything repetitive with your hands for a long time, chances are you’ve felt it: numbness in the base of the thumb, pain in the wrist, or a weak feeling in your hand. These sensations can come from a lot of things, but the symptoms add up…
Kary Mullis invented polymerase chain reaction (PCR) in 1985 creating a revolution in molecular biology techniques. But it hasn’t stopped there. PCR has greatly evolved over the years. Today, we stand at a point, where we can clone micro RNAs (miRNAs) in real time! Due to miRNA size (about 18-21 nucleotides long) and varied expression levels,…
The precision and accuracy of even the best calibrated pipette can be wiped out if you choose the wrong kind of tips. Depending on the experiment you are doing, the wrong kind of tips can also make your pipette a source of contamination, lead to waste of precious samples or reagents—or even cause you physical…
Fourier Transform Infrared spectroscopy (FTIR spectroscopy) is a useful and exquisitely sensitive technique used to identify and quantify unknown compounds, as well as study fine molecular details. However, to obtain a meaningful IR spectrum, it is not only important to prepare the sample correctly but also to learn how to clean the apparatus that houses…
Here’s a few things to take into consideration when starting up a new lab. Starting anything new is understandably overwhelming, but let’s break it down and go through the main points of designing your own laboratory. Purpose of Your New Lab The purpose and function of your proposed lab sets the course for the tasks…
SAGE, or serial analysis of gene expression, is a technique that enables you to digitally analyze the entire gene expression profile of a cell(s). Before this technique, scientists were limited to studying a few gene’s expression at once by a technique called the expressed sequence tag approach. The coolest part of SAGE is you don’t…
Sonication is mostly used during preparation of protein extracts to help break apart the cell. Although most lysis buffers have buckets of detergent that lyse cell membranes, sonication just gives an extra hand in breaking everything apart. Sonication also breaks up, or shears, DNA in a sample—preventing it from interfering with further sample preparation. Have…
It’s often said that great leaders have a knack for bringing out the best in those that follow. In turn, followers enjoy the work they do and will take the initiative to soar far above and beyond what is asked of them. A less effective scientific leader may unknowingly squander potential that might have flourished…
Some techniques can sound very dry but this isn’t one of them! SAGE was first described and published by Velculescu et al. in 1995. At the time, techniques like RNA blotting and expressed sequence tagging were used to study gene expression. However techniques like these were slow and very limited. The speed of SAGE and…
Over the last few decades, PCR, next-generation sequencing, and microarray technologies have taken blood-based research to a new level. Modern blood-based applications range from DNA fingerprinting, whole genome sequencing, blood banking to liquid biopsy, and many more. Regardless of the application, pure, intact, double-stranded stranded, and highly concentrated DNA extraction from whole blood is an…
When you perform genomic DNA extraction from whole blood, low yield or low quality DNA can result in many issues. No matter your intended downstream application—qPCR, next generation sequencing, Sanger sequencing, and so on—you need high quality DNA. We’ve made this step-by-step guide to assist you in getting the highest possible DNA yield and quality, and…
There is a growing trend in using microalgae as the expression system for heterologous proteins. However, I find most protocols dealing with microalgae available online are not that great or informative! So I would like to share my experience in using Chlamydomonas reinhardtii as the model microorganism. Before you start expressing your protein, you need…
For many scientists the most intimidating aspect of undertaking a PhD isn’t the long hours in the lab or the uncertain nature of the job length in academia that follows it. It’s the thought of attempting to write up 4+ years of work into a single cohesive thesis! The thesis writing process can vary greatly…
In the 30 odd years since its invention, the polymerase chain reaction (PCR) has become the bread and butter technique of molecular biologists. The secret to its indispensability lies in its simplicity and versatility. Numerous variants of the technique have been developed; one of these, real-time PCR, has become the method of choice for quantitative…
We have all been to awful talks—hours of slides crammed with data, given by presenters who assume you know as much as they do. But hopefully you’ve also seen a great scientific talk. A talk in which you’re walked through a story, eagerly anticipating each question and data point, until you finally reach a conclusion…
Do you use pre-packed Superdex 75 or Superdex 200 columns for gel filtration chromatography? Ever wonder if other media could better address your purification needs? Look no further. Your quest ends here! But if you’re looking for information on gel filtration principles, check out this earlier article. Choosing a Column for your Gel Filtration Experiment…
Do you use biotinylated secondary antibodies in your immunohistochemistry? You could use polymers instead. They are a great time-saving reagent.
Two years ago, all I knew was third BASE in my baseball field and the cutter ball from the pitcher. Now, I know a lot more about lab-based BASES and cutters: REBASE and NEBcutter. While they sound like baseball terms, REBASE and NEBcutter are tools for working with restriction enzymes. Read on to find out…
While you can observe mitotic cell cycle progression using immunofluorescence, flow cytometry is a great tool to delineate details that aren’t apparent by chromosomal morphology alone. DNA stains are a great way to get a general idea of what your cells are up to. There are also a number of other stains you can use…
Mice are an extremely powerful research tool, but they do take extra time and effort. While you can purchase mice from vendors like Jackson Labs or outsource your genetic engineering to a number of companies, it’s often necessary, and more economical, to start a breeding colony. Even if you get your mice commercially, you’ll probably…
Lasers were once called “a solution looking for a problem.” The word—which is an acronym for Light Amplification by Stimulated Emission of Radiation—used to conjure up images of deadly weapons from Sci-Fi movies and TV series. However, their increasing use in everyday life, first in CD players and then in barcode scanners and pointers, have…
Why do we need scientific collaboration? There is no science without collaboration: science is incredibly social. When you publish a paper or even a conference abstract, you collaborate with editors or a committee to produce an outcome (successful journal or scientific event) together. So, you have to understand the principles of collaboration even if you…
Researchers have always been in search of model organisms that can be used to study and explore biological phenomena to make discoveries that can be extrapolated to more complex higher organisms like humans. Of the various model organisms developed and used, starting from the ubiquitous E. coli and S. cerevisiae to the humble D. melanogaster…
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