Olwen Reina
I am a Clinical Research Coordinator at the U.S. Department of Veterans Affairs with a background in basic research, writing, mentoring and teaching. I studied Natural Science at Trinity College Dublin, Ireland, specializing in biochemistry with immunology and I am currently undergoing ACRP (Association of Clinical Research Professionals) certification. In my spare time, I enjoy studying HTML/CSS and SEO, doing acroyoga, making kombucha, salsa dancing, voluntary community projects and eating sushi. Feel free to send me a note with any writing opportunities or to say hello.
Articles by Olwen Reina:
Making the Most of Quiet Days in the Lab: From Gloomy to Glorious
It’s Monday morning. You arrive in the lab armed with a large coffee and feeling rested after a non-lab weekend. You check your email and calendar and peek into your PI’s office. Today will be a rare non-experimental day, a day that some love and others dread: a day to clean up and get ready…
SAGE Part 2: LongSAGE, RL-SAGE and SuperSAGE
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…
Vital for Soup, Vital for Labs: Serial Analysis of Gene Expression (SAGE), part 1
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…
Time to Instigate Nested PCR
How to Obtain a Purer PCR Product and Reduce Non-specific Amplification Unless you’ve gotten your hands on some miraculously specific primers, amplification of only your target sequence without non-specific amplification can be very challenging. Thankfully, a clever and surprisingly simple solution is at hand! A Quick Recap of the Basics In PCR, you design your…
My job as a Clinical Study Coordinator
Clinical Trial Coordinator, Clinical Study Coordinator, and Clinical Research Coordinator are all names for the same job and refer to the person responsible for the day-to-day running of human trials. Usually when I tell someone that I’m a Clinical Study Coordinator, they have no idea what that means. I guess it’s like when someone tells…
The BOOM Method for Nucleic Acid Purification: The Ultimate Chick Flick?
The Boom method, or Boom nucleic acid extraction method, is a solid phase extraction technique for isolating nucleic acids from a solution of biological matter. This is just a fancy way of saying you use this technique to expose and remove the nucleic acids from a cell. First developed by William R. Boom, the Boom…
3 Carcinoma Cells, 2 Stromal Cells and a Partridge in a Pear Tree: An Introduction to Cell Co-Culture
The first thing you learn about culturing cells is proper aseptic technique and avoiding contamination. After that you’ll learn all the ins and outs of culturing your project’s specific cell line(s). What may not have been covered, is co-culturing, and I don’t just mean ethnic diversity in the lab! Co-culturing is the indirect or direct…
Comparing Viral Vector Expression Systems
Some viral vectors are the little black dresses of cloning and expression experiments: They work for almost any occasion and always give you the results you were hoping for. Other vectors are more like ballgowns that only come out of storage for special occasions. Let’s wade through all the information out there and take a…
Top 10 Tips for Phenol-Chloroform Extractions and Ethanol Precipitations
Phenol-chloroform extractions and ethanol precipitations can be a royal pain, but here are some tips to help you get tip-top results!
Protein Extraction and Solubilization using the TRIZOL® Method
Extracting protein from tissue samples and cultured cells is Step #1 in many biochemical and analytical techniques. Before you can do a Polyacrylamide Gel Electrophoresis (PAGE), a Western blot, or mass spectrometry you need to extract your protein. Nowadays, a lot of labs have switched to kits for their protein extraction but these kits can…
Expanding Possibilities: Why You Need to Look into Viral Transduction
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…
The Nope-Nope-Nevers of Using a Flow Cytometer
There are some wonderful toys in the lab that enable us to open up a whole new world in science. One of those is a rather pricey and an incredibly sensitive laser-based apparatus capable of counting and sorting cells, detecting biomarkers, and engineering proteins: the flow cytometer. By propelling cells through the path of the…
Origami in Nature: Protein Structure Prediction
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…
Native Versus Denaturing Gels
We’re already gone through the basics of how gel electrophoresis work, compared common gel types like agarose and polyacrylamide and even explored some alternatives. Now let’s look at the native versus denaturing gels. You’ll be a speGEList in no time! Denaturing Gels We’ll start with this one, as it’s very self-explanatory. Denaturing gels are exactly…
When PCR Gets RACE-y: From Unknown mRNA Segments to Sequenced cDNA
Normally you need two primers to amplify your segment of interest – one for the 3′ end of your segment of interest and one for your 5′ end. But if you don’t know the sequence of the regions you’re hoping to amplify this can be a problem! Rapid Amplification of cDNA Ends (RACE) is a…
How to Clean and Maintain Scales
Spring time means spring cleaning! Baby birds are hatching, the days are getting longer, there are butterflies everywhere and you feel inspired to do a good deep clean of your lab scales. We can’t help you sing like Snow White so that animals come help you clean but we can help you get your scales…
Get To Know Your DNA Polymerases
While most may think standard Taq is the backbone of PCR, there are many other DNA polymerase options out there. The polymerase you use has a significant impact on the efficacy of your PCR, specifically on the product yield, the purity of the product and the faithfulness with which the starting product is transcribed. Sometimes,…
Fuzzy Wuzzy Problems: Achieving and Maintaining a Contamination-free Incubator
When you share an incubator with a number of people it can be very hard to keep a clean shop and months, or more, of work can be lost due to contamination. The two biggest sources of bugs in an incubator are: the water pan the containers being put in and out. Both of these…
Problems amplifying GC-rich regions? Problem Solved!
No, it isn’t you that’s the problem, and you’re certainly not alone if you’re having trouble amplifying GC-rich sequence and/or understanding why GC-rich sequences are causing such problems in the first place! Amplification of GC-rich sequences by PCR has been an irritant for scientists for decades! When we say “GC-rich” we mean ?60% of the…
Capillary Gel Electrophoresis: An Alternative to SDS-PAGE?
When you think about separating proteins, do you think about separating them using a gel? Specifically using SDS-PAGE? If you answered “yes”, it is for good reason. SDS-PAGE is ubiquitous in molecular biology labs because it is good at separating proteins. However, SDS-PAGE takes a lot of time and is labor-intensive. So let’s expand your…
Seamless Ligation Cloning Extract (SLiCE) Explored and Explained
Traditionally, if you’re hoping to clone a DNA/RNA fragment (or insert) into a vector, such as a BAC you would need: Expensive exonucleases, called restriction enzymes: pacman-like enzymes that chomp at specific sequences in your destination vector or fragments to be inserted (often just “inserts”). Sequence homologies between your inserts and your destination vector, called…
PCR on a shoestring: Build Your Own PCR Machine
Maybe you’re a teacher hoping to do something different, maybe you’re a student trying to drag out their funding, or maybe you just want to build something really cool. Did you know that PCR used to be done by hand? Imagine three water baths with thermometers, a timer going off every few minutes, and a…
Polymerase Incomplete Primer Extension (PIPE) Cloning Method
PIPE PCR is a ligase-independent, restriction enzyme-free cloning strategy like SLIC (link to my SLIC article), SLiCE and CPEC. The PIPE method eliminates sequence constraints and reduces cloning and site mutagenesis to a single PCR step followed by product treatment. It is fast, cost-effective and highly efficient. The key step is designing the primers; one…
How to Be Greener – The Environmentally Friendly Guide to PCR
Science is an expensive business and those who use high energy-demanding techniques may not even realize just how expensive they are. The Cost of PCR Let’s looks at PCR. You need to pay for the machine, all the ingredients including expensive enzymes, a freezer and a fridge for your ingredients, tubes and caps, not to…
The 10 Unspoken Rules of Working in a Lab
There are so many unspoken rules to working in a lab! It’s unnerving what will cause frayed nerves to snap, people not to trust you and a good relationship to turn sour. Here are some of the rules I’ve learned. Feel free to add more in the comments section below. 1. Thou Shalt Not Touch…
Finding Nemo: Understanding Single Cell Isolation and PCR Amplification
Every protocol for single cell PCR can be broken down into two steps. In the first step, the cells are isolated by micromanipulation, laser capture microdissection, flow cytometry, or by direct micropipetting. Next, the genetic material is processed by PCR to amplify your sequence of interest. Here, we’ll go through the different options for isolating…
Six Ways to Measure T Cell Responses
T cells can be problematic to characterise because they have a wide variety of subtypes and because of the technical difficulties of studying the membrane-bound T cell receptor, but there are situations where you want to be able to do this such as analysing the degree to which immunological memory has been induced to measuring…
Letting Go of Your Ligase: Transfer PCR
When I buy a new sweater, I love finding out that it goes with several pairs of pants, the scarf that’s an awkward color and the earrings I haven’t worn yet. PCR is like this sweater – it goes with almost everything and molecular biology is taking full advantage of this using it at every…
Say Goodbye to Restriction Enzymes and Ligases: An Introduction to Sequence and Ligase Independent Cloning (SLIC)
SLIC, or sequence and ligase independent cloning, was developed by Li in 2007 and published in Nature Methods. What makes it a Nature Methods worthy protocol? Unlike other forms of cloning, SLIC does not require restriction enzymes or a ligase! Seriously! Don’t believe me? Why not have a go for yourself? I’ve detailed the main steps below to get you started. How it works To…
Thermal Asymmetric Interlaced PCR (TAIL-PCR)
What do bunnies, coins and PCR have in common? They all have tails! (ha ha!) Thermal asymmetric interlaced PCR or TAIL-PCR is used to sequence and analyse unknown DNA fragments that are adjacent to known sequences. Think of it as being rather like networking. You know you want to get to know someone so you…
Which Cytokine Will I Get? How to Stimulate Human Cytokine-Producing Cells
Cells are like people: depending on their current environment, past experiences and their genetic make-up they will react differently. Treat cells in different ways, and they will produce different cytokines. There are a lot of protocols out there for stimulating cells. Depending on the species of cells you plan to stimulate, different protocols are available…
Tips for a Happily Functioning Tissue Culture Room
You walk into your tissue culture room to find a window open, the incubator’s humidity tray empty and a pipette lying on its side in the hood on a used glove… After you have found and torn to shreds the person responsible for this monstrous act (!!), consider posting the below tips to help those…
How to Clean a Tissue Culture Incubator
A few years ago, I was doing research in a lab in Ireland. Our lab, among many others, was moving to a new building. Everything was chaotic. Half our equipment was in the old building and the new lab was creepishly empty. The fire alarm went off every few days. There was a constant…
Don’t Have the Blues: Make the Lac Operon Work for You
Glucose is the preferred food source for E. coli, however when glucose levels drop, E. coli need to look for other ways to feed themselves. One way in which they accomplish this is to replace glucose metabolism with lactose metabolism. The induction and control of lactose metabolism is complicated and its process has been exploited…
A Beginner’s Guide to Next Generation Sequencing (NGS) Technology
The completion of the Human Genome Project in 2003 ushered in a new era of rapid, affordable, and accurate genome analysis—called Next Generation Sequencing (NGS). NGS builds upon “first generation sequencing” technologies to yield accurate and cost-effective sequencing results. Fred Sanger sequenced the first whole DNA genome, the virus phage ?X174, in 1977. In that…
The 9 Online Calculators You Need to Know About
When you think of a “calculator”, you probably think of the plastic gadget in your lab desk drawer or an app that came with your phone. But there are so many helpful calculators online that do a lot more than just add and subtract numbers. Here is a list of some of the wonderfully convenient…
The Lac Operon Explained
An operon is a functioning unit of genomic DNA that contains a group of genes controlled by a single promoter. Put simply, these genes share information needed to create the tools for a particular task so they share a promoter ensuring they’ll all be transcribed together. The lac, or lactose, operon is found in E.…
Heating up agar? Just add a cup of water and avoid the glitter and crumbs
It’s ironic how much folklore and superstition comes with being in science. “That’s a lucky pipette”, “playing Bach for your cells will help them grow”, “always make your own solutions”; we all have our own tips. Some of them might be well-founded others not so much… Tips from trusted colleagues can be very helpful though.…
The History of PCR
As with some of the greatest discoveries in science, from penicillin to microwave ovens and play-doh, PCR was discovered serendipitously. Thanks to the work of many scientists, including Watson and Crick, Kornberg, Khorana, Klenow, Kleppe (so many K’s…) and Sanger, all the main ingredients for PCR had been described by 1980. Like butter, flour, eggs,…
How to Pick the Right Scale for Your Needs
There are many things that vary from one scale to the next. When picking which scale to buy or use, there are a few things to take into account: the two biggies being the maximum capacity and the readability range (also known as how sensitive the measuring system of the scale is). As both these…
Mischief in the Mastermix: Bothersome Bubbles
It happens to the best of us. You’re minding your own business and suddenly out of nowhere your mastermix is a bubble bath and your primers are enjoying a froth party. Let’s talk about how to deal with these foamy fiends! When you’re making up your mastermix, you could have a variety of ingredients going…
Facing Your Laboratory Freezer: Dos and Don’ts For Defrosting Day
Your stomach clenches. Sweat snakes down your torso. The world seems to slow down. You begin the long, terrifying walk down the corridor. Your mind calls out to you to, “Run! Run now!” but you soldier on until you reach the door and knock. There is no escaping the wrath you will evoke when you…
Don’t Be Arrested for B.I.T.E. (Bunsen Ill-Treatment and Endangerment)!
B.I.T.E., or Bunsen Ill-Treatment and Endangerment, happens every day. In the time since you started reading this article, somewhere out there, a Bunsen burner has been mishandled. This is a dark subject and while some flinch at the thought of discussing it (some stories may be too dark for the public to handle) this writer…
The A-Z of PCR Variants
The wide range of applications of PCR has led to an ever-growing list of variants of the technique. While some are optimizations to suit specific requirements and are very similar to basic PCR, others completely turn the technique on its head to formulate novel creative applications in various fields. This article lists some variants of…
The Establishment of the Nobel Prize
Let’s play a game. I’ll say a word and you say what comes to your mind. Ready? Go! Cat… Kitchen… Doctor… Airplane… Nobel… I have no idea what you said when I said cat but I’d say most of you said “prize” when I said Nobel. Alfred Nobel’s name is most often remembered because of…
The different Phases of PCR and Why They Are Important
PCR (Polymerase Chain Reaction) is a biochemical technique developed by Kary Mullis in 1983 that is used to create large quantities of a sequence of DNA. Since this method of mass-producing DNA was first introduced, it has become significantly less labour intensive, more economical, and more routine. The technique relies on a few key players…
Red light/Green Light In Aseptic Technique: When Is The Flame OK?
My mom is a microbiologist and so I was a lot more informed about bugs than most kids. In fact, I probably gave more than one classmate nightmares with my talk of there being 10 times more bacteria that make up the human body than human cells. I remember my mom working by a Bunsen,…
10 Ways to Abuse a Pipette
It seems like every movie that needs a shot of a scientist doing their sciencey-thing either gets the person to pour one pretty liquid from one flask into another or to stare intensely at a test tube with a look of knowing so much more than you ever could. Another favorite shot is of someone…
Agarose versus Polyacrylamide: Not All Gels Are Created Equal
Like athletes running on turf versus sand, the gel you run your DNA through can highly affect your results. The two main types of gels that people use for DNA electrophoresis are agarose and polyacrylamide (PA) gels, but figuring out the differences can be confusing. Basically, you choose a gel based on two main factors:…
Gel Electro-For-Whatsit? Breaking Down How Gel Electrophoresis Works
Run to red! It’s a mantra I learned when first using gel electrophoresis to separate DNA molecules. This can save you a lot of frustration and humiliation in the lab (stage right: a complaining scientist who swears the equipment is broken as a supervisor facepalms in embarrassment). But what about how does this jell-o like…
Choosing the Correct Enzyme for PCR
A wide variety of enzymes are available for PCR and RT-PCR and the optimal choice depends on a range of factors specific to your experiment. Some of these factors will now be explored to help you to make the most suitable and cost effective choices when ordering. PCR Type and Other Factors to Consider First,…
