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Vicki Doronina

Vicki did her PhD in Molecular Biology at the University of Edinburgh. She had been working as a postdoc in several Russel group UK universities, while honing her skills in scientific and creative writing. She is now a pen for hire. Check out my proudest achievement, which may be useful for you: The BiteSizeBio Guide for Protein expression

Articles by Vicki Doronina:

How to Set up Your Elution Experiment

What do DNA mini preps and protein immunoprecipitation experiments have in common? They start differently, but they end with the same, critical stage – elution. But what exactly is elution, and what is the point? The Terminology First, let’s start with some basic terminology: Elution – extracting one material from another by washing with a…

15 Oct 2019 DNA / RNA Manipulation and Analysis

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…

08 Oct 2019 Cells and Model Organisms

An 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…

30 Jul 2019 Cells and Model Organisms

Isolating Bacterial RNA from Blood

For many decades, the only way to detect sepsis – bacterial growth in blood – was isolating the bacteria and growing bacterial colonies on a special medium. This was done by first spinning down the blood, which brought the blood cells and bacteria into the pellet. The pellet was spread on a blood agar plate…

08 Apr 2019 DNA / RNA Manipulation and Analysis

The Beginner’s Guide to Reading Plasmid Maps

Very often plasmid maps, especially historical ones that are hand-drawn by a long-forgotten PhD student, are a puzzle. What are these arrows and boxes? Where do I start? Don’t worry, we have a crash course introduction into deciphering plasmid maps. Familiarizing Yourself with Your Plasmid of Interest Let’s start with a classic plasmid: pBR3221. It…

11 Mar 2019 DNA / RNA Manipulation and Analysis

Greenhouse 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…

07 Mar 2019 Cells and Model Organisms

The 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…

14 Feb 2019 Cells and Model Organisms

RNAseq Library Preparation: From Cells to cDNA

RNAseq libraries, also called whole transcriptome shotgun sequencing libraries, provide a snapshot of cellular processes. This allows the researcher to gain information regarding changes in transcriptome in response to environmental changes, during disease, or after a drug application. RNAseq libraries also allow for the detection of mRNA splicing variants and SNPs. RNAseq libraries have virtually…

11 Feb 2019 DNA / RNA Manipulation and Analysis

Laser in a droplet

When you hear about a laser, you likely imagine a medium-size apparatus with a light beam coming out of it, not a bacterium in a drop of liquid. Well, Turkish and British scientists went beyond ordinary imagination – they expressed a fluorescent protein in E.coli and suspended live bacteria in droplets. Illuminated droplets served as…

31 Jan 2019 Microscopy and Imaging

To Sonicator and Beyond – Large Cell Volume Lysis Methods

At some point you have to leave small-scale cell lysis and move to large culture volumes for experiments currently in vogue, be it microarrays, total RNA libraries, or large-scale pull-downs for interactome or metabolome analysis. And at this point, you have to change your lysis method from an on-the-bench in eppendorfs to one capable of…

29 Jan 2019 Basic Lab Skills and Know-how

Breaking 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…

15 Jan 2019 Cells and Model Organisms

4 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…

11 Jun 2018 Cells and Model Organisms&DNA / RNA Manipulation and Analysis

Fishing for Kinases with Multiplex Inhibitor Bead Assays

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…

18 May 2018 Protein Expression and Analysis

Top Five Methods for Primary Antibody Labeling

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…

04 May 2018 Protein Expression and Analysis

Nil by Mouth: Evolution from the Glass Pipette to the Robot

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…

14 Mar 2018 Soft Skills and Tools

Why 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…

07 Dec 2017 Cells and Model Organisms

Flashing Red Signs During a Job Interview

In all the stress of having a job interview, it’s easy to forget that it takes more than one to tango. In fact, a job interview is like a new flat mate interview. While your prospective boss and colleagues are interviewing you and assessing your fit for the lab, you should also keep your eyes…

23 Aug 2017 Personal Development&Survive and Thrive

The Sandwich Technique: How to Dish Out Critique

How time flies. One day you are giving your first presentation in front of your fellow students, seemingly the next you are listening to a presentation by your own student. And frankly, the talk is awful. It’s twice the time limit, the student weaves around the topic as a drunken sailor, and she acknowledges her…

19 Jul 2017 Dealing with Fellow Scientists

Top 5 of the most commonly used cell lines!

Cell lines are an invaluable scientific tool. They allow us to dissect the internal workings of tissues in a controlled environment without the ethical implications of working with whole organisms. Starting with the first successful immortal cell line HeLa, the number of available cell lines has since diversified into a plethora of options. Just like model…

13 Apr 2017 Cells and Model Organisms

Setting up a Fermentation or Perpetuum Mobile Cell Culture

Some names are confusing. For example, ant-lion is not an ant – or a lion. Likewise, fermentation in the scientific sense does not involve using a ferment or brewing beer. In science, fermentation is the setting up of a long-term culture of eukaryotic or prokaryotic cells. Fermentation is invaluable in providing a steady flow of…

10 Apr 2017 Cells and Model Organisms

How to Use Proteases to Purposefully Digest Proteins

In this article I will not talk about ‘wild’ proteases, which destroy cellular proteins in your lysates like wolves destroy sheep. Instead, I’ll be talking about the shepherd dog proteases—purified, tame and useful to digest proteins your research. In Protein Research and Crystallization Several programs can predict your protein domains. However, we wet biologists know…

25 Aug 2016 Protein Expression and Analysis

How to Improve Plasmid Yield Using Antibiotics

After the initial excitement of growing and isolating plasmid DNA, routinely preparing plasmid mini/midi/maxi preps gets boring. You definitely want a way to squeeze the maximum amount of plasmid DNA out of your culture. Good news—you can increase your plasmid yield using antibiotics. Keep the Pressure On to Improve Plasmid Yield Remember that you need…

23 Aug 2016 DNA / RNA Manipulation and Analysis

How to Become a Medical Writer

If there is one profession that benefited from globalization, it is the medical writer. While the university research groups shrink and global biomedical companies fire their research stuff, medical writing companies are expanding, providing stable jobs with good salaries. The American Medical Writers Association (AMWA) reported in 2011 that the median salary of an experienced…

08 Aug 2016 Career Development & Networking

How to Express Proteins Across Kingdoms: Prokaryotes vs Eukaryotes

In the sci-fi novel Terminal World by Alistair Reynolds, a planet consists of zones with defined characteristics of matter interactions on a subatomic level. These conditions permit different levels of technology sophistication in various zones. For example, in the “Steamville zone” nothing more complicated than steam engines works – electronic schemes fuse irreversibly. Something like…

09 Jul 2016 Genomics and Epigenetics

What To Do About Rust in Your Incubator

Ideally, your tissue culture incubator should be polished stainless steel, gleaming and immaculate like a surgical theatre. And I am sure you keep it in order, like new. It’s just sometimes you start in a lab where the incubators already have brown spots – rust. There’s Rust in My Incubator! Usually rust occurs because of…

09 Jul 2016 Equipment Mastery and Hacks

Sanger Sequencing: How the Genome Was Won

I’ve never run a sequencing gel in my life, but people around me did, and they spent a lot of time on getting it just right. Although the principle described by Sanger in 1975 sounds straightforward (1), sequencing gels are very long and very thin – less than a millimeter thick! They were easy to…

09 Jul 2016 Genomics and Epigenetics

How to Deal with Stress of a Research Project Examination

A scientist’s life is full of stress. An experiment is not working— stress, experiment working but producing results opposite to the previous one— stress, somebody using the last of the reagent you need now— more stress. But these are unexpected stresses, small and overcome easily. The ‘planned stresses’ such as meetings with your supervisor or…

09 Jul 2016 PhD Survival

More Than a Clever Name: Northern Blots

You might think Northern Blots are an old-fashioned technique. However, qRT-PCR is prone to false positives and negatives, and reviewers may require Northern Blot confirmation of your qRT-PCR results. So sometimes Northern Blots are a necessary evil.

09 Jul 2016 DNA / RNA Manipulation and Analysis

Lifecycle of a Scientific Technique

Research laboratory techniques come and go now faster than ever. What is very cool today will not fly even in a thesis tomorrow. This article provides an overview of the method lifecycle.

09 Jul 2016 Fun Stuff

Burning bright: a brief history of ethidium bromide DNA staining

For several decades, Ethidium Bromide (EtBr) was the molecular biologist’s default dye for DNA staining. Now, EtBr is being consigned to the history books. It’s time to have a historical look at where it all started.

09 Jul 2016 DNA / RNA Manipulation and Analysis

How Sweet is Your Protein: Using Enzymes to Study Glycosylation

Most eukaryotic proteins exist as several isoforms, differing in posttranslational modifications, which allows them to perform slightly different functions or the same function under slightly different conditions. A common posttranslational modification of proteins is glycosylation.

09 Jul 2016 Protein Expression and Analysis

The Lab Detective: Finding the Right Blot Detection Method

When it comes to registering the signal output of your Southern/Northern/Western/probe hybridization, you are spoilt for choice these days. You can go all retro and use X-ray film. You can go digital and use a phosphorimager. Finally, you can go fluorescent and use a fluorescence detector. So, what are the pros and cons of each…

09 Jul 2016 Protein Expression and Analysis

Top Tips for Yeast Microscopy

Microscopy is one of the fun parts of working with yeast. If you fix your cells, you can get a snapshot of the structures. Live cells microscopy using fluorescent proteins tagged proteins is even better, as you can see the dynamics and cell machinery working before your own eyes. Light Microscopy to Check for Contamination…

19 May 2015 Microscopy and Imaging

Career Highlight: Technical Officer

An ad about a Technical Officer position is usually nebulous. For example: “The post holder work as part of a technical team and provide both routine and specialist services in support of undergraduate, postgraduate, outreach and revenue-earning activities.” What Does a Technical Officer Do? In fact, a technical officer role can be summarized in two…

18 May 2015 Career Development & Networking

Top Tips on How to Prevent Cell Line Cross-Contamination

Recently we wrote an article about widespread cell culture contamination and how to detect it. This follow-up article will provide practical tips on avoiding cross-contamination in the first place. Be Cautious While Working The first way of cross-contaminating cultures is by accidentally mixing two cultures together, which may lead to an unintended co-culture or the displacement…

22 Apr 2015 Cells and Model Organisms

Gene Synthesis: Cloning of The Future?

I remember the time when elves and wizards walked the Earth and DNA oligonucleotide synthesis was $5 a nucleotide. But the world has changed, nobody thinks twice about ordering an oligo. Whole gene synthesis, which is synthesis of long oligos and their assembly into a very, very long oligo. With prices of around 25–35 cents per…

20 Apr 2015 DNA / RNA Manipulation and Analysis

Cell Culture: a Case of Mistaken Identity

While working in a UK university, I met a researcher who loved Italy much more than the UK. I asked her why she had left her favourite country. She told me that before coming to the UK, she had a 2-year fellowship in Italy where she was getting some promising results and had the chance…

20 Apr 2015 Cells and Model Organisms

Banish the Background with Toxin–antitoxin Cloning Systems

One of the most annoying traits of “classical cloning” is an imperfect system of discriminating between the clones containing an empty vector and vector with insert after cloning. Even when your self-ligation control plate is empty, you can have a lot of colonies containing an empty vector on the “vector + insert” plate. Even the blue-white…

16 Feb 2015 DNA / RNA Manipulation and Analysis

Assembling the Puzzle: Cloning with Compatible Cohesive Ends

Consider a jigsaw puzzle. While most of the pieces have a different picture on their surface, all pieces fit together in an interlocking pattern. As unlikely as it may seem, restriction enzymes from different organisms can produce interlocking pieces of DNA – so called compatible cohesive ends (CCE). These are pieces of DNA, which fit…

17 Oct 2014 DNA / RNA Manipulation and Analysis

Look Ma, No Kit!: A DIY Method for Isolating Yeast Genomic DNA

I recently moved to a different research institute and was happy to discover that my new lab had not one but several different kits for yeast genomic DNA isolation. I like trying new kits and protocols. I especially like trying new kits when they promise, like the Olympics, to yield results that are “Swifter, Higher,…

08 Oct 2014 DNA / RNA Manipulation and Analysis

A Sneak Peak at ‘The Bitesize Bio Guide to Protein Expression’ – a Bitesize Bio eBook

If I piqued your interest in the first post about my new e-Book ‘The Bitesize Bio Guide to Protein Expression – a Bitesize Bio eBook’ check out this excerpt from the book explaining what an expression system is and how to choose the right one.  What is an expression system anyway? There was a time…

23 Sep 2014 Protein Expression and Analysis

Have I Got Good Protein Expression News for You

While the art of reading hand poured sequencing gels is forgotten as the next generation sequencers spit out genome after genome, protein expression still often requires sweat, tears and a lot of luck. I think this happens not because there is something different about protein expression in comparison with sequencing, but because people do not…

21 Sep 2014 Protein Expression and Analysis

Stand By Your Poster

A lot of scientists hate presenting posters. Because more often than not, you stand near your carefully designed, full of great results placard, all alone, while there is a crowd gathered two posters down. There are some conclusions you could come to: You might think that the popular poster author’s work is brilliant – unlike…

08 Sep 2014 Writing, Publishing and Presenting

Dpn I The Strange

If you ever used a site-directed mutagenesis kit or ligation-independent cloning, then you also used restriction enzyme Dpn I. But what does it do and more interestingly, why? Restriction enzymes and methylases: the yin and yang of bacteria Usual restriction enzymes, the toolkit of genetic engineering, are one half of the “yin and yang” pair…

15 Aug 2014 DNA / RNA Manipulation and Analysis

Seven Frivolous Reasons Not to Attend a Conference

Scientific conferences are a peculiar throwback to XIX century, when bearded white men in wool suits were meeting in ale houses to discuss the latest experiment they did at home – once. In our time of instant communication and telepresence, conferences are obsolete and I’ll tell you why. 1. The main reason not to go…

13 Aug 2014 Fun Stuff

Kick Start Your Research With Crowdfunding!

Like most scientists, you rely on grant monies to fund your research. Sustaining it depends on your ability to devise promising new ideas, collect new data and show proof-of-concept before writing another proposal to keep the cycle going. Only the best-of-the-best pilot projects seem to make the cut for experimentation when scarce lab funds are…

06 Aug 2014 Inspiring and Thought Provoking

Shooting Trouble During Cloning

As frustration goes, cloning is often up there with trying to thread a camel through the eye of a needle. You do everything carefully: prepare your vector and fragment DNA, cut them as the restriction enzyme manufacturer instructs (complete digest in five minutes!), ligate, transform and go home in anticipation of a good number of…

04 Jul 2014 DNA / RNA Manipulation and Analysis

Tips for Heating up Agar in the Microwave

One of our readers posted the following question to us and we decided to pass it along to everybody’s favorite microbiology expert, Aunt Yersinia: For one year I am working in different research laboratories, after I got from school. I keep wondering why EVERYBODY is using pre-made Agar solutions for pouring plates, and EVERYBODY is…

17 Feb 2014 Basic Lab Skills and Know-how

Open Access Vultures

If ideas are born as a heresy and die as superstition, many enterprises are born for the bettering of humanity and serve as a source of scam at a later stage. For example, a couple of years ago Amazon was full of 30-40 page ‘books’ on obscure topics such as 18th century shipbuilding.  When a…

15 Jan 2014 Uncategorized

My favorite laboratory Freebie

I love free stuff. Maybe it’s because I am from the former Soviet Union, where there wasn’t enough stuff around, let alone free. Or maybe a little happiness about getting something for nothing is universal, but I am still amazed that companies are giving away things – whether they are useful, not so useful and…

09 Dec 2013 Equipment Mastery and Hacks

How to scale up a PCR reaction

Scientific creativity and repetitive tasks do not go well together.  There is nothing worse than having to repeat the same task over and over again – I know somebody who quit science because of this and became a castle curator. So how do you minimise the amount of one of the most repetitive tasks –…

02 Dec 2013 PCR, qPCR and qRT-PCR

What makes a good collaborator?

In its beginning science was a solitary pursuit: most of the papers in scientific journals prior to the 20th century have just one author.However, the change in scientific culture from “publish when you are really sure about the results” –(it took Darwin many years after he wrote The Origin of Species  to publish it) –…

11 Nov 2013 Dealing with Fellow Scientists

Focus on Isoelectric Focusing

Isoelectric focusing electrophoresis (IEF) of proteins is nowhere near as popular as its cousin – sodium dodecyl sulphate-polyacrylamide gel electrophoresis aka SDS-PAGE. While in both methods the proteins are denatured, IEF is a gel-based electrophoretic separation of proteins using difference in their overall charges. The sodium dodecyl sulphate – SDS part of the usual gel…

21 Oct 2013 Protein Expression and Analysis

How to Odentify Protein Motifs from Protein Sequences

Wouldn’t it be great to put your nucleotide sequence into a program and get back a 3D-structure of your protein and a full description of its functions? In theory, because the protein 3D-structure is determined by the aminoacid sequence, given the right algorithm and a powerful enough computer, this should be simple.  In practice, because…

07 Oct 2013 Protein Expression and Analysis

Do science and copyright mix? (or: if you love your writing, set it free)

American academic and political activist Lawrence Lessig  argues that digital technologies allow all of us to change from passive consumers of culture to the its creators. Producing books, newspapers and movies in the 20th century required a lot investment into manufacturing and distribution, which made most of the population unable to take part in a…

30 Sep 2013 Writing, Publishing and Presenting

Bad Reference? It’s Not the End of Your Science Career

The conventional sequence for getting a new job in science (or anywhere else) goes like this: 1) Apply for job 2) Get an interview 3) Ace the interview 4) Pray that your references hold up. So if you had a bad relationship with your last boss, you’re in trouble. Because no matter how well you…

18 Sep 2013 Career Development & Networking

Book review: ‘How to Write and Publish a Scientific Paper’ by Robert A. Day and Barbara Gastel

One of our PhD students recently became silent and withdrawn. I couldn’t understand why: he is getting a lot of results, has many friends and a popular and easy-going person in general. Then I’ve heard that our PI had told him to write a draft of his first paper and had an idea why he…

16 Sep 2013 PhD Survival

Easy Yeast RNA isolation without the Trizol

Recently BsB author Yevgeniy Grigoryev shared a total RNA isolation protocol. The one I use is even simpler – no expensive Trizol, which is a mix of phenol and some salts, all that is required is some Tris, SDS and phenol/chloroform mix. I have never used this protocol on non-yeast cells but I am almost…

09 Sep 2013 DNA / RNA Manipulation and Analysis

Where to publish negative results

I met a final year PhD student once, who told me a sad story. His supervisor had a plausible idea that exercise reduces the chances of developing bowel cancer. To test the hypothesis, the student made a transgenic mouse with an increased incidence of bowel cancer and got the mice to run (or not run)…

21 Aug 2013 Writing, Publishing and Presenting

Alternatives to presenting your science with Powerpoint

I was shocked recently at a seminar called  “Writing with style” by the Manchester University writer-in-residence, Chris Simms. He opened by saying that he has never done a presentation using Powerpoint in his life. What? Surely biologists and PowerPoint presentations (PPT) go together like biologists and white lab coats. They teach you to make PPTs…

29 Jul 2013 Writing, Publishing and Presenting

Book Review: “Like a Virgin”, by Aarathi Prasad

While modern humans have a broad selection of contraception options, reproducing is still limited to the “egg + sperm = baby” theme whether in the bedroom or in a test-tube.  The Amazon review of Aarathi Prasad’s book, which my husband keeps calling “A lucky virgin”, promises the book “delivers an astonishing exploration of the mysteries…

15 Jul 2013 Inspiring and Thought Provoking

Science and the Media – Dos and Don’ts

Have you ever wondered how the media can write (often cringingly inaccurately) about a recently published scientific paper? Attending Standing up for Science media workshop organised by the Sense about Science charity shed a lot of light on this issue for me There are times when the media are hungry for any news, mostly during…

03 Jul 2013 Science Communication & Ethics

10 Top Everyday Items Useful in the Lab

Every research lab is full of equipment specially designed for specific technical and experimental requirements, unfortunately this means said equipment is often expensive. Thankfully there are simple and cheap everyday items which can help you with your experiments and generally make life a lot easier. 1)  Perforated metal ladle – to fish out samples from…

26 Jun 2013 Equipment Mastery and Hacks

Brahe’s Battle: Kickstarting Science With Rap

“Science” and “rap” are not the two words I expected to find in one sentence. How very small-minded of me. Much to my surprise I discovered that in 2010 Bitesize Bio had a BioPop Rap Battle between nationally-recognized Tom McFadden and a relative newcomer, Science Rapper. In this epic battle between the Cassius Clay and…

05 Apr 2013 Science Communication & Ethics

The Tale of Two Lab Management Strategies

According to the philosopher of science Thomas Kuhn, experimental science relies more on  scientists’ emulation of each other as apposed to theoretical knowledge; e.g. it’s more like craft, which is transferred from person to person through teaching and observing, rather than anything else. Chosen by a group leader, a lab-management strategy is self-sustaining, so I…

03 Apr 2013 Dealing with Fellow Scientists

Meet your microbes: take part in the American Gut Project

“No man is an island” said  John Donne. But if he were, every healthy man or woman would be a lavish, tropical, densely populated island. Recently, I talked to a Knight wants you to help him explore that island. Interested? Confused? Read on… The population of the human island is, of course microbes. Humans have…

20 Mar 2013 Genomics and Epigenetics

Chemistry Spies: pH meters, Buffers and You

The pH meter is probably the least understood and most abused piece of equipment in the biological lab, probably because it is an undercover agent from chemistry and only a rare biologist likes chemistry. Look over there, it stands in the corner of the lab, covered in dust, glass probe encrusted with crystals. In a…

04 Mar 2013 Basic Lab Skills and Know-how

Book Review: “Coalescent”, by Stephen Baxter

This is not just one book, but loosely interconnected, two and a bit – a historical novel, a biological thriller and a science fiction short story – under one cover. The historical novel is about a girl growing up in Britain in the 5th century A.D., while the Roman rule disintegrates. Now, I am not…

18 Feb 2013 Inspiring and Thought Provoking

When Dr Harry met Dr Sally

Logically and statistically, a lab romance (= a romantic relationship between members of one lab) should not work. Most relationships fail sooner, rather than later and working in the same lab will be extremely awkward after the split, which is rarely amicable. And even when the lab romance does work becoming a long term relationship,…

14 Feb 2013 Fun Stuff

Common Sins When Weighing Out Chemicals

You can really tell when Honours Project students start working in the lab on their projects: the pH meter probe is suddenly floating in water and the weighing area is a mess, because nobody had time to explain “the weighing etiquette”. Fret no more! We will spell it out and you can print it out…

13 Feb 2013 Basic Lab Skills and Know-how

The Reproducibility Initiative: Let Them Eat Cake!

Despite obvious differences between the Korean professor-biotechnologist Hwang Woo-suk and German-born postdoc Jan Hendrik Schön, who used to work in the US on semiconductors, both of these scientists have something in common. Since Hwang Woo-suk’s and Schön’s groundbreaking articles were published in Nature and Science, nobody has been able to reproduce their results  and the…

01 Feb 2013 Writing, Publishing and Presenting

Second Chance Saloon: How to Western Blot a Coomassie-stained gel

In her article How to Get Perfect Protein Transfer in Western Blotting, Emily Crow recommends Coomassie staining your gel after transfer to the membrane to check the quality of the transfer. A good transfer should not leave behind proteins and PVDF membrane, stained by 0.1% Ponceau S in  5% phosphoric acid and destained with water…

21 Jan 2013 Protein Expression and Analysis

What Is Open Access Anyway?

It is a truth universally acknowledged that free cheese exists only in a mousetrap, and even there it’s free only to the end user. So it’s no wonder that the traditional system of most scientific publications through publishing houses seems to be fair. A publishing house (PH) employs editors as well as technical personnel to…

07 Jan 2013 Writing, Publishing and Presenting

Book Review: ‘The Selfish Gene’, by Richard Dawkins

A few popular science books rise above the genre and become pop-stars of the book world – bestsellers. Even fewer among them change public discourse and, finally, culture. The Selfish Gene (TSG) by Richard Dawkins is one of these rare books. Published in 1976, TSG is not only still in print, but according to the…

04 Jan 2013 Inspiring and Thought Provoking

Restriction Enzyme Wars: The Natural Function Of Restriction Enzymes

Parents  of small children attending nursery know that the period of time from September to June is a succession of colds and flues for the whole family – children with their underdeveloped immune system exchange viruses, creating new potent strains. Well, that’s probably how bacteria feel all the time in the natural environment teeming with…

14 Dec 2012 DNA / RNA Manipulation and Analysis

Antibiotic Stability: Keep Your (Gun)powder Dry

The stability of an antibiotic depends on its chemical structure, method of isolation (from natural sources or chemical synthesis), and the mechanisms of inactivation. First generation antibiotics isolated from natural sources, such as penicillin, are the most unstable, followed by its semisynthetic derivatives (such as ampicillin and carboxycylin).  Aminoglycosides (kanamicin, spectinomycin, etc.) are more stable.…

30 Nov 2012 DNA / RNA Manipulation and Analysis

Can a New Peer Review Paradigm Decrease Time to Publication?

Peer-reviewing scientific papers is one of the greatest (if not the greatest) bottlenecks of scientific articles publishing. You – a final year PhD student or postdoc at the end of a grant – submit a manuscript to a Top Journal and are happy to hear from the editor that it’s been sent to reviewers. A…

16 Nov 2012 Writing, Publishing and Presenting

Top Ten Tips for TAP

Tandem affinity purification (TAP) is a versatile technique allowing the isolation of proteins for various purposes including Western blot and mass-spectrometry. The target protein is fused with protein A from streptococcus and the calmodulin binding domain, which together comprise the TAP-tag (for an introduction to TAP-tagging, see this article). To purify a TAP-tagged protein from…

14 Nov 2012 Protein Expression and Analysis

Book Review: “The Double Helix”, by James Watson

Is it just me, or are there not many well-written scientific memoirs around? Even the words “scientific memoir” brings up an image of a long and boring book. There are a lot of good books written about scientists, but not by scientists. Maybe it’s because the scientists are trained to write logically, objectively and dispassionately:…

19 Oct 2012 Inspiring and Thought Provoking

DEPC: The Wicked Witch of RNA?

If you have ever worked with RNA, you know about DEPC (diethylpyrocarbonate). You add it to water at a concentration of 0.1%, shake or stir, incubate at 37°C for two hours or at room temperature overnight and, as if targeted by a magic bullet, the RNAses that may have been in the water are gone.…

10 Oct 2012 DNA / RNA Manipulation and Analysis

How To Handle A British Supervisor: A Foreigner’s Guide

The United Kingdom, formerly known as Great Britain, has a long scientific tradition. British academic institutions are among the best in Europe and possibly the world (there is a potential conflict of interest here: while the author is not British by birth, she has spent many years studying and working in the UK). It is…

26 Sep 2012 Dealing with Fellow Scientists

How to Amplify Difficult PCR Substrates

During my postgraduate studies, I did literally one PCR reaction with a pre-optimised protocol on a not especially difficult template. So my karma came back with vengeance, when as a part of my first postdoc I had to amplify a template containing a 35 bp-long GC-rich stem-loop, which proved to be extremely difficult. This was…

14 Sep 2012 PCR, qPCR and qRT-PCR

Zero Tolerance: A Perfectionist’s Guide to Aseptic Technique

Arguably, molecular biology is impossible without microbiology – even if you work exclusively with transgenic mice, you may one day need to amplify a vector in E. coli. And microbiology is definitely impossible without good aseptic technique. The main principle of good microbiological practice is a zero tolerance approach: it’s good to be a little…

29 Aug 2012 Cells and Model Organisms

How to Do a Kit-free Midiprep

Commercial kits are supposed to be to homemade protocols what lifts are to stairs: they should work faster and save you physical exertion. However, in many cases, taking the staircase (e.g. the DIY approach) works better in some ways – and it is always cheaper. BitesizeBio has previously published protocols for homemade plasmid minipreps. I’d…

23 Jul 2012 DNA / RNA Manipulation and Analysis

Got Phage? Here’s how to get rid of it.

Summertime… The birds are singing, the trees are growing. Your tissue culture has sprouted yeast contamination, your yeast culture is happily growing bacteria. Your bacterial culture was growing calmly and predictably, dividing every twenty minutes, but suddenly its optical density has dropped, and it’s full of some sort of filaments and clumps. Or you did…

18 Jul 2012 Cells and Model Organisms

How to Be The Lab Bastard

We all know them. You might even be one. The Lab Bastard is the one who considers himself (or herself!) superior to all other mere mortals in the lab. He would never degrade his talent by doing communal jobs in the lab, but swans around, absolutely sure that his experiments are most important and his…

03 Jul 2012 Dealing with Fellow Scientists

The Easiest Yeast Transformation Protocol on Earth

There are several yeast transformation protocols around, and most of them require a lot of steps: overnight starter culture, dilution and growth to logarithmic phase, several washes, and so on… These protocols work very well since they have been optimised for maximum transformation efficiency, which is needed for applications like library construction. But they are…

22 Jun 2012 Cells and Model Organisms