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Dr Nick Oswald

I started Bitesize Bio on a Macbook on my kitchen table in 2007 while in my 7th year of working as a molecular biologist in biotech. My aim was to share the know-how that I had acquired from the school of hard-knocks in the lab, so that others could learn from my mistakes and small victories. Nowadays my mission is to facilitate the gathering of hardcore know-how from whole spectrum of bioscientists and share it here on Bitesize Bio to create a super-mentor that any bioscientist can turn to for much-needed guidance.

Articles by Dr Nick Oswald:

Ethanol Precipitation of DNA and RNA: How it Works

Using ethanol precipitation to isolate or concentrate your nucleic acids? Find out how this routinely used technique works, and get tips to produce the best results.

An image of beer bottles and mugs denoting ethanol used for ethanol precipitation
30 Mar 2021 DNA / RNA Manipulation and Analysis&New England Biolabs

Does Your h-index Measure Up?

How do you measure how good you are as a scientist? One way is the h-index. Discover what this is, and learn about the pros and cons of using it to assess your scientific career.

A scrabble-type tile showing a letter h next to a hand showing a sign language letter h to represent an author's h-index
16 Mar 2021 Writing, Publishing and Presenting

6 Laboratory Sterilization Methods

Effective laboratory sterilization methods are essential for working with isolated cell lines. Read our guide to the top 6 sterilization techniques to banish those bugs.

Yellow 'Cleaning in Progress' floor sign to represent effective laboratory sterilization methods
09 Mar 2021 Basic Lab Skills and Know-how

How to Make the Perfect Agar Plate Every Time

Agar plates are the foundation of many experiments – make sure your plates are perfect every time with these 8 tips and start your experiment ready for success!

gloved hands holding up an open perfect agar plate
02 Mar 2021 Cells and Model Organisms

10 Tips on Writing a Research Poster

A scientific research poster can be a great tool for drawing people into a conversation at a conference. We’ve pulled together our 10 top tips to help you prep perfect posters.

A blurred photograph of an event exhibition to represent a scientific conference and someone presenting a scientific research poster
18 Feb 2021 Writing, Publishing and Presenting

10 Ways to Use Your “Dr” Title for Good and Evil

So you might be wondering why you bothered with all those years of failed experiments, committees, over-bearing supervisors, thesis writing, and thesis defending. Well, no matter where life takes you, you can now call yourself “Dr” whenever you want. And that can be more useful than you might think…

A model of Dr Who's police box Tardis on a white background to represent ways to use your Dr title for good and evil
16 Feb 2021 Fun Stuff

What Is a Cq (Ct) Value?

Don’t stay confused by Ct values! We’ll guide you through what they are, how to calculate them, and troubleshooting issues.

Image of a qPCR plate, to highlight importance of ct value in qPCR
17 Nov 2020 PCR, qPCR and qRT-PCR

What’s The Problem With Ampicillin Selection?

Resistance to the antibiotic ampicillin is commonly used as a selection marker for plasmids in gene cloning and protein expression in E.coli and other bacteria. While it can be incredibly useful tool, there can be problems using this selection marker that you need to be aware of if if you plan on using it. This…

17 Dec 2019 DNA / RNA Manipulation and Analysis

Antibiotics Used in Molecular Biology

Antibiotics are used in a wide range of techniques in molecular biology including molecular cloning and are important for treating pesky mycoplasma contamination in cell cultures. They can also be used to maximize your plasmid yields by reducing protein synthesis, in certain circumstances. The aim with this post is to provide an easy reference to…

10 Dec 2019 DNA / RNA Manipulation and Analysis

How to Avoid Accidental Plagiarism and Academic Fraud [BMA Podcast]

In the modern research environment we have all of the information we need to work with right at our fingertips – just a cut and paste away. And that makes it very easy for even the most well-meaning scientist to accidentally stumble into plagiarism. Most of us think of plagiarism as simply copying someone else’s…

16 Jun 2017 Writing, Publishing and Presenting

How to Cope With Overwhelm in the Lab: Taming Your Inbox

Look around you in your lab, your institution, and even in the world in general and you’ll see how much we all gravitate towards stress and overwhelm. Stress is just the workplace norm. Overwhelm means you are working “hard enough”. Being so occupied that you are frantically buzzing around from one task to another means…

05 Jun 2017 Organization and Productivity

The Easier Way to Write a PhD Thesis

Without good planning and preparation, writing your thesis can be a nightmare. Here are some tips on how to make the process a whole lot easier.

phd thesis
10 Aug 2016 Writing, Publishing and Presenting

The Essential PCR Troubleshooting Checklist

Routine PCR? Let’s be honest, there’s no such thing. Even with the simplest PCR reaction things can go wrong, so you need to have a good checklist of ideas for PCR troubleshooting and rectifying the problem. Today I have brainstormed all of the ways I can think of to approach problems with standard PCR reactions.…

27 Jul 2016 PCR, qPCR and qRT-PCR

E.coli Electroporation vs Chemical Transformation

This is the first in a three part series on the transformation of E.coli. By the end of this you should be an expert on E.coli transformation and on which strains to choose for different applications. If you’re already an expert, I hope it’ll be an enjoyable refresher for you. In either case, please comment…

26 Jul 2016 DNA / RNA Manipulation and Analysis

How SDS-PAGE Works

What does a stacking gel do? This and other questions about SDS-PAGE answered!

13 Jul 2016 Protein Expression and Analysis

Perfectionism: Are you on the downward spiral?

Do you fear failure every time you do an experiment? Do you feel constantly stressed about obtaining poor results? Do you feel personally culpable when an experiment goes wrong? If you answered “yes” to any or all of these questions, you may be suffering from perfectionism. For a scientist, this is a particularly damaging trait…

09 Jul 2016 Personal Development

5 DNA Ligation Tips

DNA ligations can be frustrating. Sometimes they don’t work for no obvious reason. Our top 5 DNA ligation tips should improve the efficiency of your ligations, and will hopefully increase your cloning success rate! 1. Aliquot the ligase buffer The ATP in the ligase buffer is essential for the DNA ligation reaction, but is broken down…

DNA Ligation Tips
09 Jul 2016 DNA / RNA Manipulation and Analysis

Top Tips to Keeping Your Logbook in Shipshape

Unless you are one of those rare breeds that do organization naturally, setting a system in place to archive your experiments takes practice and perseverance. It’s hard to imagine when you are doing an experiment for the 100th time that you will ever forget how to do it; but a year down the line, when…

09 Jul 2016 Organization and Productivity

How to Shut Off Background Lac Expression in LB

Here’s a tip that you may find useful if you are expressing proteins in E.coli using a lac promoter-based expression system, e.g. pET, in LB medium (L-broth). Lac expression systems are typically induced in the lab using IPTG (isopropyl-beta-D-thiogalacto- pyranoside), which is a non- hydrolyzable analog of lactose, the natural inducer of the lac operon.…

lac expression
09 Jul 2016 Protein Expression and Analysis

PCR Problems? Try an Additive

You’ve tried all the usual stuff, and checked the primer sequences twice, but still can’t get that PCR fragment amplified. It’s time to enter the strange world of PCR additives. Over the years a variety of additives have been shown to enhance PCR reactions in certain situations. Here is a summary of some of the…

09 Jul 2016 PCR, qPCR and qRT-PCR

Get Your Clone 90% Of The Time with Ligation Independent Cloning

Are you stuck in cloning hell?, Tired of doing ligations that don’t work? Want a faster, more efficient cloning procedure? You should try ligation independent cloning. A growing number of researchers swear by ligation independent cloning methods because they are simpler and more efficient than conventional cloning and as a recent convert to their ranks,…

09 Jul 2016 DNA / RNA Manipulation and Analysis

10 Tips for Consistent qPCR

Quantitative PCR (qPCR) uses fluorescent dyes or probes to visualize the amplification of specific DNA sequences as it happens (i.e. in real time). The dyes or probes fluoresce when they bind to newly amplified DNA, and the amount of fluorescence emitted is proportional to the amount of DNA (or mRNA) present in the original sample. By detecting newly synthesized DNA…

consistent real-time PCR
09 Jul 2016 PCR, qPCR and qRT-PCR

Why Do Enzymes Have Optimal Temperatures?

Every biologist is familiar with the profile of the rate of an enzymatic reaction versus temperature as shown in the figure. We know that enzymes from E. coli or warm-blooded animals tend to have an optimum around 37°C, while those from thermal vent bacteria have much higher optimal temperatures. Surprisingly, I find that many biologists…

09 Jul 2016 Protein Expression and Analysis

The Basics: How Phenol Extraction of DNA Works

Phenol extraction is a commonly used method for removing proteins from a DNA sample, e.g. to remove proteins from cell lysate during genomic DNA preparation. It’s commonly used, but not commonly understood. If you want to know how it works so you can show off to all of your friends… read on. The basic protocol…

09 Jul 2016 DNA / RNA Manipulation and Analysis

Quick reference: Determining DNA Concentration & Purity

The most comprehensive way to evaluate DNA concentration and purity is to use both UV spectrophotometeric measurements and agarose gel eletrophoresis. This quick reference guide gives an overview of the information that can be derived from both. UV spectrophotometric measurement of DNA concentration and purity DNA itself, and most of the common contaminants found in…

09 Jul 2016 DNA / RNA Manipulation and Analysis&New England Biolabs

5 Tips on Vector Preparation for Gene Cloning

One of the most crucial steps in any cloning procedure is the preparation of the vector. Get it wrong and your chances of success will be drastically reduced. The overall aim for a good vector preparation is to obtain a fairly concentrated stock of undamaged, fully digested plasmid DNA that is free from contaminants. Missing…

09 Jul 2016 DNA / RNA Manipulation and Analysis

What’s The Problem With Ampicillin Selection?

Ever wonder what those small colonies, like satellites, surrounding a larger E. coli colony on your LB with ampicillin plates were? Or why, when you picked that colony, it never had the plasmid you just transformed? Well, it’s because those satellite colonies are “protected” from the ampicillin by the big colony. Read on for more… Ampicillin…

09 Jul 2016 DNA / RNA Manipulation and Analysis&New England Biolabs

Omics Software Galore!

If you are looking for Omics software, then I suspect the G6G Directory of Omics and Intelligent Software need be your only stop. From the name it will come as no surprise that this website is a directory of Omics and AI software. On the Omics side it lists software for: Genomics Gene Expression Analysis/Profiling…

omics software
09 Jul 2016 Genomics and Epigenetics

Non-specific Binding? Tips to Sharpen up Your Western Blot

In the previous installment of this series on western blotting, we addressed potential sources of error when your final product is completely bare. But alternatively, what do you do when too much background is the problem? You may have beautiful bands of interest—but if there is a bunch of non-specific binding, your quantification and data…

Image of a pencil sharpener to depict sharpening western blot image by handling non-specific binding
15 Mar 2016 Protein Expression and Analysis

Fast-track your Ampicillin Plasmid Transformations

Most of us use pretty standard transformation protocols for E.coli. Yours probably goes something like this: – Thaw the competent cells on ice – Add DNA – Electroporate (or incubate then heat shock for chemically competent cells) – Add rich medium (LB or SOC) – Incubate at 37°C (or appropriate temperature) for 30-60 minutes –…

19 May 2015 DNA / RNA Manipulation and Analysis

Codon Usage Analysis

Problems with expressing your gene? One of the potential stumbling blocks in heterologous gene expression is incompatible codon usage. Every amino acid can be encoded by more than one codon, and for every amino acid each organism has a favorite codon that it tends to use more often than the others. The availability of tRNA…

05 Mar 2015 Protein Expression and Analysis

DIY Electrocompetent E. coli

If you buy competent E.coli regularly, you’ll know that they are pretty expensive. So the cost of screwing up a cloning or transformation experiment is pretty high in terms of money, as well as your time and sanity! But you don’t need this extra worry because despite what their high commercial cost would suggest, making…

02 Feb 2015 Protein Expression and Analysis

10 Do’s and Don’ts for PhD Students

My PhD is rapidly becoming a distant memory. Before nostalgia completely obscures my recollections of this chapter of my career, I thought I’d jot down some pointers for prospective and current PhD students. These are mainly based on things I wish I had done during my PhD, or mistakes I have seen others make. I…

29 Dec 2014 PhD Survival

20 Ways to Increase your Productivity

No matter how efficient you are, it’s always possible to improve your productivity and improving your productivity means that you get more of the rewards you are trying to obtain: results, publications… or dare I say it, money. Here are 20 ways to improve your productivity. Some are focussed toward improving the productivity of bench…

17 Dec 2014 Organization and Productivity

DNA Ligation: How it Works

It takes a real effort to keep your basic knowledge of molecular and cell biology fresh, in addition to everything else you have to do. Wouldn’t it be great to if there was a place where you could find easy-to-read articles that allow you to brush-up on those basics in just a couple of minutes?…

05 Dec 2014 DNA / RNA Manipulation and Analysis

Sleigh or Wormhole: Has Santa’s Delivery Method Evolved?

We all know the traditional Christmas Eve scene of Santa flying in his sleigh through the crisp night air, pulled by his troop of reindeers. Over the years, debate has raged in the scientific community as to just how he could be pulling off this feat. We still don’t know how he does it. But…

01 Dec 2014 Fun Stuff

Stop Pushing, Start Enjoying and Get Better Results at the Bench (and in Your Life)

Most of the time, research (and life!) can feel like a struggle. Constant deadlines, incessant demands, pressure to get results, grants, job, publications – and dealing with irritating colleagues and bosses. You know what I mean. The struggle saps your energy, and removes the color from your life. It reduces your capacity to focus on your…

24 Nov 2014 Inspiring and Thought Provoking&Personal Development

The Basics: How Alkaline Lysis Works

Alkaline lysis was first described by Birnboim and Doly in 1979 (Nucleic Acids Res. 7, 1513-1523) and has, with a few modifications, been the preferred method for plasmid DNA extraction from bacteria ever since. The easiest way to describe how alkaline lysis works is to go through the procedure and explain each step, so here…

08 Oct 2014 DNA / RNA Manipulation and Analysis

How to: Get Better Plasmid midiprep Yields

I get many people complaining to me about poor DNA yields from commercial plasmid plasmid prep kits. In this article I will explain the main pitfalls in plasmid isolation and how to avoid them.

12 May 2014 DNA / RNA Manipulation and Analysis

Breaking Up is (Not That) Hard to Do: Sonication for Cell Lysis

To answer some of the more interesting research questions, you often need to get a good look at what’s going on inside the cell. Whether you’re running a Western blot or measuring enzyme activity, many assays require access to the materials (e.g. proteins, DNA, subcellular fragments) contained within the cell walls. There are several ways…

19 Aug 2013 Protein Expression and Analysis

One Part Science, Two Parts Murder: A Book Review of “The Poisoner’s Handbook: Murder and the Birth of Forensic Medicine in Jazz Age New York” by Deborah Blum

The canonical motto in Toxicology is ‘the dose makes the poison.’ That is, enough of anything can kill you. But, as Deborah Blum notes in the end of her book, “poison by water doesn’t unnerve us. The real scare comes from those elements and compounds whose toxicity is measured in drips and drops.” In The…

15 May 2013 Inspiring and Thought Provoking

Damage control: One thing you must always to do ensure your data is reliable

Whenever you make up a solution or use a purchased reagent in the lab, you trust the work of a whole army of people and equipment. If any one of those links in the chain has a technical problem or makes a mistake, then your reagent might turn out to be faulty. And that can…

15 Apr 2013 Organization and Productivity

RNases: Their baddie super-powers explained (and how you can defeat them)

RNases are like the baddie super-heroes amongst laboratory enzymes. They are omnipotent, destructive and seemingly indestructible. This is because they were created by evil overlords, for the sole purpose making life difficult for the brave scientists who battle every day to produce high quality, intact RNA preps. Ok, I’m joking about the overlords part.  But…

12 Mar 2013 DNA / RNA Manipulation and Analysis

How To Deal With People Stealing Your Reagents

I have been fortunate enough that in my career to date I have rarely experienced the problem of other people stealing my reagents. However, one PI told me of her experiences working in a US laboratory where things had got so bad people brought their reagents home at the weekends! Working in a research laboratory…

17 Dec 2012 Dealing with Fellow Scientists

Competition!! Join us for the Bitesize Bio Blowout

I’ve always liked December, mainly because Christmas and my birthday fall in that month. But this December we are also celebrating moving into the Rolls-Royce of office spaces, at Nine, The BioQuarter in Edinburgh (photo above). This puts us right in the heart of the bioscience community in Edinburgh and turns the Scottish Centre for Regenerative…

26 Nov 2012 Fun Stuff

How to Write Your Thesis Right

After years of hard work in the lab, having to sit down and write everything up can be a daunting and difficult task. Here are a few tips that I picked up during my thesis write-up that might help to make the process that little bit easier. Back up This is probably the advice most…

01 Nov 2012 Writing, Publishing and Presenting

Don’t Miss Bioconference Live…

It’s that time of year again…time for BioConference Live! The 6th Annual Life Sciences BioConference Live virtual event kicks off September 12-13, then will be available on-demand for three months following. This free online-only event will bring scientists from all around the world together exclusively online, to learn about the latest advances in life sciences and topics…

10 Sep 2012 Of Interest

Run More Organized Experiments using LabGuru’s Free Electronic Lab Notebook and iPad App

Back in 2010, Bitesize Bio’s senior editor, Jode Plank wondered whether the release of the iPad would eventually see us ditch the paper lab notebook in favor of more searchable, organized and legible electronic lab books. Electronic lab books have been around for a while, but the disconnect between the desktop computer – and to…

09 Apr 2012 Organization and Productivity

10 Ways to Work RNase Free

Working with RNA? What fun! Those little, nearly indestructible RNases are everywhere – on your skin and mucous membranes, in the water and (some of the) enzymes you use, on lab surfaces, even in airborne microbes! Here are 10 ways to keep the RNases at bay, and keep your precious samples safe:

Image of someone filling vials with pipettes to represent successful postdoctoral interview preparation
01 Apr 2012 DNA / RNA Manipulation and Analysis

Make Every Day As Effective As Deadline Day

I’m sure you’ve heard of Parkinson’s Law, or at least the modern-day generalisation of it. It states that “Work expands so as to fill the time available for its completion.”  When I first heard this, back in the mists of time, I thought Mr Parkinson was damn right, had a chuckle at a very accurate…

03 Aug 2011 Personal Development

Tell Good Stories About Yourself To Get The Job

In our recent webinar on 10 Tips to Maximize Your Job Hunt Success, career development author and guru, Peter Fiske give an excellent tip on acing interviews that I’d like to highlight. Peter’s assertion is that one of the most important things you can do to prepare for a job interview is to construct and…

25 Jul 2011 Career Development & Networking

Three Approaches to Site-directed Mutagenesis

Site-directed mutagenesis studies can be extremely useful for elucidating the function of a gene or protein, or for creating variants of an enzyme with new and improved functions. There are now many approaches available for generating site-directed mutants, whatever your purpose. In this post I’ll summarize three techniques that will enable you to produce a…

20 Jul 2011 DNA / RNA Manipulation and Analysis

Top 10: Worst Lab Smells

Time for a bit of fun. Here are my top 10 worst lab smells, in reverse order. Please share your worst smells in the discussion! 10. I’ll start off gently with Latex Gloves. Not truly a offensive smell, just a little off-putting 9. Ever stewed a turnip for far too long? No. If you did,…

08 Jul 2011 Fun Stuff

Make Your Manuscripts More Readable in 5 minutes per Day

We scientists are all so focussed on getting our work published that many of us seem to forget something very important; that publication is just the beginning. After publication is when our manuscripts really have to do their essential work of communicating our science to our peers. If no-one reads the manuscript, we might as…

30 Jun 2011 Writing, Publishing and Presenting

Easily Organise Meetings with a Free Tool: Doodle

Organising lab meetings, journal clubs and even lab get-togethers can be a bit of a hassle, with emails flying about and spreadsheets coming out of your ears. Luckily, thanks to some nifty, free online tools you can remove the pain of being the resident meeting organiser forever. The best of these at I’ve seen is…

28 Jun 2011 Organization and Productivity

Use Less Vector, Killer Cut for Success in Plasmid Cloning

Here’s an all-too-often repeated scene in the lab: First thing in the morning, you approach the 37°C incubator with trepidation, open it and through one half-open eye you take a look at the LB plate that you spread your ligation-reaction-transformed E.coli aliquot onto. Looks good – thousands of colonies. Emboldened, you take your “no ligation…

27 Jun 2011 DNA / RNA Manipulation and Analysis

How To Read Manuscripts (and anything else) Twice As Fast

I always thought that doing a speed-reading course would be a good thing to do as a scientist. With the amount of literature we need to consume, speed-reading (the art of reading faster without reducing comprehension) would save a lot of time. But it turns out that you don’t really need to spend any cash…

13 Jun 2011 Taming the Literature

Should You Use Magnetic Beads for Immunoprecipitation?

Sepharose beads are porous, which gives them a high surface area for interaction with proteins and allows them to hold a lot of liquid. This is perfect for the application that they were originally designed for: purifying milligrams of protein in columns. When immunoprecipitation (IP) – a small-scale technique for pulling specific proteins out of solution using…

08 Jun 2011 Protein Expression and Analysis

Careers for Scientists – Business Development Manager

Looking for a new direction in your career? This is the latest in our new series of articles that focus on careers for scientists.  When we started this series, we thought you’d be interested in finding out about who does what behind the scenes at Bitesize Bio, and how we got here.  I interviewed our…

08 Apr 2011 Career Development & Networking

BioConference Live 2011: Free Online Conference for Life Science Professionals

BioConference Live is fast becoming a permanent fixture on the Bitesize Bio office calendar. And this year is no exception. This two day, all-online event brings speakers on a huge variety of topics right to your desktop and is a great way to catch up with the latest and greatest in the life sciences without…

02 Mar 2011 Of Interest

Super-Charge Your Skills and Career: New Web Seminars at Bitesize Bio

Our new webinar series has something for every biologist – take a look.

04 Feb 2011 Of Interest

Careers for Scientists – Editorial Manager

Looking for a new direction in your career? Well you’ve come to the right place. This is the first in our new series of articles that focus on careers for scientists.  We’ll be looking at jobs that are off-the-beaten-track (and sometimes on no track at all) and ones that are certainly not on the standard…

24 Jan 2011 Career Development & Networking

BioPop Rap Battle: Tom McFadden vs Science Rapper. Who Gets Your Vote?

Get ready for a battle between two red-hot rappers who have smashed onto the BioPop scene in the last year. Introducing the Contestants Tom McFadden Tom McFadden, a former Stanford biology course instructor-turned scientific communicator  emerged from the California BioPop scene (BioRap branch) with his hit single Regulatin’ Genes, which saw him featured in national newspapers like The…

29 Nov 2010 Fun Stuff

Nervous About Speaking in Public? Here’s Some Advice You Should Ignore

Books, training manuals and blog posts on speaking in public have a really bad habit of glossing over the issue of nerves. Even I did it in a post I wrote back in 2007. Here’s the advice I gave: Accept that you are going to be nervous and embrace it. There will always be some…

24 Nov 2010 Writing, Publishing and Presenting

5 Ways to Use Coffee to Power Up Your Research, Career and Lab Group

Coffee is powerful stuff, but did you ever think of using it for….

27 Oct 2010 Dealing with Fellow Scientists

Should You Use Calf Intestinal Alkaline Phosphatase (CIP) in Plasmid Cloning

CIP has been around for a while, but there is a better alternative.

18 Oct 2010 DNA / RNA Manipulation and Analysis

What’s Wrong With News Reporting of Science?

A focus on two blog articles by Martin Robbins that pull apart the tangled web of science news reporting.

12 Oct 2010 Writing, Publishing and Presenting

10 More iPhone / iPad Apps for Bioscientists

In the time since Bala wrote his article for us about iPhone apps for bioscientists, many individuals and companies have jumped on the bandwagon to deliver some great new apps that you might find useful in the lab. Here’s my pick of the 10 best apps available at the moment: 1. Pubmed Library Price $9.99/£5.99…

06 Oct 2010 Software and Online Tools

Use Cell Banks to Save Time Growing Routine Cultures

If you regularly grow up the same bacterial culture, whether it’s the strain that expresses your favorite protein, the culture you make your competent cells from, or just your regular control strain, it can be a bit of a pain growing it up from scratch each time. Before you even get to grow your actual…

01 Sep 2010 Cells and Model Organisms

Say Goodbye USB Sticks, Hello Dropbox

When you’re writing up your latest report, next paper or your PhD thesis, its best to get out of the lab and work somewhere where there are fewer distractions. Normally that means stuffing all of the work files you need onto a USB stick (or emailing them to yourself) so that you can work on…

21 Jun 2010 Software and Online Tools

So You Think You Know PCR?

Well, after much anticipation, we finally got the Bitesize Bio seminars off the ground with a rip-roaring presentation from SYBR Green I and Lightcycler inventor, Carl Wittwer. Carl’s talk took us from the early days of rapid cycle PCR to the development of the Lightcycler through to the diversification of real time PCR  into different…

24 May 2010 PCR, qPCR and qRT-PCR

Free Online Bioconference, Astronaut Included

Back in November 2009, we told you about a ground-breaking new concept from the people at BioconferenceLive – a whole three day conference, complete with lobby, exhibitor booths and great presentations, held entirely online. Suzanne and I were  “there” (in a virtual sense), attending some of the talks and manning the Bitesize Bio booth, and…

11 May 2010 Of Interest

A Facelift, Questions and World Class Seminars

We have been working furiously for the past 6 months to bring you a new, improved and dramatically upgraded Bitesize Bio. And now we are now ready to share. So what’s in the new version? The first thing you’ll notice is the facelift. But the new logo and colors are just the start. The site…

08 May 2010 Of Interest

Does Anyone Know the Funny Handshake?

Greg Petsko, President of the American Society for Biochemistry wrote a very interesting article recently in which he drew attention to the parallels between the PhD/Postdoc system and the medieval trade guilds, and the problems our profession faces because it is drifting away from that system. In the trade guild system the right of an…

31 Mar 2010 Lab Statistics & Math

How Plasmids Became Embroiled in The Cold War

The humble plasmid. We now know it so well, but as little as 60 years ago the field of extra-chromosomal heredity was decidedly murky. Not only was it the subject of great debate, conflict and friction within the scientific community, it was even used as a politico-religious tool during the Cold War! The origin of…

17 Feb 2010 History of Biology

Becoming an Expert, Brick by Brick

As a newcomer to a research lab, looking at the seasoned, experiment-beaten postdocs around you, it can be easy to fall into the trap of thinking that the task of acquiring their level of knowledge and expertise, and of making any sort of impact within the lab and wider community, is huge and daunting. But…

10 Feb 2010 Personal Development

Evernote: Never Lose Data or Ideas Again

Evernote is an amazing FREE application that could change the way you record, store and retrieve your data, in the lab as well as at home. The idea behind Evernote, as shown on the right, is to allow you to capture all of your ideas and put them into your personal database on Evernote’s servers…

21 Jan 2010 Software and Online Tools

How is Lab Grade Water Purified?

There’s something in the water, and it would love to go after your experiments. Straight out of the tap, water contains microorganisms, endotoxins, DNase and RNase, salts and other impurities that could gobble up your experiment in one bite. Of course we avoid this drama completely by using purified water from which these nasties have…

11 Jan 2010 DNA / RNA Manipulation and Analysis

The Best of Bitesize Bio 2009

Before we get our brains fully back into gear after the festive season and embark on what we hope will be a momentous year for Bitesize Bio (watch this space, we’ve got some cool stuff in store), we thought this would be a good time to look back at the best articles we published in…

06 Jan 2010 Of Interest

How To Make Fewer Mistakes In The Lab

How often do you make errors in the lab that ruin a good experiment? Rather than flaws in experimental design, I mean errors like forgetting to add a reagent, pipetting the wrong amount or following a protocol step wrongly. Especially early on in your career, errors like this can be a real drain on your…

23 Nov 2009 Basic Lab Skills and Know-how

Which is Best: TAE, TBE or Something Else?

TAE or TBE, which is best? Well, of course, it depends on what you want to do. Here are the pros and cons of both: TBE (Tris-borate-EDTA) is a better conductive medium than TAE (Tris-acetate EDTA) so is less prone to overheating so use TBE for long runs Borate is an enzyme inhibitor so TBE…

19 Nov 2009 DNA / RNA Manipulation and Analysis

Does (Should) Your Lab Rock?

My PhD was a soul-less affair. It was also rock-less, jazz-less and pop-less. And all because my supervisor was of the opinion that music in the lab was a distraction that reduced concentration and our ability to do the job. “Rubbish!”, I thought, “Nothing helps you through a mindless task like splitting cells, pipetting or…

16 Nov 2009 Dealing with Fellow Scientists

A Halloween Treat: 10 Molecular Bio Tips

This Halloween we want to treat you with some molecular biology goodies in the shape of 10 juicy tricks. We’ve been bringing you advice since August 2007, but some of our readers may just be discovering our hallowed grounds. Join us in bringing some of these old tricks back to life. 1. Save money by…

30 Oct 2009 DNA / RNA Manipulation and Analysis

Even Better Free Molecular Biology Software: Serial Cloner

In 2007, I wrote a couple of articles on the best free software for molecular biologists on Mac and PC. One of the highlights of those lists was a fantastic cross-platform for in silico DNA cloning, sequence analysis and visualization, called Serial Cloner (move over VectorNTI!). The creator of Serial Cloner, Franck Perez, contacted me…

08 Oct 2009 DNA / RNA Manipulation and Analysis

Spare a Thought for the Old Scientists

You youngsters don’t know how easy you’ve got it. Kits, outsourcing and improved practices are making research easier and easier. At least in theory (who are we kidding?). In the old days things were much tougher, and many wiley old scientists bear the scars, mental and physical, of carrying out techniques that were mind numbing,…

25 Sep 2009 Dealing with Fellow Scientists

Open Access Publishing Is Not Perfect, Yet

No-one would disagree with the goals of open access publishing: free access to scientific literature for all. If you work in an institution or small company that can’t afford to pay journal subscription fees you’ll know the problems that lack of access can cause. But publishing costs money, and someone has to pay those costs.…

24 Sep 2009 Writing, Publishing and Presenting

BiomedExperts: An Alternative Way to Search The Literature

If you have ever looked closely at Pubmed, you might have noticed that it’s not easy to search for all publications by a single author, to see everything that your collaborator has published or to see what the top people in your field are publishing. Pubmed just isn’t set up to allow you to focus…

12 Aug 2009 Taming the Literature

How to Shine in a Small Biotech Company

So you finally got your PhD (or your masters or batchelor’s) and you are making the big switch to a small biotech company. You will probably have been hired for the specific skill set that you have built during your training, but now you have to learn to apply those skills to solve real world,…

05 Aug 2009 Career Development & Networking

Tech Clinic #4: Can a single E.coli take up 2 plasmids?

The following question was emailed to Bitesize Bio by Beheroze Sattha and I gladly took up the challenge, and I immediately knew the answer. Or so I thought. After delving extensively into Pubmed, Genes V (I know, I need a new version) and Molecular Cloning I have come up with an answer, but it is…

31 Jul 2009 DNA / RNA Manipulation and Analysis

Why Bioscientists Should All Buy Macs

Macs are great and there are a lot of reasons I recommend them to anyone who asks my opinion on which computer they should buy. But for bioscientists, perhaps the best reason to buy a Mac is summed up by one word: Mekentosj. Mekentosj is dedicated to producing fantastic software that addresses the needs of…

22 Jul 2009 Organization and Productivity

Delivering Effective Criticism

Criticism is not just valuable, it is essential for a person’s development as a scientist, or anything else for that matter. Well that’s not entirely true. Not all criticism is valuable, it has to be the right kind of criticism. It has to be constructive and better still, well delivered in order to inspire the…

16 Jul 2009 Dealing with Fellow Scientists

Join Our Twitter Experiment

I have watched, with some bemusement, as the internet phenomenon that is Twitter has grown and grown, then grown some more. I say bemusement because it didn’t really make much sense to me. But millions of internet users can’t be wrong (ok, I know they can be) so I decided to take a look myself.…

08 Jul 2009 Software and Online Tools

10 More Firefox Add-ons for Scientists

Way back in October 2007, I wrote an article on 10 Firefox add-ons for cell and molecular biologists. I think Firefox is a brilliant browser and it’s open source add-on contributors make it more useful every day. Apparently, Bitesize Bio readers agree because that Firefox article has remained firmly established in our top 10 most…

06 Jul 2009 Software and Online Tools

How to Become a World Class Speaker

Really great presentation skills. Some people in science seem to have them, and some don’t. I am one of the don’ts. Sure, I can get up in front of people and talk when needed, but it won’t be a polished performance by any means. I can get my message across but my delivery is not…

16 Jun 2009 Writing, Publishing and Presenting

10 Stupid Lab Safety Mistakes

Keeping safe in the lab really only requires one thing: common sense. But if you look at what people are doing in the lab, you might think that that common sense isn’t so common after all. What are the most stupid things you have seen people do in the lab to put the safety of…

15 Jun 2009 Lab Safety

A Quik Way Around Partial Restriction Digests

No matter how many times you look at it, it’s not going to change. You are planning your next cloning experiment, but there’s a problem. The only restriction enzyme that cuts in a suitable position on your plasmid vector also, as luck would have it, cuts in another position elsewhere in the vector so you…

04 Jun 2009 DNA / RNA Manipulation and Analysis

15 Ways to Make Contacts at Conferences

Going to conferences normally involves a significant investment of time and money. So it’s important to get as much as you can out of them. One of the most valuable things you can get from a conference is contacts. These can build into a network of people that will be valuable to you throughout your…

20 May 2009 Career Development & Networking

Super-Easy Mind Mapping

I’ve talked about the benefits of mind-mapping before. It’s a fantastic technique for note-taking, brainstorming and organising your thoughts. I am a big fan of using mind-mapping software, as opposed to paper, to construct mind maps because, for me, the paper versions quickly get unwieldy and messy. FreeMind has been my software of choice for…

13 May 2009 Software and Online Tools

RPM Does Not Equal RCF

RPM and RCF are two units that can be used to describe the speed of a centrifuge. Although they may look similar, they are oh-so-different and confusing them has resulted a disastrous end to many an experiment. So let’s set it out in black and white to make sure you don’t succumb to the same…

11 May 2009 Equipment Mastery and Hacks

The Best Way to Desalt DNA for Electroporation

After ligation, the method you use for desalting your sample prior to electroporation is critical, especially if your ligation is inefficient, according to a study by Schlaak et al [1]. Under standard electroporation conditions, the electric field of 12-18 kV/cm generated in a 0.1mm-gap electroporation cuvette means that the conductivity of the sample must be…

20 Apr 2009 DNA / RNA Manipulation and Analysis

Why You Should Never Trust a Patent

If you search the literature using a comprehensive search engine like Google Scholar, you will get several types of articles listed. Most of them are peer reviewed journal articles and many are patents. But beware of an important distinction between the two: Although patents can contain useful information, they are not authoritative because they are not…

17 Apr 2009 Taming the Literature

Super Fast Immunoblotting

Sometimes a new product comes along and you just know that it is going to make your life easier. The SNAP i.d. protein detection system from Millipore falls into that category. In a nutshell, SNAP i.d. is a nifty little gadget that fits in to the immunoblotting protocol after the membrane transfer step. There it…

30 Mar 2009 Protein Expression and Analysis

Reasons to be a Scientist Part II

Scientists often complain about the job, and here on Bitesize Bio we are no different. For an example, take a look at my rant about why not to be a scientist – written about a year ago after a particularly frustrating couple of weeks in the lab. Very recently, I decided to leave bench science,…

16 Mar 2009 Inspiring and Thought Provoking

Take it Easy – Learn by Osmosis

Undergrad courses teach you to learn in a specific way. You have to cram in as much information into your brain as possible, hold it in there, then regurgitate as much of it as possible on exam day. Of course, actually understanding what you are talking about, and working from basic principles, helps but the…

09 Mar 2009 Personal Development

How To Get Great DNA Sequencing Results

There is nothing more frustrating than getting back rubbish data from a DNA sequencing run, especially when you are waiting for an important result. For example, confirmation of that clone you have been trying to get for the past three months! A lot of the time, the quality of sequencing data is within your control.…

19 Feb 2009 DNA / RNA Manipulation and Analysis

Networking For Scientists

No scientist is an island, not even a great scientist like you. A good network of professional contacts is as essential to your career as hard work at the bench. This is because your network can open many doors that no amount of good bench work could. Access to unpublished information, collaborations and job opportunities…

05 Feb 2009 Career Development & Networking

5 Ways to Use your Google Search Box

Did you think that your Google search box was just for searching the web? If so then think again – those folks at Google are the masters of innovation (you only have to look at where they work to see that). So it’s not surprising that they have made their search box cleverer than most.…

10 Dec 2008 Software and Online Tools

What you need to know about OD600

If you use a spec to measure cell density, you may be making a very common mistake and taking inaccurate measurements as a result. Specs are often used for measuring the density of suspension cultures, but the mistake that many people make is to record the OD given by the spec as an absolute value.…

08 Dec 2008 Protein Expression and Analysis

Why You Shouldn’t Worry about Getting Results

Everyone is worried about getting results, aren’t they? Results are what you need for success in science – they are essential for bringing the funding in. But focusing on results per se is not a good way to work because, as a scientist, you can’t “get” results. You can’t “make” them happen. Essentially in every…

17 Nov 2008 Personal Development

Are you growing in your career?

Where do you want to be, career-wise, in 1, 3, 5 or 10 years? Is the position you are in at the moment helping you to reach that goal, or are you stagnating? These are questions I think everyone should be asking themselves at least a couple of times a year. Career Growth During Study…

03 Nov 2008 Personal Development

Powerpoint: Lose the bullets

Powerpoint is a double-edged sword. There’s no doubt it makes putting together a presentation easier. Those who worked with slides, overhead projector films and the like in the years B.P. (Before Powerpoint) will testify to that. But Powerpoint’s ease of use also makes it easy to abuse, and bullet points are the most abused feature…

30 Oct 2008 Writing, Publishing and Presenting

Inspirational Talks at TED

Imagine bringing some of the world’s greatest talkers and thinkers in a conference and challenging them to give the best talk of their life, on whatever they want to talk about. Wouldn’t that be an amazing event? And if someone videoed all of the talks and put them on a website, what a great resource…

14 Oct 2008 Inspiring and Thought Provoking

Project Planning Made Easy

Whatever field you work in, effective project planning can make your work much more efficient, and make your like much easier. Liquid planner is a unique, online project planning interface that is free as long as your project has three or less team members. Liquid Planner has a nice interface for defining tasks and constructing…

08 Oct 2008 Organization and Productivity

It’s A Small World

Small Worlds is a new initiative organised by Alan Cann at the University of Leicester (and of the excellent Microbiology Bytes) that aims to encourage scientists to use the immense power of web 2.0 in their professional lives. Alan points out that although scientists were the pioneers of the internet, we have been slow to…

06 Oct 2008 Career Development & Networking

When SDS-PAGE Goes Bad

You are not alone. Everyone makes a hash of their protein gel sometimes but this resource can help you work out what went wrong, and feel better for seeing gels even worse than yours.

30 Sep 2008 Protein Expression and Analysis

5 ways to Damage DNA

Your DNA samples are precious so take care of them! Here are 5 ways that DNA can be damaged, so now you now what to avoid in the future.

10 Sep 2008 DNA / RNA Manipulation and Analysis

Scientists – Get Networked

Networking has never been easier. Here are 5 sites designed to help scientists to build professional networks.

08 Sep 2008 Writing, Publishing and Presenting

Pubmed + RSS + iGoogle = Easy Lit Updates

The simple solutions are always the best. Here is a simple but powerful way to combine Pubmed, RSS and iGoogle to keep up with the literature.

13 Aug 2008 Taming the Literature

Agarose Gels Do Not Polymerise!

Ever heard of polymerising agarose gels? I haven’t. If you think you have, read this.

06 Aug 2008 DNA / RNA Manipulation and Analysis

RNase and DEPC: Dispelling the Myths

DEPC. IF you work with RNA, you’ll know this stuff. It’s vital for ridding solutions of RNases that would otherwise destroy your work. But just how well do you know it?

04 Aug 2008 DNA / RNA Manipulation and Analysis

Draw Your Calculations, xThink does the Math

Tired of tapping away at that calculator? Why not draw your equation instead with XThink’s natural interface online calculator.

30 Jul 2008 Software and Online Tools

Using People Skills to Get that Job

Advice from a job interview master on how to get land a technical job, even if your technical skills aren’t as good as the competition’s.

21 Jul 2008 Career Development & Networking

The Price of PBS These Days!

What’s more expensive, gas (petrol) or PBS? Here’s a comparison between what you are paying for reagents and what you are paying at the pump.

15 Jul 2008 Basic Lab Skills and Know-how

Southern, northern, western (and eastern?)

This is the story of how one of the most famous and quirky naming conventions in biology came into being.

Southern, northern, western (and eastern?)
09 Jul 2008 Protein Expression and Analysis

TiddlyWiki: A 21st Century Roladex

Meet TiddlyWiki – a great piece of software that you can use to build your own wiki on a (USB) stick.

01 Jul 2008 Software and Online Tools

Calculate your Fudge Ratio, Manage Lab Time Better

Calculating your fudge ratio can help you get your work done on time and get home before dark. Here’s how.

24 Jun 2008 Personal Development

How to Make Accurate Stock Solutions

Biology researchers have a bad habit of doing accurate assays using semi-accurate tools. Here are some suggestions on how to sharpen up the accuracy of your assays.

23 Jun 2008 Basic Lab Skills and Know-how

How Accurate are Your Pipettes?

You probably use and rely them more than any other tool in the lab, but just how accurate are your pipettes?

19 Jun 2008 Basic Lab Skills and Know-how

4 (Well, 5) Facebook Applications for Biologists

Would you like to pretend you are still working while you “Facebook”. These biology-related Facebook applications will help.

17 Jun 2008 Software and Online Tools

A Simple Lab Notebook Admin System

As far as your lab work is concerned, your lab book is the source of all knowledge. Making it easy to find things in there will help. Here’s how to do it.

10 Jun 2008 Organization and Productivity

How to reduce your lab’s environmental impact

Bioscientists are generally nature-lovers at heart, but the average bio lab is incredibly wasteful. Here are some ways to reduce your lab’s environmental impact.

05 Jun 2008 Organization and Productivity

This Week’s Best of the Kit

Lazy DNA ligation, low carbon footprint bunsens and back-to-basics E.coli… they’re among our picks of the kit for this week.

03 Jun 2008 DNA / RNA Manipulation and Analysis

Avoiding the Lure of The Internet

The internet is a great tool, but can also be a real source of distraction. Here are five ways to avoid it’s lure while working, and stay productive.

31 May 2008 Organization and Productivity

How I Chose a “Grad School” (UK edition!)

In the US it’s called Grad School, but in the UK we just call it “doing a PhD”. Here’s how I chose my PhD position, and some resultant advice for those currently looking for a PhD.

27 May 2008 PhD Survival

Scientist, GSOH. Seeks Similar.

How does the lonely scientist find that special someone with whom they can share their copy of Molecular Biology of The Cell?

20 May 2008 Dealing with Fellow Scientists

How to Refold 653 Insoluble Proteins

An introduction to the Monash protein folding database, which contains protocols for refolding over 600 different proteins from inclusion bodies.

15 May 2008 Protein Expression and Analysis

Sequence and Ligation Independent Cloning

Could ligation independent cloning get any better? Well here is a technique that is sequence AND ligation independent.

14 May 2008 DNA / RNA Manipulation and Analysis

Don’t Overdo The Multi-tasking

Multi-tasking used to be my favourite way to get ahead. During my PhD I saw others around me working extremely long hours in the lab and not really having much of a personal life and quite early on I made the decision that this was not for me. Although I enjoy my work, having a…

07 May 2008 Organization and Productivity

Would you Sterilise Growth Media With A Microwave?

Several peer-reviewed articles advocate using microwaves for sterilization, but would you trust microwave-sterilized growth medium?

06 May 2008 Cells and Model Organisms

Re-cycling Electroporation Cuvettes

If you have ever worked out the price of an electroporation cuvette you will realise that, at several dollars each, they are worth recycling. Accounts on how amenable electroporation cuvettes are to recycling vary, but I find that as long as you treat them well it is possible to use single cuvette many times. It’s…

30 Apr 2008 DNA / RNA Manipulation and Analysis

Structured Digital Abstracts – Easier Literature Searching But Not Democratic

FEBS Letters is this month carrying out an interesting experiment that could make literature searching easier for both humans and computers. The experiment centres on Structured Digital Abstracts (SDA). SDA are extensions of the normal journal article abstracts that describe the relationship between two biological entities, mentioning the method used to study the relationship. Each…

24 Apr 2008 Writing, Publishing and Presenting

What is your Life Changing Book?

Leading scientists in a variety of fields gave their recommendations on life changing books at New Scientist yesterday. This makes pretty interesting reading – and certainly throws up some ideas for adding to your bookshelf. Among the 17 recommended books were volumes as diverse as Animal Rights by Peter Singer, which turned Primatology expert Jane…

23 Apr 2008 Personal Development

Climb The Career Ladder Faster With These Cover Letter Tips

Cover letters are possibly the most important documents you will write in your career because they can open or close the door to your dream job. But, surprisingly, people often under-estimate their importance and assume that they are just the lesser companion to the CV/resume. Of course, that’s not the case. Your cover letter should…

16 Apr 2008 Career Development & Networking

Control Your Lab Computers From Home

If you have computers in the lab that you would like to access from home, this might be for you. LogMeIn.com offers a free remote desktop service that allows you to take control of a remote computer. Perfect if, while relaxing after dinner, you remember that you forgot to turn off the HPLC at work…

14 Apr 2008 Software and Online Tools

5 Products That Could Make Your Lab Life Easier

Today I was browsing through the “new technologies” section on the Biocompare website. Apart from the amazing but super-expensive automation equipment that most of us unfortunately have little chance of getting our hands on (at least at the moment), five products caught my eye as being useful for improving techniques widely used by researchers. I…

10 Apr 2008 DNA / RNA Manipulation and Analysis

5 More Tips for DNA Gel Extraction

Problems with DNA gel extraction can be a real show-stopper since this is such a routinely used procedure. But, even if you are having no particular problems, it’s always nice to try and pick up some information that might improve your technique just that little bit. Probably for these very reasons, Suzanne’s article 10 Tips…

08 Apr 2008 DNA / RNA Manipulation and Analysis

How To Become A World Expert In Your Field

Only a handful of people ever become world experts in their field. The rest attain somewhere between a functional and world expert level of knowledge. So what makes the best better than the rest? Are they born with greater knowledge? Intelligence? Inner strength? Well, the latter is the more likely. Although some world experts are…

31 Mar 2008 Personal Development

Lazy Cell Lysis

For routine procedures involving cell lysis, it’s good for the lysis to be… routine. Of course there are many good and freely available lysis buffer recipes but for convenience and reproducibility you can’t beat pre-made lysis buffers. Focusing on lysis for protein extraction, here are some of the reagents available for fast and efficient lysis…

27 Mar 2008 Protein Expression and Analysis

Church Scaremongering on Stem Cells

Injecting human DNA into a non-human egg is a “monstrous” undertaking, of “Frankenstein” proportions, according to the Catholic church. Next they’ll be telling us that The Earth is flat. These comments, delivered in an Easter sermon by a high-ranking Cardinal, are part of the Catholic church’s recent campaign against The Human Fertilisation and Embryology Bill,…

25 Mar 2008 Science Communication & Ethics

3 More DNA ligation Tips

A while back, I wrote an article on 5 DNA ligation tips that could improve the efficiency of your cloning procedures. It proved to be quite a popular article so here are another 3 tips that might make your ligations even better!

19 Mar 2008 DNA / RNA Manipulation and Analysis

Top 10: iGoogle Gadgets for Molecular and Cell Biologists

I finally signed up for Google Reader last week after reading Bala’s great post last week on Google Reader for Academics. Setting this up brought my attention to iGoogle, another very useful Google service. iGoogle allows the user to create a personalised start page. One of it’s main features is the ability to add all…

17 Mar 2008 Software and Online Tools

Easier DNA Sequence Manipulation

If you regularly use online DNA sequence manipulation programs, your life might be about to get just a little easier. At Bitesize Bio, we were becoming tired of jumping from site to site to get the sequence manipulation tools we needed. One site for reverse complementation, another for translation and yet another for restriction analysis……

10 Mar 2008 DNA / RNA Manipulation and Analysis

Ethidium Bromide: The Alternatives

How can you avoid the perils of exposing DNA to UV light during cloning procedure? Use an alternative DNA stain! Ethidium bromide is not your only option. In this article, we will compare the available DNA stains that can be used in electrophoresis to clarify the options available to you. Ethidium Bromide The classic DNA…

Ethidium Bromide alternatives
03 Mar 2008 DNA / RNA Manipulation and Analysis&Biotium

10 Unmissable Bio Flick and Pic Galleries

A picture tells a thousand words. So I suppose a movie tells 24,000+ words per second. Whether you use them for educating, self-study or just for your viewing pleasure, photos and movies of biological concepts and processes are a valuable resource. Here are ten of the best bio flick and pic galleries from around the…

28 Feb 2008 Fun Stuff

Turn Away from the (UV) Light

This is a story that could strike fear into your heart if you use UV light to visualize DNA that you later intend to clone. Read on if you dare. A while back I was doing a project where I had to make a mutation library of a plasmid. There are a number of ways…

26 Feb 2008 DNA / RNA Manipulation and Analysis

Sending Plasmids: How to Avoid Jail Time and Shredded Envelopes

Whether you need to get your plasmid DNA to a lab on the other side of the world, or a few hundred miles down the road, it’s important to make sure your precious sample gets there, it is not degraded, and you don’t end up in jail. Here’s the Bitesize guide on how to send…

20 Feb 2008 DNA / RNA Manipulation and Analysis

The Best Polymerases of 2008

Yawn…. The awards season is upon us once again. Overpaid, under-worked and over-ego’d celebrities get together to slap each other’s backs and tell each other how great they are. But little do they know where the real party in town is. The 2008 Thermostable Polymerase Awards (the THEPA’s) are underway and you have a front…

14 Feb 2008 PCR, qPCR and qRT-PCR

Could You Learn Better?

Are you a visual, aural, read-write or kinesthetic learner? If you don’t know, it could be a good idea to find out. Changing the way you learn, study and take notes to suit your learning tendencies can allow you to learn faster and make your newly-acquired knowledge stay with you for longer.

07 Feb 2008 PhD Survival

Defending A Giant

The problem with being the big kid in the playground is that there will always want to be someone who wants to bring you down. And in the playground of stem cells and cloning, few come bigger than Professor Sir Ian Wilmut. In recent years, Prof. Wilmut has been hounded through the courts and in…

05 Feb 2008 Science Communication & Ethics

Love in Mendel’s Garden

It’s February… the end of winter is in sight and with Valentine’s day approaching, romance is in the air in Mendel’s Garden. In case you don’t know it, Mendel’s Garden is a delicious box of brain candy – a phenylethylamine-packed, monthly collection of blog articles on gene expression, development and evolutionary genetics. This month we…

04 Feb 2008 Of Interest

A New Unnatural Base-Pair

You know about adenine, thymine, guanine, cytosine. Now get used to SICS and MMO2. In this JACS article published this month, researchers at the Scripps Institute reported the identification of these two artificial bases. They are efficiently incorporated during in vivo DNA synthesis by the Klenow fragment of E.coli DNA polymerase and pair together with…

31 Jan 2008 Of Interest

Quickly Boost Your Writing Skills

Reports, grant applications, theses, manuscripts, essays, patent applications, your Nobel Prize acceptance speech. As a scientist, there are so many things you have to write. And writing them well is important. Writing clearly and with structure allows you to get your message across and avoiding grammatical errors stops you looking stupid in front of your…

29 Jan 2008 Writing, Publishing and Presenting

Warning: Dihydrogen Monoxide is Worse Than Ethidium Bromide

Please read and pass this life-saving information on to your friends. A chemical that all of us use in the lab has turned out to be highly dangerous. It is an asphyxiant, can cause severe burns and is a contributor to the greenhouse effect. Medical organizations all over the world confirm it to be responsible…

28 Jan 2008 Lab Safety

Preps in the Zyppy: How I Changed my DNA Miniprep, Gel Extraction and Concentrator Kits

Breaking up is never easy, especially when you’ve been together a long time. But when you meet the right one it’s so much easier. Here’s how I ditched my old miniprep kit for something new.

21 Jan 2008 DNA / RNA Manipulation and Analysis

BioPop: 10 Songs That Should Be On Every Biologist’s iPod

The late Francis Crick once said that “Trying to determine the structure of a protein by UV spectroscopy was like trying to determine the structure of a piano by listening to the sound it made while being dropped down a flight of stairs.” But, if you thought that protein structure determination was the closest that…

18 Jan 2008 Fun Stuff

Ligation Independent Cloning Protocol

A while back I wrote a post on a T4 DNA polymerase dependent ligation independent cloning method. In the comments, Max asked if anyone had a protocol. Since there does not appear to be a simplified protocol available on the web, I thought I would post mine for reference. It is adapted from a 2006…

17 Jan 2008 DNA / RNA Manipulation and Analysis

Who Else Thinks Biology Teaching Methods are Wrong?

I shudder to think of the way I was taught about metabolic pathways as an undergrad. Lists of mysterious names connected by arrows – all to be memorized, with little reference to how the processes actually worked on a chemical basis. Even worse – and perhaps embarrassingly for me – I was almost at the…

16 Jan 2008 Science Communication & Ethics

Work Smarter With The Molecular Biologist’s Toolbar

To (hopefully) make the life of molecular biologists everywhere a little easier, I have put together a Molecular Biologist’s tool-bar for Firefox/IE, which you can download here. It’s main feature is the multi-search box from which you can search Google, Pubmed, Scirus, Wikipedia, SwissProt and others directly, saving you from navigating to the individual sites…

14 Jan 2008 DNA / RNA Manipulation and Analysis

PlasMa DNA: Free, cross-platform plasmid mapping and analysis software

If you are looking for some free plasmid manipulation and analysis software, then you need look no further than PlasMa DNA. It’s packed with features, user friendly and looks great. Best of all, it is a cross-platform application – it works on both PC and Mac, and the files produced on one operating system can…

10 Jan 2008 DNA / RNA Manipulation and Analysis

Free Mind Mapping Software

Mind mapping is an extremely useful technique for note-taking, brainstorming and learning. In the past I often tried to use mind-mapping but the neat-freak in me was never satisfied with the messy maps I would create. However, now there is an alternative to scribbling out mind maps on paper with the availability FreeMind, a great…

07 Jan 2008 Software and Online Tools

Happy Holidays…

The Bitesize Bio team will be taking a well-earned rest over the holidays and we would like to wish our readers a very merry Christmas. Myself, Dan, Suzanne and Terry have really enjoyed bringing you the best of molecular and cell biology tips, journal articles, news, comment and other stuff over the last four months…

20 Dec 2007 Fun Stuff

Get Inside A Molecular Biologist’s Imagination

I’ve always thought that it takes a good imagination to study molecular and cell biology since we never actually see much of the molecular processes we study, dissect and hypothesize on every day. Think about the mental models you have of the processes of cytoskeleton polymerization/ de-polymerization or DNA translation for example. Aren’t they amazing?…

18 Dec 2007 Fun Stuff

8 Approaches to Random Mutagenesis

Random mutagenesis is an incredibly powerful tool for altering the properties of enzymes. Imagine, for example, you were studying a G-protein coupled receptor (GPCR) and wanted to create a temperature-sensitive version of the receptor or one that was activated by a different ligand than the wild-type. How could you do this? Firstly, you would clone…

12 Dec 2007 DNA / RNA Manipulation and Analysis

At last – an easy backup solution

When I was writing up my PhD thesis I was paranoid about data backup. Years of hard work – pictures, data-files, notes, publication lists not to mention the thesis manuscript itself – all stored on one hard drive. Copying onto CDs or detachable hard drives was fine, but what if I lost those, or they…

10 Dec 2007 Software and Online Tools

Three Entertaining Molecular Biology Movies

It’s Friday again, so nothing too heavy from me today, just a little light entertainment to ease you into the weekend. Here are three (somewhat) entertaining molecular biology-related movies from you tube.

07 Dec 2007 Fun Stuff

An Easy Lysis / Homogenization Method for Any Sample

Lysis of some microbes is easy, but for others its much more difficult – I think due to differences in the make-up of their cell wall. At the moment, one of my colleagues is preparing hundreds of cell-free extracts from microbes isolated from the environment to screen for interesting enzyme activities. Since she is processing…

05 Dec 2007 Protein Expression and Analysis

Electroporation on a (96 well) Plate

I just came across a neat device now being offered by BioRad that may interest those of you who do a lot of electroporation of difficult-to-transfect mammalian cells, where tedious optimization of the electroporation protocol itself is required.

29 Nov 2007 DNA / RNA Manipulation and Analysis

Enzyme Commission (EC) Numbers

In the early 1950’s so many new enzymes were being discovered in the burgeoning field of biochemistry that enzyme nomenclature was in danger of getting out of hand. With no guidelines on how to name enzymes, researchers simply chose their own. Some enzymes were given names, like diaphorase or Zwischenferment, that conveyed nothing about the…

28 Nov 2007 Protein Expression and Analysis

10 Simple Rules For Doing Your Best Research

Last month, Thomas C. Erren and colleagues published an editorial in PLoS Computational Biology entitled 10 simple rules for doing your best research, according to Hamming. The article provides some great philosophical guidance on setting out to do great research, drawing on advice given by the mathematician Richard Hamming during a Bell Communications Research Colloquium…

27 Nov 2007 Personal Development

Get Involved With Bitesize Bio

We’d like to invite you, our wonderful, talented readers to get more involved with this blog. Here’s a few ways you can do so: Suggest a topic you’d like us to write an article on (click here to do this) Share your knowledge… write an article for the blog. Whether have one technical tip you…

22 Nov 2007 Career Development & Networking

The Best of: Tech Tips

Bitesize Bio has gained a lot of new readers over the past few months so I thought it would be a good idea to highlight some of the articles newer readers may have missed. I’ll do this periodically to make sure none of our readers miss any of our great content. So, here are the…

22 Nov 2007 DNA / RNA Manipulation and Analysis

Free, Publication Quality Plasmid Annotation

I just came across an extremely nice piece of plasmid mapping and annotation software that I’d like to share with you. PlasMapper is a web-based application, created by staff from the University of Alberta, that automatically generates fully annotated plasmid maps from your raw sequence input. Using a database containing the sequences of hundreds of…

21 Nov 2007 Software and Online Tools

Troubleshooting DNA Ligation Problems

In any experimental procedure, getting the controls right can save you a lot of work when things go wrong by allowing you to troubleshoot the source of the problem. DNA ligation is no different. In this article, we explain how to set up a ligation reaction with a complete set of controls, and use them…

20 Nov 2007 DNA / RNA Manipulation and Analysis&Opentrons

Gene Genie #20

Here at Bitesize Bio we are very proud to have the chance to host our first ever blog carnival. Gene Genie brings together blog articles from an array of perspectives within the area of human genes, genetics and diseases. It has been a pleasure and an education reading through all of these great articles and…

19 Nov 2007 Of Interest

Online Data and Project Management

During a research project, how do you record your data, conclusions and the samples you produce? What about ideas, insights and thought-trains? It would be very useful to have a good system to easily store all of these valuable products of your work and retrieve them when you need to look at your data or…

14 Nov 2007 Software and Online Tools

Rookie Researcher Disasters

Wide eyed and wet behind the ears, the rookie researcher steps into the lab for the first time. Armed with several years’ knowledge mined from text books, lectures and undergrad labs he feels ready to take his place amongst the worldwide legions of scientists who battle daily in the pursuit of knowledge. Little does he…

13 Nov 2007 Lab Safety

Error Bars in Biology

….statistics. The very word strikes fear into the heart of many a biologist (including me). In an article published earlier this year, Cumming and co-workers of La Trobe University, Melbourne gave a very useful rundown of common mistakes made when using statistical error bars in biology and suggested a number of rules that should be…

09 Nov 2007 Lab Statistics & Math

Re-Think PCR and Win an IPhone

Robert, a Bitesize Bio reader sent me an e-mail to tip me off about a fun little contest being run by BioRad at www.rethinkpcr.com. You are invited to say how you would “re-think” PCR. At first I thought this was a technical contest, seeking real suggestions on how PCR could be improved but actually you…

07 Nov 2007 Software and Online Tools

10 Reasons NOT to be a Scientist

Ok, this week has been a bad week in the lab so far. A few weeks ago I wrote a post describing 15 reasons to be a scientist. Today I am in the mood to cross over to the dark side and give you 10 reasons NOT to be a scientist! Strangely I could only…

06 Nov 2007 Inspiring and Thought Provoking

Firefox Add-ons for Molecular and Cell Biologists

Firefox is the most popular browser on the web. This in large part due to the vast array of free add-ons that allow you to customize the browser and add features that will help your everyday work. And molecular and cell biologists are not left out. In this article I have compiled a list of…

29 Oct 2007 Software and Online Tools

Time to Think

Spare a thought for your poor over-worked neurons. In the information age, they are bombarded with input from the moment they are dragged into consciousness by the radio alarm clock each morning then throughout the day by e-mail, Google searches, RSS feeds, mobile phones, newspapers, books, blogs and more. In the post genomic era, it’s…

26 Oct 2007 Personal Development

The Invention of PCR

Few technical breakthroughs have changed the face of their field like the Polymerase Chain Reaction (PCR). Gene cloning, sequencing of complex genomes, DNA fingerprinting and DNA-based diagnostics are just some of the techniques that were either inefficient, crude or plain impossible before PCR. The technique has revolutionized biological research and biotechnology to such an extent…

24 Oct 2007 PCR, qPCR and qRT-PCR

10 Links: Cell and Molecular Biology Podcasts

Podcasts are great. I listen to podcasts every day during my commute and find them a great way to pick up information, whether it’s to learn about a new subject, brush up on something I have studied before or keep up with the news. Here are 10 molecular and cell biology related podcasts that I…

22 Oct 2007 Software and Online Tools

How to: Keep your data organized

Talented, enthusiastic scientist required. Must have good organizational skills. Do you fit the bill? With the pace of molecular biology and biochemical research quickening year on year, the importance of good organization and planning skills for researchers is becoming increasingly important. Here are 5 ways to ensure that your data is organized and easily analyzed,…

16 Oct 2007 Organization and Productivity

Solved: Heterologous Gene Expression Problems

When heterologous gene expression goes wrong it can be a real headache. Here’s my checklist for the steps to take when you encounter problems with this dark art. 1. Check the construct by sequencing the expression cassette to make sure that everything is as you expect. A lack of expression could result from a stray…

09 Oct 2007 DNA / RNA Manipulation and Analysis

Plasmid archiving at Addgene

Addgene is a non-profit plasmid repository that stores and distributes plasmids for academic labs. It’s great if you work in an academic lab and they happen to have your plasmid – drop them an order and get your plasmid in the mail. I don’t work in an academic lab, but I still love addgene… here’s…

04 Oct 2007 DNA / RNA Manipulation and Analysis

An Attractive Genomic DNA Isolation Kit

I was becoming a bit bored with the tedium of column-based kits, so when I had to isolate genomic DNA from a range of micro-organisms for a recent project I decided to try something new. Invitrogen’s ChargeSwitch genomic DNA isolation kit, which uses magnetic beads to separate the gDNA from the cell debris, seemed interesting…

03 Oct 2007 DNA / RNA Manipulation and Analysis

You Know You’ve Been In the Lab Too Long When…

This has been doing the rounds all over the web, so I thought I’d post my 10 favorites. You know you’ve worked in the lab too long when… You wash your hands before you go to the toilet You tell your family to store the milk “at 4°C”

26 Sep 2007 Dealing with Fellow Scientists

Ethidium Bromide: A Reality Check

The hysteria among molecular biologists about our old friend ethidium bromide has long been an irritation to me. Researchers are rightly wary of this potential carcinogen. More recently this wariness has been whipped up into a witch hunt by companies touting “safer” alternatives and disposal methods. While I don’t for a minute think that we…

26 Sep 2007 Lab Safety

Choosing a Competent E.coli Strain

Of all the of competent E. coli cell strains available, which one should you choose? The choice of strain to use in a given experiment is determined in large part by the nature of the experiment and the set of traits that best fit it. In this article I summarize some of the most important…

24 Sep 2007 DNA / RNA Manipulation and Analysis

The World’s Fastest Miniprep?

I love this great time-lapse video entitled “a day in the lab”. If only minipreps were this fast and easy!

20 Sep 2007 DNA / RNA Manipulation and Analysis

Competent E.coli: To buy or not to buy?

Buying competent cells from commercial suppliers is convenient, provides a guarantee of quality and gives access to strains with a variety of in-built traits that assist with things like maintenance of plasmid integrity (more on these traits later). However, this can be an expensive business.

20 Sep 2007 DNA / RNA Manipulation and Analysis

15 Reasons to Be a Scientist

Just for fun, here my top 15 reasons for being a scientist. Add your own reasons in the comments below if you so wish. 1. Not being stuck behind a desk all day every day 2. Conferences… see the world for free 3. Understanding some of the fundamentals of life and the universe 4. Getting…

18 Sep 2007 Fun Stuff

One Tube PCR Cloning Method

I love shortcuts, and this one is very good. Chun-Ming Liu of Plant Research International has a number of molecular biology protocols on his website,  but my favourite is his One Tube PCR Cloning Method. The protocol involves simply putting the vector, insert, restriction enzyme, ligase (and in his case polymerase for polishing the ends)…

14 Sep 2007 DNA / RNA Manipulation and Analysis

10 Tips for Better Presentations

I have been at a conference today and don’t have too much time to write this, so this will be a quick article. After watching lots of speakers of varying competence, I thought that it would be good to outline some tips for great presentations. Speaking is an integral part of a scientist’s job, and…

12 Sep 2007 Writing, Publishing and Presenting

The Dark Side of Gene Synthesis

After writing my recent article on custom gene synthesis, I came across an article in the excellent Seven Stones systems biology blog that highlights the potential dark side of this emerging technology. The article describes a recent Nature Biotechnology commentary by B??gl et al 2007 in which executives from the DNA synthesis industry discuss regulation…

10 Sep 2007 DNA / RNA Manipulation and Analysis

10 links: Free PC Software for Molecular Biologists

Here is a list of 10 pieces of great molecular biology software for PC users that I hope you will find useful. I am not a regular PC user myself so I have not tested all of these out so if any of these are no good, or if you have any favorites you’d like…

10 Sep 2007 Software and Online Tools

10 links: Free Mac Software for Molecular Biologists

I’ve put together this list of 10 pieces of free molecular biology software for Macs. I hope you will find at least some of it useful. If any of your favorite free programs are not included, please e-mail me and I’ll add them or you can leave a comment with a link. If you are…

10 Sep 2007 Software and Online Tools

Easier Gene Cloning With Positive Selection Cloning Vectors

Isn’t it a pain digesting, purifying and dephosphorylating your cloning vector prep to eliminate prevent high background in your ligation/transformation? A new generation of positive selection cloning vectors promises to eliminate all of that hassle by killing off any vector that has not taken up the insert you are trying to clone. Positive selection cloning…

06 Sep 2007 DNA / RNA Manipulation and Analysis

Custom Gene Synthesis: A PCR alternative.

Artificial gene synthesis was first reported in 1972 when a group of researchers at Massachusetts Institute of Technology synthesized a complete yeast alanine tRNA gene. Synthesis of the first peptide- and protein-encoding genes ensued in the following decade. Since then, synthetic biology has advanced in leaps and bounds, and custom gene synthesis, a one-time expensive option for…

05 Sep 2007 DNA / RNA Manipulation and Analysis

Better Pubmed Journal Searches

Ever get too many hits from your Pubmed searches? Using field tags allows you to generate more specific searches than keywords alone, saving you from trawling through hundreds of irrelevant articles.

31 Aug 2007 Taming the Literature

DNA replication, transcription and translation in action

While browsing you tube I came across this really nice animation of DNA replication, transcription and translation complete with imaginative sound effects. I hope you enjoy it as much as I did.

29 Aug 2007 DNA / RNA Manipulation and Analysis

Low cost DNA gel documentation

Equipment for photographing DNA gels stained with ethidium bromide (or other fluorescent dyes), doesn’t have to cost thousands of dollars. These days, great pictures can be obtained with a standard digital camera and an orange filter. Here’s how.

29 Aug 2007 DNA / RNA Manipulation and Analysis

My favorite PCR polymerase

What do you get when you cross a Pyrococcus DNA polymerase with a dsDNA binding domain? …a highly processive, high fidelity, lighting fast PCR work-horseThose Finnish wizards at Finnzymes have made that work-horse a reality with their Phusion polymerase. I had been meaning to try out this enzyme for quite a while, but never got…

28 Aug 2007 PCR, qPCR and qRT-PCR

Plasmid Cut & Paste with Quikchange

I recently had a problem where I needed to cut out an expression cassette (a promoter coupled to a coding sequence) from one plasmid vector and paste it into another containing an expression cassette so I could get tandem expression of the two genes. The recipient vector had no suitable restriction sites for performing this…

28 Aug 2007 DNA / RNA Manipulation and Analysis

Zyppy Plasmid Miniprep Kit

Zymo research have launched a new plasmid miniprep kit that not only is has the coolest name of any kit on the market but is, the manufacturers claim, the fastest means of plasmid purification available.

24 Aug 2007 DNA / RNA Manipulation and Analysis
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