Recent Articles

qPCR: RNA quality and why it matters

Gene expression analysis plays a pivotal role in a wide range of studies, including biomedical analysis and diagnostics. Of all the methods available for gene expression analysis, quantitative real-time PCR (qRT-PCR) is the most rapid, […]

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20 Ways to Increase your Productivity

Saying goodbye to 454: how to choose your next NGS platform

PIER, HIER and Mannich: Antigen Retrieval in Immunohistochemistry

Overview of Protein Turnover using 35S: how to prevent trashy data and uh-oh moments

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NGS: The final frontier

Obtain NGS-Grade™ Quality: Extract, Purify, & Fragment Nucleic Acids from FFPE Tissue with the Covaris Process

HAMID KHOJA
Principle Scientist at Covaris

Sponsored by:
 
 
NGS: The Final Frontier

The Fundamentals of Sample Preparation for Next Generation Sequencing

NANDITA MULLAPUDI, PHD

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Protein Analysis, Detection & Assay

Overview of Protein Turnover using 35S: how to prevent trashy data and uh-oh moments

The half-life of a protein is an important factor in many molecular biology studies. If your thesis has anything to do with proteins then your graduate advisory committee will ask about half-life, so start […]

Think You Need Cells to Make Your Protein? Think Again! Use In Vitro Translation.

Do you need purified recombinant protein? But you don’t have the time or facilities for cell culture and purification? Try using in vitro translation (IVT) instead! IVT is like your own miniature protein factory. […]

The Nature of Denaturing (Protein Gels, that is!)

You've nurtured your cells for weeks, perfected your experimental conditions, and nailed down all the controls. You've harvested your cells and gently lysed them, now you're ready to look at the proteins. What's one […]

The Five X-Factors in Bacterial Protein Production and Purification

Every protein is unique and thus every protein has its own set of production and purification challenges – many of which cannot be predicted. Therefore to successfully produce and purify your favorite protein you […]

Insane in the Membrane! PVDF vs. Nitrocellulose – Which One Comes Out on Top?

When it comes to Western blotting, there’s no denying it: Your membrane is a key player. After all it is the physical scaffold that holds your precious samples and it needs to be up […]

Microscopy & Imaging

PIER, HIER and Mannich: Antigen Retrieval in Immunohistochemistry

When you fix your tissue samples with paraformaldehyde (PFA) the proteins in your sample become covalently cross-linked. This is good to preserve the ‘architecture’ of your tissue sample. However, this cross-linking can become a […]

Microscope maintenance: changing and aligning your mercury burner

Mercury burners are one of the most common light sources used in fluorescence microscopes, producing a wide spectrum of wavelengths making them a great light source for viewing your samples. But they do have […]

Imaging at ‘LightSpeed:’ Novel EMCCD Camera Mode Brings Speed and Flexibility to Super-Resolution Imaging

Imagine trying to photograph a cheetah running at full-speed without moving your camera. It sounds tedious, but it’s the kind of handicap many researchers face when imaging high-speed molecular events in super resolution, such […]

What is Electron Microscopy and Its Applications?

You likely know your way around a light or confocal microscope, but what if you need to see outside the optical range of these microscopes? Enter: Electron microscopy. Electron microscopes or EMs can increase […]

A Beginners Guide to The Point Spread Function

Suppose that you have a tiny fluorescent object, such as a 10nm-diameter fluorescent bead or even a single fluorescent molecule, and you try to observe it under a fluorescence microscope.  Provided that the object […]

Nucleic Acid Purification and Analysis

Plasmid v Genomic DNA Extraction: The Difference

If you want to isolate plasmid DNA, you crack your cells open and carry out a miniprep, trying very hard not to get any contaminating genomic DNA in your sample. If you want genomic […]

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 […]

Better Plasmid Midipreps Part II: What Causes Low Yields?

Recently we received a question from Bitesize Bio reader Sonia after our article How to: Get Better Plasmid Midiprep Yields. She asked: "What could be the problem when one sample gives a good yield while […]

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. […]

When Glycogen is not Your Friend – Isolating RNA from Glycogen-Rich Tissues

Bitesize Bio has had a lot to say about RNA isolation, mainly because it is one of the most anxiety-producing requirements for molecular biology; especially when you are first starting out (although isolating proteins […]

Next Generation Sequencing

Saying goodbye to 454: how to choose your next NGS platform

The Rise and Fall of the 454 Sequencer  The GS20 454 sequencer, released in 2005, was the first next-generation DNA sequencer to hit the market, and its feats quickly dazzled the scientific community. As […]

The Real Cost of Sequencing in 2014

We are now living in the era of the $1000 genome. Unfortunately, most of us are still paying significantly more than this for a genome, or an equivalent amount of data in the form […]

A Beginner’s Guide to Next Generation Sequencing (NGS) Technology

The first whole DNA genome to be sequenced was the virus phage ΦX174, in 1977, by Fred Sanger. In that same year, Sanger developed the future backbone of the “genome era”: DNA sequencing technology. […]

Beware The Bane of Batch Effects

A promising study on using gene expression to develop personalized treatments for ovarian cancer. A report of surprisingly high levels of differential gene expression among different ethnic groups. The announcement of previously unsuspected levels […]

Sequencing the microbiome: re-discovering our invisible allies

Scientific breakthroughs have profound effects on how we view and treat the world that surrounds us. Especially in the microscopic level, scientific discoveries provide the only understanding we have of Nature. One such case […]

PCR & Real-time PCR

qPCR: RNA quality and why it matters

Gene expression analysis plays a pivotal role in a wide range of studies, including biomedical analysis and diagnostics. Of all the methods available for gene expression analysis, quantitative real-time PCR (qRT-PCR) is the most rapid, […]

Overhang PCR

Have you ever “accidently” forgotten to add the Kozack consensus sequence to the start of a coding genes? Or forgotten to include the stop codon? Did you clone something, then realize you wanted to […]

An Essential Toolbox for qPCR Users

Today, PCR is as common a feature to the lab as pipettes and beakers. The majority of us regularly need to amplify our DNA or RNA samples, sometimes for an ‘everyday’ PCR run just […]

Top Ten websites to help you with your PCR experiments

Whether you are embarking on a PhD in molecular biology, trying to amplify a new gene, analyzing gene expression by qPCR, or trying to solve a PCR problem, you will probably resort to a […]

Taking the Pain, Challenge and Rage out of PCR: The BitesizeBio Guide to PCR

Polymerase Chain Reaction, better known simply as PCR, has come a long way in the past 30 years. For those of you old enough to remember the not so ‘good old days’ when PCR […]

Flow Cytometry

All sorted? Getting the best out of your cell sorting facility

If you are bringing cells to a core to be sorted there are a few things you can do to optimise your sorting and will help the core staff. Here are a few hints: 1) Know […]

Immunophenotyping: Identifying Who’s Who in the Cellular World

Figuring out what’s what When studying cells and cell subsets (and cell sub-subsets, and so on!!) we need ways to identify and classify every single cell. This will allow us to individually analyse each population […]

Fixation and flow cytometry

Fixation is routinely used in histology and cytology Labs the world over as a way of keeping cells in stasis at a particular point to ensure that, by the time they are examined, they […]

Using Flow Cytometry for Fluorescence Resonance Energy Transfer

A marriage of sorts Fluorescence resonance energy transfer, or FRET, is often done using a microscope, which means it can be difficult to analyze large numbers of cells in one sitting. One way to […]

Where Are My Cells: Part 2

The golden rule of flow cytometry, especially cell sorting is: ‘Put good cells in and get good cells out’. When you sort you might not get good cells out and you may not get […]

Cell / Tissue Culture

Cell Counting with a Hemocytometer: Easy as 1, 2, 3

Many biological applications such as microbiology, cell culture, blood work and many others that use cells require that we determine cell concentration for our experiment. Cell counting is rather straightforward and requires a counting […]

Which Cytokine Will I Get? How to Stimulate Human Cytokine-Producing Cells

Cells are like people: depending on their current environment, past experiences and their genetic make-up they will react differently. Treat cells in different ways, and they will produce different cytokines. There are a lot […]

Tips for a Happily Functioning Tissue Culture Room

You walk into your tissue culture room to find a window open, the incubator’s humidity tray empty and a pipette lying on its side in the hood on a used glove… After you have […]

Getting in Deep: How to Deep Clean a Tissue Culture Hood

One of the most exciting aspects of being a biologist is getting opportunities to examine how and why living organisms behave the way they do. We have technology that enables us to obtain images […]

Seven Things That Really Annoy Me About Tissue Culture

The tissue culture facility can be one of the most important places in the lab.  Many researchers spend hours in the hoods isolating primary cell lines and tissue, generating samples for western blot analysis, […]

Cloning & Expression

The Basics: How Does DNA Ligation Work?

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 […]

Say Goodbye to Restriction Enzymes and Ligases: An Introduction to Sequence and Ligase Independent Cloning (SLIC)

SLIC, or sequence and ligase independent cloning, was developed by Li in 2007 and published in Nature Methods. What makes it a Nature Methods worthy protocol? Unlike other forms of cloning, SLIC does not require restriction enzymes or a ligase! Seriously! Don’t believe […]

Dressing Up Your Oligonucleotide

Oligonucleotides are those smallish bits of DNA or RNA that we rely so heavily on for many of our molecular biology experiments. In their naked form, they are single, inert strands of DNA or […]

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 […]

How to identify supercoils, nicks and circles in plasmid preps

One of my favorite things to do with a student the first time they work with plasmid DNA is to have them run an agarose gel containing 2 samples:  uncut plasmid DNA, and plasmid […]

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