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Shoba Anantha

Shoba is currently Director Of Business Development at IBM in Wisconsin. She has a PhD in Biology from the University of North Carolina at Charlotte.

Institution : IBM
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Articles by Shoba Anantha

Touchdown PCR: A Primer and Some Tips

Touchdown PCR: A Primer and Some Tips

By Shoba | July 9, 2016

When I first heard of touchdown PCR, I thought of a landing aircraft, which, as it turns out is not a bad way to think about it. But despite it’s amenability to analogies and dreadful puns (see title), touch-down PCR (TD-PCR), a very useful technique for improving PCR amplification specificity, is trickier that it might…

An image of test tubes to depicts how to clean a water bath.

10 Tips for Pipetting Perfection

By Shoba | November 28, 2011

Several years ago as a freshman in a research lab, the very first project I received was to pipette incremental micro-volumes of H2O onto a piece of parafilm. Boring! Weighing the liquid on parafilm and comparing the weight between 10 replicates for each micro-volume continued for a week before I touched anything else in that…

Touchdown PCR: A Primer and Some Tips

Eliminate PCR Amplicon (but not real-time PCR?) Carry-Over With UNG

By Shoba | October 8, 2010

Using UNG is a great trick for PCR amplicon decontamination, but is it any good for rtPCR?

Touchdown PCR: A Primer and Some Tips

PCR: The Right Way to Decontaminate and Eliminate False Positives

By Shoba | April 9, 2010

PCR is highly sensitive, but the downside of that very property is that it makes the technique prone to producing false-positives. In labs where PCR is a staple, like the one I work in, any false-positives are more often than not due to amplicon contamination. A broken capillary or a PCR plate left carelessly at…

An image of spinning plates to depict how to build a plate centrifuge.

How to Build a Plate Centrifuge for $25

By Shoba | March 12, 2010

Find out how to build a plate centrifuge using a salad spinner. Gathering the components is as complicated as it gets!

Touchdown PCR: A Primer and Some Tips

qPCR: Plexor vs Hydrolysis Probes

By Shoba | September 4, 2009

Hydrolysis probes, commonly also referred to as TaqmanTM is a very popular chemistry for real-time PCR. In this article I will compare hydrolysis probes with PlexorTM. But first, a quick overview of hydrolysis probes. Hydrolysis probes, an overview Hydrolysis probes are a popular detection chemistry for monitoring sequence-specific amplification in RTPCR. Just like with  SYBR…

Touchdown PCR: A Primer and Some Tips

qPCR: Plexor and SYBR compared

By Shoba | August 24, 2009

In my last article I introduced you to the Plexor System. And from that we already know that while in reactions that user SYBR Green for detection, fluorescence increases with accumulation of PCR product, with Plexor the fluoresence decreases. Today I want to compare some other well-known features of SYBR Green chemistry and see how…

Touchdown PCR: A Primer and Some Tips

Get the qPCR Fluorescence Low Down with Plexor

By Shoba | August 20, 2009

In real-time PCR, there are two primary ways to detect amplicons using fluorescent monitoring. One is intercalator-based dyes such as SYBR Green, and the other is probe-based techniques (hydrolysis or hybridization probes). All of these methods share a similar mechanism of measuring increasing fluorescence during amplification. But there is another completely different way to quantitatively…

Touchdown PCR: A Primer and Some Tips

Controls and Tips for TA cloning

By Shoba | June 23, 2009

Controls are obviously extremely important when setting up experiments. Without them, meaningful interpretation of the experimental results can be impossible. I say obviously, but in my previous job as a technical services scientist, you’d be surprised at how often I found myself talking to customers about the importance of controls. One customer commented, during our…

Touchdown PCR: A Primer and Some Tips

Solved: Low Yields in Cell-Free Protein Synthesis

By Shoba | April 21, 2009

In my last article, I introduced Cell-Free Protein Synthesis. Today I want to talk about a major bottleneck in in vitro cell-free protein expression; low yield. Most often, paying attention to the important factors such as template purity and design, transcription and translation inhibitors, and potassium and magnesium concentration will solve any problems with low…

Touchdown PCR: A Primer and Some Tips

An Intro to Cell-free Protein synthesis

By Shoba | March 2, 2009

Cell-free protein synthesis (aka In vitro translation) refers to protein production in vitro using lysates generated that provide the cellular machinery necessary for synthesis. The lysates can be of bacterial or eukaryotic origin. It is a useful alternative to in vivo synthesis for generating protein for the study of things like: protein:protein interactions (pull-down assays,…

Touchdown PCR: A Primer and Some Tips

Quantitative RT-PCR: One-step or Two-step RT?

By Shoba | February 16, 2009

qRT-PCR (quantitative reverse transcription-polymerase chain reaction) is now the gold standard technique for mRNA detection and quantification, sensitive enough to enable quantification of RNA from a single cell. The reverse transcription (RT) step is the main source of variability in a qRT-PCR experiment, so an optimal reverse transcription is essential for a reliable and successful…

Touchdown PCR: A Primer and Some Tips

Tips for Eukaryotic Cell Transfection

By Shoba | January 29, 2009

Transfection of eukaryotic cells is a routine but sometimes tricky procedure. There are several transfection reagents available on the market, but sometimes the old methods are the best. I find that the simplest, fastest and cheapest transfection method for eukaryotic cells is calcium phosphate mediated transfection (1). It’s main advantage is that, since Ca2+ is…

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