A Better Way to Be Sure: How a compound management tool can help with tissue extractions

Mar 09, 2015

compound-management-postA Problem with Extractions

Imagine the following scenario:

You’ve engineered in reduced expression of YPI (your protein of interest), identified 200 potential individuals that may have the appropriately low YPI levels, and now you need to extract protein from those 200 samples to verify. How much extraction buffer do you add to each sample?

As high-throughput technologies become more widespread in biology labs this type of scenario has become increasingly frequent, especially if you substitute DNA, RNA, or other compounds for protein. For efficient extraction from tissue, most protocols provide guidelines on how much extraction buffer to add per weight of sample. While there’s often some room for error, reproducibility and extraction efficiency are improved when the ratio of extraction buffer to tissue is optimized, which in turn increases the reproducibility and data integrity of downstream assays. When you’re only working with a few tissue samples at a time, weighing each sample is easy to do. But when you’re trying to process a hundred or more samples, weighing each one is impractical. In these situations many researchers simply approximate sample weight, which can lead to variability in extraction efficiency.

But what if you could measure the volume of every sample in a 96-well plate in thirty seconds, and know exactly how much buffer to add?

A Brief Side Trip to Compound Management

Just like with tissue extraction, it turns out that knowing how much sample volume is in a well can be a critical parameter for pharma teams. When running screens with small molecule compounds, the compound libraries are typically stored in multiwell plates with compounds suspended in DMSO. Each time a new assay is run, aliquots of compound are removed from the stock plate, although not all samples are used with every assay. Over time, small inconsistencies in the volume removed can add up to slightly less (or more) compound left in the stock plate, with a worst-case scenario being an unexpectedly empty well. In addition, the DMSO can absorb water, potentially damaging the dissolved compound. If a sample well has a larger volume than expected, this could indicate a compromised compound, and then all bets are off on what the assay results mean.

Our team originally developed the Artel VMS™ to help a big pharma team know—not just calculate based on expected volume removals—how much compound they had left in each well of their stock plates. We soon realized that this ability to measure actual volume in each well had applications beyond compound management.

Back to the Solution for the Extraction Problem

As discussed above, when you have a 96- or 384-well plate with tissue samples—or seeds, tail snips, other solids, liquids, or homogenates—knowing how much they weigh can help optimize extraction conditions, increasing reproducibility and extraction efficiency.

Now, thanks to the problems facing that big pharma compound management team, researchers needing to process tissues in multiwell plates can quickly and directly measure the volume of their samples in each well of their plate (it’s not the weight but it’s a good metric to describe how much sample you have). The VMS can measure sample volumes in each well of a 96-well plate in thirty-five seconds or just under two minutes for a 384-well plate. Take a look at this recent poster from the SLAS2015 Conference to see how well this process works for measuring seed volumes in a 96-well plate. And then think about how much more reproducible your studies might be when you can know sample volume instead of approximating.

Additional Resource

About the Author

bill-giganteBill Gigante

Bill Gigante, Mechanical Engineer at STRATEC Biomedical, has over 10 years of experience supporting small molecule compound management. As a Research Engineer at Amgen, Bill designed and supported automation related to compound management. In his role at STRATEC Biomedical he is contributing to the design of medical devices as well as championing a device for volume detection.