As a follow-up to our recent Documenting Specimen Storage post, here are some key specimen storage tips:

Do:

1.  Keep cross-contamination in mind when storing your specimen samples.  If you work in a lab where researchers are going to be working with acombination of bacteria, yeast, cell cultures and viruses, make sure to store each so that cross-contamination is not a possibility in incubators, freezers, and tissue culture hoods.  Use a labeling system to dedicate specific lab areas.
2.  Use an electronic management system for tracking and managing specimen to streamline collections throughout your lab.  Use a centralized web-based system, such as Labguru’s cloud management system, to create a uniform database for all researchers to upload, track, change and label samples.
3.  Consider digitizing your organization and labeling of samples with barcoded or numerically based identification system.  Did you know that patient-related sample mislabeling (in both academic and hospital settings) cost an average of $712 per mistake?  Research labs dependent on large libraries and expensive cell lines for screenings stand to lose even more.  Digital labeling systems based on computers and automated tracking will largely reduce human-related laboratory errors.
4.  Consider professional storage, tracking and management for your sample collections, especially if they are large libraries that are expensive to procure and/or copy. Specialized companies will assign dedicated management teams to track new samples and manage current collections, even handling monitoring of freezers and chain-of-custody storage.  If your samples are of high importance, are rare, or expensive, it’s worth a try to leave them in professional hands.
5.  Establish strict, laboratory-wide guidelines for specimen collection and sample storage practices.  There are numerous templates from other labs posted online as a resource guide.  Enforce uniform training in the lab, and have managers and group leaders periodically ensure guidelines are followed.

Don’t:

1.  Use rudimentary means, such as an Excel spreadsheet, to track specimen storage across the lab.  This is probably the biggest mistake labs make with regard to their inventories, and is a recipe for mislabeling, experiment error and other preventable disasters.  Everyone in the lab will have their own system for tracking samples, their own nomenclature, and even their own style of recordkeeping, none of which might make sense to lab mates.  Instead, opt for a group-wide online management system (see Do #2.)
2.  Store specimens in the wrong type of box or tube.  Mind when samples will need to be stored in specialty automation tubes for screening or aliquoting by robotics equipment.  Similarly, depending on the necessity of long-term storage at -20, -80 °C or liquid nitrogen, choose tubes and boxes that can withstand temperatures with minimal effect on sample quality.
3.  Work with, collect, ship or store specimens without a group standard operating procedure in place, ensuring that proper training and enforcement of procedures are followed.  SOPs mean that uniform procedures are followed by all group members, which will minimize troubleshooting if experiments don’t work or collaborators have questions.
4.  Ignore biosafety guidelines for samples designated Biosafety Level 3 and higher.  These will require their own SOPs, training and possibly personal protective equipment,  even if group members are working remotely as guests in another lab.  For work exclusively within your own lab, consider hiring a biosafety and biocontainment expert to help streamline training and implementation within federal regulations and guidelines.
5.  Forget to select the right label for sample storage – consider where the sample will be stored, what the conditions are that it will be exposed to in both storage and experimentation (barcode scanning, for example), and what materials the label is made of so that it can withstand all of these without falling off or losing legibility.

Do you have any other specimen storage tips? We’d love to hear from you – leave a comment below! 

If there is something that students quarrel passionately about it is over shared resources. Now, “resource” is a BIG term covering everything from tips for your pipettes to your PI’s time. Today I will talk about shared equipment and how to try and manage the lab in such a way that your machines will serve you efficiently.

The problem and its solution
So the problem is quite obvious – in almost all cases there are more users than copies of the same device which means that some sort of queuing or scheduling is required.

In many cases, each piece of shared equipment or device has a person who is responsible for its maintenance and user guidance. However, in many cases the device resides outside of their lab, and he/she has a hard time monitoring users and correct usage of the device. Thus it is common that shared devices have a calendar listing users’ schedule for work on the device. This is a practical and low cost solution that serves well though it has its own weaknesses, mainly in regard to user monitoring.

For one thing, people tend to be lazy to register for the device, even if it is just fifty feet away from their lab. This of course leads to the device being taken by another user or worse, being used without any knowledge as to who used the device previously (in case of a technical problem, misuse or sullying). Moreover, when it comes to periodic maintenance it can be practically impossible to assess the working hours the machine has been through if there is no counter. Another important issue is user registration: when the device has a paper calendar anyone can reserve a time and start using the device, even if he/she has never received any formal guidance.

Of course, all the above can change once the device calendar is moved to a web-based calendar, such as Google calendar. Why is using a web-based calendar such an improvement over classic paper calendars?

• First of all, if a new user would like to reserve a time on the device, they have to approach the person in charge to register him for the specific calendar. At that point the person in charge will make sure the new user knows how to correctly operate the device.
• Second, the person in charge can easily monitor who’s using the device at any time point, and if there is a failure, they can easily contact the user through the user’s email and without the need to decipher cryptic fonts and phonetic writing styles.
• Third, the person in charge can calculate how much time the device has been used since the last maintenance checkup and thus easily maintain the equipment according to the manufacturer’s recommendations.
• Fourth, all users can view the schedule and plan their experimentation without the need to leave their chair or lab room. Cancellation of a reservation is as easy as registration, thus making the most of the device’s allocated time.

This strategy has one major drawback and that it is digital and the data or part of it can be accidentally deleted by a careless user. This problem can be circumvented by locally saving the calendar each month and thus generating a backup.

Have you shed tears over shared equipment? Care to share with us tips on how to handle shared equipment? We’d love to hear from you!

The sequencing of the Saccharomyces Cerviciae (yeast) genome in the mid-1990s revolutionized genetics, allowing researchers to use deletion mutants to study regulation of eukaryotic cells.  The primary techniques up until now have included yeast two-hybrid arrays for studying protein-protein interactions and tetrad dissection for mutation analysis.

The advent of high-throughput genomics to analyze cytotoxicity, programmed cell death, drug target screens, and other disease pathways has revolutionized traditional yeast experimentation methods.  Specimen are now arrayed in libraries, ranging from mid-size collections targeting certain proteins or gene families, to large whole-genome arrays such as the synthetic genetic array to study thousands of genes simultaneously.  Gene knockouts of up to 6,000 genetic mutants can be purchased for study.

Because of their expanded availability and whole-scale approach at a relatively inexpensive cost, genetic yeast libraries and knockouts have become vessels of drug discovery and cell biology across disciplines and areas of study.  Microarray genetic screens have been used to study everything from aging factors, a “Green Screen” cytotoxicity array for various toxic compounds, the regulation of various oncogenes, and even the genetic yeast factors in the development of sauvignon blanc wines!

Because yeast libraries have expanded from small batches for protein experimentation and genetic knockouts to arrays of thousands of genes, it has incurred several challenges to library management.  The biggest of these is classification, nomenclature and cataloging. Most yeast cDNA expression libraries run in the several thousand dollar range from major specimen providers.  Additionally, facilities such as the Y2H screening facility at Indiana University that have set up large-scale Y2H analysis for labs not adept at yeast manipulation and biology still return all samples and do not provide long-term storage.  As such, labs must apportion proper space for storing yeast libraries, and protocols for avoiding cross-contamination issues, especially if the lab is also conducting experiments with cell and bacterial cultures and if multiple researchers within the group will be handling the same library.  Along these lines, using a proper specimen collection tool will facilitate knowing where in the lab the libraries are stored (if they dictate special individual storage), proper labeling of individual wells (which can number in the thousands) or any subcollections thereof, and catalogues of gene names for quick analysis and cross-reference of screening experiments.

The pros of working with yeast—short propagation time, ease of maintaining cultures, relative ease of transformation, and simplified DNA genetics for higher eukaryote research—allow labs whose focus doesn’t necessarily lie in traditional genetics or molecular biology to address disease or cellular mechanisms.  My own undergraduate advisor, whose training and specialty is in bioorganic chemistry, is using yeast as a host for investigating lead and other heavy metal poisoning pathways.  The downside to this expanding multi-disciplinary popularity for yeast is that labs must develop relevant protocols, sample storage, train students and staff on handling. All of this requires an enormous amount of organization and planning.  Utilizing resources, such as yeast protocol collectives from established professors, the wiki-based Saccharomyces gene database and forming collaborations is another excellent way to broaden your group’s expertise in experimenting with yeast, while still addressing the primary global aims of the research.

The bottom line for any researcher is cost and efficiency.  Across multiple disciplines, some of the biggest concerns involving yeast research are the cost for custom-made or pre-made libraries, screening robotics and facility use, and reagents for screens and protein experiments.  Taking advantage of collaborations, along with some of BioData’s recent tips on laboratory communication, academic mentorship and research management will go a long way towards helping your lab integrate sophisticated yeast screening technology and experiments.