Zully Santiago receives honorary award for her work in The Writing Center

ZullyThis past summer our student (and the 2014 PRISM Symposium Best Poster Presentation winner) Zully Santiago received an Honorary Award presented by both the Department of Sciences and the Department of English for her contributions at the John Jay Writing Center. Professor Artem Domashevskiy, Zully’s research advisor, told us that “for many years now Zully has worked at the Writing Center, specializing in teaching John Jay’s Biochemistry students how to read and write scientific manuscripts in both The Journal of Biological Chemistry and Biochemistry Journal style formats, because I require lab reports in my Biochemistry classes to be submitted in those formats.”

Zully graduated in the spring, and will be attending CUNY Graduate Center to begin her Ph.D. studies this fall. Prof. Domashevskiy notes that “Zully is a very gifted, intelligent, creative, and hardworking young woman. I believe she will have a bright future as a researcher and academician and will become an exceptional professional in her field.”

10 Common Mistakes Made by Newbie Researchers – Part 3

By Zully Santiago, PRISM Undergraduate Researcher, Spring 2013 through Summer 2014SantiagoZully

Part 3 – Be a Responsible Labmate

8)     Mistake: You break something or spill something.

Solution: If you break glass, no big deal. Simply throw the glass out in the glass waste in a safe manner. Try to find all the pieces and so on. However, if there was a corrosive substance (or dangerous substance in anyway) in a container and it is now on the floor, do not touch it. Go ask for help. You can contact your mentor, any professors that may be around on the floor, or call security. Hopefully after your biohazard training, you’ll be able to handle simple spills and have information in order to contact someone for more dangerous spills. Again, know what you are working with and its hazards.

9)     Mistake: You need to go to class, so you rush cleaning, or you don’t clean at all because you’ll come back later.

Solution: If this happens, try to leave your mess in the most convenient way possible so that your lab mates can do their work, and leave a note. If your mess is potentially dangerous, call your mentor or a lab partner to help you take care of it. Nevertheless, make sure you clean up after yourself since the lab is shared. Don’t leave anything for someone else to clean. It isn’t fair or right to do so. Remember, not only are you the researcher, you are also your own lab technician, so no one is responsible for your mess other than yourself.  If you planned properly, you should have more than enough time to clean up after yourself. If someone leaves a mess, try to find out what everything is and clean it up for your own safety, and let your mentor know about it so that it doesn’t happen again.

10)     Mistake: At the end of the experiment, you place everything in a single waste container or attempt to throw the waste down the sink. You know better than this.

Solution: Again, if you understand how your chemicals work in your experiment, you will know how to dispose of them properly. Many chemicals cannot be put down the sink and many other chemicals will continue to react when mixed together, so think carefully. If you have multiple steps in a reaction, think about the intermediates, the chemicals used in each step, and find out if it is safe to put them all together. When in doubt, ask someone or play it safe and make separate waste containers if needed.

10 Common Mistakes Made by Newbie Researchers – Part 2

By Zully Santiago, PRISM Undergraduate Researcher, Spring 2013 through Summer 2014SantiagoZully

Part 2: Understand your Experiment Before Beginning

5)     Mistake: You quickly get a simple protocol or a recipe for your experiment (or, if you are lucky, you have a kit’s instructions). You immediately perform the experiment, but it fails horribly, and you have no idea what went wrong. You automatically assume the protocol, kit, or recipe is wrong and you did everything correctly.

Solution: Understand the experiment before you do it. Understand what every single chemical does and what role it plays in the experiment. I would say most failures in an experiment are human error by the scientist overlooking something simple but important. My rule, don’t touch a chemical unless you know what it does, how to care for it, what role it plays in your experiment, and how to safely dispose of it. If your experiment uses a kit, thoroughly understand how the kit works. If it is being used for separation, what kind of separation method is it? If it is chromatography, what kind? If it is a gel, how does it separate? What comes out first? Understand all the components of the kit before using the kit.

Often protocols that you find online or in books will not cover important details such as proper care and considerations for the chemicals you are using such as light sensitivity, reactions with moisture and air, temperature concerns, reactions with certain plastics, and so on. Also, keep in mind that time and exposure to the environment can heavily weigh on the experiment. A big overlooked factor is the shelf life of reagents. Remember, often when chemicals are exposed to water, hydrolysis occurs, slowly degrading the chemicals over time. So the chemical may have a long shelf life in its store-bought form, but it may have a very limited shelf life once in solution. This is a big issue for antibiotics and DTT.

Also, repeatedly thawing out and freezing chemicals or proteins can also severely degrade them. Record how often your reagents are thawed out or aliquot small amounts at a time so that you can use those amounts when needed rather than thawing out the whole stock container each time. The protocols and kits usually assume you know what the chemicals do and how to handle them—which often you don’t, so google everything or go to the company website and read up on your experiment and the reagents before handling them. When working with kits, thoroughly read the material that comes with it as it has detailed information on handling all the components of the kit.

6)     Mistake: You do an experiment, and it works! Or it fails! Who knows? Either way, you got some type of result…but you didn’t write anything down.

Solution: Again, it’s easy to follow protocols and recipes, but what matters are the specifics! What did you use? What conditions? What temperatures? What amounts? What chemicals? What order? How long? Again, there are so many factors involved in getting results outside of what is mentioned in the protocols. You need to document your steps and what has occurred. Based on your observations you may find better ways of doing the experiment. Or based on your observations, you have resolved a huge problem! However, we won’t know unless you write it down. In my experience, I rarely follow the protocol exactly; often I find better tweaks that provide good yields for my experiment, but I record deviations as well as observations. Moreover, if something goes wrong, often there are good scientific blogs on company websites and third party websites that talk about the same problems you may have had in the lab, so it is important that you record your observations because these forums and blogs may help resolve what went wrong and how to fix it.

7)     Mistake: You do the experiment from memory.

Solution: Never do your experiment from memory. You should always have the protocol or your previous observations handy just in case something turns out different. However, the main issue with trying to do an experiment from memory is that you will often forget a step, usually an important one. I see this happen a lot when students make buffers at the total volume desired, but they didn’t adjust the pH, so that added volume was not accounted for.

10 Common Mistakes Made by Newbie Researchers – Part 1

SantiagoZullyBy Zully Santiago, PRISM Undergraduate Researcher, Spring 2013 through Summer 2014

Part 1: Prepare, Prepare, Prepare

1)     Mistake: The same day you plan on doing the experiment is the same day you gather all the reagents, glassware, and any other materials required for the experiment…only to realize that you do not have the reagents or materials needed to actually conduct the experiment.

Solution: Plan your experiments two weeks in advance. So if you plan on making a gel next Thursday, make sure you have all the necessary reagents to make the buffer and the gel itself today. Also, today, you should check and make sure the tank is working and that you have all the parts. If you need your glassware autoclaved, make sure you do that in advance. Make sure you have everything you need way in advance of doing the experiment, so look over your experiment in detail before considering running it.

2)     Mistake: You want to do an experiment, but you are afraid without someone guiding you through it, so you keep putting it off until someone shows you.

Solution: The more you read and understand how your experiment works, the less guidance you will need. If you start thoroughly understanding your experiments when they are easy (usually in the beginning), the easier it will be for you to become independent. Ask questions regularly, but attempt to answer them yourself first! Seek out answers from various sources. This facilitates critical thinking. When you get stuck or you want to confirm your reasoning, then go to your mentor. Remember, however, that you are supposed to be the expert and the most knowledgeable person about your project, so go do it.

3)     Mistake: You are not able to finish an experiment in time.

Solution: Plan your experiment in advance (see Mistake #1). Even if you are doing an experiment for the first time, before you even attempt to do it, make sure you have all your reagents and materials that are needed. After, read through the protocol again and look for incubation periods. If there are any time periods, double the time required and add an hour just for prepping (gathering/cleaning glassware, labeling and so on). This should give you enough time to actually do the experiment (provided you don’t make any mistakes or have to start over). If you are using instrumentation, make sure it works and is calibrated in advance. I personally like to have a whole free day if I am doing a brand new experiment or working with a brand new instrument. I won’t touch an instrument or apparatus that I have never used before until I have read and watched videos handling them. YouTube has everything, and often company websites have videos on how to use their instruments. Sometimes you can imagine doing the experiment and planning out what glassware and materials you will need, but there always seems to be something overlooked, so give yourself more time to make mistakes.

4)     Mistake: You haven’t been in the lab for a while because of school or other projects. You are not sure where you left off, but you attempt to continue your experiment as planned and the next step fails horribly.

Solution: Check your samples and instruments before you use them! Run a small sample and see if it is working before you proceed to the next big step. For example, if you had proteins or DNA in storage for a while, run a gel and see if you are getting the bands you are supposed to. The same rule applies anytime you use an instrument. Run a standard and see if everything is working properly before you use up your samples.


Alumni Spotlight – Christopher Pedigo (PRISM ’09) Earns American Heart Association Fellowship and Other Accolades

Christopher Pedigo, a PRISM alumnus who graduated in 2009, is steadily pursuing his goal of starting his own biomedical research lab.  With just one more year to go in pursuit of his PhD in Molecular and Cellular Pharmacology at the Miller College of Medicine in the University of Miami, Christopher has already published several scholarly articles and received accolades for his work.

Pedigo Blog 1While at John Jay, he worked under the mentorship of Dr. Yi He on a project published in the January 2013 issue of the Journal of Environmental Science and Health, titled “Bioaccessibility of arsenic in various types of rice in an in vitro gastrointestinal fluid system.”  After he graduated, Christopher spent two years as an adjunct instructor at John Jay and Borough of Manhattan Community College, while continuing to perform research in the labs of both Dr. He and Dr. Nathan Lents.

In 2009, Christopher was accepted into his PhD program and started research with his PI, Dr. Sandra Merscher, and co-mentor, Dr. Alessia Fornoni.  Their work investigates novel causes of Diabetic Kidney Disease (DKD), which affects 40% of diabetic patients, as potential therapeutic targets.  Consequently, Christopher and his lab are looking at the role of circulating factors on the glomerulus in vivo in mouse models and in vitro in the podocyte.

He is co-first author on the publication, “Sphingomyelinase-like phosphodiesterase 3b expression levels determine podocyte injury phenotypes in glomerular disease,” published in the Journal of the American Society of Nephrology. In this study, Christopher and his colleagues show that SMPDL3b levels are differently regulated in two glomerular diseases and that these levels determine the type of damage caused by certain circulating factors (more specifically sUPAR).

Christopher earned an American Heart Association Fellowship to help him continue his research and eagerly awaits word on his pre-doctoral NIH F31 fellowship application.  Travel grants awarded to Christopher are allowing him to visit various U.S. locales in order to advance his research and develop his expertise. Christopher is one of five PhD students nationally to receive the Tutored Research and Education for Kidney Scholars grant that will afford Christopher the opportunity to take a week-long kidney physiology class in Maine.  Other travel grants also allow him to attend the Kern Lipid Conference this summer in Vail, Colorado and to attend the American Society of Nephrology Conference in Philadelphia this fall.

PRISM is very proud of Christopher’s accomplishments since graduating John Jay and wishes him the best of luck in all of his academic endeavors.