Chapter 1 General

1.1 Accessing Lab Accounts and Spaces

1. The lab has a Google Drive Folder that we use for documentation and inventory. It should be kept as up-to-date as possible.

2. The lab has a Slack, which we use for quick messaging and lab-specific threads.

3. Request to be added to our lab’s listserv by emailing its current handler, Alex Sorets. This is generally used for longer, lab-wide announcements.

4. Email our current building manager, Ross Denham, for access to Olin Hall 004A, 117, 118, 119, and 213A, and for after-hours access to the building. Have Ethan CC’ed on the email so he send his approval to your email.

5. Our lab also has 3 calendars to schedule general lab events, book specific hoods, and to book time on our microscope. Request access to these calendars: Lippmann Lab Calendar, Lippmann Lab Microscope, Lippmann Lab 118 Small Hood.

6. Create an iLabs account. The first time you log into your account, you will need to add “Lippmann, Ethan (VU) Lab” to your groups. You should use the menu on the left side of the screen and click on “Manage My Groups” to request access.

7. Send an email to the Vanderbilt IT Department asking for access to our lab’s shared network drive. Include your VU NetID in this email.

  - Addresses for different computers:

PC:  \\vu1file.it.vanderbilt.edu\lippmannlab\

Mac: smb://vu1file.it.vanderbilt.edu/lippmannlab/

8. Finally, our lab has a Github that we use for code versioning and internal sharing.

1.2 Becoming an effective researcher

There is no set formula to facilitate a productive research career but our general expectation is that you will:

• Spend 40-60 hours a week in the lab environment. This includes actual bench work and time at your desk spent updating your lab notebook, organizing data, writing papers, planning new experiments, etc. Learning and innovation in the laboratory is partly through osmosis and casual conversations, so make an effort to be around your peers during normal working hours. You may choose to spend some time outside the lab if you are in the process of writing a paper, but more work is inevitably done inside the lab and student office compared to at home.

• Do your work when it needs to be done. Wet lab work often necessitates experiments at strange hours (e.g. 6 hour time points) or on weekends. Our policy is that you do your work on schedule. Then, if your schedule is free during the week or weekend, take your time off accordingly. I often left work at 3pm during graduate school if I knew I would be pulling a 9-5 on Saturday. Your schedule is your own to set (aside from individual and group meetings) as long as I know you are striving to meet the research goals we have set together. Burnout is a real problem, and we try to avoid it at all costs, but accountability is equally important.

• Preparation, preparation, preparation. Putting together an experimental design by yourself and together with other lab members (especially Ethan) can save days or weeks of unnecessary delays by identifying potential pitfalls, proper control conditions, etc. Always think in great detail about the experiment before you do it!

• Be honest with your data - to Ethan and yourself. Falsifying data is obviously grounds for immediate dismissal from the lab. However, you must also be careful to not bias yourself on what your results actually mean. If you do an experiment three times, and get three different answers, you can’t simply report the one that worked the way you thought it should. Always follow the scientific process and determine what you did that gave you these different results. Your common sense and observational skills are often the most valuable tools in your research.

• Read, read, read. Our lab pursues diverse research areas – this is not an accident. All the knowledge I accumulated, which drives the research ideas and grant proposals, was accumulated from years of reading anything I found interesting. If I saw an editorial on an interesting topic, I read it and then read or browsed all the relevant citations associated with it. If I attended an interesting seminar, I thought about the ways we could incorporate that work into our lab’s efforts and subsequently browsed papers written by the seminar speaker. However, while I am an excellent resource for both broad and esoteric knowledge, I cannot be your go-to source of information on every topic. Your will have to read primary literature and reviews to build your knowledge base. If you are reading a paper and don’t understand a technique, protein, system, etc. that was used, look it up! Wikipedia is a surprisingly helpful for learning biology, and you can find a Youtube video for almost any experimental technique these days. Surprisingly, you can also follow scientists on Twitter who often discuss their recent work or work of their peers, with excellent summaries.

• Stay current on the literature. Set up automatic email alerts from Nature, Science, Cell, and their daughter journals. Then, set up your My NCBI account on PubMed to give you monthly updates on a variety of keywords relevant to your projects. You can use your Vanderbilt account to log into My NCBI by choosing “See more 3rd party sign in options” and searching for Vanderbilt. You also access the Vanderbilt library through Google Scholar by adding all the Vanderbilt Library options to your library links in your Google Scholar settings. The more you know about current findings and techniques that may be relevant to your research, the more novel and innovative you allow yourself to be. This is definitely a skill that should be carried with you after graduate school.

• Keep a personal library of the papers you read. Use whatever program you want. The majority of the lab uses Zotero because it’s free and compatible with Microsoft Word for adding a bibliography to a manuscript. This saves a lot of time when trying to track down things you have read and want to cite.

• Keep your lab notebook up-to-date. One of the more annoying events in research is having an experiment fail, then trying to remember what you may have done wrong rather than simply tracing the written details on paper. Your lab notebook should be by your side every day as you work, and you should be writing in it constantly. We buy lab notebooks in bulk from Amazon, so you can get a new one whenever you need it.

• Attend campus seminars that are relevant to your research, and probably a few that you simply find interesting. Hearing a prominent researcher talk for 45 minutes is often more productive than reading 10+ of his/her papers. Likewise, a talk may not be releated to your work, but the techniques being used are. Sign up for email alerts on semiar postings in other departments on campus. Commonly attended seminars include the Chemical Engineering Seminar, Biomedical Engineering Seminar, Stem and Progenitor Cell Interest Group (SPRING) meeting, and the Alzheimer’s Disease Journal Club. Furthermore, the number of virtual conferences has also grown in the past year due to the pandemic. Virtual seminars that may be of interest include the CZI Weekly Webinar, Brain Barriers Virual Seminar Series and Tissue Talks.

• Rely on the experience of others. Everyone is here to help, particularly given the diverse expertise in our lab. The success of the lab depends on effective teamwork and appropriate integration of new members. When you become the senior lab member, be sure to return the favor to your junior colleagues.

• If you want to build something: The lab has a 3D printer and CNC machine. McMaster-Carr has an amazing catalog of parts, fitting, materials, etc. VIIBRE has an excellent machine shop and offers technical advisement, and we have a small machine shop in the basement of Olin where the CNC is housed. The Vanderbilt Institute of Nanoscale Science and Engineering (VINSE) in the Engineering and Science Building (ESB) has a variety of instruments and a clearn room. Leon Bellan’s lab (Mechanical Engineering) has built some interesting new microfluidic capabilities and is an excellent technical resource. Basically, if you think you can design and build something to assist your research, you should. The ability to “hack” cell culture and instrumentation is an incredibly useful skill for any career trajectory.

1.3 Safety

Appropriate personal protection equipment (PPE) should be used. Shorts are fine in the summer, but they must always be accompanied by close-toed shoes. Protective eyeware is required if you are in lab longer than 10 minutes, and especially if you are using any chemicals or the liquid nitrogen. Lab coats are optional in the main lab for routine work but should be donned for chemical handling. Lab coats are required during cell culture. We provide everyone with their own safety glasses/goggles and cell culture lab coat.

1.4 Fellowships

All lab members are expected to apply for external funding. For graduate students, this includes the NSF GRFP, NDSEG, NIH F31 fellowship, and AHA pre-doctoral fellowship. I am cognizant that certain students are not competitive for certain fellowships, but every student-earned fellowship provides more money that can be spent on supplies and equipment. Current and previous students have uploaded their applications to Google Drive for internal sharing. There is also a collection of grant examples called the Edge for Scholars (EFS) Funded Grants Library.

1.5 Lab Upkeep

Labs are inevitably messy and disorganized, but there are certain steps that need to be taken to ensure safety is maintained and reagents aren’t wasted.

• Label the details on everything you make. What if you pH a buffer to 7.4, but it should have been 8.4? Will you remember these details if your experiment doesn’t work and the bottle wasn’t labeled? Also know the shelf life of the reagents you prepare. Expired reagents can cause similar headaches. It is up to you to know how long a particular solution will be active before needing to prepare a new one! Additionally, please make sure that you put your initials on your reagents when you label them so that other lab members know who to contact if they have questions.

• When a product arrives, label it with the date it was received and then opened. See above.

• When the product arrives, make sure it’s stored properly. Fridges, -80 Freezer, -20 Freezers, flammables cabinet, acid/base cabinet, etc.

• If you buy a new reagent, add it to our lab Chemical Inventory. Print out its MSDS form and add it to the in-lab binder. Last, add the compound to our Vanderbilt ChemTracker Inventory. When you sign into the ChemTracker Inventory, you will skip set up, and you should be able to select “Lippmann Lab” on the left side of the screen.

• Treat reagents appropriately. Does your reagent need to be desiccated? If so, put it in the right place. Is your reagent anhydrous or hygroscopic? If so, wrap the cap in parafilm to prevent moisture accumulation. And so on… If you are unsure how to store, use, or dispose of a reagent, talk to a senior lab member.

• Handle antibodies, growth factors, and small molecules appropriately, and always label tubes with dates.

  • Always use sterile microfuge tubes and work in the biosafety hood when preparing anything that will be added to cells!

  • If an antibody arrives frozen, thaw it on ice and aliquot into individual tubes before refreezing (typically 5 \(\mu\)L per tube).

  • If you buy a new antibody, add it to our Antibody Inventory.

  • Growth factors will typically arrive as lyophilized powders. Reconstitute them according to their instructions (the product sheet should specify water, PBS, dilute HCL, etc.), add 0.1% human serum albumin, and store as working aliquots in the -80 freezer.

  • Freeze/thaw of proteins leads to loss of biologyical activity! Once an antibody or growth factor is thawed, you should not refreeze it, but you can store whatever you don’t use in the fridge for 1 week. This ensures that these expensive reagents don’t get needlessly wasted.

  • Small molecules are typically resuspended in water or DMSO. Check the data sheet before reconstituting and check to see if the reagent is light-sensitive (store in an amber microfuge tube). Then, distribute into microfuge tubes and refreeze. For small molecules in DMSO, if the stock solutions won’t be used for >1 month, wrap the cap of each tube in parafilm to prevent water uptake. If a layer of liquid has formed above the frozen sample, discard it for fear that its activity may be compromised. Additionally, small molecules are typically added to the cells’ media the day that you will add it to the cells; exceptions will be noted during training or in the protocols.

• Make sure that the liquid nitrogen tanks are filled and its records are current. Our cell stocks are virtually irreplacable if the liquid nitrogen tanks fail or run dry. Everyone plays a part in making sure their levels are suitably high. Likewise, when you bank cells or remove a vial, be sure to update either the small tank spreadsheet or the big tank spreadsheet so we know exactly which lines and how many vials we have on hand.

• Be a good lab citizen and clean up after yourself. When you leave the cell culture suite or the lab, there should be no traces that you ever did an experiment. If you use the last of a reagent or are planning on using a significant amount of a reagent, make sure you order more so that you do not affect other lab members’ experiments.

• The lab works together to make sure the lab spaces are functional, clean, and well-stocked. We rotate the schedule for dishwashing and autoclaving. Specific lab duties and equipment liaisons can be also found in this folder.