Lab resources

NAVIGATION

Lab Policies

Lab Safety

Lab Equipment

Work with Human Subjects

Lab Policies

So you are here, now what…

Welcome to the Greathouse Lab at Baylor University. In this memo, I set out to describe my expectations of myself as a mentor and you as a part of the project and lab. Some elements are simply practical ‘dos’ and ‘don’ts’ but many touch on the issues of collaboration and team science.

My goal as a mentor is to support and empower each team member to articulate and achieve his/her goals within the team’s vision. As a mentor, I am committed to helping you develop scientific skills and learn the nuances of microbial genomics. I strive to help you achieve success along your chosen career path through assisting with networking, identifying opportunities, and tackling complex scientific question. Most often I can do this by assembling the resources and sharing the formative successes and failures I (and others) have faced along the way. I may or may not be the right mentor to you at every stage (due to my own professional and academic limitations), but I will try to be a resource for identifying others who can help guide you in that role.

1. Lab meetings

A Greathouse lab meeting is every week (varies from semester depending on teaching schedule) for approximately 1 – 1.5 hours. This is an informal meeting in which people ‘open up their notebooks’ and talk about what they’ve worked on since the last meeting. It’s also a great time to bring analyzed data and discuss how to interpret or visualize the central findings. Admittedly, most people use powerpoint slides at this point to guide the discussion. The lab meeting schedule is posted on the OneNote along with upcoming meetings and my travel dates. At lab meeting, I will discuss hiring decisions that are in progress; e.g. potential post-docs, students, and staff. I will also let you know about my upcoming deadlines – proposals, talks. This is a private meeting and everything discussed here is considered in confidence. Attendance is mandatory – if you are running over or have a conflict on a particular day, let me know.

2. Outside meetings

• Attendance at one outside meeting a year is typically supported and encouraged. There are myriad of larger and smaller meetings. Think about what you want to learn, whom you want to meet, etc.
• You should receive pre-approval before registering for a meeting. I try to balance how many people from the lab attend the various meetings and who is going to submit what lab projects.
• A student can attend more than one meeting a year if for example s/he is presenting a talk, looking for a job.
• You can present your own unpublished work, recognizing the balance between the benefit of interacting with colleagues and possible competition to publish. However, you are not allowed to present or discuss other lab members’ unpublished data or even the experiments that are underway without specific permission from the lab member and myself. Similarly, if you give me pictures or slides of your unpublished work, I will not present it without specifically discussing this with you.

4. Travel

• Send me an email with the BU TAF travel form filled out and include your preferred departure time and date, hotel, and return. If there is a meeting rate for hotels, there is some flexibility about you booking your own hotel room. Remember everything needs to be booked about a month in advance for domestic, non-sponsored travel. Please ask me for details before you consider foreign or sponsored travel.

5. Money and property.

• Do not pay for things personally and expect to be paid back. There is no ‘petty cash’ for me to reimburse you.
• Please let me know when reagents or equipment needs to be ordered WELL IN ADVANCE.
• You cannot take a computer or other device (projector) off campus without a property pass.

6. My work habits

• My core hours at work are 8:30 AM to 6 PM. My teaching schedule is usually on Tuesdays and Thursday, but varies by semester, but is posted on my door.
• Usually e-mail is the best way to reach me. I usually read and respond to emails in the morning before 8 AM and throughout the day.
• If I have not responded to an email in 2 days, feel free to bug me. Sometimes I don’t know the answer and need to find out.
• If I’m traveling, I will try to tell people this in advance at lab meeting.
• If I’m on vacation and do not plan to respond to e-mails, I will turn on my ‘out of office’ automatic response.
• If you really need to contact me immediately, my cell phone number is 443-676-4776. I probably have the ringer turned off. Email, text, phone the number above.

7. My expectations of your work habits

• Maintain core hours that are allowed by your student work schedule, and for which we have agreed upon. I do understand that people value a flexible work schedule. It will not always be possible to accommodate this when you are running an experiment with other lab members or collaborators.
• On occasion, I may need you to work over the weekend if I have a grant or manuscript deadline.
• Respond to emails, even just to give me an estimate of when you will have an answer for me, within 2 days.
• Turn on your out of office automatic response if you are sick/on vacation and do not plan to respond to e-mail.

9. Notebook, record keeping

• All molecular biology experiments should be stored in notebooks, real-time data on OneNote and data archived on a https://github.com/GreathouseLab when submitted and finally published. All primary data for a manuscript should also be stored on the lab OneNote archive for wet (bench) work or on https://github.com/GreathouseLab for data analysis.
• Electronic notebooks should be kept on https://github.com/GreathouseLab – of course I expect that you will be keeping a hard copy of any data and analysis in a notebook as well.
• Primary sequencing data are stored by Baylor College of Medicine and/or on the Kodiak servers under the Greathouse user group – if you need access contact Mike Hutchinson. I require documentation of all coding scripts (Stata or R code) to repeat the analysis if needed at a later date. This means that if you write any analysis code, you will need the data file and Stata .do or R Markdown file that can run this analysis to generate the results.
• For all publications that use primary data and statistical analysis, I require for publication either a Stata .do code file or R markdown file that can generate the entire analysis with one data file (with notes so that it can be adequately reproduced).

10. Authorship, publication

• By no means are you allowed to submit a manuscript by yourself (this will constitute automatic dismissal) having to do with any data produced or review of literature we have conducted. This is a task I take very seriously and have to make sure all co-authors and collaborators are given ample time to approve before submission.
• If you are submitting an abstract for a meeting, please send it to me at least 2 days in advance for approval. If it’s an abstract that you’ve submitted previously, please still let me know. Sometimes there is authorship or other considerations based on who else is attending the meeting. If collaborators are authors, please send 5 days in advance so that we can give others a reasonable amount of time to read and decide if they want to be included.
• When you make a significant intellectual or experimental contribution to a project, then you will typically be an author on the manuscript.
• However, there have often been considerable resources devoted to a project before you ever receive the samples/data to analyze (e.g.; development of an IRB approved protocol, recruitment of patients). Even if others do not contribute a figure to a paper, they may also deserve authorship.
• Authorship (including order of authors) is always discussed before a manuscript is submitted from the lab.
• Within one month of final acceptance it the responsibility of every author (and particularly the first author) to ensure that all data and scripts are archived with me on the shared drive. I may get requests for data or data used to generate a figure months and years after publication.

11. Collaboration

• Do not send or give reagents to someone who asks you for them. Send them on to me. We may have received the reagent from another lab and not be allowed to share it. Or we may not be able to freely distribute reagents (especially clinical samples) without paperwork and justification. Or the person requesting the reagent may be a direct competitor of an existing collaborator.
• Please do not initiate a new collaborations, copy me on initial email interaction. I ultimately assume responsibility for all transactions (sequencing, cell lines, clinical samples).
• If there is a misunderstanding or a conflict with a collaborator – talk to me. Hopefully this won’t happen because you will consult with me first if you feel uneasy about an email or interaction. Remember that the lab may have multiple interactions with this lab or individuals that could be impacted. We might also have a history with this individual that helps to explain what you perceive to be an odd response.

12. Media Contacts

• If you are contacted by an outside news or media person/entity about your work that was published, congratulations! But please let me know first BEFORE you agree to talk them. I will need to vet the source and give my approval.
• If want to blog, vlog, or podcast your published work that’s great, I support your scientific endeavors. However, please do NOT write or speak about any unpublished data, especially critical for patents or industry partnerships

Lab Safety

All of our lab safety record keeping is located on this website (Bioraft login: Bioraft link). It is your responsibility to keep your training up to date; you and I will be notified if training is required. For any emergencies please review these documents:

• Laboratory Emergency Response Guide;
• Chemical Spill Instruction Sheet;
• Fire Extinguisher Notes.

Go to this link for waste pick up forms or request disposal/pickup.

Alternate links:

• Laboratory Emergency Response Guide
• Chemical Spill Instruction Sheet
• Fire Extinguisher Notes

Lab Equipment

-80 C freezer:

• Whenever ice builds up on the edges and corners of inside doors, use ice scraper to remove. If this is not performed, doors can be damaged.
• Unit will vacuum seal after opening, if you need to open it again, turn the knob on the left side of the unit to release the vacuum seal.
• This dial has an ice pick for when ice builds up. If can be used from the inside or the outside. However, due to the location of the unit, from the inside will be most efficient. Life the bottom of the top freezer to access the area.
• Inside doors are removable, if they build up ice, remove them and put them in the sink. Since both doors are the same size, it does not matter if you interchange them.

Incubators:

• Shelves go in so that the with lip facing down is facing you
• CO2 stops blowing when outer door opens
• Cleaning 70% ethanol or 10% bleach but NOT recommended
• Water pan has cover to direct air flow
• Wipe down back (take off panels) before start it up
• Cold finger condenses and it drips down to pan
• Little bit of condensation is ok
• Lots of condensation is bad, check that out
• Copper and UV light to help prevent contamination
• UV light is safe to use, comes on for 10 min after door is opened
• If bad contamination, take everything out, autoclave everything and leave UV light on for 24 hours

Filter for DI and Molecular grade water:

• Let me know if any of the DI water lights are red continuously. I will Call Evoqua for replacement

CO2 Tank:

• when on, left gauge should read between 5 and 10 psi. (tube pressure) Left gauge should read between 1000 and 500 psi (tank pressure)
• blue/green knob is the control to the tube to the incubator; the left gauge corresponds to the pressure in the tube
• black knob is turned completely to the left; turning to the right increases tank pressure
• to turn tank on and off, see open/close valve located at top of tank
• to shut off co2 to incubators, make sure green/blue valve is turned down

Autoclave:

1. Check the water level on the front exhaust tank. If it is at high level mark, replace with fresh water up to the low level mark. Be careful about the position of the exhaust hose.
2. Turn the power switch to on. Ensure that pressure gauge reads 0 MPa. Ensure that the cover lock light is not lit.
3. Open the cover.
4. Make sure the drain valve (underneath exhaust tank) is closed. Pour water (normal sink water) into the chamber until the water level is slightly below the heating cover surface (approx. 3.5 L)
5. Place autoclave tape over item (caps should be loose!). Place items to be sterilized inside the basket(s), ensuring they are not overlapping. Place basket(s) inside chamber (smaller basket on top).
6. Make sure the digital display shows a temperature below 60 degrees C.
7. Close the cover.
8. Use the select button to select one of the 4 sterilization cycles [1) liquid, 2) steri., 3) melt, 4) instrument.] Then use the arrow buttons to select the specific program within the cycle (1, 2, or 3.) Refer to list to determine the different programs/cycles. For Biohazard trash use program for liquid sterilization and double bag! Afterwards place in black trash bag and put in standard lab trash can for pick up
9. Press the start button if no further modifications to settings needed.

After cycle is completed

10. Buzzer will sound. Ensure that the pressure is lowered to 0 MPa and that the cover lock lamp is not lit.
11. Pull up the handle slightly to open the cover and wait until no steam comes out. Then open the cover slowly.
12. Take out the sterilization objects when steam has been purged completely from the chamber. Make sure they are cool first! Or use autoclave gloves.
13. Set the power switch to off.
14. Drain off the heating water by opening the cover, opening the drain valve.
15. Close the drain valve after draining water.

Work with Human Subjects

If you are participating in or working with data from studies with human subjects, you MUST complete CITI training BEFORE working with any subjects or data:

IBC Required Training

IBC regulatory training for all investigators and lab personnel in BSL1, BSL2, or BSL3 Labs is completed through CITI. All required CITI training should be completed before submitting protocols to the IBC. Incomplete training will delay review and approval. Many additional IBC training modules are available to investigators through CITI. The IBC encourages investigators to access these modules as you see fit to facilitate your own research or instruction, and to use them as a resource in your teaching and mentoring of student investigators.