Lab guide - SIWLab/Lab_Info GitHub Wiki

Lab guide, Wright Lab, EEB Toronto Welcome to the lab! We want your time here as an undergraduate/graduate student, postdoctoral fellow, research associate to be as fulfilling as possible- your time here should give you an opportunity to learn, contribute to science, publish your research, develop your career goals, and be part of an inclusive and welcoming community. This guide provides some notes on resources, expectations, and supports available, and is meant to be a living document that will evolve and be updated over time.

Department and University Resources/expectations

Department code of conduct, statement of values, and allyship network: EEB has developed a code of conduct and statement of values, along with an Allyship Network that can provide support to anyone who has had problematic experiences such has harassment and discrimination- these resources can all be found here: https://eeb.utoronto.ca/equity-diversity-inclusion/

Student Mental health hub: https://mentalhealth.utoronto.ca/

Accessibility Services https://studentlife.utoronto.ca/department/accessibility-services/

Office of research integrity, including policy on ethical conduct of research: https://research.utoronto.ca/research-integrity/research-integrity

Note: My door is open to discuss any issues related to the above topics- I can help connect you with any additional support you may need. Expectations for everyone Be present (virtually and/or in person). Attend lab meetings, seminars, your office hours, lectures for classes you TA, meetings with your colleagues, and department events. It’s fine to work flexibly, but respond promptly (within 1-2 business days) to your labmates and collaborators via email and Slack. Keep people informed if you need to step away for any reason. For any group lab activities we will continue to make hybrid options available, recognizing that people’s circumstances vary broadly. Of course we recognize that there are a number of reasons why you may need to step away from being present (health, family, etc.); please keep me informed when/if you need to step away. If you are sick and/or test COVID positive please stay home until you feel better. Expectations around evenings, holidays and weekends: Work-life balance is essential, and I don’t expect people to be regularly working evenings and weekends. Our research mostly does not require us to work weird hours, with rare exceptions such as fieldwork/plant care. That said, some people like to work weird hours and we respect that too. How people set their balance is a personal decision, and I may send messages at off-hours if I get an opportunity to do so, but I don’t expect to get responses from people over Slack/email during evenings, holidays and weekends, and may well not respond to messages until the work day starts. . Ask for help. Respect your labmates’ time and listen to their boundaries, but don’t waste your own. If someone else has information or experience you need, ask them. If you’re worried about damaging equipment or interfering with someone else’s experiment, ask them. There’s a middle optimum point between trying things out oneself and seeking help when needed. Give yourself the chance to work out the problem independently, but don’t stay stuck. Be helpful. Value your own time and set boundaries, but remember that part of your role in the lab is exchanging knowledge with your fellow scientists. Answering their questions helps you develop your scientific communication and mentoring skills, and the challenge of explaining a concept or protocol will deepen your own understanding. Paid forward principle: getting help from others now will pay forward in you helping the next lab member. We all have useful expertise to share with others and contribute. Be respectful. Speak politely to your labmates. Do not make assumptions about them based on their background, age, sexuality, gender, ethnicity, disability status, etc (see EEB code of conduct above). Listen to them and do not touch them without their consent. Do not talk about them behind their backs. Respect and share common spaces and resources (e.g. the lab / lunchroom / servers). Be kind, including to yourself. Everyone here is smart. So are you! Distinguish yourself by being considerate and compassionate as well. Science can be hard, so when things are difficult that is often a reflection of the challenges of being at the cutting edge of research rather than personal ability. Manage yourself. Learn how you work best and what conditions you need to perform well. We recognize that there is not one single model for this. I can provide some ideas of work strategies, but won’t know what works best for you. Be self-aware of your emotions and behaviour and how that might affect other people. Push yourself to improve and take care of yourself and your wellbeing. Ask for help when you need it.

What you can expect from me as a mentor ...

Regular meetings to discuss plans and progress (weekly or biweekly, depending on project stage and needs) Early intensive discussions to plan projects, and late intensive writing support A balance between supervision and allowing independence- I want to be there to help guide, but also want you to have the space to flesh out your own directions on a project- this balance should evolve over time (e.g. early PhD more step-by-step direction, later in the thesis more self-guided) Opportunities for skills training Letters of recommendation An academic supervisor provides letters of reference and recommendation for their mentees. Aim for at least two weeks notice and a last-minute reminder. Networking support I will connect you with other faculty, students, and postdocs who might serve as future mentors and collaborators. For lab members interested in careers outside of academia, he will send you to relevant resources. Transparency about funding I will keep you informed about grant renewals, how much you can claim in conference reimbursement, how much is being spent on lab resources, etc. Support in interpersonal issues If you clash with another lab member, Stephen will help resolve the situation or find appropriate resources to do so. Inclusion in recruitment I understand that new students and postdocs need to work with all of us, and will take your input about prospective lab members seriously. Support As your adviser, I have your back and want to see you succeed. I will support you when you’re facing problems, and will help seek out any additional support you may need. Boundaries I care about you, but our relationship is first and foremost professional. Everyone understands that you have your own friends and family.

What I can expect from you as an advisee As an MSc student…. Attend orientation events Take required classes Have timely committee meetings Set regular research goals in consultation with Stephen and evaluate progress on those goals regularly Meet regularly with me As an early (year 1-3) PhD student … Attend orientation events Take required and elective classes Have timely committee meetings Meet regularly with me Set regular research goals in consultation with Stephen and evaluate progress on those goals regularly Appraise! As a senior (year 3+) PhD student …

Start taking a more active role in mentoring undergrads and early PhD students Think about your career goals and research your options (research academia, teaching academia, industry, government, muffin bakery). Set regular research goals in consultation with me and evaluate progress on those goals regularly Make steady and timely progress on thesis chapters- publishing as you go is not always feasible but is often the best approach for both career and defence planning Look for opportunities to improve skills relative to career goals (e.g. teach your own classes, take a data science workshop) As a postdoc …

take an active role in training and mentoring PhD students Set regular research goals in consultation with me and evaluate progress on those goals regularly Further develop your career goals and explore options for next steps

The lab as a whole …

Timely communication about things you need from me (e.g. letters of recommendation, signatures on reimbursement forms, etc.) Openness about how your work is going and what problems you’re having Organization and data management so that future lab members can follow up on your work Awareness that I also have time constraints and commitments, including some that come up unexpectedly Responsible conduct of research (do not falsify your data, embezzle funds, harass your colleagues, abuse your undergraduate colleagues, or neglect your obligations as a TA and labmate)- see department and university links above

Wet lab Lab Safety and Guidelines: It is crucial to be well informed about the lab guidelines primarily for your own safety and for others. It is natural to be excited about a new lab opportunity or an experiment and at the same time it is equally important to be a responsible member. While it is important to understand what is being done and why, please feel free to ask any lab member you are unsure or confused about anything. Maintain Your Lab Notebook : Use of a lab notebook is an important part of your experiment. Typically, lab books are lab properties and must remain in lab even after you finish your research. There are several kinds or lab note books available in the market and some are more comfortable with the online versions as well. The best practice to maintain a great lab book is to write down details for everything you do in an organized fashion. Please remember, it is never too much information when comes to your lab book and you don’t take a chance to miss a point may be in next 6 months or a year. If you maintain an online document, please share with the supervisor (PDF would be great) before you leave so that another person can continue your research smoothly. You can keep a copy (scan/photocopy) of your lab book for personal use. Always record your observation/data as accurate as possible and never go back and make a correction. Prepare Your Own Solutions: It is a good practice to prepare your own solutions for an experiment to avoid any confusion or error. However, common solutions (e.g. electrophoresis buffer) can be used from the common container and refilled when exhausted. For other consumables (e.g. Ultrapure water, TE buffer etc.) it is recommended to make an aliquot for your own use and keep the main bottle as ‘pure’ as possible. Avoid Moving Equipment: Moving equipment (small or big) from one area to another may lead to major confusion and subsequently leading to inconsistencies in experimental results. For example, we have dedicated areas and equipment sets (Pipettes, Hot Plate, Tube Racks) for DNA and RNA extractions to avoid cross contamination. For example, RNAse used in DNA extraction may be a challenging issue for RNA extraction if any of the equipment are contaminated with RNAse). We typically do RNA extraction in fume hood and DNA extraction on a reserved benchtop area reserved for molecular biology work. Greenhouse/Growth Chamber Related Work: If your research project involves growing plants in the greenhouse/growth chambers, it is equally important to follow the standard guidelines set by the Growth Facilities staff (https://gf.eeb.utoronto.ca/). When preparing soil mix or preparing pots in the potting room, it is important to clean up any left-over soil from the benches or floor before you leave. Also, restrict your visits to the zone you are assigned to minimize transmission of pests between zones. It is always a challenge for the researchers and facility staff members to effectively control the common pests (e.g. Aphides, Thrips, Fungi gnats). Do not forget to clean the zone/growth chamber after accomplishing your project. You can use the available vacuum cleaner in hallways of the greenhouse when available. Leaf Tissue/Sample Collection: It is crucial to collect leaf/tissue sample as accurately as possible following standard/stipulated guidelines. Healthy and very young leaf tissue is ideal for DNA/RNA extraction. Double check both the leaf surfaces for Aphids or Thrips and avoid collection of plant tissue damaged by pests or pathogens. To avoid contamination, use gloves and wash fingertips and tweezers with 70% Ethanol in between two samples. Collect 30-50 mg fresh tissue in 2-mL round-bottom tubes (Sarstedt) for tissue collection as these are suitable for downstream processing during DNA/RNA extraction. It is equally important to label the tubes using Permanent Markers (e.g. VWR) and not Sharpie or similar marks as the latter tend to wipe out when flash frozen in LN2 or stored at -80°C freezer. Use of a short and unique tube label is encouraged along with detailed information in Lab Notebook or Spreadsheet. Detailed protocol for tissue collection is available on Lab GitHub account here (to be prepared). Handling Liquid Nitrogen (LN2): Plant tissue collected in 2 mL tubes are flash frozen in Liquid Nitrogen and stored in -80 freezer for DNA/RNA extraction. Temperature of LN2 is -196°C under normal atmospheric pressure (nitrogen exists as a liquid between the temperatures of -210°C and -196°C) and therefore should be handled very carefully. Individuals working with LN2 should always wear Cryogenic Gloves to avoid potential cold burns. Always carry LN2 in designated Dewar or shatterproof storage vessels. Use Dewar for long term storage and shatterproof vessels for tissue collection. Return the left over LN2 to the Dewar after finishing the tissue collection. Environmental Health and Safety (Safety First): University has policies to attend mandatory safety trainings for all lab personnel. All students should take two mandatory courses (EHS002 and EHS803) and keep up to date as required by the EHS. More information can be obtained here (https://ehs.utoronto.ca/). One can Register for Training using ‘My EHS’ Training from the link here (https://ehs.utoronto.ca/training/my-ehs-training/). My EHS Training is ONLY accessible from the U of T campus network. Autoclave Training is usually offered during the beginning of a semester but may also be available based on need. For Autoclave training you can also email directly Carlos [email protected] for upcoming sessions. In Case of an Emergency (Fire, Serious Injury): Please call 911 and/or Campus Police (416 978 2323). You can also call Emily or Stephen for a lab emergency (any time) or between 8.00 AM – 9.00 PM for other queries.

Github link to computational tips and resources, and additional protocols https://github.com/SIWLab