RESOURCES

Laboratory: The Li lab is located on the 9th floor of the Leslie Dan Faculty of Pharmacy (LDFP) Building at the University of Toronto St. George Campus. It comprises approximately 2,800 sq.ft of combined research and support space.

·   Main laboratory rooms (940, 950, 960)

·   Two tissue culture rooms (947, 949)

·   Cold room (4°C)

·   Freezer Room (with -80°C freezers, cell line storage freezer, and ultra-centrifuges)

Office: The Li lab student/trainee offices are immediately adjacent to the laboratory rooms. Every trainee is provided with a desktop/monitor. Available software includes Microsoft Office (full suite), Snapgene, FlowJo, ImageJ, EndNote, Python, and Console. Dr. Li’s office is on the same floor, adjacent to the lab and student/trainee office.

Animal: Mice are housed in a dedicated room in an animal care facility affiliated with University Health Network (UHN) and U of T. Routine care will be provided by Animal Resources personnel.  Trained veterinarians are available for consultation at all times. All animal care protocols are reviewed and approved by the AAALAC-accredited institutional animal welfare committee (IACUC).

Equipment list of Li Lab

·       Lambda workstation (GPU: 4 X NVIDIA H200 NVL 4-Way NVLink Bridge)

·       Lambda workstation (GPU: 2 X NVIDIA Geforce RTX 4090)

·       Agilent Biocompatible 1260 HPLC

·       Shimadzu HPLC

·       Buchi-815 Flash chromatography system with UV and ELS detection

·       Buchi-850 Flash chromatography system with UV and ELS detection

·       Biotek 460 plate washer and dispenser

·       Biotek Cytation-1 microplate reader

·       Biotek Cytation-5 multimode Imager plate reader (shared)

·       Flow cytometer (cytoFLEX S, shared)

·       Dynamic Light Scattering System (ZETASIZER NANO-ZS, shared)

·       Agilent Biostack automation system

·       NanoDrop One/OneC Microvolume UV-Vis Spectrophotometer

·       Promega Quantus Fluorometer

·       Opentrons automatic liquid handler robots (Four)

·       Universal Robots UR50e

·       Microfluidic pump system for nanoparticle formulation

·       Thermo MaxQ4000 orbital shaker (Two)

·       Corning cell counter

·       Thermal Mixer (Two)

·       Benchtop refrigerated microcentrifuges (Three)

·       Thermo Sorvall refrigerated centrifuge

·       Eppendorf New Brunswick Innova 44/44R Incubator Shaker

·       Eppendorf 5804 Centrifuge

·       BioRad PCR Thermocycler (Three)

·       CO2 incubator for cell culture (Four)

·       Inverted microscope

·       Labconco Freeze Dryer

·       -80°C freezer

·       -30°C freezer (Three)

·       4°C refrigerator (Three)

·       Cryo-storage tanks (Two)

·       Vacuum ovens (Two)

·       Chemical fume hoods (Three)

·       Biosafety Cabinets/Laminar Flow hoods (Three)

·       BioRad ChemiDoc MP Imaging System (shared)

·       BioRad CFX Opus 384 Real-Time PCR System (shared) 

Core Facilities: All Li lab members have training and access to the core facilities and services below.

1.     Centre for Pharmaceutical Oncology (CPO, 12th floor of the LDFP Pharmacy building; free access to members)

·   Flow cytometer (cytoFLEX S)

·   LC-Mass spectrophotometer

·       Multimode lmager plate reader and Fluorescence Microscopy (Biotek Cytation 5)

·   Dynamic Light Scattering System (ZETASIZER NANO-ZS)

·   Confocal Microscope

·   BioRad qPCR

·   Beckman Coulter Ultracentrifuges (Two)

·   BioRad ChemiDoc Imaging System

2. Princess Margaret Genomics Centre

·   Microarray scanners

·   Liquid handling robots

·   Real-time PCR machines

·   DNA/RNA extraction and purification instruments

·   Agilent bioanalyzer 2100 for nucleic acid quality control

·   High-performance computing (HPC) clusters for data analysis

3.     STTARR Innovation Centre

-       Preclinical Imaging Core

·   IVIS spectrum imaging system for fluorescence and bioluminescence imaging

·   High-resolution 3D ultrasound and photoacoustic imaging system

·   Small animal 1T, and 7T MRI

·   Clinical 1.5T MRI for imaging large animals

·   MR-guided HIFU at 1.5T and 7T

·   PET-CT, PET-MR, SPECT-CT-PET

·   MicroCT imaging system

·   Image-guided, flat-panel cone-beam CT radiation therapy units

·   Veterinary support through the Animal Resource Centre

-       Histopathology core

The STTARR pathology core services all research laboratories within UHN, academic institutes, and industry sponsors on pre-clinical research projects with full histopathology services including formalin-fixed paraffin-embedded (FFPE) tissue services, frozen tissue services, microtomy, immunohistochemistry, in situ hybridization, and H&E staining.

4. Translational Infrastructure

With two fully equipped operating rooms, intraoperative imaging capabilities (Fluoroscopy, Fluorescence Imaging), and a clinical bore size MRI with HIFU, STTARR provides infrastructure and offers support for translational research.

5. Ontario Centre for the Characterisation of Advanced Materials (OCCAM) in the Department of Chemical Engineering & Applied Chemistry at UofT

·   700 MHz Agilent DD2 NMR Spectrometer

·   600 MHz Agilent DD2 NMR Spectrometer

·   Two 500 MHz Agilent DD2 NMR Spectrometers

·   400 MHz Agilent VnmrS NMP Spectrometer

·   400 MHz Varian MercuryPlus NMR Spectrometer

·   400 MHz Bruker Avance III NMR Spectrometer

·   300 MHz Varian MercuryPlus NMR Spectrometer

·   Hitachi CFE-TEM HF3300

·   Hitachi VP-SEM SU3500

·   Hitachi UHR-SEM SU8230

·   Hitachi HR-SEM S4500

Institutional environment

Investigators at the U of T have a rich history of close networking and productive collaborations while writing grants and manuscripts and overseeing multidisciplinary science programs. The U of T provides an environment that is intellectually rich and in which cross-fertilization of ideas and collaboration between departments and Faculties is encouraged and supported. LDFP is located at the southeast corner of the U of T campus and the heart of the Discovery District, which is a concentrated mix of research labs, hospitals, biomedical companies, and finance/business support services located in Toronto’s downtown core. It is close to the Toronto Academic Health Science Network (TAHSN) teaching hospitals and other scientists studying gene therapy and animal disease models in hospital-based research centers. The LDFP supports a diverse and rich environment for cross-departmental collaboration and interdisciplinary endeavours through the launch of PRiME, a Precision Medicine initiative at the U of T. This concentrated core will provide frequent collaborative work and extensive support to the PI’s group, resulting in high-quality and innovative research.

The following research partners are all located within 15 minutes of walking distance.

·   Terrence Donnelly Center for Cellular and Biomolecular Research (Donnelly CCBR)

·   SickKids Research Institute

·   Centre for Research in Neurodegenerative Disease (CRND)

·   Banting and Best Diabetes Centre (BBDC)

·   Molecular Design and Information Technology (MDIT)

·   Ontario Cancer Institute (OCI)

·   Toronto General Research Institute (TGRI)

·   Toronto Western Research Institute (TWRI)

·   St. Michael's Hospital

·   Women’s College Hospital

·   Samuel Lunenfeld Research

·   The Centre for Addiction and Mental Health (CAMH)

·   Toronto Rehabilitation Institute

·   MaRS

Welcome to the Li Lab! 🎉

As you embark on your research journey, my goal is to help you excel and navigate common pitfalls. To achieve this, I’d like to share my thoughts on the core research abilities that will be beneficial throughout your studies in our lab and beyond:

1. Reading literature

2. Generating innovative ideas 

3. Designing experiments 

4. Analyzing data

5. Writing a compelling paper

6. Submitting the paper and doing revisions

7. Presenting your work

1. Reading Literature

Reading literature is the foundation of any successful research project. This stage requires the ability to learn quickly and summarize effectively. Begin by immersing yourself in good review articles (feel free to reach out to me or your senior peers if you need recommendations on which papers to start with 😎), which provide a broad overview of new knowledge in your field. These sources will help you understand the current state of research and identify key themes and trends.

As you progress, engage critically with these texts. Instead of passively reading, question the motivations behind the research, the technical contributions made, and the results obtained. Practice summarizing each paper in three sentences: what motivated the research and what new contributions it made. This exercise will sharpen your ability to distill complex information into its essence. 

Gradually narrow your focus to specific and impactful research problems that pique your interest. This process will help you identify gaps in the existing literature where you can make a meaningful contribution. Remember, the goal is not just to understand what has been done but to identify what remains and is worth exploring.

2. Generating Innovative Ideas 

Once you’re familiar with the literature, it’s time to generate your own ideas. This stage requires summarization, reflection, and sensitivity. Summarization involves identifying the similarities, advantages, and disadvantages of existing methods.

Then reflect on how different papers relate to each other: Who improved upon whom? Who supplemented whose work? What is the fundamental contribution of each piece? Does it introduce new knowledge or leverage existing technologies for new applications? How could you redesign this research to publish it in a better journal? Understanding these relationships will give you a clearer picture of the research landscape.

Sensitivity to gaps and deficiencies in existing research is the starting point of innovation. Sometimes, this sensitivity is a matter of research intuition or talent, but more often, it’s a skill that develops with experience. The more papers you read and understand, the more attuned you become to spotting weaknesses and opportunities for improvement. I also encourage you to discuss your ideas with others, especially those from different fields, as this can provide fresh perspectives and spark new insights.

3. Designing Experiments 

With a promising idea in hand, it’s time to design experiments. This stage requires strategic thinking and planning. Start by aligning your experimental design with your idea, motivation, and contribution. Choose appropriate comparative experiments and data that will help you test your hypothesis effectively.

When designing experiments, ensure that your results can be compared with the right benchmarks. It’s not enough for your results to be impressive in isolation; they must highlight your contributions effectively. Think of your experimental design as a strategic plan that combines various elements to showcase your work’s novelty and impact.

Consider the entire experimental process from start to finish. What resources will you need? What potential obstacles might you encounter? How will you measure success? By thinking through these questions in advance, you can design experiments that are robust, efficient, and informative.

4. Analyzing Data

Critical analysis is essential at this stage. Once you have your experimental results, evaluate them thoroughly. Does the result validate your hypothesis? Is the result strong enough to surpass the benchmarks in the literature or impress future reviewers? When results are not as expected, don’t panic—it’s not the end of the world. Understanding the reasons behind unexpected results can often lead to valuable insights and new directions for your research.

If a method doesn’t work and isn’t essential from a big-picture perspective, be decisive in skipping it and exploring new avenues. This ability to pivot is crucial in research. Sometimes, letting go of an idea is a wise way to make room for a better one. Keep an open mind and be willing to adapt based on what the data reveals.

5. Writing a Compelling Paper

With solid data in hand, it’s time to communicate your findings effectively by writing a compelling paper, which requires logical thinking and clear communication. Develop a strong narrative that seamlessly connects the motivation, methods, results, discussion, and contributions into a coherent and engaging story.

Start by outlining your paper. Clearly state the motivation behind your research, the methods you used, the results you obtained, and the significance of these results. Each section should flow logically into the next, creating a cohesive and persuasive argument for your work.

Storytelling is particularly important for novel ideas. Your paper should not just present data but also convey the significance and potential impact of your research. Aim to make your paper both informative and engaging, capturing the reader’s interest while clearly communicating your findings.

6. Submitting the Paper and Doing Revisions

Beyond impact factors, study the journal’s acceptance styles and preferences to find the best fit for your paper. Look for journals that have published similar work and whose audience will be interested in your findings. Take the time to read the submission guidelines and understand the journal’s requirements. Tailor your submission to meet these guidelines, increasing the likelihood of acceptance. This strategic approach ensures that your work reaches the right audience and has the maximum impact.

Understanding what the reviewer is truly asking is critical. When you receive feedback, take the time to analyze it carefully. Address the reviewer’s comments thoughtfully, supplement experiments if needed, perform necessary statistical analyses, and revise your article accordingly. Sometimes, reviewers may misunderstand certain aspects of your work. In such cases, be prepared to argue your points clearly and logically. Provide additional evidence or clarification to support your arguments. This iterative process enhances the quality of your research and strengthens your arguments.

7. Presenting Your Work

Once your paper is accepted, effective presentation and communication skills can help disseminate your findings and inspire others. Whether you’re speaking at a conference, presenting to a small group, or discussing your work informally, being able to deliver your findings clearly and concisely is crucial. Our group meetings and student seminars provide good opportunities for you to practice. 

Beyond these core research abilities, some general qualities including accepting failure, persevering before achieving success, maintaining a positive outlook, and balancing research with life will sustain you through the challenges of this research journey. 

Don't hesitate to reach out if you have any questions or need further guidance. I'm here to support you every step of the way.

Cheers,

Bowen

Summer 2024

Summarized Notes from Nature Masterclasses

A strong paper not only presents great research but also tells a clear, engaging story.

Key Elements of a High-Impact Paper: 

• Broad Impact: Will researchers in other fields find the conclusions novel or of scientific significance? Could these conclusions directly influence research or thinking in other domains?

• Significant Impact: Do your findings potentially reshape thinking or approaches in related scientific fields? Is there clear evidence that your conclusions contribute to advancing knowledge in your area?

Tips for Abstract

• Introduction and Context (Why did you do the work?) 

Clearly state the gap in knowledge or the practical problem your work addresses. 

Examples: 

“We don’t know the reason for A.” 

“B is a practical problem, and a solution is needed.” 

“C occurs frequently, but the underlying cause remains unclear.” 

• Scientific Question (What did you aim to answer?) 

Specify the key research question or hypothesis your study addresses. 

Example: 

“We aimed to answer D, which is critical for understanding [subject].” 

• Methods (How did you do it?) 

Briefly describe the key methods or approaches used to answer the research question. 

Examples: 

“We measured/calculated/analyzed X.” 

“We used method Y to address the problem.” 

• Findings (What did you show?) 

Summarize your key findings in a clear and concise manner. 

Example: 

“We found that X is [describe the main finding].” 

• Implications and Conclusions (What does this mean?) 

Highlight the significance of your findings in the broader scientific or practical context. 

Examples: 

“This improves the understanding of A.” 

“This provides a solution for B.” 

“This could help explain C and offers new insights into the problem.”

Tips for Introduction 

• Context (Why this study matters): Provide background information relevant to your audience, setting the stage for the importance of your work.

• Focus (Key studies and rationale): Gradually lead readers towards the gap in current knowledge and clearly state the aim of your study.

• Findings (A preview): Provide a brief summary of the key findings or contributions of your work.

Tips for Results

• Present your data clearly and logically using precise, concise language. Organize different segments of your results with clear subheadings.

• Figures should be self-explanatory and understandable without reading the text. Make sure axes, labels, and legends are clear.

• Avoid cramming too much data into one figure. If needed, split it into multiple figures, each focusing on a different aspect.

• Use tables only for data that can’t be easily visualized. They should complement figures, not duplicate them.

Tips for Discussion

The discussion section serves as the bridge between your results and the broader scientific context. It is where you interpret your findings, address their significance, and place them within the framework of existing research. Writing an effective discussion requires careful thought, logical flow, and a clear balance between humility and confidence. Below is an in-depth guide to help you craft a compelling discussion section.

1. Start with a Summary of Key Findings

The opening of your discussion should clearly summarize the main findings of your study. This sets the stage for deeper analysis and helps readers understand the take-home messages.

• Use concise language and avoid excessive repetition of results.

• Highlight only the most significant outcomes and their direct implications for your research question.

• Keep this section brief yet impactful, ensuring the reader has a clear understanding of your major contributions.

Example phrases:

“This study demonstrates that…”

“The data revealed that…”

“Our findings show that…”

2. Interpret the Findings in Detail

This is the heart of the discussion. You need to explain what your results mean and why they matter. Address the following:

Biological, technical, or theoretical implications: What do your findings reveal about the mechanisms, processes, or systems studied?

Significance: How do these findings contribute to the broader scientific field?

Context: 

• How do your results align with or diverge from the expected outcomes or established theories?

• Break your interpretation into logical sections, such as addressing specific hypotheses or questions. 

• Be specific in your explanations, but avoid overstating the significance or drawing conclusions that your data do not fully support.

Example phrases:

“These findings suggest that…”

“One potential explanation for this result is…”

“Our data provide evidence that…”

3. Compare with Previous Studies

A critical part of the discussion is relating your results to the existing literature. This shows how your work fits into, challenges, or advances current knowledge.

• Highlight agreements and inconsistencies: If your results align with previous research, explain how they support established findings. If they differ, propose potential reasons for the discrepancies.

• Use specific examples from past studies to strengthen your arguments.

• Make sure to properly cite the studies you reference and discuss their relevance to your work.

Example phrases:

“These results are consistent with those reported by…”

“Our findings contrast with previous studies, which have shown…”

“This discrepancy could be due to differences in experimental conditions such as…”

4. Acknowledge Limitations of the Study (optional)

Acknowledging the limitations of your study demonstrates transparency and scientific rigor. It also helps reviewers and readers understand the boundaries of your conclusions.

Common limitations might include:

• Small sample size

• Variability in experimental conditions

• Lack of generalizability to other systems or populations

• Discuss how these limitations might affect the interpretation of your findings without undermining your overall conclusions.

Example phrases:

“One limitation of this study is…”

“While our data are promising, further research is needed to address…”

“This study does not account for…”

5. Propose Future Research Directions

• Building on your findings and their limitations, suggest specific future studies. This demonstrates the broader impact of your work and provides a roadmap for advancing the field.

• Identify gaps in the current research and propose how they could be addressed.

• Suggest follow-up experiments, potential collaborations, or alternative methodologies.

• Highlighting future research directions also shows your awareness of the bigger picture and the next steps in scientific discovery.

Example phrases:

“Further studies could explore…”

“Future research should focus on…”

“These findings pave the way for investigations into…”

1. How to write a literature review (60 min video) Link

You will learn

• What do reviewers look for in a literature review?

• How to conceptualize and write a review?

• Common myths about literature reviews.

2. How to identify research gaps (12 min video) Link

You will learn

• What is the research gap?

• Steps for identifying the research gap.

• Tools for identifying research gap.

3. How to find relevant research papers? (15 min video) Link

You will learn

• How to conduct a basic search?

• Save searches and set up alerts. 

• How do you download and export searches?

4. How to write an abstract (40 min video) Link

You will learn

• Why a good abstract is important?

• What is the ideal length of the abstract?

• What to include in the abstract?

5. How to secure funding? (60 min video) Link

You will learn

• How to write a grant application?

• What do funders look for in grant applications?

• Tips for winning grants.

6. How to use Gen AI in research (53 min video) Link

You will learn

• How has Gen AI impacted research?

• How to use Scopus AI search tool?

• Future of Gen AI in research

7. How to write a cover letter for your manuscript (8 min video) Link

You will learn

• Importance of a good cover letter

• How to write a strong cover letter?

• What to include in the cover letter?

8. How to respond to reviewers' comments? (37 min video) Link

You will learn

• Understanding reviewers’ comments

• How to write a response to each comment?

• How to increase your chances of paper acceptance?