Saturday, 30 January 2016

MICB 306

MICB 306 (with Dr. Danielle Krebs, Dr. Francois Jean)
  • Course Taken: MWF 12-1pm (September 2015 - December 2015)
  • Format: Dr. Krebs lectures half the term, then Dr. Jean lectures the end. Dr. Krebs' section primarily focuses on general life cycles of viruses using certain viruses as case studies. Dr. Jean talks specifically about three viruses (Hep C virus, Dengue virus, Ebola virus) and goes into depth about how they hijack the host and what treatments are available.  
  • Grading Scheme: 2 Midterms (20%, 25%), Final (45%), Online quizzes (10%)
  • TextbookVirology: Principles and Applications (J. Carter and V. Saunders), 2nd edition
  • Class Average: 81% 
  • Personal ExperienceA very straight forward course with a decent amount of memorization, but nothing outrageous. The weekly online quizzes are easy, and mainly try to keep the students caught up with the material. It is essentially an extension of what was covered in MICB 202. The midterms and final are also extremely fair. Great course if you are interested in viruses. While Dr. Krebs is not as strong lecturer as Dr. Kion, she is able to still communicate the material effectively. Dr. Jean is much more knowledgable about viruses; however, his notes are very difficult to follow. Most likely, you will need to make your own notes. This is a required pre-req for MICB 406/407 (virology seminar courses). 

MICB 430

MICB 430 (with Dr. Kronstad, Dr. Hallam, Dr. Jefferies)

  • Course Taken: Thursday 1:30 - 5pm (rarely went to 5pm)
  • Format: Each professor "taught" for 1/3 of the course. Students present every other week about an assigned primary literature article in partners. One student will present the paper while the second student will present the implications & critique the paper. Thus, each student will present twice for each professor--once as a reviewer, once as a critic.
  • Grading Scheme: Unsure, but I assume each professor's section is worth 1/3 of the grade. 
  • Textbook: none
  • Class Average: 92%
  • Personal Experience: This course may be a lot of work depending what papers you get assigned, and how comfortable you are at reading primary literature. Often the papers are out of your field, so you would need to read one review to understand the significance of the paper. If you want weekly journal club on various papers, and work on your presentation skills this course is for you. While it may be a bit of work every other week, the benefit is that there is no midterm or final and most students do extremely well in the course. The class size is about 10 students since typically only Honours students take the course. 
Answers to readers' questions: 
  • Can non-honours people take it? Yes, non-honours people often take it. My year we had 12 people in the course, and only 5 people were honours. Talk to Dr. Kion to register.
  • Do you recommend it for people not familiar with primary literature, can you become better at reading papers/ presentations? This is a great course to get better at reading papers since it just forces you to read way more than you would otherwise read. When I did the course, we had to present fortnightly; however, this may have changed since then. This course does not “teach” you how to read papers, but it does make you improve. You tend to present the papers with a partner, so you and your partner can bounce ideas/ struggle through the paper together. If you get really stuck, you can always go to the prof. They tend to be super helpful, and easily approachable. One thing to remember is when you present, only present the figures which depict the main point(s) of the paper and not every single figure.

Thursday, 28 January 2016

MICB 402 and MICB 412

MICB 402 (with Dr. Kenneth Harder, Dr. Georgia Perona-Wright)

  • Course Taken: T/Th 9:30am (September 2015 - December 2015)
  • Format: Dr. Harder teaches the first half, Dr. PW teaches the second half. Dr. Harder will mainly focus on innate immunity and ask you to read 6 primary literature papers on the topic (except for one cancer immunology paper)
  • Grading Scheme: Dr. Harder's Section (25% in-class midterm, 25% take home), Dr. PW's Section (35% take home, 25% final)
  • Textbook: none
  • Class Average: 76% 
  • Personal Experience: Given the class size is quite large, MICB 402 tries to disguise itself like a seminar course; however, at the end of the day, it remains a traditional lecturing course. Dr. Harder's section primarily focuses on experimental design & techniques. Although he suggests to pre-read the papers prior to class, he ends up going over each paper pretty slowly each class. Depending on how many questions people ask in class, he might run out of time before the midterm and you will be expected to read & understand the remaining papers. If you are comfortable reading primary literature, this course is not overly difficult. For Dr. Harder's midterm + take home, write FAST! Both tests are very long (not overly difficult but tedious), so plan accordingly. This year is Dr. PW's first & last year teaching MICB 402 (she accepted a position in Scotland), and previously it was Dr. Jefferies teaching the latter portion of the course. For Dr. PW, she typically used Tuesday to go over the background/ significance of the paper and Thursday to go over the experiments. Rather than focusing on experimental design, she emphasized immunological concepts & details. The papers she chose were focused primarily on the adaptive immune system especially Th2 response to helminth infections/ co-infections. Again, majority of her papers were not overly difficult but demonstrated key themes in advanced immunology. Her exam + take home was much more reasonable in terms of length and difficulty.
  • Note: Dr. Perona-Wright has accepted a faculty position back in Scotland and will not be teaching at UBC next year. :( 
Answers from readers' questions:

  • Was tutorial mandatory? What is tutorial like? Tutorial was not mandatory for us in the sense that attendance was not taken. I think we were highly encouraged to go, but most of us did not. Tutorial was going over methodology used in the papers we talked about in the course, and how to interpret data. However, I think the course may have changed since I took it with Dr. Harder & Dr. Perona-Wright in 2015/2016.


MICB 412 (with Dr. Pauline Johnson, Dr. Kenneth Harder)


  • Course Taken: T/Th 9:30am (January 2016 - April 2016)
  • Format: Dr. Johnson teaches the first half, Dr. Harder teaches the second half. Dr. Johnson focuses on the balance between our microbiota and maintaining homeostasis. Dr. Harder will mainly focus on cancer immunology. This course is a seminar-based course which means students are assigned a topic and are required to present ~15 minutes, 10 minutes questions on that topic. 
  • Grading Scheme: Dr. Johnson's Section (35% class presentation, 10% participation, 5% written report), Dr. Harder's Section (35% presentation, 10% participation, 5% written report)

  • Textbook: none
  • Class Average: 88%
  • Personal ExperienceThis course used to be 18 - 20 students; however, this year the course had around 25 students. Given the time constraints, students will present one 15 - 20 minutes presentation for each professor + 10 minutes of questions. Dr. Johnson prefers presentations that focus on content (based on reviews) while Dr. Harder prefers presentations that thoroughly explain one or two primary papers' methods + results. Besides presenting, you are expected to participate during the rest of the classes by asking questions. Finally, near the end of each half, you are expected to write a ~3 page summary of the topic, synthesizing all the talks. 
  • Advice: If you are uncomfortable with presenting, I highly suggest practicing beforehand to ensure your presentation falls within the time limit. In addition, if you are unsure what areas to focus on, you can ask the professor. 

Tuesday, 5 January 2016

MICB 447

MICB 447 (with Dr. Dave Oliver)

  • Course Taken: Tuesday 8am, Tuesday Lab (September 2015 - December 2015) You end up going into the lab regardless of lab day though.
  • Format: Working in groups of 3/4 for the entire term where you design and carry out an original research project. There are weekly lecture and team meeting. At the end of the course, you will publish a primarily research article in JEMI or if your paper is really good, JEMI+. 
  • Grading Scheme: Multiple schemes depending which gives you higher grade (depends on primarily lab notebook, midterm, project proposal, lab report)
  • Textbook: Optional Lab Book $10 (also posted online for free)
  • Class Average: 86%
  • Personal Experience: You learn a lot from this course from experimental design, lab techniques, to working in a team. Pick a group you work well with not necessarily your friends. Even the simplest project will often take triple the amount of time expected, so perhaps consider a less ambitious project. Do not trust any reagent you did not personally make yourself! Remember that this is a course, and mistakes will happen but that is how everyone learns. If possible, do not take directed studies with this lab course since this course will take A LOT of outside time. A rough estimate will be 16 hours per week for each team, and possibly more at the end of term. When deciding a project, it might be easier if your project did not ask a question where the experiment either worked or did not. 
Answers from readers' questions: 
  • Choose a good group to work with. I think groups work best if people have different lab experiences and strengths (ie. organization skills, writing, experimental techniques, troubleshooting). Also, ensure that everyone has time to come into the lab outside of the course time.
  • When you choose/ design a project, choose a project where at no point it hinges on a “yes/ no” answer. For example, what are the effects of caffeine vs does caffeine do this? Cause when it comes to writing up, it is easier to talk about the broader question than a yes/no question. If you can work on multiple parts of the project at the same time, it will save you time. For example, optimizing both protocol A and B at the same time before combining the two for your proper experiment. You can see the projects people did in previous years here: https://www.microbiology.ubc.ca/undergraduate/jemi
  • Read as much as possible before you dive into your project. The more pre-planning you do, the less troubleshooting you’ll probably run into.  

Thursday, 10 September 2015

How do I ____ ?

How do I send from my UBC alumni account if I chose to forward my email? 

For Gmail, go to "Settings" --> "Accounts & Imports" --> "Send mail as" --> Add another email address you own.
  • Email: UBC alumni account 
  • Server: smtp.gmail.com 
  • Port: 465 (choose SSL) 
  • Username: yourgmail@gmail.com 
  • Password: (your gmail password)

Sunday, 16 August 2015

Tolerance: the Future of Transplantation

“Live life, pass it on” reads an advertisement designed to increase potential organ donors. With more than 1,000 transplant waiting list patients dying per year in the UK, organ availability and transplant success rates are key to serve a constantly increasing demand for organ transplants.
Transplant centres across the world require more donors.
Photo from Geralt
Though transplantation was first explored in 1902, it was not until 1954 that the first successful human kidney transplant operation was performed. 50 years down the road, transplantation is considered the best possible treatment for most individuals with organ failure. Patients with severe kidney failure often prefer a single transplant procedure to a four-hour dialysis treatment three times a week. In addition, over a period of ten years, each successful kidney transplant patient saves the NHS (UK’s National Health Services) £24,100 ($49,355 CDN) per year compared to dialysis treatment. 
A successful kidney transplant saves $49,355 CDN per year compared to dialysis
However, transplantation has numerous challenges including organ rejection, infections, and cost. Organ rejection is when the body’s immune system recognizes the donated organ as “foreign” and attacks it. If the donated organ is continuously attacked, the organ becomes non-functional. There are three categories of rejection based on when the rejection occurs: hyperacute (within first few hours after transplant), acute (within first year after transplant), and chronic (a year or more after transplant). These organ rejection categories are believed to be initiated by different aspects of the immune system such as the recipient’s antibodies (proteins that recognize foreign objects) or white blood cells.

Organ rejection is one of the biggest risks of transplantation
Photo from http://spacesick.blogspot.ca/2009/07/organ-rejection-shirt.html
In order to minimize the potential for rejection and increase transplant success, multiple protective measures are taken. First, the donor must meet certain physical requirements. However, as deceased donors are becoming older, more obese, and less likely to have suffered trauma-related death (ie. died from organ failure), fewer organs are considered suitable for donation. In addition, the patient and the donor must be a closely matched by three immune components; the patient cannot have antibodies that recognize the donor’s cells, and the patient’s blood and human leukocyte antigen (HLA) type must be compatible with the donor. As a result, even though organs are in high demand, 12% of suitable organs are not transplanted due to a lack of compatible patients. Despite these protective measures, the recipient’s immune system may still recognize the donated organ as foreign and reject it. As a result, we have to resort to non-specific immunosuppressants. This poses a problem as this also suppresses other essential immune system functions, and causes the patient to be extremely susceptible to infections.

Immunosuppressants have improved acute organ rejection rates, but not chronic rejection rates
Photo from Stevepb
Thanks to recent improvements in immunosuppressive drugs, immunosuppressants have decreased acute organ rejection rates, but chronic rejection still remains a significant problem. For example, 93% - 97% of donated adult kidneys are still functioning well a year after surgery, but this drops to below 75% after ten years.  Not only do immunosuppressants become less effective at decreasing the risk of organ rejection over time, but chronic use of immunosuppressants has many challenges including patients’ reluctance to continue taking drugs, risk of infection, and long-term monetary cost (around £5,000 per year for each patient).
93%-97% of patients survive one year following kidney transplantation
~75% of patients survive ten years following kidney transplantation
Rather than improving current immunosuppressive drugs that repress the entire immune system, a major goal of transplantation research is to tailor the immune response to accept the newly transplanted organ by persuading the immune system to tolerate donor organs while still retaining its ability to respond to other disease-causing agents. The ability to induce tolerance would counteract the risk of acute and chronic rejection while eliminating the need for lifelong immunosuppressive therapy.
Tolerance is a major goal of transplantation research
Photo from DasWortgewand
A potential avenue for inducing tolerance is through “mixed chimerism”, where the host and donor bone-marrow-derived elements co-exist in the recipient. Mixed chimerism is effective in transplantation because donor blood cells can migrate to the host thymus and “teach” new T cells, a type of white blood cell, to ignore the donated organ without using immunosuppressants. This ensures the new T cells generated in the host are tolerant of elements from both the host and donor. An additional benefit of mixed chimerism is that severe depletion of patient’s bone marrow cells is not required unlike traditional transplantation techniques. This is extremely advantageous because in retaining some of their own own bone marrow cells, the recipient still has aspects of a working immune system as a backup system in case the donor organ is rejected.

Mixed chimerism could be an effective because it "teaches" new white blood cells called T cells.
Photo from Geralt
One major barrier that we still have to overcome is graft-vs-host disease (GVHD). GVHD is when the donor’s T cells from the donor’s transplant migrate into the recipient’s tissues and attack the “foreign” recipient’s body by recognizing HLA, which is contrary to organ rejection that is initiated by the host’s immune system. It is typically associated with stem cell or bone marrow transplant, but can also occur in some organ transplants. GVHD can lead to acute or chronic and include symptoms such as skin rash, muscle weakness, and selective damage to the liver and gastrointestinal tract. Since transplants often occur without perfectly matching HLA, balancing inducing tolerance via mixed chimerism while avoiding GVHD remains a challenge.

Lung transplant rejection with H&E stain
In general, most tolerance-inducing methods have been based on blocking an essential aspect of white blood cell activation known as co-stimulation. Co-stimulation ensures white blood cells can become fully functional and replicate properly. Blocking this co-stimulation essentially dampens the immune system and allows mixed chimerism to occur. In animals, antibodies that target a particular co-stimulatory pathway have been shown to allow mixed chimerism through reducing the immune inflammatory response. However, translating this process into humans has been challenging due to complications with blood clotting.
Xenotransplantation (using animal organs for transplantation) could become a possibility with mixed chimerism tolerance induction.
Photo from Netalloy 

Overall, major leaps have been made in making mixed chimerism tolerance induction safer and less toxic, so we can expand its use in transplantation and beyond. In fact, if we are able to induce tolerance, the possibility of xenotransplantation—using animal organs for transplantation—would become a possibility. Despite the fact that closely-related species are  better matched immunologically, the US Department of Health and Human Services declared a moratorium on primate-to-human transplantation in 1999 due to the potential risk of virus transmission. Today, xenotransplantation is focused on pigs because of their organ size and physiologic similarity to humans, and favourable breeding characteristics. Early research in xenotransplantation focused on monkeys due to their similarity with humans. While pigs can be slightly genetically modified to be more “human-like”, tolerance induction remains a critical keystone to future xenotransplantation applications and the key to solving our organ shortage dilemma.

References: 

Tuesday, 2 June 2015

Popular Elective Courses for First Years


What are electives? 
  • Electives are simply courses that are not explicitly stated in your degree program. They can be courses related to your field or courses in a different faculty. Some students prefer taking "easy" electives while some students choose harder ones. 
What are popular electives for Science students (with little/no pre-reqs)? Useful = red

Arts
  • CLST 301: The Technical Terms of Medicine and Biological Science
  • ECON 101/102: Micro & Macro Economics
  • ENGL 110: Approaches to Literature
  • ENGL 112: Strategies for University Writing
  • MUSC 103: Intro to Music Theory
  • MUSC 119: Intro to Music Technology
  • MUSC 326A: Music Appreciation
  • PHIL 120: Introduction to Critical Thinking (cannot take if you have 90+ credits)
  • PHIL 125: Introduction to Scientific Reasoning
  • PHIL 220: Symbolic Logic I
  • PHIL 433A: Bio-Medical Ethics
  • PHIL 435A: Environmental Ethics
  • PHIL 460A: Philosophy of Science
  • PHIL 464: Philosophy of Biology
  • PSYC 101/102: Intro to Biological & Cognitive Psych + Developmental, Social, Personality, and Clinical Psychology
Science
  • BIOL 300: Fundamentals of Biostatistics
  • CPSC 110: Computation, Programs, and Programming
  • EOSC 110: The Solid Earth: A Dynamic Planet
  • EOSC 114: The Catastrophic Earth: Natural Disasters
  • STAT 200: Elementary Statistics for Applications