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

Tuesday 26 May 2015

Survival Guide for Incoming UBC Students

Congratulations! You are accepted to UBC. Now what...

Home for the next 4+ years

(textbooks, choosing residence, course registration, popular UBC unofficial sites, preparing this summer)

Popular First Year Electives

How do I ___? 
As I receive questions, I will do my best to post answers here

Summer Survival Guide (#1-5) for Incoming UBC Students



  1. DO NOT buy your textbooks until the first day of class, and definitely not from UBC Bookstore
    •  Even if you are extremely eager, ask a friend who has previously taken the course if it is worth buying the textbook. Often on the first day of class the professor will emphasis whether or not the textbook will be essential for the course. Be sure to ask if previous textbook editions will be compatible with the course. 
    • For cheap places to buy textbooks, Discount Textbooks is on campus and has good selection or there are multiple Facebook groups where students buy/sell their textbooks. 
  2. I want to live in residence, but should I choose Place Vanier, Totem Park or Walter Gage? 
    • Location:

    • Vanier and Totem are traditionally for first years. There are residence advisors (RA) on each floor and they work hard to create a great community within the residence. Since Vanier and Totem are typically full of first years, it may be difficult to study in your dorm sometimes despite quiet hours especially if you are in the upper years. However, if you want to meet new people your own age, these are definitely residence to choose. It can a bit noisy especially if you live on the first floor of the residence, but typically during finals it is pretty quiet.
    • Walter Gage is typically for second years and up since it requires students to cook their own meals (or eat out a lot). Students have their own room, but share a bathroom & kitchen with 5 other roommates. The noise level depends on your roommates, but most people are quite understanding. It is harder to meet people outside your "quad". 
    • Proximity to Classes: 
    • Unless you are in Sauder (light blue) or Pharmacy (fuschia), be prepared for some walking around
    • First year chemistry, biology, physics are typically in the blue rectangle area (regardless of faculty, so yes including APSC); however, math and English are often in MATH or BUCH
    • A lot of arts courses are taught at BUCH (purple rectangle), but there are other arts buildings including geography, asian studies, and psychology. 
    • Bus Stop: 
      • The main bus loop (yellow star) is quite far away from Totem or Vanier; however, there are community shuttles that go to the other UBC residences. 
      • If you are coming home late or have a lot of things to carry (ie. groceries), make sure you bring a friend if you live at Totem or Vanier!
        • If you do not feel safe on campus, call AMS Safewalk (free walking or shuttle around campus until 2am daily). 
    • Rooms + Pricing (details available)
      • Vanier: Double ($5062), Single ($5800 or $6223 depending on building)
        • Plus mandatory meal plan (minimum: $4,125.50)
      • Totem: Double ($5062), Single ($5800 to $6962*) 
        • Plus mandatory meal plan (minimum: $4,125.50)
        • * with private bathroom
      • Walter Gage: 6-Bedroom Suite ($6592 from September - April)
        • No mandatory meal plan
  1. What courses should I register for? 
  2. What are popular UBC-related unofficial sites? 
  3. How can I prepare for university this summer? 
    • I don't recommend reading ahead or any "academic" work because university is quite different than high school in terms of what exams are like and what professors expect. It is hard to prepare for something you don't understand.  
    • Be prepared to get out of your comfort zone! Meet new people! Enjoy your last free summer because chances are you will be working full-time for the rest of your summers until you graduate.

Monday 25 May 2015

MICB 322 & MICB 323

MICB 322 (with Jennifer Sibley)

  • Course Taken: M 1pm, W Lab (September, 2014 - December, 2014)
  • Format: The course is pretty relaxed, and Ms. Sibley is more concerned about everyone understanding concepts than getting "perfect" results. There are not a lot of lab reports except for the couple at the end. Be prepared to have to go in on one or two days after your lab day for simple things like moving your bacteria to the fridge, or counting colonies. 
  • Grading Scheme:  Midterm, Lab Reports, Final
  • Textbook: Lab Book from MISA (around $30)
  • Class Average: 80%
  • Personal Experience: The TAs and Ms. Sibley are great at making sure no one feels stressed. The final was surprisingly harder than expected, but other than that the course is quite low-stress. Labs typically do not take the entire 4 hour period especially if you work quickly. Make sure you have 30 min the day before and after your lab period to set up / finish your experiments (ie. inoculate bacteria, count colonies) or beg a friend. For MICB 322, the lab work is done in pairs (the person sitting next to you) and the lab reports are done alone. However, you share the data so you typically end up working together.

MICB 323 (with Ehleen Hinze)

  • Course Taken: M 1pm, T Lab (January, 2015 - April, 2015)
  • Format: The course involves lots of partner work especially for lab reports, so I suggest pick a partner beforehand to ensure you will be able to work well together. There is a weekly lecture beforehand with in-class assignment (for participation). Ms. Hinze is a bit pickier than Ms. Sibley, but overall the class is still relatively relaxed compared to the 1st and 2nd year CHEM labs. 
  • Grading Scheme:  Midterm (10%), Lab Reports (43%), Lab Technique (5%), Data Quality (2%), Lab Book (3%), In-class participation (2%), Final (35%)
  • TextbookLab Book from MISA (around $30)
  • Class Average: 80%
  • Personal Experience: Marking tends to be a bit inconsistent and it really depends on how nice your TA is. There are slightly different expectations between MICB 322 & MICB 323 especially in terms of figure captions. The final was also harder than expected, and the amount of work for lab reports is slightly greater than MICB 322. 

Thursday 21 May 2015

MICB 325

MICB 325 (with Dr. Thomas Beatty)

  • Course Taken: MWF 10am (January, 2015 - April, 2015)
  • Format: Flipped-classroom style where readings are posted beforehand and lectures are devoted to iClickers. The first half of the course is devoted to essentially understanding plasmid maps, cross-overs and blue-white screening. The second half of the course is a month and a half long case study on how one could determine the signalling pathway of a microbe (Cartenoid synthesis in R. capsulatus). Unfortunately, while the course content is extremely interesting, a lot of people did not feel prepared enough going into the exam because we only saw one case study and did not get a lot of practice. There is homework due twice a week online, but we did not get feedback even at the end of the course. 
  • Grading Scheme:  35% Midterm, 50% Final (Note: if you miss the midterm even with an excuse, your final will be 85%), 2% Homework Participation, 7% Homework Accuracy, 6% iClicker Participation 90%+ and with up to 2% bonus if a certain percentage is correct
  • Textbook: None
  • Class Average: 78%
  • Personal Experience: Overall, while the content is interesting I found the lecture style not conductive to learning. Dr. Beatty tends to get confused with his own iClicker questions or his questions are poorly worded, so in a 50 minute lecture you will only do about 4 questions. The way midterm marks are distributed was not ideal where 4 long-winded true and false questions were worth 40% of the midterm while a short answer was only worth 5%. However, this was fixed for our final despite the final being longer than expected. The final was difficult especially if students have not been exposed to cloning schemes before since most of the questions were "explain this unexpected result". 
  • Advice: Practice problems are your friend especially the plasmid map questions. 

MICB 418

MICB 418 (with Dr. John Smit)

  • Course Taken: T/Th 11am (January, 2015 - April, 2015)
  • Format: Traditional lectures where he does not use slides or post notes, and he simply talks and students have to take notes. Dr. Smit does record all his lectures in case you miss a day or you missed a setence, and provide packages of all the diagrams he describes. Tutorials (optional) are used to review material and the TA is great. The exams are short answer, definitions, and T/F. People tend to find the T/F tricky because it is based on extremely detailed points, and if you get it wrong you get -1. Each T/F tends to be worth 3 points each. 
  • Grading Scheme: Option 1 (Final-70%, Midterm 1-30%) or Option 2 (Final-50%, Midterm 1-25%, Midterm 2-25%) if you decide to hand in Midterm 2, your mark will count regardless if you did poorly or not
  • Textbook: None
  • Class Average: 73% 
  • Personal ExperienceOverall, I found this course very interesting, but it was also the most content dense course I have taken so far. The topics covered include classic biotechnology (beer, wine, bread making with sampling!) and modern biotechnology (antibiotics, drugs, antibody production, R&D methods, patent and clinical trial process). Be prepared to spend a lot of time with this material to do well. Dr. Smit is a great lecturer and he structures each of his lectures very well and simple to follow especially when you take notes. I would recommend taking this course, but only if you have time to study/ keep up with the material otherwise consider taking it as a Credit/D/Fail course. 
  • AdviceDefinitely an interesting course, but it is extremely content heavy and lots of memorizing. Do not take this course if you are looking for an easy elective. 

CPSC 301

CPSC 301 (with Dr. Ian Mitchell)

  • Course Taken: T/Th 9:30am (January, 2015 - April, 2014)
  • Format: Lectures are relatively slow-paced, and only goes through "tricky" aspects rather than teaching how to code. All his lecture slides are posted on his website. The course first uses Scratch (https://scratch.mit.edu/) and then uses Python 3 + BioPython. Lectures typically are used to only clarify concepts and not teach, and Dr. Mitchell expects students to read the textbook to get the basic concepts. There are a lot of iClicker and in-class group worksheets for participation marks. The labs are done in pairs, and are the most helpful part of the course. Often it will take the entire lab section to finish the lab, and some people need to finish the "after-lab" section later. The lab worksheet + the programs you write will be due the next Wednesday online, and the TAs typically mark and return the labs 1.5-2 weeks later. The TAs are extremely helpful. 
  • Grading Scheme: Midterm (20%), Final (40%), Lab Exam (Must pass to pass course, 0%), Labs (20%), Class Participation (10%), Best Score among midterm, final, labs (10%)
  • Textbook: Practical Programming: An Introduction to Computer Science Using Python 3 (Paul Gries, Jennifer Campbell, Jason Montojo)
  • Class Average: 82% 
  • Personal ExperienceOverall, I found this course relatively easy and fulfilled its purpose of introducing students to basic programming. Scratch is very intuitive to use and is a good introduction to students who have never programmed before. The course uses Python 3 with Anaconda distribution (which already has many packages including BioPython and PIL). In the lab, the goal is to get the same output as the problem set. However, in the midterms & exams, it is expected that you understand what each step does and what the computer will end up remembering. The in-class worksheets are a good reflection on what to expect on exams. Dr. Mitchell can be difficult to understand when he lectures especially if you are not up to date on the readings. 
  • Advice: If deciding between CPSC 110 and CPSC 301, it depends on how much more CPSC you want to do. CPSC 301 primarily focuses on Python which is extremely useful and immediately applicable to many research fields. The course is a great introduction to programming for students with a biology background. CPSC 110 uses Dr. Racket which can be a tedious program and not directly applicable to use outside CPSC courses; however, it teaches good programming habits. You will need CPSC 110 to take more advanced computer science courses. 

MICB 301 & MICB 302

MICB 301 (with Dr. William Mohn)

  • Course Taken: MWF 10am (September, 2014 - December, 2014)
  • Format: Lectures with topical readings + group assignments, and one bioinformatics project. He has a lot of iClicker questions throughout the term for participation marks (no answers posted). Dr. Mohn writes his own notes and the class uses them as the "textbook". Make sure you stay on top of the readings, otherwise the iClicker questions are completely meaningless. He allows for a lot of discussion in the class, and occasionally people ask relatively off-topic questions which is annoying. The readings can sometimes be quite long, and the topical readings + group assignments are relatively easy once you figure out what they are looking for. The exams (midterm, final) are cumulative and primarily memorization based. The bioinformatics assignment is essentially a walk-through guide in how to align various DNA sequences to determine what microbes are present from that sample, and the computation is very very simple. 
  • Textbook: None 
  • Class Average: 76%
  • Personal Experience: Dr. Mohn's course is interesting because he tries to facilitate discussion. However, he is often quite vague on what he is looking for especially in the bioinformatics assignment where we had to write a 500-word "abstract". Make sure you memorize the course notes and answer tests with exactly the same wording. He does not hold regular office hours, so if you need help email him to book an appointment. 
  • Advice: If you do not have to take this course for your degree, I do not recommend taking this course as an easy elective. 

MICB 302 (with Dr. Tracey Kion and Dr. Pauline Johnson)

  • Course Taken: T/Th 9:30am (September, 2014 - December, 2014)
  • Format: Typical lecture-style course with no homework, but lots of in-class iClickers. The course is split up into 2 sections. Dr. Kion covers the basic "facts" about B cells, T cells such as class-switching while Dr. Johnson emphasizes how various aspects of the immune system gets activated. The exams are typically short-answers and very memorization heavy despite there being case-studies. Often it is best to memorize the wording/ phrases from the professors' notes to ensure the TAs will mark it correct. There is quite a bit of content, and especially Dr. Johnson's section it can get a bit confusing. There are weekly tutorials, and the TAs are typically quite helpful with clarifying pathways.  
  • Grading Scheme: Dr. Kion's Section (2 Midterms, 25% each), Dr. Johnson's Final 50%
  • Textbook: The Immune System (Parham)
  • Class Average: 77%
  • Personal Experience: Dr. Kion as usual is extremely knowledgable and a great lecturer. Her notes cover exactly what you need to know, and the textbook is not needed if you understand her lectures. Dr. Johnson is definitely more experienced with research than lecturing, and her slides often reflect the vast amount of information in the field rather than what she expects students to know/ understand. Given the nature of her section where various pathways and how the immune system "talks" to each other, there is a lot of jumping around and it can get confusing. It is often helpful to go to tutorial and do the worksheet to ensure you keep on top of the course. 
  • Advice: This is a very dense and intricate course if you are curious about the details of immunology. Drawing out pathways always help. Pre-reading may not be helpful, but reviewing afterwards definitely is. 

BIOC 302

BIOC 302 (with Dr. Justin Lee, Dr. Robert Maurus, Guest Lecturer: Dr. Adeleke Aguda)

  • Course Taken: MWF 8am (January, 2015 - April, 2015)
  • Format: Dr. Lee lectures about central metabolism (carbohydrates, amino acids) during the first half of the course, and Dr. Maurus lectures about DNA during the second half of the course. Dr. Lee posts extremely detailed notes while Dr. Maurus' only posts a basic set that needs to be annotated during the lecture. The midterm covers only Dr. Lee's material and the final only covers Dr. Maurus' material. There are tutorials each week that go through weekly problem sets (not for marks) which are helpful to ensure you are staying on track. 
  • Grading Scheme: Midterm which is essentially a Final (50%), Non-cumulative Final (50%) 
  • TextbookPrincipals of Biochemistry 5E or 6E by Lehninger (not required, but most people still own this textbook from BIOL 201). Personally, I found the online notes/ Power Points sufficient to study from. 
  • Class Average: 70% 
  • Personal ExperienceOverall, I found this course to be quite dense especially the first half, the second half is easier since it also covers experimental techniques  which is more conceptual based learning. If you are interested in learning about how various lipids, carbohydrates, amino acids, nucleotide bases are made and broken down then this course is for you. Dr. Lee is an amazing lecturer with a great sense of humour (perhaps slightly too happy for my 8am brain), he talks at a good speed with great enunciation. He takes great care to develop clear course notes that use analogies and acronyms to help students understand and remember. I would definitely recommend any course taught by Dr. Lee. Dr. Maurus is difficult to understand during lecture especially if you sit at the back of a large lecture hall. While his material is easier to grasp, his handwriting and less detailed notes make this half of the course equally challenging. The tutorials are well run by the TAs and the worksheets are helpful if you have been keeping up with the class. Good way to study for the midterm/ final is by doing the tutorial questions and drawing molecules/ pathways. Definitely recommend studying A LOT for this course.