End of Term Review – Fall 2017

What kind of things did us biotechies get into this term? Well…

We had a strong kick off to our 2017 fall term with our annual bbq.  Kits beach, biotech bingo, raffles for the coveted biotech mugs and of course, good food and good company.

biotech annual bbq

Then came our BCIT first and second year get to know each other H-bonding event at Kawawa. Hungry students + all you can eat sushi = at least half of us almost exploding. Was if fun? Definitely.

biotech H-bond

And in the midst of the never-ending mid terms that begin in October and carry us to finals, people were still awesome enough to participate in our Halloween costume contest. Three well-deserved winners were crowned: Ashley Spinelli (Manolya, 1st year), Rob (Jobo, 2nd year) and Hagrid (Rob, faculty), and there were many other creative and funny costumes including Arthur, Salt Bae, and the Joker.

biotech halloween

Finally, to celebrate our survival through finals week and with Christmas just around the corner each class held their own Secret Santa events. We couldn’t have asked for a better way to end off the term.

biotech secret santa

With the year coming to a close, its nice to take a moment and look back at all the fun times we had together. Next year will undoubtedly hold even more times to enjoy in our biotech fam😊.

Crystal Chau

Crystal Chau graduated from the UBC-BCIT Honours in Biotechnology program in 2015. During her time at BCIT, Crystal worked as a research assistant for the BCIT Natural Health and Food Products Research Group. As a part of her co-op at the Murphy Lab in the UBC Department of Microbiology and Immunology, Crystal researched on protein production in S. aureus and co-authored a published paper on heme degradation proteins. In addition to her work experience, Crystal was involved in the UBC Microbiology and Immunology Student Association as Biotechnology Representative and VP Finance. Crystal began working at STEMCELL Technologies as a co-op student in the Department of Research and Development and later was offered a part-time position until she graduated. Post-graduation, Crystal started a new position at STEMCELL Technologies as a research technologist.

How was your transition from BCIT back to UBC in terms of getting involved in extracurricular activities?

Crystal: I had a pretty smooth transition from BCIT back to UBC because I got involved with the Microbiology and Immunology Student Association (MISA). Taking the position of the MISA Biotechnology Representative allowed me to bridge the Biotechnology Degree with the Microbiology and Immunology Faculty. In the following year, I was elected to be the Vice President Finance, where I continued my involvement in extracurricular activities with MISA. I feel like being involved at UBC definitely helped me transition from our small biotechnology classes at BCIT back into the large classes offered at UBC.

How did you pick your courses at UBC? Based on your interest or the industry?

Crystal: I picked my courses at UBC based on my interest because ultimately, if you are not interested in it, you would not be able to fully appreciate what the course has to offer!

How did you balance your part time jobs and school? Was it difficult to work part-time during your time at UBC?

Crystal: Balancing my part-time jobs and school was challenging at times, but I found it very rewarding. Although time can be pretty tight during exam season or when you have major lab reports due, you learn to prioritize and better manage your time. Time management is a crucial skill to have, so I don’t think having a full plate is necessarily a bad thing!

A piece of advice for all of you coming back to UBC: don’t take CHBE and your directed studies in the same term. They are both lab-intensive courses, so it would be difficult to find a part-time job that would work well with the amount of lab time needed for school. Unless you have Hermione’s Time-Turner, these two courses would be much more manageable if you take them in different terms.

What do you think are the deciding factors that led to STEMCELL to hire you? 

Crystal: The Honours in Biotechnology program allowed me to gain many lab techniques and practical problem solving skills that made me a stronger candidate in my job applications. In addition to the extensive lab experience from our program, I also worked part-time in different labs during my studies, which allowed me further practice my technical and interpersonal skills in a work setting. Along with competency in the lab, your personality and work ethic play a large role in the hiring process as well.

How do you like working at STEMCELL? 

Crystal: I really enjoy working at STEMCELL Technologies due to their positive and supportive work environment, which inherently allowed me to explore new lab techniques and grow as an individual. My skillset has significantly diversified because I was able to participate in various projects at STEMCELL Technologies and learn from different experts in the field.

What is something you wished you had done before you graduated?

Crystal: I wished I had networked and connected with more people. Your time in university is the prime time to meet people from all around the world with different backgrounds and experiences; make good use of this opportunity!

In contrast, what is something you’re glad you did before you graduated?

Crystal: I am glad I got involved with an UBC Student Association before I graduated because it was something I had always wanted to do and would not get an opportunity to do it after I graduated. Additionally, in my last year at UBC, my friends and I did Storm the Wall, which was a very memorable experience for us and an item checked off of my bucket list!


Abhijit Parolia

Grad-1After graduating from the program in 2015, Abhijit Parolia currently studies at the University of Michigan as a Ph.D. student in Molecular and Cellular Pathology. During his undergraduate years, he held research student positions at the International Collaboration On Repair Discoveries (ICORD) at Vancouver General Hospital and at BC Cancer Research Centre (BCCRC). At BCCRC, Abhijit researched the role of non-coding genes in prostate cancer, which served as the topic of his Honors dissertation as well as his patent application for use in treatments and diagnostics. His undergraduate research at BCCRC has allowed him to become a published author of seven research papers. As a result of his accomplishments in research, academics, and community involvement, Abhijit completed his undergraduate career as a valedictorian at his UBC graduation.

How was your experience with writing your honours thesis? As a Ph.D. student now, how does working on your honours project compare to your current work?

Taking the Directed Studies course (MICB448) certainly requires more labor and commitment when compared to other courses that you can take to fulfil your Honors requirement in the Biotech program. However, I would argue it is definitely the most rewarding. The key is to find a great laboratory that studies something that really captures your scientific interest.

I opted for the 8 month Directed Studies course and worked in Dr. Yuzhuo Wang’s laboratory at the BC Cancer Research Center studying the pathogenesis of prostate cancer. Although challenging, writing and defending my Honors thesis was a great learning experience. Moreover, it served me very well when interviewing for graduate schools – I actually had my own research to talk about (a great morale booster)! My Honors project involved exploring the role of non-coding RNA genes in the initiation and progression of prostate cancer. This work really fuelled my interest in the field of non-coding cancer biology and still continues to influence the subject of my PhD project. Though still undefined, my PhD project would involve identification of novel long non-coding RNA genes underlying various aggressive characteristics of cancers (like invasion, metastasis etc.), likely via aberrant interactions with epigenetic regulators.

As an undergraduate, did you feel uncertain about what you wanted to do in the future for a career? If so, how did you cope with it?

It is very natural to have doubts in life; and even more so in your undergraduate life. Though I had a rough idea that I wanted to enter graduate school, I had absolutely no clue where to start. And when in such a situation, the key is to reach out to people who may have the answers and can guide you on the right track.

Beyond that, I think the integrated co-op program in our Biotech curriculum is its biggest strength. When I joined the Biotech program, I wanted to learn about stem cell-based organ regeneration. So, I reached out to many professors at UBC who were even remotely working in that field and inquired about any prospects of doing a co-op term in their laboratories. From these efforts, I did end up with my first co-op job in a lab at iCORD studying spinal cord regeneration. This was only to realize that de novo organ regeneration as a concept was still in the stages of infancy and may be wasn’t the right fit for me. Thus, instead of instinctively taking whatever jobs you can get, I would strongly encourage all of you to exploit these work-learn opportunities to identify what truly appeals your scientific self and help to clarify your career-related doubts.

How do you balance your personal life and academic career?

I may not be the best person to answer this question for two reasons: I am not very social and I was an international student at UBC. Meaning, I was miles away from family and had no social obligations making it a lot easier to mostly merge the two parts of my life. I truly enjoyed being submerged in my academic and work life and thus it naturally occupied a major portion of my daily schedule. However, under no circumstances, I would advise a similar work style for others. I believe that the ideal balance between the two slices of life is very subjective and every individual should honestly define it based on their personalities. There is no right or wrong tilt to this balance!

If you had a chance to tell your third-year-Biotech self (ie: 2nd year at BCIT) 1 thing, what would that be? It doesn’t have to be just one.

Not be overly stressed by the fact that you all have to soon find a co-op job. A large majority of you (if not all!) will end up with a job. But what is more essential is to find the right job rather than impulsively accepting anything you get offered. Use these work opportunities to explore disparate areas of research that interest you. Also, DO NOT rely only on the job postings by the Co-op Department. Write directly to the PIs you are interested in working with, in or outside of our university, and attached your resume. Some of them might actually reply and appreciate the independent initiative of you reaching out to them. So be smart in using your co-op work terms.

Do you like what you are studying? How do you keep that passion burning? In other words, is there a course of habitual actions which you take monthly/yearly to remind yourself of why you study Molecular and Cellular Pathology?

I enjoy every bit of what I am studying! And I think this profound interest in your subject is itself of paramount importance in retaining your motivation. The intricate molecular networks underlying cancers always fascinated me from the very beginning. It is bewildering to notice the genetic and phenotypic heterogeneity that exists both within and between tumors and yet, in essence, they are all just diseases of uncontrollably hyper-proliferating cells. In other words, cancers from two different patients can be drastically different in their genetic makeups even if they originate from the same organ. Given the rapid advancements in genetic technologies in the past decade, only now we have the right tools to make sense of this extensive heterogeneity and devise targeted and effective diagnostic and therapeutic strategies. Thus, these are exciting times to be in this field and precisely interrogate how different patterns of molecular aberrations impact the ensuing cancer characteristics. Simply put, studying what you genuinely enjoy is sufficient to ensure your enduring engagement with your research.

What was the most valuable lesson/thing that your years at BCIT have taught you?

Hands down, it has to be all the laboratory techniques I learnt and the hands-on practice I got while at BCIT. Not to speak badly of other programs, but I had some colleagues in their 4th year who had never done tissue culture before. So really pick up those wet lab skills as they will be extremely useful in your future research careers.

Were there any issues transitioning back to UBC from BCIT? Did the 2 year “transfer” to BCIT give you any issues with grad school apps or potential employers?

There were no issues as such in the transition back to UBC. The Biotech program even had a useful seminar to make the process smoother. However, I did face some issues while applying to graduate schools. Since the two institutes issue their own transcripts, it was a bit confusing to explain the joint part of the Biotech program. My graduate schools thought that I had actually transferred back andforth between the two schools which reflects a bit poorly on the candidate. So, I had to attach with all my applications a letter of clarification from the Dean’s Office explaining the entire joint degree arrangement. I did raise this point with the program heads at both BCIT and UBC; and I hope they will resolve this issue for you guys and classes to come – so have a single combined transcript.

What career would you like to pursue after your Ph.D.?

I am still actively thinking about this question. So far, I wish to continue on the academic track and hopefully start a laboratory of my own. However, I am interested in pursuing translational aspects of molecular pathology and thus would want to develop and commercialize new diagnostic and therapeutic strategies that can be adopted in the clinical management of cancers.

How did you decide where to pursue your Ph.D?

It is very easy to get caught up in the rankings of various universities while making this decision. However, I would strongly encourage that you make graduate school choices based on your topic(s)-of-interest and where the laboratories focused in that research area are housed. I applied to only four graduate schools, and picked University of Michigan because it has one of the most successful research groups exploring the non-coding aspects of cancer biology under the leadership of Dr. Arul Chinnaiyan. In fact, in your graduate application itself, it’ll ask you to list several laboratories in the university that match your area-of-interest and you would consider joining. It is generally believed that when doing your PhD, more than the institution, it is the reputation and credibility of your mentor that counts. So I would recommend, having some idea of the subject(s) that interests you, shortlist the leading laboratories in that field and then apply to the corresponding graduate schools. It is a major commitment that will take at least 5-6 years of your life, so do put in some honest upfront thought in to what subject and in which laboratory you would want to pursue your PhD.

How much control over your project did you get at the BCCRC?

When I initially joined the lab, I worked with a post-doc helping out on his project. I certainly had a good rapport with him and thus was able to learn tremendously and make some suggestions in course of that project. However, when I started working on my independently ideated project, I had complete intellectual autonomy and control on the project with prompt guidance when needed. In fact, I even had some co-op students assisting me in completing the project. However, these arrangements really depend on your PI and direct supervisor, and how they appraise your scientific capabilities. I was fortunate in having joined such an open and collaborative lab with an incredibly encouraging and supportive PI. I fear some labs can turn out to be completely the opposite and there things and the work atmosphere would be very different regardless of your capabilities.

Did you take initiative in your projects to write and get published, or were your supervisors very inclusive?

Undoubtedly, you have to meaningfully and intellectually contribute towards the project to be included as a co-author on the final manuscript. However, even if you meet that criterion, it depends on how fair and inclusive are your project leader and the PI. I would personally suggest not to bother about the authorship and sincerely work towards advancing the assigned project. Bring your own ideas to the table, suggest future experiments and highlight aspects of the project that are lacking. All of this will certainly earn you an authorship on the final manuscript in most of the cases.

Are you hiring any co-op students this year or next year?

Haha… great question! I will be applying for independent funding once I am a candidate (half way through my second year). If I do get the funds, I will certainly be hiring co-op students. Though, the university encourages to hire from the undergrads within the university, I will keep the Biotech program in mind and inquire if any of you might be interested to travel to the US and work with the ‘boring’ me.

Do you miss Vancouver?

I cannot tell you how much I miss Vancouver. It is undoubtedly the most beautiful city comprising of such diverse, polite and loving groups of people. And trust me, snow is much worse than rain so please stop complaining about it. Besides, I miss the delicious food and wide selection of cuisines that are readily available in Vancouver. So all you lucky folks, you better enjoy while you are there!

What is a nutritious yet delicious breakfast to start off the day?

Hmm… though I would prefer to conduct an extensive study using primates to unbiasedly assess the various breakfast diets, due to paucity of time and resources I would say its egg and toast with a cup of tea/coffee. And, at times, a muffin or doughnut doesn’t hurt or add to the adipose storages of your body.

Who is your favourite Biotech instructor?

I guess this is the only question you will not get a direct answer to. But seriously, all the instructors are there to help you learn and train you to be inquisitive about science. Thus, going beyond picking favorites, you’ll benefit the most by instead adapting to every instructor’s style-of-teaching and ask questions if there are doubts. In the end, it is up to you to make the most of every minute to spend at BCIT and UBC.

I wish you all the very best in your future endeavors and feel free to reach out to me if I can be of any help. Thank you for all these questions that I have tried to answer very honestly. I leave you with a quote from a famous microbiologist, Louis Pasteur. Work hard and good luck!

“Let me tell you the secret that has led me to my goal. My strength lies solely in my tenacity.”  – by Louis Pasteur

Stacks on Stacks…Of Pipette Boxes

Whenever there's free time in the lab, students fill pipette boxes to the brim to keep busy, and to help the instructors.

Racking tips isn’t a chore or a game; it’s serious business.

First of all, you should never rack tips by yourself. Always have someone to compete with, because honestly, it’s pretty boring otherwise. Now that you’re not alone, this is where the fun begins.

To win, you obviously need some sort of strategy or a trick up your sleeves. The wheels in your mind are turning fast, almost rolling in the deep like Adele. You think: “Should I systematically rack the tips row by row, or do I just dump it on the box and hope it falls into the holes?” But then there’s the problem of reaching into the plastic bag to acquire your pipette tips. Should you use one hand to grab the tip from the bag, and the other to rack it? Or would it be better to place a handful on the pipette box lid? Or you ask yourself, “Would I look pro if I rack tips while without looking at the holes?” All this time, you’re also trying to kick your colleague’s butt (figuratively of course).

Asking these questions when approaching challenges is crucial in problem solving and building personal integrity. When confronting a task, you learn to identify key obstacles, think creatively, plan a course of action, and evaluate the consequences. Quality control is just as, if not more important than conquering the problem. Do you have expectations for yourself to meet, even for tasks as menial as racking pipette tips?

If you follow this life hack, you will end up with stacks of cash. Just kidding, maybe a glorious pyramid of pipette boxes, ready to be autoclaved.

(What do you think is the best strategy to filling up pipette boxes?)

My Dye Knows What You Did in the Dark

Fun game to play at parties: cry about finals.

If the RNA samples have high salt content, voltage will be affected, resulting in weird running patterns.

Last biochem lab this week! All the RNA samples from the past few decades were collected and loaded onto the gel made last week along with tRNA ladder. In addition, UV spectrometry was used to measure five types of nucleotides (adenine, cytosine, guanine, thymine, and uracil) under neutral, acidic, and basic conditions.

Super old centrifuge. Be careful when handling this instrument because you can open the lid even when it's spinning!

Last analytical chemistry lab as well! With the lesson learned from last week, we centrifuged the samples so that filtration can be faster (but we ended up doing more samples, so I don’t know how much time was really saved here)

Remember that Tn-5 cell lines are adherent but not really! Since they get easily dislodged, when removing or adding solutions, aim at one point of the well at all time and do it slow!

Not last microbi lab just yet. This week, we titred the baculovirus in various concentrations with the uninfected Tn-5 cells. Afterwards, we had a two-day incubation with methyl cellulose overlay to restrict viral infection to adjacent cells only.

Because aminoallyluridine triphosphate (aa-UTP) was incorporated during reverse transcription for the microarray cDNA, these nucleotides can then be linked to fluorescent dye.

Last (wet) lab for genetics! After incorporating dyes (Cy-5 for IPTG-induced and Cy-3 for un-induced) into the samples, the two samples were combined with GFP and added to the microarray slide. The slide was then incubated overnight and washed the next day. We will be analyzing the data next week!

Tip of the Week: Into Darkness
To maintain the fluorescence intensity of the dyes, everything needs to be performed in the dark! That means lights off, blinds on, lock the doors, tight. Doing laboratory tasks in the dark is on a whole new level, so watch out!

Sweet Dreams are Made of Chocolate

Currently making up for low grades with high calories

When you are facing the UV spectrometer, note that the light travels horizontally in front of you. Therefore, the two clear sides of a cuvette face left and right.

Three labs happened in biochemistry this week: bromination, DNA melting point measurement, and RNA gel preparation. Bromination involved synthesis of 5-bromouracil from potassium bromide and uracil with the entire reaction monitored via UV spectroscopy. Melting point of salmon sperm DNA was determined via qPCR and SYBR green dye. RNA gel was casted (with several failed attempts) for next week’s lab.

Ground solid samples has a higher surface area, making it easier to melt and become homogeneous for analysis

The rest of the analytical chemistry labs revolved around our group presetations. For our team, we investigated the levels of caffiene and theobromine in chocolate. As Kevin warned, sample preparation took us a million years to get it right. Also, remember to do duplicates!

Tn-5 cell line is derived from cabbage looper (Trichoplusia ni) and can be cultured as adherent or suspension cells.

Virology labs began this week! To start off the trilogy of green fluorescent production (GFP) production and multiplicity of infection (MOI) optimization, Tn-5 insect cell line was cultured and infected with recombinant baculoviruses.

Dilutions are important in qPCR to ensure that threshold cycles between the two samples are distinguishable in their exponential phases

In genetics, the cDNA from reverse transcription was further treated to remove RNA and proteins. The qPCR samples were put into PCR tube strips and ready for real-time PCR while the microarray samples were air-dried and saved for labelling next week.

Tip of the Week: Bigger is Better
In chemistry, majority of the obstacle comes from sample preparation, especially if filtration is involved. Since a larger surface area increases efficiency of filtration, you want the Büchner funnels big!

Ready for School?

Houston, we have a problem: I am not ready for school!

Last term's chicken IgY sample was under forced aging study to test for stability over time. Remember to note down where they are in process system!

In biochemistry, IgY samples from last term and previously biotinylated IgY samples were assayed with sandwich ELISA involving biotin-streptavidin binding and the substrate p-nitrophenyl phospahte (pNPP). The goal was to detemine optimal reagent concentration that would allow sensitive IgY detection while inhibiting biotinylated IgY from binding. But nothing worked, so I don’t know. Google it, I guess.

A dissolved oxygen meter (top left), a pH meter (top right), an Orion specific ion meter that is attached to fluoride and nitrate ion selective electrode (bottom left), and some pretty colourful solutions (bottom right)

In analytical chemistry, two types of electrochemical measurement methods were investigated: potentiometry and voltammetry. Total ionic strength adjustment buffer (TISAB) was also used to remove interference such as protons, metals, and other ions.

The small bench-top centrifuge can fit the PCR tube strips if you switch the inside thingamajig.

In genetics, RNA isolated before spring break was analyzed on a RNase-free gel. After making sure that there is no low molecular weight smearing or high molecular genomic DNA, reverse transcription was carried out for real-time PCR and microarray next week.

Top of the Week: Pop It! Lock It! Drop It!
When using the water bath, note that floating tube racks often have small protrusions that hold the microfuge tube caps securely. This way, as temperature rises, the increasing pressure won’t literally raise the roof!

Party in the R.N.A.

Spring break is finally here!

Denaturing solution needs 2-mercaptoethanol, but you don't add it to the stock solution. Instead, pour some denaturing solution out and add 2-mercaptoethanol separately to get the desired concentration.

Biochem lab continued from last week’s samples with lithium chloride then centrifugation. The supernatant and pellet were collected for the gel electrophoresis lab. Quantity and quality of RNA was also measured with Nanodrop. Ideally, pure RNA has a A260/A280 ratio of 2.

Gas chromatography mass spectrometry (GC-MS) is a much more convenient pairing than liquid chromatography mass spectrometry (LC-MS) because the eluent is already in conditions and pressure suitable for mass spectrometry.

In revisited analytical chemistry lab, GC-MS was revisited, but this time, we analyzed the data on our own! Remember that you drag to zoom the top total ion chromatogram with the LEFT mouse button, double-click the zoomed total ion chromatogram at the peak with the RIGHT mouse button, then double-click the bottom spectrum to show Libra match with the RIGHT mouse button. This week, we analyzed various hydrocarbons, drug-screening standards, and fruit flavours.

Another (better) way to isolate RNA uses provided kits. Shown here are the Qiagen RNeasy Mini Kits.

New genetics labs, new us! After the long RT1Bα-fragment lab that lasted 1.5 term, we started anew with real-time PCR (qPCR) and microarrays! This week, RNA was isolated from IPTG-stimulated and unstimulated cultures with the Qiagen RNeasy Mini Kits. Provided kits may seem easy peasy shmeasy, but remember to add the right solutions! Be sure to distinguish Ambion DNase-free buffer, Ambion Turbo DNase, and DNase inactivation reagent. They all have “DNase” in it!

Tip of the Week: Bleach It Like It’s Hot
When dealing with biohazardous materials, remember to pour off the supernatant to diluted bleach before dumping it down the sink! Reusable glassware usually goes to the to-be-autoclaved tray, and the rest go to the biohazardous bags and boxes!

We Gonna Let It Burn, Burn, Burn, Burn

This is you pilot speaking: I am 100% done dealing with exams and 200% ready for spring break.

Because tissue is frozen in liquid nitrogen. Make sure you have proper eye protection when you grind the tissue. Frozen pieces may fly up up into the sky!

Teflon homogenizer was used to fully homogenize the cells.

In biochem, we started the RNA isolation lab for rat liver. The tissue was ground and homogenized in denaturing solution. RNA was then isolated from DNA in the supernatant after adding sodum acetate, water-saturated phenol, and chloroform/isoamyl alcohol. Finally, RNA was precipitated out by adding isopropanol. The entire process needs to be carefully executed without RNase contamination (use clean new plastic stuff instead of glassware)! Also, remember to add 2-mercaptoethanol to your denaturing solution before lab starts (guess which class forgot to add it?)

In atomic absorption spectroscopy, atoms in the samples have their electrons excited due to the flame. When the electrons drop back down to a lower energy level, a specific wavelength of light is emitted, corresponding to a characteristic colour.

In analytical chemistry, we used two types of absorption spectroscopy (AAS) — flame (FAAS) and graphite furnace (GFAAS) — to measure the amount of metals (Pb for GFAAS, Cu and Zn for flame-AAS) in water samples. This was a very fast lab with not much preparation needed. The machine even dilutes samples automatically to fit in the standard curve range!

A cell strainer can be used to create single cell suspension from ground tissue. Shown here is a mouse spleen.

Fow cytometry uses foward scatter (indicating size and refractive index), side scatter (indicating internal complexity or granularity), and fluorescence detection to differentiate cells tagged by different fluorochrome-coupled antibodies.

In microbiology, we prepared the cells for flow cytometry. First, mouse spleen single cell suspension was made through cell straining and red blood cell lysis. The cells were then tagged with fluorochrome-coupled antibodies: FITC-coupled anti-CD4 antibody targeting CD4 T cells, APC-coupled anti-CD8 antiboy targetting CD8 T cells, and PE-coupled anti-CD19 antibody targeting B cells. The second half of the lab took place in the Life Science Institute at UBC (yay! field trip!) where we used its flow cytometer to analyze the distribution of CD4 T cells, CD8 T cells, and B cells in our sample.

Tip of the Week: Water Samples
Because we are analyzing metals in water, remember to bring your own water samples to the lab! If you forgot about it, some of the possible sources in campus include washroom faucet, water fountain, eyewash station, and your own water bottle!


Assay a Little Prayer (Reprise)

Don’t forget to rate, comment, and cry because midterms be killin’ everybody out there!

This week's succinate dehydrogenase results were similar to those from last week, but there were two layers with the pink dye located in the top ethylacetate layer.

Because last week’s modified protocol did not work as well as we’d hoped, this week in biochem, we redid the succinate dehydrogenase assay with the original protocol. The reaction was stopped with trichloroacetic acid instead of ethanol. The reduced dye was then extracted by adding ethylacetate.

LC-MS/MS utilizes both compound separation of high-performance liquid chromatography (HPLC) and ion fragmentation of tandem mass spectrometry (MS/MS)

The analytical chem lab this week combined our knowledge on liquid chromatography and mass spectroscopy to not only separate compounds but also perform qualitative or quantitative analyses on them! After optimizing the fragmentor voltage, caffeine and theobromine were quantified in a tea sample. Insulin was also used to illustrate that larger fragment ions actually have lower mass/charge (m/z) value thus able to be detected by the MS machine.

Because the bags are cut then sealed and peeled every time you switch reagents, remember to leave some room (but not too much!) when you first make them. After adding the last (secondary) antibodies, it is better to have the smallest possible bag to maximize exposure of the membrane to the antibodies. Also, remember to squeeze all the bubbles out!

For enhanced chemiluminescence (ECL) detection, prepare some solution B (peroxide solution) ahead of time. When the membrane is all set, add equal amount of light-sensitive solution A (luminol enhancer solution) to the tube and pour it all onto the membrane!

The second microbiology lab wrapped up this week! Both T (anti-phosphotyrosine) and E (anti-phospho-ERK 1/2) membranes were blocked with 5% BSA/TBS. The T and E membranes were then exposed to primary antibodies (mouse anti-phosphotyrosine and rabbit anti-phospho-ERK 1/2, respectively). After several washes, secondary antibodies were added (goat anti-mouse and goat anti-rabbit, respectively). After more washes (last one with no Tween-20), enhanced chemiluminescent (ECL) detection was used to visualize the bands.

Tip of the Week: Water Bath and Labelling
If you know that the tubes will be subject to water batch, do NOT label them with tapes because they will fall off! It is better to label with permanent marker before starting the experiment as it is hard to write on wet surfaces.