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1C a t a l y s t
September 2016
September 2016 l septembre 2016
Volume 7: Issue 1
Student Science Journal - Journal étudiant scientifique
Humans Evolved From Walking Fish?Yes, You Read That Right!							PAGE 10
101 WEEK SPECIALS INSIDE!
Food Science:
Ice Cream
PAGE 8
C a t a l y s t
September 20162
THE TEAM | L’ÉQUIPE
Editor-in-Chief
Tanya Yeuchyk
Production Manager
Christine Wang
Rédacteur-en-chef
Setti Belhouari
Website Manager
Michael Leung
Authors | Auteurs
Setti Belhouari
Winston Cheung
Zerin Khan
Alek Tirpan
Yen Tran
Émilie Vaillancourt
Tanya Yeuchyk
Editors | Rédacteurs
Shobhitha Balasubramaniam
Sanmeet Chahal
Alex Chen
Alya Hammami
Connie You
Illustrations and Photographs
Itzel Lopez-Carreon
Sasha Newar
Katherine Power
Ashley Tenn
Translators | Traducteurs
Sanmeet Chahal
Setti Belhouari
Narimane Ait Hamou
Shamei Benoit Leblanc
Mihaela Tudorache
September Contents | Contenu de septembre
Articles
6
Ethical Considerations with the CRISPR/Cas9 system
8
Food Science: Ice Cream
10
Humans Evolved From Walking Fish? Yes, You Read That Right!
12
Novel Aptamer-based Therapeutic System against Cancer
14
Zika: le nouveau fléau
16
Science de la bouffe : la crème glacée
18
Les humains ont-ils évolué de poissons qui marchent ? Oui,
vous avez bien lu !
Entertainment
3
Comic Corner
11
The Accident
15
Funky Fungi
101 Week Specials
4
10 Tips for Freshman Students
5
Tips for Incoming Science Students
13
Enriching Your Undergrad Experience
3C a t a l y s t
September 2016
By: Itzel Lopez-Carreon, 2nd year CHM
By: Sasha Newar, 4th year BIO
Nous cherchons des traducteurs
et des auteurs francophones. Ça
vous intéresse? Contactez le
rédacteur-en-chef:
redacteur.uocatalyst@gmail.com
C a t a l y s t
September 20164
10TipsforFreshmenStudents
The life of a science student is definitely a challenging one. However, there is one thing that can be more challenging: be-
ing in your first year as a science student. You will be in a larger establishment among thousands of students who, just like
you, are lonesome, homesick, and stressed about their future. Do not panic! I have been there and survived. In addition to
being a second-year biochemistry student (with a minor in math), I am also your Rédacteur-en-chef. I am always asked
how I juggle so much work. In this excerpt, I hope to share with you the secrets of being a well-rounded and productive
student, especially during your first year of studies.
Though this list may seem general, it has helped me succeed my first year at University. I am sure it will help you too.
May you have a healthy, successful first year.
By Rédacteur-en-chef: Setti Belhouari, 2nd year BCH
1
Sleep well: Ensure that you have
sufficient sleep. Sleeping-in
during the weekend does not
make up for your all-nighters during
the week. For more on the importance
of sleep, be sure to read our November
2015 issue.
2
Prioritize: Put your health at the
top of your priorities list. Realize
that your assignments, laborato-
ry reports, midterms, and exams are
weighted differently. Put more time
doing practice questions to prepare for
your exams and midterms. Laboratory
reports may seem like huge tasks, but
they are not worth much of your final
mark.
3
Contact your professor: At
the beginning of the semester,
ask your professor whether you
should put a greater focus on your
textbook or your lecture notes. Office
hours are your opportunity to clarify
concepts with your professor. Get to
know your professor better; he/she
may become your research supervisor!
4
Wash your hands: Wash your
hands to prevent yourself from
catching the common cold during
midterm season. Take care of yourself.
If you are feeling sick, visit a health
care professional who will treat you
and write you a note justifying your
absence.
5
Extracurricular: Join an extra-
curricular activity. Being in at
least one extracurricular activity
will teach you how to accomplish
more with your limited time. This
will also help you learn important life
skills that are not covered during your
lectures. Many extracurricular activi-
ties organized in the University, offer
wonderful rewards such as scholar-
ships, trips abroad, gift cards, etc…
Still, be careful not to overburden
yourself with extracurricular activi-
ties. Good grades are also important
because they, too, can be equivalent to
an Admission Scholarship.
6
Procrastination: To avoid pro-
crastination, prepare daily goals.
Tell yourself, that you will finish
your organic chemistry lab report
within 3 hours. If you do, reward
yourself with an outing with friends, a
delicious restaurant dinner, or, simply,
an extra hour of sleep.
7
Confidence: Do not shake while
studying for your midterm.
Believe that everything you are
being taught is within your reach.
Never demean yourself. Never com-
pare yourself to the so-called geniuses
in your math class. Believe in hard
work.
8
Study groups: Study groups may
be important for students to learn
from one another. Nonetheless,
give yourself time to study by your-
self. Study groups have a tendency
of becoming grueling stress groups,
especially when they are held the night
before a midterm.
9
Last-minute: Before a midterm
or an exam, do not stand amongst
the mass of students who are
frantically going through their study
notes. Try to find a quiet place to relax
and stretch.
10
Enjoy: Do not attend your
lectures and your extracur-
ricular activities like they are
some sort of drudgery or punishment.
Think this way: if you pay for you
education, you’d better enjoy it.
5C a t a l y s t
September 2016
Welcome to uOttawa Science! Take a moment
to pat yourself on the back - you’ve made it to
the next big chapter of your life. Not only that,
but you have picked the most awesome facul-
ty in all of uOttawa! To help you start your
journey, I offer you an assembled collection of
wisdom for surviving first year...
Once you get your syllabi, take a calendar and
write down the dates of all your midterms. Trust
me, they come quicker than you think, and this
method will help you be better prepared. It also
helps to know in advance if you have more than
one in the same day (so that you can start cry-
ing early).
There are many groups on Facebook where you
can buy used textbooks from other students.
This is a great alternative to getting them brand
new, and can save you lots of money!
Go to your professor’s office hours when you
have a question. You’ll get the most qualified
explanation, and some profs will even give extra
hints when they see a student putting in the
effort. It also doesn’t hurt to meet your profs
one-on-one and develop a working relationship
with them.
Go to lab tutorials! They are absolutely worth
the extra class time. The TAs explain important
concepts behind the labs you have done, and
how to structure your lab report. You’ll find
them to be a major help!
You may want to consider renting a locker in
Marion from the SSA, especially if you live off
campus. It’s not expensive to rent, and it’s a very
convenient place to store your lab coat and
books during the year. You can even share one
with a friend and split the cost.
Attend your DGDs! It’s tempting to skip a
non-mandatory class, but they are very help-
ful for your understanding of course material.
Remember that the prof hand-picks what is
discussed, and the TA often goes through mid-
term-type questions.
Sometimes, your lab grade includes a TA eval-
uation. Be sure to talk to your lab TA about
their specific expectations - this might help you
achieve a better grade.
Actually do work and get caught up during
reading week. Going on vacation might improve
your mood, but probably not your GPA.
Don’t rush to buy your textbooks. Some profs
will highly recommend one, but then never use
it. Wait until you actually need a textbook to
buy it, and you might find yourself saving hun-
dreds of dollars.
Try getting involved with research at the uni-
versity! There are some great scholarship oppor-
tunities throughout your undergrad like UROP
and NSERC that will look great on your resume
- and contribute to your bank account.
Join the Catalyst, uOttawa’s student science jour-
nal! We’re looking for all sorts of contributors,
giving you the chance to get involved on cam-
pus, meet new people, and gain some experience
in science communications.
Join any other on-campus club or organization
that catches your interest! Complete lists are
available on the SSA and SFUO websites.
Most of all, make sure to enjoy your first year.
Yes, there are stressful times ahead, but it’s so
important to take the time to make memories
with your friends and explore the city as a uni-
versity student. Take it seriously, but take breaks
too.
Tips for Incoming Science Students
Good Luck!
By Editor-in-chief: Tanya Yeuchyk, 2nd year BIM
Ilustrated by: Meaghan De Jesus, 3rd year BIM
C a t a l y s t
September 20166
CRISPR/Cas9 is a genetic technology that allows for
researchers to target and alter genes, specifically ones
that cause disease and disorders.
CRISPR/Cas9, or clustered regularly interspaced short
palindromic repeats/CRISPR associated protein 9,
comprises the adaptive immune system of bacteria
against foreign DNA. It is used as a genome-editing
tool through the integration of a viral genome into the
CRISPR sequence to form CRISPR RNA. The latter can
be employed as a guide to target and cleave a particular
location within a genome using the Cas9 endonucle-
ase. In a recent study, Junjiu Huang and his team used
CRISPR/Cas9 to try and eradicate the human β-globu-
lin gene (HBB) from a human embryo (Otienna, 2015).
The mutation of this gene causes β-thalassaemia, a
dangerous disorder of the blood characterized by low
hemoglobin (β-thalassemia, 2016). Huang’s goal was to
use this system on other genetic diseases such as cystic
fibrosis in order to eliminate them from the embryonic
genome. The attempt was only partially successful and
faced several scientific and ethical challenges which led
to it being abandoned in the preliminary stages (Otien-
na, 2015). One major concern was the resulting numer-
ous, unpredicted off-target mutations, which can lead
to cell death or modification.
There are vast number of applications for the CRISPR/
Cas9 technology. We must, however, consider the as-
sociated benefits and disadvantages. A major ethical
issue arises in the event of this technology being used
on germ cells, as well as a significant loss of diversity
in a population. For example, CRISPR/Cas9 has al-
ready been used to modify rat coat pigmentation. The
problem lies in the fact that the same method could po-
tentially be used to modify human skin pigmentation
(Otienna, 2015). Such actions would not only reduce
genetic diversity, but lead to an important ethical di-
lemma.
A possible problematic application of gene editing is
parents’ ability to choose their child’s genetic features.
Since parents often wish for their child to be intelligent,
beautiful, and athletic, the frequency of genes associ-
ated with these characteristics would rapidly increase
in the population. This would lead, again, to a marked
decrease in genetic diversity. Modifications could even
lead to development of new genes if parents demand
for their children to have purple eyes or blue hair, for
example. It is arguable that children should have the
right to be born naturally and not be genetically mod-
ified without their consent. Many scientists firmly
believe that such genetic technologies should only be
used therapeutically and be kept under strict control.
In conclusion, CRISPR/Cas9 is a very powerful ge-
nome-editing tool with a promising future for disease
eradication. However, it should be highly regulated in
order to prevent unethical uses like on human embry-
os. Although funding for human embryonic genome
editing has been banned in the United States, it is
still permitted in other countries. If the technology is
pursued in these areas, what will be the future conse-
quences on the human genome?
Figure 1. CRISPR RNA binding to genomic DNA leads to recruit-
ment of the Cas9 endonuclease to the binding site. Cas9 can subse-
quently cleave the genomic DNA at highly specific location
Ethical considerations with the CRISPR/Cas9 system
By: Émilie Vaillancourt, 4th year BPS
References:
Otieno, M. (2015). CRISPR-Cas9 Human Genome Editing: Challenges, Ethical Concerns and Implications. Journal of Clinical Research
& Bioethics 6(6), 253-255.
Beta-thalassemia. (2016). U.S. National Library of Medicine: Genetics Home Reference. Retrieved from https://ghr.nlm.nih.gov/condi-
tion/beta-thalassemia
Photo Source:
Chemical and Engineering News. 2014. CRISPR/Cas9 Gene Editing Systems. American Chemical Society. 92: 37.
“
CRISPR/Cas9 is a very powerful ge-
nome-editing tool with a promising
future for disease eradication.
7C a t a l y s t
September 2016
DAT-GMAT-GRE-LSAT-MCAT-OAT-PCAT
FREE PRACTICE TESTS
ONLINE FEATURE EVENTS
LIVE & ONLINE COURSES
MCAT Classes Starting September
13th
and 27th
. Enroll now at
kaptest.com/MCAT.
www.kaptest.com
1-800-KAP-TEST
bailey.poredos@kaplan.com
C a t a l y s t
September 20168
FOOD SCIENCE: Ice Cream
Winston Cheung 4th year BIM; Yen Tran 4th year BCH
Photographs by: Katherine Power, 2nd year BIO
N
othing hits the spot like good old ice
cream on a hot summer day. The kid
in you might think that ice cream is
made from cold, sweet, and creamy fluff. Yet
what is ice cream really made of? Well, that
kid is not too far off. Cream, sugar, and air are
the three key ingredients that give rise to ice
cream’s taste and texture.
	 Inspired by Ottawa’s Ice Cream Festival,
this issue’s Food Science will educate you on
this tasty frozen treat called ice cream.
What is ice cream?
	 What exactly is ice cream? Would you
classify ice cream as a solid, liquid, or gas?
	 Ice cream is actually an interesting mix-
ture of all three phases- there is ice, cream, and
air. As a colloid (a substance with very small in-
soluble particles suspended), ice cream contains
ice crystals and air bubbles suspended in the ice
cream serum. The ice cream serum, which dis-
solves sugars, salt, and proteins, acts as the ma-
trix which holds the whole ice cream structure
together.
What makes ice cream?
	 What exactly is in ice cream? What do
we put in ice cream to make it so savoury and
sweet?
	 The cream and milk in the ice cream pro-
vide three vital components: fat, non-fat sol-
ids, such as milk proteins, and water. The sugar
sweetens the ice cream. Other flavourings and
additives, like egg yolk and vanilla, can be dab-
bled in to improve the taste.
Fats
Fat in ice cream mostly comes from milk fat,
which contributes to its richness by increasing
the creamy texture. This is because triglycerides
in dairy fat melt at the right temperature range
for us to eat. If the fats were to melt at a high-
er temperature, the ice cream would feel waxy
rather than creamy.
	 Fat in ice cream usually organizes in drop-
lets, but at times can form larger fat clusters or
even partial clusters. Fat helps to stabilize the ice
cream foam and slows down the melting rate of
ice cream, while also helping to deliver flavours
that might otherwise be insoluble in water. Due
to the fat content, we are able to indulge in the
soothing and savoury melt of ice cream.
Proteins
Proteins found in the milk can improve the tex-
ture of the ice cream via the emulsification of the
fat and the water. Emulsification helps keep the
fat droplets small to stabilise the air that will dif-
fuse into our ice cream. Milk proteins surround
each fat droplet and form a membrane, prevent-
ing fat droplets from forming fat cluster that are
too large.
Water
Water forms ice crystals inside the ice cream and
influences the structure. The crystals should be
miniscule in size to prevent the ice cream from
feeling grainy. Hard ice creams that are smooth
9C a t a l y s t
September 2016
and melt in your mouth have ice crystals that are
around 35-45µm in size. Soft ice creams have a
lower ice content. Most of the water transforms
into ice after the ice cream hardens.
	 Wait, why is the water not all ice if water
freezes at 0˚C? Perhaps this phenomenon can be
explained by the next ingredient which affects the
ice cream in more ways than just taste.
Sugar
Sugar is added to enhance the ice cream’s taste,
giving ice cream its iconic sweetness that we crave,
and furthermore affecting its structure. Much
like how salt ions can lower the freezing point
of snow in the winter, sugar molecules can lower
the freezing point of ice cream. This is known as
freezing point depression, where adding solutes
can decrease the freezing point of solvents.
	 It is important to be aware that adding sug-
ar in moderate amounts is important. If there is
too little sugar, the freezing point will not be low-
ered enough and you will end up with a hard ice
cube. Too much sugar, you have ice cream gloop
as the melting point would be too high.
Air
Air is whipped into the ice cream as the final in-
gredient to give ice cream its light texture. Each
little air bubble is 20-25µm. To further fluff up
the ice cream, more air is added, whereas richer
ice cream has less air content. The ice cream is
now flavoured and textured.
How do we make ice cream?
	 Hopefully good notes of the ice cream’s
composition were taken, as we now move onto
ice cream making.
	 The manufacturing process for ice cream is
made up of the following steps. See if you can spot
the similarities between these ice cream machines
and our yogurt factory (Read the November 2015
issue!). The manufacturing process of these prod-
ucts is similar and involves:
- preparing a liquid mix,
- whipping and freezing this mix dynamical-
ly, into a soft, semi-frozen slurry,
- adding flavouring ingredients,
- packaging or shaping,
- and further freezing (hardening) of the
product under static conditions.
Ottawa Tips:
	 Visit the Food and Agriculture Museum
to further investigate the ice cream making pro-
cess. Other processed foods, from cheese to jam
to ham, are also on exhibition for your enrich-
ment. There are so many museums to explore for
the scientists, studious or curious, who study in
the National Capital Region.
To see the French translations of our articles,
visit our website at
uocatalyst.wordpress.com/
***
Do you have personal research you want
to share? Send it to The Catalyst!
Submit your articles to
editor.uocatalyst@gmail.com
and see your name in print!
C a t a l y s t
September 201610
W
hat an odd statement, you might
think. How could humans come from
fish? Better yet, how could fish possi-
bly walk?
Well, in Dr. Emily Standen’s lab, right here at U
of O, a primitive, air-breathing species of fish called
Polypterus senegalus is being raised on land! The lab
is testing how adaptive these fish are to novel ter-
restrial environments. Earlier work by Standen et al.
(2014) raised Polypterus on land for 8 months and
the results were stunning: they showed substantial
improvements in their walking abilities on land. It was
seen that a terrestrial environment compared to an
aquatic one caused changes in the fish’s morphology
and triggered skeletal changes which helped them in
locomotion.
These results illustrated how, around 400 million
years ago, some fish used their regular fins to walk
when transitioning from water to land (Standen et al.
2014). Remarkably, the anatomical changes observed
in the Polypterus seem to mirror what is seen in the
fossil record. This gives us insight into how fossil fish-
es with similar morphologies may have taken their
first steps onto land.
Taxonomically, Polypterus are considered to be
the most basal of the ray-finned fishes and are the
most closely related to the common fish ancestor that
led to the evolution of land animals called tetrapods.
(Standen et al.2014). Polypterus are long and possess
lungs and big bony scales. At the front of their body,
they have large pectoral fins used for routine swim-
ming and walking on land. Unverified reports also
suggest Polypterus voluntarily walk between ponds as
the waters dry up (Pennisi, 2014). In this way, they
are very similar to the fossil fishes that paleontologists
think may have been the first fish to explore land.
Dr. Standen showed that land-raised fish walked
more effectively by lifting their heads slightly high-
er from the ground, holding their fins closer to their
body as well as slipping less than fish that were raised
in water (Standen et al. 2014). The terrestrial fish
also showed changes to their fin anatomy that pro-
vided more stability and mobility, both crucial factors
when moving about on land. These changes are the
result of plasticity, the ability of an animal to show
anatomical, behavioural, biochemical or physiological
changes (Standen et al. 2014).
The findings provide evidence for developmental
plasticity, which could have given our earliest tetra-
pod ancestors the ability to transition onto land. Over
a very (very) long period of time, adapting to life on
land may have accelerated evolutionary transforma-
tion from fins used for swimming into limbs used for
walking (Baker, 2014). It was speculated that these
changes would later be genetically fixed by natural
selection (Standen et al. 2014).
Many of the anatomical changes observed in
Polypterus reflect the fossil record of land-transition-
ing fish from roughly the same time period. Thus, Dr.
Standen’s team was able to hypothesize that, if ana-
tomically similar, the fossil fish could also have similar
behavioural characteristics when they first walked us-
ing their fins on land.
So, as strange as it sounds, 400 million year old
fish may have evolved into our very distant ancestors
on land!
Humans Evolved From Walking Fish?
Yes, You Read That Right!
By Alek Tirpan, 3rd Year BIM
11C a t a l y s t
September 2016
My Involvement with the Standen Lab
I have been involved with Dr. Standen’s lab since
last year. I was fascinated by the research she is lead-
ing and what it could signify for the field of evolutionary
biomechanics. I first started by creating 3-D models of
the gill arches of Polypterus from their micro CT scans
to visually represent anatomical differences between
the terrestrial and aquatic types. I then moved on to a
project on testing vision in Polypterus. Dr. Standen and
I were interested in understanding how terrestriality
affects vision in this normally aquatic fish.
This summer, I worked in the lab on an exper-
imental design to investigate the optokinetic reflex
in Polypterus. The project will consist of running the
Polypterus through optokinetic reflex tests to examine
if different environmental adaptations cause changes
to their visual acuity. We also hope to gain insight into
the advantages and disadvantages this would have
brought from an evolutionary standpoint.
The project underway is very exciting, and I hope
to share more results in the months to come.
References:
Baker, N. (2014, August 27). How fish can learn to walk. Retrieved August 04, 2016, from http://www.nature.com/news/how-fish-can-
learn-to-walk-1.15778
Pennisi, E. (2014, August 27). Fish raised on land give clues to how early animals left the seas. Retrieved August 04, 2016, from http://
www.sciencemag.org/news/2014/08/fish-raised-land-give-clues-how-early-animals-left-seas
Standen, E. M., Du, T. Y., & Larsson, H. C. (2014, August 27). Developmental plasticity and the origin of tetrapods. Nature, 513(7516),
54-58. doi:10.1038/nature13708
Image header source:
https://www.reddit.com/r/evolution/comments/3dmgbk/human_evolution_timeline_picture/?st=irxkxoic&sh=cf853468
2nd year BIO
Follow her on:
Facebook: @kpowerart
Instagram: @kpowerart
Image source: Dr. Emily Standen
THE ACCIDENT
BY KATHERINE POWER
C a t a l y s t
September 201612
Prostate cancer caused 27,540 deaths in the United
States in 2015 alone, and is one of the most common causes
of death due to cancer in men (Siegel et al, 2015). Since
tumors tend to be complex and heterogeneous, current
therapies which employ antibodies or small kinase inhib-
itors are able to only selectively inhibit a single signaling
pathway or molecule (Liu et al, 2016). Luckily, in 2016, a
team of researchers led by Liu and colleagues from Augus-
ta University engineered a novel strategy using aptamers to
suppress prostate cancer by targeting multiple oncogenic
signaling pathways concurrently.
Aptamers are oligonucleotides composed of short,
synthetic single-stranded DNA or RNA (ssDNA/ssRNA),
which can form unique secondary or tertiary structures.
They use structural recognition to bind to and interact spe-
cifically with target molecules (Ni et al, 2011). Aptamers
were coined from the Latin word aptus, meaning “to fit”,
since they bind to their targets with such a high affinity
and specificity, like a key fitting into a lock (Ellington and
Szostak, 1990). In fact, aptamers can be developed to bind
to a variety of targets, ranging from large molecules, such
as nucleic acid structures and proteins, to small molecules
like antibiotics and amino acids (Pestourie et al, 2005).
Since aptamers can be chemically synthesized and modi-
fied according to their desired applications and targets (Ni
et al, 2011), they are named “chemical antibodies” (Sun et
al, 2016). In comparison to antibodies, aptamers are much
more thermally stable with a longer shelf life; unlike an-
tibodies, they can be repeatedly denatured and renatured
(Jayasena, 1999). Most importantly, the non-immunoge-
nicity of aptamers make them ideal alternatives to antibod-
ies for in vivo applications (Ni et al, 2011).
So, how have the researchers from Augusta Univer-
sity employed aptamers to suppress prostate cancer? They
developed a novel chimera in which two small interfering
RNAs (siRNAs) specific to survivin and epidermal growth
factor receptor (EGFR) are fused between two aptamers
(Liu et al, 2016). The aptamers on both ends of the chimera
can bind specifically to prostate-specific membrane anti-
gen (PSMA), which is a protein expressed on the surface
of prostate cancer cells (Liu et al, 2016). Essentially, the
aptamers on either end of the chimera act like “two arms”
that grip PSMA in order to deliver the two siRNAs to the
prostate cancer cell for internalization. Once internalized,
the two siRNAs can inhibit EGFR and survivin. siRNAs
silence genes by binding to the messenger RNA (mRNA)
of specific genes and degrading them, which ensures that
there is no transcription. Hence, the gene will not be ex-
pressed.
“
Prostate cancer caused 27,540 deaths in the United
States in 2015 alone, and is one of the most com-
mon causes of death due to cancer in men.
Overexpression of EGFR signaling pathway and
survivin signaling pathway increases metastasis and can-
cer cell proliferation (De Luca et al, 2008; Altieri, 2013).
Since these two signaling pathways intersect at multiple
networks, targeting both simultaneously can lead to a more
global pathway inhibition for cancer cell growth (Liu et al,
2016). In fact, tumors which are resistant to EGFR inhibi-
tors can switch to the survivin pathway for recurrence and
survival (Altieri, 2008). Since these two proteins are inde-
pendently required by cancer cells for proliferation, block-
ing their production will be detrimental to the survival of
cancer cells.
Research conducted by Liu and colleagues in 2016
has indicated that the novel chimera suppresses the ex-
pression of survivin and EGFR by inducing apoptosis of
prostate cancer cells and inhibits the growth of tumor cells
in mouse models. Their models emulated middle and late
stages of prostate cancer, which are the most common stag-
es found in American males when they are diagnosed with
Novel Aptamer-based Therapeutic System against Cancer
By: Zerin Khan, 5th year Biotech
13C a t a l y s t
September 2016
prostate cancer (Medical College of Georgia at Augusta
University, 2016). Since many cancer promoters do not re-
side exclusively on the surface of cancer cells, but rather
can hide inside where drugs are unable to reach them, siR-
NAs can target these “undruggable” targets (Medical Col-
lege of Georgia, 2016). Thus, the researchers have opened
the avenue for designing combinational therapy and treat-
ments to suppress cancer growth. For clinical applications,
this research has indicated that the toxicity and immuno-
genicity need to be further examined in higher species of
animal models (Liu et al, 2016).
Aptamers can be used for a variety of medical ap-
plications, ranging from molecular recognition probes to
their roles as therapeutic agents. If aptamer research inter-
ests you, then you should consider the research conducted
at the Bioanalytical and Molecular Interaction laboratory
under Dr. Maxim Berezovski here at the University of Ot-
tawa. Dr. Berezovski’s lab encompasses many aspects of
aptamer research, including developing aptamers against
viruses and cells to create sensors and bioassays, as well
as using them to discover new surface biomarkers for live
cancer cells.
References:
Altieri, D. C. (2013). Targeting survivin in cancer. Cancer Lett, 332(2),
225–228.
Altieri, D. C. (2008). Opinion-Survivin, cancer networks and path-
way-directed drug discovery. Nature Reviews Cancer, 8(1), 61–
70.
De Luca, A., Carotenuto, A., Rachiglio, A., Gallo, M., Maiello, M. R.,
Aldinucci, D., Pinto, A., Normanno, N. (2008). The role of the
EGFR signaling in tumor microenvironment. J Cell Physiol,
214(3), 559–567.
Ellington, A. D., Szostak, J. W. (1990). In vitro selection of RNA mol-
ecules that bind specific ligands. Nature, 346(6287), 818 – 822.
Jayasena, S. D. (1999). Aptamers: An emerging class of molecules that
rival antibodies in diagnostics. Clinical Chemistry, 45(9), 1628
– 1650.
Liu, H., Yu, X., Liu, H., Wu, D., She, J. (2016). Co-targeting EGFR and
survivin with a bivalent aptamer-dual siRNA chimera effectively
suppresses prostate cancer. Nature Sci Rep, 6, 30346.
Medical College of Georgia at Augusta University. (2016, August
2). Treatment strategy has 2 arms for a secure grip on cancer.
R & D Magazine. Retrieved from https://www.rdmag.com/
news/2016/08/treatment-strategy-has-2-arms-secure-grip-cancer.
Ni, X., Castanares, M., Mukherjee, A., Lupold, S. E. (2011). Nucleic
acid aptamers: clinical applications and promising new horizons.
Curr Med Chem, 18(27), 4206 – 4214.
Pestourie, C., Tavitian, B., Duconge, F. (2005). Aptamers against ex-
tracellular targets for in vivo applications. Biochemie, 87(9-10),
921 – 930.
Siegel, R. L., Miller, K. D. & Jemal, A. (2015). Cancer statistics. CA
Cancer J Clin, 65(1), 5–29.
Sun, H., Zhu, X., Lu, P. Y., Rosato, R. R., Tan, W., Zu, Y. (2016). Ap-
tamers: Versatile molecular recognition probes. Analyst, 141(2),
403 – 415.
Advice from Your Senior Advisor:
EnrichingYourUndergradExperience
by: Yen Tran, 4th year BCH
Dear fellow science students,
Welcome to the 2016-2017 academic year.
University is an experience that builds both character and
development. Expect to develop memorization, critical thinking,
and time-priority management skills. Expect to handle multiple
assignments at once, scramble through long labs, and write ex-
ams under duress. Be challenged, but lest forget that your under-
graduate education is more than just academics and grades.
Your undergraduate goal should also seek for skill devel-
opment outside the classroom.
Think of some critical skills which you can apply just
about anywhere. Can you write and summarize key information?
Can you simplify and explain a concept to someone? Can you
discover your passion? These are the real challenges students
face, whether they are in a classroom, in a workplace, or chasing
after a dream.
Your undergraduate experience may answer these ques-
tions.
A significant part of learning is through discovery, so go
take on different roles and responsibilities. Every time I faced a
challenge, I learnt something new, whether it is a faster, better
method of accomplishing something, or insight to passion and
direction. For one thing, Winston and I have discovered pride and
joy from founding our Food Science column. Through my di-
verse CO-OP experiences, I have realized better career paths that
suit my personality and strengths. There are many great oppor-
tunities to seize and you will only know your preferences when
you try them out.
Luckily for you, our Catalyst team has put together a spe-
cial issue with success stories, suggested activities, and inspiring
articles. More than just surviving the school year, we hope that
you will enjoy reading and will find different ways to enrich your
undergraduate experience
Passionate about Science and Art but not
sure how to combine the two? The Catalyst is
looking for illustrators and photographers!
Email: production.uocatalyst@gmail.com
C a t a l y s t
September 201614
Zika: le nouveau fléau
par Hadjar Saidi, 3e année en BCH
**Cet article est écrit uniquement par Hadjar Saidi. Nous nous excusons
pour toute confusion provoquée dans le numéro de Mars 2016.**
D
epuis 2015, sévit en Amérique latine et
dans quelques autres pays du monde une
nouvelle flambée épidémique: le virus Zika.
Il a été pour la première fois découvert en Ou-
ganda, en 1947, chez des singes rhésus, et en
1952, chez l’homme. Depuis, ce virus a infecté
plus de 1.5 million de personnes à travers le
monde, principalement en Amérique latine et en
Afrique. Néanmoins, que savons-nous réellement sur
ce virus et quelles sont les complications associées
à ce-dérnier ?
“
L’organisation mondiale de la santé
(OMS) tire la sonnette d’alarme
face à cette menace inconnue qui se
propage de façon explosive à l’échelle
mondiale.
Des moustiques du genre Aedes portent le virus
et le transmettent à leur tour. Les sujets atteints
présentent généralement une fièvre modérée, des
éruptions cutanées, une conjonctivite et des dou-
leurs musculaires. Ces symptômes, assez bénins, dis-
paraissent en 2 à 7 jours. La virulence du virus Zika
provoque plutôt des complications neurologiques et
auto-immunitaires, signalées dès 2013 par les au-
torités de la santé lors de l’épidémie en Polynésie
française.
Parmi les complications auto-immunaitres, le virus
Zika pourrait potentiellement être responsable du
syndrome de Guillain-Barré. Plus fréquente chez
les adultes de sexe masculin, cette infection provo-
que une réaction auto-immunitaire contre le système
nerveux périphérique du patient. Le syndrome
peut atteindre les nerfs moteurs, qui comman-
dent le mouvement musculaire, ce qui entraine
des paralysies réversibles. La nature auto-immune
du syndrome exige un traitement immunothéra-
peutique visant à éliminer les anticorps du sang.
Par ailleurs, des sessions thérapeutiques plus
régulières seraient nécessaires pour soulager les
symptômes. Par contre, ce virus entraine des
conséquences encore plus calomnieuses pour les
femmes enceintes et atteintes parce qu’il provoque
une sérieuse malformation fœtale, la microcéphalie.
Celle-ci se caractérise par une croissance insuffisant-
edu cerveau chez le nouveau-né qui pourrait
entrainer dans les cas graves, des retards de
développement très dévastateurs et irréversibles.
Aucun traitement spécifique de la microcépha-
lie n’est disponible aujourd’hui. Les nouveau-nés
doivent être pris en charge dès la naissance par
des équipes pluridisciplinaires pour maximiser leur
dévelopment cérébrale.
Aujourd’hui, les connaissances scientifiques con-
cernant le virus Zika sont très restreintes. Les
autorités de la santé essayent de déterminer les
caractéristiques de ce virus telles que sa période
d’incubation, le rôle des moustiques dans sa
transmission. Il est aussi primordial d’élaborer au
plus vite des traitements et des vaccins ainsi que
des tests diagnostiques plus spécifiques visant à
réduire les erreurs liées à la présence d’autres
types de virus. La recherche s’active aussi
autour du lien potentiel entre le virus et
les complications neurodégénératives et auto-im-
munes. Selon les statistiques, le nombre de diag-
nostiques du virus Zika coïncident parfaitement
avec une recrudescence inexpliquée du syndrome
de Guillain-Barré et de la microcéphalie chez les nou-
veau-nés.
L’organisation mondiale de la santé (OMS) tire la
sonnette d’alarme face à cette menace inconnue
qui se propage de façon explosive à l’échelle mon-
diale. Face à ce fléau présentement incurable, la
prévention reste le seul moyen de protection.
Selon l’OMS, il est vital d’éviter les piqûres de
moustiques étant les vecteurs de cette mala-
die. Pour ce fait, l’utilisation de produit répulsifs
et de moustiquaires est fortement recommandée
dans les zones à risque. Ces conseils s’appliquent
15C a t a l y s t
September 2016
particulièrement aux femmes enceintes en vue
des conséquences possibles sur les nou-
veau-nés. Les gouvernements de pays touchés
par le virus recommandent aussi aux couples
de repousser leurs projets de grossesses de plu-
sieurs mois. Néanmoins, cette épidémie a créé
une véritable crise sociale notamment dans
beaucoup de pays d’Amérique latine, où l’accès
aux contraceptives est très limité et l’avortement
prohibé pour des raisons religieuses (sauf en cas
de viol ou de risques pour la santé de la mère
dans certains pays). Cette flambée de maladie du
virus Zika permet aujourd’hui à de plus en plus de
voix de se lever et de crier au changement
des mœurs et du code pénal dans ces pays
notamment pour le droit à l’avortement dans le
cas de diagnostic de microcéphalie. Le virus Zika
a dévoilé la faiblesse des services de la santé
face à une épidémie de cette envergure, mais
il a aussi permis de soulever des débats socio-cul-
turels nécessaires.
Funky Fungi
by Ashley Tenn,
3rd year BCH
C a t a l y s t
September 201616
17C a t a l y s t
September 2016
C a t a l y s t
September 201618
19C a t a l y s t
September 2016
C a t a l y s t
September 201620
21C a t a l y s t
September 2016

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The Catalyst September 2016 Issue

  • 1. 1C a t a l y s t September 2016 September 2016 l septembre 2016 Volume 7: Issue 1 Student Science Journal - Journal étudiant scientifique Humans Evolved From Walking Fish?Yes, You Read That Right! PAGE 10 101 WEEK SPECIALS INSIDE! Food Science: Ice Cream PAGE 8
  • 2. C a t a l y s t September 20162 THE TEAM | L’ÉQUIPE Editor-in-Chief Tanya Yeuchyk Production Manager Christine Wang Rédacteur-en-chef Setti Belhouari Website Manager Michael Leung Authors | Auteurs Setti Belhouari Winston Cheung Zerin Khan Alek Tirpan Yen Tran Émilie Vaillancourt Tanya Yeuchyk Editors | Rédacteurs Shobhitha Balasubramaniam Sanmeet Chahal Alex Chen Alya Hammami Connie You Illustrations and Photographs Itzel Lopez-Carreon Sasha Newar Katherine Power Ashley Tenn Translators | Traducteurs Sanmeet Chahal Setti Belhouari Narimane Ait Hamou Shamei Benoit Leblanc Mihaela Tudorache September Contents | Contenu de septembre Articles 6 Ethical Considerations with the CRISPR/Cas9 system 8 Food Science: Ice Cream 10 Humans Evolved From Walking Fish? Yes, You Read That Right! 12 Novel Aptamer-based Therapeutic System against Cancer 14 Zika: le nouveau fléau 16 Science de la bouffe : la crème glacée 18 Les humains ont-ils évolué de poissons qui marchent ? Oui, vous avez bien lu ! Entertainment 3 Comic Corner 11 The Accident 15 Funky Fungi 101 Week Specials 4 10 Tips for Freshman Students 5 Tips for Incoming Science Students 13 Enriching Your Undergrad Experience
  • 3. 3C a t a l y s t September 2016 By: Itzel Lopez-Carreon, 2nd year CHM By: Sasha Newar, 4th year BIO Nous cherchons des traducteurs et des auteurs francophones. Ça vous intéresse? Contactez le rédacteur-en-chef: redacteur.uocatalyst@gmail.com
  • 4. C a t a l y s t September 20164 10TipsforFreshmenStudents The life of a science student is definitely a challenging one. However, there is one thing that can be more challenging: be- ing in your first year as a science student. You will be in a larger establishment among thousands of students who, just like you, are lonesome, homesick, and stressed about their future. Do not panic! I have been there and survived. In addition to being a second-year biochemistry student (with a minor in math), I am also your Rédacteur-en-chef. I am always asked how I juggle so much work. In this excerpt, I hope to share with you the secrets of being a well-rounded and productive student, especially during your first year of studies. Though this list may seem general, it has helped me succeed my first year at University. I am sure it will help you too. May you have a healthy, successful first year. By Rédacteur-en-chef: Setti Belhouari, 2nd year BCH 1 Sleep well: Ensure that you have sufficient sleep. Sleeping-in during the weekend does not make up for your all-nighters during the week. For more on the importance of sleep, be sure to read our November 2015 issue. 2 Prioritize: Put your health at the top of your priorities list. Realize that your assignments, laborato- ry reports, midterms, and exams are weighted differently. Put more time doing practice questions to prepare for your exams and midterms. Laboratory reports may seem like huge tasks, but they are not worth much of your final mark. 3 Contact your professor: At the beginning of the semester, ask your professor whether you should put a greater focus on your textbook or your lecture notes. Office hours are your opportunity to clarify concepts with your professor. Get to know your professor better; he/she may become your research supervisor! 4 Wash your hands: Wash your hands to prevent yourself from catching the common cold during midterm season. Take care of yourself. If you are feeling sick, visit a health care professional who will treat you and write you a note justifying your absence. 5 Extracurricular: Join an extra- curricular activity. Being in at least one extracurricular activity will teach you how to accomplish more with your limited time. This will also help you learn important life skills that are not covered during your lectures. Many extracurricular activi- ties organized in the University, offer wonderful rewards such as scholar- ships, trips abroad, gift cards, etc… Still, be careful not to overburden yourself with extracurricular activi- ties. Good grades are also important because they, too, can be equivalent to an Admission Scholarship. 6 Procrastination: To avoid pro- crastination, prepare daily goals. Tell yourself, that you will finish your organic chemistry lab report within 3 hours. If you do, reward yourself with an outing with friends, a delicious restaurant dinner, or, simply, an extra hour of sleep. 7 Confidence: Do not shake while studying for your midterm. Believe that everything you are being taught is within your reach. Never demean yourself. Never com- pare yourself to the so-called geniuses in your math class. Believe in hard work. 8 Study groups: Study groups may be important for students to learn from one another. Nonetheless, give yourself time to study by your- self. Study groups have a tendency of becoming grueling stress groups, especially when they are held the night before a midterm. 9 Last-minute: Before a midterm or an exam, do not stand amongst the mass of students who are frantically going through their study notes. Try to find a quiet place to relax and stretch. 10 Enjoy: Do not attend your lectures and your extracur- ricular activities like they are some sort of drudgery or punishment. Think this way: if you pay for you education, you’d better enjoy it.
  • 5. 5C a t a l y s t September 2016 Welcome to uOttawa Science! Take a moment to pat yourself on the back - you’ve made it to the next big chapter of your life. Not only that, but you have picked the most awesome facul- ty in all of uOttawa! To help you start your journey, I offer you an assembled collection of wisdom for surviving first year... Once you get your syllabi, take a calendar and write down the dates of all your midterms. Trust me, they come quicker than you think, and this method will help you be better prepared. It also helps to know in advance if you have more than one in the same day (so that you can start cry- ing early). There are many groups on Facebook where you can buy used textbooks from other students. This is a great alternative to getting them brand new, and can save you lots of money! Go to your professor’s office hours when you have a question. You’ll get the most qualified explanation, and some profs will even give extra hints when they see a student putting in the effort. It also doesn’t hurt to meet your profs one-on-one and develop a working relationship with them. Go to lab tutorials! They are absolutely worth the extra class time. The TAs explain important concepts behind the labs you have done, and how to structure your lab report. You’ll find them to be a major help! You may want to consider renting a locker in Marion from the SSA, especially if you live off campus. It’s not expensive to rent, and it’s a very convenient place to store your lab coat and books during the year. You can even share one with a friend and split the cost. Attend your DGDs! It’s tempting to skip a non-mandatory class, but they are very help- ful for your understanding of course material. Remember that the prof hand-picks what is discussed, and the TA often goes through mid- term-type questions. Sometimes, your lab grade includes a TA eval- uation. Be sure to talk to your lab TA about their specific expectations - this might help you achieve a better grade. Actually do work and get caught up during reading week. Going on vacation might improve your mood, but probably not your GPA. Don’t rush to buy your textbooks. Some profs will highly recommend one, but then never use it. Wait until you actually need a textbook to buy it, and you might find yourself saving hun- dreds of dollars. Try getting involved with research at the uni- versity! There are some great scholarship oppor- tunities throughout your undergrad like UROP and NSERC that will look great on your resume - and contribute to your bank account. Join the Catalyst, uOttawa’s student science jour- nal! We’re looking for all sorts of contributors, giving you the chance to get involved on cam- pus, meet new people, and gain some experience in science communications. Join any other on-campus club or organization that catches your interest! Complete lists are available on the SSA and SFUO websites. Most of all, make sure to enjoy your first year. Yes, there are stressful times ahead, but it’s so important to take the time to make memories with your friends and explore the city as a uni- versity student. Take it seriously, but take breaks too. Tips for Incoming Science Students Good Luck! By Editor-in-chief: Tanya Yeuchyk, 2nd year BIM Ilustrated by: Meaghan De Jesus, 3rd year BIM
  • 6. C a t a l y s t September 20166 CRISPR/Cas9 is a genetic technology that allows for researchers to target and alter genes, specifically ones that cause disease and disorders. CRISPR/Cas9, or clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9, comprises the adaptive immune system of bacteria against foreign DNA. It is used as a genome-editing tool through the integration of a viral genome into the CRISPR sequence to form CRISPR RNA. The latter can be employed as a guide to target and cleave a particular location within a genome using the Cas9 endonucle- ase. In a recent study, Junjiu Huang and his team used CRISPR/Cas9 to try and eradicate the human β-globu- lin gene (HBB) from a human embryo (Otienna, 2015). The mutation of this gene causes β-thalassaemia, a dangerous disorder of the blood characterized by low hemoglobin (β-thalassemia, 2016). Huang’s goal was to use this system on other genetic diseases such as cystic fibrosis in order to eliminate them from the embryonic genome. The attempt was only partially successful and faced several scientific and ethical challenges which led to it being abandoned in the preliminary stages (Otien- na, 2015). One major concern was the resulting numer- ous, unpredicted off-target mutations, which can lead to cell death or modification. There are vast number of applications for the CRISPR/ Cas9 technology. We must, however, consider the as- sociated benefits and disadvantages. A major ethical issue arises in the event of this technology being used on germ cells, as well as a significant loss of diversity in a population. For example, CRISPR/Cas9 has al- ready been used to modify rat coat pigmentation. The problem lies in the fact that the same method could po- tentially be used to modify human skin pigmentation (Otienna, 2015). Such actions would not only reduce genetic diversity, but lead to an important ethical di- lemma. A possible problematic application of gene editing is parents’ ability to choose their child’s genetic features. Since parents often wish for their child to be intelligent, beautiful, and athletic, the frequency of genes associ- ated with these characteristics would rapidly increase in the population. This would lead, again, to a marked decrease in genetic diversity. Modifications could even lead to development of new genes if parents demand for their children to have purple eyes or blue hair, for example. It is arguable that children should have the right to be born naturally and not be genetically mod- ified without their consent. Many scientists firmly believe that such genetic technologies should only be used therapeutically and be kept under strict control. In conclusion, CRISPR/Cas9 is a very powerful ge- nome-editing tool with a promising future for disease eradication. However, it should be highly regulated in order to prevent unethical uses like on human embry- os. Although funding for human embryonic genome editing has been banned in the United States, it is still permitted in other countries. If the technology is pursued in these areas, what will be the future conse- quences on the human genome? Figure 1. CRISPR RNA binding to genomic DNA leads to recruit- ment of the Cas9 endonuclease to the binding site. Cas9 can subse- quently cleave the genomic DNA at highly specific location Ethical considerations with the CRISPR/Cas9 system By: Émilie Vaillancourt, 4th year BPS References: Otieno, M. (2015). CRISPR-Cas9 Human Genome Editing: Challenges, Ethical Concerns and Implications. Journal of Clinical Research & Bioethics 6(6), 253-255. Beta-thalassemia. (2016). U.S. National Library of Medicine: Genetics Home Reference. Retrieved from https://ghr.nlm.nih.gov/condi- tion/beta-thalassemia Photo Source: Chemical and Engineering News. 2014. CRISPR/Cas9 Gene Editing Systems. American Chemical Society. 92: 37. “ CRISPR/Cas9 is a very powerful ge- nome-editing tool with a promising future for disease eradication.
  • 7. 7C a t a l y s t September 2016 DAT-GMAT-GRE-LSAT-MCAT-OAT-PCAT FREE PRACTICE TESTS ONLINE FEATURE EVENTS LIVE & ONLINE COURSES MCAT Classes Starting September 13th and 27th . Enroll now at kaptest.com/MCAT. www.kaptest.com 1-800-KAP-TEST bailey.poredos@kaplan.com
  • 8. C a t a l y s t September 20168 FOOD SCIENCE: Ice Cream Winston Cheung 4th year BIM; Yen Tran 4th year BCH Photographs by: Katherine Power, 2nd year BIO N othing hits the spot like good old ice cream on a hot summer day. The kid in you might think that ice cream is made from cold, sweet, and creamy fluff. Yet what is ice cream really made of? Well, that kid is not too far off. Cream, sugar, and air are the three key ingredients that give rise to ice cream’s taste and texture. Inspired by Ottawa’s Ice Cream Festival, this issue’s Food Science will educate you on this tasty frozen treat called ice cream. What is ice cream? What exactly is ice cream? Would you classify ice cream as a solid, liquid, or gas? Ice cream is actually an interesting mix- ture of all three phases- there is ice, cream, and air. As a colloid (a substance with very small in- soluble particles suspended), ice cream contains ice crystals and air bubbles suspended in the ice cream serum. The ice cream serum, which dis- solves sugars, salt, and proteins, acts as the ma- trix which holds the whole ice cream structure together. What makes ice cream? What exactly is in ice cream? What do we put in ice cream to make it so savoury and sweet? The cream and milk in the ice cream pro- vide three vital components: fat, non-fat sol- ids, such as milk proteins, and water. The sugar sweetens the ice cream. Other flavourings and additives, like egg yolk and vanilla, can be dab- bled in to improve the taste. Fats Fat in ice cream mostly comes from milk fat, which contributes to its richness by increasing the creamy texture. This is because triglycerides in dairy fat melt at the right temperature range for us to eat. If the fats were to melt at a high- er temperature, the ice cream would feel waxy rather than creamy. Fat in ice cream usually organizes in drop- lets, but at times can form larger fat clusters or even partial clusters. Fat helps to stabilize the ice cream foam and slows down the melting rate of ice cream, while also helping to deliver flavours that might otherwise be insoluble in water. Due to the fat content, we are able to indulge in the soothing and savoury melt of ice cream. Proteins Proteins found in the milk can improve the tex- ture of the ice cream via the emulsification of the fat and the water. Emulsification helps keep the fat droplets small to stabilise the air that will dif- fuse into our ice cream. Milk proteins surround each fat droplet and form a membrane, prevent- ing fat droplets from forming fat cluster that are too large. Water Water forms ice crystals inside the ice cream and influences the structure. The crystals should be miniscule in size to prevent the ice cream from feeling grainy. Hard ice creams that are smooth
  • 9. 9C a t a l y s t September 2016 and melt in your mouth have ice crystals that are around 35-45µm in size. Soft ice creams have a lower ice content. Most of the water transforms into ice after the ice cream hardens. Wait, why is the water not all ice if water freezes at 0˚C? Perhaps this phenomenon can be explained by the next ingredient which affects the ice cream in more ways than just taste. Sugar Sugar is added to enhance the ice cream’s taste, giving ice cream its iconic sweetness that we crave, and furthermore affecting its structure. Much like how salt ions can lower the freezing point of snow in the winter, sugar molecules can lower the freezing point of ice cream. This is known as freezing point depression, where adding solutes can decrease the freezing point of solvents. It is important to be aware that adding sug- ar in moderate amounts is important. If there is too little sugar, the freezing point will not be low- ered enough and you will end up with a hard ice cube. Too much sugar, you have ice cream gloop as the melting point would be too high. Air Air is whipped into the ice cream as the final in- gredient to give ice cream its light texture. Each little air bubble is 20-25µm. To further fluff up the ice cream, more air is added, whereas richer ice cream has less air content. The ice cream is now flavoured and textured. How do we make ice cream? Hopefully good notes of the ice cream’s composition were taken, as we now move onto ice cream making. The manufacturing process for ice cream is made up of the following steps. See if you can spot the similarities between these ice cream machines and our yogurt factory (Read the November 2015 issue!). The manufacturing process of these prod- ucts is similar and involves: - preparing a liquid mix, - whipping and freezing this mix dynamical- ly, into a soft, semi-frozen slurry, - adding flavouring ingredients, - packaging or shaping, - and further freezing (hardening) of the product under static conditions. Ottawa Tips: Visit the Food and Agriculture Museum to further investigate the ice cream making pro- cess. Other processed foods, from cheese to jam to ham, are also on exhibition for your enrich- ment. There are so many museums to explore for the scientists, studious or curious, who study in the National Capital Region. To see the French translations of our articles, visit our website at uocatalyst.wordpress.com/ *** Do you have personal research you want to share? Send it to The Catalyst! Submit your articles to editor.uocatalyst@gmail.com and see your name in print!
  • 10. C a t a l y s t September 201610 W hat an odd statement, you might think. How could humans come from fish? Better yet, how could fish possi- bly walk? Well, in Dr. Emily Standen’s lab, right here at U of O, a primitive, air-breathing species of fish called Polypterus senegalus is being raised on land! The lab is testing how adaptive these fish are to novel ter- restrial environments. Earlier work by Standen et al. (2014) raised Polypterus on land for 8 months and the results were stunning: they showed substantial improvements in their walking abilities on land. It was seen that a terrestrial environment compared to an aquatic one caused changes in the fish’s morphology and triggered skeletal changes which helped them in locomotion. These results illustrated how, around 400 million years ago, some fish used their regular fins to walk when transitioning from water to land (Standen et al. 2014). Remarkably, the anatomical changes observed in the Polypterus seem to mirror what is seen in the fossil record. This gives us insight into how fossil fish- es with similar morphologies may have taken their first steps onto land. Taxonomically, Polypterus are considered to be the most basal of the ray-finned fishes and are the most closely related to the common fish ancestor that led to the evolution of land animals called tetrapods. (Standen et al.2014). Polypterus are long and possess lungs and big bony scales. At the front of their body, they have large pectoral fins used for routine swim- ming and walking on land. Unverified reports also suggest Polypterus voluntarily walk between ponds as the waters dry up (Pennisi, 2014). In this way, they are very similar to the fossil fishes that paleontologists think may have been the first fish to explore land. Dr. Standen showed that land-raised fish walked more effectively by lifting their heads slightly high- er from the ground, holding their fins closer to their body as well as slipping less than fish that were raised in water (Standen et al. 2014). The terrestrial fish also showed changes to their fin anatomy that pro- vided more stability and mobility, both crucial factors when moving about on land. These changes are the result of plasticity, the ability of an animal to show anatomical, behavioural, biochemical or physiological changes (Standen et al. 2014). The findings provide evidence for developmental plasticity, which could have given our earliest tetra- pod ancestors the ability to transition onto land. Over a very (very) long period of time, adapting to life on land may have accelerated evolutionary transforma- tion from fins used for swimming into limbs used for walking (Baker, 2014). It was speculated that these changes would later be genetically fixed by natural selection (Standen et al. 2014). Many of the anatomical changes observed in Polypterus reflect the fossil record of land-transition- ing fish from roughly the same time period. Thus, Dr. Standen’s team was able to hypothesize that, if ana- tomically similar, the fossil fish could also have similar behavioural characteristics when they first walked us- ing their fins on land. So, as strange as it sounds, 400 million year old fish may have evolved into our very distant ancestors on land! Humans Evolved From Walking Fish? Yes, You Read That Right! By Alek Tirpan, 3rd Year BIM
  • 11. 11C a t a l y s t September 2016 My Involvement with the Standen Lab I have been involved with Dr. Standen’s lab since last year. I was fascinated by the research she is lead- ing and what it could signify for the field of evolutionary biomechanics. I first started by creating 3-D models of the gill arches of Polypterus from their micro CT scans to visually represent anatomical differences between the terrestrial and aquatic types. I then moved on to a project on testing vision in Polypterus. Dr. Standen and I were interested in understanding how terrestriality affects vision in this normally aquatic fish. This summer, I worked in the lab on an exper- imental design to investigate the optokinetic reflex in Polypterus. The project will consist of running the Polypterus through optokinetic reflex tests to examine if different environmental adaptations cause changes to their visual acuity. We also hope to gain insight into the advantages and disadvantages this would have brought from an evolutionary standpoint. The project underway is very exciting, and I hope to share more results in the months to come. References: Baker, N. (2014, August 27). How fish can learn to walk. Retrieved August 04, 2016, from http://www.nature.com/news/how-fish-can- learn-to-walk-1.15778 Pennisi, E. (2014, August 27). Fish raised on land give clues to how early animals left the seas. Retrieved August 04, 2016, from http:// www.sciencemag.org/news/2014/08/fish-raised-land-give-clues-how-early-animals-left-seas Standen, E. M., Du, T. Y., & Larsson, H. C. (2014, August 27). Developmental plasticity and the origin of tetrapods. Nature, 513(7516), 54-58. doi:10.1038/nature13708 Image header source: https://www.reddit.com/r/evolution/comments/3dmgbk/human_evolution_timeline_picture/?st=irxkxoic&sh=cf853468 2nd year BIO Follow her on: Facebook: @kpowerart Instagram: @kpowerart Image source: Dr. Emily Standen THE ACCIDENT BY KATHERINE POWER
  • 12. C a t a l y s t September 201612 Prostate cancer caused 27,540 deaths in the United States in 2015 alone, and is one of the most common causes of death due to cancer in men (Siegel et al, 2015). Since tumors tend to be complex and heterogeneous, current therapies which employ antibodies or small kinase inhib- itors are able to only selectively inhibit a single signaling pathway or molecule (Liu et al, 2016). Luckily, in 2016, a team of researchers led by Liu and colleagues from Augus- ta University engineered a novel strategy using aptamers to suppress prostate cancer by targeting multiple oncogenic signaling pathways concurrently. Aptamers are oligonucleotides composed of short, synthetic single-stranded DNA or RNA (ssDNA/ssRNA), which can form unique secondary or tertiary structures. They use structural recognition to bind to and interact spe- cifically with target molecules (Ni et al, 2011). Aptamers were coined from the Latin word aptus, meaning “to fit”, since they bind to their targets with such a high affinity and specificity, like a key fitting into a lock (Ellington and Szostak, 1990). In fact, aptamers can be developed to bind to a variety of targets, ranging from large molecules, such as nucleic acid structures and proteins, to small molecules like antibiotics and amino acids (Pestourie et al, 2005). Since aptamers can be chemically synthesized and modi- fied according to their desired applications and targets (Ni et al, 2011), they are named “chemical antibodies” (Sun et al, 2016). In comparison to antibodies, aptamers are much more thermally stable with a longer shelf life; unlike an- tibodies, they can be repeatedly denatured and renatured (Jayasena, 1999). Most importantly, the non-immunoge- nicity of aptamers make them ideal alternatives to antibod- ies for in vivo applications (Ni et al, 2011). So, how have the researchers from Augusta Univer- sity employed aptamers to suppress prostate cancer? They developed a novel chimera in which two small interfering RNAs (siRNAs) specific to survivin and epidermal growth factor receptor (EGFR) are fused between two aptamers (Liu et al, 2016). The aptamers on both ends of the chimera can bind specifically to prostate-specific membrane anti- gen (PSMA), which is a protein expressed on the surface of prostate cancer cells (Liu et al, 2016). Essentially, the aptamers on either end of the chimera act like “two arms” that grip PSMA in order to deliver the two siRNAs to the prostate cancer cell for internalization. Once internalized, the two siRNAs can inhibit EGFR and survivin. siRNAs silence genes by binding to the messenger RNA (mRNA) of specific genes and degrading them, which ensures that there is no transcription. Hence, the gene will not be ex- pressed. “ Prostate cancer caused 27,540 deaths in the United States in 2015 alone, and is one of the most com- mon causes of death due to cancer in men. Overexpression of EGFR signaling pathway and survivin signaling pathway increases metastasis and can- cer cell proliferation (De Luca et al, 2008; Altieri, 2013). Since these two signaling pathways intersect at multiple networks, targeting both simultaneously can lead to a more global pathway inhibition for cancer cell growth (Liu et al, 2016). In fact, tumors which are resistant to EGFR inhibi- tors can switch to the survivin pathway for recurrence and survival (Altieri, 2008). Since these two proteins are inde- pendently required by cancer cells for proliferation, block- ing their production will be detrimental to the survival of cancer cells. Research conducted by Liu and colleagues in 2016 has indicated that the novel chimera suppresses the ex- pression of survivin and EGFR by inducing apoptosis of prostate cancer cells and inhibits the growth of tumor cells in mouse models. Their models emulated middle and late stages of prostate cancer, which are the most common stag- es found in American males when they are diagnosed with Novel Aptamer-based Therapeutic System against Cancer By: Zerin Khan, 5th year Biotech
  • 13. 13C a t a l y s t September 2016 prostate cancer (Medical College of Georgia at Augusta University, 2016). Since many cancer promoters do not re- side exclusively on the surface of cancer cells, but rather can hide inside where drugs are unable to reach them, siR- NAs can target these “undruggable” targets (Medical Col- lege of Georgia, 2016). Thus, the researchers have opened the avenue for designing combinational therapy and treat- ments to suppress cancer growth. For clinical applications, this research has indicated that the toxicity and immuno- genicity need to be further examined in higher species of animal models (Liu et al, 2016). Aptamers can be used for a variety of medical ap- plications, ranging from molecular recognition probes to their roles as therapeutic agents. If aptamer research inter- ests you, then you should consider the research conducted at the Bioanalytical and Molecular Interaction laboratory under Dr. Maxim Berezovski here at the University of Ot- tawa. Dr. Berezovski’s lab encompasses many aspects of aptamer research, including developing aptamers against viruses and cells to create sensors and bioassays, as well as using them to discover new surface biomarkers for live cancer cells. References: Altieri, D. C. (2013). Targeting survivin in cancer. Cancer Lett, 332(2), 225–228. Altieri, D. C. (2008). Opinion-Survivin, cancer networks and path- way-directed drug discovery. Nature Reviews Cancer, 8(1), 61– 70. De Luca, A., Carotenuto, A., Rachiglio, A., Gallo, M., Maiello, M. R., Aldinucci, D., Pinto, A., Normanno, N. (2008). The role of the EGFR signaling in tumor microenvironment. J Cell Physiol, 214(3), 559–567. Ellington, A. D., Szostak, J. W. (1990). In vitro selection of RNA mol- ecules that bind specific ligands. Nature, 346(6287), 818 – 822. Jayasena, S. D. (1999). Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clinical Chemistry, 45(9), 1628 – 1650. Liu, H., Yu, X., Liu, H., Wu, D., She, J. (2016). Co-targeting EGFR and survivin with a bivalent aptamer-dual siRNA chimera effectively suppresses prostate cancer. Nature Sci Rep, 6, 30346. Medical College of Georgia at Augusta University. (2016, August 2). Treatment strategy has 2 arms for a secure grip on cancer. R & D Magazine. Retrieved from https://www.rdmag.com/ news/2016/08/treatment-strategy-has-2-arms-secure-grip-cancer. Ni, X., Castanares, M., Mukherjee, A., Lupold, S. E. (2011). Nucleic acid aptamers: clinical applications and promising new horizons. Curr Med Chem, 18(27), 4206 – 4214. Pestourie, C., Tavitian, B., Duconge, F. (2005). Aptamers against ex- tracellular targets for in vivo applications. Biochemie, 87(9-10), 921 – 930. Siegel, R. L., Miller, K. D. & Jemal, A. (2015). Cancer statistics. CA Cancer J Clin, 65(1), 5–29. Sun, H., Zhu, X., Lu, P. Y., Rosato, R. R., Tan, W., Zu, Y. (2016). Ap- tamers: Versatile molecular recognition probes. Analyst, 141(2), 403 – 415. Advice from Your Senior Advisor: EnrichingYourUndergradExperience by: Yen Tran, 4th year BCH Dear fellow science students, Welcome to the 2016-2017 academic year. University is an experience that builds both character and development. Expect to develop memorization, critical thinking, and time-priority management skills. Expect to handle multiple assignments at once, scramble through long labs, and write ex- ams under duress. Be challenged, but lest forget that your under- graduate education is more than just academics and grades. Your undergraduate goal should also seek for skill devel- opment outside the classroom. Think of some critical skills which you can apply just about anywhere. Can you write and summarize key information? Can you simplify and explain a concept to someone? Can you discover your passion? These are the real challenges students face, whether they are in a classroom, in a workplace, or chasing after a dream. Your undergraduate experience may answer these ques- tions. A significant part of learning is through discovery, so go take on different roles and responsibilities. Every time I faced a challenge, I learnt something new, whether it is a faster, better method of accomplishing something, or insight to passion and direction. For one thing, Winston and I have discovered pride and joy from founding our Food Science column. Through my di- verse CO-OP experiences, I have realized better career paths that suit my personality and strengths. There are many great oppor- tunities to seize and you will only know your preferences when you try them out. Luckily for you, our Catalyst team has put together a spe- cial issue with success stories, suggested activities, and inspiring articles. More than just surviving the school year, we hope that you will enjoy reading and will find different ways to enrich your undergraduate experience Passionate about Science and Art but not sure how to combine the two? The Catalyst is looking for illustrators and photographers! Email: production.uocatalyst@gmail.com
  • 14. C a t a l y s t September 201614 Zika: le nouveau fléau par Hadjar Saidi, 3e année en BCH **Cet article est écrit uniquement par Hadjar Saidi. Nous nous excusons pour toute confusion provoquée dans le numéro de Mars 2016.** D epuis 2015, sévit en Amérique latine et dans quelques autres pays du monde une nouvelle flambée épidémique: le virus Zika. Il a été pour la première fois découvert en Ou- ganda, en 1947, chez des singes rhésus, et en 1952, chez l’homme. Depuis, ce virus a infecté plus de 1.5 million de personnes à travers le monde, principalement en Amérique latine et en Afrique. Néanmoins, que savons-nous réellement sur ce virus et quelles sont les complications associées à ce-dérnier ? “ L’organisation mondiale de la santé (OMS) tire la sonnette d’alarme face à cette menace inconnue qui se propage de façon explosive à l’échelle mondiale. Des moustiques du genre Aedes portent le virus et le transmettent à leur tour. Les sujets atteints présentent généralement une fièvre modérée, des éruptions cutanées, une conjonctivite et des dou- leurs musculaires. Ces symptômes, assez bénins, dis- paraissent en 2 à 7 jours. La virulence du virus Zika provoque plutôt des complications neurologiques et auto-immunitaires, signalées dès 2013 par les au- torités de la santé lors de l’épidémie en Polynésie française. Parmi les complications auto-immunaitres, le virus Zika pourrait potentiellement être responsable du syndrome de Guillain-Barré. Plus fréquente chez les adultes de sexe masculin, cette infection provo- que une réaction auto-immunitaire contre le système nerveux périphérique du patient. Le syndrome peut atteindre les nerfs moteurs, qui comman- dent le mouvement musculaire, ce qui entraine des paralysies réversibles. La nature auto-immune du syndrome exige un traitement immunothéra- peutique visant à éliminer les anticorps du sang. Par ailleurs, des sessions thérapeutiques plus régulières seraient nécessaires pour soulager les symptômes. Par contre, ce virus entraine des conséquences encore plus calomnieuses pour les femmes enceintes et atteintes parce qu’il provoque une sérieuse malformation fœtale, la microcéphalie. Celle-ci se caractérise par une croissance insuffisant- edu cerveau chez le nouveau-né qui pourrait entrainer dans les cas graves, des retards de développement très dévastateurs et irréversibles. Aucun traitement spécifique de la microcépha- lie n’est disponible aujourd’hui. Les nouveau-nés doivent être pris en charge dès la naissance par des équipes pluridisciplinaires pour maximiser leur dévelopment cérébrale. Aujourd’hui, les connaissances scientifiques con- cernant le virus Zika sont très restreintes. Les autorités de la santé essayent de déterminer les caractéristiques de ce virus telles que sa période d’incubation, le rôle des moustiques dans sa transmission. Il est aussi primordial d’élaborer au plus vite des traitements et des vaccins ainsi que des tests diagnostiques plus spécifiques visant à réduire les erreurs liées à la présence d’autres types de virus. La recherche s’active aussi autour du lien potentiel entre le virus et les complications neurodégénératives et auto-im- munes. Selon les statistiques, le nombre de diag- nostiques du virus Zika coïncident parfaitement avec une recrudescence inexpliquée du syndrome de Guillain-Barré et de la microcéphalie chez les nou- veau-nés. L’organisation mondiale de la santé (OMS) tire la sonnette d’alarme face à cette menace inconnue qui se propage de façon explosive à l’échelle mon- diale. Face à ce fléau présentement incurable, la prévention reste le seul moyen de protection. Selon l’OMS, il est vital d’éviter les piqûres de moustiques étant les vecteurs de cette mala- die. Pour ce fait, l’utilisation de produit répulsifs et de moustiquaires est fortement recommandée dans les zones à risque. Ces conseils s’appliquent
  • 15. 15C a t a l y s t September 2016 particulièrement aux femmes enceintes en vue des conséquences possibles sur les nou- veau-nés. Les gouvernements de pays touchés par le virus recommandent aussi aux couples de repousser leurs projets de grossesses de plu- sieurs mois. Néanmoins, cette épidémie a créé une véritable crise sociale notamment dans beaucoup de pays d’Amérique latine, où l’accès aux contraceptives est très limité et l’avortement prohibé pour des raisons religieuses (sauf en cas de viol ou de risques pour la santé de la mère dans certains pays). Cette flambée de maladie du virus Zika permet aujourd’hui à de plus en plus de voix de se lever et de crier au changement des mœurs et du code pénal dans ces pays notamment pour le droit à l’avortement dans le cas de diagnostic de microcéphalie. Le virus Zika a dévoilé la faiblesse des services de la santé face à une épidémie de cette envergure, mais il a aussi permis de soulever des débats socio-cul- turels nécessaires. Funky Fungi by Ashley Tenn, 3rd year BCH
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