Tag Archives: biology

Math isn’t just something to do with numbers

Posted on April 6, 2016 by | Leave a comment

Perhaps contrary to our believes, science is a work in progress, it always has been. The right ideas don’t just pop up in people’s dreams , serendipity is not here to save the day every day. Paradigm shifts don’t happen all the time, more than often hypotheses after hypotheses are proven wrong before a right one will come up. Wrong science is not necessarily bad science, and this paper, although in the wrong, will prove the point.

In 2015, Prof. Daniel Coombs , a mathematical biologist, and his research team at the University of British Columbia published a paper regarding a mathematical model. This model aims to predict the time take for a T-Cell  to reach an Antigen Presenting Cell (APC)  within a Lymph Node. Although the model failed to do it’s intended job, none of the works will be wasted. Many of the works still provide a solid foundation for future works such as an even simpler models to help better understand our immune system

Before we continue, we have to understand the basics of the human immune system.  A T-cell is a type of a white blood cell  that goes out and searches for pathogens. During an infection, APCs such as Dendritic Cells  will take up parts of a pathogen (antigen) and move to the lymph node to wait for a matching T-cell. A T-cell will get activated by binding to an APC  and proceed to activate B-cells which produce antibodies, subsequently destroying the pathogens. Thus, for our immune system to start functioning, a T-cell must come in contact with the APC that has the matching antigen.

The following video will help explain how Coombs and his colleagues devised their model for predicting the time a T-cell needs to find an APC.

Visual Representation of the T-cell. Wikimedia Commons by BruceBlas.

Visual Representation of the T-cell. Wikimedia Commons by BruceBlas.

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Source : SCIE300 Group 2

Credit to: Daniel Coombs, Alana Lee, Ivan Fong, Ryan Tran and Shayini Kanageswaran

To recapitulate, this model is characterised by having only four parameters:

  • Radius of the lymph node – R
  • Radius of APC – r
  • Diffusive constant – D
  • Boundary trapping parameter K.

r is very small compared to R, larger D equals faster the T-cell movement, and K ranges from 0-1.

This is very impressive since according to Coombs, previous models rely on at least 15 parameters to predict the exact same biological phenomenon. Were this model to correctly predict the time a T-cell will take to reach an APC, it would be at the forefront of its field. But as we have not-so-subtly hinted previously, this was not the case. The predicted time was too long compared to reality.

However, the simplicity of this model is where it excels. While other models which gave more accurate results were very complicated to compute with top of the line machines, this model can be hand computed. This model also managed to do this without losing its integrity on explaining the mode of action of a T-cell when finding an APC within a lymph node with only 4 parameters.

The following podcast contains information on the limitations, further research and improvements and our personal questions about the study.

Credit to: Daniel Coombs, Ivan Fong, Alana Lee, Ryan Tran and Shayini Kanageswaran

-Shayini Kanageswaran, Ivan Fong, Alana Lee and Ryan Tran

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Hybrids: the good, the bad, and the … natural?

Posted on April 6, 2016 by | Leave a comment

What do you think about when you hear the phrase ‘genetically engineered crops’? Do you think they’re inherently bad because they’re not ‘natural’?

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Zebroid – hybrid of zebra and donkey.  Image from Wikimedia Commons

Well, maybe you should think twice before answering, because hybridization is a process commonly found in nature. Basically, hybridization is cross-breeding between two species with different genes. In animals it’s pretty distinct in appearance, but in plants the main changes are on a chemical level. These changes are what affects the taste, smell, or defence mechanisms of the plants. Therefore, people might find a useful application to them, as hybrids may be grown as crops with better qualities, such as stronger resistance against diseases and insects. That’s why researchers are interested in exploring the genes of various plants to find the benefits, which humanity can use.

How the mystery unveiled

Dr. Celine Caseys in her lab. Photo by Alex B.

Dr. Celine Caseys in her lab at UBC. Photo by Alex B.

For example, Dr Celine Caseys and her colleagues at the University of Fribourg, Switzerland, examined the hybridization process between two types of trees from the Poplar family. Their methods involved collecting poplar leaves in three European regions and then looking for certain chemicals, responsible for defending trees from insects. More details on this research in the video below.

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Video: Benefits of Hybridization in plants by Henry Liu and Jan Jenko, Group 5

Practical use

The research revealed that hybrids are capable of creating better defence mechanisms by more efficiently producing chemicals against insects. This might have a practical application for productional growing of plants (like for biofuel) and, furthermore, for farming purposes, since the plants will require less pesticides, therefore growing crops will cost less. More on the benefits and potential drawbacks of hybridization in the podcast.

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Podcast: Benefits and drawbacks of hybridization by Alex Budkina, Group 5

As we learned from above, studying the effects of hybridization is really important, because despite all potential benefits, there are still some danger behind the artificial modification of genes, such as  endangering wild populations. Therefore, humanity must consider the  “ecological consequences”, according to Dr.Caseys, of creating genetically engineered plants. We still know too little about the process, so more studies of natural hybridization will help us to unveil the mysteries behind it.

~ Group #5: Alex Budkina, Henry Liu, Jan Jenko

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Posted in Biological Sciences, Issues in Science, Outreach Project, Uncategorized

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Visions of a Greener Earth

Posted on April 6, 2016 by | Leave a comment

Have you ever been watering plants and wondered just how much water was being absorbed by plants? Is the water you’re using to soak your garden even being put to good use by the plants? It turns out, plants contain an extensive system with complicated processes which allows them to “drink” water via osmosis. A little known fact, plants have an inner and outer layer which they use to filter water. Dr. Jetter, a researcher in the department of botany at the University of British Columbia, completed a study that aimed to figure out the function of each of those layers. He did this by examining eight different species of plants and studying the chemistry of each individual inner and outer layer.

Dr. Reinhard Jetter from UBC Department of Botany. Image courtesy of Daryl’s Camera

Our group had the pleasure of interviewing Dr. Jetter at the Biological Sciences building where he gave us further insight into his research. When our group first read his paper, we expected similar research had already been completed by scientists at other institutions but surprisingly, that was not the case. In fact, Dr. Jetter told us related research had only been done by one other group of scientists located in Germany in 2001. The video below highlights the most important components of Dr. Jetter’s research and what he found:

https://youtu.be/Ex1gqoDKbEQ

Video – Credit to Dr. Reinhard Jetter, Brian Wong, Daryl Kwok and Ying Yu

Plant cuticles were isolated. Image courtesy of Daryl’s Camera

A specially designed water chamber was used to measure how fast water passes through each layer of cuticles. Image courtesy of Daryl’s Camera

Why is this research significant? Well for one, North America suffered major droughts from 2012-2015 due to record-breaking heat waves. Acres of vegetation died off and as a result, entire ecosystems were disrupted. Additionally, water became an extremely scarce resource and states such as California were so desperate for water, they were buying it from Canada. So what are the nitty-gritty details regarding the composition of how plants control water loss? Furthermore, what are its applications to the general public? We examine this in the podcast below:

Audio –  Credit to Dr. Reinhard Jetter, Brian Wong and Ying Yu

Like all studies done in the name of science, there exist limitations. Each individual plant’s chemical components are not analogous, the water-loss barriers will vastly differ within each species. For example, in Dr. Jetter’s study, some plant species had up to 100 times water-loss prevention effectiveness versus other species. This variation is due largely to the interaction between chemical compounds within the plant itself. As a result, it would be an extremely extensive task to accurately record every individual plant species’ ability to control water-loss.

With Dr. Jetter’s research as a basis, huge potential exists in developing technologies that would drastically reduce the negative effects of drought. In the future, if scientists can fully understand and utilize the level of water loss between plant layers, vast farmlands which are highly dependent on weather conditions could be alleviated of disastrous levels of crop loss. Undoubtedly, Dr. Jetter’s research serves as the pioneering basis for a frontier of unspoken possibilities to benefit our great big green planet Earth.

-Group 3: Brian Wong, Daryl Kwok and Ying Yu

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Posted in Biological Sciences, Issues in Science, Outreach Project, Science Communication, Uncategorized

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Stop smoking to make a big difference to your health

Posted on March 21, 2016 by | Leave a comment

Nowadays, it’s hard to find a person who hasn’t heard about how harmful smoking is to our overall health. Each year, cigarette smoking is responsible for nearly 20 percent deaths in the United States and more than 6 million of people in the world died from smoking-related diseases. Smoking is harmful to every part of the body and can lead to serious health problems, such as cancer, heart diseases and respiratory problems.

 Smoking-related diseases

Smoking is one of the leading causes of cancer and it accounts for more than 30 percent of all cancer deaths in the U.S each year. The reason behind it is that smoking can trigger DNA mutations and damage the genes that protect us from cancers. Studies have shown that cigarette smoke contains more than 7000 chemicals and more than 69 of them are known to be carcinogens, which can cause varying degrees of DNA damage. As a result, people who smoke are more likely to develop certain types of cancers, such as lung cancer, throat cancer and liver cancer.

Additionally, cigarette smoking can cause heart diseases by damaging the function of your heart and the structure of the blood vessels. First, smoking produces carbon monoxide that can reduce the oxygen level in the bloodstream and hence increase heart rate to supply the body with enough oxygen. Second, some chemicals in cigarette smoke have been shown to cause the fatty plaque build-up inside the arteries. This will increase the risk of getting stroke, heart attack and atherosclerosis.

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The image shows how smoking can affect arteries in the heart. Image from National Heart, Lung, and Blood Institute.

Furthermore, smoking is also the primary cause of chronic obstructive pulmonary disease (COPD), which is a type of progressive lung disease that can cause respiratory problems and lung infections. The main symptoms of COPD include coughing, wheezing and shortness of breath. Cigarette smoking can also cause damage to lung tissues and reduce the airflow in and out of the lungs, resulting in many breathing-related problems.

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Youtube video – Smoking and its effects on Health. By iheedinstitute

Benefits of quitting smoking

Quitting smoking can lower the risk for smoking-related diseases and largely improve our overall health. Recent studies have shown that quitting smoking before the age of 40 can reduce the risk of early death from smoke-related diseases by 90 percent and increase the life expectancy by 10 years.The following graph shows the timeline of recovery effects after quitting tobacco.

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Timeline of health benefits after stopping smoking. Image from http://www.tobaccofreeco.org

In summary, cigarette smoking can cause negative health effects in many ways and it is also a major risk factor for developing cancers and other preventable diseases. Quitting smoking can help regain your health to the same level as those of non-smokers. It is never too late to stop smoking and start a healthy lifestyle!

-Ying Yu

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Posted in Biological Sciences, Issues in Science, Science Communication, Uncategorized

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Sleep loss and Obesity ?

Posted on February 29, 2016 by | 3 comments

With the cold months ending and summer coming up very soon, this means cutting down for many people. People use countless methods to help them achieve that goal such as protein powder, creatine, and diet pills. Despite all this effort, a lot of people are making this one mistake that could make it much harder for them to achieve their weight loss goal. These studies below show and strengthen correlation between insufficient sleep and factors that lead to weight gain.

Lack of sleep and 2-AG

A new study published in the journal, Sleep, was carried out by a team of scientists who focused on a type of endocannabinoid. Endocannabinoid is a class of molecule that controls physiological processes in our body. They studied a molecule called 2-AG which is associated with our ability to control our appetite. When this molecule is circulating throughout our body, it decreases our ability to control instant cravings and increases the pleasure we get from eating food we would normally think of as unhealthy and feel guilty from indulging in.

They gathered 14 healthy young adults, both male and female. Half of them were allowed to get a full nights sleep which consisted of 8.5 hours compared to the other half who were restricted to 4.5 hours of sleep. What they found was that the level of 2-AG in their body was higher consistently through out the day and remained high in the evening for those who had restricted amount of sleep.

Increased level of 2-AG would make you crave junk food you normally wouldn't

Increased level of 2-AG would make you crave junk food you normally would stay away from. Image from deckofdreams

Lack of sleep and Leptin & Gherlin

Another study that supports this claim of correlation between insufficient sleep and weight gain was also done by Prinz and Taheri. Their studies looked at the level of leptin and ghrelin in participants with restricted amount of sleep. Leptin in our body serves to suppress appetite and stimulate burning energy in our body. Ghrelin on the other hand sends signal to make us feel hungry and tells the body to store more fat. By monitoring people participants who got less than 7-8 hours of sleep, they saw decreased level of leptin and increased level of ghrelin which ultimately lead to weight gain.

Example of how reduced levels of leptin produced in mouse leads to obesity (left) compared to normal mouse (right)

Example of how reduced levels of leptin produced in mouse leads to obesity (left) compared to normal mouse (right). Image from wikipedia

Just get more sleep!

In summary, when you get less than recommended amount of sleep of 7-8 hours every night, there is increased amount of 2-AG and ghrelin and decreased amount of leptin flowing through our body. This all serves to makes us less capable of controlling our appetite, and promotes fat build up. Thinking in reverse, this means that getting sufficient amount of sleep every night would help us control our appetite and have our body burning fat like usual! This should be convincing enough for anyone wanting to lose weight for the summer to spend more time in bed at night getting some shut eye.

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video – How Lack of Sleep can Cause Weight Gain. by Howcast

 

Alana Lee

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Posted in Biological Sciences, Science Communication, Science in the News, Uncategorized

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Ocumetics’ Bionic Lens: Prefect vision for everyone?

Posted on January 31, 2016 by | Leave a comment

Are you suffering from poor vision? Do you ever complain about wearing eye glasses because they may ‘ruin’ your look? Have you ever imagined there would come a day to have perfect vision?

Recently, a new bionic eye lens named The Ocumetics Bionic Lens has got a lot of attention in media. This lens was developed by Dr. Garth Webb of Ocumetics Technology Corporation, who has dedicated his professional life to finding a way to improve and correct human vision regardless of patients’ eye conditions. This new bionic lens is able to correct human vision at all distance and give patients approximately three times vision enhancement for an entire lifetime. See the following YouTube video for a brief description of this new bionic lens.

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These specialized lenses are beneficial because they offset the risk of acquiring cataracts. This is because your eye’s natural lenses, which tend to deteriorate over time, have been replaced by these super stable bionic ones. In addition, compared to laser eye surgery, which involves corneal reshaping to improve visual acuity, this new bionic lens is perfectly safe; it does not cause any physiological changes to the eyes or other side effects that laser surgery may have, such as inflammation, astigmatism and decreased night vision.

How does it work?

According to Ocumetics’ website, this remarkable lens can be implanted into human eyes via a painless and outpatient surgery without anesthesia and hospitalization. The operation only takes 8 minutes, aiming to replace the eye’s natural lenses with the bionic ones. Ten seconds after the surgery, the bionic lenses unfold and wrap up over your eyes on its own, immediately correcting a patient’s impaired vision.

This remarkable lens looks like a small button. Image from www.cbc.ca

Is it affordable?

Dr. Webb claims the cost of the surgery is around 3000 dollars per eye. Is it overpriced? Compared to the laser eye surgery, which costs around 2000 dollars per eye, a total cost of 6000 dollars for lifelong perfect vision seems quite cheap for what is involved. In fact, this surgery may cost less than eye glasses or contact lenses in the long run because the new bionic lenses do not need to be replaced as often. Also, as the product and the technology become more mainstream in the market, the price will eventually go down.

Who can benefit from it?

The company is currently performing clinical trials on animals and blind human eyes. If the product was clinically approved to be able to cure blindness, it would be a great news for the blind. Also, for those people who are unhappy with wearing corrective lenses, this new bionic lens can provide them a better option in terms of cost, vision correction and ease of use.

Ying Yu

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Posted in Biological Sciences, Science in the News, Uncategorized

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Clinical Depression: Its Biological Mechanisms and It’s Treatments

One in four Canadians have depression that is to a degree worthy of clinical assessment, and treatment. With a number as alarming as this, why do we see that this particular mental health issue is so infrequently spoken about?

This is because there is an enormous stigma that surrounds clinical depression. In particular, polls show that 46 percent of Canadians believe that people suffering from depression are using the diagnosis as an excuse for their behaviours. This is not the case.

This stigma (held by nearly half of the nation) can be discredited by the scientific research that has gone into deciphering the physiological mechanisms of this mental health issue.

In particular scientists at the NIMH have concluded that depression is associated with a deficiency in a neurotransmitter known as serotonin. This is a di-cyclic compound that activates neurons within the central nervous system, promoting the feeling of happiness or well-being.

https://healthpsych.psy.vanderbilt.edu/2009/StopSadness_files/image010.jpg

https://healthpsych.psy.vanderbilt.edu/2009/StopSadness_files/image010.jpg

Mechanistically, serotonin is released from the axon of one neuron, and taken up through a channel protein within the dendrite of an adjacent neuron. In individuals suffering from depression, the channel protein’s ability to accept serotonin is not optimal, and essentially the feeling of happiness, and well-being elicited by the transmission of serotonin, is lost or not optimal. How is this treated?

Antidepressants are used as a treatment for this disorder by acting directly upon serotonin’s mechanism. In particular, the administration of a class of drugs known as “selective serotonin re-uptake inhibitors”  are prescribed. Essentially, this class of drugs allows serotonin to remain in the “synaptic cleft” (the extracellular space between the two neurons) for a longer amount of time. This is done by inhibiting the axon’s serotonin re-uptake channels, which are channels responsible for allowing serotonin to flow back into the axon from which it was released. Essentially SSRI’s are compounds that chemically interact with (and physically block) these re-uptake channels.  In doing so, this provides the disabled dendritic channel proteins with a longer period of exposure to the serotonin, and consequently, are able to take up near normal amounts of serotonin.

In conclusion, the symptoms felt by those suffering from depression, such as hopelessness, sadness, lethargy, and many more; are in part, caused by a proven physiological deficiency. With no control over the processes that we have discussed today, we can also conclude that those suffering from depression are unable to control particular behaviours (to a certain degree).

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Posted on January 25, 2016 by in Uncategorized

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