Category Archives: Biological Sciences

Pip, SAR, and GMOs: How UBC Researchers are Advancing our Knowledge of Plant Immune Systems

What would happen if plants couldn’t protect themselves? Well, for one, they would be prone to many different infections and viruses. Ultimately, plants would die without the ability to protect themselves. To really put things into perspective, humans would not have many of the food sources they have without plants.

Yuli Ding, a 5th year PhD student at the University of British Columbia, and her colleagues made a coincidental, break-through discovery in October 2016. Focusing on the ability of plants to resist diseases that they’ve previously encountered, called Systemic Acquired Resistance (SAR), Ding set out to determine if a specific molecule is required for this type of protection. SAR is described with greater depth in the following podcast with the researcher herself. The molecule in question was Pipecolic Acid (Pip). According to the findings of the scientists, “Pipecolic acid could be a relatively important mobile signal is the systemic acquired resistance.” In simpler terms, Pip aids in SAR by activating the process.

We had the opportunity to interview Yuli Ding about her research to help clarify some of these complex concepts. Listen to her explanations of the research in the following podcast.

What happens to plants that cannot complete SAR? Mutated plants, with a non-functional SARD4 gene, are SAR-deficient and thus unable to effectively defend against diseases. Instead of making Pip to activate SAR, a Pip pre-cursor molecule gathers in the plants – demonstrating SARD4’s importance in synthesizing Pip. Since Pip is not being created, the plants don’t exhibit SAR and are less able to defend themselves when infected by pathogens.

In this video, Yuli Ding describes how they identified SAR-deficient Arabidopsis plants, and demonstrates one of the main lab techniques, Polymerase Chain Reaction, that her team used to help identify Pip as a signal molecule.

Arabidopsis Timelapse
Music: Horizon, by Letmeknowyouanatole

Why should we care? SAR is a key process by which plants protect themselves, so SAR is an essential mechanism in ensuring the maintenance of agriculture and healthy crop yields.

Science is advancing at a rapid rate and the use of Genetically Modified Organisms (GMOs) has been increasing. A GMO is the result of a gene transfer between organisms. For example, the gene of one organism is inserted into another organism in order to improve that organism. The results of this study could be a stepping stone to creating GMOs that have better SAR, and are better able to defend against disease. Specifically, the genes responsible for synthesizing Pip could be added to immuno-compromised organisms. Genetic modification could also be used to make plants have stronger SAR or better immune systems.  Although the use of GMOs could be beneficial, GMOs pose several threats to the environment and other organisms.

What can we do with this research right now? The findings of this study could help improve the yield of crops and the number of successful crops. Farmers and agriculturalists could now focus on improving the environmental conditions of their plants to ensure that all requirements for a plant to be healthy are met. A healthy plant would increase the chances of proper SAR. All in all, a healthy plant is a happy plant!

 

By Navpreet Ganda, Pavneet Virk, and Zhongkai He.

The Body Snatcher

When you think of parasites, what comes to mind? Worms? They’re small? They’re gross? Irrelevant to our region?

Turns out these little beasts have a greater impact than you’d think. Gehman studied how a certain parasite that infects mud crabs is affected by environmental factors, such as temperature. Her research enriched the pool of knowledge regarding the parasite model! This means, information known about a specific parasite can be applied to similarly behaving parasites. For example, Gehman’s findings help us better understand the malaria parasite! For additional significance of her research, please listen to this podcast.

Audio credit: https://soundcloud.com/evelyn-chen-827562817/so-project

                                                                                              

Why are parasites important to you?

With globally increasing temperatures it’s possible for new parasites to surface in different regions and affect us, either directly or indirectly.

Parasites require the presence of a host to survive and the abundance, distribution, and susceptibility of the host affects the parasite. To evaluate these factors, Gehman and her colleagues studied factors within 10 estuaries and observed the abundances of hosts and parasites in each region.

screen-shot-2016-11-30-at-3-35-42-pm

Image Credit: Andy Tucker, Georgia University

They studied a castrating barnacle parasite that infects the mud crab. Mud crabs reside in oyster reefs and rely on them for protection. This parasite establishes itself within the mud crab and changes its behavior and reproduction patterns,  effectively taking over its body. Infected mud crabs have a sac under their body which makes them unable to get into the oyster reef, leaving them vulnerable to their predators.

As shown through this video, you can see the sac on the mud crab.

https://www.youtube.com/watch?v=vGo32jzqQAI&feature=youtu.be%20

Video taken from: https://www.youtube.com/watch?v=vGo32jzqQAI&feature=youtu.be

It was shown that regions with varying abiotic and biotic factors influenced the abundance of this parasite.

Host Size

Host size was the biggest predictor of parasite infection as larger mud crabs would be infected more often. Smaller crabs would not have enough energy to sustain the parasite, but larger crabs have more energy to sustain the parasite and may also be older, increasing their susceptibility to infection.

Water Depth

As this parasite has free-living larvae it migrates further in deeper waters because it flows with the water circulation. Therefore, in deeper waters there is a higher rate of infection.

Predator Abundance

Areas with higher predator abundance both could increase and decrease the infection prevalence. In deeper waters, mud crabs are trying to avoid their predators and that can increase infection in those individuals. However, predators that feed on infected crabs can also decrease the infection in that population.

screen-shot-2016-11-30-at-3-52-03-pm

Image credit: Andy Tucker, Georgia University

At first glance, it is hard to see this paper’s significance, but after understanding how this relates to us it is clear how important it is. There has been little evidence for how the ecological structures will change due to environmental factors which is why Gehman’s research about these tiny organisms is pivotal. More research in this area could solidify the parasite-model, allowing us to better understand the impact parasites have on human health.

So how many more bodies will be snatched as global warming continues?

 

»Group 5

Evelyn Chen, Nikeisha Dass, Riaz Vejdani, Jane Wanjiru

The Ediacaran Enigma

In biology, there’s a metaphor known as the universal tree of life that expresses the idea that all organisms are part of a big happy family, descending and evolving from the same common ancestor. It’s proved to be a pretty good rule of thumb too, as analysis has given most organisms a place somewhere in the branches of this metaphorical tree. Now, pay attention to how I emphasized “most”, because there’s an exception to this rule – one group of puzzling animals, known only from fossils, that has defied scientists’ attempts to place them on the tree of life and relate them to other organisms. They are the Ediacaran animals – grouped together and named after the period of Earth’s history they lived in (likely because “what the hell are these things” wasn’t very scientific).

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Artist’s impression of an aquatic Ediacaran environment. Image Credit: Smithsonian National Museum of Natural History via Flickr (CC BY-SA 2.0)

Eloquently described by the scientific community as looking like “mud-filled bags” or “quilted mattresses”, these bizarre animals first appeared in our fossil record about 600 million years ago, and are the earliest known multicellular organisms. Yet despite being the first, Ediacarans share no clear relationship with later multicellular life, or any other known life for that matter. Usually related organisms have at least some distinctive trait in common (for example, all Cnidarians have stinging cells), but while some Ediacaran animals shared a few passing similarities with sponges or jellyfish, for the most part they were too different from pretty much anything that came before or after them to be considered related to them: they were too complex and large compared to life before them, yet they also had body shapes that were completely alien compared to any forms of life after them. As a result, Ediacaran life is often described as “enigmatic” – or scientist speak for “really weird”.

dickinsoniacostata

Dickinsonia costata, an iconic Ediacaran organism. Note “quilted” appearance. Image Credit: Wikimedia Commons (CC BY 2.5)

Further hammering home the strangeness, despite fossils of Ediacaran organisms being found practically everywhere, all Ediacarans abruptly vanished from the fossil record 540 million years ago, and no-one is entirely sure why.

In short, these multicellular organisms suddenly showed up, disappeared just as suddenly, and are so unrelentingly bizarre that they can’t be definitively linked to any other lifeforms we’ve seen on this planet.

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Paleontologist Guy Narbonne examining Ediacaran fossils at Mistaken Point Ecological Reserve, Newfoundland, Canada. Image Credit: Wikimedia Commons (CC BY 2.0)

Now, before you scream “aliens!” at me, there are actually some reasonable hypotheses as to what the heck Ediacaran life was, why it has no clear relationship to other known life, and why it just disappeared. For example, one hypothesis suggests that the Ediacarans were a “failed experiment” in multicellular life by Mother Nature, having been out-competed to death by later life evolved from unrelated lifeforms (in fact, scientists have traced the origins of modern animals back to the Cambrian explosion, an event that coincidentally happened… wait for it… 541 million years ago). Regardless, given the “we can’t ever know for sure” nature of prehistoric biology, it’s likely that Ediacaran life will remain an intriguing biological mystery for years to come (and my personal favourite footnote in our otherwise fairly predictable biological history).

~ Kimberly

Fidgeting Is Not a Problem, It is a solution

” Stop fidgeting and focus,” said every parent, but should we really stop it? Every time somebody assumes that you are not paying attention because you are fidgeting the opposite is probably true. Nowadays, with the high level of stress in our lifestyle, the necessity of finding ways to focus is more pressing than ever. Most of us mindlessly fidget with something while we ponder a project, listen to a lecture, study, or work through a problem.

CREDIT: www.saywhydoi.com

Why Do We Fidget And How Does It Help?

According to a study, “If something we are engaged with is not interesting enough to sustain our focus, the additional sensory-motor input that is mildly stimulating, interesting, or entertaining allows our brain to become fully engaged and allows us to sustain focus on the primary activity in which we are participating.” To put it in simpler words, we all have something called “floating attention” which means that whenever we are trying to pay attention to something usually a part of our brain is bored and starts to focus on other irrelevant things. The researchers believe that brain needs to focus on something else so that it can actually clears itself to take the information it really needs to focus on. Fidgeting distracts this part of our brain and helps us to focus on what we are reading, hearing, or seeing.

In a recent study researchers at Princeton University and the University of California, Los Angeles, found that mindless doodling can boost memory and increase concentration. Moreover, students who take lecture notes in long hand, rather than on a laptop, learn the lessons more deeply and give better answers to conceptual questions. Recently researchers at NewYork University (NYU) have begun studying the reason behind fidgeting.

https://www.youtube.com/watch?v=BDwcDyQbQV0&feature=youtu.be

Credit: http://www.wsj.com

Fidgeting Tools

Fidget toys are something that you probably already use without even knowing. For the NYU study, researchers have asked people to  post photos and videos of their fidgeting toys, with descriptions of their benefits (website). The researchers plan to classify the objects based on the sense they provide. We should consider that the huge difference that separates a fidget tool from other distractions is that it’s used for the enjoyment of itself, not to achieve any particular goal. For instance, playing an iPhone game or drawing a specific painting can’t be considered as fidgeting because these actions have a certain goal.

Most people are embarrassed from their habit of fidgeting and they found it to be often distractive for others. I was always looking for a good fidget gadget that can satisfy my needs and not distract my friends. Very recently Matthew and Mark McLachlan created a Fidget Cube  with six different sides that each satisfy one fidgeting need. This amazing product will be available in the market next month and people can pre-order it for a price of 22$ from this website.

CREDIT: www.boredpanda.com

 

-Sahba Mozaffarian

Nanotechnology; size does’t matter

Just a few weeks ago the Nobel Prize in Chemistry was awarded to a group of three brilliant men, Jean-Pieree Sauvage, Fraser Stoddart and Bernard Feringa. Over the past few decades, these three have developed molecular machines that can do a variety of work,  allowing for infinite applications.

To begin, the sizes of the machines are amazing, being measured on the scale of nanometers. To put this into perspective these machines would be 1000 times smaller than a single strand of human hair! It is quite mind-boggling to imagine how humans could build such tiny machines and this was one of the biggest obstacles in designing the molecular tools.

There had been many methods attempted to build the machines, from building small machines that would be used to build smaller machines repeating this process until a macroscopic end product had been created. Another method was  layering individual atoms and dissembling in various parts to shape a molecular machine. Finally the method used by the Nobel Prize winner’s consists of forming a new mechanical bond that allows linkages to occur without any chemical interactions. Further manipulation and these interacting molecules can be rotated, spun and twisted independently of each other.

An explanation of molecular machines. Video from https://youtu.be/vELfuiUpKM0.

The applications are immense. Molecular computer chips are one of the many things being created with the molecular machines. The computer chips are able to store data in them and compared to today’s computers hardware are miniscule. With further developments I would imagine that one day the entire computer’s hardware will be of molecular size. The computers will likely be even more compact and lightweight too!

One unique invention by researchers is the creation of a nano-car. These tiny vehicles consist of chemicals that build its chassis and rotating molecules as wheels. When I read about this I imagined researchers combining this molecular car with the molecular computer that could be use to sense and see the surrounding environment. Doctors could use this machine to travel the human body, patrolling for diseases in humans by programming the computer to sense the changes in the body. This isn’t too far fetched as the idea of tiny machines travelling through the human body has been brought up before.

The nanocar. Image from https://cdn0.vox-cdn.com/thumbor/ItfIwlmbPGDqVpOXuPVErG0ygrA=/800x0/filters:no_upscale()/cdn0.vox-cdn.com/uploads/chorus_asset/file/7221875/Screen%20Shot%202016-10-05%20at%206.36.46%20AM.png

The nanocar. Image from https://cdn0.vox-cdn.com/thumbor/ItfIwlmbPGDqVpOXuPVErG0ygrA=/800×0/filters:no_upscale()/cdn0.vox-cdn.com/uploads/chorus_asset/file/7221875/Screen%20Shot%202016-10-05%20at%206.36.46%20AM.png

Novel batteries are under development as well. The molecular machines are used to roll up polymers (long strings of joined chemicals) into an unorganized mess upon radiation with light. This mess could then unravel, releasing the energy used to initially twist up the polymer. This process essentially would harness the light energy, as it was what powered the motor to coil up the previously straight polymer.

As the era of molecular machines are still in its infancy there will be many more discoveries and applications found in coming years. As Bernard Feringa said “Through natural sciences, we can go far beyond the limits imposed on nature by evolution”, what exactly these limits are, we will have to wait and see.

-Tristan Jeffery

Something You Should Know about Seafood

Recently, a news article draws my attention as it highlights the adverse effects on humans due to increased mercury level in the ocean. According to this article, mercury content of shallow ocean layers has tripled since the industrial revolution, and therefore has posed a serious threat to seafood security and human health.

Mercury

Mercury

In fact, mercury contamination is not a new topic. It comes from a variety of sources, and artisanal mining is one of the major causes. Mercury has been used in many developing countries to extract gold for decades, and countless humans and children living in these regions have been suffered from it. Overuse and misuse of mercury not only affects livelihood near the region, but also affects humans globally.

I have read through some studies and have found out that Hg concentrations in liver and muscle of seabream after exposed to MeHg for 10 to 30 days are considerably higher than controlled seabream. The longer time fish is exposed to MeHg, the more significant change will be caused. Seafood is an important component of humans’ daily diet because of its high nutrient content. In addition to increased mercury level in the ocean, bioaccumulation and biomagnification occur with human’s long-term consumption of Hg-contaminated seafood. For example, tuna is a common fish in our menu but has a high Hg concentration. MeHg poses multiple threats to human health. Common symptoms are sleep difficulty, memory loss, headaches, and weakness etc. Some well-known diseases, such as Minamata, are the adverse effect caused by consuming contaminated seafood.

 

Teriyaki Tuna.

Teriyaki Tuna.

However, because it is a global and complicated issue caused by multiple reasons, there is no universal solution to stop increasing mercury level in the ocean. As a result, we need to be careful about our seafood selections. Pregnant women and small children should restrict their fish intake, because they are most vulnerable to the toxic metals accumulating in seafood. One day, humans will probably have to stop consuming seafood in order to survive from mercury contamination.

A Post-Antibiotic Future is Probable

The discovery of antibiotics (drugs used to fight pathogenic bacteria) revolutionized medicine in 1930’s and ’40’s. Today, these wonder drugs eradicate 548 million bacterial infections successfully every year. Prior to this, bacterial infections were mostly fatal; cholera for instance had a mortality rate of 80% as opposed to today’s less than 1%; without surgery, appendicitis and bacterial meningitis had a mortality rate of 100% as opposed to today’s less than 10%. However, the recurrence of the pre-antibiotic era is very probable due to what The World Health Organization is currently considering one of the world’s most serious health crisis – antibiotic resistance.

What is antibiotic resistance?

Antibiotic resistance is the natural phenomenon in which certain bacteria continue to divide and multiply in the presence of an antibiotic. This happens because like most organisms, bacteria are subject to natural selection (a process in which organisms more suited for their environment survive and multiply while the less-suited ones die). Therefore, when bacteria are exposed to an antibiotic, most die; those that evade the effects of the antibiotic continue to divide, generating a new resistant colony; this evasion is possible due to random mutations or through the possession of unique genes transferred from bacteria to bacteria.

Image from Wikimedia Commons

Selection of antibiotic-resistant bacteria. Image from Wikimedia Commons

Since 1930’s, antibiotic resistance has always been offset by the continuous production of new antibiotics. However, due to antibiotics overuse and lack of advancement in developing new drugs, resistance rates are catching up! Last year, bacterial species resistant to our last resort antibiotic, colistin, was reported in China; this resistance is very worrying as colistin remains the best drug for tackling antibiotic-resistant infections unresponsive to the strongest antibiotics.

What are the effects of antibiotic resistance?

Antibiotic resistance has negative effects in our society. Out of 250,000 patients that acquire antibiotic-resistant bacteria in Canada, 8,000 pass away. This number is larger than the combined number of deaths from breast cancer, AIDS and traffic accidents! With time, it will grow larger due to the gradual loss of antibiotics effectiveness. Therefore, procedures dependent on the use of antibiotics such as chemotherapy and surgery will be harder to complete in the future.

If nothing is done, antibiotic resistance will lead to other unpleasant circumstances. For instance, a greater number of deaths from minor bacterial infections will be observed. Due to longer periods of illness and use of stronger, more expensive drugs, increased financial costs will also result; worldwide, an estimated 1.7 billion dollars is anticipated annually based on infections from one group of resistant bacteria. Lastly, use of stronger medication to treat infections will result in more side effects for patients.

How can we decrease the rates of antibiotic resistance?

Besides finding new treatment alternatives, avoiding overuse of antibiotics is the most effective way to combat antibiotic resistance. It is estimated that 50% of antibiotics  prescribed to humans are for viruses. We should aim to avoid taking antibiotics if they aren’t needed. In addition, finishing all prescribed antibiotics is crucial to minimizing the chance of nurturing antibiotic-resistant bacteria.

Let’s Rock on! Finding Conservation Strategies for Rockfish

Presently, fisheries provide 19% of the global protein and employ 200 million people worldwide. It is a huge economic industry with designated areas in the oceans to catch fish. Since the beginning of commercialized fisheries, where the activity grew from an individual occupation to an immense industry involving catching, transporting, cleaning and selling fish products, the amount of fish in the oceans has steadily declined due to overfishing. Overfishing happens when  more fish are caught than can be reproduced and the population is unable to fully recover to its previous numbers. Fish can be more vulnerable to overfishing if they have a longer life span, slower reproduction rate, slower development and are larger in size.

A commercialized method of fishing called longline used for catching rockfish.

A commercialized method of fishing called longline used for catching rockfish.

Rockfish, found inshore of Vancouver Island in British Columbia are commonly overfished because they possess all of these characteristics. Large fish are the ideal target for fisheries because it is less catch effort for a higher biomass. The yelloweye rockfish, found in BC grows to be a massive 40 lbs. A rockfish lives for approximately 100 years, making them vulnerable to overfishing because it takes a tremendous amount of time to recover when these older fish are removed from the ecosystem. In contrast to most species who hatch their newborns in eggs, rockfish offspring come out swimming so these young fish are quickly exposed to commercialized fishing. Rockfish are fully developed at age 20, making quick reproduction nearly impossible if overfished. These factors contribute to a slower population recovery time; if rockfish are extensively overfished, it will take generations to rebuild their population to prior numbers.

A large yelloweye rockfish (approximately 30 lbs.) caught on the Queen Charlotte Islands, BC.

A large yelloweye rockfish (approximately 30 lbs.) caught on the Queen Charlotte Islands, BC.

As result of overfishing the rockfish’s ecosystem, inshore of Vancouver Island will be destabilized. Within every oceanic ecosystem, each species is interconnected within the food chain. If rockfish are endangered it will not only threaten the productivity and interactions within the ecosystem, but also accelerate fishery collapse leading to job loss and economic downfall.

The distribution of rockfish conservation areas along the coast of British Columbia.

The distribution of rockfish conservation areas along the coast of British Columbia.

In order to counteract this extinction of rockfish and its lasting effects, a conservation strategy for rockfish has been developed by the Department of Fisheries and Oceans. Decreasing mortality is critical for rebuilding the rockfish population so different systems of fishing are being developed to limit rockfish being caught and released, which ultimately kills them. Furthermore, certain areas will be closed to fishing with the objective of ending the accidental catching of rockfish while ensuring that their habitat will not be compromised.

You can help with rockfish conservation by:

  • Reporting any fishing in closed fishing areas to the proper authorities.
  • Frequenting restaurants that serve only ocean-friendly seafood.
  • Ensuring you avoid over consumption of rockfish which is typically called the Red Snapper or Rock Cod at restaurants and grocery stores.

All of these conservation strategies and individual contributions will give the rockfish time to recover their population here in British Columbia.

-Genevieve Carpenter-Boesch