Little Forests, Big Problems.

In many places, there have been drastic increases in deforestation for urbanization and agriculture. Increases in the availability of housing and the space to grow foods may seem to benefit society at first glance, but urbanization and agriculture are not without their downsides. Wooded areas must be deforested to prepare land for construction and agricultural development, resulting in the destruction of natural habitats that are home to many plants and animals. As a result, endangered local wildlife will face challenges in avoiding extinction. Although humans have taken measures in attempts to preserve these forested ecosystems by preserving portions of natural forests within urban and sub-urban areas, this method of preservation is not as effective as it appears.

In this mini documentary, we will walk through Vancouver’s very own Pacific Spirit Regional Park and highlight the challenges that wildlife may face in smaller forests as a result of the continual urbanization.

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From the video, we introduced Adriana Suarez-Gonzalez, a ph.D student in the department of Botany at UBC. In her 2007 study, “Pollen limitation and reduced reproductive success are associated with local genetic effects in Prunus virginiana, a widely distributed self-incompatible shrub,” Adriana Suarez-Gonzalez shows in the video that some fruit-bearing plant species, (such as the Prunus virginiana, more commonly known as the chokecherry that her research revolves around) in fragmented forests (explained in the video) are less successful at reproducing compared to those in larger, continuous forests. Since plants are lower down the food chain, animals find it hard to sustain themselves.

Photo of choke cherries, courtesy of Born 1945 on Flickr Creative Commons

The video gave us a great idea about how fragmented forests affect animals attempting to sustain themselves, but to fully understand why fruit production is a problem, we must look at reproductive barriers of plants in fragmented sites. To understand the challenges that certain fruit-bearing plants face, Ms. Suarez discusses both ecological and genetic factors influencing the reproductive success of the chokecherry in the Podcast below. 

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In short, the podcast shows that ecological factors involve the quantity and quality of pollen available to the plant, and genetic factors involve the effects on the genetic structure of the plant as a result of biparental inbreeding (the fertilization of plants by closely related members of the same species). These two factors put together overall affects the reproductive success of the chokecherry.

Through Adriana’s research on this model berry, we can finally grasp the idea of how fragmentation can affect the health of the ecosystem as a whole. While we may not think much of a simple berry, we can appreciate how much it actually has to offer to animals that depend on it. It is true that chokecherries are abundant and therefore not an immediate problem to wildlife that depend on it, but Adriana’s research offers a argument in how the biodiversity in continuous forests offers similar fruit-bearing plants greater success, and as a result, the success of animals that rely on it.

 

By SCIE300-212 Group 2: Bailey Lei, Leslie Chiang, and Kia Sanjabi

References:

Cunningham SA. 2000. Depressed pollination in habitat fragments causes lowfruit set. Proceedings: Biological Sciences 267: 1149–1152.

Bosch, Maria, and Nickolas M. Waser. “Effects of local density on pollination and reproduction in Delphinium nuttallianum and Aconitum columbianum (Ranunculaceae).” American Journal of Botany 86.6 (1999): 871-879.

Kulling, Sabine E., and Harshadai M. Rawel. “Chokeberry (Aronia melanocarpa)–a review on the characteristic components and potential health effects.” Planta medica 74.13 (2008): 1625-1634.

 

The Bacterial Breakdown of Dietary Fibre in the Gut

It has been known for many years that humans consume a type of dietary fibre called xyloglucan; however, how it’s degraded in the human gut has always been unclear. A recent study published in Nature now indicates that xyloglucans (XyGs) are broken down by a specific type of bacteria that we have in our digestive system. Dr. Harry Brumer from the University of British Columbia collaborated with the University of Michigan and University of York to isolate the gene in the bacteria responsible for this process.

XyGs are found in the cell walls of fruits and vegetables such as lettuce, tomatoes, and eggplants. According to Dr. Brumer “it’s [been] known for many years that our gut bacteria could ferment [XyG] and turn it into short chained fatty acids which we can then uptake and get energy from.”

The following video outlines how bacteria help our body digest this specific type of dietary fibre:

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Gene knockouts were performed to isolate the specific set of genes in the bacteria, Bacteroidetes Ovatus (B. ovatus), responsible for degrading XyGs. By doing this, they were able to see how taking out these specific genes would affect the growth of these bacteria.  Dr. Brumer explains the importance of having B.ovatus in our gut: “our own genome only encodes very few dietary enzymes that break down carbohydrates so that’s really the key thing about these gut bacteria.”

To further help him understand how this process works, three-dimensional computer models were built of the enzyme made by B.ovatus. This gave Dr. Brumer a visual understanding of how the degradation of XyGs occurs at the molecular level.

So how is this relevant to the general public?  In the following podcast, Dr. Brumer explains the basics of his research on dietary fibre degradation and its importance for the average human being.

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As Dr. Brumer explains, “we’ve existed for thousands of years not knowing anything about what’s going on in our gut but the more we know, the more we can positively impact that.”  Dr. Brumer goes on to add that “if you go an antibiotic regiment, you actually damage the bacteria population in your gut. When you link that together with what we know about the capacity of these bacteria to break down complex carbohydrate, dietary fibre, you realize that well maybe you want to think a little but about balancing your antibiotic treatment.”

According to Dr. Brumer, “you are much better eating a vegetable rich diet.” Nevertheless, he does not “advocate [one to be a] complete vegetarian” either. “You need meat to provide protein and it can be challenging for people who are on a strictly vegetable based diet to get enough protein” in their body through alternative sources. Therefore, it is essential to keep a balance between both.

In summary, we harbour a symbiotic relationship with the bacteria in our gut. So keep your gut bacteria happy and they will keep you healthy!

 

Blog post by Ramen Kaur Sandhar, Sean Liu, and Sam MacKinnon

Image by Sam MacKinnon

Sea lampreys help scientists fill in gaps in our evolutionary history

A group of researchers at the University of British Columbia recently found that sea lampreys, an ancient species of jawless fish, appear to respond to stress much more differently than scientists originally thought.

Many species of lampreys are parasitic. Sea lampreys lack jaws and have suction-cup-like mouths that are lined with teeth, which they use to latch onto fish and suck their blood.
Source: Shutterstock.

The paper, which was published in General and Comparative Endocrinology in 2013, detailed a two-year-long experiment that culminated in some unexpected results. The researchers were attempting to determine whether previous assumptions about stress regulation in lampreys were true. By injecting lampreys with certain chemicals, called hormones, that are turned into “stress hormones” in other vertebrates, the researchers checked the lampreys’ blood levels for these “precursors” and for the stress hormone, cortisol, to see whether lampreys also turned each of these precursors into cortisol.

Click image to enlarge.
Simplified diagram of the classic stress response seen in many vertebrates.
Source: Jenny Labrie.

For years scientists had assumed that lampreys, like other fish, had a stress response that involved the same three types of hormones – corticotropin-releasing hormone (CRH), adrenocorticotropin (ACTH), and cortisol – that are seen in humans and other animals. These three hormones and their involvement in the stress pathway is discussed in the video below, as well as what is already thought to be true about the evolution of the stress pathway.

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The researchers found that, similar to other animals and to fish, lampreys do respond to CRH with increased levels of stress. CRH is a precursor to stress hormones in different species; in humans it is cortisol, which has been popularised over the past few decades as the concept of “stress” has received increasing amounts of attention – both from academia and the popular media. The lampreys injected with CRH displayed increases in their own type of cortisol, indicating that they were indeed experiencing stress in response, just as humans would.

Unexpectedly, the lampreys did not respond to several types of ACTH that they were injected with. In both humans and other fish, ACTH is the hormone that is released in response to CRH and eventually stimulates cortisol release, which causes classic signs of an activated stress response (e.g., increased heart rate).

What does this mean? Well, yes, scientists were once again mistaken; lampreys are not just like every other fish. But why should this matter? Who cares about this 505-million-year-old fish?

Click image to enlarge.
Source: Wikimedia Commons. Originally illustrated by Ernst Haeckel, and published in ‘Generelle Morphologie der Organismen’ (1866).

As it turns out, we all should. Contrary to popular opinion, scientists don’t know everything there is to know about human evolution, but we can fill in some of our knowledge gaps by studying lampreys. A better understanding of stress regulation in lampreys helps us better understand how this system has evolved since the time of these early vertebrates. Humans diverged from lampreys 500 million years ago, and we are related to them – as uncomfortable a thought that may be for some people. This link means that lampreys may be key to understanding the origins of biology in many higher vertebrates – including humans!

Perhaps for this reason alone it is worthwhile to strive to conserve lamprey species, and this research does also have implications for protection of certain lampreys, as discussed in the podcast below.

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Some have hailed the sea lamprey as an up-and-coming “evolutionary developmental model of choice.” Clearly, even blood-sucking parasites have their place in nature’s plan.

Text, video, and podcast by Jenny Labrie, Kelly Liu, Rubina Lo, and Kathy Tran.

References

Close, D.A.; Yun, S-S.; Roberts, B.W.; Didier, W.; Rai, S.; Johnson, N.S.; and Libants, S. (2013). Regulation of a putative corticosteroid, 17,21-dihydroxypregn-4-ene,3,20-one, in sea lamprey, Petromyzon marinus. General and Comparative Endocrinology, 196: 17-25.

Kimura, M. (1969). The rate of molecular evolution considered from the standpoint of population genetics. Proceedings of the National Academy of Sciences of the USA, 63(4): 1181-1188.

Nikitina, N.; Bronner-Fraser, M.; and Sauka-Spengler, T. (2009). The sea lamprey Petromyzon marinas: a model for evolutionary and developmental biology. In K. Behringer (Ed.), Emerging model organisms: a laboratory manual (pp. 405-421). Cold Spring Harbor, NY: CSHL Press.

Further reading

The hormone, cortisol

The sea lamprey and its cousin the Pacific lamprey

The stress response

Lampreys in the news

Scientists find genes linked to human neurological disorders in sea lamprey genome

Sea lampreys provide a unique solution to gene regulation

Lamprey research sheds light on nerve regeneration following spinal cord injury

Lampreys give clues to evolution of immune system

Saving Nature’s Music: Tracking the Migration of Swainson’s Thrush

Every year, billions of animals travel long distances in a process called migration. Although animal migration has occurred for millions of years, and is  the largest biological event on Earth, there is still a lot that scientists do not understand.

Songbird migration is especially difficult to track because most birds travel alone at night. Previously, scientists used unique identification markers called bands to track birds. Banding is a very limited technique, as it only provides scientists with two locations of the migratory routes.  This technique provides no information on how the birds got from point A to point B.

Swainson’s Thrush (Catharus ustulatus) with light-level geolocator
Photo: Kira Delmore

Kira Delmore, a PhD student at the University of British Columbia, used cutting-edge technology called light-level geolocators to track the migration of the Swainson’s Thrush from June 2010 to July 2011. She found that Swainson’s Thrushes in Vancouver and the Sunshine Coast took dramatically different routes to reach their wintering grounds than birds in Kamloops.

“A migratory divide is something where two populations come into contact but they migrate in different directions. [Previous studies] suggested that a divide existed and we’ve been able to confirm this with the geolocators… it’s really the first time that this has been done,” said Kira.

Light-level geolocator
Photo: Morgan Haines

Geolocators weigh about four grams and record light intensity data that researchers use to estimate location. Using this information, Kira was able to determine the different migratory paths taken by both groups of the Swainson’s Thrush.

 

This video contains more information on geolocators, how researchers catch birds, and discusses a special type of migration called loop migration that Kira was able to document.

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Not only do songbirds provide natural music, they are  important for the ecosystem. If we continue to see declines in their populations, many other species will also suffer.

Kira’s findings have helped identify several locations that are important to the Swainson’s Thrush. “These guys are migrating huge distances, they’re tiny, they need to acquire all the resources they can when they stop. So its really important that these locations are conserved so they can acquire those resources to complete this migration.”

The following podcast contains more information on the importance of songbirds and their conservation.

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Being able to understand the impact of migratory divides will help researchers gain insights into evolution. Now, Kira is trying to uncover “the genes that are associated with migration and migratory routes.”

Light-level geolocators are smaller than a quarter, yet are poised to help solve a mystery as large as the Earth itself. It stands as a testament to the power of science; its ability to use something so small to help understand something so big.

By Morgan Haines, Qianhui Sun, and Nitish Khosla

Delmore, K. E., Fox, J. W., & Irwin, D. E. (2012). Dramatic intraspecific differences in migratory routes, stopover sites and wintering areas, revealed using light-level geolocators.Proceedings. Biological Sciences / the Royal Society,279(1747), 4582.

Come again? Researchers figure out how our ears tune out of conversations

 Have you ever had a conversation that was so boring that you found yourself tuning out? Did you instead find yourself focusing on some other noise be it a conversation nearby or the chirping of a bird?

The human ear has the incredible ability to focus on sounds of specific frequencies while simultaneously filtering out background noise. This is why we can sustain conversations in loud atmospheres. How the human ear carries out this incredible feat has been unknown until recently.

File:Anatomy of the Human Ear.svg

Ear: Source Wikimedia Commons – the Ear

On March 18, 2014, a research team led by MIT graduate student Jonathan Sellon published a paper that uncovered this mystery. They found that the size of the tiny nanopores in the tectorial membrane (a small, viscous inner-ear structure) played a key role in sound filtration. The researchers studied genetically mutated mice that had different sized pores in their tectorial membranes.

Before we go on to discuss the findings of this study lets take a brief look at how sound travels in the ear and the function of the tectorial membrane. When sound waves travel in the air they compress air molecules into compressions. When these compressions enter the ear canal and encounter the ear drum they cause it to vibrate. These vibrations in turn cause the 3 small bones of the middle-ear (the malleus, the incus and the stapes) to jiggle and push upon the cochlea, a fluid-filled spiral structure that looks like a snail shell.

 File:Organ of corti.svg

Tectorial Membrane: Source Wikimedia Commons – the tectorial membrane

Lining the inside of the cochlea are small hair cells that are covered by the tectorial membrane. The tectorial membrane has small pores known as nanopores (on average 40nm in diameter in mice). When the vibrations reach the cochlea, the tectorial membrane within slides back and forth over the layer of hair cells. This induces electrical signals to be sent to a special part of the brain that processes sound. You can think of the tectorial membrane as a carpet sliding across a wooden floor and the friction that arises as the electrical signals triggered.

So, what did the researchers find?

The researchers had 2 main findings. Firstly, they found that mice with smaller pores in their tectorial membranes could focus on sounds over smaller frequency ranges while those with larger pores could not focus on sounds as well. Secondly, they found that mice with larger pores could hear sounds over a greater range of frequencies (they have a greater overall sound sensitivity) as compared to mice with smaller pores. Therefore, optimal hearing is achieved by intermediate sized pores.

What makes this study particularly exciting is that Scientists have yet to make hearing aids that can select frequencies like the natural ear does. With these new findings better hearing aids can be produced.

So, the next time someone catches you not listening to them you can always blame your tectoid membrane!

Fardowsa Yusuf

Jonathan B. Sellon, Roozbeh Ghaffari, Shirin Farrahi, Guy P. Richardson, Dennis M. Freeman, Porosity Controls Spread of Excitation in Tectorial Membrane Traveling Waves, Biophysical Journal, Volume 106, Issue 6, 18 March 2014, Pages 1406-1413, ISSN 0006-3495, http://dx.doi.org/10.1016/j.bpj.2014.02.012.
(http://www.sciencedirect.com/science/article/pii/S0006349514001891)

http://www.dailymail.co.uk/sciencetech/article-2585686/What-dear-Researchers-discover-tiny-nanotunnels-ear-let-tune-conversations.html

http://www.wired.com/wiredscience/2014/03/ear-nanopores-hearing

Hooked on Hookah

Compartments of a Hookah via http://upload.wikimedia.org/wikipedia/commons/0/0f/Hookah-lookthrough.svg

Hookah (also known as shisha or narghile) is a waterpipe that is used to smoke tobacco, flavoured molasses , and other substances. Its origins date back to India several hundred years ago. It was popularized when it first arrived in Turkey during the Ottoman empire. The actual smoking instrument itself is called a hookah where as the tobacco that is soaked in honey or tobacco is called shisha. There are different compartments that make up the apparatus such as the bowl, windscreen, hose, stem, water container, ashtray, and the gasket. The flavoured tobacco or non-tobacco molasses mix is packed into the bowl, covered with tinfoil, and then hot coals are placed on top.  The smoke passes through the water chamber and is then inhaled by the user. Hookah comes in many different flavours such as grape, chocolate, and mint.

In recent years, shisha has become more and more popular, especially among younger people. It is also become more and more common in different media such as music and television. Along with this increase in acceptance in the North American culture specifically, there is also a  notion that hookah isn’t that harmful, or at least not compared to other substances such as cigarettes. But is it really?

There is a misconception that smoking hookah is relatively safe. The charcoal used to warm up the tobacco produces large levels of carbon monoxide, metals such as arsenic, lead, and nickel, plus carcinogens. The amount of smoke that is inhaled during a shisha session is also troublesome. A normal sitting lasts around 45 minutes to an hour which translates to a few hundred puffs of heavy drags. The smoke is associated with an increased risk in developing ailments such as heart and lung disease. Sharing the mouth piece with other participants also increases the risk of transmitting diseases such as oral herpes or hepatitis.

A glimpse into the past of Hookah via http://upload.wikimedia.org/wikipedia/commons/9/98/Stanis%C5%82aw_Chlebowski_-_Turecki_hookah.jpg

Another misconception related to hookah is that it is not thought to be addicting. Smoking tobacco with a hookah delivers nicotine to your body, the addictive portion of cigarettes. The reality of the matter  is that smoking hookah is just as dangerous as smoking cigarettes, if not more.

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Vdeo comparing the hookah and cigarettes

Image of Hookah smoke being blown out via http://www.theepochtimes.com/n2/images/stories/large/2011/08/14/Shisha-81316107.jpg

Non-tobacco hookah is the healthier alternative to smoking tobacco with a hookah, but it is still dangerous in it’s own right. It is important that the general public is properly educated about the adverse effects of this practice to avoid unexpected health problems. This problem has led countries like Canada to crack down harder on this substance for the best interest of its residents. It is best to avoid these harmful products, but if you do indulge, moderation is best.

Zohaib Mahmood

REFERENCES:

http://www.quitshisha.com/blog/social-effects-of-shisha/12-secrets-you-should-know-about-shisha/

http://www.cdc.gov/features/hookahsmoking/

http://www.mayoclinic.org/healthy-living/quit-smoking/expert-answers/hookah/faq-20057920

http://www.health.umd.edu/sites/default/files/Hookah%20Brochure-%20Final_0.pdf

http://www.theguardian.com/society/2011/aug/22/shisha-smoking-how-bad-is-it

http://www.hookahu.com/pages/Hookah-Components.html

Exercising regularly leads to better memory

Working out and exercising for most people mean a healthy lifestyle and a way to stay fit. At the same time, this may not appeal to some people because they are simply not into physical activity and would rather spend the time doing something else they prefer. A new study by Professor Art Kramer and his research team from University of Illinois now show that exercising regularly for at least six months to a year can lead having better memory and an increased improvement in problem solving skills. This adds on to what scientists’ previous know about the benefits of exercising.

A simple task like jogging can lead to better memory

Previously, the benefits of exercise were all found to be based around better health, lowering cardiovascular diseases, and such. The new idea of better memory that comes with exercising can be one major factor that leads to more people exercising. This idea was tested by combining neuroimaging work  with

Neuroimaging (image of brain activity) was one technique used in Kramer’s study

studies in brain networks. For someone with a regular exercise routine of 15 to 45 minutes per day, their neuroimaging shows more activity as more oxygen was pumped into their brain. An improved cognition, increased attention span, and the ability to multitask are also benefits found with exercising in both young and older people. The major reason to this is due to the size of the hippocampus increases by 2% due to regular exercise and this part of your brain is essential for memory storing, forming, and organizing. When you hippocampus increases by 2%, it also means that the aging of your brain decreases by a maximum of years. This is very valuable to older adults because their risks of getting dementia and Alzheimer’s disease are also decreased when this occurs.

Hippocampus – important for retaining information

Many, especially students, might argue that taking out an hour out of their day is a difficult task due to school, study, work, and other arrangements; however the amount of time wasted each day surfing the web, watching TV, and being unproductive can definitely be used on going to the gym or heading out door for a light jog. For any of you reading this and have tried to find ways to memorize material better for exams, it’s time for you to get off the computer and head out for a quick jog.

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Work Cited

Nikolaidis, A., Voss, M., Loan, V., Erickson, K., & Art, K. (2013). Fmri correlates of transfer in training with a complex task. Journal of Cognitive Neuroscience, , 162-162.

Van Praag, H., Shubert, T., Zhao, C., & Gage, F. (2005). Exercise enhances learning and hippocampal neurogenesis in aged mice. Journal of Neuroscience, 25(38), 8680-8685. doi:10.1523/JNEUROSCI.1731-05-2005