Category Archives: Biological Sciences

A new and natural pathway to nitric oxide!

Nitric oxide (NO) is one of the most widely-produced gases in the human body, and has been shown to play a major role in the function of the cardiovascular, nervous, and immune systems. This means that it has implications in the treatment and management of many conditions such as erectile dysfunction, muscle soreness, and Type II diabetes. Despite the numerous processes in which nitric oxide play a role, there are only two known routes of production in living organisms. 

Research jointly published by the Institute of Pharmaceutical Biotechnology at the Zhejiang University School of Medicine in Hangzhou, China and the Department of Chemistry at the University of British Columbia examined one alternative method to the production of nitric oxide. In this pathway, two enzymes are used to generate a chemical compound known as streptozocin that creates NO as a byproduct.

Simplified schematic of the two reactions that occur to produce the N-nitroso compound streptozocin and nitric oxide (NO) as products

This work provides support to the idea that there may be alternative routes to the synthesis of this critically important compound. We spoke to Alyssa Henderson about her work on the project, her experience with research in general, and some of the challenges she faced while working on this publication.

Streptozocin is part of a larger class of N-nitroso compounds, which are identified by the presence of an -N-N=O group in its structure. Alyssa’s research was motivated by the natural presence of N-nitroso compounds in natural products. It was proposed that these compounds, and the biological pathway of its production, could be significant in the production of NO.

Tests were done with a solution containing components of E. coli and stzE (one of the enzymes isolated from the genome of streptozocin), and it was found that stzE is necessary to produce the compounds involved in the second step of the process. 

The next step in this two-enzyme pathway was similarly isolated from the streptozocin genome, and was found to be necessary for the production of the products shown below. Alyssa’s research suggested that nitric oxide is produced in the conversion of compound 3 to compounds 4 and 5, which is catalyzed by stzF.

Structure of the products generated from the second step of the two-enzyme pathway.

In order to explore how widely distributed these genes are, Alyssa’s team found 40 enzyme pairs with similar functions to the stzE/stzF enzyme pair in a variety of soil-dwelling and plant-associated bacteria, which further supports the idea that natural routes to nitric oxide synthesis exist. 

Cell cultures of some of the soil-dwelling bacteria found to have similar enzyme functions to the stzE/stzF pairs

The significance of enzymes in these soil microbes is discussed in the podcast below:

While this paper doesn’t fully explain all of the possible processes that may be involved in the natural production of nitric oxide in the environment, it sets the stage for important advancements in the field.

Stranger danger, the scary truth about invasive species

Source: Greenberg

Some are sharp, some are spotted, and some are beautiful looking, but all invasive species are bad for public lands. Invasive species are organisms that cause ecological or economic harm in a new environment where it is not native. An invasive species can be introduced to new ecosystems through the ballast water of ocean-going ships, intentional and accidental releases of species, aquarium specimens or bait and other means.   

Dog Strangling Vine: Ontario’s Invading Species

Some nonnative species don’t cause harm but those that do can cause the extinction of native species. They often compete with native organisms for resources, reduce biodiversity and alter natural habitats. For example, in Toronto, the dog-strangling vine is an ongoing problem in meadows and understories. In meadows, the plant acts as a filter on plants that are smaller or weaker in competing for resources and takes over the whole landscape. In understories, they were found to replace plants of similar niches. To learn more about this invasive species, watch the interview with expert Darwin Soudhi below. 

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Invasive species thrive and flourish at new locations because of the right biological properties that allow them to grow quickly in numbers. Once they secure their location, they usually reproduce and spread quickly and out-compete native plants and animal species for resources. Most invasive species can survive in a variety of different habitats and climate regions. They often are free of predation and disease. 

These changes, small or large can result in huge economic impacts and fundamental disruptions in all ecosystems. No matter where they came from, how they got here or what trouble they bring, invasive species are a serious concern and immediate action needs to be taken. For more information on how you can help reduce the effects of invasive species, listen to the podcast linked below.

https://soundcloud.com/jumpysnake/so-podcast-final/s-rEmNg

-Ryan Chew, Cindy Liu, Noah Rudlowski

The pUgly Truth About Flat-Faced Dogs

Image of a pug

Pugs are universally loved and instantly recognizable; yet their iconic face may be the reason for many of their health issues. Courtesy of Charles

Dogs unite and bring joy like little else can.  The sight of their cute noses snuggling up to us can make us feel better and melt even the steeliest of hearts, yet their little snouts may be one of the biggest problems hounding the health of our furry family members.

Pugs are one of the most instantly recognizable dog breeds in the world because of their flat snouts. Like other dogs with flat snouts, pugs are known as brachycephalic and suffer from numerous breathing complications. One of the most fatal of these complications is brachycephalic syndrome and occurs during times when a dog overexerts itself due to excess activity or heat and is not able to oxygenate its blood in time, leading to death.

Most people think that susceptibility to this disease depends on breed, however research published in 2015 by a team from the Royal Veterinary College in the UK suggests otherwise. The researchers looked at 700 dogs of varying breeds and found that the risk of these dogs suffering from brachycephalic obstructive airway syndrome increased very quickly for dogs with shorter snouts. In the study, no dog whose snout was at least half the size of its head was affected with breathing issues, while 80% of the dogs whose snout was less than a tenth of the size of their head suffered. The research seems to present definitive evidence for the added health risks for flat faced dogs, yet the number of pet owners that buy these breeds increase daily.

Many Dogs

Note the differences in how the snout portrudes in the breeds of dog pictured above. Courtesy of Wikimedia Commons

The shape of an organism is hugely important in the wild. Species live and die based on how well their adaptation suits their environment. However, dog breeds are unique. Due to our close relationship with the species, new dog breeds are usually the result of artificial breeding. Short snouts are specifically bred for in dogs because some people love how it looks. While individuals are certainly within their rights to choose to adopt a dog whose aesthetic they like, it seems cruel to subject a living animal to a lower quality of life in order to preserve their look. As the demand for these cute animals increases, unethical or unqualified breeders are pushing these genetic lines to the extreme in order to provide a product that they think consumers want.

For a solution to this issue to be effective it must change some of our fundamental buying behaviours. We cannot let the idea of genetics being a product completely overrule the idea of a dog as a living, breathing organism with rights. Dogs provide us with unconditional love and companionship, the least that we could do for them is make sure that they can breathe properly.

Finally, I have attached a link for owners of dogs with flat faces with helpful videos to help you identify abnormal noises in times of exertion from your dog.
Cambridge University Department of Veterinary Medicine

– Souvik Maiti

Researchers Looking into 2 Week Allergy Treatment

Globally, 220-520 million people suffer from food-related allergies that range from mild discomfort to being the cause of death. Chances are, there is someone in your course affected by this chronic illness. Currently, there are no approved treatments for these allergies other than completely omitting them from your diet, using antihistamines or epinephrine when allergy symptoms appear, or oral immunotherapy. However, it’s very difficult to avoid cross-contamination, especially when you need to eat food someone else has prepared and immunotherapy takes 9-12 months, causing allergic reactions along the way. But what if there was a way to desensitize, even completely remove the immune systems’ response to food that cause allergies in as little as 2 weeks without causing a reaction?

From a small study released on Nov 14, 2019, the researchers from Sean N. Parker Center for Allergy and Asthma Research at Stanford University has found that when targeting the alarmin IL-33 (a signal that initiates inflammatory responses) in peanut-allergic people with etokimab (an antibody injection) there was a 73% increase in the tolerance threshold for the allergy compared to the placebo group. These people could eat moderate amounts of peanuts (no more than 300 mg) 15 days after the injection without having to be expose to the allergen beforehand. This percentage dropped to a 57% increase after 45 days.

Since this is a relatively new study, there are still some improvements to be made on the procedure itself. The sample of the double-blind experiment was only 20 adults with 15  adults receiving estimable and 5 adults receiving the placebo, and the results were self-reported, which can cause a lot of variability in the data. However, the results from this small experiment was promising, and personally, I hope that etokimab will be available for the public use in the next few decades. It would be extremely helpful to eat out without having to worry about being rushed to the hospital due to accidental contamination or even just to see what peanuts would taste like.

-Sharon Li

Is Antibiotic Resistance Our New Biggest Threat?

Throughout history, our advancements in medicine have allowed us to live longer, prevent the spread of certain infectious diseases, fight infections and overall improve our quality of life. However, in recent years some of the important medical breakthroughs we have made as a society have been threatened by antibiotic resistance.

What is antibiotic resistance? In short antibiotic resistance is when antibiotics become less effective at treating the desired infection. It is caused by bacteria who evolve to be able to resist the drugs intended to kill them, so without antibiotics to terminate them, these bacteria begin to flourish and can cause persistent infections which could potentially ultimately lead to death.

A comparative view of non-resistant bacteria and drug resistant bacteria. Image Source: flickr

According to a 2018 study, in 2018 antibiotic resistance rates in Canada were 26%. According to projected models an increase in antibiotic resistance rates in the future could severely impact Canada’s economy. The study states that if resistance rates were to increase to 40% and a possible worse case 100% by 2050, Canada’s economy would be smaller. It could cause a decrease in the employment force which is said to likely have the largest impact in labour intensive jobs. On a global scale, antibiotic resistance could also have severe socioeconomic consequences. It is believed that the cost of treatment for resistant bacterial infection could approximately be 700 US dollars. This will have the largest impact on those who have a lower income and could potentially increase the presence of a socioeconomic divide. So, aside from the obvious medical impacts of antibiotic resistance, there is the various associated issues that arise which can decrease societal progressions.

Currently scientists are attempting to find solutions to this serious threat. A biotechnology company called Genentech has recently had a team of scientists that have developed a drug that can more easily penetrate the cell membranes of certain bacteria. Additionally it proved to be effective against various multidrug-resistant forms of some of these bacteria. Although this drug development is in its early stages, it could be very impactful in reducing antibiotic resistance and solving some of the resulting issues.

 

Image Source: flickr

This week (November 18th– 24th) is considered World Antibiotic Awareness Week, which is important in spreading awareness to the public about how to effectively use antibiotics to mitigate potential increases in antibiotic resistance. Some common ways that you can decrease antibiotic resistance rates are:

  • Follow your medical prescription properly (don’t skip medication days)
  • Don’t take antibiotics for infections such as a cold or the flu
  •  Try to with the help of a doctor see if there are possible solutions to provide comfort aside from the use of antibiotics.

Simple steps like these can be impactful in decreasing antibiotic resistance rates and gives us the power to fight against this looming threat.

 

 

-Shania Mander

Fatal Familial Insomnia: Dying without sleep

Sleeping. Source: Flickr

What if one day you woke up and didn’t have the ability to fall back to sleep again? Unfortunately, this is the devastating reality for almost 50 families around the world today.

Fatal Familial insomnia (FFI) is a rare neurodegenerative disease caused by prions, which are abnormal forms of normally harmless proteins found in the brain. Since this mutation is dominant, in that one copy of this mutated gene can automatically lead to its expression, this disease affects both males and females equally. Furthermore, individuals with FFI normally present symptoms of this disease between the ages of 20 to 61 years old. These symptoms include an onset of dementia, speech problems, and coordination problems.

Dementia. Source: Flickr

 

The tragic family curse

Generation. Source: Flickr

FFI is a genetic disease, thus it is able to be passed on through generations. Fortunately, however, if one parent has this genetic mutation, there is only a 50% chance that it would be passed on to their offspring. Nonetheless, the following generations that receive this mutation eventually succumb to this disease without escape.

This inevitable disease causes death of neurons in the brain and the first symptoms are apparent at around the age of 50 and are followed by four symptomatic stages.

There are four stages that individuals with FFI encounter. The first stage is insomnia, which is followed by the second stage of hallucinations and severe panic attacks. The third stage is defined by weight loss and the total loss of the ability to sleep and lastly, the fourth stage is marked by dementia. Each of these stages are short as the rapid progression of FFI causes death within 12 to 18 months.

The main cause of death from this disease is due to progressive physical and mental deterioration, which is the consequence of one of the fatal symptoms of FFI, the inability to sleep.

 

Searching for a cure

FFI is a subtype of prion diseases which itself has no cure. Additionally, since FFI is a rare disease, it is still incurable as there has been limited research done on this disease. However, there are some potential treatments that are being examined today.

Currently, there is an ongoing 10-year trial being conducted on individuals that carry this genetic mutation. In this study they observe the effects of the antibiotic doxyclycline on pre-symptomatic patients, as researchers believe the use of this antibiotic may be an effective way to prevent FFI in individuals who carry this disease.

Sadly, effective long-term treatments for FFI are non-existent. Therefore, presently, short-term treatments are being used. One of these treatments include the used of sedatives, such as sleeping pills, which can temporarily help manage the symptoms of insomnia. However, its effectiveness varies from person to person.

Although FFI is a rare disease, it still affects families around the world today. Therefore, without a cure, this leaves families hopeless for their future ahead. However, with research currently being conducted, hopefully this can provide individuals with FFI a fighting chance to overcome this disease.

– Karina To

Increased screen time can lead to deficient brain development in children

Have you ever seen a tablet or phone given to a child as a solution periods of crying or whining? Giving an infant a portable device is an easy and harmless remedy to infant tantrums right?

Not exactly, a recent study published by JAMA pediatrics reveals that an increased amount of screen-based media use can lead to lower language retention and literacy skills in prekindergarten children.

Child playing with tablet Source: PxHere

Researchers studied 69 children from ages 3-5, to determine a possible existing relationship between screen-based media use and brain development. From their study, they were able to conclude that children with an increased screen time, compared to the guidelines of the American Academy of Pediatrics (AAP), showcased a lower microstructural organization and myelination of white matter tracts that support language and literacy skills.

Myelination of white matter tracts is crucial to the cognitive development of infants as it involves the formation of a myelin sheath around a nerve to allow the a quicker displacement of nerve impulses in the brain.

Cross section of human brain, the lighter parts are the white matter and the darker parts are grey matter. The white matter is coloured white because of the myelin that surrounds the nerve fibers in the brain. Source: Wikipedia

From their research, lower amount of white matter in childrens’ brains lead to a decreased level of derivation of meaning of objects, symbols, and letters, which scientists believe plays a crucial role in literacy development.

To develop these conclusions, scientists analyzed the results of a ScreenQ survey (completed by the child’s parents), which is based off of four main factors of the AAP guidelines involving the child’s access to screen, their frequency of use, the content viewed, and interactivity or co-viewing. From the survey, the researchers compared the survey results to MRI scans of the the children’s brains and also to results from a series of communication tests designed for children with developing literacy skills.

The solution to these neurobiological risks in children may be very tricky as screen-based devices can be found in almost every household and are used daily by the general public. However, a way to prevent deficiencies in child brain development can be to follow the guidelines proposed by the AAP. Some of the recommendations are:

  • For toddlers younger than 18-24 months, avoid any form of media other than video chatting
  • For children ages 18-24 months, only allow children to watch media with parents (co-viewing) to begin communication development though watching and talking with parents
  • For children ages 2-5, allow only 1 hour a day of media exposure (educational programming) through co-viewing if possible.

To see another take on the topic, how portable device use may be beneficial to child cognitive development, check out this video:

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-Bernice Huynh

From Waste to Treasure: Civet Coffee

masked palm civet

Masked Palm Civet (Image is in the public domain. Taken from WPClipart. https://www.wpclipart.com/animals/wild_cats/civet/Masked_Palm_Civet.png.html)

Would you go out of your way to eat someone else’s poop? If you posed this question to most people, chances are high that they would look at you like you’re crazy and shuffle away before they have to experience anything else that comes out of your mouth (and possibly other orifices). However, for many people from Indonesia and around the world, the most exquisite coffee comes from only one source; the digestive tract of the Asian palm civet (Paradoxurus hermaphroditus).

 

The Producer:

Civets are not notorious caffeine hounds, and instead eat coffee cherries for the sweet fruit pulp. They are mostly solitary animals, and prefer to wander about for tasty cherries at night. Even though berries and fruits make up a large portion of the civet’s diet, they are actually omnivorous, eating little mammals and insects as well.

Civets were naturally found in South East Asia, especially in Indonesia where the practice of harvesting civet coffee started. Since then civets have been introduced to multiple islands in the region as far as Japan due to growing demands for the coffee.

The Process:

Kopi luwak, as it is known, is named after the Indonesian words for coffee kopi, and the civet, known locally as luwak.

Kopi luwak is made from Coffea arabica and Coffea canephora, the two major cultivated coffee beans around the world. What makes kopi luwak special however is the addition of the biochemical reactions on the coffee bean as it passes through the civet’s digestive system.

The traditional method for the collection of these ‘processed’ beans involves collecting the feces of wild civets from piles at the edge of their territory called civetries. The partially undigested beans are then cleaned, further processed to remove undigested fleshy layers of berry, and roasted. These roasted beans can then be brewed into coffee normally.

Indonesian farmer holding digested, uncleaned, unroasted coffee beans.

Indonesian man holding kopi luwak beans before they have been cleaned or roasted. This is the product coming from the civet. (Image is in the public commons, from user HaztechGuy, Wikimedia Commons)

The Difference:

In order to understand the differences between kopi luwak and non-civet coffee, Dr. Massimo Marcone, a professor at the University of Guelph did multiple comparative analyses of the differences between kopi luwak and non-civet C. canephora harvested in the same region during the same time in 2002. Using a method called SDS-PAGE to identify proteins in the civet-coffee bean he found that the digestive juices in the gut of the civet had caused significant degradation of proteins in the coffee beans.

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For more detail on SDS-PAGE please watch the short video above (3:16)

Proteins are long chains made up of amino acids, and digestion causes the links between subsequent amino acids to break up, allowing the heat from the roasting process to ‘hit’ more of the proteins in the coffee bean.

Marcone argues that the maillard browning reaction, on having access to more amino acids would have a significant impact on the aroma and flavour of the roasted beans.

The Cost:

Whether or not the change in flavour and aroma profile enhances the experience of drinking the coffee is up for debate between professional coffee tasters (called Q Graders). What isn’t up for debate is that the coffee can fetch prices of up to $600 CDN per lb. As a comparison, the price of silver is currently trading at about $280 CDN per lb.

Perhaps the more depressing cost however remains the cost on the welfare of the civets who are being caged in larger and larger numbers to keep up with the global demand for kopi luwak. These caged civets in many instances are force fed only coffee cherries (recall that civets are naturally omnivorous), and stored side by side in cramped battery cages.

Kopi luwak is  a fascinating method of processing coffee coveted by many coffee connoisseurs around the world, but production has to take into account the tangible ecological costs of harvest.

Civet in a cage looking very sad

Civet in a Battery Cage (Taken by user surtr, Flickr Commons, https://creativecommons.org/licenses/by-sa/2.0/, https://www.flickr.com/photos/29297680@N00/5609840328)

– Souvik Maiti

Bacteria Can Change Shape to Avoid Antibiotics?!

Can bacteria now consciously make the decision to change its’ shape to avoid being targeted by antibiotics? This article titled “Bacteria caught changing shape to evade antibiotics” seems to think so. However, upon reading this article, I discovered that it’s not that the bacteria makes the conscious decision to change its’ shape in order to avoid being targeted by antibiotics, but rather, the environment that the bacteria is in allows it to shed its’ cell wall. The title of the article is extremely misleading, and can cause undeserved panic because it is implying that bacterial organisms that are damaging to humans have evolved to the point where humans can no longer control them.

TEM of L-form bacteria from Mark Leaver of Newcastle University

If you continue to read the article, you’ll also discover that this certain strain of bacteria can’t evade all antibiotics. It can only make antibiotics that target the cell wall of the bacteria ineffective. There are antibiotics specifically made for targeting cell walls because there aren’t any human cells with cell walls, which makes it easier for the antibiotics to target the right cell. However, bacteria can shed its’ cell wall under non-hostile conditions such as an environment with high sugar concentration. By shedding that wall, the bacteria makes itself harder to detect by the antibiotics and our own immune system. That means that there is one less thing to differentiate the bacteria cell from our own human cell.

With a strong and healthy immune system, the L-form bacteria can eventually be destroyed. It is a little bit more complicated for people with weaker immune systems because they need help from antibiotics, but the antibiotics are ineffective because bacteria will stay in their L-form until the antibiotics leave the system, in which case the cell wall forms again.

Ultimately, there is no need to be worried that bacteria have evolved to consciously change its’ shape to avoid being targeted by our immune system or by antibiotics because it doesn’t. All the bacteria is doing is performing the functions it is programmed to do, like setting up protection against a hostile environment whether it is with a cell wall or without one.

-Sharon Li