Category Archives: Issues in Science

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.

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

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

Mars: The New Earth?

If Earth becomes inhabitable due to the alarming rate at which climate change is occurring, is there a possibility for humans to live on Mars?

Previously, the idea of human life proliferation on Mars was mainly expressed in science-fiction. However, a recent study reveals a new application of a material to make Mars habitable for human life.

picture of Mars

Source: Pixabay

Scientists have investigated a new approach to the obstacle of terraforming Mars and making it a habitable planet through the usage of silica aerogels.

Silica aerogel is a solid and transparent material with extreme low density, and thermal conductivity. Its structure is composed of microscopic networks of silicon oxide; therefore, allowing it to be an extremely porous material with 97% of its volume composed of air. Because of these factors, currently, aerogels are widely known for its use as insulators and can be found in wetsuits, firefighter suits, skylights, windows, rockets, paints, cosmetics, and even on NASA’s Mars Rovers.

picture of silica aerogel Source: NASA

Scientists believe that due to its insulating properties, when placed in the atmospheric regions over surface areas that are ice carbon-dioxide rich on Mars, a 2 to 3cm layer thick of silica aerogel could allow constant visible light to transmit onto the surface and melt the Mars’ solid carbon dioxide into gas. The aerogel would trap the carbon dioxide gas to mimic the Earth’s greenhouse gas effect and as a result, allow for base photosynthesis to occur, perhaps granting the beginnings of life proliferation on our neighbouring planet. Additionally, this porous material is found to successfully block both ultraviolet and infrared radiation and its thermal conductivity characteristics can raise temperatures underneath to above the melting point of water, without the need for any internal heat source. The discovered key features of this material could provide scientists with the early steps to Mars’ terraformation.

The application of the silica aerogel can be tested in hostile environment currently on Earth that mimic the environmental conditions on Mars, such as Antarctica and Chile’s Atacama desert to study its effectiveness. However, additional factors to the living conditions on Mars such as atmospheric pressure, nutrient availability and dust deposition still need to be considered in this on-going research.

Although this discovery does not provide us with a solution to the Earth’s climate change, this new application of the aerogel could shift the focus on the solution to global warming indefinitely. Through this finding, perhaps the there is a possibility for humans to live on Mars after all.

More information about the synthesis of the silica aerogel can be found here:

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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

Deepfake Technology: Can you Tell what’s Real and Fake?

Artificial Intelligence (AI) has improved remarkably since its invention. It has a variety of uses from data analysis, robotics, and applications in the medical field. All these advancements have made impressive societal impacts, however are recent progressions in AI contributing more harm than good to society?

Generative adversarial networks (GAN’s) are a dual AI system which can simply be defined as AI’s which work against each other to improve each other. One AI system considered the generator, develops content and the other AI system determines whether it is fake or not. Every time the secondary AI correctly establishes that a generated piece of content is fake, it provides feedback to the generating AI so that it can improve at producing more believable content. This is an example of machine learning, as the AI systems are continuously bettering themselves from experience without the need to be specifically programmed. This AI technology is considered a neural network as it was created to resemble a human’s neural network, so that the computers will learn like humans.

This leads us to the question as to why GAN’s can be considered harmful? This is because GAN’s are used to create Deepfakes. The term deepfake is used to describe video and audio recordings which have been generated through machine learning. These videos are not real but can be very convincing.

The above video shows a side by side comparison of Robert De Niro and Al Pacino in the film Taxi Driver. In the original film Robert De Niro is the actual actor, however in this video through the use of deepfake technology the actor Al Pacino looks just as authentic as the lead.

                                                     Source https://en.wikipedia.org/wiki/File:Woman_1.jpg#filelinks

Another example of the power of GAN’s is the image above. The picture is a generated image from a GAN and despite how real or familiar this person looks the image is not of a real person. Sites such as “this person doesn’t exist”  are an entertaining way to witness the abilities of these GAN’s, as on this site every time you refresh the page a new generated image of a fake person is displayed.

For purposes like film production, the use of deepfake technology could actually be quite helpful, however it could also be used for much more damaging motives. Technology like this could be used for propaganda in political campaigns. For example videos could be produced of political candidates saying damaging words which would impact their campaign, however these videos could all be fake and a product of deepfake technology. This causes the overall manipulation of information. Additionally this causes a serious impact in the way information is communicated to the public. It also could potentially decrease the public’s trust in true information as it will become harder to decipher what is real from what is fake.

In a study earlier this year researchers had found that although currently it still takes technical skill and a team effort to produce realistic simulations of people’s faces, it is slowly developing to becoming a more automated and accessible technology. If a wider range of people have the ability to use this there are countless ways this technology can be applied; good and bad.

To prepare for this potential increase of deepfakes making its way online, we should be wearier and more critical of videos and information we are presented in the media and online. It is important for us to be aware of the presence of deepfakes so that we can be less susceptible to believing in false information.

 

 

-Shania Mander

Mars: the new Earth?

With the alarming rate of climate change occurring on Earth, will the planet the we call “home” eventually become uninhabitable?

Although it was previously believed that human life could only survive on Earth, a recent study reveals a way to make Mars habitable.

picture of Mars  Source: Pixabay

Instead of trying to make Mars more similar to Earth through atmospheric modifications, Scientists have discovered a new approach to the obstacle of finding a second habitable planet through the usage of silica aerogels.

This material, when placed over regions that are ice-rich on Mars could allow constant visible light to transmit onto the surface for photosynthesis to occur. It could also block ultraviolet radiation and even raise the temperatures underneath to above the melting point of water, without the need for any internal heat source. In addition to these factors, scientists believe that a 2 to 3cm layer thick of silica aerogel get could potentially be equivalent to the Earth’s atmospheric greenhouse effect, thus allowing the beginnings of life proliferation on our neighbouring planet.

Silica aerogel is a solid material with extreme low density, and thermal conductivity. It is an extremely porous material and is currently widely known for its use as an insulator. Currently, aerogels can be found in wetsuits, firefighter suits, skylights, windows, rockets, paints, cosmetics, and even nuclear weapons. However, this new application of the aerogel could shift the focus on the solution to climate change and global warming indefinitely.

The application of the silica aerogel can be tested in hostile environment currently on Earth, such as Antarctica and Chile’s Atacama desert. However, additional factors to the living conditions on Mars such as atmospheric pressure, nutrient availability and dust deposition still need to be considered in this on-going research.

But, through this discovery, perhaps the idea of living on Mars not too far-fetched after all.

Image of Fingers Source: flickr

– Bernice Huynh

Dogs: more than just cute!

Angus, one of two “super sniffer” dogs trained to alert their handler when they detect C. difficile. Source: Vancouver Coastal Health

We’ve all seen (or heard of) drug-sniffing dogs, but what about bacteria-sniffing ones?

Since 2016, a team from Vancouver Coastal Health has been tweaking a program that trains dogs to alert their handlers when they detect the scent of C. difficile. Over an 18-month period, the two dogs (Angus and Dodger) that have been trained for this role have detected 391 areas at Vancouver General Hospital where this bacteria was found.

Clostridioides difficile, more commonly referred to by its shorthand C. difficile or simply C. diff, are the leading cause of nosocomial (or hospital-originating) infectious diarrhea. Formerly known as Clostridium difficile, the bacterium was renamed late last year to more accurately portray the genus it falls in.

Angus and Dodger were trained with scent training kits from the Scientific Working Group on Dog and Orthogonal detector Guidelines (SWGDOG), which allowed them to identify the distinct odour of C. difficile. Microorganisms smell due to the variety of volatile chemicals they produce in response to various external factors. In the specific case of C. difficile, it is often described as having a sickly sweet or particularly foul smell.

The symptoms of a C. difficile infection can range from mild abdominal cramping to life-threatening sepsis and inflammation of the colon. The full range of symptoms can be found here. Most cases occur after taking antibiotics, which may kill both the good and bad bacteria in your gut – these are known as your gut microbiota. 

Without your normal gut microbiota, C. difficile can take advantage of this “clean slate” and proliferate in your intestine, throwing off the balance of good and bad bacteria. Within a period of several days to a few weeks, infected patients will start to show symptoms – the most common being diarrhea. Ideally, somebody with symptoms of infection will have tests done by a doctor and undergo treatment if necessary.

The progression of infection and the post-infection considerations are shown below in this graphic published by the Centre for Disease Control:

The progression of a C. diff infection. Source: Centre for Disease Control

In a study published by the Canadian Journal of Infection Control, it was found that 82% of contaminated surfaces were found in common areas. These included washrooms, hallways, and waiting rooms. Even with the most stringent sanitization procedures, it was relatively easy to find in areas that are commonly overlooked! 

One of the areas that tested positive for C. difficile contamination was inside a toilet paper dispenser – something that I personally would never think to sanitize. 

While there’s still a lot of work that needs to be done before we can train dogs to safely detect all sorts of infectious bacteria, the developments of the canine scent detection program are notable steps in the right direction. 

For more information about canine scent detection of C. difficile in Vancouver-area hospitals, you can learn more here and through this page.