The Power of Acceptance

Posted on March 22, 2020 by | Leave a comment

When life throws us curveballs, we’re often told to hit them out of the park. However, in a recent study, researchers at Yale University found that when individuals were presented with negative stimuli, those who merely accepted their situations experienced less pain and unpleasant emotion than those who reacted naturally to the stimuli.

First, the researchers introduced participants to the concept of mindfulness, which practices the acceptance of a situation. Then, participants were placed in two different groups: one subject to high heat on the forearm, and the other subject to negative images.

Through brain scans, the team observed that participants who practiced mindfulness had reduced activity in regions of the brain concomitant to pain response and negative emotion upon stimuli compared to those who reacted. Furthermore, the participants self-reported that they experienced significantly less negative affects when they accepted their situations.

Figure 1. Participants (n=16) experienced more negative affects upon seeing negative vs. neutral images (a), and upon feeling hot vs. warm temperatures (b) when they chose to react instead of accepting. The * indicates p<0.05, *** indicates p<0.0001, and error bars indicate standard error. (Credits: Kober et al. (2020))

Mindfulness is already practiced by patients suffering from chronic pain and depression, but these findings show the power that acceptance has even on individuals who have never meditated, and the team believes that mindfulness is a good way to temporarily regulate the intensity of pain and negative emotions.

HOW DOES MINDFULNESS WORK?

Scientists are still unsure of how meditation elicits responses in the brain; perhaps mindfulness allows us to feel more in control of our circumstances when we’re having negative experiences, or it reminds us that we have enough strength to make it through whatever. Nonetheless with this technique added to our repertoire, the next time life throws us a curveball we will be more prepared to deal with it.

-Athena Wang

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Microwave misconceptions: What actually happens when food is heated?

Posted on March 21, 2020 by | Leave a comment

There are several misconceptions regarding microwave ovens, many of which are simply not true. In fact, one of the most abstract claims made about microwaves is that they can cause cancer. As scientists, we understand that this is not the case. Microwave ovens exploit high wavelength radiation at the lower energy region of the electromagnetic spectrum, which is not particularly dangerous. It is thus important to dispel some of the misconceptions regarding microwave ovens, especially the myths about radioactivity and poor protection.

SEATTLE, WA – SEPTEMBER 20: An “Amazonbasics Microwave,” which can be controlled by Alexa, is pictured at Amazon Headquarters shortly after being launched, on September 20, 2018, in Seattle Washington. Amazon launched more than 70 Alexa-enable products during the event. (Photo by Stephen Brashear/Getty Images)

Radioactive species are not generated in a microwave oven

Radioactivity involves the emission of radiation from spontaneous decay of unstable atomic nuclei. Energy is lost through the release of elementary particles, such as gamma-ray photons, from the nucleus or from electron shells as x-rays. Fortunately, microwave ovens do not release these high energy species, nor do they produce such high energy species. Most microwaves use a magnetron to generate either pulsed or continuous microwaves. In the magnetron, beams of electrons are made to follow curved trajectories, in vacuum tubes, through the combination of electric and magnetic fields. The consumer microwave magnetron emits 2.45 GHz microwaves. This frequency is quite low, which corresponds to low energy. What this means is microwaves do not have enough energy to remove electrons from the food being heated. What they will do is generate heat by inducing molecular vibrations, breaking hydrogen bonds, and allowing for ionic migration of free salts in an electric field.

Microwave ovens are well protected

While the microwave door might seem simple, it is actually inherently complicated. Many different components are used to form the protective door. One of those pieces is known as a choke. In a study conducted by Kusama et al., it was found that the structure of the choke derived in a finite-difference time-domain (FDTD) analysis was very similar to the experimentally designed choke structure. This structure was also found to obtain the maximum shielding effect. While there were many parameters and factors, they assessed the metal lengths (S1 and S2) and the angle (theta). They calculated the radiation power P2 exiting the choke by changing the three previously mentioned parameters. One rather interesting finding from their paper was the effect of the angle on the shielding. This portion was conducted at fixed metal lengths of 4.00 mm and 9.01mm for S1 and S2 respectively.

Angle (theta)[Deg] 0 15.52 26.56 33.69 45.00 56.31 63.40 70.56 90
Approximate Shielding effect [dB] 21 18 27 35 29 22 18 17 16

From the data, it is evident that the shielding length changed with the angle, and the optimum angle was found to be 33.69o. This theoretical structure (S1 4 mm, S2 9.01 mm,  33.69o) was found to resemble the empirical structure, and thus the choke has been designed shield effectively. Hence, the choke and other components, which reflect microwave radiation, provide apt protection and prevent the release.

Don’t believe everything you read online; Microwaves are safe. Let me know what your opinions are in the comments.

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LEGO: Is it more than just a kids toy?

Posted on March 21, 2020 by | 4 comments

With everyone staying at home due to recent events, a common struggle is finding ways to pass the time. You remember having a box of LEGO bricks lying around, but you think to yourself “Building with LEGO? Nah, that’s just a kid’s toy!”. However, LEGO bricks are more than just a construction toy, they are also a technological marvel both in manufacturing and function.

The LEGO group first patented their iconic LEGO brick design in 1958 in Billund, Denmark. Modern LEGO bricks are made of ABS plastic, a copolymer of acrylonitrile, 1,3-butadiene and styrene, which is formed into its distinct brick-like shape using the injection molding process.  The molds are designed to produce LEGO pieces accurate to up to five-thousandth of a millimeter (0.005 mm), which is around half the thickness of a human hair. This results in a piece defect rate of 0.0018%. In other words, the LEGO manufacturing process produces 18 defective pieces out of every 1 million total pieces produced.

Left to right: Structures of styrene, acrylonitrile and 1,3-butadiene, the main components that make up the plastic used to make LEGO bricks. Source: Sigma-Aldrich

LEGO bricks have become an iconic construction toy due to the endless building possibilities they present. LEGO bricks are connected together through round nubs on top of the brick, known as studs, to tube-based cavities on the bottom of the brick. For instance, six LEGO bricks that are two studs wide by four studs long, commonly referred to as a 2×4 brick, can be combined in 915,103,765 unique ways. This number was determined computationally by mathematics professor  Søren Eilers from the University of Copenhagen in 2005.

(Photo credit: Mark Rubinchik)

Although a LEGO brick may seem like a simple piece of plastic, there is a lot more to it than meets the eye. Next time you’re looking for something to do, why not pull out some LEGO and see how many combinations you can make!

-Mark Rubinchik

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Vaccination and Herd Immunity

Posted on March 21, 2020 by | 2 comments

Herd immunity is often generated through vaccination or widespread infection. For the current Covid-19 pandemic, many scientists and experts advocate social distancing to avoid overwhelming hospitals while buying more time for the inventions of vaccines and treatments. Why is vaccination favored by scientists and medical experts than a widespread infection? How is herd immunity achieved through vaccination?

What is herd immunity?

Herd immunity refers to a means of protecting a whole community from disease by immunizing a critical portion of its populace. Vaccination protects the vaccinated person but also the people who are not immunized. However, to achieve herd immunity, we need a certain percentage of people in a community to be vaccinated.

Herd immunity, the result of a high immunization rate. Source: The National Institute of Allergy and Infectious Disease (NIAID)

To reach the herd immunity threshold, different vaccination coverages which depend on the basic reproduction number (Ro) are required. Vaccination coverage is the estimated percentage of people who have received specific vaccines. For example, measles, a highly contagious virus, has a Ro value between 12 and 18. This high Ro value calls for a high vaccine coverage which is 92-94%. In other words, to reach the herd immunity threshold, at least 92% of the population needs to be vaccinated.

The higher the vaccine coverage the better…

Does it mean that measles will die out as long as 92% of the population is vaccinated against measles? The answer is no. Dr. Plans-Rubio, an epidemiology expert in Europe, found a significant negative correlation (P<0.05) between the incidence of measles in 2017–2018 in different countries of the European Union and measles vaccination coverage with herd immunity levels in the target measles vaccination population during 2015–2017. According to Dr. Plans-Rubio, low percentages of measles vaccination coverage with two doses of vaccine and the resulting low herd immunity levels explained measles incidence and persistence of measles in the European Union in 2017-2018. To eliminate the measles virus in the European Union, W.H.O must improve routine measles vaccination coverage and conduct supplementary measles vaccination campaigns.

Linear correlation coefficient p
Coverage with two doses of measles vaccine − 0.533 0.003
Coverage with one dose of measles vaccine 0.523 0.004
Coverage with first dose of measles vaccine − 0.332 0.079
Coverage with second dose of measles vaccine − 0.559 0.002
Prevalence of individuals with vaccine-induced measles protection (Iv) − 0.580 0.001
Herd immunity gap (94.5 − Iv)a − 0.580 0.001

(Table source: European Journal of Clinical Microbiology & Infectious Diseases)

Relating to Covid-19 pandemic

Without measles vaccines, we would not have lowered the mortality rate of measles and reached herd immunity in most countries. The novel coronavirus, similar to measles, is also contagious. To lower the mortality rate of Covid-19 and reach herd immunity, the corresponding vaccine is required. Hence, every single one of us should practice social distancing to avoid overwhelming our healthcare system while scientists strive to invent the corresponding vaccine.

 

Reference:

Plans-Rubio Pedro. Low percentages of measles vaccination coverage with two doses of vaccine and low herd immunity levels explain measles incidence and persistence of measles in the European Union in 2017–2018. European Journal of Clinical Microbiology & Infectious Diseases, 2019; 38, 1719-1729. DOI: https://link-springer-com.ezproxy.library.ubc.ca/article/10.1007%2Fs10096-019-03604-0#Sec2

-Pricia

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Sugar Chemistry: A Pathway to Antibiotics

Posted on March 18, 2020 by | 1 comment

We’ve all heard it endlessly as kids. Don’t eat too much sugar, it’s bad for you. However, what if I told you that sugars aren’t all that bad and in fact, careful changes to its chemistry can lead to life-saving drugs, such as antibiotics! Just last year, researchers at the University of British Columbia, led by Stephen Withers, found a unique way to tinker with sugars’ chemical structures by using molecules in bacteria. The same bacteria found in our poop!

A view of E. Coli, the bacteria that was used by Wither’s and his team. Credits: The Philadelphia Inquirer

Sweet…but what are they?

Before we go further, let’s start with a simple question: What exactly are sugars? Sugars are molecules shaped like hexagons which are often joined to other molecules known as “acceptors”. In a way we are kind of like sugars; we find someone we like, confess how we feel, and they accept our love! Right? Wrong. As we all know the last part rarely happens and this is the same in sugars, as chemists have yet to find easy ways to join the sugar and acceptors. Luckily for sugars (and unluckily for us), Mother Nature has come up with some solutions, using helper molecules known as enzymes.

Curious as to what type of sugars chemists work with? There’s no ambiguity here, chemists use the same molecules found in sugar cubes. Yes! The ones you put in your coffee. Credits: The Verge

a solution under our noses…

Instead of struggling to find ways of joining sugars and acceptors, Wither’s team thought: Why not just use these enzymes? In other words, hijack Mother Nature. To make their idea a reality, they extracted sugar-specific enzymes from E. Coli, a bacterium that lives inside the human digestive tract. Their efforts gave them 175 sugar-specific enzymes, and from this they chose 8 enzymes that were most specific to the type of sugars and acceptors they were interested in.

“With the 8 enzymes in hand, Withers and his team could now easily make these sugar-acceptor linkages” is what I would like to report; however, things are never so simple. It turns out that the sugar-specific enzymes they got from E. Coli did the exact opposite of what they wanted. Instead of forming sugar-acceptor linkages, they were specialized in breaking them.

Unsurprisingly the savvy researchers expected this and already had a reliable strategy to reverse-engineer these enzymes from linkage breakers to linkage makers. You may be wondering how they re-purposed something to work completely opposite of what it was intended for. To reconcile this, think of this example: hammers. If you’re feeling angry one day you would likely use the hammer to smash things. However, if you’re feeling innovative one day, the hammer would help you build things by hammering in nails. These enzymes are similar; an enzyme that breaks sugar bonds differs very little from one that builds sugar bonds.

more than just a bond…

Sugars go way beyond than just satisfying your sugar fix. They are molecules essential to the maintenance and regulation of not only your body, but in most living things! Because they are found everywhere, including infectious bacteria, sugar-based molecules serve as effective antibiotics, however making these drugs are difficult. Why? Well as mentioned before, chemists have trouble making these sugar-acceptor bonds; however, the research done by Wither’s team show that this will not remain the case. On a lighter note, they also created a sugar-based molecule that had nothing to do with health; detergent. This just further shows that these bonds are far-reaching and relevant in many contexts.

Story source

Armstrong, Z.; Liu, F.; Chen, H.-M.; Hallam, S. J.; Withers, S. G. Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides. ACS Catalysis 2019, 9 (4), 3219–3227.

-Kenny Lin

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Posted in Biological Chemistry, Chemistry News, Organic Chemistry

Gold: Precious in a Different Way

Posted on March 17, 2020 by | 2 comments

Let’s face it, to most people gold is just an over-glorified rock with no real value; however, that’s not the case at all! Just this month, researchers from University College London have created a novel light-activated coating that kills infectious bacteria. The key ingredient? Gold.

upgrading with gold…

The invention of a bacteria-killing coating sounds ingenious; however, Hwang’s team was actually not the first to come up with this idea. Previous studies have already shown that coatings incorporating the chemical crystal violet can adequately kill bacteria. The problem was that the coating had to be light-activated by UV rays, which harm the skin by promoting skin cancer.

This was exactly the problem Hwang’s team looked to solve; to make a coating that did not require harmful wavelengths of light. They overcame this challenge by incorporating small clusters of gold into a polymer containing crystal violet. The result? Now this new coating could effectively eliminate bacteria upon activation with low intensity white light – the level of light found in offices.

Concentration of bacteria (CFU/mL) across three conditions after 6 hours exposure to low-intensity white light. Star indicates bacterial concentration is undetected. Sample size = 6 per treatment, error bars are standard deviation. Adapted from Hwang et al.’s data

The figure above perfectly illustrates their result. Statistical analyses show that bacterial concentration does not significantly differ between the violet crystal and control (no coating) condition. This indicates that low-intensity white light cannot activate the bacterial-killing function in the violet crystal coating. What’s interesting is that addition of gold with the violet crystal, reduces the bacterial concentration significantly to near zero values, indicating successful activation.

More than a novelty…

The results of Hwang’s study are truly impactful. It is well known that hospitals are a hotbed for infectious bacteria. In fact, 27% of surfaces in hospital rooms are contaminated with bacteria even after regular and thorough cleaning. As such, applying the coating on these surfaces will definitely reduce the chances of contracting a hospital-related disease. Who would have thought? Not only is gold more than just a hunk of rock, it can also save lives.

-Kenny Lin

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Global Warming Continues to Climb: The Pressure of Heat Stress Rises Just as Quickly

Posted on March 16, 2020 by | 1 comment

Every year the days continue to get hotter and it’s becoming very noticeable and soon it will become unbearable. As time moves forward, the effects of global warming continue to only get worse. With CO2 levels rising with no sign of slowing down, global average temperatures will rise with it. First introduced in 1975 by Wally Broecker, it has been noted that average global temperatures have rapidly been increasing since the early 1900s. Eventually the temperatures will become more than simply uncomfortable and will reach hazardous levels.

Figure 1: History of global surface temperature since 1880. Source

According to this research published in the journal Environmental Research Letters by Li et al. the result of increasing temperatures will result in an increase in cases of heat stress. Worst case scenario It could affect more than 1.2 billion people annually by 2100. That is potentially 4 times the number of people affected by heat stress presently.“Every bit of global warming makes hot, humid days more frequent and intense. In New York City, for example, the hottest, most humid day in a typical year already occurs about 11 times more frequently than it would have in the 19th century,” said lead author Dawei Li

Heat stress is caused by the body’s inability to cool down properly through sweating. This can cause body temperatures to rise rapidly with high temperatures damaging the brain and other vital organs. Various forms of heat stress include (in order from mild to extreme conditions): heat rash, heat cramps, heat exhaustion, and heat stroke. Without emergency treatment, heatstroke can cause permanent disability or even death.

Figure 2: Projected changes in global average temperature under four emission pathways. Source

Annual exposure to extreme heat and humidity are projected to affect areas currently home to about 500 million people if the planet heats 1.5°C and nearly 800 million with 2°C. The planet has already warmed by about 1.2°C above late 19th century levels.

An estimated 1.2 billion people would be affected with 3°C of warming, as expected by the end of this century under current conditions.

-Adrian Emata

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Inexpensive and rapid test to detect Lyme disease

Posted on March 16, 2020 by | 1 comment

A Great Challenge

Lyme disease is the most common vector-borne infectious disease in North America and Europe. Caused by the spirochete bacterium Borrelia burgdorferi, it is characterized by a rash in infected skin and leads to major symptoms if left untreated. Though many tests have been developed to diagnose this disease, the currently available tests are expensive and lack sensitivity (true positive rate) when it comes to the early stages of the infection.

 

Fortunately, a team of scientists from The University of California, Los Angeles, has recently developed a new inexpensive and trustful way of detecting this infection. They claim that this new procedure does not need previous training to be implemented, and that its sensitivity can be greater than 90%.

Figure 1: Lyme disease testing procedure. Adapted from ACSNANO

How does it work?

Figure 2: Illustration of the complexed reactions that lead to identification of the lyme disease. Adapted from ACSNANO

This novel test consists of a paper based multicomplex vertical flow assay, where small paper layers are covered in various disease-specific target proteins that interact with different antigens present in human samples. The protein-antigen interaction results in an observable change in colour. Upon the completion of the test, they generate a colour pattern that can be analyzed by a computer or even a smartphone. This allows possible diagnosis of the disease within minutes and increases specificity (true negative rate) and sensitivity in its early stages. The test has also been optimized with positive and negative controls to avoid false diagnoses, and it is enclosed in a 3D printed case for easy handling.

 

Major Improvements to Technology

Figure 3: Reported data on test sensitivity, specificity and Area Under the Curve. Adapted from ACSNANO

Previously used examinations could cost up to 400 USD per test, and their average time for diagnosis is currently over 24 hours. They also have very low sensitivity to the early stages of the disease, with values of less than 50% being reported. As mentioned by the authors, this assessment has a material cost of 0.42 USD per test which greatly reduces costs for diagnoses. They also report values of sensitivity of over 90% in early stages of Lyme disease and a specificity value of 87%. Nonetheless, this team of researchers have demonstrated the correct diagnosis of the disease in a matter of minutes making this process efficient, easy and available to the public at a reduced cost.

 

-Aron Engelhard

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“The Crow and the Pitcher” and Close Packing of Equal Spheres

Posted on March 16, 2020 by | 1 comment

 The Crow and the Pitcher

The Crow and the Pitcher is one of Aesop’s Fables, which tells a story of: A thirsty Crow found a high and narrow-neck pitcher with a little water in it, the crow could not reach the water no matter how it tried. Suddenly, the crow came up with an idea: picking up some small rocks and dropping them to the pitcher. With each pebble, the water rose higher and higher. Finally, the crow drank the water.

The Crow and the Pitcher, Aesop’s Fables. (Copyright: Milo Winter)

This story is very inspiring to many children, it told them to think flexibly when facing problems. However, is it possible for the crow to drink the water with rocks in real life?

Close Packing of Equal Spheres

The problem in the Crow and the Pitcher is that after the crow dropped rocks to the flask, the water filled the space between rocks first, then it raised the height of water. How much water was needed to fill the space between rocks, this is the closest packing problem.

The Close Packing of Equal Spheres was first put forwarded by Kepler in the 17th-century. Kepler thought that the close packing of equal spheres in a three-dimensional space looks like the following:

The cannonball stack: an “FCC” latice. (Copyright: Wikipedia)

The close packing of equal spheres can be widely found in chemistry, such as crystal structures of Magnesium and Copper atoms. It was calculated by Carl Friedrich Gauss that the greatest fraction of space occupied by spheres – that can be achieved by close packing of equal spheres is 74%. In other words, if the water in the pitcher is 26% (volume) or less, the crow cannot drink the water no matter how many rocks it put in the pitcher.

The close packing of equal spheres also called the Hexagonal Close Packing. In 2017, the scientist proved that the Hexagonal Close Packing is the densest arrangement in the three-dimensional space.

 How can the crow drink the water in the pitcher? 

Is there a way that the crow can drink the water in the pitcher without 26% of water? Mathematicians said that by combining the truncated octahedrons, tetrahedrons and octahedrons (2:1), or truncated cubes and octahedrons (1:1), or gossip mirrors and truncated cuboctahedrons (3:1), the crow can easily drink all the water in the pitcher.

Alternative ways for the crow to drink water in the pitcher. (Copyright: ScienceDirect)

If it is hard for the crow to find the above rocks, it can also combine multiple shapes of rocks to get the water in the pitcher. Moreover, some scientists tested the effect of shapes of flasks on the increasing heights of water in flasks by using the Close packing of equal spheres. They found that the height of water in Erlenmeyer-flask-shaped flasks has the fastest increase. However, where can you find an Erlenmeyer flask? -A chemistry lab. It’s absolutely a bad idea to drink solutions in a chemistry lab.

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Biodegradable, what does it really mean?

Posted on March 16, 2020 by | 5 comments

Plastic pollution is one of the major issues effecting the marine environment today.

A study published on February 13 2015 by Science investigated the input of plastic into the oceans from land. Using worldwide data, the study estimated that 192 coastal countries generated 275 million metric tons (MT) of plastic waste in 2010 alone, with 4.8-12.7 million MT of that waste entering the ocean.

Marine debris that was washed ashore covers a beach on Laysan Island in the Hawaiian Islands National Wildlife Refuge. (Susan White/USFWS)

What is bioplastic?

Bioplastics are plastics that are partially made of biological materials like wheat, maize, and tapioca.  Being made of biological material does not mean that bioplastics can be broken down by fungi and bacteria. Essentially, being bioplastic does not necessarily mean that the material is truly biodegradable.

Examples of non-biodegradable bioplastics include bio-based Polyethylene terephthalate and Polyethylene which make up everyday items such as bottles and carry bags.

There are bioplastics that can degrade in the environment, given specific conditions. For example, Kale et al. published a study in 2007 that investigated the biodegradation of polylactide bottles. The study found these bottles degrade after 30 days when buried in soil, at relatively high temperatures.

What is biodegradable plastic?

The definition of biodegradable is the break down of substances into inorganic materials, such as water and oxygen.

“This word ‘biodegradable’ has become very attractive to people trying to make quick bucks on it,” explains Ramani Narayan, a professor of Chemical and Biochemical Engineering at Michigan State University, who helped develop biodegradable corn-based plastic.

Typically, companies make plastics that degrade into smaller particles faster and then claim that they are ‘biodegradable’ says Narayan. Figure 2 shows the relative rates of degradation of various materials. Even though they are claimed to be biodegradable, they still take large amounts of time to degrade into smaller particles – which are no better for the environment.

Figure 2: Image depicting the relative rates of degradation for various materials. Obtained from creative commons.

Why does this matter?

The general public does not know the difference between bioplastics and biodegradable plastics. They also do not know that companies use the term ‘biodegradable’ lightly – and just because plastics claim to be biodegradable does not mean they actually are. This would cause people to assume that using and disposing of bio- and biodegradable plastics is safe for the environment, when that is not the case.

This discarded plastic would eventually find its way into the ocean, further increasing the plastic pollution in the marine environment. Plastic debris in the ocean is known to increase the rate of ingestion, suffocation and entanglement of hundreds of marine species – often resulting in death.

It is important to know the distinction between bio- and biodegradable when using plastics, such that they can be disposed/recycled in the appropriate manner.

The easiest solution would be to minimize your plastic use entirely, to reduce the rate of plastics entering the ocean and reduce the endangering of wildlife.

 

-Chantell Jansz

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