Do you see in black and white?

“What does Red look like to you?”, and “Are you like a dog then?” are some of the many questions people suffering from colour blindness get once their genetic deficiency is uncovered. Not only are these questions woefully ignorant, but they are grossly exaggerated from the implications of the term “blindness”. This occurs since people normally attribute blindness as a condition in which an individual cannot see whatsoever, however in reality even individuals who are considered “blind” have some visual perception. In accord with this, colour-blind people are not absolutely blind to colour, with many simply having difficulty differentiating between shades of colours such as green or red. This is why colour-blindness is identified in the spectrum of Colour Vision Deficiency, or CVD for short.

Most people understand that we see things because of our eyes, but don’t actually understand how this happens, and as a result they also have difficulty understanding how CVD occurs, so a short description is provided here. In the eye, the retina is the component which receives incoming light and transmits the corresponding information to the brain resulting in colour perception. This is done by the approximately 6 million cone cells, which are categorized into the red, green, and blue types, and all individually respond to different wavelengths of light. Colour vision deficiency occurs when an individual’s eyes are unable to sense certain wavelengths of light under normal conditions due to some issue with their cone cells.

With this description, it is still difficult to visualize what it really means to be colour vision deficient, since you can’t simply switch off your cones to experience this, whereas you could close your eyes to simulate blindness. To put it simply, people with CVD, such as myself can’t see quite as wide a range of colours that a person with normal colour vision can (a great description of this can be found at this website). The outcome of this is mainly confusion for the CVD individual, with common interactions such as “Do my shoes and dress match?”, “Can you pass me the red backpack?”, or “The red line shows X, while the green line shows Y” leading to misunderstanding. Granted that such interactions can be quite humorous, the individual is often left feeling oblivious and naïve. So next time you meet someone who is colour-blind, just saying “Your eyes are pretty” will probably make their day.

Why Do Onions Make Us Cry?

Via Wikimedia Commons

While I love cooking with onions, I absolutely hate cutting them. The stinging I feel when I slice through an onion is a sensation that I am very familiar with; however, I am not as familiar with the reason why. Like me, researchers were unsure what exactly happens between slice and tears, until a recent study on the structure of the enzyme responsible for the burning sensation when cutting onions, Lachrymatory Factor Synthase.

It was known that, when chopping onions, the broken cells’ cytoplasm releases amino acid sulfoxides that the onion enzyme, allinase, converts to volatile sulfenic acids responsible for the onion’s aroma and flavor. Another enzyme that is released as the cell breaks is lachrymatory factor synthase, or LF synthase. This enzyme converts select sulfenic acids into propanethiol S-oxide, another volatile sulfur gas that, when reaches the water in our tears, produces sulfuric acid. The acid irritates our eyes, which produces the burning sensation and more tears, further increases the burning. While research on allinase, a common enzyme found in plants responsible for producing volatile compounds, is well known, LF synthase is a new idea to the process.

Before 2002, it was believed that allinase produced the tear causing gas from the beginning of cell rupture; however, when a Japanese food company tested the theory, they discovered another enzyme, LF synthase, is really responsible. In order to really understand the complete mechanism, researchers needed to know the structure of LF synthase. And now we do.

Researchers in Ohio wanted to know what LF synthase looked like to gain insight into the enzyme’s role in the onion’s volatile gas mechanism. To do this, they analyzed the structure of the enzyme through X-ray crystallography after crystallizing the enzyme.  When compared to the structure of other plant proteins, they were able to identify the enzyme’s active site and propose a mechanism of propanethiol S-oxide production.

With this new piece of the puzzle, we now have a greater understanding of why we cry when chopping onions. Perhaps, one day, they will use this information to produce onions that do not result in tears. Until then, I will continue to dread making French onion soup.

Perhaps you could also try this man’s trick to cutting onions without tears. YouTube Preview Image

 

Lori Waugh

 

A New Nonstick Coating makes life easier

Have you ever attempted to scoop out the remaining honey with fingers in a container? Have you ever squeezed really hard to get the last bit of a toothpaste? Is the little bit clingy glue in the bottom of the bottle really annoyed you when you try to use it?

A company called LiquiGlide discovered a new nonstick coating can let the above problems go away. The basic idea is to use this special coating to make the inside of container slippery so that the liquid will slide back into the bottom instead of sticking to the lid and drying there. In addition, a test by Consumer Reports in 2009 indicated that much of what we buy never makes it out of the container and is instead thrown away — up to a quarter of skin lotion, 16 percent of laundry detergent and 15 percent of condiments like mustard and ketchup. Therefore, If this material is widely used in daily life, we can save resources and reduce waste.  Bingham plastics is the most common material that is used in traditional container manufacturing. Bingham plastic is named after Eugene Bingham, a chemist who proposed the mathematical properties. This material is highly viscous and does not flow without a strong push.

This picture shows the average waste and the differences between new nonstick coatings and traditional coatings. (source)

The key to success this technology is to find a material that has superhydrophobic surfaces. Superhydrophobic surfaces are non-wettable surfaces with high water contact angles and facile sliding of drops. The superhydrophobic surface is rough under a microscope. Water rolls up into balls, sitting on the tips of the rough surface, but mostly on air trapped between the droplet and the rough surface. The droplets roll off easily. In this new material,  the lubricant binds more strongly to the textured surface than to the liquid, and that allows the liquid to slide on a layer of lubricant instead of being pinned against the surface, and the textured surface keeps the lubricant from slipping out. However, finding a proper material is not easy. If the microscopic roughness is damaged, water will flow in and displace the pockets of air, then stick to the no-longer-slippery surface. Since air can dissolve into the water if superhydrophobic surfaces are submerged in water for long periods, it will become rough. As a result, detergents or lotions will stick on the wall of containers.

This picture describes how superhydrophobic surface works in this new material. (source

In the future, the company wants to explore further on the industrial applications including coatings for petroleum storage tanks and pipelines. If these applications can succeed, less energy needed to push materials through the pipes,  fewer chemicals required cleaning the pipes.

 

 

 

 

 

Written by Nancy Ma

Efficient Removal of Heavy Metal Ions from Water by Nanoporous Thin Films

The term heavy metal refers to any metallic chemical element that is toxic or poisonous at low concentrations. The most common heavy metals include mercury (Hg), arsenic (As), chromium (Cr), cadmium (Cd) and lead (Pb).

Heavy metals are natural components of Earth’s crust. They are non-degradable. They enter our bodies via food, drinking water and air. At very low concentrations, some heavy metals, such as copper and zinc, are essential to maintain the metabolism of the human body. However, at higher concentrations they can cause poisoning and put our lives at risk. For example, high levels of lead (II) cations can hinder brain development in children who drink from contaminated sources and cause organ damage to people of all ages. Similarly, water supplies contaminated with cadmium (II) cations cause the weakening of bones and damage our kidneys and livers.

Heavy metals are dangerous because they tend to bioaccumulate. In other words, their concentrations increase in our bodies over time. They are stored faster than they are broken down or excreted.

Heavy metals can enter a water supply by industrial and consumer waste, or from acidic rain breaking down soils and releasing heavy metals into streams, groundwater and other water sources.

In order to remove the heavy metals from our water supplies, Weidman and co-workers functionalized nanoporous thin films of poly(acrylic acid) (PAA) with glutathione and cysteamine. Glutathione and cysteamine are peptides that exist in many organisms to counter the accumulation of heavy metal ions. For example, glutathione, which is found in many plants and animals, can bind to the metal ions and remove the ions from transport pathways within the organism.

Coupling glutathione to PI−PS−PAA films can remove over 93% of heavy metal ions for drinkable water. (Source: Weidman et al., 2017)

Unlike the conventional packed bed processes, which require long residence times for effective removal of heavy metals; the nanoporous films have a lot of built-in functional groups, which allow the coupling of glutathione and cysteamine to the groups. The ready attachment of glutathione and cysteamine to the films enable efficient removal of toxic heavy metals from water supplies.

The thin films were tested with cadmium (Cd2+) and lead (Pb2+) ions. Results showed that the films could remove over 93% of the heavy metal ions. Furthermore, in mixed ion solutions, the capacity and removal rates of the films did not reduce. After repeatedly regenerating the films, the films showed no loss in capacity.

The percent of metal removed in the solution containing cysteamine-functionalized films (left) and in the solution containing glutathione-functionalized films (right). (Source: Weidman et al., 2017)

In conclusion, these thin films provide a sustainable platform for the efficient purification of lead- and cadmium- contaminated water sources to safe levels.

-Jennifer Liu-

New skin from transgenic stem cells

Gene therapy is a promising medical development that can save people suffering in perilous diseases. One outstanding case of gene therapy is transplanting transgenic skin cells to replace over 80% (0.85 m2) of a young boy’s outer layer of skin (called the epidermis), effectively treating a severe skin disease called junctional epidermolysis bullosa (JEB) without long-term adverse effects. This accomplishment was published by Professor Michele de Luca and the collaborating medical team from Ruhr-Universität Bochum’s burn unit and the Center for Regenerative Medicine at the University of Modena (Italy), on November 8, 2017, in the journal Nature.

JEB is a disease caused by mutations in any of three genes that encodes a protein called laminin, which anchors the epidermis to the dermis, the inner layer of skin. Failure to do so results in fragile skin with low mechanical resistance and elasticity, manifesting as blisters and wounds in many areas and increased vulnerablility to infections. The patient in the study had extremely severe JEB caused by mutation in one gene and lost an amount of skin equal 80% of his total body surface area, including arms, legs, chest and back.

mutation in the laminin protein (not shown) causes detachment of the epidermis (outer skin) from the basemebt membrane and inner skin (dermis) in junctional epidermolysis bullosa. source: https://ghr.nlm.nih.gov/condition/junctional-epidermolysis-bullosa

The treatment started two years ago in 2015, with doctors removing a small area of normal skin to establish skin cultures, which were artificially infected (transduced) with a virus (called a retroviral vector) carrying the normal laminin-encoding gene. After growing the cells to 0.85 m2 , the new skin was sequentially grafted on sites of exposed inner skin, using either plastic or fibrin as the adhesive base. Both graft types were equally effective: the regenerated skin did not blister or damage after pinching; furthermore, after 21 months followup, the grafted skin did not produce antibodies by the body, indicating it was safe and the body recognizes it as belonging to itself. The new skin regenerates monthly by a small number (about 5% of the skin after 8 months) of long-lived stem cells called holoclones, which could regenerate themselves and develop into half-differentiated cells (meroclones) and almost fully differentiated cells (paraclones), which cannot divide further but replace old cells and gradually disappear. 

general stem cell therapy scheme. Skin cells from the patient are harvested and a virus introduces the desired gene into the skin culture to create genetically modified cells. Source: https://stemcells.nih.gov/info/Regenerative_Medicine/2006Chapter4.htm

However successful it was, the treatment was actually pretty risky. The retroviral vector could insert, or integrate, the normal laminin gene anywhere in the patient’s genetic blueprint and disrupt other normal genes and cause unregulated tissue growth, resulting in tumours or cancers. Fortunately, genetic sequencing of the transplanted skin revealed that the normal gene was inserted mostly in regions not coding for proteins (introns and intergenic regions) with only 5% inserted in protein-encoding regions, but these genes were not involved in cancer. In addition, the transplant did not cause specific cells to survive better than others and cause tumour formation. However, long term monitoring is still required.

While this technology is currently limited to injuries with an intact dermis, it is less invasive and more effective than surgery as it does not entail infections, and it could be applied to early diagnosis stages to prevent skin diseases as well as restoring large areas of damaged skin. This is a new treatment for epidermolysis bullosa, a condition affecting 500 000 people worldwide, and a major stepping stone to developing stem-cell therapies for many debilitating diseases.

Written by Jenny Zhong

Human Brains in Rats?

Picture of neurons. Source: https://commons.wikimedia.org/wiki/File:GFPneuron.png#/media/File:GFPneuron.png

The idea of a human-animal hybrid has long been a part of science fiction, but so far has been a highly impossible task. However, recent studies have resulted in the first steps taken towards doing this in reality, involving implanting a miniature human brain into a lab rat.

This miniature human brain is called an organoid, which previously were created in petri dishes made from human stem cells, and grew new neurons similar to how full-size human brains do. Prior testing on these organoids were focused on researching how brain diseases such as Alzheimer’s and Zika virus develop, however this research was limited as the organoids were not attached to any biological system.

This is where researchers, such as Dr. Isaac Chen, came up with the idea of implanting the organoids into rats. Chen’s team had attached the visual cortex portion of the organoid to rats, which was shown to have connected properly as neurons in the organoid were fired when light was shined into the rat’s eyes. A separate lab also successfully connected blood vessels of rats to the organoids, allowing blood flow and growth.

Picture of a lab rat. Source: https://commons.wikimedia.org/wiki/File:Albino_Rat.jpg#/media/File:Albino_Rat.jpg

However, there was a big problem that caused this research to come to a halt: ethics. Organoids are no where near the size of an operating human brain, nor have they shown the growth required to reach human intelligence. Even when attached to a rat, there are no signs of increased intelligence or growing consciousness. What this does imply, however, is that there is a potential for a rat to grow thoughts like a human with advancements in this process. Where can science draw the line between ethical testing on rats and testing on rats that can think like humans?

Currently, the closest thing to an ethical rule is the moratorium against implanting human stem cells into early embryos of vertebrates, but the organoids are not direct stem cells, and the test rats were fully developed. Perhaps laws need to be set to restrict organoid size before implant, or a certain development limit for the rats, as younger rats are likely to develop with the human neurons intertwined? The ethics behind these experiments are hazy, but the results of these experiments are highly beneficial for society, as it provides potential solutions for horrific neurological diseases.

While limits should definitely be set on this kind of experimentation, scientific progress should not be limited. We must continue to strive towards supporting our society and those who are diseased, and as long as the ethical boundaries of this experimentation is understood well, it deserves to be investigated.

Stretching the Mussels

Many everyday products such as tire rubber rely on their ability to stretch. These materials are mainly consisted of a type of polymer called the elastomer which  can flex without breaking and return to the original form. However, a big limitation of elastomer materials is the lack of strength. A group of researchers has developed a tough but still flexible elastomer but they were inspired by an unusual creature, the mussel.

Mussels (Wikimedia Commons)

Elastomers are structurally shapeless polymer strands with only a few chemical cross-links in between, In order to strengthen the elastomer, the density of the strands must be increased but a denser and more structured polymer would result in a stiffer and more brittle material.

Mussels form a tough and flexible polymer to secure to the surfaces in rough intertidal zones. The researcher at UC Santa Barbara’s Materials Research Laboratory were inspired by this natural polymer and they developed a way to maintain elasticity while increasing strengths in elastomeric polymers.

The research focused on a dry polymeric system which is different from previous research which was limited to wet systems. The researchers utilized a mussel inspired iron coordination complexes into a dry polymeric system. The iron coordination provides a self-healing mechanism which can reform broken cross-links therefore maintaining the material’s flexibility but increases the toughness.

They found that the iron incorporated polymers do not store energy when it is stretched. It disperses the energy then slowly recovers to the original shape. This material can be very useful in everyday uses to absorb contact such as the inside of a helmet or the coating of a phone case.

Polymers that contain metal coordination are not widely used and researched. This research opens up possibilities to change a polymer’s properties by the uses of metals. Further research into this field has the potential to optimize functionality and durability in many everyday applications.

Science discovers can come from anywhere. Chemistry advancements often happen in the laboratory but the inspiration is  all around us. This research’s method of developing a tough elastomer will allow for more research into the relationship between elasticity and strength of elastomers.

A Clear Perspective wins Nobel Prize

Joachim Frank, Richard Henderson, Jacques Dubochet have claimed this year’s Nobel prize in chemistry taking biochemistry and medicine to a new era. The trio earned the prize for cryo-electron microscopy which is an imaging technique that allows researchers to see proteins and other large bio molecules with atomic precision. Knowing where all the pockets are in molecules helps chemists to get drugs to fit into them which makes imaging techniques vital to understand in order to treat diseases. However, researchers have had really powerful tools for imaging bio molecules for a while. Specifically, X-ray crystallography and nuclear magnetic resonance spectroscopy.

So why this one is so important is because the most decorative methods have short comings. NMR spectroscopy works best for small bio molecules – which is a drag if you want know what a virus looks like for example and if you want to use X-ray crystallography the bio-molecules you are interested in has to crystallize which not all bio-molecules do. Cryo-electron microscopy gets around these problems without sacrificing resolution. Generally speaking, electron microscopy, uses an electron beam rather than light to magnify samples to atomic resolution. But plain old EM isn’t optimized for living things and their molecules. Hitting bio molecules with an electron beam which can damage or destroy them. And electron microscopes work in vacuum which can also damage or destroy bio molecules. Today we are seeing virus and proteins and other structures like never before thanks to cryo-EM.

Cryo-electron microscopy of proteins has advanced from the low resolution image on the left to the detailed image on the right. Attribution: National Institutes of Health

Understanding how Cryo – em overcomes this challenge relies on the fact that the proteins stay in a very thin layer of liquid nitrogen and then they are frozen. The thin layer of nitrogen that they are frozen in allows them to be protected from the beam of electrons that hit them and hence they are not damaged.

Although freezing the samples protect them an electron microscope, ice crystals actually interfere with imaging. In 1982, Jacques Dubochet and his team found they could vitrify water by adding ethane that had been chilled by liquid nitrogen. Vitrify water is a glass like structure and randomly ordered rather than crystal like and hence it doesn’t interfere with imaging. Another obstacle for Cryo-em was image processing power. Early stages of the technology resulted in fuzzy images of proteins and averaged to a whole protein. In the coming years, computers get better and researchers get better in using the technology.

Presently there is an avalanche in Cryo em technology leading to sharper and better images.

Comparison of X-ray Crystallography to Cryo-Electron Microscopy Attribution: Nature

We talked about biology, medicine and a little bit of physics, you must be thinking how does this all fit in with chemistry. Allison Campbell, the president American chemical society states: “To me this is all about chemistry because this enables us as scientists to look at molecules and the arrangement of atoms in molecules and the resulting structure. And that’s all about chemistry”.  I believe the Nobel prize has mostly to do with biochemistry and less about chemistry. Although, the imaging technique can be used to design new targeted drugs for certain proteins it is still mostly a biological advancement rather than a chemical advancement. Maybe a chemistry advancement will win a prize on grounds of biology in the future. Till then we can enjoy crisp images that were only part of a fantasy decades ago.

 

Garvit Bhatt

Daily products, how safe are they?

As we live our daily life, there are some products we need to use on a daily bases. One of the products we cannot leave out is shampoo. Even though we use shampoo everyday, we may have to pay close attention to what it is made of.

(CC0 Creative Commons, From Pixabay)

Shampoo contains many chemical substances. There are many people who try to avoid chemical substances and it is not difficult to find those who make their own shampoo or choose products that are made of organic sources. Why do we need to care about the product which so many people on earth use daily without questions?

Many shampoo products contain 1,4-deoxane and diethanolamine, which are used to make bubbles and make the shampoo more efficient in cleansing. These substances can be hazardous to us, damaging nervous system and even causing cancer if exposed for a long time.

structure of 1,4-dioxane (Source: Wikimedia Commons)

structure of diethanolamine (Source: Wikimedia Commons)

1,4-dioxane is not used as a material to make a shampoo, but rather, it is produced during the process of making shampoo, depending on the substances used. Therefore, it is very difficult to avoid 1,4-dioxane completely. Researches have found that 1,4-dioxane can be absorbed through skin or be inhaled to cause serious damage. If we are exposed to 1,4-dioxane, it can cause irritation on mucous membranes of eyes and nose, and dizziness. If with great exposure for a long time, it can even cause death.

Diethanolamine, on the other hand, is widely used as a surfactant to make shampoo. It can be absorbed through skin as well, causing irritations to skin and eyes, and further damage kidney.

To avoid these hazards, it is best to use products that does not contain 1,4-dioxane and diethanolamine if possible. Also, minimizing the time of use and amount of shampoo will help preventing them from being absorbed into skin. Even though everyday products are used by many people for a long time and seem safe, we would need to think more about what exactly we are using.

Dangers of Artificial Food Colouring

Artificial food dyes are additives that are used to enhance the colour of various foods. The food industry has used food colouring as a tactic for many centuries to make food look more appealing to consumers. Would you rather eat a colourless lollipop, or a rainbow coloured lollipop? Although artificial colouring is widely used, it is linked to a number of health problems such as cancer in animals and increased hyperactivity in children.

Lollipop (By Graham and Sheila)

For many of us, it is almost impossible to go a day without consumption of artificial colouring. Colouring agents are found in beverages, candies, cereals, and in most processed foods. Health Canada has permitted 13 colouring agents that are considered safe, including Brilliant Blue (or Blue #1), Allura Red (or Red #40) and Tartrazine (or Yellow #5), the 3 most common colouring agents.

In “Food Dyes: a Rainbow of Risks”, CSPI (Center for Science in the Public Interest) revealed health issues linked to nine food dyes. For instance, Citrus Red 2, which is used for colouring the skins of oranges, is toxic to rodents and is linked to bladder tumor. Yellow 5, which is used in beverages, cereals, and yogurts, may be contaminated with cancer-causing chemicals and is linked to hypersensitivity reactions in children.

A study published in 2007 also found that artificial colours increased hyperactivity in children. The results were achieved from 267 studies in 3 year old and 8/9 year old children. The children were given a placebo drink, or a drink containing artificial colouring equivalent to the amount of colouring found in two bags of sweets. The children consumed the drink everyday for a total of 6 weeks. During the study period, three measures of behaviour, the ADHD rating scale, the hyperactivity scale and the classroom observation code were used to study the hyperactivity in children. The researchers found that the results were consistent with those from other studies.

Top: Chocolates coloured with Brilliant Blue. Bottom: Chocolates coloured with natural spirulina (By John Penton)

Although there are potential health effects linked to artificial food colouring, I still want my M&M’s chocolate and Jell-O to be coloured. Thankfully, more companies are looking for natural alternatives to replace artificial colours and meet the public’s desire for natural products. Natural colour sources such as cyanobacteria Spirulina can replace Brilliant Blue, curcumin from turmeric can replace yellow, and chlorophyllin from chlorella can replace green. Furthermore, Health Canada has set many restrictions to limit the amount of food colours that can be used, and the types of food the colours can be added to. However, if you are concerned and want to limit artificial colours in your diet, look for food labels that say, “no artificial colours”, or shop at grocery chains that do not sell food with artificial colouring, like Whole Foods Market.

An interesting video that talks more about the potential health effects of artificial food colours is shared below.

YouTube Preview Image

 

Carmen Chu