Category Archives: Admin

Are we a step closer to synthesizing people ?

Posted on November 25, 2017 by | 1 comment

Having a trouble making friends? How about building a friend?! New research at the University of Harvard by Pang Yui has brought us one step closer to synthesizing living beings.  Synthesizing animals and people seems like an impossible task but it’s definitely more attainable now thanks to this fascinating research. You might be surprised what this new finding has to offer.

Many different types of cells make up the human body. DNA strands, which are the building block of genetic material in the body form the different types of cells.  In our body,  base nucleotides known as the A, C, G, T, which have the potential to fold into 3D structures make up DNA. Hydrogen bonding between the base pairs of nucleotides determines base pairing.  For example, As and Ts and Cs and Gs bind to each other. In order for the cell to grow, develop, and repair itself, many changes occur in the DNA to allow cells to replicate. 

Related image

Figure 1. A photo demonstrating the base pairing in DNA structure

For many years, people understood the complex machinery behind DNA replication. Can we synthetically make DNA? Scientists have previously tried to make copies of DNA in test tubes. However, this technique known as PCR is limited to amplifying DNA segments. It might be a Nobel-prize winner technique but definitely, we cannot rely on PCR to build large strands of DNA.  Pang Yui, a researcher at the University of Harvard developed a new method that allows pre-designed sequences of DNA to autonomously grow. The Primer Exchange Reaction (PER) is a method that offers autonomous and programmable features that have very diverse applications in the field of synthetic biology. Some of these applications involve the engineering of molecular devices, that are capable of synthesizing large DNA nanostructures.  These nanostructures are able to sense environmental signal in the cell which allows them to grow autonomously and carry different functions. This method represents advances in the field of molecular robotics since pre-designed DNA molecules can be programmed to self-assemble in 3D structures, that are able to carry certain functions and tasks. 

Autonomously growing synthetic DNA strands

Figure2. The method of Primer Exchange reaction which gives rise to autonomously grown DNA that is able to carry different tasks. Image credit: Wyss Institute at the University of Harvard 

The method of PER needs very basic requirements. Firstly, you need “an engine” in the form of Single-stranded DNA that has the potential to partially pair with itself. Secondly, you need a primer that is complementary to the piece of single-stranded DNA. Through a series of elongation and displacement reactions, the primer is able to copy the sequence of DNA in-situ.Once these reactions are over, the DNA is expelled and is allowed to be recycled in this process to make large strands of DNA.  

This method represents the future of technology. If we can program DNA to do specific tasks and functions, we can definitely synthesize people. All you need is making proteins which are crucial in many cellular processes. If this new research is able to synthesize proteins, we are one step closer to synthesizing animals and people who can keep our company.

By: Tarek El Sayed

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How do airbags work? Deadly poison in your car’s air bag!!!

Posted on November 20, 2017 by | 1 comment

Have you ever wondered how do airbags work? Do you know airbags are not inflated by any compress gas source but rather the product of a chemical reaction?? The reagent of the reaction is a really Toxic salt called sodium azide, NaN3, but is it gonna KILL you???

Under normal condition, this salt is really stable. However, if it’s heated, the salt will decompose immediately and give sodium and nitrogen gas as products.

2NaN3 → 2Na + 3N2

The equation above describes how sodium azide falls apart. It is noticeable that after the reaction, the total volume of the chemicals increased since there is only solid before reaction. And it can be calculated that under standard state condition, 130 grams of sodium azide produces about 67 liters of nitrogen gas which can inflate a normal airbag immediately (in 0.03 s!!) as the sensor detect a collision!

The following video shows how fast an airbag will expand!

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You may notice that nitrogen isn’t the only product of this reaction. It produces sodium, too! Sodium is a quite reactive metal and will form sodium hydroxide (click to see the hazards) which is a strong base when reacting with water. Thus it would be hazardous if it got into your nose or eyes. To minimized the risk, sodium azide is always mixed with other chemicals which convert sodium metal into less hazardous salts. The most commonly used chemicals are potassium nitrate and silica.

It can be seen from the equations above that the final products of the overall reaction are nitrogen gas and Na2K2SiO4 which is a harmless alkaline silicate (click to see the hazard).

Overall, the airbag does contain toxic substances, but it is quite stable and sealed inside your car. It will NOT kill you definitely!!! When the airbag is inflated, all the toxic chemicals will be converted into harmless substances which are nitrogen gas and alkaline silicate.

Written by Xuan Wang

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The Life Saving Reaction: Chapter II

Posted on November 15, 2017 by | 1 comment

As chemistry students we usually have to defend our choice of studying chemistry against the ceaseless attacks from friends and relatives. Therefore, beside boosting the food production and saving many lives, the Haber-Bosch process is a strong argument for how chemists can change the world. Simply the Haber-Bosch process produces ammonia from gaseous nitrogen and hydrogen under high temperature and pressure (500oC, 200 atm) . Since ammonia is the key component in chemical fertilizers, the Haber-Bosch process is responsible for the annual production of the food that keeps around 7 billion people alive nowadays.

But the story of the life saving reaction does not end here, a recent modification to the Haber-Bosch process is about to write a new chapter.

In may 2017, researchers from Waseda University and Nippon Shokubai Co. Ltd. achieved a highly efficient ammonia synthesis at low temperature, with the highest yield ever reported. In the paper that was published in Chemical Science, R. Manabe et al. used an Ru catalyst and applied electric field to achieve the reported synthesis. Although the activity of Ru catalyst for ammonia synthesis in mild conditions was reported in 1972, the rate of the reaction was very slow due to the high activation energy. Here is where the finding of the paper becomes interesting.

In the presence of an electric field and hydrogen or a compound containing hydrogen to carry the ions through the reaction, the activation energy can be significantly reduced. Instead of N2 and H2 dissociation followed by N-H bonds formation, protons add up to the N2 molecule and facilitates the N-N bond cleavage. In other words, in the presence of an electric field the reaction proceeds in an associative mechanism rather than a dissociative mechanism. The addition of the proton to the N2 molecule is an example of proton hopping, in which the proton keeps jumping from one molecule to an other.

Figure (1): The steps of the associative of mechanism in the presence of an electric field

As demonstrated in the figure (1), N2 first binds to the Ru catalyst through one N atom. A proton hops non binding N. Another proton hops to the binding N, and the nonbinding N associates to the metal center. The formation of N2H molecule in an electric field releases the energy that supports the endothermic cleavage of the N-N bond. However, the figure does not include the dissociation of the H2 molecule which is catalysed by the Ru. When ammonia is produced in acidic conditions, an ammonium ion is produced which carries out the hopping process which is the first step in the figure.

This news is significant for many reasons. First, the production of ammonia consumes more the 1% of the world’s produced energy. Saving this energy would have significant economic and environmental applications. Second, the use of ammonia as hydrogen carrier for Hydrogen fuel is currently studied, and low-energy synthesis of ammonia might be required soon. Finally but most importantly, you can have a crushing argument for how chemistry can change the world!

 

 

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Is Quantum Cliché?

Posted on November 13, 2017 by | Leave a comment

The word “quantum” is often over-used, sometimes in contexts where it is not remotely applicable, much to the annoyance of scientists. However, quantum mechanics, the often misunderstood field of physics relating to the motion and properties of particles on nanometre scales, actually does have more effects on our day-to-day life than many people realize, and more of these effects continue to be discovered. Technological innovations which were made possible by the study of quantum physics are the most commonly cited examples of quantum mechanics in day-to-day life, but recent research is leading scientists to believe that quantum phenomena may be at play in nature as well.

Recent studies have shown evidence of a phenomenon unique to quantum physics, called coherence, being at play in the process of photosynthesis. Coherence is a property of waves which is observed in quantum mechanical particles, because one of the key results of quantum mechanics is the fact that particles are not discrete, but actually waves. Waves can be in phase or out of phase, depending on how their troughs and peaks line up with each other. If they line up in a consistent pattern, then two waves are said to be coherent. In quantum mechanics, two particles being in a coherent state means that the wave functions that describe them are coherent with one another. Usually systems tend towards decoherence, because particles’ wave functions become less well-defined as they interact with the environment, making them in phase with each other in some places, and out of phase in others.

These figures demonstrate the difference between coherent and incoherent waves. The coherent waves above add to form a well-defined wave, while those below add to form a wave with randomly varying amplitude and phase
Credit: Wikimedia Commons

The classic Schrodinger’s cat thought experiment, in which a cat is both alive and dead at once, is one of the most well-known examples of quantum mechanics. It is made possible because the cat exists in a superposition of different states, which are able to be added together because they are coherent.

An illustration of the structure of photosystem II, as found in cyanobacteria
Credit: Wikimedia Commons

When plants convert light from the sun into energy, they initially use the energy from incoming photons to move electrons, in what is called a charge transfer. The process of charge transfer is exceptionally efficient, and without this efficiency, photosynthesis as we know it would not be possible. In a recent paper in Nature, researchers described their analysis of a reaction centre where charge transfer occurs, called photosystem II, and detailed how their results demonstrate that the high efficiency of charge transfer in photosynthetic processes is due to quantum coherence. The researchers obtained photosystem II protein complexes from spinach leaves, and analyzed the quantum states of these complicated species using lasers. They observed evidence of quantum coherence during charge transfer and proposed that “this coherence allows the sampling of the energy landscape (or switching between pathways) until the system finds the optimal route towards charge separation.” Clearly, this kind of “sampling of the energy landscape” could not be predicted without knowledge of the strange phenomena which are described by quantum mechanics.

This research demonstrates that the word “quantum” should not only be conjured up when thinking about the future of computers, and peddlers of pseudo-scientific products, but also when out for walks in the forest, or biting into a crisp apple, both of which might not be possible without the quantum phenomena that allow photosynthesis to be a viable process.

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Do you see in black and white?

Posted on November 13, 2017 by | 1 comment

“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.

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A New Nonstick Coating makes life easier

Posted on November 13, 2017 by | 2 comments

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

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New skin from transgenic stem cells

Posted on November 13, 2017 by | 1 comment

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

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Daily products, how safe are they?

Posted on November 5, 2017 by | 4 comments

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.

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WAKE UP. Take a coffee nap.

It’s late afternoon now. You had your perfect cup of coffee in the morning, but the day has taken its toll on you. Shall you go for another cup? Or perhaps a nap to wake you up?

I recommend to you not either or, but both! Yes, the best of both worlds: the coffee nap.

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Coffee Nap: a cup of coffee then a nap (see, I google “coffee nap” and I get sleeping animals). 

Left: Wikimedia Commons – Julius Schorzman.  https://commons.wikimedia.org/wiki/File:A_small_cup_of_coffee.JPG

Right: Pixabay – Scheeze. https://pixabay.com/en/cat-sleeping-nap-bed-portrait-pet-2092451/

Why aren’t coffee naps a trend? Scientists discovered two decades ago that drinking a cup of coffee, then napping for 20 minutes will boost your energy way more than a regular nap or coffee. Sleepy people who took a 15-minute coffee nap before being tested in a driving simulator scored higher. Research also says that coffee naps wake you up more than face washing, bright light, taking breaks, and coffee or napping separately.

So how do coffee naps work? First let’s learn how caffeine wakes you up.

Caffeine, a chemical in coffee, enters your bloodstream about twenty minutes after you drink it. It makes it way to your brain where it fills receptors which are normally filled by adenosine, another chemical. This happens because caffeine is similarly shaped to adenosine.

The chemical structures of caffeine and adenosine. Note how similar they are: they both have N (Nitrogen), O (Oxygen), and ring structures in their chemistry.

Wikimedia Commons: Edgar181. https://commons.wikimedia.org/wiki/File:Caffeine_and_adenosine.png

What does adenosine do? Adenosine builds up in your brain with each moment you are awake, and when it fills receptors it makes you sleepy. But when caffeine blocks adenosine, you don’t become sleepy.

A nap works in a similar way. Sleep doesn’t block, but removes adenosine from the brain. But if you sleep for more than twenty minutes, you fall into a deep sleep and become less alert when you wake up. So short, power naps are actually effective!

Now let’s put caffeine and napping together. First your nap removes adenosine from your brain so the receptors are less filled. Then, at twenty minutes, caffeine comes in and blocks more receptors than it could have without the help of adenosine. The result? Your afternoon rescue.

So take that coffee nap! Even half-sleeping for twenty minutes will be helpful, and you can also drink other caffeine beverages.

As for me, even though I still don’t drink coffee, and can’t nap either, I will give it a shot. Let me know how it goes for you!

Cheers,

Ivy Wu

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Posted on November 2, 2017 by in Admin

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Why people have 5 fingers?

Posted on October 31, 2017 by | 5 comments

Have you ever wondered why you have five fingers?? We have been using our hands for more than twenty years and you may have the same question as i do which is why we have 5 fingers.

To better understand the reason, let’s look at a special case of “polydactyly“. In short, polydactyly refers to the situation where there are more than five fingers in a hand (or foot). There are two types of polydactyly which refer to Type A and Type B. In Type A, the extra finger can function properly like other fingers and have a complete bone structure.  In Type B, the extra finger is non functional and  seems to be “floating”.

Type A of polydactyl http://https://en.wikipedia.org/wiki/Polydactyly

Type B of polydactyly http://https://en.wikipedia.org/wiki/Polydactyly#/media/File:Polydactyly_Left_Hand.jpg

To answer our question in the beginning, we have to know the cause of Type A. The duplication of the entire finger is due to an abnormal function of a gene called “Sonic hedgehog” gene or”SHH” gene which plays an important role in the growth of digits on limbs and organization of the brain. During the fifth week of an embryo development, SHH gene will synthesize a signalling protein called  Sonic hedgehog protein which act on the ulnar side of the “hand” (at the black dot in the picture) and fingers start to form.

Hand of an embryo
https://dissolve.com/video/Human-embryo-close-developing-face-rights-managed-stock-video-footage/002-D30-11-319

When the concentration of the SHH signalling protein is lower than common level, less than five fingers will form. When the concentration of the SHH protein is too highly, it will result in Type A of polydactyly.

This is the reason of how five fingers formed, but you may still wondering that why five-finger structure is common. This is the result of evolution. About 380 million years ago, quadrupedalism can have six, seven even eight fingers depending on different species. Due to evolution, it has been simplified into a five-finger structure which ensure both the flexibility and the grasping ability. This is the reason why we all have five fingers not six or four.

Written by Xuan Wang

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