Monthly Archives: March 2020

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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Posted in Biological Chemistry, Inorganic Chemistry

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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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Posted in Analytical Chemistry, Biological Chemistry, Chemistry News

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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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Teaching Resonance to Undergrads: How Hard Can It Be?

Posted on March 16, 2020 by | 3 comments

Resonance structures are a tough concept for chemistry students to understand, and the way they’re being taught has a significant impact on how well they retain the concept. A pair of researchers from the University of Nebraska and the University of Virginia’s Chemistry departments show that explaining the limitations of resonance drawings gives a better understanding than explaining the benefits.

 

The study, published March 13th of this year, took 180 students across 2 different organic chemistry classes with 2 different professors. The first professor focused on highlighting how accurate and beneficial resonance drawings are towards the understanding of the deeper chemistry. The second professor focused on the limitations and shortcomings of resonance drawings, and this approach gave a more accurate understanding of the underlying chemistry.

Reliability of Findings

Quantifying a student’s understanding of a concept is no easy task, so the researchers had to cover multiple facets of understanding. They asked students three questions relating to the underlying understandings of resonance contributors of enolates; written description of resonance hybrids, draw the resonance hybrids, and predict the carbon-oxygen bond length. The answers students gave are graphed below, and show that students in Professor 2’s class had a better understanding of all 3 concepts.

Examples of answers for students asked to draw an enolate resonance hybrid: (a) hybrid structure with correct partial charges (correct answer), (b) hybrid structure, (c) major resonance contributor, (d) minor contributor, and (e) example of other structures (incorrect). Source: Xue, D., Stains, M.

Students’ understanding of resonance hybrids between two professors analyzed through (a) written descriptions of the resonance hybrid, (b) drawings of the resonance hybrid, and (c) carbon-oxygen bond length predictions. Source: Xue, D., Stains, M.

This study did a great job of explaining the ways in which students can misunderstand resonance hybrids, and the pitfalls that professors need to stray students away from. However, teaching styles are not quantifiable, only qualitative observations can be made. This makes any differences possibly anecdotal. Further uncertainty is introduced by limiting the categories that a given student’s answer could fall under. This could “round up” some students to appear to understand more than they do, or vice versa.   Professor 2 also had 8 fewer students than Professor 1. This means Professor 1 had 109.4% the number of students that Professor 2 had, making the population sizes of the two groups significantly different in size.

Despite these possible problems with the methodology and certainty of this research, I think we can all empathize with how tough these concepts were at first. And to lighten the tone, I’ll share this analogy that Professor 2 used in his class to help his students learn. Hope it brings a smile to your face!

Analogy used by Professor 2 to teach about resonance. Source: Xue, D., Stains, M.

  • Griffin Bare

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Posted in Organic Chemistry

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New method found to build artificial blood vessels!

Posted on March 16, 2020 by | 4 comments

Figure1, yellow: Number of People died on the kidney transplant waitlist, blue: Number of people removed from the waitlist classified as “too sick”. Source

 

As the research shows, there are more than 114000 people in the United State on the waiting list of life-saving organ transplants. On average, there will be one new name added to the list every ten minutes, and 20 people die because of the lack of available organs every day. Research team from the University of Minnesota Medical School has published their new founding in Nature Biotechnology on March 11st, 2020. Their research proved the possibility to build artificial blood vessels in a pig, which has the potential to provide ultimate blood vessels for human organ transplants.

How did they come up with the idea?

“There is so many chronic and terminal diseases, and many people are not able to participate in organ transplantation,” said Daniel, a cardiologist who accepted heart transplantation before, “About 98 percent of people are not going to be eligible for a heart transplant, so there’s been a huge effort in trying to come up with strategies to increase the donor pool. Our approach looked at a pig.” Due to the physiological similarity between human and pigs, scientists have done similar studies of using pig insulin to treat human diabetes. These historical researches give scientists confidence and also an existing platform to study.

What is the benefit of choosing pigs?

Figure 2:Acute rejection Anti-CD3 Donor DC. Source

Transplant rejection is a process of transplanted tissue rejected by the recipient’s immune system. According to the research done previously, there are 50-80% of patients would have at least one rejection episode. This symptom is due to recipient’s body cannot adapt to a “foreign” tissue and the immune system would fight against the transplanted tissue. Transplant rejection always causes severe consequences, and a lot of patients would have to remove the tissue immediately.

Daniel Garry, the leader of the research team came up with an idea to avoid transplant rejection. They took mature cells scraped off from a patient’s skin, reprogram these cells and eventually inject them into a pig embryo. This process would develop patient’s own genetic information in pig’s body. Thus, patients will get their own “blood vessels” which can greatly avoid transplant rejection. Mary, coworker of Garry said: “These blood vessels would be engineered and could be utilized in these patients to prevent those kinds of life-long handicaps, if you will.”

The first phase of their study has been approved by the University of Minnesota’s Stem Cell Research Oversight committee. “While it is a first phase, there’s pretty solid proof of concept,” Mary said. “We believe that we’ve proven that there’s no off-target effects of these cells, so we’re ready to move forward to later gestational stages.” This study will eventually benefit millions of people who are suffering from transplantation surgery. Also, this study shines lights and give hopes to modern organ transplantation studies.

-Vicky Gu

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Posted in Biological Chemistry, Popular Science

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Symmetry in a single crystal – space group frequency

Posted on March 16, 2020 by | 1 comment

If you are the one who has experience of working in a synthetic laboratory, you might come across a single crystal. Have you ever noticed that the inner structure of the crystal is arranged symmetrically?

The symmetry of molecules, atoms, or ions in a single crystal

A single crystal does not grow randomly. It grows in an ordered manner so that a particle can have three-dimensional symmetry to another particle in the crystal. The symmetry between the particles is described as a space group. Easily speaking, the space group is a way to represent the spatial pattern of molecules, atoms, or ions in a single crystal. There are 230 space groups based on group theory, and a well-defined crystal structure shows one of the space groups.

Figure 1. An example of the space group “P 1 2 1” of a SiO2 crystal. The capital letter P stands for “primitive lattice”, the numbers 1 and 2 represent “1-fold and 2-fold rotation axes”, respectively. The left figure shows SiO2 molecules arranged in a unit cell and the unit cell is described as the Cartesian coordinates a, b, and c. The right figure shows the same unit cell with SiO2 molecules, but b axis is perpendicular to the screen. (Source: http://aflowlib.org)

Statistics of space groups

Molecules, atoms, or ions prefer to be arranged in a certain space group although they have 230 options. The database in Cambridge Crystallographic Data Centre (CCDC) contains more than one million crystal structures, and the number increases every day. The data centre reported that 986,061 structures show fully defined space groups. Interestingly, 34.4 % and 24.9 % of the structures have the space group “P 21/c” and “P -1”, respectively (Table 1). The key point is that more than 50 % of crystals, which you may come across in a laboratory, have particles arranged in either the space group P 21/c or P -1.

Table 1. Top 10 frequently occurring space groups. SG and CSD stand for space group and Cambridge structural database, respectively. (Source: CCDC, published in January 2019)

– Young Cho

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Surgery can activate cancer cells, but aspirin stops metastasis

Posted on March 15, 2020 by | Leave a comment

When patients are diagnosed with breast cancer, the cancer cells have already metastasized to another part of the body. However, the number of cancer cells involved in this process is negligible, and current equipment cannot detect them. Cancer cells after metastasis remain inactive, which seems unlikely to threaten patients’ health. Nevertheless, those dormant cancer cells are time bombs. One way to set them off, surprisingly, is through cancer surgery.

Recent research led by Dr. Robert Weinberg of the Whitehead Institute found the mechanisms that may explain why surgeries activate the hidden cancer cells. They designed a set of comparison experiments based on mice that injected with breast cancer cells and observed how breast cancer developed in different conditions.

To simulate the postoperative recovery process, scientists implanted sterile sponges in the mice injected with breast cancer cells. This “unnatural” design may be controversial, but it maintains all animals experiencing the same experimental conditions.

“Weinberg gets some pushback because he works on artificial systems, but this is often the only way to expose fundamental principles of biology.” said biologist Sui Huang, professor of the Institute for Systems Biology, who was convinced by this experiment.[1]

Figure 1. (A) Schematic illustrating the experimental design. Mice had been previously wounded by sponge implantation at one or two distant sites. (B) Tumor diameter during the one-month experiment. (C) Tumor incidence as a function of time (n = 9 to 10 per group) for the experimental and control group. Data are plotted as means ± SEM. P values were calculated using the Mann-Whitney test (P < 0.05). Source: Translational Medicine Science

One month after the surgery, researchers tested the number of cancer cells that remained in mice’s bodies. Figure 1 summarizes the results: for those that accepted the surgery, 60% of mice developed tumors in other parts of the body. While in the comparison group, the value is only 15%. Based on the results from 270 mice, Weinberg concluded that surgery could accelerate the cancer cell metastasis and even facilitate tumor formation.

The reason for the effect, as explained in the paper, has to do with the immune system. During the surgical wound recovery process, the inflammatory response restricts the immune system. Therefore, the “guard cells” cannot effectively monitor the cancer cells, resulting in metastasis and tumor formation.

Figure 2. Tumor diameter after the injection of cancer cells into previously unwounded (left) or wounded (right) mice treated with saline or meloxicam (n = 15 mice per group). Data are plotted as means ± SEM. P values were calculated the Mann-Whitney test P < 0.0005. Source: Translational Medicine Science

The good news is common pain killers, such as aspirin, can efficiently inhibit this process. Scientists found that many nonsteroidal anti-inflammatory drugs can effectively suppress tumor formation resulting from surgical wounds. Figure 2 shows that the wounded mice had a constant tumor size at around 2mm after given meloxicam, while the comparison developed tumors at average 5mm. Note the experiment only tested meloxicam; aspirin was also proved to be effective in the follow-up research.

Although the results are quite delightful, whether we can apply the same experiment to humans remains unclear. Weinberg pointed out that the aim of the investigation is not telling people not to trust lumpectomy or other tumor surgeries but develop a more effective treatment for postoperative recovery. He hoped that this research would promote further experiment on human and test whether drugs like aspirin has the same effect in the human body.

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Posted in Biological Chemistry, Organic Chemistry

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What is N95? ——The knowledge about face masks

Posted on March 3, 2020 by | 2 comments

Facing the outbreak of the new coronavirus, all kinds of face masks were sold out in the blink of an eye. More and more people seem to start to realize the importance of face masks.  But, do face masks really work? and how they work?

The answer largely depends on what type of face mask you are wearing.

Classification of Face Masks

According to the design of the face masks, the general ranking of the protective ability is (high to low): N95 masks> surgical masks> ordinary medical masks> ordinary cotton masks. But in the case of the new coronavirus, the most effective type of face masks are medical-surgical masks and masks filtering 95% or more of non-oily particles, such as N95, KN95, DS2, FFP2, etc. At present, China’s medical face masks are mainly divided into three types: medical protective masks with the highest protection level, medical-surgical masks commonly used in invasive operating environments such as operating rooms, and ordinary disposable medical masks.

 

How Face Masks Work?

Usually, medical face masks are made of non-woven fabrics, and its raw materials are mainly Polypropylene. And polypropylene layers are arranged to form an SMS structure.

SMS structure makes face masks capable to block floating particles while allowing airflow in and out the face masks. In this structure, the key material that brings the virus filtering effect is a high density, electrostatic layer lies in the middle: melt-blown non-woven fabric. When small particles like viruses get close to the melt-blown nonwoven fabric, it will be immediately captured by the electrostatic field and adsorbed on the surface of the non-woven fabric, and therefore prevent the virus gets into the body.
Yicheng Zhu

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Posted in Biological Chemistry, Organic Chemistry, Popular Science, Uncategorized

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