Trash to Treasure

Wouldn’t it be great to convert something that is harmful, yet naturally occurring in the environment to something that is useful to the human kind? That is exactly what a few researchers led by Dr. Da Deng at Wayne State University in Detriot did.

Multi-colored algae blooms may sound like one of nature’s many beauty wonders, however it is far from wonderful. Typically, these harmful algal blooms (HAB) consists of massive growth of one or more phytoplankton species, blooming up to a concentration of hundreds to thousands of cells per millilitre. These blooms of varying size can cover the surface of water for weeks. Some blooms are large enough, they can even be seen from space!

This satellite image capture algal bloom in Lake Erie Basin, taken on July 28, 2015. source: Nasa Earth Observatory

This satellite image captures the algal bloom in Lake Erie Basin, taken on July 28, 2015. source: Nasa Earth Observatory

In 2011, the algal bloom that occured in Lake Erie broke the record of worst algal bloom ever observed, topping the chart at 10 of the 10-point severity index. In August, 2014, the Toledo water crisis in Lake Erie left nearly half a million people without safe drinking water. Although the exact cause of algal bloom is yet to be determined, scientists believes that are many contributing factors including: water temperature, sunlight, current and presence of essential nutrients like nitrogen, carbon and oxygen. Although only a few algae species produce toxins, the effects they have on humans and aquatic life are detrimental as the toxins make their way up the food chain into animals we eat.

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[Video Courtesy to: Ohio Sea Grant]

Dr. Da Deng and his team of researchers aimed to reduced HAB in freshwater lakes by converting it to something useful. The team collected samples of  toxic HABs from Lake Erie, and converted it to hard carbon by heating it in argon gas at high temperatures of  700-1000 °C. Hard carbon, often derived from petroleum made from biomass, is an ideal electrode (electric conductor used to connect non-metallic part of the circuit), used for sodium-ion batteries. The final electrodes created by the researchers consists of 80% hard carbon (derived from algae), 10% black carbon and 10% binder. The scientists found that overall, the sodium electrode had a high capacity of up to 440 mAh/g in the first cycle. However, there were some issues of irreversible capacity loss after the first cycle, resulting in a lower capacity of 230 mAh/g.

Although, Lithium-ion batteries are more dominant in use right now compared to Sodium-ion batteries, sodium is more abundant and could potentially replace the more-expensive Li-ion batteries in the future. However, more extensive research still needs to be conducted to increase the stability and capacity issues with these algae-derived sodium electrodes to improve their performance in the future. The researchers also noticed that the temperature of which the algae was heated also affected its stability and capacity performance. This is something scientists can take in account as they aim to improve this discovery.

 

 

DNA TAKE ON A NEW ‘SUPERCOILED’ SHAPE

The iconic double helix of DNA that James Watson and Francis Crick first published in 1953 was not the end of DNA structure as new Study revealed.The double helix of DNA was just a tiny fraction of a real genome.It consists of 12 DNA base-pairs that later formed building blocks of DNA known as helical ladder.

DNA structure is made up of almost 3 millions base-pairs that must fit into nucleus of a cell which is just 10 micrometers across, thus DNA must really have to coil to fit into nucleus.

To get the bigger picture according to the new research,the researchers recreated DNA molecules in the lab. The researchers forced DNA strands to coil and recoil it at the same for several turns using short circular snippets of DNA that is made up of many base-pairs.
The researchers the discovered a panoply of a breathtaking new shape of DNA.YouTube Preview Image
Supercomputer simulations show how the dynamic motion of the supercoiled DNA causes its shape to change constantly to form a myriad of structures.

Most of which have different shape of DNA like handcuffs or sewing needles.Others through their coiling shape look like rods.
Supercoiled DNA strands

Photo credit: LIVESCIENCE/Thana Sutthibutpong

To make this ‘supercoiled’ DNA strands visible in the human body,researchers inserted an enzyme called human topoisomerase II alpha into the body to show how this ‘supercoiled’ DNA look like in the body.
The enzyme relaxed DNA twisted DNA in human body.This new discovery of ‘SUpercoiled’ DNA was reported today (oct 12) in the Journal Nature Communications posted by livescience that the structural shape of DNA created in the lab resembled the strands of DNA found in the cell nucleus.

The DNA samples were then froze and used a special form of microscopy to capture the first-ever images.
According to James Watson and Francis Crick, DNA helix is formed when complementary base-pairs like adenine and guanine are bound together which is now being contradicted by the new simulation of DNA in the new study that these base-pairs peel apart when the helix is unraveled.

The new discovered has shown us the complexity of the structure of DNA.It is now beyond double helix and it is so interesting to see how ‘supercoiled’ is DNA.

KUOL BIONG

Tragic Island Threatening Our Marine Life

Have you heard about a huge floating island of plastic? You may not believe it, but there it is in the central North Pacific Ocean, called the Great Garbage PatchThe size of the garbage patch is enormous estimated about twice the size of Texas! Charles Moore, the scientist who first discovered the garbage patch, mentioned that the garbage island will even likely double in size in the next ten years. The Great Garbage Patch has become a discourse of environmental debate for its adverse effects on marine life.

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Source: Flickr Commons

Though there are various types and sizes of debris, the majority of the marine debris consists of plastics. Algalita Marine Research Foundationan organization that studies sampling the marine debris to determine the density of plastic debris in the pacific garbage patch, analyzed the increasing ratio of plastic to zoo plankton by weight. This means that the concentration of plastic debris is increasing, contaminating the largest biome on Earth. Increasing accumulation of plastic debris leads to the biological loss by entanglement and ingestion. Every year, over 100000 ocean animals become trapped in marine debris and unfortunately, many of them die. In addition, many marine organisms ingest plastic debris, mistaking them as their food source, being poisoned and starved.

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Author: Chris Jordan Source: Wikimedia Commons

The chemical toxicity in plastics is another factor that deteriorates marine ecosystem. Plastic debris not only contains organic contaminants, but it also contains persistent organic pollutants such as pesticides and petroleum hydrocarbons, which are resistant to environmental degradation: they will remain in the water, aggravating and propelling the speed of contamination of marine life. Also, the high concentration of contaminants causes lethal threats to marine ecosystem as they accumulate in their body through ingestion. Contaminants, such as phthalates and Bisphenol A (BPA), adversely affect reproduction in many marine animal groups, disrupting the development of amphibians and inducing genetic abnormality. BPA acts as a feminizing agent that produces an estrogenic effect in fish. It also affects the processes of sex hormones and disrupts growth, insulin signaling, bone development and brain development. Furthermore, bioaccumulation of chemicals can occur; persistent organic pollutant can accumulate in the fatty tissues of organisms and higher the trophic level, the greater potentially the negative effect on birth or mortality of marine animals.

From the serious damages caused by the garbage patch, people have to be aware that we have caused the destruction of marine life. The environment constantly lets us know through diseases or disasters that it needs care, and people must pick up on the cues and change their behavior in order to save the world from a dark future!

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YouTube video courtesy of: National Geographic

By InHye(Lisa) Kim

I commented on :

Adrian Li’s post on Vitamin C. Miracle Cure or Wannabe Dud or Neither?

Grace Kim’s post on Almost there! Universal blood for all.

Julia He’s post on My Grandma Can Become Stronger by Eating Apples and Tomatoes.

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Kidneys Grown in Petri Dishes Claimed to Be Functional When Transplanted in Animals

 

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Source: Flickr Commons. Credit to: Alpha

This past decade has been an exciting time for regenerative science. Developmental biologists have been striving to discover new methods to grow organs such as hearts, brains, muscles, and even a hamburger patty from stem cells. As of only this September, kidneys grown in Petri dishes have been shown to be functional in animal studies!

Japanese researcher Dr. Shinya Yokote and his team have come across a scientific breakthrough within the stem cell research field in their recent early edition paper published on September 21st, 2015.

The early edition paper claims that transplant of lab-grown kidneys from stem cells are fully functional – in the sense that they can generate and excrete urine – in their animal studies with rats and pigs. Other groups in the past have generated half functioning kidneys that could generate urine when transplanted into animals, but not excrete it – a disorder known as hydronephrosis.

Dr. Yokote’s group managed to overcome hydronephrosis by inventing a new system within the rat’s body for the stem cell-generated kidneys to excrete their waste in to prevent hydronephrosis. They biologically engineered a persistent drainage tube to the kidney and connected it to a temporary bladder which was transplanted along with the kidney. This new system would empty its waste to the animal’s real bladder when it became full. The scientists named this system the “stepwise peristaltic ureter,” (SWPU) and believe that this could be the future of kidney transplantation.

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A picture of the SWPU system that were used to transplant into rats. Source: Yokote, S., Matsunari, H., Iwai, S., Yamanaka, S., Uchikura, A., Fujimoto, E., Matsumoto, K., Nagashima, H., Kobayashi, E., Yokoo, T. (2015). Urine excretion strategy for stem cell-generated embryonic kidneys. PNAS Early Edition September 21, 2015. doi: 10.1073/pnas.1507803112

Although this discovery could impact millions with kidney failures in the future, readers should be warned that this is only an early access article. The researchers have not shown any empirical data to support their claims in their early access article. Those interested should keep a keen eye open for the full paper to be released!

By Justin Yoon

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Is in vitro meat the future meat source?

 

Cell Culture, Author: Umberto Salvagnin, Source: Flickr Commons

Cell Culture, Author: Umberto Salvagnin, Source: Flickr Commons

While “Humans no longer raise animals for food” is still a science fantasy in TV shows like Star Trek, growing meat from a Petri dish as one solution to achieve this goal is no longer a far-fetched dream.

Around 2000, Morris Benjaminson, has successfully produced fish fillet from goldfish skeletal muscle in the lab, and deep-fried their result. “It looked and smelled pretty much the same as any fish you could buy at the supermarket,” says Benjaminson (Scientific American).

Two years ago,  two people tasted the in vitro beef muscle prepared as a burger patty at a news conference in London for the first time.

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[by youtube channel Maastricht University Cultured Beef]

They both agreed that the texture was quite close to meat. “I know there is no fat in it so I didn’t really know how juicy it would be, but there is quite some intense taste,” said one taster.

We seem be able to see lab-grown meat in production fairly soon. However, would in vitro meat be our future meat source even if they taste no different from natural meat?

I think there are some obvious advantages. First of all, in vitro meat allows us to control its nutrition content, hence it can be much healthier than farmed animals. Secondly, reducing animal farming can significantly reduce animal cruelty, the burden on land use, and animal waste. Last but not least, from a environmental point of view, in vitro meat can even reduce green gas emissions. For example, cattle farming is infamous for their Methane emissions (Food and Agriculture Organization of the United Nations), and Methane has a global warming potential 72 times more than carbon dioxide over a 20-year-period based on a 2007 report by  Intergovernmental Panel on Climate Change (IPCC).

Name: Confined animal feeding operation, Author: SlimVirgin, Source: en.wikipedia

Name: Confined animal feeding operation, Author: SlimVirgin, Source: en.wikipedia

However, people do argue that there might be some disadvantages that we should look out for. For example,  Science Friday  has pointed out a few down-sides such as reduction on animal by-product, and the $300,000 price tag for a beef burger patty. However, I think these are trivial problems given that animal by-products have already been largely replaced by artificial materials, and the scientists were quite confident about cutting the price down. The most interesting point is that they mentioned that it is just like industrial revolution, artificially producing natural product is always going to cost more energy, which is not necessarily a good thing for the environment. I agree that it does seem like more energy cost is inevitable, but energy related environmental damage is something that we have already been working on for years, and it is up to us to prevent it from very beginning.

All in all, I think with a combined effort with other solutions that we have already been working on such as animal farming regulation, and a global effort on reducing green house gas emission, there is definitely a place for in vitro meat to benefit us to some extend in the future.

By Sainan Liu

Almost there! Universal blood for all.

Researchers of The Centre for Blood Research and The Chemistry Department in University British Columbia (UBC) have been experimenting to generate an enzyme that makes eight different blood types to be the safe universal blood for everyone.

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Blood transfusion (source: Flickr Commons)

As it is generally known, our blood type lies into four major groups: A,B, AB and O. Also, there are positive types and negative types on each four types. Overall, eight different blood types differentiate from each other by additional sugar structure that lies on the surface of the red blood cells which decide presence or absence of antigens. Failure in performing correct blood transfusion can bring life-threatening situation due to immune responses to patients. The importance of correctly identifying the blood type and its transfusion to the patient in need is absolutely critical in the matter of life and death. An example of wrong blood type transfusion can be found in the link.

Drawing from the above importance of identifying blood for patients, the blood type O is known as universal blood because type A and B share the same core sugar structure as type O.  More specifically, only type O negative can be called universal blood because type O positive can not be transfused to patients who have negative blood type. Blood type O negative can be donated to patients with negative blood types as well as positive blood types. The universal blood type O negative is the key to blood transfusion; one which is in need, but not enough of.

Above diagram indicates blood type O as universal donor due to absence of antigen.

Therefore, David Kwan (UBC Chemistry department), Jayachandran Kizhakkedathu (UBC the Centre for Blood Research) and others are in process of finding a way to create an enzyme that can cut off the additional sugar structure (antigen) on surface of the blood cell so that all blood types can be donated and transfused safely as blood type O. Such research is the breakthrough in the clinical use of blood transfusion in saving the lives of critical patients.

Researchers used a new technology called directed evolution to generate the “sugar(antigen)-cutting” enzyme. Through directed evolution technology, researchers were possible to insert mutation gene into the gene that codes for the enzyme. Currently, thanks to their efforts, the enzyme under research became 170 times more effective at cutting majority of antigens in type A and B.

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[Credit to: City]

Since the enzyme cuts majority of antigens but not all, the research is still underway. Human immune system is critically sensitive to even tiniest of antigens; adding to the importance of the successful research. This study needs further improvement before the enzyme can be used for clinical use.

by Grace Kim.

Does storing data using light make computers lighter?

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The image represents a memory cell, with the yellow patch being the phase-change material called GST, which sits on a waveguide

When it comes to new enhances to computers everyone wants faster response times and overall better performance. A team of researchers from top ranked universities found a way to increase computers performance by changing the way they access and store data.

Data stored on a computer needs to be there when power is is either on or off. This is called non-volatile memory and devices that have this property are CD’s, DVD’s and hard disks. Although devices like these provide data storage, they are really slow compared to CPU. Exactly how slow? Same as email and pony express.

This is a huge step in technology since it would allow computers to become much faster overall. It would also help the CS community deal with technical difficulties that arise from memory accesses like blocking an execution path until memory read/write is complete. The earlier example is hard to handle with today’s technology, since it introduces many possible hard-to-discover errors that may cause abnormal behavior.

This problem encountered in Computer Science is called the von Neumann bottleneck. Even though you can increase the performance of the CPU, you still waste many cycles waiting for memory/hard disk to respond to the requests. “There’s no point using faster processors if the limiting factor is the shuttling of information to-and-from the memory”, explains the University of Oxford’s Professor Harish Bhaskaran, leader of the research project, in a statement.

Professor Harish Bhaskaran and together with his team have built the world’s first all-photonic non-volatile memory chip. The chip provides incredible data reads and writes given we are using light and not electronic signals. However that is not the only major property of it; it also allows for simultaneous reads and writes, a world first as well.

The next steps of this projects are deploying the chip and integrating it with existent configurations in the industry, as well as building interfaces with different modules.

Radu Nesiu

Credit: Image by Wolfram Pernice