Category Archives: Analysis

Is the Secret to Longevity in our Genes?

Posted on November 20, 2017 by | Leave a comment

Increasing life expectancies of the world. (Source: Wikimedia Commons)

Lifestyle and luck aside, the average human in the twenty-first century has a life expectancy of 80 years. For many people this may seem like a long time, but what about people who live to 100 years old or even older? Is there some secret to longevity they are not telling us?

The small fraction of the population who live to the age of 100 or more are called centenarians. An even smaller fraction of people, who live to be significantly older than 100 are supercentenarians. If you ask them what it takes to live a long life, you will get a wide range of answers: “morning walks and chocolate”, “tell the truth”, “raw eggs and no husband.” Although these answers cannot be directly correlated with longevity, scientists are looking for answers in our DNA.

It is true that a supercentenarian will have few than usual DNA variations known to increase the risk of heart disease, Alzheimer’s disease and other ailments, but researchers believe there is more to it than just luck. They suggest that there is a genetic code that actively protects against aging. This could explain why some supercentenarians are actually more healthy overall, than centenarians in the final months of their life.

DNA strands: Possibly hold the answer to longevity. (Source PublicDomainPictures)

Finding this sequence this is understandably hard since this “survival” phenotype is so rare and nonspecific. Of the billions of A’s, T’s, C’s, and G’s that make up our genetic code, it is hard to distinguish where these mutations occur and even more difficult to collect enough genotypes to confirm the theory.

Despite the odds, researchers published an article that identifies new variants in chromosomes 4 and 7 associated with extreme survival and reduced risk for diseases. The study used 2,070 individuals who were the one percentile of survival for the 1900 U.S. year and analyzed their genomes. They found that there are longevity-associated variants (LAV) and survival to extreme age at death (eSAV) variants, LAV being more common in centenarians. Although this far from confirms proof of a healthy aging gene, it a step forward in unlocking the secrets of living a long, healthy life.

-Mya Dodd

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Method of the Year: Cryo-electron Microscopy

Posted on November 14, 2017 by | Leave a comment
Cr to Nicolae Sfetcu

High Resolution of Detailed Structures (Credits to Nicolae Sfetcu)

About one month ago, Jacques Dubochet, Joachim Frank and Richard Henderson awarded the Nobel Price in Chemistry 2017 for developing the cryo-electron microscopy. The National Institutes of Health named cryo-electron microscopy ‘method of the year’. Cryo-electron microscopy can image frozen-hydrated specimens in native state without dyes at low temperatures through electron microscopy. Using this technology, scientists have produced three-dimensional images to target cancer drugs and demystify the Zika virus.

Cancer drug target visualized at atomic resolution (credits to NIH Image Gallery)

Actually, the development of cryo-electron microscopy has a long history. Previously, scientists used cumbersome dyes, stains or labels to visualize cell function, which would change the behaviour of the cell function and only provide a coarse two-dimensional image. This made scientists hard to understand molecular biology clearly since how the components in the cells looked like and what functions they performed remained unknown.

However, from 1975 to 1986, Joachim Frank stitched two-dimensional micrographs together to yield a sharp three-dimensional image. In 1990, Richard Henderson used this principle to visualize a protein in three-dimensional down to atoms with an electron microscope. In the early 1980s, Jacques Dubochet discovered that water would form a solid shell without freezing by rapidly cooling a specimen before putting it in an electron microscope, which could keep biological structures in original shape during scanning. They produced the desired atomic resolution in 2013. And researchers can now routinely produce three-dimensional structures of biomolecules.

Combining these theories, scientists could take biologically-accurate snapshots of the tiniest units of life. This technology helps scientists understand diseases better and develop better drugs. For instance, scientists found unique parts of the pathogen’s structure in the Zika virus and identified a potential target for a vaccine.

Improving resolution by cryo-EM (credits to NIH Image Gallery)

Engineers have developed better hardware to help improve cryo-electron microscopy by visualizing detailed structures instead of shapeless blobs. Scientists claim that the limited physical knowledge confines the resolution bt they will obtain better visualizations of biological structures in the coming year.

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Zika Virus…a Cure for Brain Cancer?

Posted on October 30, 2017 by | 2 comments

 

A summary of ZIKV Photo from: Google Images

ZIKV is a virus that is spread by daytime-active Aedes mosquitoes. The infection mostly causes very mild symptoms similar to Dengue Fever. Babies in the womb can have slightly more adverse effects such as brain malformations and birth defects. Researchers studied how ZIKV was causing these problems for babies. One main concern that arose was that ZIKV was causing the death of stem cells which are in high abundance in babies.

Recently experts have been studying how to use ZIKV to treat brain cancer, specifically glioblastoma. Glioblastoma is a type of brain cancer that is very common in adults and can grow and spread quickly. Due to its rapid growth, glioblastoma is tricky to treat and the common treatments, radiotherapy, chemotherapy and surgery, are unable to fully remove it.

Taking the knowledge that ZIKV targets stem cells in babies, researchers investigated whether or not ZIKV would target cancer cells in adults as they have relatively few stem cells. An article published in The Journal of Experimental Science reports the findings of this experiment. In living mice and donated human brain tissue samples, ZIKV was seen to kill the cancer cells. This is a huge step forward in the research.

Human trials are still some way away but so far the results look promising. The next step before human trials is to try and modify the virus to make a tamer version with the same effect on the cancer cells. This ensures that patients will be safe from other symptoms when treated.

For a general summary of the research conducted, the following YouTube video is informative:

YouTube Preview Image

Although the research is still in its early stages, I feel that it could have a lot of potential once human trials begin. This could lead to a treatment for cancer that is more effective than what we have today.

~ Sajni Shah

References:

1) Zhe Zhu, Matthew J. Gorman, et al. “Zika virus has oncolytic activity against glioblastoma stem cells.”  Journal of Experimental Medicine Oct 2017, 214 (10) 2843-2857.

2) Roberts, Michelle. “Zika virus used to treat aggressive brain cancer.” BBC News, BBC, 5 Sept. 2017, www.bbc.com/news/health-41146628.

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SI Units Are Changing, But Will We Have To As Well?

Posted on October 22, 2017 by | 2 comments

The SI units that we know and love today were first published in 1960, but they will be undergoing redefinition in the next few years. But don’t panic just yet!

First, a little history. The International System of Units is the metric system. The abbreviation SI stems from Système international (d’unités) in French. It is based on the metre-kilogram-second (MKS) system of units, in which meters, kilograms, and seconds were the base units.

The SI units are founded on seven base units for seven independent quantities. These units are the meter (m), kilogram (kg), second (s), kelvin (K), mole (mol), ampere (A), and candela (cd). All other units are derived from these seven. For example, the unit of force is a Newton (N), which is equal to 1 m×kg×s-2 in base units.

The SI base units. Depiep: Wikimedia Commons

Metrology is “the science of measurement, embracing both experimental and theoretical determinations at any level of uncertainty”, as defined by the Bureau international des poids et mesures (BIPM).

Changes are made to SI units to ensure stability over the long-term by linking the definitions to invariable constants.

Currently, the kilogram is defined by “the mass of the international prototype of the kilogram”, kept in a vault in Paris. If this sounds vague to you, you’re in agreement with the BIPM and metrologists around the world.

The international prototype of the kilogram is a block of platinum-iridium. However, objects like this one can easily lose or gain atoms or molecules from the surrounding air. In comparison to the prototype, official copies may no longer have the same weight. The prototype has an uncertainty of zero for now, but this is expected to rise.

Official copies of the kilogram are changing. Elizabeth Gibney Nature

SI was designed to be able to evolve as new derivative units are added and old definitions redefined. These changes are discussed at the General Conference on Weights and Measures held by the BIPM. The next conference will be held in Versailles in November 2018.

The latest revision was discussed October 16th-20th 2017 in Paris. In this new system, the base units will be defined in relation to a fundamental physical constant such as the speed of light c or the Planck constant h.

The new, revised SI units. Elizabeth Gibney Nature

These changes won’t affect the way we measure or the measurements we make in our everyday experiments, so we can continue on the way we did before. However, those operating at the absolute highest precision can now rest a little easier.

-May Constabel

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Consider Third Hand Smoke When Choosing a Home

Posted on October 16, 2017 by | 4 comments

Are you planning to move into a new home? Most people have heard about second hand smoke being bad for your health, but have you ever heard about third hand smoke? Third hand smoke is residual tobacco smoke pollutants that can remain in an environment up to months after the last use of tobacco. These pollutants settle on dust and surfaces such as carpets and fabrics. They can be reemitted into the air and inhaled, ingested, and absorbed through the skin. When choosing a home, is third hand smoke important enough of a factor to affect your decision?

Smoke Lingering in an Indoor Environment Credit to Wikipedia Commons

Researchers at the San Diego State University found third hand smoke to be very persistent, with significant levels remaining in homes vacant for 2 months even after they were cleaned and prepared for new occupants.

Third hand smoke levels were measured in 100 homes of smokers and in 50 homes of non smokers before and after the occupants of the homes changed. With the original occupants of the homes still present, the homes of smokers were detected to have levels of third hand smoke around seven times higher on living room surfaces and on living room dust when compared to the homes of non smokers. Levels of third hand smoke were measured again two months after these original occupants moved out and new non-smokers moved in.  The levels of third hand smoke on dust and on surfaces still exceeded health thresholds in more than half of these homes.

Urine samples for the new occupants in former homes of smokers and in former homes of non-smokers were analyzed, and the new occupants in homes of former smokers had an astonishing 3 to 5 times higher levels of tobacco pollutants present in their urine.

They found that third hand smoke levels in the air in homes of former smokers decreased after the change of occupancy, since polluted air can easily be recycled through air circulation and ventilation, but levels of third hand smoke on dust and surfaces remained high. So if you are planning to move into a new home especially with a newborn child, you should take care in choosing a home since infants and young children exhibit behaviours such as crawling and hand to mouth contact which exposes them to the high levels of third hand smoke found on dust and surfaces.

When choosing a new home, definitely try to avoid homes with excess levels of third hand smoke by knowing the history of the recent previous occupants. Knowing about the presence of third hand smoke can protect you and your family from the negative health effects of third hand smoke!

-Gareth Lee

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Why are dogs so friendly?

People started raising dogs about 14,000 years ago. Dogs are believed to be the very first domesticated animals. I have a dog as well, a 4-year-old German Shepherd called BeiBei. BeiBei came to my home when he was only three months old. At first, he was naughty and a little bit ‘aggressive’ (because nobody had ever told him not to bite and biting was his particular way to play with others), but finally he became a clever, loyal and friendly grown-up.

A photo of BEIBEI and me. (credit to baojing Jin, My mum)

For centuries, dogs are considered as the best friends of humans. When it comes to dogs, ‘friendly’ must be the first word popping up in most people’s heads. However, wolves, another species from canis, were first cultivated by humans due to some evolutionary advantage but nobody succeeded at all. And even baby wolves were not likely to be docile.

So have you ever thought about why, exactly, dogs are much more friendly than wolves or other kinds of animals? The answer remained unknown until 2010, when a study on DNA of dogs and wolves was published by Bridgett, a geneticist from vonHoldt of Princeton University, and colleagues.

The core difference was discovered in a gene related to social behaviours called WBSCR17, which claimed that the gene difference makes dogs so friendly and influences dogs’ domestication. Gene difference is also the reason why dogs can be trained to sit or shake hands using food rewards while you might be dead right away if you are trying to do the same things to wolves.

He sat down in order to get the frisbee from my hand. (credits to myself)

So a new project comparing the DNA of domestic dogs and wolves raised by humans was carried out then. In the experiment, dogs seemed to pay more attention on humans than wolves. Analyzing the DNAs of them, genes called GTF2I and GTF2IRD1, other than WBSCR17, are different. In addition, these genes are also related to the social behaviours in humans. What’s more, WBSCR17 genes help dogs adapt themselves to live with humans. Similar, other domestic animals, namely cats and mice, have genes of the same functions enabling them to be tamer than wild animals.

So now you can answer the question: Why are dogs so friendly? The reason is just a handful of changes in special genes, GTF2I and GTF2IRD1 and WBSCR17. From the perspective of genetics, dogs are indeed good friends of humans.

-Xinyue Chen

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Posted on October 2, 2017 by in Analysis

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Effects of hot and cold steeping methods on antioxidant activity in tea

Posted on September 18, 2017 by | 1 comment

Antioxidants are molecules that protect your cells from damage, and tea is bursting full of them, but have you ever wondered whether steeping your tea in hot or cold water affects its antioxidant levels? Is the difference even significant enough to worry about? Researchers at Università Politecnica delle Marche tested the effects of steeping temperature on antioxidant levels in black, green, white, and oolong tea.

                             

Black Tea                     Green Tea                       White Tea                    Oolong Tea

All images from Wikipedia Commons

 

The results showed that antioxidant activity is generally higher in tea brewed with hot water, but using statistics, this difference was found to be significant only for green tea. White tea deviates from this trend, showing statistically higher levels of antioxidants when brewed with cold water.

Two different analyses were conducted to measure the antioxidant ability of the four teas. Each analysis independently yielded similar results.

Fig 1: Antioxidant level measured in units of (mM GAE), showing statistically higher antioxidant levels for white tea brewed with cold water and for green tea brewed with hot water. Black and Oolong tea brewed with hot water showed higher antioxidant levels, but was not statistically significant.

Venditti E, Bacchetti T, Tiano L, Carloni P, Greci L, Damiani E. Hot vs. cold water steeping of different teas: do they affect antioxidant activity?. Food Chemistry. 2010 Apr 15;119(4):1597-604.

 

The researcher’s findings suggest that different types of teas contain different types of antioxidants, which are sensitive to different steeping temperatures. The effect of steeping temperature on tea depends on which antioxidants are present. For example, white tea brewed using cold water yielded higher antioxidant levels because some antioxidants may be degraded at higher temperatures. Brewing at lower temperatures preserved those heat sensitive antioxidants. Another example is brewing green tea, where tea brewed with hot water yielded higher antioxidant levels because some antioxidants may be extracted from the leaves efficiently only at higher temperatures.

Whether you prefer black, green, white, or oolong tea, and whether you prefer hot or cold brewing methods, all of these types of teas contain many antioxidants and are a healthy drink choice. Therefore, it is more important to drink the type of tea you like best, brewing it with the method that you prefer, which will ensure that you continue to consume this healthy drink!

-Gareth Lee

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