Category Archives: Science in the News

Evolution Can Be More Random Than You Think

Charles Darwin’s Origin of Species postulated that evolution takes a directed approach toward increasing fitness. A recent discovery suggests that evolution doesn’t always need to have a direction. Dr. Matthew Pennell’s findings suggest that evolution on a chromosomal level can have a high degree of randomness.

Dr. Matthew Pennell, an evolutionary biologist specializing in Computational Biology at the University of British Columbia, recently wrote a paper that gives more insight on evolution, entitled Y-Fuse? Sex Chromosome Fusions in Fishes and ReptilesIn this paper, Dr. Pennell uses software and algorithms to determine the factors that drive sex chromosome fusions. Unlike traditional biologists, Dr. Pennell does all of his work on his MacBook instead of using pipettes and microscopes.

Source: Wikimedia Commons, Dr.Pennell uses computational approaches, such as Mathematica for his research.

Source: Wikimedia Commons, Dr.Pennell uses computational approaches, such as Mathematica for his research.

This video, courtesy of universityofbc via Youtub, introduces UBC Killam and NSERC postdoctoral fellow, Dr. Matthew Pennell and talks about his research

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“The simple fact that Y autosome fusions are way more common than W or X or Z, suggests it’s probably just random, which is a kind of interesting and cool result that this huge thing in our genome and across all genomes is just random chance, and this random chance explanation is the most consistent with our data.”

 -Dr. Matthew Pennell

During his graduate studies, Dr.Pennel was part of a team that integrated chromosomal information of thousands of species into an electronic database called The Tree of Sex, which we describe in further detail in our podcast below.

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Now that we know randomness is involved in sex chromosome evolution another question arises: Is sex determination an absolute process? 

As we will soon see there are species, such as the Stickleback fish that change their sex determination system from XY, to ZW, to temperature controlled and so on. However, does this mean that we humans might experience such a change in the future?  

Source: Flickr Commons, Huamns have 22 pairs of autosomes and 1 pair of sex chromosome

Source: Flickr Commons, humans have 22 pairs of autosomes and 1 pair of sex chromosome

“They keep reinventing how they make males and females and this is really interesting and crazy because making males and females is the most basic thing animals do….But they keep switching around how they make males and   females, which I think is pretty cool.”

-Dr. Matthew Pennell

In addition, we were fortunate enough to have the opportunity to interview Dr. Pennell:

https://youtu.be/9obgQ7mI5Ac

Before the interview with Dr. Pennell, our group had a lot of difficulty understanding the premise and messages of the paper. Dr. Pennell provided us with simple insights on the different facets of the evolution of sex chromosomes – from the creative variety of ways that nature determines sex in species, to the mechanisms which drive sex chromosome fusions. Although a lot of these concepts were hard to understand at first, the premise of the paper is very simple to understand – computational biologists often work with real world data sets (ie. “The Tree of Sex”, and try to fit their models to them to determine the relationships between the scientists’ predictions and what’s really happening. In this specific paper, Dr. Pennell and his team concluded that the different models did not relate to the given dataset and the explanation for the real data is attributed to randomness.

 

We would like to give a special thanks to Dr. Matthew Pennell for his time and explanation of his paper.
Authors: Justin Yoon, Julia He, Radu Nesiu, and Matt Golf (Group 2)

Looking deep within a cell, super resolution microscopy technique improved by researcher at UBC

What do you think is the smallest scale visible through a light microscope? Bacteria in micrometers? Guess again. The answer is thousands of times smaller. Last year, a Nobel Prize in Chemistry was awarded for the development of super-resolved fluorescence microscopy, which brought the imaging scale down to nanometers (billions of times smaller than a meter). Recently, Reza Tafteh, a PhD candidate from the University of British Columbia further improved on this technique. The specific version of super resolved microscopy Reza improved on is called single-molecule localization microscopy (SMLM), and it allows scientists to image deeper into a target cell with greater accuracy. An interview with Reza is available in this podcast: 

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The computer system used to operate Reza’s microscope, photo credits: Ivan Lan, Reza Tafteh

As Reza explained in the podcast, SMLM achieves high resolution through image reconstruction. Imagine looking into a traditional microscope like looking down on the city of Vancouver at night from an airplane above. It is hard to tell the contour of the city with the limited lighting. Using fluorescence on the target sample is like turning on the building lights in the city, allowing us to observe things that aren’t normally visible under the moonlight. Now imagine that these lights are constantly on and extremely bright. If the location of the lights are too close together, many of them may seem blended with each other. This makes it harder to tell apart (or resolve) smaller structures such as narrow streets from one another; which in this case is like trying to resolve narrow structures within cells. SMLM reduces this effect by turning the lights on and off at different times for different parts of the city, which you can find more details in the podcast and the video.

However, the traditional SMLM technique isn’t perfect. Alongside major limitations in stability mentioned in the podcast, another major limitation is the distortion of an image caused by changing refractive indices through several different media, just like a pen appearing bent when inserted into a cup of water. Refractive indices varies from the cover-slip to the media (the substance the cell is placed in for imaging), and from the media to the cell.

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Refractive Index difference causing image refraction. Source:Flicker Commons, Author: Mohammad Tajer

Reza Tafteh has improved on both of these limitations. His approach can produce stabilized images with reduced distortion when imaging deep into samples. Here is a video of him demonstrating his stabilization technique.
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Reza is now trying to push the limits of SMLM even further, he sets his eyes on improving the technique’s inability to image live cells, while continuing to increase the resolution and clarity of microscopy images. It is exciting to think that specific cellular structures such as heart cell calcium receptors can be observed in unprecedented detail. It is not hard to imagine the many biological fields that can benefit from this microscopy technique. Reza’s improvement on SMLM  can potentially lead to better understanding of molecular biology, which may one day lead to new treatments for diseases such as central core disease.

Music and sound material used in podcast:

A sincere thank you to Reza Tafteh for participating in this project.

By: Group 3, Brian Cheng, Esther Lo, Ivan Lan, Sainan (Stephanie) Liu

The CRISPRs Fever

You may remember from biology textbook that we can edit genetic material using restriction enzymes, a DNA-cutting protein structure. Using this we can learn about gene functionalities, search for disease treatments or increase yields of crops. Controversially, it also made unnatural creations possible. However, different gene targets require different enzyme structures, just like to open different doors you need different keys, and making these “keys” turns out to be complicated, expensive and time-consuming, which might have kept most of the “fantasies”, such as “super human” or other wired things, away from reality for now for better or worse.

by PuraVida_Fotografie from Google Image "genetic mutation" Labeled for reuse

by PuraVida_Fotografie from Google Image search “genetic mutation”, labeled for reuse.

However, what if all the “doors” also have the same type of “digital locks”, and all you need to change is the password? CRISPRs (clustered regularly interspaced short palindromic repeats) turns out to be this “lock”. It contains repeated sequences sandwiched with spacers (unique genetic information) in between. The spacers are external virus genes kept in bacterias and served as the “criminal records” so that when invasion happens again, the bacteria can send an “army” of gene-cutting enzymes, called Cas9, to cut the recognized viruses’ DNA apart.

"Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA" by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki - Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

“Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA” by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki – Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

In 2012, scientists have proven that instead of making restriction enzymes for different genes, we can simply replace these “criminal records” and use the same Cas9 “armies” to cut desired genes with much less time and cost. You can find the details in this following video.

YouTube Preview Image[by McGovern Institute for Brain Research at MIT]

Nature , Science and many major media have unanimously deemed CRISPRs to be a revolution. Radiolab has discussed its ethical controversies as if the realization of the technology is right around the corner. It has been portrayed as such a simple and approachable method that people even claim to provide CRISPR DIY kit for experiments at home.

However, I think despite these attentions,  the reality is that we are still far from ready to harness CRISPRs. Although many researches has already been using it to edit genes in a variety of bacterias, plants, and animals within a short 3-year period, few studies focused on the limitations and functions of CRISPR itself. Some research was done too early without waiting for the technology to mature, such as the research using human embryos, which has resulted in a less satisfactory result. Some researchers commented that CRISPR can be less accurate than expected and may not be the most efficient and cost-effective solution for certain problems on Quora. Scientist Konstantin Severinov on Quanta Magazine also pointed out that it is still unknown whether defending invaders is the major usage of CRISPRs since many of these spacers appear to be genes of viruses that are long gone. It might be a good time now to slow down and maybe build the technique from ground up concretely first.

by Sainan Liu

Lethal Adaptations In Nature: Tapeworms linking infection and cancer

Parasites are some of the oldest and basic forms of life on the planet. Each and every species having honed their specific traits to leech and infest their host often through millions of years of natural selection. It’s a scary thought, to say the least. And one particular widespread parasitic species has recently been discovered to have made significant jump. Tapeworms.

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Tapeworm proglottids (50cm in length)
Author: Nathan Reading via Flickr Commons

It’s a certain parasite that I’m quite concerned about every time I pick up an egg sandwich at local gas station. Tapeworms often infest the digestive tract of animals and use their hosts are intermediary stages in their life cycle. In the case of humans, that infection is usually caused by consuming undercooked foods. The photo of a vomited tapeworm above was taken from a pregnant 26-year-old patient who had been living in East Africa. As you can see, they can grow immensely large in your intestine without any symptoms (one of the optimal traits of a model parasite).

If that wasn’t enough to make your skin crawl, a study published in 1999 found that up to 75 million people may carry the dwarf tapeworm with 25% of children affected in certain areas. When taking a much closer look with an electron microscope (image below), you can clearly see that tapeworms have an effective adaption on its head: suckers, muscular grooves, and hooks to latch onto your inner digestive system. Though rarely lethal, newly published research has uncovered a potentially deadly link between these worms and cancer.

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Hymenolepis microstoma (rodent tapeworm)
Author: Magdalena ZZ via Wikimedia Commons

A brief report was published this past week in the New England Journal of Medicine, detailing an unprecedented case of a tapeworm (or any parasite of that matter) transferring cancer cells into a human. The team of American researchers led by Dr. Atis Muehlenbachs from the Centers for Disease Control and Prevention claim it to be the first reported case of its kind. Easing public fears, it’s also been described as extremely unusual and rare.

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Source: The New England Journal of Medicine

The story begins in Columbia in 2013 when a 41-year-old man stumped local doctors of his deteriorating condition. He was ill, losing weight, and struggling with a prior HIV infection. Upon further examination, a CT scan of his lungs showed many tumorous growths which were made of cells not identified as human. That shocking revelation prompted them to contact scientists at the U.S. CDC.

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Figure 1 (A). Radiographic and Pathological Features of Malignant Hymenolepis nana.
(Muehlenbachs et al. 2015)
Source: The New England Journal of Medicine

The CDC center in Atlanta found the cells to be much smaller than human ones. Ten times smaller. Eventually, a genetic analysis found the strange cells had DNA from Hymenolepis nana (the dwarf tapeworm). The current theory is that the HIV patient’s compromised immune system and a mutation in the tapeworm caused this spread of cancerous cells from parasite to host.  For a more detailed explanation of the biological mechanisms involved, check out the helpful video below courtesy of the New England Journal of Medicine.

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It’s important to note that original patient died before he was correctly diagnosed. However, perhaps the results of this investigation may prove to be fruitful for others in the future as millions of people suffer from both tapeworms and HIV.

Tragedy aside, one has to admire how amazing this discovery is. For myself, I’m so impressed by the international collaboration of medical experts as well as the nature of the case. Even the language used in the original paper sounds very dramatic, Invasion of human tissue by abnormal, proliferating, genetically altered tapeworm cells is a novel disease mechanism that links infection and cancer.”  (*I’ve underlined some phrases to emphasize their impact.)

It feels like something out of the TV show House MD: a medical mystery, bizarre clues, the elusive search, and the extraordinary resolution. It’s the kind of passion that I believe Muehlenbachs shares.

“We were amazed when we found this new type of disease – tapeworms growing inside a person, essentially getting cancer, that spread to the person, causing tumor…” – Dr. Atis Muehlenbachs of the U.S. CDC

Furthermore, I’m sure this case will spark a new field in medical research of cross-species oncology. I admit that this mutation may not be very beneficial to the tapeworm as it prematurely kills off its human host and may end up being a once-in-a-life phenomenon. Nonetheless, it’s a great example of how a parasite can dramatically change the relationship with its host and how we should approach treatment of unknown diseases.

By Paul Yi

Commented on:

Esther Lo’s Green Rush in Canada

Matthew Golf’s Free Speech for Science in Canada

Luxi Xu’s Work-Life Balance

 

Brains and games in 21st century – How do video games affect us?

There is a lot of debate regarding how video games influence our brains development and whether or not games are beneficial or damaging. Scientists have examined both sides and the question that needs to be answered is whether games are beneficial or they are transforming us into machines.

digital mindcredits: http://guardianlv.com/2013/08/researchers-develop-mind-control-using-the-internet-video/

Some studies show that prolonged exposure to video games has negative effect both on the body and the brain. Games decreases attention span, increase the risk of obesity and violent games decrease sensitivity towards aggression. The implications are troubling since decreased attention implies lower academic performance and obesity is a health risk factor. Furthermore it is shown that decreased sensitivity towards aggression not only makes us consider aggressive behavior acceptable but it also increases the chance that we will become aggressive.

aggressive gamers

credit to: http://yoursinglesourcefornews.com/ academics-debunk-theory-linking-violent-video-games-with-aggression/1379/

Another fact that must be considered is repetitive tasks in games. Because there are lots of games that become repetitive and have reward systems that encourage that behavior gamers are exposed to lose of creativity. Since repetitive tasks are better suited for a computer we could ask ourselves if our mind is encourage to become a basic processing unit.

However, there is another side of games which was investigated by researchers and the findings encourage people to become casual gamers. The benefits from games are as follow: better cooperation skills, adaptation to new challenges, fast reaction time and better attention to details.

brain-skills-games

credits: http://www.jklmgames.co.uk/how-games-can-train-the-brain

Besides the standard types of games we should also consider games that involve movement (e.g. some Nintendo Wii games) which are shown to motivate exercise. Those type of games should become encouraged in populations with increased risk of obesity, where the reward system should be tailor for the customers.

The tricky part of the games is the reward system which acts as a drug since it releases dopamine which is the hormone for excitement. Using this we can develop games that can stimulate people to learn and train. A study done on surgeons  showed it is possible to increase job performance via gaming. Here is a TED talk about games and how we can use them to construct a better world.

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Based on what we seen so far casual consumption of non-violent games have beneficial effects, however one must take extra care since crossing the line and becoming an addict can severely impact us.

Radu Nesiu