Category Archives: Biological Sciences

Studying DNA has never been easier…Thanks to eVITTA!

There’s one thing that every single one of us has in common with each other and all other living beings. It’s the fact that we carry DNA in our cells. DNA is an important molecule that has all the inherited information about how a living thing will look and function. A strand of DNA is like an extremely long sentence that uses only four letters – in fact, the length of the human DNA is 600 billion letters long! Can you imagine how hard and time consuming it would be to read? That is why scientists at The University of British Columbia (UBC) have developed a new and exciting application called easy Visualization and Inference Toolbox for Transcriptome Analysis, or eVITTA for short. eVITTA simplifies analyzing RNA (a type of DNA) and not only makes the process more efficient, but improves scientists’ understanding of its information as well.

The kind of DNA information that eVITTA works with is called the “transcriptome”. The transcriptome is the full set of RNA, which are the copies of DNA, within a cell. Analyzing the information in the transcriptome is crucial; for the past few decades, it has been one of the most used techniques for investigating diseases and their mechanisms.

The analysis of transcriptome data, however, is very tedious and time consuming. You have to retrieve the data, examine it, and then compare it with other transcriptome datasets to draw a conclusion. This involves several steps and different types of programs, which can be inefficient. eVITTA was created to combine the many steps of transcriptome analysis into one simple, user-friendly interface. This speeds up the process of transcriptome analysis immensely!

The tedious process of analyzing long strands of DNA is simplified with eVITTA.
Image Credit: CI Photos/Shutterstock.com

evitta was born out of excess data!

One of the many topics that sparked our interest was understanding the circumstances surrounding the creation of eVITTA. As Dr. Yan of UBC’s Taubert Lab puts it:

This whole project was born out of our need to pass on data. We have a lot of transcriptome data from past years that no one has gotten around to analyzing…. so during the pandemic, we started digging into those data and developing visualization modules and we realized we can actually make this into an app so that we can feed more data and generate visualizations

The team behind eVITTA

To discuss the different aspects of eVITTA and to delve deeper into this project, UBC’s Shayan Abbaszadeh sat down for a virtual interview with PhD candidate Judith Yan from the department of Cell and Developmental Biology at UBC. Dr. Yan is one of the many faces behind eVITTA at the Taubert lab and has worked tirelessly to bring this idea into fruition. Our podcast describes her role in realizing the gaps in efficient transcriptome analysis and building eVITTA with the rest of the Taubert Lab during the COVID-19 pandemic. Outside of eVITTA, Dr. Yan’s lab work in the Taubert Lab usually involves using model organisms such as roundworms to study stress responses and applying that knowledge to better understand human diseases. 

How does eVITTA make analyzing RNA so simple?

To grasp the scope of this research, first and foremost, it is important to understand transcriptome analysis. Dr. Yan describes transcriptome analysis as a powerful tool that examines how RNA, a copy of DNA, is used in a cell, tissue or organism. This involves taking out the whole RNA from a sample, getting it sequenced (i.e. decoded), and subsequently obtaining information from that data.

An exploration of gene patterns is one of the main aspects involved in effective transcriptome analysis.  A gene is a section of DNA that carries a specific piece of information. A crucial aspect of analysis is understanding that some genes are turned on at higher rates than others. According to Dr. Yan, once there is a count for these different genes, the numbers can be interpreted to reveal useful information about “what some of these genes are doing” and “what processes and gene sets are actually being changed“. Finally, there needs to be effective visualization techniques of the different data sets and the data needs to be validated against previously published data. 

All of these functions are achieved through eVITTA; a user-friendly, web-based interface that streamlines the multiple steps of transcriptome profiling. Watch this short video to become familiar with the 3 modules of eVIITA; easy-GEO, easyGSEA, and easyVizR, and realize what effective transcriptome analysis looks like!

The challenges of transcriptome analysis and how evitta addresses them

In our podcast, we focused extensively on the motivations behind the creation of eVITTA, specifically in relation to challenges associated with transcriptome analysis and how eVITTA deals with these challenges in ways that previous methods could not. Dr. Yan alludes to the use of the ‘overrepresentation approach’ (ORA) in previous technologies that has the flaw of only being able to represent a small subset of gene changes. As Dr. Yan puts it: “you’re missing out  on a lot of information and biologically… you are not able to capture the less severe changes. eVITTA on the other hand, focuses on entire sets of genes instead of just one gene, allowing scientists to observe gene changes across the board. 

Additionally, previous technologies did not allow for the organization of data because “oftentimes it is very tedious to do multiple comparison because you have many different subsections that you want to look at“. eVITTA prevents the dumping and mislabeling of gene data which expedites the process of discovering important biological patterns. This platform has already been proven to be highly effective in studies involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and roundworms (C.elegans). 

Dr. Yan’s research using eVITTA involves the starvation response of C.elegans roundworms. (credit: Taubert lab)

what does the future hold for eVITTA?

Our podcast also discusses the future of eVITTA and the team’s plans for further expansion. Dr. Yan and her team plan to add more algorithms to analyze the expression of different genes at a more in-depth level. The team also want to add more visualization options to provide more choice for gene dataset analysis. Finally, they are planning to update eVITTA’s databases by adding more datasets to the application. These ideas and more are discussed in our podcast below!

As transcriptome profiling provides major insight regarding diseases and illnesses, the optimization eVITTA can provide may be increasingly vital for today’s society. For instance, if transcriptome analysis can be conducted more efficiently, crucial findings in disease mechanisms may be discovered sooner. As a result, treatments and health regulations can be created more quickly, potentially saving lives and preventing disease spread. Additionally, eVITTA’s user-friendly and web-based interface makes transcriptome profiling accessible to more biologists around the world and would therefore greatly benefit the research community.

– Heather Cathcart, Kaushali Ghosh, Parham Asli, Shayan Abbaszadeh

 

 

 

Enzymatic Browning in Granny Smith Apples

Introduction

Browning is the darkening of the flesh that occurs shortly after fruits such as apples and pears are cut, exposing the flesh to air. Although browning is not toxic to humans since the pigment is composed of melanin, browning makes the fruit unsightly and unappetizing to eat . The main cause of browning is polyphenol oxidase (PPO), an enzyme that catalyzes the first two steps of converting the amino acid tyrosine into melanin in the presence of oxygen. Physical and mechanical stresses from slicing fruit physically damage the cellular structure of the flesh, which catalyzes PPO activity as it becomes exposed to oxygen .

Why Do Apples Turn Brown After You Cut Them? | Let's Talk Sciencefrom lets Talk science

what is an effective tool to delay apple browning?

Past studies have investigated the effects of different consumable solutions on browning, and citric acid, found naturally in fruit juices, was identified to be a moderate to a high inhibitor of browning . Citric acid is able to slow the onset of browning by lowering the pH of PPO’s environment so that the pH is outside the optimal pH range of 6-7 required for PPO to oxidize the flesh . Although other agents such as chelators and antioxidants can also inhibit PPO through reduction and inhibition, citric acid is more commonly found in foods, especially fruit juices that, when applied to apples, are more likely to preserve the apples’ taste

ReaLemon 100% Lemon Juice, 15 Fl Oz Bottle, 1 Count - Walmart.comfrom Walmart

Despite citric acid being an effective tool for delaying browning, the concentration at which its effects last for an extended period of time is unknown. Therefore, lemon juice was chosen since it is known to be composed of approximately 6% citric acid . Lemon juice also contains other acids, like ascorbic acid and malic acid, but their concentrations are negligible since citric acid comprises about 95% of the acid content of lemon juice . Granny smith apples were used as they are a common fruit consumed in households and are known to brown quickly after being sliced. It was hypothesized that lemon juice will delay the onset of browning due to the citric acid making the juice’s pH too acidic for polyphenol oxidase to initiate the conversion of tyrosine into melanin. If lemon juice delays browning, then the surface area of browning that appears on apple slices over a set period of time would decrease as the concentration of lemon juice the apple is exposed to increases.

Conclusion

This result shows that  increasing lemon juice concentration results in the decrease of browning due to the low pH of the juice compared to the pH that browns apple flesh. These results provide insight for future studies to find more effective anti-browning agents and to further investigate environmental temperatures to avoid to delay browning.

—–Chenyang Luo

Reference

Son, S. M., Moon, K. D., & Lee, C. Y. (2001). Inhibitory effects of various antibrowning agents on apple slices. Food Chemistry, 73(1), 23-30

Tinello, F., & Lante, A. (2018). Recent advances in controlling polyphenol oxidase activity of fruit and vegetable products. Innovative Food Science & Emerging Technologies, 50, 73–83. https://doi.org/10.1016/j.ifset.2018.10.008 

Tortoe, C., Orchard, J., & Beezer, A. (2007). Prevention of enzymatic browning of apple cylinders using different solutions. International Journal of Food Science & Technology, 42(12), 1475-1481.

Yapo, B. M. (2009). Lemon juice improves the extractability and quality characteristics of pectin from yellow passion fruit by-product as compared with commercial citric acid extractant. Bioresource Technology, 100(12), 3147–3151. https://doi.org/10.1016/j.biortech.2009.01.039 

What If We Killed All the Mosquitoes?

We all hate those little pests that only come out in the summer just to bite you and give you the little bump that itches for, what feels like, all eternity. More than 3,500 different species of mosquitoes exist, but only a small percentage of those species actually bite humans. For example, the Anopheles gambiae species carries malaria and the Aedes aegypti species spreads Zika fever. Furthermore, only the female mosquitoes are equipped with the appropriate stylet to pierce your skin.

Anopheles gambiae sucking blood
Credit: Wikipedia

So that begs the question, what would happen if we killed all the mosquitoes on Earth?

How It Affects the Food Chain

Animals that have mosquitoes as their primary food source, like bats, birds, frogs, fish and dragonflies, would likely have to change up their diet. This could potentially lead to their predators changing up their diet in some form as well, since their mosquito-loving prey would be hunting in other areas. So there would be some ecological impact.

Red-eyed tree frog
Credit: Wikipedia

However, it likely wouldn’t be all that detrimental to the food chain. Eventually other insects/animals would fill the void in the food chain left by mosquitoes and possibly be less annoying to humans and other animals.

How Would we benefit?

Hundreds of thousands of people would be saved. Malaria is a disease that still runs rampant in Africa. 95% of all cases and 96% of all deaths originated in the region, with children under the age of 5 making up 80% of the deaths in Africa. So eliminating the mosquitoes would increase the quality of life in many areas around the world and save a countless number of lives each year.

So why don’t we just do it?

Simply eradicating an insect species that lives all across the globe just isn’t feasible. Locating and killing every single mosquito is just not possible. However, it has been tested on smaller scales. 

Aedes aegypti on a leaf
Credit: Wikipedia

Scientists have genetically modified some male Aedes aegypti. The male carries a gene to stop their offspring from developing properly resulting in death before being able to reproduce. This has proven to be successful. However, it is still not feasible for total removal of mosquitoes across the globe since it would require genetically modifying millions of mosquitoes.

-Darryl Ma

The future of male birth control is within reach!

Now here’s something you may not know… condoms are over 5000 years old! That’s right, some of the first forms of birth control date back to thousands of years ago, and while the condom has made huge strides in the millennia that have passed since then, the only other option that exists for men in birth control is a vasectomy that may be hard and often costly to reverse. Well, that is until recently! A new scientific breakthrough has allowed scientists in The United States to design a male contraceptive pill that is 99% effective in preventing pregnancies in mice and is awaiting human trials!

there is a significant discrepancy in the contraceptive options available to women as opposed to men, signaling the need for more balance. Getty Images/Peter Dazeley

How does it work?

The male body needs a certain nutrient called retinoic acid, a form of vitamin A, for fertility, sperm formation and sexual drive. The male contraceptive pill, which was first unveiled at the 2022 American Chemical Society’s spring meeting a few days ago, is equipped with certain compounds that block crucial proteins from binding to retinoic acid receptors (RAR), hence allowing for reliable and reversible sterility in male subjects. The compound was administered orally to mice for a 4-week period. Not only did the compound result in a dramatic decrease in the mice’s sperm count, it also had no observable side effects. Better yet, once they stopped administering the drug, the mice regained the ability to give birth in 4-6 weeks!

In order to minimize potential side effects, the chemicals within the drug were designed such that they would specifically bind to RAR. This way, surrounding tissues will not be affected. But more importantly, the chemists and pharmacologists responsible for developing this drug at The University of Minnesota, attribute its success to the fact that it is completely non-hormonal!

The pill targets Vitamin A and has been shown to cause sterility in male mice. Getty Images/Canopy

what makes a non-hormonal pill better?

Up until now, there have been numerous attempts to create a male contraceptive pill, but any compound that has thus far reached the clinical trial stage, exclusively targets the male sex hormone testosterone. Unfortunately, this may  be accompanied with a slew of side effects including increased cholesterol levels, weight gain, depression, and increased risk of cardiovascular disease. This is why current efforts have been targeted towards the non-hormonal pathway to developing a male contraceptive pill.

When can the world expect to see the pill?

Clinical trials are set to begin by the end of 2022. The researchers behind the pill have teamed up with a private company, YourChoice Therapeutics, to achieve this goal. While there is actually no guarantee that the pill will replicate the same results in humans, there is a high level of optimism that the pill can be marketed to the general public in 5 years or under. Jesse Mills, director of the men’s clinic at UCLA jokes “It’s hard to ask a mouse about moodiness or fatigue or other side effects that may manifest in human studies”. Nonetheless, the current pill offers more promise than previous options.

Research associates at The University of Minnesota announce that the pill is ready to begin clinical trials in 2022. CTV News

 

Live long and eat chocolate

The history of chocolate

Photo Credit: Stocksy/Cameron Whitman

If you can’t imagine life without chocolate, you’re fortunate you were born after the 16th century. In the past, chocolate only existed in Mesoamerica as a bitter, foamy drink. Historically, not only chocolate has been used to associate with mood-lifting, but also provides scientifically supported physical health benefits. 

The secret of chocolate 

Flavanols, are a group of compounds that is the most abundant in cocoa, have strong antioxidant and anti-inflammatory effects that protect our cells from damage. As a result, consuming cocoa could help us age well and minimize our risk of getting cardiovascular diseases and cancer, and other diseases. 

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Video:Healthy Cocoa: The Story of Cocoa Flavanols

Can Consuming Cocoa Help Us Age Better?

Dr. Yanbin Dong, a geneticist at the Medical College of Georgia, and his team are looking for answers to prove the effeteness of cocoa. They studied the blood of 600 individuals aged 60 and older who participated in the world’s largest experiment to evaluate the efficacy of a cocoa supplement as well as multivitamin on reducing heart disease, stroke, and other diseases.

Dr. Yanbin Dong. Credit: Mike Holahan, Augusta Chronicle

“People believe that eating chocolate is good for you,” Dong said, adding that global enthusiasm for the sweet treat has outpaced scientific evidence of its benefit in humans.

The COSMOS Trial (COcoa Supplement and Multivitamin Outcomes Study), led by Brigham and Women’s Hospital and the Fred Hutchinson Cancer Research Center, collected data from 21,444 men and women to analyze The impact of a cocoa extract supplement and/or multivitamins on common health problems.

Inflammation is a major factor in ageing and common conditions such as heart disease, stroke, Alzheimer’s disease, cancer.

Dong and his colleagues will focus on ageing, including so-called “inflammaging” and epigenetic ageing, which are both considered good indicators of our biological age. Biological age considers key factors that influence your health and wellbeing, such as genetics and lifestyle, rather than just the year you were born. He also performs more standard ageing tests on these people, such as blood pressure and cognitive function tests.

From the study, dark chocolate, in particular, is frequently appreciated for its health benefits as a natural and good source of antioxidants, as well as iron, copper, and other heart-healthy nutrients. According to Dong, eating chocolate has been shown to lower cholesterol, blood pressure, cognitive decline, and boost the immune response to invaders such as the coronavirus.

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video : Cocoa: Food of the Gods | Simon TEDxUniversityofGroningen

As a result, not all chocolate gives health benefits. It is specifically the cocoa in chocolate that has been linked to positive outcomes–the higher the percentage of cocoa, the more active compounds that are present to provide health benefits.

Written by Yeonjun Choi

Become a pro about PROtein

How much protein have you eaten today? If you are not sure how much protein you consumed today, you might want to make sure you are getting enough protein in your diet. Protein contributes to how our body’s everyday functions. Thus, it is time to become a pro about protein and learn the importance, benefits and how much protein you should have.

 

What is protein?

Proteins are the building blocks of life and are the second most important macromolecule (large molecule) in the body. The protein molecule is made up of twenty different building blocks commonly known as amino acids. These amino acids make up the protein molecule chain and come in all shapes, sizes and functionality depending on the length and formation of the amino acids that form this chain. You may have heard and might be wondering, why does the human body need to consume protein when it can produce it on its own? Well, within your body and out of the 20 amino acids, the body can only create 11 nonessential amino acids. Accordingly, it cannot produce the essential ones that account for the other nine of them. Therefore, the human body needs to consume these essential amino acids through foods/supplements as it is vital for functions such as tissue repair, growth of bones and muscles, and transportation of oxygen/nutrients, to name a few.

 

Caption: What is protein and why is it so important?                                                    Source: https://www.youtube.com/watch?v=CzBGa8KnM3Q

 

PRO-tein tips on consumption

We know protein is crucial for health, but what is the limit for consumption – what happens if we consume insufficient or excess amounts? The optimal protein intake amount for a somewhat inactive average man or woman is 56 grams and 46 grams per day, respectively. This amount translates to about 0.36 grams of protein per pound (g/lb) of body weight, according to the Recommended Dietary Allowance (RDA). The RDA is the average daily intake of a nutrient to fulfill the essential nutritional requirements – it provides the goal/minimum amount to consume to stay healthy. Knowing that 0.36 g/lb of protein is the ideal amount, what are the consequences of having a lack of or an excess intake in the amount of protein? Studies have shown that insufficient and excess quantities of protein for long durations restrict bodily function. For protein deficiencies, individuals will develop mood changes, weakness and fatigue, and hair, skin and nail problems. Whereas for an excess intake, dehydration, kidney damage, and increased cancer risk and heart disease may occur.

 

Caption: Do you need more protein than you think? Well, you might need more protein in your diet depending on your lifestyle.                                                         Source: https://www.youtube.com/watch?v=JeKn-ym6sgE

 

Do you want to be a PRO-tein athlete?

Although there are dire consequences for consuming an excess amount of protein, sometimes it is desirable depending on muscle mass, physique goals and how active an individual is. For athletes, protein intake increases by almost double the amount (1.4 to 2.0 g per kg of body weight) as more energy is used up and the body requires more nutrients to recover and repair muscles. Additionally, protein is essential for muscle growth and boosts metabolism, which assists in burning calories to a greater extent.