Tag Archives: Genetics

Pip, SAR, and GMOs: How UBC Researchers are Advancing our Knowledge of Plant Immune Systems

What would happen if plants couldn’t protect themselves? Well, for one, they would be prone to many different infections and viruses. Ultimately, plants would die without the ability to protect themselves. To really put things into perspective, humans would not have many of the food sources they have without plants.

Yuli Ding, a 5th year PhD student at the University of British Columbia, and her colleagues made a coincidental, break-through discovery in October 2016. Focusing on the ability of plants to resist diseases that they’ve previously encountered, called Systemic Acquired Resistance (SAR), Ding set out to determine if a specific molecule is required for this type of protection. SAR is described with greater depth in the following podcast with the researcher herself. The molecule in question was Pipecolic Acid (Pip). According to the findings of the scientists, “Pipecolic acid could be a relatively important mobile signal is the systemic acquired resistance.” In simpler terms, Pip aids in SAR by activating the process.

We had the opportunity to interview Yuli Ding about her research to help clarify some of these complex concepts. Listen to her explanations of the research in the following podcast.

What happens to plants that cannot complete SAR? Mutated plants, with a non-functional SARD4 gene, are SAR-deficient and thus unable to effectively defend against diseases. Instead of making Pip to activate SAR, a Pip pre-cursor molecule gathers in the plants – demonstrating SARD4’s importance in synthesizing Pip. Since Pip is not being created, the plants don’t exhibit SAR and are less able to defend themselves when infected by pathogens.

In this video, Yuli Ding describes how they identified SAR-deficient Arabidopsis plants, and demonstrates one of the main lab techniques, Polymerase Chain Reaction, that her team used to help identify Pip as a signal molecule.

Arabidopsis Timelapse
Music: Horizon, by Letmeknowyouanatole

Why should we care? SAR is a key process by which plants protect themselves, so SAR is an essential mechanism in ensuring the maintenance of agriculture and healthy crop yields.

Science is advancing at a rapid rate and the use of Genetically Modified Organisms (GMOs) has been increasing. A GMO is the result of a gene transfer between organisms. For example, the gene of one organism is inserted into another organism in order to improve that organism. The results of this study could be a stepping stone to creating GMOs that have better SAR, and are better able to defend against disease. Specifically, the genes responsible for synthesizing Pip could be added to immuno-compromised organisms. Genetic modification could also be used to make plants have stronger SAR or better immune systems.  Although the use of GMOs could be beneficial, GMOs pose several threats to the environment and other organisms.

What can we do with this research right now? The findings of this study could help improve the yield of crops and the number of successful crops. Farmers and agriculturalists could now focus on improving the environmental conditions of their plants to ensure that all requirements for a plant to be healthy are met. A healthy plant would increase the chances of proper SAR. All in all, a healthy plant is a happy plant!

 

By Navpreet Ganda, Pavneet Virk, and Zhongkai He.

Key protein in spinal cord regeneration found

Researchers at Duke University have identified a key protein used in spinal cord regeneration in zebrafish. The findings were presented in the November 4 edition of the Science journal.

An adult female zebrafish. Authorized for redistribution by the copyright holder. Retrieved from https://en.wikipedia.org/wiki/Zebrafish.

An adult female zebrafish. Authorized for redistribution by the copyright holder. Retrieved from https://en.wikipedia.org/wiki/Zebrafish.

While zebrafish can completely regenerate their spinal cords even after it is severed, humans cannot. This makes spinal cord injuries (SCI) one of the most debilitating injuries for humans, as ability to walk and sense can be impaired. As SCI can be permanent, many patients require lifelong assistance with daily activities, resulting in loss of autonomy.

Diagram of the spinal cord. Image in the public domain; retrieved from https://en.wikipedia.org/wiki/Spinal_cord_injury

Diagram of the spinal cord. Image in the public domain.

When a zebrafish’s spinal cord is undergoing regeneration, a bridge forms. The first cells (a cell is the basic functional unit of all living things) project lengths many times their own size and connect a wide length of the injury. This is followed by nerve cells, and after eight weeks, new nerve tissue has filled the gap formed by the injury, reversing the zebrafish’s paralysis.

Nerve cells in the brain. Shared under the Creative Commons license. Retrieved from https://en.wikipedia.org/wiki/Neuron.

Nerve cells in the brain. Shared under the Creative Commons license. Image by UC Regents Davis campus.

The researchers looked for genes (the basic functional units, made up of DNA, that instruct the body how to make proteins) whose activities changed throughout this process, and they focused on a protein called connective tissue growth factor (CTGF), as they found more of it in the supporting cells (glia) that formed the bridge within two weeks of the injury than before.

Glial cells in a rat brain. Public domain. Retrieved from https://en.wikipedia.org/wiki/Neuroglia.

Glial cells in a rat brain. Public domain.

This finding is important because it provides a direction for research in achieving full recovery of function in patients with SCI. Although the researchers say that CTGF alone will probably not be enough for spinal cord regeneration due to scar tissue (new tissue that forms after injuries) in mammals, now that CTGF has been identified as a key protein for regeneration, it could be used with other proteins and therapies. The researchers expect that studies on CTGF will move towards mammals like mice.

In addition, knowing this new information about CTGF can lead research towards similar proteins. Indeed, the researchers themselves have indicated plans to study the other secreted proteins they observed when looking for genes with altered activities throughout the zebrafish’s healing process.

Permanent SCI have debilitating physical and psychological effects on their patients, their families, and the support system around them. An estimated 24-45% of people with SCI suffer from depression, and the suicide rate can be as great as six times of the general population. In fact, in young people with SCI, it is suicide that is the leading cause of death and not physical complications of the injury itself. The psychological impact is tragic, which is one of the reasons why I believe that improving patient outcomes for SCI is one of the most pressing needs for modern medicine, and also why I hope research funding continues to go towards spinal cord research.

-Jasper Yoo

CRISPR; A tool that can almost fix everything

CRISPR, sounds like a type of vehicle or a new gym supplement. In fact CRISPR is a new piece of technology, possibly the greatest finding of the century. CRISPR, short for Clustered Regularly Interspaced Short Palindromic Repeats, is a genome-editing tool that was first found in bacteria. Japanese scientist Yoshizumi Ishino at the University of Osaka was the first to discovered CRISPR in 1987.

CRISPR is used as part of the immune system defence in bacteria. It has the ability to sense when viruses inject their DNA into the cell; sending out proteins that recognize the foreign DNA, cutting it up into non-functioning pieces to prevent an infection. The sent out proteins are able to recognize virus genomes by incorporating the injected viral DNA into its own genetic material, using this as a template to find the invading DNA.

How bacteria use the CRISPR/Cas system against viral infections. Image from https://upload.wikimedia.org/wikipedia/commons/5/5f/Crispr.png

How bacteria use the CRISPR/Cas system against viral infections. Image from https://upload.wikimedia.org/wikipedia/commons/5/5f/Crispr.png

Many of you may be thinking, cool so the bacteria has a way of protecting itself from invading viruses but how does this effect humans? Until now there have not been accurate DNA cutting technology but with CRISPR we have one. As discovered by Doudna Lab, it is possible for scientists to create templates that match the gene they want to remove from genetic material, allowing them to cut out any gene they want. For a concise explanation check out Carl Zimmer’s, on behalf of  BI science, description of how CRISPR works in the video below.

This allows for endless possibilities. Genetic diseases, like sickle cell anemia, can be cured using CRISPR. Simply make a template that matches the mutated gene, remove it with the CRISPR  and add a functional gene. The individual will no longer suffer from sickle cell anemia. Scientists are even looking at the possibility to modify the human germ layer, allowing for ‘designer’ babies to be made. We are still a long way from designer babies though, as it is illegal to do genetic experiments that alter the germ layer in many countries, as well as the possibilities of errors arising during the procedure that have not been fixed.

Scientists are also exploring CRISPR’s applications on plants. Want to produce plants that can survive harsher climates and produce better products, modify the genome by removing and inserting genes of interest. For instance, the State University of New Jersey is working with grape plants to edit their genes to be resistant against fungus using CRISPR.

Unfortunately CRIPSR technology won’t be used for several years. Research is only being done on animal models and human cells right now, as the errors of CRISPR are still trying to be fixed along with arguments around it’s ethics. The templates made to match genes may accidentally match up with similar genes in the body, which would lead to mutations in human genes that could potentially be fatal. Although still under work, CRISPR has the potential to cure many diseases and provide a higher quality of life for everyone.

-Tristan Jeffery