Your Diet and Cancer: pHacts and pHiction

This is a companion article to the feature Not so Basic After All: The Role of pH in Cancer Therapy.

Based on your reading of the article above, you may be wondering if an acidic diet can cause cancer, or if you can prevent cancer with a basic diet. While the results of the baking soda study might make it seem that way, science points to a more nuanced reality. 

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CRISPR-Cas9: How to Hack Your Genes

Our genes control everything from our height and hair color to our chances of developing cancer, heart disease and any number of other conditions. Sometimes it can seem like our genes rule our lives, but what if we could turn the tables and edit our own genes?

Scientists have used a tool called CRISPR-Cas9 for years to change the DNA of bacteria, plants and animals. Now, some researchers have started using this tool in humans to treat diseases that were previously uncurable. But as promising as this tool is, there are a lot of potential negative consequences, too.

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats (but you don’t need to remember that). It’s a particular pattern in the organization of DNA building-blocks. This pattern acts like a huge, flashing alarm to Cas-9, a protein that can cut up DNA. Cas-9 can attach itself to the DNA sequence using a special RNA molecule that has the same pattern. The RNA and DNA fit together like a zipper and this lets Cas-9 recognize and cut out that part of the DNA.

After this system was discovered in 2012 in bacteria, scientists quickly started using CRISPR-Cas9 for their own research. Previously, there had been other ways to edit DNA, but these methods either required weeks of breeding animals before the changes took hold, or they encountered severe limitations on how big the gene they wanted to edit could be and where on the gene it could be edited. CRISPR-Cas9 solved a lot of those problems. With a little tweaking of the Cas-9 protein, scientists could use CRISPR-Cas9 to not only delete genes but also add and change genes, as well!

In just a few years, scientists began using CRISPR-Cas9 on hundreds of different projects. Scientists at Imperial College of London, for instance, used CRISPR-Cas9 to create mosquitos that were unable to procreate so they couldn’t spread malaria. Conservationists have used the system to study how coral reefs are affected by climate change. A group of researchers in Brazil and Ireland has even created naturally spicy tomatoes by inserting the gene for capcasin (the molecule that gives peppers their heat) into the genome of a tomato.

Despite this surge in the use of CRISPR-Cas9 in animals and plants, doctors were slow to adopt the system as a way to treat genetic diseases, and for good reason. As powerful as CRISPR-Cas9 is, it requires scientists to know exactly which gene they want to change. For many diseases, even if we know that they are genetic, we don’t know which gene is the culprit. This means scientists need to perform a lot more research into the causes of the disease before a good gene therapy can be made. For a few diseases with very well-known genetic causes, though, doctors got to work creating cures as soon as they were sure the treatment would be safe in humans.

Most recently, CRISPR-Cas9 has been used to treat a form of hereditary blindness called Leber congenital amaurosis. This disease happens when one of 14 genes that are vital for keeping light-sensing cells in your eyes healthy is mutated. Patients with one of these mutations are either born blind or lose their sight soon after birth, and there is no way to restore their sight. A clinical trial at the Oregon Health and Science University is using CRISPR-Cas9 to edit one of these faulty genes, CEP290.  For this trial, a special form of CRISPR-Cas9 that targets CEP290 is injected directly into the patient’s eye. It sounds uncomfortable, but this way the gene will only be edited in the eye, and not anywhere else in the body. It’s too early in the trial to report any results, but if it works, this will be the first CRISPR gene therapy used in human patients.

This is an example of CRISPR-Cas9 therapy done right, but unfortunately, it has also been done very wrong. The most infamous example is the CRISPR editing of babies that were born in China in 2018. Scientist He Jiankui used CRISPR-Cas9 to edit the genomes of twin embryos. The twins’ father was HIV-positive, so He removed the CCR5 gene, which codes the protein that HIV uses to enter a cell. The babies were born without issue, as far as we know, but there are many problems with the way He went about making this therapy happen.

It’s not known what the long-term effect of deleting CCR5 will be on the babies. Because the embryos were edited when they were only single cells, the changed gene will be present in every cell in the entire body. This means, unlike the eye-specific CRISPR-Cas9 treatment, any part of the body could be affected by the deletion of CCR5. We don’t know what the consequences of that wide-spread deletion will be.

It’s also very likely that the treatment was unnecessary. HIV transmission from mother to child is very common, but developing HIV from having an HIV positive father occurs only in extremely rare cases. So, even if the children don’t develop HIV, it doesn’t mean that it was because of the CRISPR-Cas9 therapy.

As we start to discover more about the ways that our genes inform our health, we’ll be able to use CRISPR-Cas9 to cure a whole host of diseases that were previously untreatable. But we have to rigorously check the data to justify the use of this technology. So, when the next big CRISPR cure comes along, look into how the scientists decided which gene to change and whether they know what the full effect of this change will be. CRISPR-Cas9 may have given us the power to change our genes, but with this power comes the responsibility to do it right.

Maggie Colton is a 4th year undergraduate at the University of Chicago studying cancer biology. When she’s not in the lab, she enjoys baking and playing her tuba.

Periodic Pandemonium: Exploring Chemistry’s Rule-Breakers

When I tell people that I study chemistry, the response is usually some version of “You must be bright” or “I hated that class” or, put more simply, “Why?”  I’ve grown used to defending my love for chemistry, and I’ve often pointed to its straightforward nature as the source of my affection. I liked that the elements on the periodic table are arranged according to trends in their chemical properties, and that we can infer things about an element’s behavior by its position.   An element’s electronegativity (the tendency to attract electrons), for example, increases as you move from left to right and from bottom to top across the table. The size of the atom, meanwhile, increases from right to left and from top to bottom. In class, I labeled different chunks of the periodic table to signify alkali metals, transition metals, lanthanides, actinides, halogens and other categories of elements with neatly-defined criteria for membership.  As a straight-A student and a type-A personality, I appreciated how chemistry was so orderly, how there was always a right answer.   

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Who Cares About Climate Change Anyway?

You might be worried about the future of our planet. It may seem like there is no good news about climate change and that nothing is being done to stop it. Of course, you can contribute as an individual to lowering your carbon emissions; this can include all of the things we keep hearing about – recycle more, stop using plastic, eat less meat, drive less – but even if we all change the way we live to lower our individual carbon emissions, the dent we make in the world’s overall emissions will unfortunately be minuscule compared to reduction we need to make a true difference. So, what can we do beyond this? And how are other people dealing with this? 

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How to Properly Wear a Face Mask and Gloves

Last week, the CDC told us that we should wear face masks to prevent the spread of SARS-CoV-2, the virus that causes COVID-19. But we’ve noticed that some people are wearing them improperly, where they’re not actually protecting themselves and the people around them. We wanted to provide some guidance on how to wear face masks (and gloves) in the right way to keep you safe:

First, we wanted to remind you that the idea behind wearing a mask, N95 or not, is about preventing you from spreading SARS-CoV-2 to others if you already have it. The CDC wants you to assume that you’re infected because, even if you do have it, there’s a good chance you won’t have any symptoms. For your mask to truly protect you, it needs to seal to your face and it needs to be made from a material that keeps tiny viruses out. Your cloth mask can’t do that, unfortunately. The reason the CDC is recommending cloth masks is because N95 masks are hard to find and need to be saved for healthcare workers.

We’re sorry we can’t provide you with better news about masks, but that’s the reality we must deal with today. It’s a new world, and we have to work with what options we have available to us.

Fortunately, we know a little more about how SARS-CoV-2 spreads though, so there’s still a lot you can do to protect yourself.

For instance, we know the virus spreads through droplets, like from spit and snot. That means it can spread by coughing or sneezing on someone, or even by speaking to or breathing on someone from within 3-6 feet. That means you need a that covers both your mouth and nose, as tightly as possible. Whether or not a good-fitting mask is not available, stick the social distancing rules to avoid the virulent breath of others.

If you do have a good-fitting mask, once you put it on, don’t touch or move it. By touching your mask with your potentially contaminated hands, you are going to get the virus on your mask, making it easy to inhale it and make yourself sick. The best way to adjust or remove your mask is to handle it only by the elastic around your ears/the strings on the back of your head.

Also, hopefully you’ve figured this one out on your own already, but your mask won’t work if it’s sitting on your chin. It won’t work if it’s only over your mouth. Don’t laugh; we’ve seen many people pulling their masks down in public to smoke or to speak with others in close proximity. You might as not be wearing a mask at all at this point!

Next, let’s talk about rubber gloves. The SARS-CoV-2 live on surfaces for up to three days, and naturally, this might cause you to want to wear rubber gloves while you’re outside. But while you’re doing that, just keep in mind that rubber gloves just act as another layer of skin. The gloves themselves are a surface, too, and they can get contaminated just like your skin, so you still need to avoid touching your face even if you’r wearing them and you need to replace the gloves as often a you’d wash your hands.

Even with a mask and rubber gloves, make sure you maintain a distance of six feet from others. This is the best way to prevent the spread of the virus. The easiest way to do that is to just stay home. Please do so as much ask you can. Stay safe out there!

The Discovery of Vaccines: Then and Now

In the doctor’s office, a little toddler smiles joyfully as the doctor releases the plunger and withdraws the syringe from his arm. This was the first of a series of shots that he was scheduled to receive as part of his vaccination regimen. The doctor applies a bandage to the toddler’s arm, adds the vaccination to his records, and asks the family if they had any questions before leaving for the day.  

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Coronavirus, Corona Beer, and Corona Bread

Everyone is hearing about the coronavirus, and, of course, Corona beer is not having any of it. Maybe they’ll try renaming it, but that’s not going to happen any time soon. I’m going to assume that you probably know that a coronavirus isn’t called that because of the beer. It’s called that because of the Latin term for ‘crown,’ which the virus looks like.

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Mixing a Phage Cocktail to Combat Bacterial Infections

In 2013, when Tenzin Kunor was in his last semester of college, he learned that he had a type of tuberculosis (TB) that was resistant to the typical drugs that are used to treat TB. At first, he thought it was a bad cold because he had been experiencing chest pains, a sore throat, and coughing. When it got to the point that it was painful to walk, he received his diagnosis: multidrug resistant TB. This bacterial infection requires special medications, and takes a long time to resolve. For Tenzin, it took two years.

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Control Diabetes Before It Controls You: How Group Visits Improve Care

In Greek mythology, after escaping his prison, Icarus soared close to the sun, despite his father’s instructions to fly neither too high nor too low. His wings of feathers and wax melted before he plummeted to his death. In modern day, patients with type 2 diabetes similarly seek to escape their symptoms at the doctor’s office, and they receive instructions just as difficult—maintain a level of blood sugar that is neither too high nor too low, or face harsh consequences.

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Fun Facts About Pi(e)

We are sad to say we had to cancel our annual Pi K Fun run because of the coronavirus. Everyone’s health and safety is a priority for us, and we don’t want to put anyone at risk of sacrificing either. We really feel bad that you’re missing this yearly tradition, so to make it up to you a best as we can, we collected some fun facts about pi(e) in all its forms. We hope you enjoy!

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Mini-Brains and Soufflés? More Alike Than You Think

Mini-brains—that’s right. It sounds like something from Frankenstein, doesn’t it?  

I gazed in awe as my mentor showed me these ‘mini-brains,’ aka cerebral organoids. Much like soufflés, mini-brains must grow without falling apart and require a lot of care and patience. They ‘rise’ to the challenge of helping physicians and scientists better understand the brain and develop treatments for diseases that affect us and our loved ones. 

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Why You’re Not Dead Yet – A Crash Course on Fighting the Flu

You’re sitting at home, watching TV, and then, suddenly, you feel it. Did your throat always feel so dry? Was your nose that stuffed up this morning? Then, you realize it. You heard someone cough near you on the train yesterday morning, and now, you’re one of the 60 million Americans each year who’ve caught the flu

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The Impossible Burger: Is it Really That Impossible?

Let me preface this by saying that I’m not vegan, vegetarian, or even pescatarian. I’m not any of the -arians. But I am a foodie. So when I heard about the Impossible Burger, a plant-based “beef” burger, I had to try it. Unlike other plant-based burgers, where you can see the beans and corn that are squished together to make the patty, the Impossible Burger truly resembles a beef burger.

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