shaliva – BioQuakes

Author: shaliva

Diving into the Sea of Gene Editing

On April 17, 2024

Have you ever wondered why some people travel across the world just to go snorkeling or scuba diving? The answer is simple, Coral. Coral is one of the most beautiful organisms in the ocean. While coral is amazing, its looks are not all that it achieves. Coral is home to 25% of marine species while also feeding close to half a billion humans. Coral has such a huge impact on the world we live in, yet pollution and global warming are slowly taking out tons and tons of beautiful coral from our oceans. Although there are over 6,000 species of coral, we are going to narrow it down to just 1,500 and analyze the “stony corals” ability to build reef architectures.

Phillip Cleves is a scientist at Carnegie Melon who set out to use cutting-edge CRISPR/Cas9 genome editing tools to reveal a gene that’s critical to stony corals’ ability to build their reef architectures. Cleves highlights the ecological significance of coral reefs, emphasizing their decline due to human-induced factors like carbon pollution. Carbon emissions lead to ocean warming, causing fatal bleaching events, and ocean acidification, hindering reef growth. This acidification is particularly detrimental to stony corals, as it affects their ability to form skeletons made of calcium carbonate. Understanding the genetic basis of coral skeleton formation is a key research area to address this issue.

You may be wondering, what is CRISPR? CRISPR is like a genetic toolbox that scientists can use to edit DNA. Imagine DNA as a big instruction book that tells our bodies how to work. Sometimes, there are mistakes in the instructions, like a typo in a recipe. CRISPR lets scientists find and fix these mistakes. They can cut out the wrong parts of the DNA and put in the right ones, like editing a sentence in a book. This helps researchers study how genes work and could one day help treat diseases by fixing genetic errors. Using CRISPR, Cleves and his team were able to identify a particular gene called SLC4y which is required for young coral to begin building. The protein it encodes is responsible for transporting bicarbonate across cellular membranes. Interestingly, SLC4γ is only present in stony corals, but not in their non-skeleton-forming relatives. Together, these results imply that stony corals used the novel gene, SLC4γ, to evolve skeleton formation.

Finally, in AP Biology, you learn about genetics, the study of how traits are passed down from parents to offspring through DNA. CRISPR technology is like a super-advanced tool that geneticists use to manipulate DNA. It’s kind of like having a magic eraser for genetic mistakes! CRISPR also brings up the potential for gene editing in humans although sometimes it is seen as unethical. What genes would you edit if you had the chance?

To kill one, you must kill them all

By shaliva

On February 27, 2024

In Student Post

Throughout your life, I bet you have heard hundreds of people mention the words cancer and chemotherapy, but have you ever wondered what this treatment does inside your body? Chemotherapy is a treatment method for cancer that involves the use of powerful drugs to kill cancer cells or stop them from growing and dividing. These drugs can be administered orally, intravenously, or through other routes and may cause various side effects due to their impact on rapidly dividing cells throughout the body. Doctors have not yet found a way to target only cancer cells. This means that chemo will attack all rapidly dividing cells including hair, the digestive system, and more. Finally, a recent study has found that chemo does not work the way that doctors have thought for many years.

Before I get into the discovery, I want to explain the process of mitosis and how cancer cells can divide so rapidly. In AP bio, we learned that mitosis is a fundamental process in cell division where a single cell divides into two identical daughter cells. It consists of several stages: prophase, Prometaphase, metaphase, anaphase, and telophase, followed by cytokinesis. During prophase, the chromosomes condense, the nuclear envelope breaks down, and spindle fibers form; in metaphase, the chromosomes align at the cell’s equator; in anaphase, sister chromatids separate and move towards opposite poles; finally, in telophase, new nuclei form around each set of chromosomes, completing the division process. In a normal cell, the rate of division is controlled by chemical signals from special proteins called cyclins. However, Cancer cells can divide without a signal; resulting in an extremely fast and dangerous pace of reproduction. For decades, researchers have believed that a class of drugs called microtubule poisons treat cancerous tumors by halting mitosis, or the division of cells. Now, a team of UW-Madison scientists has found that in patients, microtubule poisons don’t stop cancer cells from dividing. Instead, these drugs alter mitosis — sometimes enough to cause new cancer cells to die and the disease to regress. Beth Weaver, a professor in oncology and cell and regenerative biology found this discovery quite shocking. When hearing about this discovery she said “For decades, we all thought that the way paclitaxel works in patient tumors is by arresting them in mitosis. This is what I was taught as a graduate student. We all ‘knew’ this. In cells in a dish, labs all over the world have shown this. The problem was we were all using it at concentrations higher than those that get into the tumor.” With this discovery, scientists were inclined to see if other microtubule poisons work the same way. This led to an experiment conducted by Mark Burkard.

In Burkard’s experiment, he used tumor samples from breast cancer patients who had received standard anti-microtubule chemotherapy. They measured how much of the drugs made it into the tumors and studied how the tumor cells responded. They found that while the cells continued to divide after being exposed to the drug, they did so abnormally. This abnormal division can lead to tumor cell death. In normal cell division, a cell’s chromosomes are split into two identical sets. Shockingly, weaver and her colleagues found that microtubule poisons cause abnormalities that lead cells to form three, four, or even five poles during mitosis while still only creating one copy of chromosomes. This then forces the chromosomes to be pulled in more than two directions causing the genome to scramble.”So, after mitosis you have daughter cells that are no longer genetically identical and have lost chromosomes,” Weaver says. “We calculated that if a cell loses at least 20% of its DNA content, it is very likely going to die.”. This experiment was crucial to the development of cancer treatment because it was able to take the scientists off the path of attempting to completely stop mitosis and instead has them attempting to screw it up. With this new finding, what else do you think scientists have missed in some of their treatments?

The Long Term Effects of COVID-19 Hidden Behind the Fog

By shaliva

On December 7, 2023

In Student Post

COVID-19 was one of the biggest pandemics in United States history. It changed everything including schooling and many other aspects of life, but do you ever seem to forget what life was like before COVID-19? You may be thinking am I just getting old? Why am I losing my memory? Well, findings in Nature Medicine have shown that you may be suffering from what they are calling “Brain Fog”. This Brain Fog can result in recurring memory and concentration lapses that can make it difficult to function every day. You may be thinking, how does this even relate to COVID? Well, It is believed that this brain fog is developed from blood clots triggered by COVID.

Before we get into the brain fog, I want to explain how the body first reacts to COVID-19 entering your cells. AP Bio we learned, that your body activates its innate and adaptive immune systems. First, the innate system releases mast cells which release histamine along with macrophages that secrete cytokines. Cytokines are small proteins that are crucial in controlling the growth and activity of other immune system cells and blood cells. When released, they signal the immune system to do its job. We then see natural killer cells take out any damaged or infected cells while cytokines attract smaller phagocytes called neutrophils and digest pathogens. Along with the Innate response we see the Adaptive response. The adaptive response relies on B lymphocytes and T lymphocytes. The B lymphocytes create the humoral response while the T activates the cell-mediated response. Both are just as important but different. When T-helper cells recognize the antigen it triggers both responses. In the cell-mediated response, the T-memory cells prevent reinfection while the T-killer cells go and kill any infected cells. In the Humoral response the B-plasma cells, secrete antibodies that bind to and neutralize the pathogen which is then engulfed by a macrophage, while B-memory cells also prevent reinfection. Even with all this protection people may still be left with long last symptoms including brain fog.

To find out if this brain fog really came from COVID, a psychiatrist from Oxford named Maxime Taquet took samples of over 1,800 people in the U.K. who had been hospitalized due to COVID-19 and made 6 six-month checks on their symptoms. When examining the blood, they found that people who still had “brain fog” tended to have elevated levels of at least one of two proteins. The first protein is called a D-dimer protein which is produced when a blood clot breaks down. Patients with high amounts of D-dimer tend to have memory problems yet the cognitive side seems to still be intact. Doctors believe these effects were caused by blood clots in the lungs, which lead to low oxygen levels in the brain. The second and seemingly more dangerous protein to find mass amounts of is fibrinogen. This protein is produced in the liver and causes clotting to stop bleeding. When patients have elevated amounts of fibrinogen during COVID-19, they seem to have memory loss along with scoring poorly on the cognitive test. These patients show signs of dementia. Taquet believes that fibrinogen may have caused blood clots in the brain or somewhere else that directly affects the brain.

After hearing about the findings Resia Pretorius was very excited. From her own research, she has found connections between COVID and brain fog. She believes that the spike protein of COVID binds to the fibrinogen and causes it to change shape. But she believes this discovery can help determine ways to cure long COVID symptoms. So have you been affected by COVID’s brain fog or are you just getting old?

The Shell that has a lot to tell

By shaliva

On October 22, 2023

In Student Post

Sea Turtles are one of the most fascinating creatures in the world. When snorkeling in the middle of the Caribbean you hope and pray that you get to swim along with one of these wonderful creatures. But little did you know, they have millions of years of history hidden within their shells. Currently, only 7 species of sea turtles are alive, among the seven are those in the genus Lepidochelys: the olive ridley and the Kemp’s ridley. These two species are some of the most popular in the Caribbean Sea yet we know so little about their history. Until…

A group of paleontologists found remains of a turtle shell in 2015 in the Chagres Formation on Panama’s Caribbean coast. This turtle shell happened to be 6 million years old and it represents the oldest known fossil evidence of Lepidochelys turtles.

When analyzing the fossil, the scientists discovered preserved bone cells called osteocytes. These bone cells are the most abundant in the vertebrates and have nucleus-like structures. To test for genetic material the group used DAPI, a blue-fluorescent DNA stain. The test was successful and they were amazed because this was the first time DNA remains have been found in a fossilized turtle that is millions of years old. Not only does this discovery bring understanding to the biodiversity present in Panama millions of years ago, but it also brings a whole new topic of molecular paleontology.

Molecular paleontology is a study of ancient and prehistoric biomatter including proteins, carbohydrates, lipids, and DNA that can sometimes be extracted from fossils. The understanding of how these complex molecules such as DNA and proteins can be preserved in fossils will continue to help scientists now to understand how soft tissues can be preserved over time. In Unit 1 of AP Bio, we are introduced to DNA. DNA is a fascinating molecule that carries most of the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms and many viruses. It is composed of two long strands forming a double helix structure. Each strand is made up of nucleotides, which consist of three components: Deoxyribose Sugar which makes up the backbone, a Phosphate group that contributes to the backbone structure, and a Nitrogenous base whose sequence encodes genetic information. At this point you may be thinking, why is this turtle so special? Can’t they find DNA in every fossil? Well, you would be shocked; before the discovery of DNA in this 6 million-year-old turtle, scientists were simply amazed by discoveries of DNA over 1 million years old. This is because DNA consists of sequences of base pairs that are chemically linked along the sides of a double-helix structure, resembling a twisting ladder. Being an organic substance, the constituent parts of this helical structure can deteriorate naturally over time. In the absence of active cellular processes within a living organism to repair and replicate DNA, it can degrade relatively quickly, rendering its components meaningless. Although DNA is plentiful and easily obtainable from living organisms, the task of retrieving viable DNA becomes increasingly challenging with extinct organisms, especially the further back in time they lived. All of these reasons indicate why this singular turtle fossil has more to tell about our genetic code than the millions of other fossils we have found over millions of years. Before reading these articles I had never understood how we were able to learn so much about animals and their ways of life just by a single fossil. But this discovery begs the question of why the DNA was able to survive so long within the shell of a turtle and not in the million of other animals around the world?

BioQuakes

AP Biology class blog for discussing current research in Biology

Author: shaliva

Diving into the Sea of Gene Editing

To kill one, you must kill them all

The Long Term Effects of COVID-19 Hidden Behind the Fog

The Shell that has a lot to tell

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