DNA Repair in Yeast

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DNA damage is often responsible for many types of diseases such as cancer. In cells, the most common type of DNA damage is the double strand break (DSB). Cells have many rescue methods to repair their broken DNA. This summer, I worked at a lab and helped a postdoc on her project in studying the role of sumoylation in promoting DNA checkpoint in yeast.

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In summary, once a DSB is detected, a cascade of proteins are recruited, as shown in the diagram above.  One result of the DSB repair process is cell cycle arrest, also known as the checkpoint response. While the cell cycle is arrested, the cell initiates homologous recombination, which is the main repair mechanism for a DSB. This is when sumoylation of the common protein, RPA occurs.

There is evidence of a link between the checkpoint response and the sumoylation of RPA. By creating many yeast strains with varying genotypes, we study how the sumoylation of RPA is involved in the checkpoint response.

Screen Shot 2017-11-19 at 6.10.03 PMI went through the process shown to the left for each strain. Beginning with mating, the entire process takes about a week. At first I experienced some trouble with primers for PCR, and with my mentor’s help, we troubleshooted our process. Within a week, we managed to fix the issue and come out with beautiful gels. This was a valuable laboratory experience for me since I learned how to go about analyzing and correcting my methods. By the end of the summer, I built about 12 different strains that will be useful in understanding the significance of sumoylation in DNA damage checkpoint.

The most tedious but one of my favorite parts of this experience was learning how to dissect yeast tetrads. I spent hours at the dissection microscope carefully separating each of the four clumped spores and placing them carefully in rows on the plate. The next few days I would watch them grow into neat little rows of colonies, and then proceed to select and analyze each colony.

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This experience allowed me to thoroughly explore the processes of homologous recombination and the DNA checkpoint in a model organism, yeast. I was excited to have such an excellent opportunity to study and understand the unique proteins involved in the steps of DNA repair firsthand. As I learned each of their roles, I became more and more fascinated in the complexity of the cell’s processes. With this enthusiasm, I look forward to studying biology in the future.

Click below to see more of my notes!

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Life in the Lab

AP ART ii 2016-2017: Concentration

This series of art reveals the life in the lab that is unseen by the naked eye. Within a lab, there is more life than one could ever imagine. After all, biology is the study of life. Whether it be flora or fauna, large creatures or microscopic cells, they play a vital role in our scientific advances in medicine and technology and should be recognized and respected.

Jennifer Guo, AP Art II, Concentration #1, MHS 2017

Jennifer Guo, AP Art II, Concentration #2, MHS 2017

Jennifer Guo, AP Art II, Concentration #3, MHS 2017

Jennifer Guo, AP Art II, Concentration #4, MHS 2017

Jennifer Guo, AP Art II, Concentration #5, MHS 2017

Jennifer Guo, AP Art II, Concentration #6, MHS 2017

Jennifer Guo, AP Art II, Concentration #8, MHS 2017

Jennifer Guo, AP Art II, Concentration #9, MHS 2017

Jennifer Guo, AP Art II, Concentration #10, MHS 2017

Jennifer Guo, AP Art II, Concentration #12, MHS 2017

Jennifer Guo, AP Art II, Concentration #111 MHS 2017

Smorgasburg

4.15.17 // Smorgasburg
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Feasting on Ramen Burgers, Nachos, and Tacos

Smorgasburg is the ultimate food festival of New York City. Beginning in April and continuing every Saturday until October, there’s no better way to welcome the warm weather of the spring and the heat of the summer. This bustling fair is located in New York’s East River State Park, framed by the waters of the East River and the skyline of Manhattan. Over my spring recess, I had the chance to spend the day at Smorgasburg with my friends, and it was unforgettable to say the least.

Whether it be the burgers or the tacos, the ice cream or the doughnuts, the foods at Smorgasburg are not only delicious, but also gorgeous and unique. I highly recommend the noodles (Noodle Lane), the Unicorn rolled ice cream (Roll ‘n Chill), and the chipotle shrimp taco (Takumi Taco). I’ll definitely be back later in the season to try even more food!

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Roll ‘n Chill

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Takumi Taco

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John’s Juice

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Noodle Lane

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Wowfulls

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People’s Pops

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Raindrop Cake

Basics of Microglia

Microglia are important neuronal cells of the central immune system. As their name suggests, microglia are the smallest type of neuroglia, but they have proved to be the fastest and possibly the most intelligent. Microglia migrate independently around the brain to maintain neural circuits and activity. In this way, the brain is protected from microbes, cleaned of cancerous/defective cells, and maintained in optimal condition.

Origins

Microglia are first created from the early mesodermal tissue of the fetus and migrate to the brain where they proliferate. As the brain develops, microglia replenish themselves independently, but the presence of abnormalities causes microglia to make more new cells.

STRUCTURE

In its resting state, microglia are seen as cells with long branches and tendrils. If they detect microbes or injury to nerves, they transform into an ameboid form, retracting their tendrils and increasing the size of their cell body to be able to engulf microbes and debris. Observation of this process, called “microglial activation,” proves that microglia are certainly the most active cells of the brain.

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Roles

Microglia are closely related to macrophages, as evidenced by their similar roles in maintenance and protection through gobbling up pathogens and debris.

Normally, microglia are distributed evenly throughout the brain, each with its own “territory” (15-30 µm) to strictly patrol. They are responsible for protection and maintenance of synapses and will move out of their territory in order to cluster around sites of trauma or infection.

Because of their active role in the brain, scientists are studying the functions of microglia- in relation to the abnormalities that occur in neurodegenerative diseases such as  Alzheimer’s and Parkinson’s disease.

Exponents and Logarithms

Today, we will be reviewing how to graph and solve exponential and logarithmic equations.

Exponential functions start very, very small and grow rapidly. It is commonly used to calculate interest, half-life, or population growth.FullSizeRender 87
Just as subtraction opposes addition and division opposes multiplication, logarithms oppose exponents. The logarithmic function is the inverse of the exponential function.

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The most important thing to remember is that you may get an answer that does not satisfy the equation. When dealing with logs and exponents, always make sure to check your answer.

Matrices

Matrix: A rectangular array of numbers, symbols, or expressions, arranged in rows and columns

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I spent an hour to rewrite my notes on matrices today. If you have time, I highly recommend rewriting notes, picking out the most important definitions and explanations. With some colors and diagrams, this method creates an excellent study guide! Afterwards, I always make sure I have enough time to do plenty of practice problems.

Cell Division

Why do cells divide?

The continuity of life is based upon the reproduction of cells. The single-celled amoeba divides to produce an entirely separate organism, while multicellular organisms such as humans arise from single cells via cell division. Furthermore, cells are not immortal and must be renewed, as seen in the creation of new red blood cells in bone marrow. Thus, there are 3 purposes for cell division: reproduction, growth and development, and tissue renewal or repair.

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Basic overview of Mitosis

Eukaryotic cell division consists of mitosis (the division of the nucleus) and cytokinesis (the division of the cytoplasm). FullSizeRender 84

FullSizeRender 86Interphase: cell growth and copying of chromosomes in preparation for cell division
  • First Gap (G1) represents the first part of interphase during which the cell grows and functions normally.
  • DNA begins to replicate and cytoplasm increases in Synthesis (S).
  • In Second Gap (G2), the cell checks for DNA damage that may have occurred during S phase and will proceed to Mitosis (M) phase once all necessary proteins are present.
  • Centrosomes duplicate, each with two centrioles.
  • Chromatin has not condensed yet and is not visible. The nuclear envelope and nucleolus are still present.
Prophase: The first step in Mitosis
  • Chromatin fibers condense into discrete chromosomes, each with 2 sister chromatids.
  • The nucleolus disappears.
  • Mitotic spindle (microtubules) begins to form.
Prometaphase: Chromosomes released from the nucleus
  • Nuclear envelope disintegrates.
  • Microtubules from the centrosome attach to the chromosomes via the kinetochore (on the centromere).
Metaphase: Chromosomes line up
  • Centrosomes are each at opposite poles.
  • Chromosomes are guided by the microtubules to the metaphase plate at the equator of the cell.
Anaphase: The shortest stage of Mitosis
  • The two sister chromatids separate and migrate to opposite poles.
Telophase and cytokinesis: two identical daughter cells are formed
  • Nuclear envelope and nucleoli reappear to enclose each group of chromosomes.
  • The cell splits into two new cells.
  • Cleavage furrow is formed in animal cells; cell plate in plants.

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Prokaryotes (bacteria and archea) reproduce by binary fission, in which the chromosome simply replicates and the two chromosomes actively move apart to form two identical organisms. Remember, prokaryotes have no nucleus and have a single circular chromosome that contains their genetic information.

Controlling Cell division

While cell division is an essential part of life, it would be disastrous of cells had no way of regulating this process.

  • The cell cycle is regulated largely by the accumulation of cyclin that combines with cyclin-dependent kinase to form MPF. The G2 checkpoint is only passed when there is a sufficient amount of MPF.
  • Platelet-derived growth factor (PDGF) promotes cell division by allowing the cell to pass the G1 checkpoint and begin preparing for mitosis. This is used by platelets to clot blood.
  • External factors also play a role. Density-dependent inhibition prevents cells from overcrowding, allowing them to only grow as a single layer. Cells may also exhibit anchorage dependence in which they will only divide if attached to a substrate such as tissue.

The loss of control of the cell cycle cause cells to divide abnormally, forming tumors. These cancer cells have no means of regulating cell division and will multiply rapidly.

The ability to reproduce and regulate cell division is essential for the continuity of life.

Sources: Campbell Biology 9th Edition

Thoughts on Art

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I’ve been exploring art as a hobby ever since I was young. Art class has always been a big part of my life. Actually, when I was young, I didn’t appreciate art as much I do now. Weekly art classes often seemed like a chore to me since I would often be learning basic skills instead of actually creating my own pieces, which at first, was frustrating. But in the end, I thank myself for enduring those long hours of lessons. Now, I am able to create my own pieces by focusing on creative thinking without struggling too much with technical skills. These hours of practice and my developing passion for drawing made me into the artist I am today.

Artists are always learning from drawing books, art teachers, or their peers. Art pushes me to think outside the box and become bolder in risk-taking. I’ve recently started working much more with wet mediums such as oil paint and watercolor. In addition, my concentration pieces this year are digitally rendered with Adobe Photoshop, a technique I am working hard to master. Thus, with every artist I meet, I am introduced to more and more new and exciting aspects, whether it be classic or modern, graphic design or fine art. Ultimately, I’ve learned that style has infinitely many fascinating forms.

Check out my regularly updated collection of artwork!

Walking Toby

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I’ve been busy, but here’s a quick post //

Yes, I walk my cat. Well, not exactly. I’m not really walking anywhere; it’s considered more like sitting outside while my cat walks around the porch. It seems anticlimactic, but Toby loves it. He begs to go out nearly everyday, and I try to give as much time as possible for this activity, especially on the weekends.

Cats are intelligent and naturally curious, and in Toby’s case, staring through the window wasn’t enough for him. Though I have to supervise him, I often am able to do some reading or listen to music as I sit with him. In addition, having Toby’s attention on the outside world helps with normally-arduous tasks such as nail-clipping and brushing out knots in his fur. All in all, it’s a pleasant experience for both of us. So if you have a cat willing to tolerate harnesses, I would highly recommend this activity. Not only do you get make your cat happy, but I guarantee you’ll get a few compliments for how cute you and your cat are as well!

The Importance of Sports

Staying fit isn’t the only reason you should play a sport. Participating in athletics, especially in high school, gives you the opportunity to destress, reset, and refocus right after a long day of school. As many of you know, I love playing volleyball. I’ve been playing since 8th grade, and I can honestly say that it’s one of the best decisions I have ever made for myself. I have made many friends and learned important lessons from my coaches and my own experience on the court. Through cheering on my teammates and talking loud on the court, I developed the outgoing personality I have today.

Volleyball requires reflex, focus, and determination. Even when losing, it’s important to keep pushing against the other team. But when playing not-so-great teams, it is also important to stay humble and never, ever lower yourself to their level; always aim to be the best and never pity the other team. As my coach once said, “I don’t care who we’re playing: I want to see blood on the court.” After 4 years of volleyball, I have come to realize that winning against a worse team does not nearly feel as good as doing well against a better team, even if we lose. It’s important to always strive for better, no matter how good you are.

Throughout the experience of playing during games and practice, mistakes will always be made, but making a mistake is a key process in learning. From knowing what I did wrong, I am able to focus on what I need to do in the right way to do it. Refocusing after a mistake is critical to success. This lesson was crucial not only to volleyball, but also to many of my successes in school. Instead of getting bogged down by my mistakes, I used my failures to help me succeed in the future.

I encourage you to go out and try a sport with a friend or even just yourself. Although I come home at 6 or 7pm nearly everyday after-school during the fall season, I have absolutely no intentions of skipping practice or quitting volleyball just to have more time to do work. Even during the off-season, I intend to keep playing club volleyball. Playing a sport benefits both your mind and body, plus it’s always great to have an opportunity to bond with new people.