Category Archives: Biochemistry

By Olivia Tran July 18, 2022

Juana Garcia/The Cougar

So, youve decided you want to be a doctor. Welcome to the pre-med world at UH it can be a long and crazy ride, but if youre confident you want to be a physician and are willing to work hard towards your dream, you can get there. As someone who initially felt lost, here are a few things I wish Id known going in.

You can major in anything and still be pre-med. No major is better than another for medical school admissions, so pick something that interests you and that you can do well in. While majors like biology include many of the prerequisite classes required for medical school and surround you with other UH pre-meds, non-science majors can add variety to your courses and allow you to meet people outside your pre-med bubble.

Most medical schools require general biology, general and organic chemistry, biochemistry, physics, statistics, English and advanced biology, for example genetics, regardless of major. Check the UH pre-health website to see what classes count towards these.

Do your best to do well in them- schools look at biology, chemistry, physics and math grades. Being engaged in class will make it easier to do well in future courses and exams and secure strong letters of recommendation.

Community service goes a long way as a pre-med student, as it shows your desire to help those around you. Whether you tutor middle school students through a campus organization or help at a nearby animal shelter, try to show consistency and initiative in something that matters to you.

You can even create service projects as you gain more experience. Student organizations can help you access volunteer opportunities and leadership roles.

Clinical experience can be anything from volunteering in a hospital to working as a medical scribe. In contrast, shadowing means you follow a doctor around and observe their daily activities. Its essential to have both to understand the realities of the medical field maybe youll find its not for you, and thats OK.

These experiences can be hard to find, especially if you want a specific schedule, location or salary. So youll have to be proactive and get used to cold calling. Since UH is near the Texas Medical Center, you can find many opportunities that are just a short car or Metro ride away.

While research isnt strictly required, medical schools appreciate applicants who show critical thinking and scientific inquiry. Opportunities include wet lab pipetting, mice work, computer modeling, translational and clinical research, health disparities and even research completely outside of health.

Most UH labs are willing to take on undergraduates, but you must be eager and persistent when asking to join. Cold emailing to ask for a meeting with the professor in charge of the lab, the principal investigator, is a typical way to start. You can also reach out to the Office of Undergraduate Research and Major Awards.

Non-medical employment can pay the bills and boost your application. Being a waitress or cashier shows you have people skills, are dependable and can balance a real job with school. These often pay more than entry-level clinical jobs, so its something to consider if you find yourself strapped for cash.

Dont forget to keep up with what makes you, you. Whether rock climbing, drawing or just getting boba with friends, these activities can help you de-stress and can also be put on your application if they are significant to you.

I put this last because you dont need to stress about it yet. The Medical College Admissions Test consists of four sections- chemistry/physics, reading, biology/biochemistry and psychology/sociology.

Students usually take it between sophomore and junior year at the earliest, with most taking it during the spring semester of their junior year if they want to enter medical school right after graduation. The most important thing you can do to prepare as a freshman is to do well in your relevant classes and retain the material.

If you feel overwhelmed already, dont be. No one is perfect in all these aspects nor capable of focusing on all of them simultaneously. Medical schools understand if your circumstances prevent you from doing as much as youd like. Be sure to check out the UH Pre-Health Advising Center website for more detailed information, and best of luck as you begin your journey.

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Tags: med school, premed, student life

Excerpt from:
Advice: How pre-med freshmen can start preparing now - The Cougar - The Daily Cougar

How does a nose remember that its a nose? Or an eye remember that its an eye?

As scientists probe the question of how cells remember what kind of cells they are supposed to be, or their genetic lineage, its important to understand how cells express different genes without changing the DNA sequence itself.

But studying this subject is difficult: Researchers can purify the proteins that drive genetic expression, put them in a test tube and watch them bind. But doing so inside the nucleus of cells, their native environment, has been so far impossible.

Study: HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization (DOI: 10.1126/sciadv.abk0793)

Now, a team of researchers at three University of Michigan labs have been able to track how a protein binds to its chromatin substrate within a living cell by establishing a collaboration that combines state-of-the-art ultra high-resolution imaging, synthetic protein design and computational modeling. Their results are published in Science Advances.

The biological question that were asking is, How do cells actually remember past experiences? And how do these experiences also lead to cells establishing distinct identities, as it happens in the case of the human body where you have lineages of cells that form neurons, or blood cells, or brain cells, and all actually maintain their identities for many generations,' said lead author Kaushik Ragunathan, assistant professor of biological chemistry at the U-M Medical School.

An example I like to think about is that if you chop off your nose, you dont get a hand growing there, even though the genome in your nose and the genome in your hand are exactly the same.

Cells control how and which genes are expressed from a copy of the DNA sequence held within each cell, despite that sequence being the same across all cells in the body. One way they control expression is by changing how tightly the DNA is packaged within the nucleus using proteins called histones. Histones can be modified through the addition of small chemical tags that regulate how tightly the DNA is wound around them and thus whether the genes can be expressed.

Proteins that have the ability to read, write and erase these histone tags explore the DNA within the nucleus of the cell very rapidlyon the order of milliseconds, according to Ragunathan. Ultimately, all this epigenetic information needs to be inherited across generations, but the recognition of these tags is a complicated process that involves chromatin binding and proteins meeting and interacting with each other amidst the chaos of all other possible competing interactions within the cell.

Being able to understand each step of the processand therefore enabling control of how the epigenetic information is inheritedintrigued co-author Julie Biteen, professor of chemistry and biophysics.

Biteen uses single-molecule fluorescence imaging to track individual proteins inside cells. Her lab can see where these proteins are relative to the chromatin, and Ragunathans expertise is in the molecular mechanisms underpinning how histone modifications and histone-binding proteins interact. These two worlds needed to come together so that the biochemistry of what happens in a test tube outside of cells could be tested to figure out what happens inside of them.

The timing of this process is critically important to ensure that the right genes are silenced at the right place and at the right time, Biteen said. What hooked me on this project is that in vitroin a test tubeyou can purify two proteins, watch them bind and see how good that binding is, or what is the affinity for one another. That tells you what can happen in the cells, but not what does happen in the cells.

Biteen and Ragunathan worked with Peter Freddolino, associate professor of biological chemistry, and computational medicine and bioinformatics at the U-M Medical School, to combine computer modeling with their experimental results.

This is really where our collaboration becomes really powerful, Biteen said. On one hand, seeing molecules is very helpful and knowing how fast the molecules move helps a lot in terms of understanding what is possible inside the cell, but here we could take a leap forward by perturbing the system even in unnatural ways in order to understand what these different motions of molecules in the cell actually mean.

While epigenetic marks are tremendously important for maintaining different tissues in complex organisms like humans, they also play an important role in regulating genes of single-celled organisms such as yeast. The team focused on a type of HP1 protein in yeast cells called Swi6. This family of proteins binds to a specific type of histone modifications in the cell to enforce gene silencing. By integrating fluorescent labels with Swi6, Bitees lab watched Swi6 move inside the cells nucleus.

While Swi6 searches for the correct binding site on DNA, it moves quickly, Biteen said. When it finds its target, it slows down significantly. The movement of a protein within the cell is akin to gears in a car and things can move at different speeds based on whom proteins interact with.

From these spaghetti tracks that we get inside the cell, we then figure out how much time they are spending searching and how much of the time they are spending bound, Biteen said. The amount of time they spend not moving tells us about how strongly theyre interacting and their biochemical properties.

While Biteens lab can measure movements in the cell on the scale of tens of milliseconds, much of the biochemistry happening in the cell is happening even faster, she said. Freddolino took this experimental information and developed models to estimate the ability of the Swi6 proteins to jump between the binding states that were identified in experiments.

Freddolinos modeling took into account the experimental measurements and the possible biochemical properties, which includes how the Swi6 molecules interact in the cell. These interactions include molecules that freely float in the solution of the cell, molecules that have bound to DNA, and molecules that are holding hands with each other, he said.

My lab wanted to come up with a more fine-grained model that estimated what was the most likely set of molecular states of the proteins and their ability to jump between those states, that would then give rise to the imaging data that Biteens lab created, Freddolino said.

Having this numerical model allows us to do the computational experiments of what happens if the protein binding is twice as fast as we think. What if its 10 times as fast as we think? Or 10 times slower? Could that still give rise to the data? Very happily, in this case, we were able to show that the relevant processes were really being captured in the fluorescence microscopy.

After identifying the binding properties of natural Swi6, the researchers tested their findings by redesigning Swi6 from its components to see whether they could replicate some of its biochemical properties, Ragunathan said. This allowed the researchers to determine that the imaging and modeling conducted in the first part of the paper reflects how the protein was binding in its native environment.

Can we do what nature did over the course of millions of years and make a protein that in many ways has properties similar to that of Swi6 in cells? Ragunathan said. In vivo biochemistry, which is what weve decided to call this, was not something that was ever thought to be possible inside living cells, but we have shown this is entirely feasible by using imaging as a modality. We are using this project as a foundation in order to understand how these epigenetic states can be established and maintained across generations.

Read this article:
U-M researchers track protein binding, build synthetic proteins to study gene expression - University of Michigan News

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WEST LAFAYETTE, Ind. Clint Chapple, distinguished professor in the Purdue University College of Agricultures Department of Biochemistry, has been elected to the National Academy of Sciences. NAS membership recognizes achievement in original research and is widely regarded as one of the highest honors in science and technology.

Chapple will be among approximately 2,400 active U.S. NAS members. Academy members elect a maximum of 120 U.S. researchers and 30 international members annually for outstanding professional achievement and commitment to service.

Election into the NAS is an outstanding honor for scientists, and Clint is most deserving, said Karen Plaut, the Glenn W. Sample Dean, College of Agriculture. He is a top-notch scholar who has received awards for research, teaching and mentoring students. We are elated he has been recognized for his contributions to his field, and we are proud to have him as part of our faculty.

Andrew Mesecar, head of the Department of Biochemistry, said, He was elected to the National Academy because of his forefront contributions to his field. He is world renowned for that and for his service to the plant sciences community. This is what the world sees. What the world doesnt see is an exceptional leader who is willing to sacrifice for the greater good of the department.

The NAS specifically noted Chapples work in understanding the biosynthesis of lignin, the hardening component in plant cell walls that serves various important biological functions. In Chapples nearly 30 years at Purdue, his study of lignin has expanded along with its applicability to pulp and paper production, animal feedstocks and biofuels.

The plant cell wall is a fundamental part of the plant body, Chapple explained. Starting in 1993, my group was able to learn about the fundamentals of what enzymes and genes are important for plants to make lignin in the cell wall. We were able to manipulate their expression and learned to reprogram the plant to make a lignin that might be more suitable for a variety of applications. Overall, we learned a lot in the process.

Plaut noted that Chapple also has been instrumental in advancing plant sciences initiatives that have strengthened research and teaching in the College of Agriculture. Chapple co-founded and directed the Center for Plant Biology, which hired 10 new assistant professors to work across multiple disciplines within the center, funded as part of the Institute of Plant Sciences.

Investment in plant sciences through Purdue Moves and its successor, Purdues Next Moves, has helped sustain an environment in which Chapples research has flourished. He credits his former and current graduate students and postdocs for their contributions:

Ive had great people in my lab, many of whom are in industry or faculty members at other universities, he said.

Chapple values his NAS election as affirmation from highly accomplished peers.

If you can move the needle in terms of human knowledge and get paid for it and have fun! thats a great opportunity, he said. Ive been very fortunate.

Media contact: Maureen Manier, mmanier@purdue,.edu

Source: Clint Chapple, chapple@purdue.edu

Agricultural Communications: 765-494-8415;

Maureen Manier, Department Head, mmanier@purdue.edu

Agriculture News Page

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Purdue biochemistry professor Clint Chapple named to National Academy of Sciences - Purdue University

Ziff graduated from James Madison High School in Vienna, Virginia, but because her father works for the State Department, the family moved to different countries every few years, she said.

Her experiences of science classes varied from place to place, she said. In Bogot, she and just four peers would get to their 7 a.m. AP biology course, where the instructor encouraged them to be curious and used a Socratic method of inquiry. In Rome, her AP chemistry course was more traditional.

As the family moved around the world, she danced wherever they went.

It was often a way to connect with my peers in different countries, Ziff said. When my family moved to a new place including Venezuela, Italy, Colombia, Spain or the U.S. I would search for a new dance studio and enroll, and it not only continued my practice, but helped me make local friends and learn the language.

After Ziff studied with the Kibbutz Contemporary Dance Company in Northern Israel several times, and then the danza180grados conservatory in Madrid, Spain, she decided that this pursuit of experiences in movement was not just a hobby and she would put more effort into it. The program in Israel was especially demanding and intensive, she said. She returned to the Israeli dance company for five months during a gap year before coming to UVA.

That was a turning point. I knew I wanted to continue studying dance in college, said Ziff, whose mother is Israeli. I wanted to major in biochemistry and minor in dance because Im interested in the details.

She added that she was increasingly interested in the more intricate pathways of life, how tiny fragments of us transform and interact, literally on the molecular level.

She acknowledged that studying chemistry and practicing dance require different kinds of learning, but there are similarities, as well.

There are many small parts that make up the molecular intricacies of the bodys regulation, and changing a few of those parts can have rippling effects, Ziff said. As I learned more about dance, I realized that small changes in body language, style, music choice, lighting and a host of other factors within a piece of choreography can completely shift its mood and meaning.

Despite its small size, UVAs dance program, housed in the Drama Department, offered some mighty strong opportunities for a motivated student like Ziff, who had to get even more creative during the COVID-19 lockdown.

She joined the Miller Arts Scholars, an interdisciplinary arts program that offers a variety of resources for undergraduates to pursue their artistic dreams. The students meet in required seminars, work with faculty and visiting artists, and plan projects and events in their fields. They not only have to present a proposal for a project, but also follow up with a report on the outcome.

For a project last year, Ziff choreographed and created a dance film, learning how to record and edit a performance. In 2020-21, she also earned funding for a Rising Third-Year Arts Award, originally to attend an intensive training session at the American Dance Festival in New York City. When the pandemic prevented that, she and fellow student Kiana Pilson, another Miller Arts Scholar in Dance and arts awardee, commissioned an original duet from acclaimed choreographer Helen Simoneau, to be performed at the UVA Dance Programs Virtual Spring Dance Concert. They produced the piece as a dance film.

See more here:
Class of 2022: Ziff Balances Mind and Body With Biochemistry and Dance - UVA Today