BeaBiochemist

Paving the Way in Research for Diverse Perspectives: Meg Palacio

Anonymous — Wed, 15 Nov 2023 22:20:43 +0000

Paving the Way in Research for Diverse Perspectives: Meg Palacio Anonymous (not verified) Wed, 11/15/2023 - 15:20

Leading as an Inclusive Researcher

Advancing diversity, equity, and inclusion of historically excluded students in STEM has been a large part of my identity and effort throughout my graduate school journey. As a Chicana, I recognize the barriers imposed upon disadvantaged groups and know that I would not be where I am today without the aid of programs that increase support for diverse students in science. I felt a responsibility to give back to the same community that helped me to succeed as a young researcher. So, I have been involved in various outreach and mentoring programs such as the Society for the Advancement of Chicano and Native Americans in STEM (SACNAS), Peer-2-Peer mentoring, Summer Multicultural Access to Research Training Program (SMART), Longmont High School SMART Program, STEM Routes, and the Uplift Program. I also co-founded and was the former chair of the Biochemistry Department’s DEI committee. Outreach work is what can inspire the next generation of scientists and it is critical that we create an inclusive environment for all identities to be able to thrive.

My Research: Biochemistry for Creating New Tools for Human Health

My research focuses on elucidating the role of biomolecular condensates in transcription regulation. Biomolecular condensates are membraneless liquid droplets that possess a high concentration of local proteins and/or nucleic acids. These condensates offer spatiotemporal control of protein function and could be utilized by the cell to regulate processes such as transcription. Specifically, most of my efforts have focused on developing a fluorescent assay to simultaneously visualize in real-time condensate formation and human RNA polymerase II transcription using a defined reconstituted in vitro system. I knew this project was a great fit for my thesis research because it combined researching the regulation of a fundamental process with the development of a new method or tool. Additionally, the implication of biomolecular condensates in coordinating transcription is a relatively new idea and subsequently, there are a lot of available questions that need to be addressed so we can better understand the underlying mechanism. Finally, I also find studying human transcription intriguing. It a complex orchestration of a multitude of proteins and nucleic acids where the precise timing is critical for proper gene expression.

My Life's Journey

Biochemistry truly fascinates me, every organism surrounding us survives because of all these thousands of intricate biochemical interactions. I am inspired by the idea that I could be someone who contributes to understanding how these interactions regulate processes that give rise to life. I chose CU ��«��Ƶ because it felt like an environment where I could succeed. Graduate students here appeared to be genuinely happy. They were working hard in lab and simultaneously enjoying their weekends hiking or spending time with friends. These students were publishing in top journals and still finding time to enjoy life. That dynamic is exactly what I wanted in a program. Additionally, the research in the biochemistry department and the CU community is astounding and the faculty are easy to talk to despite their impressive backgrounds. Plus, who wouldn’t love the Rockies in their backyard?

Meg looks to go above and beyond to provide resources for causes where she's directly plugged in, “I hope to secure additional funding for causes important to me and one of those programs is the Longmont High School SMART Program, an afterschool program in a largely Hispanic community that exposes students to protein structure, function, and modeling.” Download Meg's CU ��«��Ƶ Biochemistry journey.

The Taatjes Lab - BCHM

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A Creative and Community Minded Researcher - Clair Huffine

Anonymous — Tue, 26 Sep 2023 20:57:20 +0000

A Creative and Community Minded Researcher - Clair Huffine Anonymous (not verified) Tue, 09/26/2023 - 14:57

Clair Huffine is a 2025 PhD candidate in the Cameron Laboratory. She recently won the 2023 Biophysics Supergroup Outstanding Research Presentation Award; is a 2023 P.E.O. SCHOLARS Award applicant; and in 2022 was an NIH/CU Molecular Biophysics trainee and received Honorable Mention for GRFP - the NSF Graduate Research Fellowship Program.

A Creative and Community-minded Researcher

Giving back gives me energy. In addition to board service with S.C.O.P.E (Science Community Outreach Program and Education), I co-founded QSci: Queers in STEM in order to build a thriving community for LGBTQ+ students, staff, and faculty. Additionally, I am a member of P.E.O., a women’s philanthropic organization whose mission is to fund women’s education at all levels, high school to graduate school. With a love for all things green, I spend my weekends backpacking, tending my jungle of houseplants (complete with my “jungle-cat” Kiki), or fly fishing. I also work as a freelance artist, primarily creating digitally painted landscapes or graphic design work for board games. These skills have been transferable to my scientific career with creating compelling scientific figures for my papers and presentations, increasing community engagement with monthly QSci Posters, and crafting memorable and attractive logos for S.C.O.P.E. My portfolio can be found at clairhuffine.com.

Research: Biochemistry for Climate Change

Bacterial cells are often thought of as lacking subcellular organization. However, bacteria do in fact possess both membrane-bound regions as well as, unique from eukaryotes, protein encapsulated regions in order to accomplish incredible biochemical feats. In Dr. Jeffrey Cameron’s lab, I use time lapse fluorescence microscopy to track the redox state inside the carboxysome, which are protein-encapsulated bacterial microcompartments that house the CO2-fixing machinery for cyanobacteria (commonly known as blue-green algae) and allow them to efficiently remove CO2 from the atmosphere and convert it into sugars and biomass. Having always been driven by the plight of climate change, I hope to provide insight into this CO2-capturing mechanism to ultimately offset increasing atmospheric CO2-levels and slow climate change. I plan to pursue a career focused on addressing climate change through applied research and scientific outreach.

My Life's Journey

I grew up in northern Virginia and with a biology and chemistry degree in hand and moving from one mountain range to the next, I began my graduate degree at the ��«��Ƶ the Fall of 2020. I wanted to pursue my graduate degree that held inter- and intra-lab teamwork in science as an ideal. I couldn’t help but notice how collaborative and welcoming the scientific environment at CU ��«��Ƶ was. Students and faculty alike were enthusiastic to share their work, make new interdisciplinary connections, and support their peers in any way possible. I joined through the Interdisciplinary Quantitative (IQ) Biology program, which focuses on crossing disciplinary boundaries, encouraging collaboration, and developing computational skill sets.

Clair has a volunteer mindset about life, “Science does not occur in a vacuum; dissemination of research and engagement of the wider community is essential for scientific progress. As such, I have volunteered time across several organizations to foster connections, act as a scientific liaison, and spark excitement about cutting edge research driving science forward..” Not to mention, when she's not in the lab, Clair is using her creative talents to support interesting graphics for student-led groups she is involved in, as well as creative illustrations for scientific papers. Download Clair's CU ��«��Ƶ Biochemistry journey.

The Cameron Lab - BCHM

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Nicole Marie Hoitsma Recognized as a 2023 Damon Runyon Fellow

Anonymous — Wed, 16 Aug 2023 20:32:20 +0000

Nicole Marie Hoitsma Recognized as a 2023 Damon Runyon Fellow Anonymous (not verified) Wed, 08/16/2023 - 14:32

Damon Runyon Cancer Research Foundation awards $3.9 million to exceptional early-career scientists

Nicole Marie Hoitsma, PhD [HHMI Fellow], with her sponsor Karolin Luger, PhD, at University of Colorado, ��«��Ƶ, has been named one of 13 new Damon Runyon Fellows by the Damon Runyon Cancer Research Foundation.

The Damon Runyon Cancer Research Foundation has named 13 new Damon Runyon Fellows, exceptional postdoctoral scientists conducting basic and translational cancer research in the laboratories of leading senior investigators. This prestigious Fellowship encourages the nation's most promising young scientists to pursue careers in cancer research by providing them with independent funding to investigate cancer causes, mechanisms, therapies, and prevention. In July 2023, the Board of Directors announced at 15% increase in the Fellowship stipend, bringing the total to $300,000 over the award's four-year term.

“Over the past three decades, the rate of cancer mortality in the U.S. has dropped by a third, saving an estimated 3.8 million lives. This is because of earlier diagnoses, a better fundamental understanding of the genetic changes that take place in a cancer cell, and personalized treatment options like targeted therapy and immunotherapy. Damon Runyon scientists have been a part of each and every one of these advances,” said Yung S. Lie, PhD, President and CEO of Damon Runyon. “We fund the best young talent—risk takers and innovators. I am confident that because of the research being done by our scientists, this trend will continue, such that ultimately cancer will be a fully treatable disease. My optimism is shared by the cancer research community.”

Hoitsma's Research:

Human cells have complex mechanisms to repair DNA damage, such as that caused by exposure to sunlight or chemical substances. If DNA is not properly repaired, however, it can lead to cancer. In fact, faulty DNA repair has been associated with the initiation and progression of all types of cancer and is often targeted in cancer treatment to stop uncontrolled cell growth. A better understanding of how cells naturally defend against DNA damage will allow for the development of better drugs to treat cancer. Dr. Hoitsma aims to investigate specialized proteins, known as chromatin remodelers, that make damaged DNA accessible for repair. This research will provide insight for the development of novel therapeutic strategies to target these critical pathways. Dr. Hoitsma received her PhD from University of Kansas Medical Center, Kansas City and her BS from South Dakota State University, Brookings.

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A Blooming Scientist: Emily Kibby

Anonymous — Wed, 31 May 2023 14:51:49 +0000

A Blooming Scientist: Emily Kibby Anonymous (not verified) Wed, 05/31/2023 - 08:51

Emily Kibby is a 2025 PhD candidate in Biochemistry in the Aaron Whiteley Research Group. She became an NIH Signaling and Cellular Regulation Trainee in 2020 and in 2021 received a Graduate Teaching Award.

A BLOOMING SCIENTIST

It was only in high school that I started to appreciate chemistry and developed an interest in biology. Up until then I thought I might be a writer and most likely an educator - following in the footsteps of my parents. I became fascinated with understanding the molecular mechanisms that serve as the foundation for life. As is true for many people, I would say the mentorship I’ve received (and given) and the people that I have worked with have been really important parts of my development as a scientist.

RESEARCH: WHERE MICROBIOLOGY MEETS BIOCHEMISTRY

I focus on understanding bacterial immune systems, and investigating the many ways that bacteria have to protect themselves from viruses and other threats. I’ve always been fascinated by the diversity of microbes and the interactions in host-pathogen conflicts, so I love working on a system where both the host and the pathogen are microbes! I think I’m always going to be fascinated by the same things that I love now, but that might expand to looking at the immune systems of other organisms like fungi or archaea, and I anticipate that I will also broaden the strategies I use to answer scientific questions. Genetics are and will always be an incredibly powerful tool to answer the types of question I am excited about, but I’m hoping to learn and use other strategies to investigate microbial conflict systems. Emily’s first first-author paper was just published in Cell (Volume 186, Issue 11, P2410-2424.E18, May 25, 2023)!

MY LIFE’S JOURNEY

I chose the CU ��«��Ƶ Department of Biochemistry because I really loved the collaborative and supportive community found in this department - not to mention the excellent shared facilities and science. I arrived at CU ��«��Ƶ as a first-year grad student Fall of 2019 and managed to experience most of the first year in person before we were shut down due to COVID. Professor Aaron Whiteley started his lab in January of 2020 and after initial rotations, I found the Aaron Whiteley Lab was a great fit with my research interests! Mentoring and teaching are in my DNA and early-on I became involved in undergraduate mentoring, tutoring students through the Student Academic Success Center, and volunteering with Partnerships for Informal Science Education in the Community (PISEC) and the Science Community Outreach Program and Education (SCOPE). Along my journey toward a PhD I’m hoping to learn new skills and strategies for framing, communicating, and investigating exciting scientific questions, and then putting those strategies into practice to do some cool science! Because I have received really helpful mentorship, I wish to continue mentoring others and get other young scientists excited along the way. When I’m not in the lab, I enjoy the many outdoor activities accessible in ��«��Ƶ, playing volleyball, and other group activities that our community is known for! I hope that my career will lead me to an academic environment where teaching is paramount - but never removed from the joy and application of the research.

Emily has an inquisitive mindset about life, “I just love that biochemistry gives a window to better understand the molecular strategies used by us and other organisms to live. “Life” as we think about it is already so incredible, the fact that we can understand it on a molecular level and that we still have so much to learn has always been really exciting to me. I also love that biochemistry has so many applications for making life on this shared planet better for everyone.” Not to mention, when she's not in the lab, Emily is using her teaching mindset to tutor and mentor undergraduate students and provide support to her fellow graduate students. Download Emily's CU ��«��Ƶ Biochemistry journey.

Aaron Whiteley Research Group - BCHM

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A Dedicated Science Champion: Calvin Voong

Anonymous — Mon, 17 Apr 2023 20:47:11 +0000

A Dedicated Science Champion: Calvin Voong Anonymous (not verified) Mon, 04/17/2023 - 14:47

Calvin Voong is a 2024 PhD Candidate in Biochemistry, Biophysics, and Molecular Biology in the Goodrich-Kugel Research Group. In 2019 he received a Graduate Teaching Award; in 2021 he received a Department Service Award; and in 2023 was a member of the Graduate Recruiting Team.

LOS ANGELES LEADS TO BOULDER

I grew up in the greater Los Angeles area in a historically underrepresented community, where the expectations were centered on being diligent and working hard – a necessity to make ends meet. During my undergraduate studies, I commuted to Long Beach State University from my family home, which often led me to being on the road around 6am and leaving for home later into the evenings. The combination of long days and familial expectations were mentally and physically challenging for my studies, but I made it! However, when I went to graduate school, I wanted to do things differently; I wanted to focus on creating a healthy lifestyle while being diligent in my studies and scientific endeavors. CU ��«��Ƶ Biochemistry gave me that opportunity and access to world-class facilities, to people who are curious - collaborative – supportive, to advisors who made time for their students, to a great community, and to a healthy outdoor environment.

MOLECULAR CURIOSITY TO SYSTEMS RESEARCH

I have always had an interest in understanding the molecular details and I am excited about drug design and biomolecular tool development. Through my research journey, I have developed an appreciation for the basic sciences – wanting to better understand the molecular details of how a system works - where I can modulate different properties of a particular biomolecular system to learn and explore. My current research path focuses on investigating how a DNA binding protein, HMGB1, navigates the structure of a nucleosome. As an architectural DNA binding protein, HMGB1 can modulate the local chromatin environment to help facilitate the binding of other transcription factors to their cognate DNA binding sites. Previous biochemical assays have shown that HMGB1 interacts with DNA and parts of the nucleosome; however, it is unclear from this set of literature how HMGB1 utilizes these different modes of interactions to help it search for DNA binding sites in the context of chromatin. Hence, to investigate this phenomenon, my research uses single-molecule microscopy to study the binding kinetics of HMGB1 on nucleosomes. Having a better understanding of how HMGB1 navigates the architecture of a nucleosome will allow us to better understand the mechanisms by which HMGB1 helps transcription factors bind to their cognate DNA sequences.

MY JOURNEY

��«��Ƶ has become my home. I am grateful for the opportunities that have allowed me to put all my energy into my academics and research pursuits, I am grateful for the complete support of my advisors and fellow lab members, and I am incredibly grateful that I have been given opportunities to explore my scientific endeavors by allowing my curiosity to lead the way. Being a full-time graduate student without needing to work multiple jobs to get me through my degree has been vital to my growth and success. Additionally, giving back to the community has been important to me, as I have co-created the CU Biochemistry Peer-to-Peer mentoring program to support the first-year graduate students, spearheaded the in-person recruitment process to support our administration, and trained a myriad of up-and-coming scientists to be confident and efficient in what they do. My experience giving back to the CU ��«��Ƶ Biochemistry community has been incredibly fulfilling. Coming from a low socioeconomic background, where many of my peers did not have the opportunities to pursue their academic goals and aspirations due to financial and cultural constraints, I am motivated to give back and support those like me. I am bringing forward ideas, creating opportunities in education for those around me, and encouraging the growth and development of those I work with. The CU ��«��Ƶ Biochemistry program has allowed me to grow, and in turn, allowed me to give back to the very community that fostered my success.

Calvin has a pay-it-forward mindset, “Success, and joy, is fostering education and opportunity for the underserved in scientific fields by building programs that offer paths into biotech or pharmaceutical development careers. I want this to be part of my life’s journey througout my career." Not to mention, when he's not in the lab, Calvin is using his photographic skills in documenting the excitement of science and his fellow graduate students. Follow Calvin's updates at decalvino.com or download Calvin's CU ��«��Ƶ Biochemistry journey.

Goodrich-Kugel Research Group - BCHM decalvino.com

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All in the Family: Camila Sousa

Anonymous — Sun, 31 Jan 2021 19:45:07 +0000

All in the Family: Camila Sousa Anonymous (not verified) Sun, 01/31/2021 - 12:45

Sometimes life tells us we’re meant to do something. In Camila Sousa’s case, it started young, growing up in a house in ��«��Ƶ with not one but two PhD scientists for parents. Camila’s mom is a molecular biologist, and her dad, Marcelo Sousa, is a principal investigator here in the Biochemistry Department. Camila is in her Junior year, pursuing dual majors in Biochemistry and MCDB, and working in the esteemed Cech Lab on DNA methylation enzymes.

Choosing CU Biochem

Camila remembers hearing her parents talking shop often as a child. She doesn’t describe their influence as pressure, but rather as fostered curiosity: “I was always interested in what they were discussing. Growing up I’d always wonder how things worked at a molecular level—and my parents would quickly explain.” Camila wasn’t satisfied with the answers she got and decided to follow in their footsteps. “Biochemistry is the best approach to our molecular understanding as it relates to biological processes.” She’s quite matter of fact in saying this, almost as if she’d been raised by scientists.

As a born and raised ��«��Ƶite, Camila decided to stay true to her roots and enroll at CU, where she says she’s glad to avoid paying rent. However, perhaps most enticing were the ample research opportunities available through the Biochemistry department: “The research opportunities at CU Biochem were much more independent than other programs—real independent research opportunities versus a more railroaded experience assisting on someone else’s project.” As for out of state options, Camila felt that spending twice the money on tuition wasn’t worth the potential added value. Instead, Camila followed in her parents’ footsteps and decided to major in both MCDB and Biochemistry, choosing the two for their complementary approaches to similar subject matter.

For example, after taking immunology this past semester, which is an MCDB class, Cech Lab held a journal club where she learned about a specific receptor involved in immune responses. “The paper in our journal club focused on the structure of the protein and how it interacts with nucleic acids, whereas the MCDB paper focused more on the protein’s enzymatic cascade and broader cellular effects.” Even with the continued support from home, transitioning from high school to college was a big step for Camila. The increased independence presented a major challenge to overcome:

“You have to want to learn, want to do well, be generally interested in what you’re doing. It can be a challenge to figure out your learning language—how you want to study to get the information you need. Study habits were probably the most difficult to figure out. Also, questions—you have to go to the professor, they won’t be on your back checking if you understood. I have a free tutor in my parents, but I’ve noticed a different approach now that I’m in college—they’re forcing me to think for myself more rather than feeding me information.”

Conducting Research

Camila’s favorite classes thus far have leaned toward her father’s favored discipline. Though she hasn’t taken many upper-division courses yet, her favorite thus far has been Principles of Biochemistry. As with other Biochem majors, as an underclassmen Camila’s schedule focused on foundational Chemistry, Biology and Mathematics to prepare her for the integrative nature of biochemistry. When it came time to take Principles, Camila enjoyed how the course brought things together, remembering focusing on the various instruments that populate biochemistry labs, learning how they work and how typical workflows produce data. She also flourished in Molecular Cell Biology 1 which centered on the Central Dogma of Biology: DNA replication, transcription, and translation. “I liked this class because it started getting to the edge of our knowledge in that field. The professors wouldn’t have answers to the questions we’d ask.” Camila had found her home pressing the frontiers of human understanding, in exploring those childhood questions her parents never quite answered.

Soon unsatisfied with the answers to her big questions available in her lectures, Camila decided she would pursue research. She started by volunteering in her dad’s lab, doing inventory, organizing chemical shelves, and doing odd jobs for grad students. Camila (charitably) describes it as ‘getting acquainted with the lab,’ not really research, but a foot in the door.

If you’re interested in research, get into a lab in whatever way you can. I started off doing inventory and cleaning the fridge, because I really wanted to get into a lab! I started emailing professors the summer between freshman and sophomore year, so not a ton of class experience. I shared my class experience, my majors, and told them I was interested in their work.

Today she’s in the Cech lab, which focuses on RNA biology. Camila is currently assisting a post-doc working on chromatin-associated proteins—modulators that indirectly control gene expression by modifying the molecular structure of the chromosomes that house our genes. Camila’s project is specifically focused on DNA methyltransferase 1 (DNMT1), an important enzyme responsible for methylating DNA that her postdoctoral mentor previously identified. Methylation is the process of attaching a methyl group to a specific site on a gene where it can affect transcription—usually blocking it. We call this process epigenetic because it presents an indirect way of affecting the Central Dogma, namely transcription, without modifying the specific nucleotide sequence of our genetic instructions. As Camila reminds me, it’s also a dynamic process, “the gene in question can be methylated or de-methylated whenever it needs to be activated.” Camila’s day-to-day includes synthesizing the RNA transcripts her team has identified as interacting with DNMT1, while preparing for upcoming binding studies between the RNA and the methylating enzyme, which she says will provide a better picture of what the interactions look like.

Why is DNA methylation so important? Abnormal DNA methylation patterns are found in many cancers. According to Camila, in some cancers there is a pattern of dysregulation preventing DNMT1 from methylating appropriately, meaning cell cycle checkpoints can be missed, anti-tumor factors are ignored, and cancerous cells begin dividing unchecked. Quantifying exactly how these compounds interact can give us greater insight in how these abnormal methylation patterns come to be, making Camila’s work foundational to developing targeted therapies. Importantly, as biochemists work to decode the machinery responsible for DNA methylation, we move closer to developing bioengineered treatments for all genetic disease with sequence specificity. For instance, imagine targeting the mutated hemoglobin-Beta allele (responsible for Sickle cell anemia) for methylation while allowing the other copy to continue producing healthy red blood cells, all while harnessing the human body’s own cellular machinery.

Looking Ahead

Beyond her world of RNA-oncology, Camila is excited where biochemistry as a field is heading. She excitedly tells me about some technology in development her father shared with her:

Right now, we don’t have a method of figuring the structure of a protein based on its amino acid sequence even though it represents the totality of the code. However, Google is working on a machine learning program [AlphaFold] that can predict and visualize protein structure based on the amino acid sequence alone. I haven’t worked with structural biology yet, but structure is quite difficult, especially for insoluble proteins like membrane proteins. It can be a challenge to purify, difficult to work with lots of subunits, so this would be a major boon to the field.

A boon indeed, as the author’s own research would benefit immensely from this sort of plug-and-play amino acid decoding. Once scientists can consistently predict protein structure, we move closer to predicting interaction and function. Google’s AlphaFold2 technology may eventually allow scientists to circumvent expensive experimental methods for determining protein structure, like X-ray crystallography and cryo-election microscopy, entirely.

Though Camila hasn’t had as much free time given her ongoing research, she used to be an avid ballet dancer, taking classes and performing with her troupe “once in a blue moon”. Aside from ballet, both of Camila’s parents were born outside the U.S. (dad is Argentinian, and mom is from Germany), so she’s had ample opportunities to see the world: “I got to go to Italy for ten days around 2018—we started in Venice, looped north, then ended in Rome. We had two full days to do nothing in Venice, and by the end it felt like I’d seen everything twice! I loved going to the historical sites, that’s part of why I love traveling.” Unfortunately, COVID has put both travel and research plans on hold for the time being. In the meantime, Camila continues to plan her next round of experiments and life after ��«��Ƶ. She’s thinking grad school, almost certainly in Molecular Biochemistry, but she hasn’t settled on a topic beyond human health. Wherever she goes, Camila wants to continue exploring the mechanisms behind human diseases. We’re excited to see where Camila’s research eventually takes her, as she’s sure to make a big splash wherever she lands.

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Life of a Postdoc: Stephanie Moon

Anonymous — Mon, 21 Sep 2020 22:50:40 +0000

Life of a Postdoc: Stephanie Moon Anonymous (not verified) Mon, 09/21/2020 - 16:50

Dr. Stephanie Moon is working on ridding the world of disease. Beginning with an early obsession with finding a cure for chicken pox, Dr. Moon set her sights on RNA viruses, a family which includes some of the most prolific killers in human history: HIV, Zika, Hepatitis C, Ebola. Part of the challenge with these RNA viruses is the extremely rapid rate at which they can mutate, which means much shorter periods for natural selection to promote nasty traits such as immunoresistance and rarely, resistance to vaccination. Dr. Moon has spent the past five years as a post-doctoral research associate here at CU Biochem exploring just how RNA viruses make us sick.

Dr. Moon joined Professor Roy Parker’s lab as a Howard Hughes Medical Institute and Linda Crnic Institute for Down Syndrome’s postdoctoral research fellow to look at how disrupted RNA degradation affects development and function in humans. As one of her lab’s senior researchers, a significant component of her role involves sharing the lab’s work with the broader scientific community. “It’s a huge component of working in a lab—networking. I was initially attracted to CU Biochem by the prospect of having Roy as a mentor, and since then I’ve found over the past few years our department is one community working together to tackle some really important questions.” She fondly remembers her first trip to Europe—a seminar where she presented the lab’s research—as one of the perks of her postdoctoral experience at CU.

These postdoctoral fellowships are a critical step in the careers of many professional scientists. Postdocs conduct research while gaining the necessary experience and skills to compete for faculty or industry research positions. Part of a postdoc’s job is applying for fellowships, i.e. actively seeking out funding streams for continued research. According to Dr. Moon, “you need to be in constant communication with your mentor throughout these application processes.” When it comes time to move on from the postdoc position, mentors can help navigate complex applications for competitive professorships or industry research positions that can take upwards of a year, and their connections and support can help you build a professional network beyond one's alma maters.

New American doctorates typically do a single postdoc for no longer than five years, while European scientists are more likely to take multiple positions and spend more of their early careers conducting postdoctoral research. Some funders explicitly limit funding to a set duration, reinforcing the expectation that graduates move on to more permanent positions. For relative newcomers such as Dr. Moon, improved benefits and compensation provide intrinsic motivation to forge ahead. While professorships allow for greater autonomy and permanence, they are highly competitive: “I’ve had colleagues who’ve had success after a year, while some have been successful after six or seven years. Multiple postdocs are becoming more prevalent in the United States, but the goal is still to keep the total time around five years.”

Preparing for a Career in Science

Dr. Moon grew up in rural Colorado, studying biology and chemistry at Fort Lewis College, working as a hospital lab technician post-graduation before eventually earning her Ph.D. in pathology from Colorado State University. She found transitioning to graduate school especially challenging due to her limited research experience “in a small lab, at a tiny school,” and a scarcity of micro-and-cellular biology course offerings at Fort Lewis. In terms of course offerings, Dr. Moons says CU Biochem students are much freer to choose courses tailored to a specific field of interest. She recommends all aspiring scientists develop core skills in writing, statistics, and computer science. “We do a lot in this field to visualize and analyze data, and a lot of that can now be streamlined with coding.” Dr. Moon also recommends current students utilize CU Biochem’s large research community as a critical resource: “One of the great opportunities for our undergrads is the ability to tailor their education to their goals, interact and work with professional scientists from their first semester, conduct real research, and publish work. For instance, Parker Lab is home to an undergrad named Gabe Tauber who’s already co-authored multiple publications.”

Given the chance, Dr. Moon would have worked harder to seek out undergraduate research opportunities, “especially if studying at a smaller school; look out for internships and research positions at larger schools and in bigger cities during your summer and spring breaks.” As a grad student, Dr. Moon often looked to social media for these research opportunities: “Twitter can be a valuable resource for finding and pursuing research, as you’re instantly connected to the global scientific community”. CU Biochem frequently posts information on research opportunities, seminars, and networking events to Facebook, Twitter, and Instagram. “You should also practice grant-writing and apply for funding as early as possible—I’ve been able to conduct research here [at CU] because of competitive postdoctoral fellowships such as these.” In January, Dr. Moon accepted an Assistant Professorship at the University of Michigan. While Dr. Moon may have moved on, we look forward to meeting our next group of postdocs and following our CU Biochem grads as they begin their own postdoctoral careers.

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Engineering our Future: Tina Boville

Anonymous — Mon, 21 Sep 2020 22:37:14 +0000

Engineering our Future: Tina Boville Anonymous (not verified) Mon, 09/21/2020 - 16:37

Though she sounds every bit the polished Silicon Valley CEO while discussing spin-ups, revenue streams, and funding runways, Dr. Tina Boville first describes herself as “a huge nerd.” via Zoom. A CU Biochem doctoral alum, Tina grew up on Anne McCaffrey’s science-fantasy series Dragonriders of Pern, which heavily incorporates themes of terraforming, genetic modification, and the celestial future of humanity. These stories inspired in Tina the belief that we can and should engineer our own lives for the better. Because of that vision, she is now an MIT Technology Review Top Innovator under 35 (awarded to “exceptionally talented innovators whose work has the greatest potential to transform the world,” the founder of her own company, and already putting her science to work improving lives.

Tina first joined our community as an undergraduate in MCDB. Like many scientists of note, Tina's undergraduate experience was somewhat unmemorable. However, while pursuing her bachelor’s, Tina landed an internship at pharmaceutical giant Amgen here in ��«��Ƶ that would prove quite the boon. After graduating, Tina stayed on with Amgen for a couple of years prompting her decision to return to CU for a PhD in Biochemistry. While she didn’t know what her next step would be, “teaching was something I enjoyed, and thought was important.” So, as a doctoral student, Tina joined CU’s Graduate Teaching Program, which she quickly rose to lead. Though she says she loved her teaching opportunities, it was another experience at CU that would provide a platform for Tina to reach for the stars of her childhood novels.

Going Green

It was here at CU Biochem that Tina set the foundation for her future entrepreneurship at CU Green Labs. First piloted by then Kuchta Lab postdoc Kathryn Ramirez-Aguilar in 2007, CU Green Labs was one of the first programs of its type in the nation, improving sustainability in research through equipment sharing, recycling, and energy-saving incentives. Today, it is recognized as a national leader, host to the International Institute for Sustainable Laboratories Conference in 2019. Kathy described Tina as an “amazing person,” and made sure to note “[Tina] recently took the time to share via Zoom her career path with my current CU Green Labs student assistant and give advice for when they leave CU to look for that next step in their career,” while setting up the interview for this piece.

Working with Kathy Ramirez-Aguilar, Tina would become program lead for the [then] recently built Jennie Smoly Caruthers Biotechnology Building, where she worked to improve sustainability in reagent purchasing and waste disposal without compromising the science of JSCBB’s research groups. Tina’s own achievements include the ubiquitous pipette box recycling bins you’ve seen around campus: “The work with CU Green Labs set me up on thinking about Green Chemistry.”

What is Green Chemistry, you might ask? In Tina’s words, Green Chemistry is “a catch-all for what we do, and not that new of an idea.” Tina cites the American Chemistry Society’s 12 Principles of Green Chemistry as a sort of Messianic tablet for her work, which proscribes ways chemistry can be made safer and more efficient. Dicta include designing for energy efficiency, reducing derivatives, and maximal incorporation of material into products during synthesis. The aim of the ACS principles, and Green Chemistry on the whole, is “making processes more efficient.” This all may sound a bit dry, until one considers just how integral chemistry is to our everyday lives.

Take, for example, the Lithium cobalt(III) oxide in your phone battery, the cetirizine you take to manage pollen allergy, the all-trans retinoic acid in your acne cream, or the liquid crystal cholesteryl benzoate forming the words on this screen. For our phones to call, for our trains to run, for our loved ones to get better, these compounds need to be synthesized: “We really need to make those chemicals, they’re critical.” However, producing such compounds in the quantities we need (which are increasingly engineered by us) can be a costly and wasteful process. Often even the precursors need precursors, and only a small fraction of the starting materials end up in the final product. Enter Aralez Bio, co-founded by Tina in 2019, and noncanonical amino acid (ncAA) synthesis.

Scaling Up

After the University of Colorado, Tina won a prestigious Resnick Prize Sustainability Fellowship at the California Institute of Technology where she began working with Nobel Laureate Frances Arnold on directed protein evolution. Working with Professor Arnold, Tina would develop a novel enzymatic pathway capable of synthesizing stable amino acids beyond the 20 that form the building blocks of all life on earth. It would also serve as the foundation for Tina's push into the private sector. These resulting noncanonical amino acids can then be used to form a dizzying array of novel compounds in what Tina aptly calls “chemical LEGO.” Most importantly, and not unlike our own physiology, the enzymes used to make these ncAAs are preserved during synthesis. The result: no more exorbitant waste to product ratio, and a growing set of new blocks to build with: “Just like LEGOs, you need different pieces to be able to build Yoda, or Luke.” Without the pieces, processes like drug synthesis are slow, wasteful, difficult to standardize. For pharmaceutical companies, this means reducing the economic and environmental cost of drug manufacturing while scaling new drugs to market demand more quickly. As Tina puts it, “enzymes hit 10 of the 12 Principles,” so, after her fellowship, Tina used her postdoctoral work to co-found Aralez Bio with postdoctoral lab mate Dr. David Romney, and Prof. Arnold as an academic co-founder.

According to Tina, bringing a professor on in an advisory role is “common for companies spinning out research worked on in that [investigator’s] lab.” Although not necessary for biotech startups, Tina says advisors “typically have good experience on the relevant tech and can provide insight on directions the field will be headed.” With Tina’s vision and Dr. Arnold’s experience, Aralez Bio is making impressive progress on its mission: “We can now make hundreds, and will be able to make thousands of kilograms [of ncAAs] by the end of our program.” This summer, Tina also secured a Shaw Rocket Fund award for Aralez Bio, a clean tech grant program through Caltech for companies working to reduce hazardous waste and greenhouse gas production.

Though Tina says she sees the impact of COVID on her industry, she and her company show no signs of slowing down. Aralez Bio recently moved from a shared business incubator to a standalone facility to comply with social distancing guidelines—a move not possible for many smaller outfits who’ve been forced to suspend operations in response. Funding streams have also been slowing as the pandemic continues. For her part, Tina has been working to source lab equipment from auctions held by other labs who weren’t so lucky: “Running a business is a totally different set of skills—it doesn’t matter if you’re a really smart scientist.” Fortunately, Tina appears to have exactly the skills she needs, and the scientific world is taking notice.

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Biopharma Innovator: Celso Espinoza

Anonymous — Mon, 22 Jun 2020 07:25:15 +0000

Biopharma Innovator: Celso Espinoza Anonymous (not verified) Mon, 06/22/2020 - 01:25

Dr. Celso Espinoza is a senior drug discovery investigator with the biopharmaceutical firm AbbVie. Originally a component of Abbott Laboratories, AbbVie split in 2013 to focus on new drug discovery, and Celso followed. Since then, Celso has been a part of many major therapeutic breakthroughs including the immunosuppressor Humira, and mood stabilizer Depakote. These successes have grown AbbVie into a 47,000+ employee publicly-traded company, and Celso is now a senior investigator managing a team of scientists searching for new cures. We caught up with Celso to learn how he leveraged his CU Biochem Ph.D. into a flourishing career in pharmaceutical research, and to share memories of the department’s early days.

From the Gridiron to the Bench

Celso started his scientific career, as many undergraduates do, interested in medicine. Unlike many, he was also playing inside linebacker for Cal State – Sacramento’s football team. Celso took to interdisciplinary research at Cal State under Drs. Roberts and McCarthy, who encouraged graduate studies at a number of programs, including CU ��«��Ƶ’s Chemistry and Biochemistry Department (we officially split in 2018). “They said you know whatever you do, find someone you can get along with; so, during [CU’s] rush week, I met Jim [Goodrich].” Needless to say, they got along. Dr. Goodrich, coupled with mountain views, hiking and biking trails, and a departmental emphasis on genome-wide investigation, made CU Biochem Celso’s first choice for earning a Ph.D. Despite his undergrad research experience, Celso recalls his first weeks building a foundation of transferrable skills under Jim’s guidance:

After meeting Jim, and working for him, I wanted to be more like Jim, thinking creatively. I really enjoyed being in his lab. You don’t come in with all the tools, so he had to work really hard to teach me everything. He taught me how to think, problem-solve, and be efficient, and I really appreciated his help.

Outside of finding an influential mentor, Celso fondly remembers his time in ��«��Ƶ spending time with faculty and peers outside of the lab. He enjoyed participating in the annual departmental retreats, where graduate students would share their most recent findings with the rest of the department and spend time with faculty and classmates in an informal setting. He also vividly remembers taking long bike trips organized by faculty, particularly a grueling 2-day, 40-mile bike ride through Rocky Mountain National Park with current CU Biochem instructor Dr. Rico Stephen.

Transitioning to the Private Sector

After earning his Ph.D. under the tutelage of our Dr. Goodrich, opportunity struck again, this time with the esteemed epigeneticist Dr. Bing Ren at the University of California San Diego, a pioneer in CHIP-seq technology. Once his postdoctoral fellowship under Dr. Ren concluded, Celso moved into biopharmaceutical research and development, where he has been a key investigator in some major therapies. Day-to-day, this means conducting experiments and analyzing results, not unlike a primary investigator at a private institution, albeit with a bit more vertical hierarchy. Celso manages a team of scientists (focusing on genomic and transcriptomic approaches in his case), sets research agendas, and communicates results to other research groups and AbbVie’s corporate offices:

I go to about one conference a year to stay up to date in the field. In the private sector, you may have to travel to various sites to work with different teams, but you don’t share your results with other organizations as often. In my work, I work with microbiologists, chemists, folks doing clinical trials, and we all come together to answer a research question. There are typically a lot of channels to go through before we are ready to present our findings to the public.

The Future of Biopharma

Celso believes biopharma may be the next industry to see seismic changes, not unlike the personal computing industry in the Eighties:

Look at Steve Jobs; he figured out how to put everyone together with the iPhone. If someone could do that with genomics, they’d be a billionaire. If you look at companies who are doing whole-genome sequencing, like 23 and Me, they’re just beginning to use the data we get from someone’s genome. Genetic counseling, pharmaceutical research, it's bigger than all of us. We’re starting to learn how the genome works across each layer—epigenetics, RNA, DNA. Ιt would be nice to have a clear answer, but we still don’t know just how far the frontiers like RNA go.

In Celso’s field, this means understanding the function and interactions of a growing proportion of the human exome and proteome it encodes, at a clarity that allows identification of nucleotide-level changes responsible for pathology. For example, Celso’s group has most recently focused on how the body metabolizes drugs and variance in reaction to therapies. Recent breakthroughs in bioinformatic software, big data cloud computing, and our collective understanding of the genetic code of life mean Celso’s predictions may not be so far away. Perhaps one of our own Biochem Buff readers will be the pioneer Celso envisions.

Building Bridges

When asked how aspiring biochemists might replicate Celso’s professional successes, he recommends engagement and passion. Celso’s time at CU Biochem included participation in Biophysics Club and RNA Club, where he forged friendships and fostered a growing professional network:

These are skills I still use today. It’s very important to be able to communicate and provide positive feedback. You also have to find a passion. If you’re not passionate about your work, it’s going to be a long, long journey. In my field, a lot of people on the outside forget that for [pharmaceutical researchers], the patients come first. Helping people get better, that’s our main motivation.

As part of the Goodrich Lab, Celso focused on mechanisms of transcription, a novel approach at the time.

Most of the things I worked on in grad school were mechanisms. [Jim’s] lab was a transcription lab, but there weren’t any people studying the function of RNA, so I took over a project finding the secondary structure and figuring out which part of RNA binds to proteins, which led to more research into epigenetic mechanisms.

The work would prove integral to Celso’s transition into pharmaceutical research. Today, Celso develops 3-D assays to understand the function of various sequences within the human genome, with the end goal of identifying genes responsible for phenotypic variance associated with disease, and then using that understanding to develop therapies that target these pathways.

Goorich/Kugel Lab - BCHM CU ��«��Ƶ Jobs AbbVie CU ��«��Ƶ Biophysics Program

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Dealing with Adversity: Graycen Wheeler

Anonymous — Fri, 05 Jun 2020 19:37:06 +0000

Dealing with Adversity: Graycen Wheeler Anonymous (not verified) Fri, 06/05/2020 - 13:37

Graycen Wheeler is a 6^th year graduate student in BCHM's Liu Lab. She was initially attracted to CU Biochem by the strong web presence and diversity of research in the department’s labs. During graduate recruitment, “the interview process wasn’t nearly as anxiety-inducing and I felt natural interacting with grad students and prospective advisors.” Graycen joined the department with good grades and plenty of undergraduate research experience, but a couple of challenges along the way quickly taught her that success would require new skills, a little luck, and a lot of persistence.

Finding a Home

For many grad students, the first year of grad school induced a crisis of identity; Graycen and her classmates rotated between labs while establishing professional relationships, brushing up on research skills, and preparing for her written exams, all while taking a rigorous course-load. “A lot of people say being in graduate school is a break from your real life—and it’s not. You have to constantly assess what you’re giving up to stay in school.” Compounding these stressors, at the end of her first year, Graycen received the disappointing news that her first choice for a permanent lab was no longer accepting graduate students. Furthermore, her written exams were scheduled a few short weeks after first-year students join their labs.

Graycen stuck with it, and after “wandering into a microscopy lab,” fell in love with systems biology: “I loved the huge tangled mess of cell-signaling. With microscopy, there’s also lots of programming and image analysis which is always a delight.” Graycen had completed her first two rotations based on her undergraduate experience with structural biology. The opportunity to moonlight in multiple labs with varying research focuses before making a choice was a major draw, even amongst related programs at CU, for Graycen, it paid off. In her new lab, Graycen felt “like a mad scientist from a cartoon looking over my microscope.” She also made new friends, including a lab mate that she now plays tabletop games with: “I found my roommate and some great friends through that game. That’s a great benefit of this program—close ties to other departments.”

Beyond the Bench

It was these friends that Graycen turned to for support when she learned that she had failed her written comp test: “I was playing in a departmental softball league, and we had a game the day I found out that I had failed.” Some of the faculty that had administered her exam were playing, and needless to say, it was the last place she wanted to be. After the game, Graycen decided to hang out with some teammates where she received kind and encouraging words from her peers. “Grad school is hard, no matter what program you choose. There will always be times that it sucks; it felt great to be surrounded by people who reminded me of that.”

Over the intervening years, Graycen has added writer, producer, and podcast host to her CV thanks to her work with CU’s blog Science Buffs. Graycen writes for Science Buffs and is a co-host and co-producer for the Buffs Talk Science podcast: “Science Buffs wanted to start a highly produced podcast a la Radio Lab on NPR, but these would take 6+ months to produce without a big staff. We were working on an idea for a podcast that we could get out in a reasonable time frame.” Graycen takes full advantage of the format: “I get to say, ‘asking on behalf of the non-scientist’ and pretend you’re asking for the regular listeners out there. The podcast is a great chance to talk to people I’d normally be intimidated by in a more informal setting.”

Sharing Science

Graycen has also found that the format has a disarming effect on expert guests: “Everybody is pretty nervous to go on a podcast, so they end up a lot less intimidating; we have professors and other experts over for dinner and discuss their research in a more informal setting. The interviews themselves are also a blast.” Graycen and her co-host have managed to parlay several of their interviews into game nights. Graycen’s favorite stories to tell are about bad scientists: “Our first episode on Buffs Talk Science was on Ryan Zinke, who was a scientist for the Trump administration. He was constantly offering his professional opinion ‘as a geologist’ when he had never worked as a geologist and had only studied geology briefly in college. I like stories with a little bit of controversy, which leaves listeners to formulate their own opinion.”

When she’s not in the lab, working on a new story, or dominating faculty in softball, you might find Graycen mountain biking: “The single tracks in Eerie are great. The prettiest trail I’ve been on was in Bailey, which also happens to be the Bigfoot sighting capital of Colorado.” She also keeps bees, which she inherited from a former classmate who’s now doing patent law in New York. Follow Graycen’s work on Science Buffs and on Twitter @grrriosa.

Liu Lab - BCHM Science Buffs Blog Buffs Talk Science Podcast @grrriosa - Twitter

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