Category: Being a Scientist

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Gone Fishing: Teaching Bioinformatics With Skate DNA

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As computers have advanced over the past few decades, researchers have been able to work with larger and more complex datasets than ever before. The science of using computers to investigate biological data is called bioinformatics, and it’s helping scientists make important discoveries, such as finding versions of genes that affect a person’s risk for developing various types of cancer. Many scientists believe that almost all biologists will use bioinformatics to some degree in the future.

A cluster of various-sized dots connected by glowing lines.
Bioinformatics software was used to create this representation of a biological network. Credit: Benjamin King, University of Maine.

However, bioinformatics isn’t always included in college biology programs, and many of today’s researchers received their training before bioinformatics was widely taught. To address these gaps, the bioinformatics cores of the five Northeast IDeA Networks of Biomedical Research Excellence (INBREs)—located in Maine, Rhode Island, Delaware, Vermont, and New Hampshire—have worked together to offer basic bioinformatics training to students and researchers. The collaboration started in 2009 with a project where researchers sequenced the genome of a fish called the little skate (Leucoraja erinacea) and used the data to develop trainings.

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Making a MARC at Vanderbilt

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“What we’re trying to do is support the students’ attachment to being a scientist, to becoming part of the community,” says Douglas McMahon, Ph.D., the Stevenson Professor of Biological Sciences at Vanderbilt University in Nashville, Tennessee, and a co-director of Vanderbilt’s Maximizing Access to Research Careers (MARC) program. MARC focuses on undergraduates from diverse backgrounds who are in the biomedical sciences and plan to pursue a Ph.D. or M.D./Ph.D. degree after graduation.

Sim Plotkin in front of a brick building.
Sim Plotkin.
Credit: Allyson Arserio.

For years, NIGMS has funded MARC programs throughout the United States and its territories; Vanderbilt joined their ranks in 2020. In June of that year, Dr. McMahon and Katherine Friedman, Ph.D., an associate professor of biological sciences at Vanderbilt and co-director of its MARC program, welcomed the initial cohort of six rising juniors. “MARC is a great opportunity because it focuses on helping people reach their Ph.D. goals who don’t really have others around them who know how to get there,” says Sim Plotkin, a molecular and cellular biology major. “For me, that’s really helpful because I’ll be the first in my family to graduate from college.”

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Accelerating the Development of Tests for Endometriosis and Cancer

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NIGMS’ Small Business Technology Transfer (STTR) program works toward more effective methods for patient screening, diagnosis, and treatment.

Translating lab discoveries into health care products requires large investments of time and resources. Through STTR funding, NIGMS supports researchers interested in transitioning their discoveries and/or inventions into products. Here are the stories of three researchers working with the XLerator Hub, one of the funded programs that supports six southeastern IDeA states and Puerto Rico.

Ending Diagnostic Delays for Endometriosis

A headshot of Dr. Idhaliz Flores-Caldera. Dr. Idhaliz Flores-Caldera.
Credit: Courtesy of Dr. Flores-Caldera.

Idhaliz Flores-Caldera, Ph.D., a professor of basic sciences and OB-GYN at Ponce Health Sciences University in Puerto Rico, has studied endometriosis for nearly 20 years. Endometriosis occurs when endometrial tissue, which typically lines the uterus, grows elsewhere in the body. Dr. Flores-Caldera first had the idea for a noninvasive diagnostic test for the disorder about 10 years ago. But it was only when she learned about funding opportunities from the XLerator Hub that she saw a path to validating her preliminary research findings and eventually commercializing her test.

Dr. Flores-Caldera applied for and was accepted into the hub’s proof-of-concept program, Ideas to Products, which funds researchers to flesh out ideas they want to commercialize. “I am very appreciative of how the program has provided me with tools and knowledge about commercializing a product and the process of patenting a product,” she says. “In general, scientists aren’t educated on this important topic.”

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Pathways: The Imaging Issue

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Cover of Pathways student magazine showing geometric shapes, pom-pom-like structures, and text that reads, Dive into the microscopic world. What do you think this image shows? Hint: It’s NOT an underwater scene! (Answer inside). Cover of Pathways student magazine.

NIGMS and Scholastic bring you our latest issue of Pathways, which focuses on imaging tools that help scientists unlock the mysteries of our cells and molecules. A better understanding of this tiny world can help researchers learn about the body’s normal and abnormal processes and lead to more effective, targeted treatments for illnesses.

Pathways is designed for students in grades 6 through 12. This collection of free resources teaches students about basic science and its importance to health, as well as exciting research careers.

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COVID-19 Vaccine and Therapeutic Trials ACTIV-ate in West Virginia

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Hands in medical gloves drawing liquid from a vial into a syringe with a model of SARS-CoV-2 in the background. ACTIV clinical trials will evaluate the safety and efficacy of COVID-19 treatments and vaccines. Credit: iStock.

Since the virus that causes COVID-19, known as SARS-CoV-2, was first reported in late 2019, scientists have launched hundreds of studies on strategies for diagnosis, prevention, and treatment. To prioritize the most promising vaccine and therapeutics candidates, streamline clinical trials, and coordinate regulatory processes, the National Institutes of Health (NIH) and the Foundation for the NIH have established the Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) partnership. ACTIV brings together eight government entities, 20 biopharmaceutical companies, and four nonprofit organizations.

The public-private partnership provides infrastructure, subject matter expertise, and funding to efficiently bring the most promising therapeutics and vaccines into clinical trials. Five ACTIV therapeutic trials are underway. NIGMS-supported Institutional Development Award Program Infrastructure for Clinical and Translational Research (IDeA-CTR) networks reach historically underserved areas and populations, which are important participants in such trials.

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Fight Against COVID-19 Aided by Sepsis Researchers

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Oblong light-blue structures with red spots in the middle connected to the surface of a sphere. Spike proteins on the surface of a coronavirus. Credit: David Veesler, University of Washington.

Since the start of the COVID-19 pandemic, researchers from many areas of biomedical science have worked together to learn how this new disease affects the human body, how to prevent its spread, and how to treat it. Severe cases of COVID-19 and cases of sepsis share many symptoms. Sepsis is the body’s overactive and extreme response to an infection. It’s unpredictable and can progress rapidly. Without prompt treatment, it can lead to tissue damage, organ failure, and death.

Sepsis has similarities with some cases of COVID-19, most likely because the two conditions trigger the same reactions at the cellular level. Researchers have studied these reactions in sepsis for many years.

“When we look back on 2020 and the speed with which progress was made against COVID-19, two features will stand out,” says John Younger, M.D., a member of the NIGMS Advisory Council who recently co-chaired a working group on advancing sepsis research. “The first is how quickly the biotechnology community came together to develop vaccine candidates. The second, and arguably the most immediately impactful, is how caregivers and clinical researchers were able to rapidly refine the care of COVID-19 patients based on decades of experience with sepsis.”

This post highlights a few of the many sepsis researchers supported by NIGMS who are applying their expertise to COVID-19.

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Career Conversations: Q&A with Organic Chemist Osvaldo Gutierrez

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Osvaldo Gutierrez, Ph.D., was born in Rancho Los Prietos, a small town in central Mexico where his grandmother served as a midwife. Seeing how his grandmother helped people through her work inspired Dr. Gutierrez to pursue a career where he, too, could help people. His family emigrated to the United States when he was young. Despite challenges he faced in a new country, he graduated from high school, attended community college, and was accepted to the University of California, Los Angeles. He originally planned to become a medical doctor, but an undergraduate research experience sparked an interest in chemistry, and he ultimately earned a Ph.D. in the field.

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Year in Review: Our Top Three Posts of 2020

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Over the year, we dove into the inner workings of cells, interviewed award-winning researchers supported by NIGMS, shared a cool collection of science-themed backgrounds for video calls, and more. Here, we highlight three of the most popular posts from 2020. Tell us which of this year’s posts you liked best in the comments section below!

The Science of Infectious Disease Modeling

Oblong light-blue structures with red spots in the middle connected to the surface of a sphere. Spike proteins on the surface of a coronavirus. Credit: David Veesler, University of Washington.

What does “modeling the spread” (or “flattening the curve”) mean, and how does it apply to infectious diseases such as COVID-19? Learn about the science of infectious disease modeling and how NIGMS supports scientists in the field.

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Expert Advice on Starting a Lab

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During our Starting Your Own Lab webinar, attendees asked so many insightful questions that we ran out of time to respond to all of them. So we asked nine NIGMS early career investigators to tackle the most popular ones in short videos, which were featured on our social media. Now, you can watch the whole series on our YouTube channel.

1. What advice do you have for postdocs searching for a faculty position?
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Preparing Students in Puerto Rico for Biomedical Careers

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“There’s knowledge to seize in Puerto Rico, and our program is letting students know that they have a really important role to play in solving local problems, that they are part of the solution,” says Isar P. Godreau, Ph.D., a researcher at the University of Puerto Rico (UPR) Cayey Institute of Interdisciplinary Research.

Dr. Godreau, along with fellow researchers Mariluz Franco-Ortiz, Ph.D., at UPR Cayey Institute of Interdisciplinary Research, and Raymond Louis Tremblay, Ph.D., at UPR Humacao, directs an NIGMS Innovative Programs to Enhance Research Training (IPERT) grant. The UPR IPERT supports undergraduates throughout the university’s 11 campuses.

Resources Reach Thousands

Dr. Ortiz standing with other standing and kneeling students in a classroom, smiling and waving. Dr. Franco-Ortiz (second from right) with students during a Coaching for Resiliency workshop session. Credit: Ivonne Bayron-Huertas, Ph.D.

Furthering NIGMS’ goals to create a highly skilled and diverse biomedical workforce, UPR IPERT provides undergraduate students from economically disadvantaged families with skills development and mentoring opportunities. One of the program’s main components is a series of Coaching for Resiliency workshops, which cover topics such as dealing with stress, managing family expectations, and handling financial challenges. A coach leads each group that includes about 10 to 15 first-year students and half as many second-year or higher students who act as peer mentors.

The coaching sessions help students connect with one another and with mentors. “One of the main accomplishments beyond the numbers is the power of networking,” says Dr. Franco-Ortiz. “The power of networking at different levels—from student mentors and faculty mentors at the UPR campus as well as abroad—is so crucial in terms of helping students who are looking for next steps.”

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