Tag: Training

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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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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Decades of Dedication: Angela Wandinger-Ness Recognized for Outstanding Mentoring

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“Each person has something that they uniquely want to do, and as a mentor, you have to help uncover that,” says Angela Wandinger-Ness, Ph.D., the Victor and Ruby Hansen Surface Endowed Professor in Cancer Cell Biology and Clinical Translation in the department of pathology at the University of New Mexico (UNM) School of Medicine. “You have to put opportunities in front of them. You see what excites them, and then you steer them.” Dr. Wandinger-Ness is among this year’s honorees of the Presidential Award for Excellence in Science, Mathematics and Engineering Mentoring (PAESMEM).

Dr. Wandinger-Ness, Amber Rauch, and Melanie Rivera standing together in a laboratory. Dr. Wandinger-Ness (left) with former undergraduate trainee Amber Rauch (center) and current Ph.D. trainee Melanie Rivera. Credit: Angela Wandinger-Ness, Ph.D.

The PAESMEM was established by the White House in 1995. This year, recipients were honored during a virtual awards ceremony. Each awardee received a grant from the National Science Foundation, which manages the PAESMEM on behalf of the White House Office of Science and Technology Policy.

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Learn Directly From Scientists Through Available Webinar Series

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Looking for more virtual learning opportunities? NIGMS recently recorded a series of 14 webinars where experts shared their knowledge on topics from infectious disease modeling to pursuing a career in biomedical science. With the start of the 2020-2021 academic year, we’re highlighting a webinar that’s particularly relevant for our Biomedical Beat readers who are educators. You can check out the whole series on the NIGMS YouTube channel.

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NIGMS Centers Build Relationships with Blackfeet Students and Collaborate on Inflammation Research

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A sign that says “Welcome to the Blackfeet Nation” next to a sculpture of two American Indians on horseback under a blue sky. Credit: Murray Foubister. CC BY-SA 2.0 Link to external web site.

As part of its commitment to cultivate a diverse and inclusive scientific workforce, NIGMS continues to nurture relationships between teaching institutions and American Indian communities nationwide to ignite student interest in biomedical science and encourage research careers. This post highlights one such collaboration between NIGMS-supported centers at Montana State University (MSU) in Bozeman and the Blackfeet Nation, a tribe of nearly 18,000 members that’s one of the largest in the United States.

A headshot of Dr. Neha John-Henderson. Neha John-Henderson, Ph.D., Montana State University. Credit: Kelly Gotham.

Neha John-Henderson, Ph.D. Link to external web site, an MSU assistant professor of psychology, first met Blackfeet Community College (BCC) students through Agnieszka Rynda-Apple, Ph.D., an MSU assistant professor of microbiology and immunology who already had a working relationship with the Blackfeet community. For about a year, Drs. John-Henderson and Rynda-Apple visited BCC interns and faculty supervisor Betty Henderson-Matthews monthly to help them interpret data collected for a student-developed project. While completing this project on the link between stress and health on the Blackfeet reservation, the researchers developed relationships with the students and faculty. They listened closely to the students’ stories, experiences, and career aspirations.

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All About Grants: Basics 101

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Note to our Biomedical Beat readers: Echoing the sentiments NIH Director Francis Collins made on his blog, NIGMS is making every effort during the COVID-19 pandemic to keep supporting the best and most powerful science. In that spirit, we’ll continue to bring you stories across a wide range of NIGMS topics. We hope these posts offer a respite from the coronavirus news when needed.

A female scientist in a lab using a pipette. Scientific research requires many resources, which all require funding.
Credit: Michele Vaughan.

Scientific inspiration often strikes unexpectedly. The Greek mathematician and inventor Archimedes first thought of the principles of volume while taking a bath. Otto Loewi designed an important experiment on nerve cells based on a dream involving frog hearts.

But going from an initial moment of inspiration to a final answer can be a long and complex process. Scientific research requires many resources, including laboratory equipment, research organisms, and scientists’ time. And all of this requires funding. Government grants support the majority of research in the United States, and the main source of these grants for biomedical researchers is the National Institutes of Health (NIH). NIH is the primary federal agency for conducting and supporting basic, clinical, and translational medical research. It investigates the causes, treatments, and cures for both common and rare diseases.

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Crowdsourcing Science: Using Competition to Drive Creativity

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Six student researchers sitting around a table and collaborating on a project. Credit: iStock.

Historically, crowdsourcing has played an important role in certain fields of scientific research. Wildlife biologists often rely on members of the public to monitor animal populations. Using backyard telescopes, amateur astronomers provide images and measurements that lead to important discoveries about the universe. And many meteorologists use data collected by citizen scientists to study weather conditions and patterns.

Now, thanks largely to advances in computing, researchers in computational biology and data science are harnessing the power of the masses and making discoveries that provide valuable insights into human health.

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PECASE Honoree Elizabeth Nance Highlights the Importance of Collaboration in Nanotechnology

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Black and white microscopic image of a capillary supplying blood to brain cells. A network of capillaries supplies brain cells with nutrients. Tight seals in their walls keep blood toxins—and many beneficial drugs—out of the brain. Credit: Dan Ferber, PLOS Biol 2007 Jun; (5)6:E169. CC by 2.5 Link to external web site.

The blood-brain barrier—the ultra-tight seal in the walls of the brain’s capillaries—is an important part of the body’s defense system. It keeps invaders and other toxins from entering the human brain by screening out dangerous molecules. But the intricate workings of this extremely effective barrier also make it challenging to design therapeutics that would help us. And as it turns out, getting a drug across the blood-brain barrier is only half the battle. Once it’s across, the drug needs to effectively target the right cells in the brain tissue. With this in mind, it’s no surprise that challenges this complex are solved through collaboration among scientists from several different specialties.

Elizabeth Nance Link to external web site, an assistant professor of chemical engineering at the University of Washington in Seattle and a recent recipient of the Presidential Early Career Award for Scientists and Engineers (PECASE), focuses her research on understanding the barriers in the brain and other cell- and tissue-based barriers in the body to see how nanoparticles interact with them. Her lab uses nanoparticles to package therapies that will treat newborn brain injury, which can occur when the brain loses oxygen and blood flow, often during or immediately prior to delivery. This damage can lead to cerebral palsy, developmental delays, or sometimes death. Early interventions for newborn brain injury can be valuable, but they need to target specific, injured cells without harming healthy ones.

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