Improving research mentor training requires new approaches.

Mentoring is essential for the success of researchers at all career stages, but not all mentor-mentee relationships are created equal. Students from historically underrepresented backgrounds often receive less mentoring than their peers, and many mentors are not trained in how to mentor effectively. To address some of these needs, Entering Mentoring, an evidence-based program for research mentor training, was developed and shown to be effective in improving mentoring. 

Of course, such programs are only useful if people have access to them. In CBE—Life Sciences Education, Spencer et al. report on the infrastructure they have created to facilitate more widespread research mentor training.

The first hurdle that must be cleared for more mentors to receive training is to have more people capable of giving the training. Therefore, the authors took a train-the-trainer approach and recruited and trained master facilitators to instruct others in how to implement research mentor training, termed facilitator training. This approach has resulted in nearly 600 people being trained as facilitators, with over 4,000 mentors receiving research mentor training.

In order to be broadly useful, training for mentors needs to be applicable in a variety of settings, including at different institutions and for researchers at multiple career stages. The original Entering Mentoring program was designed as a summer seminar for graduate students mentoring undergraduates, but it has been expanded for different research areas and for those mentoring everyone from undergraduates to junior faculty. Modules to address specific concerns, like culturally aware mentoring, have also been developed, and there are resources available for structuring the programs in a variety of formats.

Even though a person might be trained in facilitating research mentor training, actually running such workshops requires time, resources, and support, which are not always available. To help address these concerns, facilitator training workshops were restructured to include resources and strategies for overcoming obstacles to implementation, such as encouraging facilitators at the same or similar institutions to cooperatively plan.

As mentorship programs expand, quality control is necessary to ensure that workshops are productive and that resources are accessible. Therefore, assessment tools were developed for facilitators to evaluate workshops they run, and a centralized evaluation system was developed to more effectively make use of feedback.

By developing this infrastructure, better training will become more accessible for more mentors. Early results of self-reported surveys suggest that research mentor training is already being effectively implemented—ultimately helping make science more accessible and productive. 

CITATION:

Building a Sustainable National Infrastructure to Expand Research Mentor Training

Kimberly C. Spencer, Melissa McDaniels, Emily Utzerath, Jenna Griebel Rogers, Christine A. Sorkness, Pamela Asquith, Christine Pfund

CBE—Life Sciences Education Published Online: 28 Aug 2018

DOI: https://doi.org/10.1187/cbe.18-03-0034

Biology students who participated in a one-on-one homework activity with a classmate showed increased learning gains.

The huge sizes of many undergraduate science courses make it rare for a student to get valuable one-on-one interaction with a professor. Teaching assistants and student tutors can help with this problem, but an expert may not actually be required to help students attain deeper levels of understanding—simply engaging with the material with another person might be enough. In CBE-Life Sciences Education, Bailey et al. asked if a simple peer-tutoring homework assignment could help students in a general biology course learn the content.

The authors used two sections of an undergraduate biology class for non-majors. The experimental section was given peer-tutoring assignments in which two students would meet outside of class. One student, the “teacher,” instructed their peer based on a set of learning objectives. The other student, the “questioner,” asked the teacher questions about the material. After 15 minutes, the two students switched roles. These sessions were recorded, and the audio was sent to the instructors for credit. The control section was instructed to study the learning objectives on their own for 30 minutes in lieu of the peer-tutoring exercise.

Based on a preliminary assessment given at the beginning of class, the two sections were essentially equivalent in terms of starting scientific knowledge and interest. After the exercise, students in the section that completed the peer-review assignment performed better on all class tests, averaging 6% higher scores than their counterparts who studied alone.

Interestingly, the highest gains were seen for students who scored lowest on the preliminary assessment, suggesting that this peer-tutoring activity might be particularly effective for students starting out with less developed scientific skills. Additionally, students who asked more questions during the peer-review assignment were more likely to do well on the final exam.

Students in both sections were also given a survey on their perceptions of the peer-tutoring exercise, and they reported it being helpful. Students given the exercise consistently ranked it highly among the class activities that helped them learn, and students in the control section generally reported believing that being required to study with a peer would have been helpful to them. This shows that students are receptive to peer-tutoring exercises.

Although this study only reported on two sections of one class, the methods described are particularly useful to instructors due to their simplicity: the teacher/questioner peer-tutoring exercise does not take up class time, but it still gives students a chance to ask questions and verbally engage with class content. The authors conclude their paper with suggestions for instructors on implementing similar assignments in undergraduate classrooms.

CITATION:

Learning Gains from a Recurring “Teach and Question” Homework Assignment in a General Biology Course: Using Reciprocal Peer Tutoring Outside Class

E. G. Bailey, D. Baek, J. Meiling, C. Morris, N. Nelson, N. S. Rice, S. Rose, P. Stockdale

CBE-Life Sciences Education 11 May 2018; https://doi.org/10.1187/cbe.17-12-0259

https://www.lifescied.org/doi/full/10.1187/cbe.17-12-0259

You’ve probably encountered at least one diagram in a biology textbook that didn’t make any sense to you. Although these pictures are supposed to clarify ideas, sometimes they leave readers befuddled. This is a particular problem for students; experts looking at schematics are able to fall back on their knowledge of a subject, while novices cannot. To help students learn, textbook illustrations must be as clear as possible.

In a paper published in CBE-Life Sciences Education, Wright et al. examined the use of arrows in biological diagrams. They looked at two introductory textbooks and found a wide variety of arrow styles used—including fat, skinny, dashed, and curved—to convey many distinct meanings—like chemical reactions, movement, and energy transfer. They found that many arrow styles were used to represent different processes throughout the textbook, and often, arrow styles were used inconsistently within sections, or even within a single figure.

Could the inconsistent use of arrow styles be contributing to students’ confusion? The authors conducted surveys and interviews with undergraduates, concluding that, yes, students are often uncertain about the meanings of the arrows. They found that most arrow styles don’t have any intrinsic meaning to students, and while some individuals correctly make inferences from context, many end up being unnecessarily confused by the use of arrows.

This study highlights a common problem in life sciences education: ideas that seem intuitive for experts can be problematic for novices. For a professor who has been up to their neck in biology for decades, it can seem obvious that a “bouncing” arrow represents phosphorylation, but for students at the start of their education, it’s far from intuitive. The authors recommend that instructors take the time to work with students on increasing their visual literacy and discuss the common representations used in their fields to maximize understanding.

CITATION

Arrows in Biology: Lack of Clarity and Consistency Points to Confusion for Learners 

L. Kate Wright, Jordan J. Cardenas, Phyllis Liang, and Dina L. Newman

CBE Life Sci Educ March 2018 17:ar6; doi: 10.1187/cbe.17-04-0069

NIH’s National Institute of General Medical Sciences has announced that Alison Gammie will serve as the new director of its Division of Training, Workforce Development, and Diversity (TWD). The division supports a variety of research training, career development, and diversity-building activities from the undergraduate to the faculty levels.

Alison E. Gammie, PhD

With 1014 authors, an article by Leung et al. in the May issue of G3 has the largest author list of any paper published in the journal. More than 900 of those authors were undergraduate students when they performed the research.

Over several years, students at 63 higher education institutions across the US conducted an investigation far beyond the power of any individual lab. In so doing, this massive team not only advanced science, but gained valuable research skills and experience.

“By organizing the efforts of ‘massively parallel’ undergrads, we can solve problems that would defeat other methods,” says Genomics Education Partnership (GEP) program director Sarah Elgin. “At the same time, students learn how to handle the messiness of real data, to evaluate different kinds of evidence, and to justify their conclusions.”

The GEP is a large collaboration of college/university faculty coordinated from the Biology Department and The Genome Institute at Washington University in St. Louis. Their goals are to introduce bioinformatics into the undergraduate curriculum and to integrate research experience into the academic year. With this classroom-based approach, many more students can access educational opportunities normally restricted to a small number of summer research spots.

The project tackled by the GEP students was annotating and improving the sequence of the Muller F element of Drosophila fruit flies. The F element is so small that it looks like a compact “dot” alongside the other fruit fly chromosomes and is commonly called the “dot chromosome.”

Heterochromatin staining in Drosophila melanogaster chromosomes. The two dot chromosomes are visible at center. Image source: flybase.org

Intriguingly, the dot chromosome is entirely heterochromatic by many criteria, meaning that it’s made up of tightly packaged DNA, a state typically associated with repression of gene expression, low recombination rates, and regions that contain few genes. But despite being packed into heterochromatin, the dot chromosome in Drosophila is not an inert gene desert; indeed, a region stretching nearly a third the length of the chromosome (the distal 1.3 Mb) has around the same density of active genes as expected in euchromatic (i.e., non-heterochromatic) genome regions.

How has this unusual chromatin context affected the evolution of the dot chromosome? To investigate this question, the GEP team wanted to compare the dot chromosome to a euchromatic region from a different chromosome. But this exploration required high quality assembly and annotated sequence from several different Drosophila species, not just D. melanogaster, the species in which the dot chromosome has been most intensively studied.

The students used publicly available draft genome sequences for three Drosophila species, plus the high quality sequence of D. melanogaster, species separated by 40 million years of evolution. In the first stage of work, they corrected errors, such as misassembly, in the published sequences and requested additional sequencing reactions to cover gaps. “The students do a significantly better job at improving the sequence than the software does,” says Elgin. “Most programs get bogged down in the repeat sequences that are abundant on the dot chromosome.”

The students then took the improved sequence and used multiple types of evidence to annotate the start, stop, and splice sites for each gene. The evidence used by the students included conservation, expression data, and computational prediction based on sequence features.

“We think a lot of the educational benefit of the project comes from asking students to weigh the evidence; sometimes it’s contradictory, sometimes one clue is more reliable than another, sometimes the students need to dig a bit deeper,” says Elgin. “Basically we’re teaching them to look carefully at data and be suspicious, be skeptical.”

Each chunk of annotation was completed by at least two independent groups of students, allowing them to cross-check their findings and fix errors.

The end result was a high quality data set that allowed the team, led by GEP staff member Wilson Leung, to statistically compare the properties of the dot chromosome to the euchromatic comparison region in all four species.

This comparison revealed that most of the distinctive properties of the D. melanogaster dot chromosome are conserved across species — including genes with longer introns and more coding exons on average than the euchromatic comparison region, as well as a higher density of repeat sequences. The accumulated repeats — mostly remnants of now inactive transposable elements — can partly explain why dot chromosome genes have larger introns (the introns contain more repeats), though it doesn’t explain why the genes tend to have more coding exons.

Dot chromosome genes also showed less evidence for selection — in the form of codon bias — than the euchromatic comparison regions. This agrees with theoretical predictions that natural selection should be less effective where recombination rate is low, such as in heterochromatin. However, for D. grimshawi (a Hawaiian species that has been geographically isolated from the others), there is greater evidence for selection on dot chromosome codon bias, suggesting a higher rate of recombination than in the other species. D. grimshawi also has a lower transposon density on the dot chromosome, so the authors suggest that the density and types of transposons may affect the degree of local heterochromatin formation.

Unexpectedly, the authors found that the GC content (and therefore melting temperature) of both genes and their flanking regions is significantly lower in the dot chromosome than in the euchromatic comparison regions. Elgin says this is one of the findings from the project that she finds most fascinating, because she can’t yet explain it. “It drives me nuts!” she says. One possibility could be that the lower melting temperature enhances the transcription efficiency of genes trapped in a heterochromatic context. This might be one way that expression of dot chromosome genes is maintained at similar levels to genes from euchromatic contexts.

There are plenty more insights to be mined from the data, says Elgin. “At some point though we had to ask Wilson to stop analyzing data, because we had to start writing. One of our big goals was to publish a paper with the students as co-authors. We wanted them to be able to look themselves up on PubMed!”

Although the GEP faculty and staff wrote the article drafts, each of the 940 students listed as a co-authors had to read and approve the manuscript before submission. “Actually we got some important comments back from students,” says Elgin.

The GEP also measures the program’s educational performance. Research published last year in CBE-Life Sciences Education shows that not only do these students increase their knowledge of genes and genomes, they also report  gains in their ability to analyze data and understand the research process that are similar to students  who had performed a summer research project. Both types of learning gain — knowledge and understanding of research — were more striking when more class time was devoted to the project. Given enough time (on average, around 45 hours of class time), GEP student gains even exceeded those reported by students who had spent a summer in a research lab.

“Faculty are sometimes skeptical that this kind of project will work for their students. But the GEP includes a diverse range of schools serving different types of students, and the learning gains were similar across every category we tested. I believe any student can benefit,” says Elgin.

More students are benefiting as the GEP expands and takes on new research projects. Some of these students will continue in research careers — as Wilson Leung did after his own undergraduate research experience in a precursor to the GEP. Many other students will choose different paths, but will do so with a richer understanding of both genetics and the hard work of building new knowledge.

Citation: Leung, W. et al. (2015). Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution. G3: Genes| Genomes| Genetics 5(5):719-740 doi: 10.1534/g3.114.015966 http://www.g3journal.org/content/5/5/719.full