Nose Picking and Other Notes from the Microbiome Workshop

microbial_350x248Did you know that nose picking is useful to science? Indeed, the nasal passages have been mined, so to speak, for new insights into pathogens and the microbiome. You can now view the dirty details about this topic and many others related to the fascinating world of the microbiome on the NIMBioS YouTube channel, which now has the full line-up of talks from our recent popular Investigative Workshop: Computational Advances in Microbiome Research.

Forty-three of the top thought leaders in computational microbial community analysis techniques attended the workshop by invitation. In addition to those attending in real time, nearly 100 virtual participants viewed a live stream of the talks. A lively discussion took place on Twitter with the hashtag #CAMRws.

Workshop goals were to foster new ideas, accelerate the pace of biological discovery through dissemination of cross-disciplinary techniques, provide a starting point for new collaborations, and to identify gaps for future funding opportunities. The July 27-28 workshop was co-organized by by Jill Banfield of the University of California, Berkeley, and Curtis Huttenhower of Harvard University.

Full details about the workshop can be found at http://www.nimbios.org/workshops/WS_microbiome. More resources and discussions can be found on the workshop’s WordPress site at http://www.nimbios.org/wordpress-training/microbiome/

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Math and Biology Interface Meets Steampunk

Students show off their labeled axis, ready for data

Students at STEMPunk show off their labeled axis, ready to graph some bird population data.

Science and math educators are always looking for innovative ways to make their messages memorable  — which is why NIMBioS participated in a unique outreach event for middle school kids this week blending STEM and the science fiction genre “steampunk.”

Andrew Isenhower talks to students about what their graph shows is happening to Northern Bobwhite populations in Tennessee

Andrew Isenhower talks to students about what their graph shows is happening to Northern Bobwhite populations in Tennessee

Organized by UT engineering graduate student Caroline Bryson, the “STEMPunk” event had a festival atmosphere where students visited hands-on booths to interact with scientists, engineers and mathematicians, all in steampunk-themed costume. Steampunk is a science fiction genre that features steam-powered technology with 19th century style elements. About 35 students from all over the state, on campus for an engineering camp, participated in the event with their camp counselors and families.

Nels Johnson (center) helps students interpret their Eastern Bluebird population graph.

NIMBioS postdoctoral fellow Nels Johnson (center) helps students interpret their Eastern Bluebird population graph.

NIMBioS’ booth “Math for the Birds” featured data about changing bird populations found in the previously published Discover Birds activity book. Andrew Isenhower, a UT graduate student in wildlife and fishery biology, collaborated and brought teaching specimens to display of Eastern Bluebirds, Northern Bobwhites, and a Wild Turkey tail fan and feet. After Andrew’s introduction to the birds Kelly Sturner, NIMBioS Education & Outreach Coordinator, introduced Breeding Bird Survey data for the three species. Suzanne Lenhart, NIMBioS Associate Director for Education & Outreach, and Nels Johnson, NIMBioS postdoctoral fellow, then joined in helping the students graph the data on enormous graphs on the floor. The axis were created using duct tape. Axis labels were arranged by the students and data points graphed. Then, data points were connected using a feather boa to show trends.

After a discussion of what the graphs showed was happening to bird populations over time, Andrew provided insight behind the patterns the students observed by talking about the challenges the species have faced due to land use changes, decreasing habitat, competition with invasive species, and also the benefits that some conservation efforts have had.

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Prepare to Collaborate! Here’s How to Do It Well

What does it take to run a successful collaborative meeting? As a NIMBioS participant or organizer of an activity, you will meet and work with scientists from a variety of fields. Cross-disciplinary research can produce exciting results, but it also presents unique communication challenges.

The following is excerpted from the introductory talk by Simon Kahan at the recent NIMBioS Investigative Workshop: Many-cell System Modeling. Kahan, a research scientist at the Northwest Institute for Advanced Computing, co-organized the three-day workshop. We share it here with permission from Kahan in hopes this model for effective collaboration may prove useful to you as a participant or organizer.

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“A Preparatory Model for Collaboration”

When we meet, we will become a system of professionals with diverse expertise and a shared purpose, seated around a table, eager to collaborate. NIMBioS has made this possible, generously providing the necessary funding and facilities. We hope to make the most of this opportunity by advancing our purpose to the best of our abilities and by creating new directions or ideas that are more significant to the community than would be the additive sum of our typical individual contributions over three days. We do not yet know what that looks like. We have never before worked as this group. We will have only limited time together: time insufficient for the “forming, norming, storming, performing” phases of group development, perhaps insufficient even to remember the names of the other group members. Our hopes are therefore tempered by practical constraints.

To compensate somewhat, we can prepare ourselves. We can prepare by contemplating two roles each of us may take on during our meeting:

First, each of us may have a unique role as a participant. As a participant, we each will contribute our professional (subject) expertise. Expression of our ideas will induce others to respond and to build upon them. Through this process, we hope to create a shared understanding of what is, what challenges we face, and what actions are needed to further our purpose. Preparing to take on the role of participant means reviewing the purpose of the meeting, bringing to mind what we can contribute.

Second, each of us may take on a facilitative role. As a facilitator, we each have the opportunity to intervene in the system, adjusting the functioning of the group toward greater efficiency, as I will describe shortly. Some have described taking on concurrent roles of participant and facilitator as being “simultaneously on the dance floor and on the balcony [overlooking the dance floor].” Maintaining both perspectives is a difficult skill to master. Were we to select a person to facilitate only, we would likely lose their contribution as participant, and we would be challenged to identify enough participants with strong facilitation skills when in subgroups. Instead, we share responsibility for facilitation. We will each occasionally check-in from “the balcony” and then return to “the dance floor.” This choice sidesteps the need for an experienced facilitator. There is a large body of literature on collaboration, groups, and facilitation. More pragmatic than expecting group members to prepare by reading the literature is to present, as part of the meeting introduction, the following simple model for collaboration and corresponding interventions. It takes about ten minutes.

The Essential Components of Collaboration are illustrated in the figure below. These components are Task, Process, and Relationship, all of which manifest to some degree in every group member. The degree depends upon personality and circumstance.

The Essential Components of Collaboration

The Essential Components of Collaboration

Task is about getting things done. Group members for whom Task is key will feel satisfied when choices are made, actions are taken, and boxes are checked off. When those members are dissatisfied, they become impatient and may behave in ways that seem careless toward other group members. However, in the absence of Task, little is completed.

Process is about how the group structures its work. Group members for whom Process is key will feel most satisfied when the agenda is explicit, objectives are clearly stated, and time apportionments are respected. When these members are dissatisfied, they may demand that the group slow down or they may withdraw from participation altogether. The group may perceive them to be perfectionists. Without Process, the group risks wasting effort by solving the wrong problem or running out of time altogether due to mismanagement.

Relationship is about engaging all participants. Group members for whom Relationship is key will feel most satisfied when every group member appears engaged and satisfied. When these members are dissatisfied, they may become anxious and behave in ways that seem overly sensitive. Without Relationship, the benefit of collaboration will be suboptimal because group members’ expertise will not be fully used.

When all three components are in balance, we collaborate most effectively. That balance and the expertise required to pursue the group’s purpose is all that is needed to advance our shared purpose: no dedicated facilitator is required. For this reason, preparing to maintain balance of Relationship, Task, and Process is a worthwhile investment. Maintenance of balance is a skill requiring repeated effort to master, so having multiple group members intentionally exercising the skill is crucial.

Keeping this model in mind guides facilitation when checking-in on “the dance floor” from “the balcony.” We look for any three of the dysfunctions that indicate imbalance and intervene accordingly.

If our self or someone else seems impatient with progress, we can intervene on behalf of Task. An appropriate intervention requires creativity in response to the situation. Drawing attention toward ending the current phase of the process may address Task dysfunction. An example might be to suggest, “What other ideas are there? <pause> We seem to have collected all ideas, let’s vote!” Providing an impatient group member with something to do that serves this phase of the process serves both to address the dysfunction and provide relief to that group member: “Alex, would you be willing to write down the ideas as we all suggest them?”

If we notice a lack of direction, we can intervene on behalf of Process. Very often groups forgo Process in favor of discussion, leading to wandering. A reasonable intervention on behalf of Process that is never too early is, “Before we go any further, what is our agenda?” Even with agenda in place, groups wander. A direct intervention is appropriate and effective: “Wait! I think we are straying from the point.”

If we notice participation is imbalanced, Relationship may be an issue. However, the cause might just as well be differences in expertise in the particular topic or in engagement style (see below). What we aim to ensure is that those who have something to contribute, do contribute. We might then serve Relationship by intervening, “We haven’t heard from you for awhile: what are your thoughts?” Or, perhaps to someone who is going on at length, “Excuse me, we need to give others a chance to contribute, too.” Intervening on behalf of Relationship can be most socially awkward, but failure to do so risks suboptimal results.

Component Dysfunction Intervention
Task Stagnation

 

“What other ideas are there? <pause> We seem to have collected all ideas, let’s vote!”
“I volunteer to write down the ideas as you suggest them.”
Process Wandering

 

“Before we go further, what is our agenda?”
“I think we are straying from the point.”
Relationship Inequity “We haven’t heard from you: what are your thoughts?”
“Excuse me, we need to give others a chance to contribute, too.”

Regarding engagement style, some people can think creatively only when they are not listening. To ensure we include their contribution, we must have quiet times within the collaborative process. During those times, the process should entail individual thought and writing; simply asking participants to spend a minute writing down their ideas prior to brainstorming can facilitate increased contribution from introverts.

In summary, effective collaboration depends upon balance amongst its three components: Task, Process, and Relationship. That balance is rarely sustained without facilitative interventions. We can partially compensate for the absence of a professional facilitator by preparing our group members to occasionally step out onto “the balcony” to observe and intervene in “the dance floor” in an effort to restore balance. Even when few members do intervene, the mere awareness of the others may increase their receptivity, resulting in a smoother, more productive collaboration.

Ideas presented here are both a simplification and a synthesis of concepts in a larger body of work on group dynamics and collaboration. The particular R-P-T model resulted from experiences working with other students in cohort 17 of the Organization Systems Renewal program offered at Seattle University in 2010-12. The program is now offered through Pinchot University.

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NIMBioS also has a few tips to offer. The following web pages provide detailed instructions for how to conduct a successful Working Group and Investigative Workshop. Each page describes what Working Group organizers and Workshop organizers should do beforeduring, and after meetings to make them successful.

We are always looking for new research to support! If you are interested in requesting support for a new Working Group or Workshop, the next deadline is September 1. All areas of research at the interface of biology and mathematics will be considered, but we are especially interested in activities expanding beyond the areas of research supported to date. Potential organizers of activities in areas of molecular biology, cell biology, network biology, immunology and systems biology are particularly encouraged to submit requests. For more information about how to submit your proposal, click here.

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NIMBioS Staff, Postdocs & Graduate Students Give Middle School Girls STEM Adventures!

Highlights from last week's Adventures in STEM Camp

Highlights from last week’s Adventures in STEM Camp

Sixteen middle school girls enjoyed a fun and exciting week of STEM (Science, Technology, Engineering and Mathematics) adventures last week during a day camp organized and hosted by NIMBioS and the engineering center at the University of Tennessee called CURENT.

Girls toured NIMBioS and designed and printed 3D models of real flowers. They explored the world of mathematical modeling through activities such as acting out a predator-prey-resource model in a game called “Oh Deer!” and exploring a similar model in Netlogo in the computer lab.

NIMBioS graduate fellows Ben Levy and Christine Dumoulin and NIMBioS postdoctoral fellow Caroline Farrior assisted throughout the week. The girls interviewed Farrior about her science career as well as interviewing NIMBioS postdoctoral fellows Sandy Kawano and Angie Peace, NIMBioS Associate Director for Education & Outreach Suzanne Lenhart, and NIMBioS Web Analyst Jane Comiskey.

A field trip to the American Museum of Science and Energy in Oak Ridge, TN was included followed by a tour of the University of Tennessee Veterinary School and hospital. CURENT provided many activities for the girls about electricity and renewable energy including building solar car and windmill models. The week concluded with the girls presenting to their families all the knowledge they acquired in the week, as well as the posters that they created of themselves in their dream STEM careers.

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Congratulations to Paul Armsworth!

Paul Armsworth NIMBioS Associate Director for Postdoctoral Activities

Paul Armsworth
NIMBioS Associate Director for Postdoctoral Activities

Congratulations are in order for Paul Armsworth who has been named a James R. Cox Professor at the University of Tennessee, Knoxville. Armsworth is NIMBioS Associate Director for Postdoctoral Activities.

An associate professor in ecology and evolutionary biology, Armsworth has been affiliated with NIMBioS as one its senior personnel since 2009 when he was hired as an NIMBioS-affiliated faculty member at UT.

The three-year Cox award will provide Armsworth with a stipend of $25,500 to support his research, which integrates mathematical modeling, statistical analyses, and field surveys. Cox recipients are chosen by a committee for their excellence in teaching, scholarship, and service.

Armsworth follows in the footsteps of another NIMBioS leader who earned the honor, namely NIMBioS Director Emeritus Louis Gross. Gross used the award to help fund the NIMBioS Songwriter-in-Residence program. Cox was interested in environmental issues and music.

Previously, Armsworth was a lecturer in Population and Community Ecology at the University of Sheffield. He received a B.A. in Mathematics from Oxford University in 1996, a Ph.D. in Mathematics from James Cook University, Australia, in 2000, and a Ph.D. in Biological Sciences from Stanford University in 2003.

To read the UT press release announcing the award, visit http://tntoday.utk.edu/2015/07/08/university-honors-ecologist-paul-armsworth-cox-professorship/

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Testing the Waters: Summer Research Good Preparation

Ginny, Diya, Talon, Mariel and Ryan - just a few of our creative SRE students.

Ginny, Diya, Talon, Mariel and Ryan – just a few of our creative SRE students

The NIMBioS Summer Research Experiences for Undergraduates and Teachers (SRE) program helps prepare its participants for all the pressures and learning pleasures of graduate school, say a number of our SRE students.

NIMBioS interviewed a participant from each of this year’s five SRE projects, and several commented on how the program has solidified their desire to attend graduate school. While the participants experience eight intense weeks of research and modeling at NIMBioS, they also commended the program for all the fun they’re having alongside the learning.

Mariel Bedell

Mariel Bedell

Mariel Bedell, a pre-med major at Carnegie Mellon University, is a member of the SRE team modeling the distribution of fluid pressures in the kidney. Bedell said the SRE research has truly extended her learning well beyond the classroom. “I realized that research is very influential and inspiring to a student of any level. It is a great learning experience, far different and more encompassing than that of taking a class,” she said.

Talon Johnson

Talon Johnson

For Talon Johnson, a math major at Morehouse College, the SRE program has helped him focus on attending graduate school. Johnson is a member of the SRE team exploring the stressors in the host-pathogen interaction. He said the most valuable experience has been coding and programming in R, collaborating with others from different fields of study, and learning how to delve deep into research articles.

Parkman_sre2015_200x266

Virginia Parkman

As a dog lover, Virginia Parkman, a math major at the University of Tennessee, Knoxville, was very excited to learn that she would be studying canine distemper and applying the research to helping a local animal shelter. “This research could potentially save hundreds of dogs’ lives. With our model, we could potentially show a shelter how to protect their dogs from getting distemper and from spreading the disease,” she said.

Diya Sashidhar

Diya Sashidhar

For Diya Sashidhar, a math major at North Carolina State University, one of the best parts of the SRE program has been collaborating with students from different fields to solve a common problem. “Sometimes, modeling can be frustrating. However, with group members come different ideas and perspectives, allowing us to progress and eventually overcome our problems,” she said. Sashidhar’s project is to develop mathematical models to understand the body’s immune response to tuberculosis.

Ryan Yan

Ryan Yan

Ryan Yan, a math major at the College of William and Mary and member of the SRE project studying invasive species movements through shipping routes, summed up the NIMBioS SRE nicely: “I think as a young researcher, there’s truly no better way to become immersed in your field than in a place like NIMBioS.”

To read the full profiles and learn more about NIMBioS SRE, visit http://www.nimbios.org/sre/sre_profiles2015.

 

 

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NIMBioS Evaluation Services Now Available

NIMBioS uses a systems-based model for evaluation. The CIPP approach considers the organization as a whole, assessing the quality and significance of outcomes while still examining the inputs and processes that lead to these outcomes.

NIMBioS uses a systems-based approach for evaluation, one that considers the organization as a whole, assessing the quality and significance of outcomes while also examining the inputs and processes.

NIMBioS is pleased to now offer its considerable experience and expertise in providing external evaluation services to the STEM research and education sector, with a particular emphasis on interdisciplinary programs. Under the guidance of Pamela Bishop (Ph.D., Evaluation, Statistics, and Measurement), NIMBioS Evaluation Services provides independent, rigorous and transparent formative and summative evaluation services targeted to the unique goals of the program under evaluation.

Dr. Pamela Bishop NIMBioS Evaluation Manager

Dr. Pamela Bishop
NIMBioS Evaluation Manager

With expertise in evaluation theory, design and implementation, the NIMBioS evaluation team is capable of evaluating large-scale projects to optimize decision-making and to untangle the complexity of program dynamics in order to understand how and why the project works (or doesn’t work) for whom.

NIMBioS carries out extensive evaluations of the variety of activities it supports, which has led to peer-reviewed publications on the methods used at NIMBioS to foster interdisciplinary research and education. NIMBioS uses a systems-based approach to program evaluation of center-scale effectiveness, with particular emphasis on assessing the impacts of NIMBioS in developing cross-disciplinary collaborations and research. More than 150 systematic evaluations of NIMBioS activities and events have been conducted.

You can read more about NIMBioS Evaluation Services at http://www.nimbios.org/about/evaluation

NIMBioS also provides all of its evaluation reports online. Read our evaluation reports from all NIMBioS activities, including Working Group meetings, Investigative Workshops, Tutorials, and Education and Outreach Events.

To explore your options for evaluation with NIMBioS Evaluation Services, contact Pamela Bishop at (865) 974-9348) or pambishop@nimbios.org

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Fireflies, Farms, Food: NIMBioS SRE 2015 Underway!

The 2015 SRE's at Great Smoky Mountains National Park

The 2015 SRE’s at Great Smoky Mountains National Park

The 2015 NIMBioS Summer Research Experpience (SRE) for undergraduates and teachers just wrapped up its third whirlwind week. Already participants have gone on the annual pilgrimage to see the synchronous fireflies in Great Smoky Mountains National Park, eaten yummy food at welcome parties and barbecues, and taken part in tutorials on programming, mathematical modeling in life sciences, 3D printing and more. All have gotten off to a great start on their research projects. The eight week program is sure to go by too fast!

SRE's at the welcome party, for many of them their first night in Knoxville!

SRE’s at the welcome party, for many of them their first night in Knoxville.

The Invasive Species group meets with their mentors.

The Invasive Species group meets with their mentors.

The host-pathogen and tuberculosis SRE groups tour a local dairy farm to learn about how cattle are managed to prevent the spread of infectious diseases.

The Host-Pathogen and Tuberculosis SRE groups tour a local dairy farm to learn about how cattle are managed to prevent the spread of infectious diseases.

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Productive Working Group Leads to Special Issue

MAP Working Group, Meeting 4. (L to R): Vitaly Ganusov, Maia Martcheva, Gesham Magombedze, Eiichi Momotani, Yrjö Gröhn , Shigetoshi Eda, Yoram Louzoun, Srindand Sreevatsan, Don Klinkenberg, Suzanne Lenhart, Ad Koets, Ynte Schukken.

MAP Working Group, Meeting 4. (L to R): Vitaly Ganusov, Maia Martcheva, Gesham Magombedze, Eiichi Momotani, Yrjö Gröhn, Shigetoshi Eda, Yoram Louzoun, Srindand Sreevatsan, Don Klinkenberg, Suzanne Lenhart, Ad Koets, Ynte Schukken

The Within-host Modeling of MAP Infection Working Group has had an extremely productive few years and its work has paid off in a dedicated special issue this month of the journal Veterinary Research. Ten of the twelve papers in the issue were produced by the Working Group.

The Working Group on MAP, which stands for Mycobacterium avium subsp. paratuberculosis, held its first meeting at NIMBioS in June 2012 and wrapped up after the fourth meeting in July last year. The group comprises 16 members from diverse fields, including mathematics, statistics, epidemiology, immunology, microbiology and optimal control and is co-organized by Ynte H. Schukken, Cornell Univ.; Ad Koets, Utrecht Univ.; Srinand Sreevatsan, Univ. of Minnesota; Maia Martcheva, Univ. of Florida; and Shigetoshi Eda, Univ. of Tennessee, Knoxville.

The Working Group was established following a successful Investigative Workshop on the topic held in the summer of 2011. The chief objective of the Working Group was to develop a within-host MAP infection model, using observational data on infection patterns and within-host immune response data. Ultimately, the model aimed to provide an understanding of the progression of and mitigation strategies for Johne’s disease in ruminants, which is caused by intestinal infection of the bacterial pathogen MAP. JD causes reduction of milk production, weight loss, and premature culling of clinically affected animals. JD has been found in more than two-thirds of US dairy herds and causes the US dairy industry an estimated annual loss of hundred millions of dollars.

The special issue of Veterinary Research published this month is a compilation of work that explores and connects MAP dynamics at multiple levels.

Congratulations to this hard-working and productive Group!

If you are interested in seeking support for your research and would like to propose a Working Group or Investigative Workshop, the next deadline for support is September 1. Full details on what categories of support NIMBioS provides as well as proposal information can be found at http://www.nimbios.org/research/

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NIMBioS Welcomes New Researchers

(From left) Nels Johnson, Megan Rua, Quentin Johnson

(From left) Nels Johnson, Megan Rúa, Quentin Johnson

We’re excited to announce our new postdoctoral and sabbatical fellows who will bring their research to NIMBioS this summer and fall.

New postdoctoral fellows include:

Nels Johnson joins NIMBioS in June following a postdoctoral fellowship at Colorado State Univ. where he has been focused on the Great Plains Methane project investigating communities of methane consuming soil bacteria. At NIMBioS, Johnson will develop new, flexible community models for addressing the impact that diversity and community structure have on ecosystem function and for better understanding the biodiversity of communities across environmental gradients and traits.

Quentin Johnson joins NIMBioS in August after completing his Ph.D. in Life Science/Genome Science and Technology at the Univ. of Tennessee, Knoxville. His project centers on developing a high-throughput mathematical and computational model to identify allostery and the mechanism by which the allosteric signal is initiated and propagated in the peroxisome proliferator-activated receptor and retinoid X receptor complex, which are proteins involved in preventing growth of cancer cells.

Megan Rúa is currently an NSF postdoctoral research fellow in biology at the Univ. of Mississippi where she is conducting a 1200 seedling experiment. Starting in August, her research at NIMBioS will focus on using selective source analysis (SSA) to estimate selection due to interspecific interactions and other sources and will also involve employing meta-analysis in conjunction with SSA to examine these relationships across a broad array of hosts and their mycorrhiza.

New sabbatical fellows are as follows:

Charles Price, an assistant professor of plant biology at the Univ. of Western Australia, will work on a project to understand the physical drivers of allometric patterns in trees. Price begins his fellowship in June.

Richard Schugart, an assistant professor of mathematics at Western Kentucky Univ., begins his fellowship in August to investigate optimal treatment protocols for a bacterial infection of a wound using oxygen therapy.

And joining NIMBioS in February 2016 as a sabbatical fellow is Glenn Ledder, a professor of mathematics at the Univ. of Nebraska-Lincoln, whose project involves dynamic energy budget modeling and multi-component systems.

The next deadline for applying for a postdoctoral fellowship and a sabbatical fellowship is September 1.

 

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