View of a wooden deck with forest behind it.

Summer 2020 outlook

Summer 2020 is…. here. This year has been unpredictable at best, but some things have stayed the same. For example, summer is one of my favorite seasons in which to work in science, because things calm down when the university is not in full session and I’m not facing a deluge of emails, meetings, and myriad small interactions that accumulate to eat up the day. I’ve been taking the time to prepare my laboratory, dive deep into scientific writing, and prepare for the increased teaching load I will have starting this fall.

Manuscripts

You might think that the pandemic causing months of delayed or reduced labwork would have lightened my research load, but I’ve had more than enough to keep me occupied over this spring. Not only have I been submitting a few manuscripts for peer review at scientific journals from my time at the University of Oregon and Montana State University, but I have been working on some unanticipated manuscripts that coalesced this spring. This has included a project with a previous collaborator on diet and health, another based on soil microbial ecology led by master’s student Tindall Ouverson at MSU, and three more which were generated during my DNA sequence data analysis course that I taught this spring! Of these, I am lead author on two and contributing to the others at a variety of depths. Some require a great deal of my time, while others require only editing and review.

Students

And then there were 10! I now have three University of Maine master’s students and 4 undergraduate students performing research in my lab, as well as three other graduate students from other labs who are affiliated with us (as in, I am on their committee). In addition to training them on scientific research theory, laboratory protocols, and data management and analysis, they are getting general training in scientific literature review and critique, scientific writing and presentation, and laboratory management.

Lab space renovations

I am preparing the second of two laboratory spaces for my research, and this space hasn’t been fully renovated in years. While still very functional, there have been a number of remodeling, refinishing, and reorganization steps which needed to be taken to get it in line for biosafety level II microbiology work.

I have been doing much of this work personally, because it’s cheaper, and I have experience in basic home renovations. And, I enjoy the opportunity to put my email inbox away and let my thoughts wander to scientific theory while I use power tools.

When it is ready, I’ll be starting the wet-lab research into gut microbiology and doing more culture work to supplement the genomics work. To aid in that research, I’ve been acquiring more nifty bits of equipment.

Course materials development

Over the spring, I piloted a new course as a special topics version, and I have just been approved to teach that as an official course starting in spring 2021! This summer, I have and will continue to revise my teaching materials from the spring version to prepare them for AVS 454-554 next year.

I’ll be teaching two courses starting in fall 2020, one on animal microbiomes and one on undergraduate research for animal science students. AVS 254, on animal microbiomes, is material I have taught at other institutions with a different course focus. For that course, I will be updating the course material, adding new lectures from scratch, and revising the formatting of powerpoints. I’ll also need to make some of it more accessible for asynchronous online learning, depending on how the semester is organized this fall. This means pre-recording the lectures, and putting more effort into the online learning software I have available.

The other course I am teaching is new to me, AVS 401 (and 402 each spring), the AVS Capstone experience. I’ll be teaching students how to write scientific proposals, research papers, and give scientific presentations, as well as guiding them through participation in research along with faculty mentors. For many students, it’ll be their first experience participating in research. This year, since many students are unable to participate in in-person research and labs have been closed, it’ll be extra challenging to come up with projects, but I have some creative ideas in mind.

Works in development

In addition the above objectives, I have a number of things in development which are not yet ready to be shared in detail. These includes new research collaborations, leading a team to organize a journal special collection, and leading a team to organize and host a (virtual) mini conference meeting in the fall!

Faculty positions and summer work

Now, as an assistant professor at the University of Maine, I’m on a 9-month contract. During the academic year, I devote 50% of my time to research-related activities, and 50% to teaching/advising/mentoring– related activities. I have the option of working in the summer, or taking it off unpaid. However, my summer salary is contingent on me being awarded research funds which will pay for the work, something which is not guaranteed in this funding climate. It is generally not advisable for pre-tenure faculty to spend summers idle, and in any case, I would inevitably have to perform work of some kind over the summer to keep pace with my workload.

I am lucky enough to have start-up funding which can pay up to 2 months of summer salary per year during my first 3 years; however, I am expensive: one month of my summer salary is the equivalent of 1 full-time undergraduate researcher for 3 months, or a sizable chunk of a research project. On the one hand, I want to value my time and effort, and being paid for summer research helps close the gender pay gap for salary and retirement contributions. On the other hand, I am also forced to consider how to get work done on a reduced budget, should federal funding not come through. After all, being awarded tenure is contingent on productivity.

In May, I was adamant about taking the entire month of July off, as 2019 and 2020 have been incredulously busy and stressful and I haven’t had a vacation since Feb 2019. Now, at the end of June, I’m not sure I could take off a full summer month and still output all of the above, plus be prepared for the challenges of teaching this fall. At least my working-from-home view is more or less a vacation-scape, and some surprise home renovations will at least keep me away from electronic screens for some of it.

DNA double helix with dollar signs as a nucleotide.

Extrava-grant-za!

Today a large-scale federal grant proposal was submitted, bringing me to four proposals submitted so far in 2020 (and eight total in the 2019/2020 academic year)! I have one more that is planned for the end of May, and two more that may be submitted this summer depending on the disposition of my pending proposals. Each of these proposals takes weeks to months of planning, writing, and coordination between the research team. The proposal submitted today was 107 pages, and only some of those materials can be re-used between grants, such as descriptions of equipment and research facilities.

A stack of papers facedown on a table.
So. many. supporting documents.

The success rate for obtaining federal funding for your project varies by agency, year, and category of project/principal investigator, nicely tracked here (updated Dec 2019), and currently ranges from 8 – 30%. For example, “pilot” project (small projects to “seed” your long-term research), student-specific, or “new investigator” grants may have a higher rate of success because their applicant pool is restricted by eligibility. Competition is fierce, especially when federal agency budgets are cut or re appropriated.

If projects are not funded, they are returned with reviews from typically 2 – 4 experts in the field who provide comments and recommendations for strengthening the experimental design, or the presentation of the project itself. You might think that proposals are judged on the merit of the science alone, but the ability of the team to manage the project, and the research team, is also being evaluated. Principal investigators (researchers like me, leading the project) need to show that we have good ideas and the organizational skills to implement them, especially if the project spans multiple years or institutions.

Submitting a research proposal is worth celebrating – it represents weeks of effort – but especially during this time when we are all trying to keep our head above water, never mind accelerate or productivity. It’s important to take a few minutes to relax, work can wait, because ‘the grind’ will be there waiting for you when you get back.

Tour of the Baker Lighting Lab

For the past two months, I’ve been spending quite a bit of time writing grant proposals.  In particular; those which expand our understanding of indoor lighting on human health and behavior, the indoor microbiome, and energy usage in buildings.  These project proposals are collaborative efforts between several University of Oregon research labs: Biology and the Built Environment Center, Energy Studies and Buildings Laboratory, and the Baker Lighting Lab.  I’ll have more updates in the next few months as those are reviewed.

Siobhan “Shevy” Rockcastle, Chair of the Baker Lighting Lab, and I have been brainstorming ideas, and today I went over to the Baker Lab to check it out in person.  The Lab is decorated with concept-design lighting projects from previous students, which are not only beautiful, but extremely creative.  Here are a few of my favorites!

This slideshow requires JavaScript.

 

 

 

What I do for a living Part 5: The Indoor Microbiome

Last June, I started a position as a Research Assistant Professor of Microbial Ecology at the Biology and the Built Environment Center at the University of Oregon.  The BioBE Center is a collaborative, interdisciplinary research team investigating the built environment – the ecosystem that humans have created for themselves in buildings, vehicles, roadways, cities, etc.  With my background in host-associated microbiology, I am concerned with how the built environment interacts with biology.

dog_mud_print

Humans shed microorganisms constantly – every itch, every cough, every minute.  In fact, our buildings are littered with the biological material shed from our bodies and our microbiomes (1, 2, 3, 4).  Pets (1, 2) and plants (1, 2) also contribute, and so does outdoor air (1, 2).  In fact, the indoor environment is full of microorganisms.

 

In addition to knowing how our presence, our behaviors (ex. cleaning), and how we run our buildings (ex. ventilation) creates the indoor microbiome, I want to know how the indoor microbiome affects us back.  Not only can “sick buildings” negatively affect air quality, but they can harbor more microorganisms, especially fungi, or pathogenic species which are detrimental to our health.

My first indoor microbiome data is one that I have inherited from an ongoing project on weatherization in homes, and hope to present some of that work at conferences this summer.  Since June, a large amount of my time has gone into project development and grant writing, most of which is still pending, so stay tuned for details.  It has involved read lots of articles, going to seminars, networking, and brainstorming with some brilliant researchers.

As research faculty, I am not required to teach, although I have the option to propose and teach courses by adjusting my percent effort (I would use the teaching salary to “buy back” some research salary).  As I am not currently tenure-track, I am also limited in my ability to hire and formally mentor students.  However, I have been teaching bioinformatics to a student who recently graduated with his bachelor’s and is pursuing a masters in bioinformatics later this year.

I’ve also been keeping up with my science outreach.  I gave a presentation on my host-associated microbiome work, I marched, I volunteered for a few hours at Meet A Scientist day at the Eugene Science Center, and I’m hosting a Science Pub on “A crash course in the microbiome of the digestive tract” at Whirled Pies in Eugene this Thursday, February 8th!

 

 

Draft twice, submit once: the grant writing process

Today, the research team that I am a part of submitted a grant which I co-wrote with Dr. Tim Seipel, along with Dr. Fabian Menalled, Dr. Pat Carr, and Dr. Zach Miller. We submitted to the Organic Transitions Program (ORG) through the US Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA).  The culmination of months of work, and some 12+ hour days this past week to meet today’s deadline, this grant will hopefully fund some very exciting work in agriculture!

Research relies on grant money to fund projects, regardless of the type of institution performing the research, though commercial research centers may partially self-fund projects.  Most new research hires to universities will receive a “start-up package” which includes some funding for a few years to buy equipment, pay for a small, preliminary project, or temporarily hire a technician. Start-up funds are designed to hold a researcher over for a year or two until they may apply for and receive grant funding of their own.  Sooner or later, everyone in academia writes a grant.

startup
Cartoon Credit

Grants may be available for application on a regular basis throughout the year, but some grant calls are specific to a topic and are made annually.  These have one submission date during the year, and a large number of federal grants are due during in the first quarter of the year, a.k.a. Grant Season.  University researchers find themselves incredibly pressed for time from January to March and will hole up in their office for days at a time to write complex grants.  Despite the intention of starting your writing early, and taking the time to thoroughly discuss your project design with all your co-PDs well before you start writing to avoid having to rewrite it all again, most researchers can attest that these 20-30 pages grants can get written over from scratch 2 or 3 times, even before going through a dozen rounds of group editing.

The Bright Idea

Most large grants, providing several hundred thousand to over a million in funding over several years, require project teams with multiple primary researchers (called Principal Investigators or Project Directors) to oversee various aspects of research, in addition to other personnel (students, technicians, subcontractors).  One researcher may conceptualize the project and approach other researchers (usually people they have worked with in the past, or new hires) to join the project.  Project ideas may get mulled over for several years before they mature into full grant submissions, or go through multiple versions and submissions before they are perfected.

The grant I just co-wrote investigates the use of cover crops in Montana grain production.  Briefly, cover crops are plant species which improve the soil quality but which you aren’t necessarily intending to eat or sell.  They are grown in fields before or after the cash crop (ex. wheat) has been grown and harvested.  Legumes like peas, beans, or alfalfa, are a popular choice because they fix nitrogen from its gaseous form in the atmosphere into a solid form in soil which other plants (like wheat) can use.  Other popular cover crop plants are great at bio-remediation of contaminated soils, like those in the mustard family (1, 2, 3). Planting cover crops in an otherwise empty (fallow) field can out-compete weeds that may grow up later in the year, and they can prevent soil erosion from being blown or washed away (taking the nutrients with it).  For our project, we wanted to know how different cover crop species affect the soil microbial diversity, reduce weeds, put nutrients back into soil, and improve the production of our crop.

We designed this project in conjunction with the Montana Organic Association, the Organic Advisory and Research Council, and Montana organic wheat farmers who wanted research done on specific cover crops that they might use, in order to create a portfolio of cover crops that each farmer could use in specific situations.  As these organizations comprise producers from across the state, our research team was able to get perspective on which cover crops are being used already, what growing conditions they will and won’t work in (as much of Montana is extremely dry), and what production challenges growers face inherent to planting, managing, and harvesting different plant types.

Drafting Your Team

When you assemble a research team, you want to choose Project Directors who have different experiences and focuses and who will oversee different parts of the project.  A well-crafted research team can bring their respective expertise to bear in designing a large and multi-faceted project.  For our grant, I am the co-PD representing the microbial ecology and plant-microbe interaction facet, about a third of the scope of the grant.  We will also be investigating these interactions under field settings, which requires a crop production and agroecology background, as well as expanding the MSU field days to include organic-specific workshops and webinars, which requires an extension specialty.

Because grant project teams are made up of researchers with their own projects and goals, in addition to providing valuable perspective they may also change the scope or design of your project.  This can be extremely beneficial early on in the grant-writing phase, especially as you may not have considered the limitations of your study, or your goals are too unambitious or too lofty.  For example, the cover crop species you want to test may not grow well under dry Montana conditions, do you have a back-up plan?  However, as the submission deadline looms larger, changing the focus of your study can cost you precious writing time.  Working in a research team requires a high degree of organization, a flair for communication, and an ability to work flexibly with others.

Identifying the research question

scienceeducation
Image Credit

All grants center around a Project Narrative, and funding agencies will provide detailed instructions on how to format your project grant.  Pay strict attention- in very competitive pools your grant can be flagged or rejected for not having the appropriate file names or section headers.  The Narrative gives introductory background on your topic that details the research that has previously been published.  Ideally, it also includes related studies that you and your team have published, and/or preliminary data from projects you are still working on.  The aim is to provide a reasoned argument that you have correctly identified a problem, and that your project will fill in the knowledge gaps to work towards a solution.  Grant panels are made up of researchers in a related field, but they may not be intimately aware of your type of research.  So, you need to be very specific in explaining  your reasoning for doing this study.  If your justification seems weak, your project may be designated as “low priority” work and won’t get funded.

In our case, cover crops have been used by farmers already, but not much basic research has been done on the impacts of picking one species over another to plant.  Thus, when cover crops fail, it may be unclear if it was because of unfavorable weather, because the previous crop influenced the soil in ways which were detrimental to your new crop, because you seeded your crop too sparsely and weeds were able to sneak in and out-compete, because you seeded too densely and your crop was competing with itself, or something else entirely.

You also need to identify the specific benefits of your project.  Will you answer questions? Will you create a new product for research or commercial use?  Will organic producers be able to use what you have learned to improve their farm production?  Will you teach students?  When you are identifying a need for knowledge and describing who or what will benefit from this study, you need to identify “stakeholders”.  These are people who are interested in your work, not people who are directly financially invested.  For us, our stakeholders are organic wheat farmers in Montana and the Northern Great Plains who want to integrate cover crops into their farming as an organic and sustainable way to improve crops and reduce environmental impact.  Not only did our stakeholders directly inform our project design, but we will be working closely with them to host Field Day workshops, film informative webinars, and disseminate our results and recommendations to producers.

Crafting Your Experimental Plan

Once you have identified a problem or research question, you need to explain exactly how you will answer it.  For experiments in the laboratory or field, you need to be incredibly specific about your design.  How many samples will you take and when?  Will you have biological replicates?  Biological replicates are identical treatments on multiple individual organisms (like growing a single cover crop species in four different pots) to help you differentiate if the results you see are because of variation in how the individual grows or because of the treatment you used.  Do you have technical replicates?  Technical replication is when you analyze the same sample multiple times, like sequencing it twice to make sure that your technology creates reproducible results.  Will you collect samples which will provide the right type of information to answer your question?  Do your collection methods prevent sample deterioration, and how long will you keep your samples in case you need to repeat a test?

In addition to describing exactly what you will do, you need to explain what might go wrong and how you will deal with that.  This is called the Pitfalls and Limitations section.  Because basic research needs to be done in controlled environments, your study may be limited by a “laboratory effect”: plants grown in a greenhouse will develop differently than they will in a field.  Or, you might not be able to afford the gold-standard of data analysis (RNA sequencing of the transcriptome still costs hundreds of dollars per sample and we anticipate over 1,200 samples from this project) so you need to justify how other methods will still answer the question.

Supporting Documents

Even after explaining your research question in the Narrative and your design in the Methods sections, your grant-writing work is still far from complete.  You will need to list all of the Equipment and research Facilities currently available to you to prove that your team can physically perform the experiment.  If you will have graduate students, you need a Mentoring Plan to describe how the research team will train and develop the career of said student.  If you will be working with people outside of the research team, you will need Letters of Support to show that your collaborators are aware of the project and have agreed to work with you, or that you have involved your stakeholders and they support your work.  I was delighted by the enthusiasm shown towards this project by Montana organic producers and their willingness to write us letters of support with only a few days’ notice!  You’ll also need a detailed timeline and plan for disseminating your results to make sure that you can meet project goals and inform your stakeholders.

0619160801
Poster presentation at ASM 2016.

Perhaps the most difficult accessory document is the Budget, for which you must price out almost all the items you will be spending money on.  Salary, benefits (ex. health insurance), tuition assistance, travel to scientific conferences, journal publication costs, travel to your research locations, research materials (ex. seeds, collection tubes, gloves, etc.), cost to analyze samples (ex. cost of sequencing or soil nutrient chemical analysis) cost to produce webinars, and every other large item must be priced out for each year of the grant.  The Budget Narrative goes along with that, where you explain why you are requesting the dollar amount for each category and show that you have priced them out properly.  For large pieces of equipment, you may need to include quotes from companies, or for travel to scientific conferences you may need airline and hotel prices to justify the costs.

Begging
Cartoon Credit

On top of what you need to complete the study, called Direct Costs, you also need to request money for Indirect Costs.  This is overhead that is paid to the institution that you will be working at to pay for the electricity, water, heating, building space, building security, or other utilities that you will use, as well as for the administrative support staff at the institution. Since nearly all grants are submitted through an organization (like universities), instead of as an individual, the university will handle the money and do all the accounting for you. Indirect costs pay for vital research support, but they run between 10-44% of the dollar amount that you ask for depending on the type of grant and institution, potentially creating a hefty financial burden that dramatically reduces the available funding for the project.  On a $100,000 grant, you may find yourself paying $44,000 of that directly to the university.

comicnov9_2014_overhead
Cartoon Credit

Draft Twice, Submit Once

The Budget is by far the most difficult piece to put together, because the amount of money you have available for different experiments will determine how many, how large, and how intensive they are.  Often, specific methods or whole experiments are redesigned multiple times to fit within the financial constraints you have.  If you factor in the experimental design changes that all your co-PDs are making on the fly, having to balance the budget and reconstruct your narrative on an hourly basis to reflect these changes, and the knowledge that some grants only fund 6-8 projects a year and if you miss this opportunity you may not have future salary to continue working at your job, it’s easy to see why so many researchers find Grant Season to be extremely stressful.

Review_panel.JPG
Cartoon Credit

Featured Image Credit