Author: sueishaqlab

I'm an assistant professor of animal and veterinary studies at the University of Maine, Orono, studying how animals get their microbes. I am also the Founder and Lead of the Microbes and Social Equity working group.
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Reflecting on “suggested deadlines” for assignments

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Over the Fall 2020 semester, I changed my assignment deadline policy, creating “suggested deadlines” instead of enforced ones. I altered the language to “suggested deadline” in my syllabus semester timeline (in which I provide due dates for all assignments), I left submission portals open in the online teaching software, and I did not manually penalize grades for lateness. I made the change out of practicality for the fall semester, and I was personally pleased by the results; however, I wanted to hear from students. After being able to formally obtain student feedback during course evaluations, I wanted to reflect on that change and how I will implement it in future courses.

Previously, when grading policies were up to me, I accepted late assignments with a possible -10% grade penalty reduction per day, although I would waive it for a variety of circumstances. It was easy to enforce using online teaching software which timestamped submissions. This policy seemed to motivate some students, but in retrospect, it made students feel like they had to share their reasons for lateness and justify why they needed an extension. Not only did this late assignment policy increase the number of emails I received and time spent replying that yes, I would still accept it, but it also meant that students were sharing more personal information with me. I suspect that students who did not ask for deadline extensions probably had a reason but didn’t want to share than information in asking for an extension, and really, it is none of my business what else is going on in their life.

However, I made the decision to allow any assignments to be turned in after the due date without a penalty, in part because the pandemic shifted the amount and type of work most students were doing. Many of them reported an increased workload, having to attend remote classes in their car, trouble with internet access with so many other users on their network, and of course, power and internet outages are common in Maine when trees topple utility lines. If I had enforced assignment deadlines, then a third to a half of my students were in danger of failing the course because of lack of work, but not because of poor quality of work. This was unreasonable to me, especially in my undergraduate research course where I would be effectively be penalizing students for delays caused by their research mentors or haled research on campus.

So, I made the decision to trust my students to manage their own motivations and time management. After all, they are legal adults, they are not first years, and they have chosen to continue their education despite the financial burden and other constraints. More than that, almost all of my graded assignments with significant weight in the class are essay based, which means I can get a feel for the students’ writing voice and it is really easy to identify plagiarism by the change in tone or maturity of the writing. If being able to turn in an assignment late meant students’ could copy each other’s assignments, I should be able to catch it even without the online plagiarism checking software.

I was concerned that I would receive all the assignments on the very last day, and was dreading the avalanche of grading that would unleash on me. Instead, assignments trickled in on a regular basis, several hours to several months late depending on the students’ circumstances, some of which were later disclosed to me. Instead of getting sloppy, thrown-together assignments, I think the quality of writing and the depth of student critical thinking were improved. Students later reported being able to spend more time on the assignment when they had control over when that time could be spent. And, despite having the most students in the most difficult semester to get through, I discovered no instances of plagiarism.

I think I will make the move to suggested deadlines semi-permanent (some deadlines will be enforced based on if it is time-sensitive). The online teaching software I use can be set to assign a 0 to missing assignments, to email me when submissions are received, and to add conditions to submission portals, such as having first submitted another assignment or having received feedback on a previous assignment (like a previous draft of a paper). I can schedule automatic email reminders about assignments, email only students who are missing assignments, and students can check their grades and assignment lists online at any time. Not only does this dramatically reduce the time I spend chasing after assignments, but it gives students more agency in being able to participate in the class on their own time.

Certainly not every class can be structured this way or allow for flexible deadlines. But, I think a lot of them could be, and I think in most cases it would improve student engagement and learning outcomes. Below, you can find the comments on my two fall course evaluations, and you can check out my previous posts on curricula development or my teaching statements.

For much of the fall semester, assignment deadlines were open ended. Do you think keeping open ended deadlines (as in, you turn in things when they are ready but [not] on a specific date) next year would make this class better? Do you think you would be able to keep up with assignments without deadlines? Or do you think the deadlines help keep you on track?

My question from the course evaluations for this fall

Comments

  • I think the soft deadlines kept me in check, however it’s nice to know that if things unexpectedly get crazy for me that I won’t be penalized for taking extra time to make sure that I submit quality work.
  • I very much appreciated the flexibility in deadlines for this class as many other classes ramp up at the end of the semester. I felt as though I could control my workload with the assignments set up like this, and would recommend keeping the deadlines as suggestions to where you should be up to date in the course, but the actual submission deadline remains later in the semester.
  • You could do once a month check ins or something to verify nobody is completely slacking off. Maybe have three major deadlines to force people to keep up – one at the end of October, end of November and then the final submission?
  • The deadlines really helped keep me on track. Dr. Sue Ishaq was more than lenient with due dates and the work load, so I do not think anyone would have an excuse to not do well in this course (although this was really helpful with the troubling times humanity is facing). I think being more strict would be more fair to her as a professor and would help students not take advantage of being able to put things off and not learn the material.
  • I think the open ended deadlines was really helpful. It allowed me to put the time in when I could rather than rushing to get it done and turned in for the due date.
  • I appreciated having the due dates so I could try to get stuff in at a reasonable time but also that the deadlines were flexible so if something came up I wouldn’t turn in something I wasn’t happy with. I had a different class with no deadlines and it was horrible, I need the structure to be there but to also have the leniency for when things aren’t going well.
  • In this new quarantined world, the open deadlines were essential to academic success. While I didn’t struggle in this class necessarily, I did struggle in chemistry, pre calculus and lab with out the aid of study groups, math labs, and lab partners. Having open dead lines in this course not only affected my academic success in this course, but it also snow balled in a positive way and helped my GPA overall.
  • I think open ended deadlines with a suggested deadline would be the most helpful, because it will reduce the stress of deadlines, and allow for leeway in the case of multiple courses having work do on the same day, but it also gives a time frame around when the work should be done
  • The lack of deadlines required self–discipline but also removed the daunting aspect of the due date, which I often find myself deterred by and ultimately more likely to put off the work. I felt that the assignments were more inviting this way.
  • I think that this semester it was very beneficial to have the open ended deadlines. For me personally, I prefer to have deadlines to keep me on track, but I appreciate the flexibility of the open–ended deadlines.
  • I think having the open ended, suggestive deadlines made for a much easier semester. It took off a lot of stress to know that I could have an extra day if needed. Sometimes we get peaks in the semester where we’re slammed with work and knowing that if I needed an extra day or two to complete an assignment was really reassuring.
  • Thank you for being understanding on deadlines as this semester has been crazy, although the soft deadlines kept me on track without penalizing me for taking extra time if needed.
  • I think ended open deadlines do help due to things become crazier as the whole covid thing continues
  • I feel that open ended deadlines next year would make this class better because due to recent events in the world it is sometimes difficult communicating with project mentors. By having open ended deadlines, I know when it is supposed to be due, but if I am missing some information from someone on the project I do not worry as much about getting in trouble for handing it in late.
  • yes this is hard to juggle long term projects with weekly class deadlines. So open ended is the best for this class.
  • I believe the structure of fall semester deadlines was great.
  • I feel like open ended deadlines are very helpful because you would be able create better quality work with your research. I feel like I would be about to keep up with work without deadlines or just create the deadline for the end of the semester and put reminders.
  • I think a more strict set of deadlines could’ve been helpful as far as tracking progress. Exceptions could still be made for those struggling on a topic, or who are unable to start for some reason out of their control.
  • This semester, while everyone has been adjusting to the new way of pandemic life, the open ended deadlines were extremely helpful and stress relieving.
  • yes I think there should be soft deadlines, there is a date that it should be done but we didn’t have to have it done by then
  • Having a general guideline about when things should be turned in has been helpful, but keeping the deadlines open ended has relieved a lot of stress and has enabled me to produce better work because I was not rushed.
  • The deadlines kept me on track and having no deadlines would have me just turn everything in at the end which is bad.
  • I liked the deadlines. I would have kept all the work till the last minute if we didn’t. However, the open ended deadlines meant that even if you were behind, you wouldn’t be penalized which really helped.
  • I think open ended deadlines are a great idea because it allowed me to not feel pressured to submit something that I did not feel was ready. Without that stress, I was able to submit all of my assignments on time with the open ended deadline and not during the later one, which was helpful!

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Watch the Microbes and Social Equity seminar from Feb 17th

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Extended Health

Dr. Joshua August (Gus) Skorburg, PhD

February 17, 2021, 12:00 – 13:00 EST. 

Watch the recording.

About the speaker: Dr. Joshua August (Gus) Skorburg is Assistant Professor of Philosophy, Academic Co-Director of the Centre for Advancing Responsible and Ethical Artificial Intelligence (CARE-AI), and Faculty Affiliate at the One Health Institute at the University of Guelph in Ontario, Canada. He is also Adjunct Professor in the Fuqua School of Business at Duke University. He received his PhD in Philosophy in 2017 from the University of Oregon. His research spans topics in applied ethics and moral psychology.  

https://www.uoguelph.ca/arts/people/joshua-august-gus-skorburg

About the seminar:  Dominant views about the nature of health and disease tend to assume the existence of a fixed, stable, individual organism as the bearer of health and disease states, and as such, the appropriate target of medical therapy and ethical concern. However, recent developments in microbial biology, neuroscience, and social and personality psychology have produced a novel understanding of the individual and its fluid boundaries. Drawing on converging evidence from these disciplines, I will argue that certain features of our biological and social environment can be so tightly integrated as to constitute a unit of care extending beyond the intuitive boundaries of skin and skull. Call this the Hypothesis of Extended Health (HEH). Using the example of obesity as a case study, I show how HEH is well positioned to accommodate recent research on both the human microbiome and relationship partners. I conclude by suggesting that HEH helps us to break free from unhelpful dichotomous thinking about obesity – between individual behaviours (e.g., restraint, diet, exercise) or constraining socio-economic structures (e.g., food deserts, advertising).

About the series: Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic, medical, or political constraints that restrict available choices that may impact our health.   

Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. This speaker series explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field.  The spring speaker series will pave the way for a symposium on “Microbes, Social Equity, and Rural Health” in summer 2021.

Watch the Microbes and Social Equity seminar from Feb 10th

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An Indigenous Micro- to Meta-Narrative: Microbes and Social Equity

Dr. Nicole Redvers, ND, MPH

February 10, 2021, 12:00 – 13:00 EST. 

Watch the recording.

About the seminar: Indigenous Peoples have scientific narratives and traditions that span thousands of years rooted within concepts of relationship. The microbial microcosm itself is a lens of relationship that situates us as humans within our own communities and in the biome of the planet. How these relationships intersect and how we view them as an evolution of knowledge in theory and practice impacts how we view equity and its applications in the scientific process. This seminar will seek to bridge Indigenous knowledge traditions and scientific discourse with the intent of situating microbes and social equity within a larger relationship within research and practice.

About the series: Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic, medical, or political constraints that restrict available choices that may impact our health.   

Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. This speaker series explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field.  The spring speaker series will pave the way for a symposium on “Microbes, Social Equity, and Rural Health” in summer 2021.

Microbes and Social Equity at UMaine

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Last week, I chatted about Microbes and Social Equity with Ali Tobey, Marketing and Communications Graduate Assistant for the Office of the Vice President for Research and Dean of the Graduate School at the University of Maine. The MSE working group has been meeting for a year to discuss how microorganisms are what connects us to each other or to the environment, how microbes are involved in so much of human health, how disparities in access to basic needs can affect your health and your microbes, and how social policy can be used to resolve social inequity and improve health for all.

This spring, the MSE group and the University of Maine Institute of Medicine are hosting a semester-long speaker series. The talks range from basic to applied science, from research to education to medical practice, and touch on a variety of topics. The series is free, and open to the public, but registration is required.

The full list of speaker and registration links for the Microbes and Social Equity spring 2021 speaker series can be found here, and Ali’s piece is below:

Ishaq links gut health to social equity, advocates for policy discussion
Reblog of the story by Ali Tobey, University of Maine

Of mice and many samples

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The first mouse study of the Ishaq Lab (in conjunction with the Zhang and Li labs at Husson University) has concluded phase 1, which means that over a few short days, an incredible number of samples needed to be collected, preserved, and processed for further laboratory work (phase 2) which will take through the summer to complete.

Sample collection was made more challenging by the pandemic, because we needed to distance as much as possible, disinfect objects and surfaces, wear masks, and increase the amount of ventilation in a space. Luckily, this type of work lends itself to these types of precautions – not only did we already need to wear a significant amount of protective gear to work with mice or handle their feces, but biosafety work like this requires higher than usual ventilation and frequent sanitation of objects and spaces. Since some of this work could be performed simultaneously in different rooms, we were able to use both Ishaq lab spaces and the ‘mouse house’ to keep people distanced.

During the 40-day mouse study, ‘Team Broccoli’ collected:

  • 640 mouse body weight data measurements
  • 433 fecal samples, which were archived for possible culturing and/or sequencing
  • 400 additional samples collected over two days:
    • 40 blood samples for immune factor identification
    • 360 gut samples
      • Of which, 200 were PMA treated within 12 hours of collection for use in DNA sequencing
      • 160 of which will be cultured to isolate bacteria. This will create 1 ~ 8 isolates per sample that will need to be grown on its own plate, transferred to broth media, and then frozen with glycerol at -80C until they can be revived and studied later this year.
Stacks of petri dishes filled with culture media. The stacks are inside of a vinyl anaerobic chamber, for use with bacterial culturing.
A messy laboratory bench showing dozens of jars, bottles, and graduated cylinders, all of various sizes.
Three small, white, cardboard boxes on a black laboratory bench. The lids are off, revealing about 200 small tubes with sample names written on the lids.
Joe Balkan, performing culturing of bacteria at the anaerobic chamber. Joe is wearing a face mask, and is holding up a culture plate. There are stacks of petri dishes inside the chamber.
A person holding a mouse in a research facility. The person is wearing a hairnet, nitrile gloves, a surgical mask, and a surgical gown. The mouse with dark brown fur is sitting on the top of the person's hand. In the background, there are metal shelves with bins and containers of research supplies.
Person in a research facility holding up their arm with a mouse on it. Person is wearing a hairnet, nitrile gloves, surgical mask, and a surgical gown. They are holding their left arm up to the camera to show off a mouse with dark brown fur sitting on their arm. In the background is a metal shelf with containers of research materials.

How to choose a graduate program in STEM

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I frequently receive requests for advice on choosing graduate programs, or to work in my lab, and have conversations with graduates who are struggling with program, department, or university policies which they were not aware of when they began. I decided to put those thoughts and conversations in one place, to create a non-exhaustive list of advice and considerations for choosing a graduate program. This will mostly be applicable to STEM programs, but some aspects will be universal.

Some of this will be discouraging, because graduate school is not a thing to be entered into lightly. But, I also believe that anyone can participate in science, and that many times when people think they couldn’t succeed in science, it’s not because they aren’t good enough, it’s more of a problem with an environment that selects for just one type of researcher.

Define your goal.

What do you want to do with your career and why do you need to go to graduate school to accomplish this?

I spend more time talking people out of graduate school, or into a lesser commitment, than I spend convincing people to go to graduate school, because there is an inflated sense of the need and prestige of having a graduate degree. And, many people assume they need a degree, or the highest degree available, to get the job they want.

When I was in 6th grade, I decided I was going to be a veterinarian because I wanted to help animals, and I refused to consider other career paths which felt like a lesser calling. Three weeks into my undergraduate degree in animal science, I realized that the reality of being a veterinarian is very different from its portrayal, and it wasn’t what I wanted at all. I had only thought I wanted it because I had gotten a very limited exposure to career choices prior to going to college. I see the same mistake with people considering, or in, graduate school. I don’t mean to disparage having a veterinary or graduate degree, I just mean that the way they are portrayed to prospective students is not always accurate. Do your homework before committing to those career paths.

More than that, when you receive career advice or look into career paths, the advice tends to focus on the highlights or major types of jobs and ignore the nuance of interdisciplinary or support-level careers. Not only does this mean that everyone in animal science thinks they can only be a veterinarian or a professor to be in the field, but the way that careers are portrayed makes students think that the only suitable use of their time, and justification for massive financial burden of higher education they incur, is to go for the career with the highest prestige – whether they want that or not. Unfortunately, when students realize they don’t have the grades and the accolades to make it into the career with the most prestige, which also has the most strict entry requirements, it means students are more likely to give up entirely, consider leaving their degree unfinished, and feel guilt or shame for having failed. But here’s something no one tells you up front: choosing a different job doesn’t mean you failed to be the boss, it means you chose a different job. A veterinary technician isn’t a failed veterinarian, and a laboratory technician isn’t a failed researcher, they are performing different functions in a setting which requires collaboration from various job types.

So, I’ll ask you again, like I ask all prospective graduate students: what do you want do with your life, and do you need graduate school to get you there? This question helps you focus on creating stepwise objectives to meet your goals. Maybe you need a specific degree, or a degree in a specific field, or don’t actually need a degree at all, maybe you need an internship or professional training, and those might require a specific order to the events. Do you want to travel for work or not? Do you want to have clear definition of your job responsibilities, or the flexibility to determine your own to-do list? Do you want to be at the bench, in the field, or at the keyboard and to be doing the research, or do you want to be writing proposals and papers, and administrating the research and the lab personnel? And, do you actually want to work alone or are you alright in a social environment? Spoiler alert, most jobs in science actually require daily socialization, communication, and presentation.

All of these aspects will determine the particulars of what you need out of a graduate program and the type of degree you get. It’ll also help you in the future when you need to decide if you have met your grad school goal and are ready to move to the next phase of your life.

You can probably outline your personal goals and constraints, but defining your professional goals will take some homework. I’ve previously described the academic ladder, with descriptions of responsibilities of students, post-doctoral researchers, adjuncts and researchers, and tenure-track faculty. I have also compiled some “science journeys” into a video. Professional research blogs can be a good way to learn about life in academia, although keep in mind many labs only post about their successes and not about their failures. You can also connect with faculty on campus, and most labs will take on undergraduate (or even high school) students to participate in research. If you aren’t sure if you would be interested in research, you can ask to shadow researchers in the lab, attend a few lab meetings, or otherwise participate in a voluntary and commitment-free capacity. There are also plenty of research opportunities off campus, as well.

Volunteering for Adventurers and Conservationists for Science, collecting water samples to look for microplastics.

Define your limits.

Graduate programs can be demanding, and you may need to relocate to find the topic, project, and mentor who is right for you. Before you start applying everywhere and racking up application fees, think about your constraints, your limits, and what would be a “deal-breaker” for you. Defining your limits (especially if you have a lot of them) will feel like you are writing yourself out of the possibility of finding a graduate program that works for you. In reality, it will help you find an institution that matches your life better and will help you focus on what is really important to you. You don’t have to erase all other aspects of your life in order to be a scientist.

Often, you feel pressured to give up everything to go to graduate school or other professional degree programs. The perception is that because there are fewer available positions than applicants that you need to underbid everyone else and give up everything, essentially that you need to recruit the graduate program. You assume you have to relocate and out of your own pocket, you need to put family on hold, you need give up job benefits, and you will have to work all the time.

I’ve moved over 7,000 miles for academic jobs.

Some of that may be true, and you should think about what you are able to manage and what you can’t live without. Some of that is just perception cast by work-a-holic culture and you will be able to reject or negotiate aspects. Think of your list of limits as conditions your employer might need to meet in order to convince you to take the position.

Narrow down your interests.

What do you want to do day after day, failure after failure?

If you start to make a list of things you are interested in science and you start writing down all the cool things you saw on social media – stop right there. Science is cool, but most of the time is cool in retrospect after the work has been completed and narrative added in. Science is arduous, iterative, and requires a lot of process improvement and reflection, and that takes time and focus. You need to be able to work on the same thing day after day and maintain interest even if everything you do seems to fail everyday. Especially when you are trying to develop technical skills and analytical skills, you need to be able to focus and dive deep into your topic, and you can’t be distracted by every little thing you think is cool, otherwise you will never get anything done.

You don’t need to commit to your research interest for life, and you don’t need to have an incredibly narrow scope to your interests, but you should be able to identify a common theme or the aspect that draws you in. Which topic makes you ask “yes, and?” over and over. What cool science story made you look for a second similar story, and then a third?

Search for a program.

There are a few different types of graduate degrees available, and each have nuances about the requirements to get in, requirements to graduate, cost to you, salary and benefits to you, and approach for application and acceptance into the program. I recommend looking into programs first, to find a location and institution that best meets your personal and professional goals and limits, and then trying to find a mentor. Don’t underestimate the importance of geographic location, and the environmental and social climate you will find there. You might need to be close to family, or find a location with a job or program for a partner. And if you are used to sun, several years of overcast winters might lose their novelty.

Most people apply to multiple programs and it can take time to find the right match. If you end up applying to multiple programs at a single institution, you can ask them to waive additional application fees, something that is commonly done but not commonly advertised.

Masters of Professional Studies are designed to give you familiarity with research and build skills. MPS is not thesis-based and requires research participation but not your own research project, so it is often used for people who will be in research-adjacent jobs. Students are admitted to programs based on their GPA, exam, or other numeric qualifications, and during their first semester have to identify a research mentor and two other committee members to guide their curricula and career development. MPS students pay for their own tuition, and most program/university policies stipulate that they are not allowed salary for their research, although they usually can be paid summer research salary. MPS students are eligible for teaching assistantships, but few, if any research assistantships. Because you are categorized as students and not employees, you do not receive health insurance or other fringe benefits, but you are eligible for student health insurance plans. MPS are completed in 2 years, but can be completed over longer periods of time to accommodate working professionals.

Master of Science programs are thesis-based, and require research study in a project you co-lead. Applications may be accepted year-round or according to deadlines, depending on the program. Master’s programs are designed to last 2 -3 years (credit hour requirements make it almost impossible to accomplish in fewer than two years), and beware mentors or projects which assign you a PhD-level amount of work to accomplish in just two years. Finding funding for master’s programs can be tricky, as many universities prioritize PhD students in order to boost their Carnegie research rating, but master’s programs are needed for training the majoring of the research workforce. Typically, you are paid a salary for your master’s, including partial coverage of your health insurance, and full coverage of your tuition. Most programs do not cover full health insurance, or semester fees, both of which can cost a thousand dollars of more in each of the spring and fall semesters, but you might be able to negotiate these to be paid by your advisor. You are considered both a student and an employee, but most university policies make graduate students ineligible for university-based or even individual-based pre-tax retirement savings programs for employees, although you can configure a post-tax retirement savings plan on your own.

Doctorate of Science programs are dissertation-based and requires that you (more or less) lead a research study and have contributed significantly to the theory behind its design, or theory behind its analysis and interpretation. PhD programs are designed to take about 5 years in the US (3 years in many other countries which don’t require coursework). Credit hour requirements make it almost impossible to accomplish in fewer than 4 years in the US, and PhD time can vary between 4 – 9 years, depending on the research and other circumstances. Applications are accepted year-round for direct-to-lab admissions (see below), and once or twice a year to be considered for lab-rotation-based fellowships.

Thesis-based science programs have two paths to admission, which is not always common knowledge. You will always have to apply to the graduate college of a university and meet the qualifications set by the university, as well as the program/department. After passing initial qualification checks, the graduate school will forward applications to the department to review, and it is this step that offers two paths.

If graduate programs have a collective fund to support students (teaching or research assistantships), they might accept a certain number of students as a cohort based on their qualifications. The top number of applicants will have some sort of recruitment event in which you are shown the facilities, have a chance to talk to students and faculty, and are interviewed by the program admission committee. Applicants who are admitted as a cohort have salary provided for the first 1 – 2 years as they take classes and rotate through different research labs. At the end of rotations, you match with a lab that has money to continue funding your salary and your research. Most programs will not accept so many students to the cohort that they will be unable to find them funding to continue their graduate work.

However, because thesis-based study is a funded position, you might apply to a department as a “direct admission”. This means that you have already matched with an advisor during prior conversations, the advisor has already looked through your application, and that the advisor and the department have informally agreed to offer you a position. But, this method is entirely dependent on that advisor having funding to pay your salary, tuition, and your research costs. You need to start the conversation with a possible mentor 6 months or more before you want to begin, unless you are applying to an advertised position in their lab. Finding research funding takes 6 – 18 months because of the slow pace of federal funding review and allocation, so if your advisor needs to find funding it will take planing ahead of time. Direct admission can happen on a rolling basis, but you will still need to apply to, and meet the qualifications of, the graduate college. Because of the unpredictable nature of the funding, you can defer a direct admission offer for a year, as needed.

Interviewing and searching for a mentor.

Whether you are applying as part of a cohort or a direct admission, you will have some sort of interview. It might be a series of informal conversations with potential advisors, or a formal interview with a program admission committee. When you are going into a graduate program interview, it feels daunting, and it’s not until you advance your career enough to be on the interviewer side that you realize it is supposed to be a conversation and not a test.

The graduate interview is not really about proving your qualifications because you have already met that hurdle with your application. The interview is to match students to mentors, and to confirm your interest in research. By having conversations and interacting in real time (whether in person or via electronic chat), interviewers can assess your communication skills, and get a better idea of your goals and interests.

The graduate advising relationship is quite different from what you might have experienced with previous instructors or undergraduate advisors, so it’s important that your personal and professional goals line up with those of your advisor. It really helps if you actually get along. You’ll be working together for several years during your degree, and will maintain a mentoring relationship for a good portion of your early career after you graduate. As a member of their lab, you’ll be performing a lot of their research and representing them at conferences and other venues during presentations, collaborations, or future work. It’s important to your career and theirs that you are able to work well together.

Therefore, during your grad school interviews you should remember that you are interviewing them, as well. The interview is an opportunity for your future advisor and institution to impress you and convince you to take a position with them. This is your chance to ask them about the projects you might be doing, where former lab members are now, their expectations of you, and more. Many federal funding proposals require a detailed mentoring plan, so advisors already have an idea what your professional development might look like. Importantly, get an idea about the lab culture. Some advisors feel you should work nights and weekends and during all breaks, others feel that your contributions belong to the lab and you might not have as much access to your own intellectual property than you think. And, not every lab has made a commitment to equity and inclusion. Here’s the policy for the Ishaq Lab.

It’s also a great time to ask grad program coordinators about university policy, departmental expectations, and financial support opportunities which might affect you. Does the program provide some or all financial support for health insurance, tuition, salary, and student fees? If not, what opportunities are in place to secure these? Are you able to switch mentors if there is a professional or personal mismatch? Is childcare available for graduate students? What about time off for maternity leave, and is this paid or unpaid? Family or medical leave? What if you need to take a semester or a year off, can you get back into the program and would you lose your funding? How many papers will you need to publish, or scientific presentations to give, and will there be financial support for those costly endeavors? While no one would ask you to pay publication fees out of pocket, I have heard of researchers refusing to financially support grad student travel to conferences, despite many departments requiring students to present in order to obtain their graduate degree. Travel to scientific conferences can run to several thousand in travel and participation costs per trip, and one trip to a national-level conference could cost an entire month’s graduate student salary.

Adopt healthy habits.

If everything comes together and you’ve been accepted into a graduate program that works for you, congratulations!! I wish you the best on the next step of your journey. If you are looking for more advice for once you get there, check out my previous posts, including preparing yourself before you start by adopting good habits for organization and work-life balance.

A close-up picture of petri dishes containing a light yellow film of microbes.

2020 Year In Review

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As has become a New Year’s Eve tradition, here is the Ishaq Lab’s Year in Review for 2020! In previous years, I remarked on difficult and delightful times alike, but 2020 has been a year full of intense loss for so many, and some have unfairly borne more of that heavy weight. In reflecting on whether to go ahead with the post for this year, I chose to do so and to include a tone of optimism and hope because, for the first time in the Ishaq Lab, I am not writing the story of me, I am writing the story of we. Even though we couldn’t all be together this year, the Ishaq Lab has tried to do our best to stay connected, and I have had the pleasure of watching my new lab team work together and grow as scientists. I am proud of how they have handled this year, and I wanted to share their triumphs.

Research

2020 was the year for launching the first official projects of the Ishaq Lab, including a field project, a mouse project, and a handful of data analysis or microbial community projects.

A screenshot from a virtual lab meeting, featuring 5 women.

Early in the year, students began joining the lab, and we had our very first lab meeting, featuring Adwoa Dankwa (UM Perry lab), Alex Fahey (in the office with me), Tindall Ouverson (MSU, Menalled/Seipel lab), and Johanna Holman. Ironically, we had our first lab meeting over Zoom to facilitate students in multiple geographic areas, not suspecting we would only have virtual lab meetings this year.

The first field project was a literal one – a soil project! Because of the pandemic response in the spring and early summer, laboratory work was reduced until we could do so safely in enclosed spaces. But, we were able to launch a field project because the samples could be collected and processed by one person alone over the summer. Undergrad Nick Hershbine, who is majoring in Ecology and Environmental Sciences, has been investigating the microbial community in blueberry soil from farms around Maine. This is part of a larger project led by Dr. Lily Calderwood, and is supported by the  Wild Blueberry Commission of Maine (“Exploration of Soil Microbiota in Wild Blueberry Soils“). Nick is in the process of data analysis and interpretation, and we hope to write up the preliminary results over the winter.

The Ishaq Lab also launched its first mouse project! This is my first time managing mice, and luckily I have expert collaborators at Husson University and a stellar grad student taking the lead on those portions. I’ll be overseeing the microbial ecology aspects, done by master’s student Johanna Holman for her graduate work. Joe Balkan, a Biology undergrad at Tufts University, has been reviewing previous literature for culturing protocols, and will be joining us for two weeks over break to help with some bacterial work. Undergrad Evan Warburton, who started in the fall semester, will pick up that microbiology work from Joe at the beginning of the spring semester.

The Ishaq Lab also had its first student presentation this year, by master’s student Sarah Hosler giving a graduate seminar on her proposed research for her degree, which involves host-microbial interactions in ruminants. The first portion of laboratory work for her project will take place starting in winter break. We’re not ready to share any details, but first we will be trying out some new methodology, as well as recreating some older methodology which has fallen out of fashion.

As part of that first step, Sarah will be assisting with the Capstone project of undergrad Emily Pierce, who was awarded a UMaine CUGR undergrad fellowship to fund her work this spring. Emily will be investigating host-microbe interactions during Cryptosporidium parvum infections, something which routinely devastates newborn livestock. We had anticipated running this experiment last summer, but postponed it for safety. Emily and master’s of professional studies Alex Fahey have made good use of that delay, however, and have been spending the time reading scientific manuscripts, assembling experimental protocols, and designing their project. Alex does not need to complete a thesis for her degree, it’s more about assembling a variety of skills, so she has participated in a number of supportive activities this year.

Undergrad Jade Chin has been working on her Honor’s Thesis project, the scope of which has had to nimbly pivot over the past year as we weren’t sure what we would be able to accomplish during the pandemic. For example, we spent two months waiting for DNA extraction kits to arrive due to supply shortages and the federal disruption of the postal service. Those kits are critical to the very first step of the experimental procedures and one we could not skip. Jade will defend her Honors thesis in spring 2021, including a written thesis, an oral presentation, and even a short interview with her thesis committee, although it will be less formal and less strenuous than a graduate-level defense.

Grace Lee, an undergrad at Bowdoin College, has been working on data analysis of microbial communities associated with lobster in aquaculture, which is part of a larger project by Drs. Debbie Bouchard, Jean MacRae, and Heather Hamlin. The dataset is a large and complicated one, though with an elegant experimental design. We anticipate writing up the results beginning this winter and continuing through the spring. Grace will be joined by an undergrad who I have been mentoring in my AVS 401 Capstone class, who will be contributing a literature review for the manuscript.

Three papers were published this year, which were all part of previous projects at former positions. This included the culmination of my post-doc work in the Menalled Lab from back in 2016, and one of the small projects I participated in while at BioBE from 2017 to mid 2019.

  1. Horve, P.F., Dietz, L., Ishaq, S.L., Kline, J., Fretz, M., Van Den Wymelenberg, K. 2020. Viable bacterial communities on hospital window components in patient rooms. PeerJ 8: e9580. Article.
  2. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities. mSphere 5:e00340-20. Article.
  3. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358(15):113989. Article. This was accepted in 2019 but not officially published till 2020.

It’s very common to have a slump in publications when starting a new position, and particularly when that involves moving to a new institution and establishing a new lab group. Research can take awhile to gain momentum, especially when you need to recruit and train new lab members. Or, when those lab members have to pause their lab work for global public health reasons. The Ishaq lab isn’t worried, we’ll make up for it in 2021. With all the ongoing projects, we anticipate a handful of other papers being developed next year. I’ve also got four manuscripts that have been in review for months, a process which has also been (understandably) delayed because of the pandemic.

Five stickers advertising the Ishaq Lab, with different photos of lab equipment, bacterial culture plates, and sheep.
We tried out some designs for Ishaq Lab stickers!

Teaching

I taught three new classes this year; one that was new to me and two that I developed myself. In spring 2020, I taught a special topics version of my DNA sequencing data analysis class, which means that I got provisional approval to teach it as a one-off while I completed the full course approval. Because the data analysis class is cross-listed for undergraduate seniors and for graduate students, it needed to go through two different curricula approval processes, and curricula must be approved a certain amount of time before the first instance of the class. That class has now been formally approved as AVS 454/554. From the spring version, two scientific manuscripts are in review, and a third is in preparation while more data are added. We managed to achieve a lot in the spring class, considering halfway through the semester we switched to remote instruction only as the early throes of the pandemic descended.

The other two new classes I taught this fall, including the first part of the Animal and Veterinary Sciences Capstone Experience, AVS 401, which instructs students on writing and presenting research proposals and matches students with a research mentor to try and complete the project. It was particularly challenging to do that this fall, when many researchers still had their work on pause because of the pandemic. I’ll be continuing this class in the spring as AVS 402, in which students present what they’ve done. While only a few AVS students will pursue research as a career, they will all need to implement the scientific method and the ethos of research into their lives no matter where they end up. Being able to find, assess, and critique information are all critical skills which this Capstone Experience helps them to develop.

I taught AVS 254, Introduction to Animal Microbiomes. I’ve previously taught some of this material, but to very different student audiences, which required a lot of course development on the fly over the semester. Even with the previous material, I still needed to revise all my previous lectures to adapt to a new lecture length, add new ones to make up about half the semester, and, as our understanding of host-associated microbiomes evolves over time, the course materials needed to be updated (annually) to present up-to-date knowledge. The last lecture of the semester was a compiled video of ‘science journeys‘, featuring researchers in host-associated microbiology sharing what they work on and how they got here. You can watch the video, too!

I also spent a lot of time this fall curating the Teaching Statement portion of my tenure packet, some of which I shared as a series of posts this fall. Next spring I will have my third-year review, which will be the first official hurdle and where I get more substantive feedback from my peer committee about the trajectory of my teaching, research, and outreach as I develop my packet to apply for tenure in ~ year 5. In 2021, I have a planned blog post describing the history and process of tenure, and I will likely share other portions of my tenure packet, such as my research statement.

Presentations from my couch

As I recently posted, 2020 has been The Year of The Virtual Conference. Many conference in spring and summer of 2020 were outright cancelled, but some managed to revise their format and be held virtually later in the year. This was achieved with a combination of live-streaming and pre-recorded content, all of which became on-demand during the conference. Viewers could ask questions through a chat function, or by posting questions directly to the presentation page. While early attempts to host large virtual meetings with researchers in multiple time zones faced a steep learning curve, overall, I think many people realized the potential provided by a virtual platform. For example, without travel costs, more students and early career researchers could afford to attend, and researchers with family care, health, or other constraints could participate on their own time.

Seven of the eight planned scientific presentations of my work took place in 2020, listed here with some links to video content.

Outreach

Screenshot from an online seminar. The video of the speaker is in the upper right corner, and the title slide is the rest of the image. The seminar is "A crash course in the gut microbiome" by Sue Ishaq at the University of Maine.

Similarly, seven of the eight planned public presentations took place, with some links to video content in the list below:

  1. University of Maine Medicine seminar series (virtual), “A crash course in the gut microbiome” , Nov 6, 2020. pdf of slides with annotated comments: ishaq-ummed-gut-crash-course-20201106
  2. Genomes to Phenomes (G2P) group, University of Maine. Co-hosted a session with grad student Alice Hotopp, on gut microbes and survival of reintroduced animals. Oct 30, 2020.
  3. University of Maine Cooperative Extension Oxford County 4-H Teen Science Cafe (virtual), “Gut microbes on the farm”, Oct 15, 2020. 
  4. BioME (Bioscience Association of Maine) Virtual Coffee Hour, “What is a microbiome and where can I get one?” Oct 14, 2020. I introduced myself and my research to 65 participants, who are biomedical professionals and state representatives in Maine. 
  5. University of Maine Cooperative Extension Oxford County 4-H Jamboree (virtual), “Gut microbes on the farm”, Aug 13, 2020. Video.
  6. Invited to lead Journal Club with the Fogler Library, August 4, 2020. led a 1 hour discussion on gut microbes and survival of reintroduced animals.
  7. Albright College Science Research Institute summer program 2020, which engages grades 5-12 in research.  “A crash course in the gut microbiome”, virtual presentation, Aug 4, 2020.

I’ve also been endeavoring to promote the AVS Capstone Experience projects, in part by sharing student-written project summaries on social media and UMaine news outlets. I will do something similar at the end of the spring 2021 semester when projects are complete. And, the online conferences have gotten me thinking about how to create an on-demand virtual symposium that is open to the public…

Blog

I published 45 posts this year, including this one, and was much chattier this year with over 26,000 words total. The most popular post this year was What is academic Outreach/Extension, a sleeper post from 2017 which finally ended the popularity reign of Work-Life Balance: What Do Professors Do?. A number of posts were tied for the least popular this year with one view each, but at the bottom of that possibly-arbitrary list, was A collaborative project got published on the biogeography of the calf digestive tract!, a publication announcement from 2018.

My site had its most popular year, with just over 5,000 visitors taking >8,250 views from 112 countries, as shown in the image below. This November had a record number of visitors, with >1,100! In total, my site has had >15,200 visitors and just under 24,000 views since January 2016, more than I had imagined possible when I began. The website visitors are joined by 64 wordpress followers, 100 on Instagram, 113 on Facebook, nearly 1200 on Twitter, and 0 on Tumblr, which I set up because wordpress will auto-reblog to there, just in case anyone still uses Tumblr.

Website visitor statistics for 2020.

Life

I picked up a new hobby this year – axe throwing! I tried it at an axe bar last winter and instantly took a shine to it. We made wood targets at home and bought a few throwing axes, and while I haven’t become the maverick I had hoped, it is a lot of fun. I’ve also picked up an arguably more useful skill, basic electrical work to change outlets and light switches! We’ve been slowly updating and renovating our house, and I’m looking forward to learning drywalling and flooring next near.

Looking Ahead

2021 is anticipated to be an exciting year, and will be a combination of wrapping up current projects so some of my students can graduate, as well as progressing the graduate work of Johanna and Sarah. In my “free time”, I’ll continue to fine-tune my curricula, and it’ll be back to the writing table as I revise the research proposals that I submitted this year which were not awarded funding. Of the twelve proposals I submitted in 2020, two were awarded, one is already revised and back in review, at least two will be revised and resubmitted, and at least two new ones are planned.

I’ll be part of my first graduate thesis defense as part of the committee, as Tindall Ouverson is expected to defend her master’s in 2021 from Montana State University. Tindall’s first paper on soil bacteria in agricultural fields is currently in review, and the data analysis for two more (one of which is not on soil microbes) is underway.

I’ll also be leading the committee for Jade’s Honors thesis defense in March. Alex won’t be giving a defense to finish her degree, but she’ll still be informally meeting her committee to reflect on her academic journey and if she’s prepared for a professional career. Johanna and Sarah will soon be inviting faculty to their committees, and next year I will be chairing those meetings.

I’ll be teaching the AVS 402 Capstone class for the first time, but as I already spent the fall semester with AVS seniors in AVS 401, it shouldn’t be any trouble. Just a LOT of revising papers and giving feedback. I’ll be teaching my DNA analysis class again, and will spend the next few weeks updating the materials from last spring when I taught the special topics version. I’ll also be compiling datasets for my students to work on, and hopefully, to turn into scientific manuscripts by the end of the semester.

A number of events developed by the Microbes and Social Equity working group will come to fruition in 2021, and I will finally be able to tell you about them in detail! Stay tuned for information on a speaker series running from February through April, a hybrid (virtual and in person) symposium in June, and a public announcement of a scientific journal special collection.

I’m also pleased to say that one of my cousins will be joining the website behind-the-scenes in 2021, to add alternative text to my website images to make them more inclusive. This and other work will serve as part of the requirement for science/service hours for membership to the Science National Honor Society! I’ll leave it to my cousin to make a formal introduction in a blog post on science accessibility, but welcome to the team!

See you next year!

Sealab 2021.jpg
Image: https://en.wikipedia.org/wiki/Sealab_2021

Emily awarded an undergraduate research fellowship!

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The very first Ishaq Lab undergraduate researcher, Emily Pierce, has also been awarded the first fellowship of the Ishaq Lab!

Emily has been awarded a Faculty Fellows Research Assistantship for spring 2021 from the University of Maine Center for Undergraduate Research (CUGR)! The $1200 award will provide funds for salary to Emily and research materials, and will support her project for her AVS Capstone Experience (selected Capstone project summaries are here, but Emily’s is not included).

Portrait of Emily Pierce

Emily joined the lab in early 2020 to work on a project investigating calf health and gut microbes, but very soon after joining the lab, the SARS-CoV-2 pandemic emerged and changed the way we were able to interact on campus. Without missing a beat, Emily shifted her efforts from helping me wrangle the lab renovations and sorting out our inventory, to helping me improve my teaching materials, to diving deep into previous literature to dig up protocols for her experiment in 2021: “Ideal Conditions for Cryptosporidium Attachment and Infection.“

We’ll be performing the experiment itself over the winter break, and then using the spring to analyze the data and write them up. As part of the CUGR award, Emily will be presenting her work at the 2021 Student Symposium in April, which will be held virtually this year. You’ll have to wait till then to get more details!

“Now what? Science journeys into host associated microbiomes”

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With the closing of the fall semester, I said goodbye to the students in my AVS 254: Introduction to Animal Microbiomes class. Despite the challenges and turmoil of fall 2020, these students have been engaged, enthusiastic, and creative. After presenting lectures on the microbial communities in and on animal hosts and how they can impact health and fitness, for the final class of the semester, I wanted to close with perspectives from the broader world of science.

To that end, I compiled several videos of “science journeys”, as told by active researchers in host microbiology, with an introduction to the class/video and my own science journey. I hope to compile a new volume each year I teach the class, to gather diverse paths.

I am extremely grateful for the time, effort, and thoughtfulness of the researchers who were able to contribute during a hectic semester to volume one:

  • Edna Chiang, University of Wisconsin Madison, @EdnaChiang  
  • Dr. Kaitlin Flynn, Benaroya Research Institute in Seattle, @microkaitlin  
  • Kiran Gurung, University of Groningen, @kirangurung29  
  • Jocelyn R. Holt, Texas A&M University, @JocelynRHolt  
  • Chissa Rivaldi, University of Notre Dame, @Powerofcheez  
  • Dr. Laura Tipton, Chaminade University of Honolulu, @lauraomics  
  • Dr. Benjamin Wenner, The Ohio State University, @Bynjammin
A very close-up image of a small, dark brown mouse perched on the arm of a graduate researcher wearing a surgical gown.

The first mouse study involving the Ishaq Lab begins!

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Mice have arrived for a collaborative project on diet, gut microbes, and health in conjunction with researchers at Husson University! This is the first mouse project for the Ishaq Lab, and also my first hands-on mouse project (in my previous publications with mice, I received datasets but the mouse work was performed solely by my collaborators).

A person holding a mouse in a research facility. The person is wearing a hairnet, nitrile gloves, a surgical mask, and a surgical gown. The mouse with dark brown fur is sitting on the top of the person's hand. In the background, there are metal shelves with bins and containers of research supplies.
Person in a research facility holding up their arm with a mouse on it. Person is wearing a hairnet, nitrile gloves, surgical mask, and a surgical gown. They are holding their left arm up to the camera to show off a mouse with dark brown fur sitting on their arm. In the background is a metal shelf with containers of research materials.

This is one of my first new collaborations at the University of Maine, which began in September 2019 as I was just finding my way around campus. An established researcher at Husson University, Dr. Yanyan Li, reached out to welcome me and talk about overlap between our work. Yanyan, her husband Dr. Tao Zhang, also a researcher at Husson University, and collaborator Dr. Grace Chen at Michigan State University, had been working on beneficial compounds found in broccoli using mice as an experimental model for Inflammatory Bowel Disease (IBD). Over the past year, in consultation with IBD experts Drs. Gary Mawe and Peter Moses (who I worked with previously while at UVM!), we have written several proposals for funding to expand the project.

Johanna Holman worked for several years with Yanyan and Tao, as an undergraduate researcher and then as a research assistant. She joined the Ishaq Lab this fall to continue her work as a graduate student and add gut microbiology to her skill repertoire. This experiment will form the base of her graduate thesis, and Johanna is taking a lead role in managing the project as well as several undergraduate researchers, including Dorien Baudewyns, assisting with the mice and lab work. As an early career researcher, and new to mice, I’m extremely lucky to be able to learn from an experienced team of researchers!