Johanna sets a date for her master’s thesis defense!

Prevention of Inflammatory Bowel Diseases by Broccoli Sourced and Microbially Produced Bioactives.

Presented by Johanna Holman in fulfillment of her Master’s of Science in Nutrition degree at the University of Maine. Jul 25, 2022 09:30 – 10:30 AM Eastern Time (US and Canada)

Register in advance to attend this presentation over Zoom, which will also be held in person in 206 Rogers Hall at the University of Maine (no RSVP required). After registering, you will receive a confirmation email containing information about joining the meeting.

About Johanna

I met Johanna in the fall of 2019, when I was just establishing myself as a new Assistant Professor at UMaine and she was looking for an advisor for a graduate degree.  Right away, she impressed me with her background and enthusiasm for research.  I learned that Johanna began her undergraduate study as an art student before transitioning fluidly to science.  The ability to design visual aids and graphical representations of data is hugely important to science and sadly, not always a skill that scientists are trained to do, and Johanna has made some incredible art for her research.  

Once she became a science student during her undergraduate study, she worked in the laboratories of Drs. Yanyan Li, previously an Associate Professor (of nutrition) in the College of Science and Humanities, and Tao Zhang, Assistant Professor of Basic Pharmaceutical Sciences, both of Husson University in Bangor.  There, she performed nutritional biochemistry, worked with mouse models, and developed an idea of what she wanted to study in graduate school and pursue as a career.  Johanna continues to work closely with both researchers, especially now that Dr. Li has taken a position at UMaine. 

Johanna and I continued to plan her graduate work and career goals, she officially joined my lab as a Master’s Student of Nutrition at UMaine in fall 2020, and immediately got to work.  Not only did she begin preparations for the massive undertaking that is part of her project, but she began mentoring several undergraduates on and off campus, and started as a first time teaching assistant for the Chemistry department, which required navigating virtual labs.  She served as a chemistry TA for academic year 20/21 and 21/22, with up to 60 students per semester. For the last year and a half, she has been coordinating a large-scale research project with investigators at 4 different institutions and undergraduate researchers from 3 different institutions, involving hundreds of samples – while being a masters student, a graduate teaching assistant, and mentoring undergrads in the lab, and all during a pandemic!  She managed that all so well, that despite being a first-year graduate student, she was awarded a 2020-2021 University of Maine Graduate Student Employee of the Year award, and the 2022 Norris Charles Clements Graduate Student Award from the College of Natural Sciences, Forestry, and Agriculture. 

Johanna’s project focuses on whether consumption of specific broccoli sprout preparations will elicit changes in the gut microbiota, to the effect of improving the production of microbiota-specific bioactives that have local anti-inflammatory effects, and promoting intestinal homeostasis by reducing dysbiosis. Broccoli sprouts represent an effective, and accessible way to add dietary intervention to existing treatment and prevention strategies for IBD patients. This project is a continuation of previous research on bioactive compounds in broccoli, completed in the labs of Drs. Yanyan Li and Tao Zhang at Husson University in Bangor.  While some of the work may be similar, the skill set she has gained in her graduate work is entirely new.  For the 2020/2021 winter break, Johanna was managing a 40-mouse study looking at DSS-treatment and different preparations of a broccoli sprout diet for 5 weeks, which resulted in hundreds of samples collected, hundreds of data time points, and enough follow-up laboratory and analysis work to keep her occupied for an entire year.  She has learned how to culture bacteria in an anaerobic chamber, which is a notoriously fussy machine that requires regular attention, as well as to grow them under different conditions for biochemical analysis and enzyme activity.  She is currently learning additional histology skills, DNA extraction, DNA sequencing library preparation, DNA sequence analysis, and more. Recently, she has participated in a pilot study to develop an immunological model of IBD, using IL-10 knockout mice. While IL-10 mice have been used to study IBD, they have never been applied in this way to study the interaction of diet, microbes, and disease.

She has presented this work at the American Society for Microbiology annual meeting, and at the UC Davis Research Experience for Undergraduates (REU) symposium, and has several conference presentations planned for 2022. Johanna has an author on a paper in early 2022 for work she contributed to as an undergraduate, and is preparing 3 manuscripts generated from her masters work which will be submitted for peer review at a scientific journal in 2022.

Johanna has been accepted to the Nutrition PhD program at UMaine, and will continue working with Dr. Li and I, as well as the full research team. Based on those preliminary results, Johanna’s doctoral work will focus on developing that new model, synthesizing information from both models, and using those results to develop diet intervention trials in human patients. After her PhD, Johanna intends to conduct research at an institution here in Maine, and to continue her work connecting the biochemistry of nutrition with gut microbiology and human health.

Sue talking a selfie in the UMaine parking lot in full regalia.

2022 graduating students

UMaine and many other universities are having in-person graduation ceremonies, and welcoming students who are graduating this year, as well as those who finished in 2021 and 2020 who were not able to walk in a regular ceremony. I made it to the ceremony for the graduates, so I could cheer on Sarah, where over 400 of the more 600 total graduate students matriculating got hooded and recognized for their achievement.

This year, many Ishaq Lab members walked across the stage and off into the next step in their life.

A graduate student and a faculty member, both in full graduation regalia, posing for a photo in a gymnasium.

Sarah Hosler, Animal and Veterinary Science Master’s of Science student, who will be defending her thesis this summer and is considering her next career step.

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.

Johanna Holman, Food Science and Nutrition Master’s of Science student, who will be defending her thesis this summer and returning this fall for a PhD!

A woman in a lab coat wearing a face mask and latex gloves is using a thin yellow swab to spread bacteria on a culture media plate. She is sitting at a biosafety cabinet with the glass door pulled down.

Rebecca French, AVS undergrad who did her Capstone project as part of the squirrel pilot project I ran this past year. Rebecca won a research grant for this work. She is heading to vet school in Long Island!

Morgan Rocks, AVS undergrad who did her Capstone project as part of the squirrel pilot project I ran this past year. She is heading to vet school in the midwest!

Natalie Sullivan, AVS undergrad who did her Capstone project as part of the Cryptosporidium pilot project we are running. She is planning to work for a year before pursuing vet school.

Woman standing on the ocean shoreline.

Jade Chin, AVS undergrad who defended her Honor’s Thesis in 2021 and was awarded High Honors for it, has been in Glasgow, Scotland, for her senior year/first year of veterinary school there.

Myra Arshad

Myra Arshad, an REU student who is graduating from Stoney Brook University. She’s taking a year to work in research before pursuing a graduate degree.

In addition, we had a handful of other undergraduate students who performed their independent research for their Capstone projects in the Ishaq Lab graduate this year.

5-year anniversary of my PhD graduation!

Seems like a lifetime ago that I walked the stage and was hooded during the graduation for my doctoral degree, just 5 years ago. In 2020, most Universities have cancelled their in-person graduations due to pandemic concerns, with faint hopes that they might be able to host the opportunity for 2020 graduates “to walk” at a future ceremony. It’s a good day to reflect on the opportunities and privileges I’ve been afforded that have helped me along the way.

I defended my PhD in mid March 2015, and within two weeks had driven with Lee from Vermont to Montana, flying back to VT for the ceremony in May. In those 5 years, I moved to Montana, then Oregon, then Maine; I’ve worked for 4 different departments in 3 Universities; I’ve had several different hair styles; I adopted a dog, got married, and bought a house; applied to dozens of jobs almost every year because of the short-term appointments I held; and established a research lab at the University of Maine as an assistant professor. It’s been a pretty busy 5 years, all around. I look forward to the next 5 years, and the opportunity to help the next generation of researchers begin their journey.

Happy 1 year dissertation defense anniversary!

A year ago today I gave the public defense of my PhD dissertation!  It was a stressful day, especially because my laptop crashed just 10 minutes beforehand while I was practicing and making last minute adjustments!  Luckily, I had prepared by bringing the presentation on a flash drive, and by putting it on an online cloud drive as well.  My parents brought enough potato salad, cookies, cake, and Italian meatballs to feed the dozens of attendees and then some.  I really appreciated the friends and family that showed up to support me, some had even driven to Burlington, VT from Massachusetts just for me!  You can watch my full defense presentation on YouTube.

After a long hour of presenting my work and answering questions from the crowd, my graduate committee and I left for the closed-door portion.  For the next two and a half grueling hours, 5 field-leading researchers asked me questions about everything I had done, and what I might have done differently.  Finally, they asked me to step into the hallway while they made their final deliberations, where I nervously ate cookies as fast as I could because I hadn’t eaten in hours.  They came back out 5 minutes later smiling, and announced that I had passed!  You can read my full thesis here.

Where’d the spark go? When it’s time to break up with your graduate program.

Remember when you first met your graduate program? You got that little thrill whenever they emailed you. You started measuring the graduate student office for new drapes. You just wanted to spend all your time in the lab, and couldn’t be happier doing so. As time went on, you learned a lot about your field and about yourself. You grew as a person and became more confident in your work. Eventually, the relationship started to stagnate: you got tired of working on the same old projects, ran out of interesting classes to try, you felt like it was never going to get the next level and, well, you got bored. It happens to everyone, and it’s important to recognize the signs (1), before the relationship becomes negative.

I have seen it before. Graduate students have trouble finishing up projects and getting manuscripts published, their PIs change the subject when the time comes to set a defense date, they feel like a perpetual student, until they become frustrated at the creeping feeling of no control over their life or the pace of their career. And eventually, many of them reflect this frustration outwardly by complaining about their PI, their department, their university. This is detrimental to yourself and to the quality of your work (2) (3), to the other students around you who still have several years of graduate work to look forward to, and to prospective students (4).

And more than that, it doesn’t help you to find your next position, because you find yourself complaining to people that you probably shouldn’t open up to: people you meet at a conference, a candidate interviewing in your current department, the interviewer for your prospective job. No one likes to hear someone rag on their old boss if they might one day be the boss you are badmouthing on social media.  Nor they do they want a team member who is going to bring down the tone for the whole group.

When you are ready to move on in your career, you know, and you need to take responsibility and control of your trajectory to make it happen. Set a timeline and stick to it, sit your PI down and set a defense date, curate your CV and start applying for jobs. Not just the two jobs that you really, really want, but any job that you think you might be interested in. The post-doctoral job market is small, and it’s difficult to find a position. Don’t put all your eggs in one basket, as you may find yourself stuck in that particular graduate program if you’re not able to find a new position. The process will hone your skills as well, especially if you can get an interview. Use each opportunity, and if you don’t get the job, politely ask the interviewer how you could make yourself more competitive, or if there was an aspect of your work that was underwhelming or poorly explained.

The point is, don’t wait until you are sick of being a graduate student and can’t wait to get out, keep an eye out for your next move and be proactive about it. So put away those free t-shirts you got from vendors, get yourself some new business attire, get your CV in shape, and you’ll be surprised at how many interviewers ask for your number.

Here is another relevant and entertaining blog post on the subject.