Sarah Hosler passed her Master’s of Science these defense (we knew she would succeed)!! Sarah has worked incredibly hard over the last two years to broaden her research skills and conduct four completely different pilot projects. Her defense presentation focused on the two main projects, but was a wonderful way to see that progression all at once and to reflect on her growth as a lab manager and researcher. She has also earned the designation of “second Ishaq Lab grad student to defend”.
The defense was attended by her thesis committee, students in the Ishaq lab, collaborators on this project, friends and family, and Izzy the dog (pictured, and yes, Sarah preferred this picture of her at her defense to a portrait of herself. Sarah will officially pass after a few revisions to her thesis and a formal acceptance by the committee members, which is standard for graduate defenses.
After wrapping up a few things in Maine, Sarah will be heading to Pennsylvania to take a position as Student Program Coordinator for middle and high school aged students at Albright College, where she obtained her Bachelor’s of Science. Congrats on the defense and on the next stage of your career!
“Weaving An Interdisciplinary Microbiome Career Using Threads From Different Ecosystems”.
Johanna Holman passed her Master’s of Science these defense (we knew she would succeed)!! Johanna has worked incredibly hard over the last two years to broaden her research skills and conduct several experiments, and her defense presentation was a wonderful way to see that progression all at once. She has also earned the designation of “first Ishaq Lab grad student to defend”. The defense was attended by her thesis committee, students in the Ishaq lab, collaborators on this project, and friends and family (who brought her a flower and broccoli bouquet that can be seen in the picture below). She will officially pass after a few revisions to her thesis and a formal acceptance by the committee members, which is standard for graduate defenses.
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 mouse 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.
Prevention of Inflammatory Bowel Diseases by Broccoli Sourced and Microbially Produced Bioactives.
Sarah officially joined my lab and started as a Master’s of Animal Science student at UMaine in fall 2020, which was during an extremely tumultuous time in history, and was only a year into my Assistant Professor position here at UMaine and before the lab had built up protocols, collaborations, samples, or momentum. Collectively, this meant that Sarah was part of my work to establish a laboratory and has been blazing that trail along with me. As such, in addition to the technical and analytical skills she has been learning, she has obtained a massive amount of professional development and leadership experience.
Sarah’s research interests are the interaction between the microbial community associated with various animal species, animal health or productivity, and the environment. This work is highly interdisciplinary, and requires extensive imagination and forethought into experimental designs which can capture biological, microbiological, and environmental data. This research theory is directly in line with the One Health in the Environment research group at UMaine, as well as the Microbes and Social Equity working group – an international research collaboration which I lead-, both of which Sarah has obtained mentorship from. This graduate work has focused on developing pilot studies and new research collaborations for three major projects/lines of scientific inquiry.
The first project centered around the tracking of Cryptosporidium parvum in different-aged dairy cattle populations as well as their pens at the University of Maine’s J.F. Witter Farm. Cryptosporidium is a small protozoan; a single-celled organism, and it is found in and around water and soil, as it spends most of its life cycle in those places. Humans and animals may ingest it through contaminated water or the fecal-oral route accidentally. In very young (such as calves) or immunocompromised individuals, an infection can occur, causing diarrhea and dehydration, and leading to death in many cases. Sarah has trained multiple undergraduates on sample collection and processing, as well as cell staining and microscopy, and the project has already collected dozens of samples. As this project will proceed for at least two years, it is not the main focus of Sarah’s thesis, however she will be an author on the eventual publication and she is leading a review manuscript on cryptosporidiosis which we will submit for peer review by fall 2022.
The second project investigated pathogens in wild rodent populations in Maine, in the context of heat stress and northward-shorting range changes due to climate changes. A pilot project collected biological data and samples from live-trapped flying squirrels and white-footed mice in six locations across Maine over summer 2021. The pilot project involved three additional investigators with complementary expertise, as well as their associated student mentees. To investigate disease potential, free catch fecal samples were collected from trapped animals to identify carriage of specific pathogens, and to isolate bacteria and assess heat tolerance. Sarah coordinated the training of undergraduate students in my and other labs, including sample collection and processing, microbial culture, DNA extraction, and more.
The third project project, and primary focus of her second year, investigated the microbial communities associated with sea scallops at different life stages and associated with tank surfaces at different points in a hatchery production run. Overall, there is a dramatic lack of research into the microbial communities involved in aquaculture and fisheries and how these might impact production as well as local ecosystems. Sarah processed a large number of samples for DNA extraction and sequencing preparation, as well as microbial culturing and biofilm assessment, and trained an undergraduate on the culturing work. This project and the piloting work Sarah did has led to a small grant award and a multiple-institutional collaboration. Sarah presented some of this preliminary work to aquaculture and fisheries industry professionals at the Northeast Aquaculture Conference & Exposition/ 41st Milford Aquaculture Seminar in Portland, and the American Society for Microbiology Microbe meetings. Sarah is currently writing this manuscript which will be submitted for peer review by the end of this summer.
This graduate work was highly collaborative, and required a great deal of professionalism. Each of the three research projects that Sarah had been working on involves a primary team of faculty or animal science professionals, most of whom are on campus at UMaine but some of whom are remote at external institutions. Each of the three projects also involved 1 – 4 undergraduate students participating in the research. Not only did Sarah help me organize project team meetings, and facilitate those meetings, but she coordinated data collection and file management for those projects, as well as trained and oversaw undergraduates in the laboratory. These skills are so often overlooked in research training, and are often considered part of the background in science. However, as tenure-track faculty, I would argue that these organization and research coordination skills are the most valuable for advancing complicated projects.
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.
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.
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.
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!
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.
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, 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.
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.
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.
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.