Tag: comprehensive exam

Johanna Holman prepares to defend her doctoral dissertation!

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Johanna Holman is preparing to defend her doctoral dissertation in Microbiology on January 27th!

The presentation of her work is publically available from 10 – 11 am EST, and will take place on the UMaine Orono campus, as well as on Zoom (register here).

Johanna joined my lab in 2020, first as a master’s student in Nutrition, then as a PhD student in Microbiology. She started her research career as a lab tech for some of my long-term collaborators, Yanyan Li and Tao Zhang, back when they were at Husson University in Bangor, Maine. She joined my lab to add microbiology to her existing nutrition and biochemistry background, and at this point, it might be easier to list which projects she hasn’t been a part of. She’s performed bacterial culturing, bacterial community analysis, genomics, transcriptomcs, and protein prediction. She’s run diet intervention trials in mice and in people, and she’s trained nearly every student in my lab in the last 6 years in some type of lab work or data analysis. She has been a valuable collaborator on our intricate and lab-heavy projects, allowing the lab to coordinate up to 5 projects and 8 students simultaneously.

Johanna is a brilliant nutritional health microbiologist who uses multi-faceted research – from the lab to public health – to understand the connection between health and the microbiome. She’s led two publications from her masters (a literature review on sulforphane and the immune system, and another on a broccoli sprout diet intervention in mice); co-authored three others (a literature review on cruciferous vegetables, a similar broccoli sprout diet intervention in mice, and a different formulation of the broccoli diet); and has several more manuscripts from her doctoral work that are poised for submission to scientific journals for peer review.

She’s written graduate research proposals for the NIH and USDA. She was awarded the Charles Morris and UMaine grad student award.

She’s been a teaching assistant for chemistry and biology, with an estimated 120 students per year. She’s a graphic designer (Imaginome Designs). She grew a whole human from scratch. She’s keen to learn and has always kept an open mind to new opportunities. Johanna has been instrumental in the knowledge generation and success of my lab, and we are so luck to have been a part of her journey.

A cartoon of a woman eating broccoli, with the digestive tract shown on her shirt, and smiling microbes in the background.
A diagram with two panels, and a cartoon mouse in the middle. The cartoon mouse is eating broccoli, and a cartoon of the digestive tract is overlaid on the mouse's abdomen. Lines emanating from the broccoli point to the left panel, and show the compound glucoraphanin being converted into sulforaphane by the myrosinase enzyme. Lines emanating from the colon of the mouse point to the panel on the right, showing the same biochemical conversion by gut microbes.
A black and white portrait of Johanna Holman
A logo that says "The Broccoli Project"
A cartoon of brightly colored, smiling bacteria.
A cartoon of cruciferous vegetables
Johanna Holman standing at a wooden podium with a white board and a projection screen behind her. Johanna is presenting her master's thesis, and the title slide of the presentation is showing on the screen.
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.

Heather Richard passes her comprehensive exam and advances to doctoral candidacy!

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Heather Richard passed her comprehensive exam, which means she is advancing to PhD candidacy!! Heather’s research focuses on how land use and water infrastrucure changes the dynamics of salt marshes and their tidal creeks, which alters their microbial communities, biochemical processes, and capacity to sequester atmospheric carbon in sediment. She details that work, including field sampling and labwork protocols, as well as data visualization and major findings, on an interactive website she created to support research into salt marshes in Maine.

Heather Richard

Heather Richard, B.A., M.S.

Doctor of Philosophy Candidate, Ecology and Environmental Sciences. Heather is being co-advised by Dr. Peter Avis

Heather joined the University of Maine in 2021 as a PhD student with the Maine eDNA program and studies the impacts of bridges and roads on microbial communities in salt marsh habitats. Her background in Ecology led her to pursue a career in informal environmental education for several years before getting a Master’s degree in Marine Biology from San Francisco State University studying biofilms on microplastics pollution. Upon returning to Maine in 2016 she led local research for a coastal non-profit organization and has since been dedicated to studying coastal environmental issues relevant to Maine. She has found a true passion in bioinformatic analysis and is eager to learn new tools for data analysis of all kinds. 

The exam involved writing mini-papers around topics assigned by her committee, including decision-making and troubleshooting for sequencing data analysis, biogeochemical processes in salt marshes that drive carbon sequestration or release, and microbial ecology in coastal ecosystems. Each set of questions were released once a day for 5 days, and mini-papers took 6 -8 hours to complete and had to be returned within 24 hours. This intensive series of written exams were followed by a two-hour question-and-answer session in which Heather gave further detail on her written answers, connected basic biochemical processes to broader ecosystem-level microbial ecology, and considered furture research designs. This grueling process is the last hurdle for PhD students, and now it’s “smooth sailing” until the PhD defense. Over the next year or so, Heather will perform metegenomics sequencing data analysis from her salt marsh sites, and synthesizing microbial and biochemical data into several manuscripts which we will submit to scientific journals for peer review, and eventual publication.

Johanna Holman passes her comprehensive exam and advances to candidacy!

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Johanna passed her comprehensive exam, which means she is advancing to PhD candidacy!! The exam involved writing a research proposal on a topic outside of her main focus, and presenting her idea for an hour to her committee, who then asked detailed questions about her work and understanding of this research for over an hour.

Johanna has been with the lab since 2020, but she has actual been researching broccoli sprouts for 6 years, as she started her career with Yanyan Li and Tao Zhang back when all three were at Husson University. Johanna is a brilliant nutritional health microbiologist who uses multi-faceted research – from the lab to public health – to understand the connection between health and the microbiome. She has been a valuable collaborator on our intricate and lab-heavy projects, allowing the lab to coordinate up to 5 projects and 8 students simultaneously. Now that she is a PhD candidate, Johanna will begin designing her own research projects and trying to find funding through fellowships, to help her become an independent researcher.

A black and white portrait of Johanna Holman

Johanna Holman, B.S., M.S.

Doctor of Philosophy candidate, Microbiology

Johanna joined the lab in fall 2020 to investigate the effects of diet on the gut microbiome, and on host-microbial interactions. For the past several years, she has been working with Drs. Tao Zhang and Yanyan Li, and her project combines nutritional biochemistry of broccoli sprouts with effects on gut microbes. She obtained her master’s in nutrition in summer 2022, and returned to the Ishaq and Li labs for her PhD!

Imaginome Designs, her graphic design business

Alexis Kirkendall, Jaymie Sideaway, Aakriti Sharma, Sue Ishaq, Johanna Holman, and Lilian Nowak.
Sue Ishaq, Yanyan Li, and Johanna Holman, pose in various labs where the three research broccoli. Photo Credit: Patrick Wine, UMaine.
Johanna Holman at her ASM Microbe 2022 poster
Johanna Holman at her ASM Microbe 2022 poster
A cartoon of a woman eating broccoli, with the digestive tract shown on her shirt, and smiling microbes in the background.
Designed by Johanna Holman.
A cartoon of a bacteria eating broccoli and pooping out sulforaphane
Designed by Johanna Holman
A cartoon of brightly colored, smiling bacteria.
Designed by Johanna Holman.

Lola passes her comprehensive exam!

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Congratulations to Lola Holcomb, for passing the graduate comprehensive exam!! She now goes from being a PhD student to a PhD candidate, and for the next few years will focus on developing her own research designs and writing her thesis.

Lola standing in front of her poster which displays the results of her research on gut microbes.
Portrait of Lola Holcomb, wearing a block sweater on a beach at sunset

The exam was set by her PhD program in the Graduate School of Biomedical Sciences and Engineering, and involved writing a 6-page research proposal over the past two months, and on the day of, giving a 1-hour presentation and answering questions from her committee for up to two hours. The focus of the proposal and the presentation are a hypothetical experiment she designs on a topic that is similar to her existing research but not directly related. In that way, you can test a student’s ability to translate their existing knowledge and fact-finding skills to a totally new area and see how well they can reason through a new problem. The committee will ask students to explain their thought process, methods, and how they will assess the progress on the hypothetical project. It’s a long and arduous process, but Lola’s depth of knowledge and ability to problem-solve helped her pass with ease!