Tag: graduate award

Alexis awarded research funds from the Crohn’s and Colitis Foundation!!

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Alexis Kirkendall began her PhD with research funds awarded in her very first month!! Over the fall, she drafted a proposal to evaluate the probitoic potential of bacteria the we previously isolated from a broccoli sprout diet study. The funds were awarded from the Crohn’s and Colitis Foundation, and will help launch the research for Alexis’ dissertation!!

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    Alexis Kirkendall processing microscope slides.
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    Alexis Kirkendall, Jaymie Sideaway, Aakriti Sharma, Johanna Holman, and Lilian Nowak.
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    Logo designed by Johanna Holman.
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    Alexis Kirkendall processing microscope slides.

Effect of probiotic candidates on intestinal epithelium barrier function.

Summary

Broccoli sprouts contain precursors to anti-inflammatories which increase beneficial gut bacteria and reduce pathogens, and confer protective effects against colitis. Gut microbiota are critical to converting the precursor to the anti-inflammatory sulforaphane to sites of intestinal inflammation. We are currently investigating hundreds of bacterial isolates for their capacity to produce sulforaphane using gut microbiota samples from different parts of the intestines in broccoli sprout-fed mice. We are benchmarking these 806 isolates against standard strains with GSLs-metabolism. We hypothesize that previous broccoli sprout entrainment of bacteria can improve their capacity for GLR metabolism in the new hosts. Our immediate goal is to test the capacity of these isolates to produce SFN and reduce inflammation, and our long-term goal is to develop a dietary preparation of broccoli sprouts and a probiotic which have therapeutic effects against IBD in humans. 

Relevance to IBD

Broccoli sprouts contain plant secondary compounds, especially glucoraphanin, which is transformed into sulforaphane, an anti-inflammatory, by gut-microbiota-sourced enzymes. High fiber diets may reduce inflammation and cancer risk, and improve quality of life for colitis patients. Our research investigates a prevention/management approach which has the potential to restore host-microbial homeostasis, but also is more affordable and accessible than a dietary supplement or medical treatment. We found that certain gut microbiota metabolizing broccoli sprout glucoraphanin to anti-inflammatories such as sulforaphane, and that a broccoli sprout-supplemented diet results in sulforaphane accumulation systemically and in gut tissues, reduced inflammatory cytokines, and beneficial changes to gut microbiota. We found that these interactions between gut microbiota and broccoli sprouts reduce susceptibility of mice to chemically induced colitis and immunologically associated enterocolitis.

Lots to celebrate in the Ishaq Lab this fall!

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Ayodeji won a travel award to present at a conference and is receiving job offers in advance of his January defense date for his master’s thesis!

Ayodeji Olaniyi, B.S.

Master of Science student.

Ayodeji joined the lab in 2022, and has been investigating the Vibrio bacteria associated with different scallop hatchery tank systems. Ayodeji won a travel award from the University of Maine Aquaculture Research Institute Rapid Response Fund, to present his work at the upcoming meeting: Northeast Aquaculture Conference & Exposition (NACE) and the 43rd Milford Aquaculture Seminar (MAS)! He is also celebrating research job offers for when he defends his thesis in January!!

Marissa received a research award from the Bioscience Association of Maine, and contibuted to two papers this year!!

Marissa Kinney

Marissa Kinney 

Master of Science student

Marissa completed her undergraduate at the University of Maine in 2021, earning a BS in Microbiology and a BS in Cellular/Molecular Biology, and after graduating worked in the field of public health at UMaine’s Margaret Chase Smith Policy Center. She’s been crushing it since joining the lab in early 2023, including contibuting to the two papers listed below, being awarded a One Health and the Environment NRT Fellowship 2023 – 2024 at UMaine, and now, a research award from the Bioscience Association of Maine!!

Lola was first author on a paper that was just accepted (details soon), and contributed to a second paper that was recently published!

Portrait of Lola Holcomb, wearing a block sweater on a beach at sunset

Lola Holcomb

Doctorate of Philosophy candidate.

Lola entered as a rotating first-year GSBSE student in March 2022, and declared the Ishaq Lab her dissertation lab soon after, where she has been performing 16s data analysis for other ongoing lab projects, comparing gut microbiomes of mouse models of Inflammatory Bowel Disease with broccoli as a dietary treatment.  Lola was awarded a One Health and the Environment NRT Fellowship 2022- 2024 here at UMaine.  She led the data analysis on a paper using a Crohn’s Disease mouse model for innovate diet-microbe research.

Johanna was first author on a paper that was recently published, and contributed to a second paper accepted (details soon)!

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

Doctor of Philosophy student

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 will combine her previous work on the nutritional biochemistry of broccoli 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! She won the 2022 Norris Charles Clements Graduate Student Award and the 2020-2021 University of Maine Graduate Student Employee of the Year. She led a large mouse project which was recently published, and led much of the lab work for a second paper that was just accepted.

Alexis is returning soon as PhD student in Microbiology!

Alexis Kirkendall

Undergraduate Researcher

Alexis is from Ohio and is about to graduate a semeser early in Biology at Heidelberg University. She joined the lab through the Summer 2022 REU, continued her work remotely, and returned to Maine in summer 2023 as a research assistant for several projects related to gut microbes, diet, and Inflammatory Bowel Disease. She was just accepted into the microbiology program at UMaine!!

 

Esther joined the lab!

Esther Alaba

Doctorate of Philosophy candidate

Esther has won several awards for combining mechanistic and functional tools to investigate dietary interventions in managing metabolic diseases. Her teaching experience includes Basic Physiology, Anatomy, and Experimental Physiology courses. She is passionate about Girls’ Education and Empowerment and currently mentors several young women towards successful career development. 

Her desire to utilize bioinformatics tools for nutritional therapy brought her to Ishaq’s lab. She currently works on human and mouse data to identify the microbiome and metabolomic pathways involved in the ameliorative effects of broccoli sprouts during IBD.

Esther is being co-advised by Dr. Yanyan Li.

Marissa Kinney awarded an NSF NRT graduate fellowship from the UMaine Initiative for One Health and the Environment!

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Masters of Science in Microbiology student, Marissa Kinney, will be joining the 2023/2024 cohort of graduate students in the Initiative for One Health and the Environment group at UMaine, as she was awarded a fellowship through the group’s NSF NRT funding. She’ll be using this fellowship to cross-train in other research disciplines, and explore the economic and social factors concerning people with Inflammatory Bowel Diseases, alongside One Health co-mentor Dr. Mario Teisl, Director and Professor of the School of Economics.

Marissa joins fellow Ishaq Lab grad student, Lola Holcomb, who was awarded a fellowship by the group and started with the 2022/2023 cohort.

Marissa Kinney

Marissa Kinney 

Master of Science student, Microbiology and Animal and Veterinary Sciences

Blurb: Marissa is a Masters student who loves learning and bench microbiology. She completed her undergraduate at the University of Maine in 2021, earning a BS in Microbiology and a BS in Cellular/Molecular Biology. She devoted a large portion of her time in undergrad to research in the laboratories of Dr. Julie Gosse and Dr. Edward Bernard. Since graduating, she worked in the field of public health at UMaine’s Margaret Chase Smith Policy Center, collecting and processing data about violent and drug-related deaths in Maine. While her role at the Center was one she loved dearly, she feels a big pull towards laboratory work and academic research. She recently joined the Ishaq lab and is excited by the new opportunities this position brings. 

Marissa was awarded a One Health and the Environment NRT Fellowship 2023 – 2024 at UMaine.

Now, working in my lab, Marissa is focusing on the microbial communities in the gastrointestinal tract, and particularly in the context of broccoli sprouts in the diet and how certain gut bacteria can use them to create an anti-inflammatory compound of interest. She has been developing new protocols for using growth curve analyses and genomic assays (quantitative PCR) to identify bacteria with the capacity to use broccoli sprouts to create anti-inflammatories along different location in the gut, and under difference health or disease states. Over the next few years, she’ll also be learning DNA sequencing library preparation and data analysis, working with human subjects in a diet trial, performing experiments using mice as a model for humans, and a variety of microbiology, genomic, and biochemical laboratory techniques. Marissa’s project is part of a much larger collaborative on the use of dietary broccoli sprouts to resolve symptoms in Inflammatory Bowel Disease patients.  As part of that larger collaboration, Marissa will be meeting regularly with the various parts of the project team, including students and researchers at 4 different institutions, and helping on three different projects in the lab to build her skillset. This requires a high degree of organization and coordination, and Marissa immediately stepped into her role.

To expand the lab’s existing work on human gut microbiomes, Marissa will use the NRT training and knowledge base as an opportunity to learn techniques in social sciences and economics. IBD is highly impactful on the wellbeing of people experiencing it acutely or chronically, and there is a large social and economic burden, as well. While any IBD patient could already consume broccoli to potentially receive benefit, nuances in how gut microbes respond to diet, and fears about exacerbating symptoms, preclude this. Being able to understand dietary behaviors, and assess the economic impact of a whole-food palliative strategy, would allow us to better implement our dietary intervention.

Johanna receives a UMaine College of Natural Sciences, Forestry, and Agriculture Graduate Student Award for her research!

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Johanna Holman received the 2022 Norris Charles Clements Graduate Student Award from the University of Maine College of Natural Sciences, Forestry, and Agriculture (NSFA), for her research and academics over the last two years for her Master’s of Science in Nutrition!! This award highlights the achievements and potential for positive impact of graduate students in agriculture, is more often awarded to doctoral students who have had more years of graduate work in which to accomplish their research, give presentations, mentor undergraduates, and otherwise develop their professional skills.

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.

Despite the setbacks and challenges of the pandemic, Johanna has been extremely productive and has done an extraordinary amount in just a year and a half (from start to the time of application submission) for her masters work. Johanna is currently writing up the results of her masters work into three manuscripts that we plan to submit to scientific journals for peer review this summer. She will defend her thesis at the end of the summer, just in time to start in September as a PhD student working with Dr. Yanyan Li and I!

Artwork by Johanna Holman
Artwork by Johanna Holman

From the NSFA award page: “The Norris Charles Clements Graduate Student Award was established in the University of Maine Foundation in May 1997 for the benefit of the University of Maine, Orono, with a bequest from Laurel Clements ’48 in honor of her father, Norris Charles Clements, a distinguished Maine poultry farmer who in 1953 was honored by the University of Maine as Maine’s Outstanding Farmer. Income shall be used to provide financial assistance for rewarding outstanding graduate students in agricultural sciences and to recognize the accomplishments of graduate students whose studies have the potential to make a significant contribution to Maine agriculture. Candidates should have training and be doing research in disciplines related to Maine agriculture, such as agronomy, soil science, animal and veterinary sciences, agricultural economics, entomology, plant pathology, agricultural engineering and other disciplines the dean deems contribute significantly to the well being of Maine agriculture. Students will be chosen for awards on the basis of their high academic standing, the quality of their research and their personal integrity.”

Tindall won first prize in a graduate students poster competition!

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Congratulations to Tindal Ouverson for winning first prize in the graduate students poster competition at the 2021 Montana State University LRES research colloquium!

Tindall is a master’s of science in Land Resources and Environmental Sciences at Montana State University, working with advisers Drs. Fabian Menalled and Tim Seipel. Tindall and I have been working closely over the past three-ish years on soil microbiomes, and she is preparing to defend her thesis this May.

Check out her recently published paper: Temporal soil bacterial community responses to cropping systems and crop identity in dryland agroecosystems of the Northern Great Plains. 

Johanna Holman is awarded UMaine Grad Student Employee of the Year!

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Johanna Holman, Master’s of Nutrition student in the Ishaq Lab has been awarded the 2020-2021 University of Maine Graduate Student Employee of the Year!!!!

I met Johanna in the fall of 2019, when I was just establishing myself as a new Assistant Professor in the School of Food and Agriculture, 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.  I see this is an asset – the ability to design visual aid and graphical representations of data is hugely important to science and sadly, not always a skill that scientists are trained to do. Johanna also had a number of service industry jobs, and initially in that first meeting, she was somewhat apologetic for not having been devoted to science jobs from the start.  I countered that I was pleased to see that she has worked in other industries, specifically in difficult service-related jobs.  It is often more important to have patience, dedication, and strong interpersonal skills, such as those gained by working in customer-facing jobs.  I believe that Johanna has and will continue to succeed because of her varied education and experience.

Once she became a science student during her undergraduate study, she worked in the laboratories of Drs. Yanyan Li, 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 has 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 officially joined my lab and started 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.

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. 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 is entirely new.  For the winter break, Johanna was managing a 40-mouse study for 5 weeks, which has 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 will be learning DNA extraction, DNA sequencing library preparation, DNA sequence analysis, and will lead the generation of a large manuscript on the results.

It might seem too early to recommend a graduate student for this award after just one semester, but it is remarkable that a new master’s student could achieve all of this in their first semester during a pandemic.  I have informally mentored graduate and undergraduate students for years, and it is easy to spot the ones who will go far in science. Johanna has a highly successful career ahead of her, and I am honored to be one stop on that path.  This award will not only acknowledge the incredible amount of work she has accomplished, but it will support an early career researcher who has every quality to make research a hospitable and collaborate place.

Stacks of petri dishes filled with culture media, some of which have bacterial colonies growing on them.
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.
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.