MSE seminar today on “Advancing Queer and Transgender Equity in Science (AQTES)”

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The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

Events will be hosted January – December, 2024, once a month on a Friday, 12:00 – 14:00 pm ET. Presented over Zoom.

After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine and the UMaine Cultural Affairs/Distinguished Lecture Committee.

Register here for free!

“Advancing Queer and Transgender Equity in Science (AQTES)“

Presented by Dr. JL Weissman and other members of the Advancing Queer and Transgender Equity in Science (AQTES) working group

Dec 20, 2024 12:00 PM Eastern Standard Time

Jackie Lee “JL” Weissman (they/she) is an Assistant Professor at Stony Brook University starting Fall 2024. Her research examines how microbes survive and thrive across diverse environments. She develops new tools to infer what microbes are doing and can do from DNA sequences captured directly from the environment (“metagenomes”), aiming to improve the representation of microbially-mediated biogeochemical cycles in global climate models. She also has a special interest in using a combination of comparative genomics, population genetics, and mathematical models to understand the ancient and ongoing battle between microbes and their viruses. She believes all students, with supportive training and mentorship, can become highly-capable computational biologists, and loves to show students how a little coding can go a long way.

The newly-formed group, Advancing Queer and Trans Equity in Science (AQTES), wants to improve the field of research by making the hiring process fair and welcoming for everyone. No matter what your personal identity is, we can all agree that fair and unbiased job searches are critical to hiring the best talent. But, sometimes a poorly-organized job search prevents the people with the best talent from applying at all.

In our white paper, we give suggestions on how to host a job search that is better for everyone. We provide examples and advice on how to write job adverts, create the agenda and atmosphere for the job search, how to make the interview process more accessible for everyone by remembering that we are humans and not robots, and how to support your new faculty.

Citation for the paper: Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES). 2024. Running a queer- and trans-inclusive faculty hiring process. EcoEvoRvix repository 6791.

Perspective piece introducing the paper:  Weissman JL, Chappell CR, Francesco Rodrigues de Oliveira B, Evans N, Fagre AC, Forsythe D, et al. (2024) Queer- and trans-inclusive faculty hiring—A call for change. PLoS Biol 22(11): e3002919.

Logo designed by Alex Guillen

Marissa Kinney defended her master’s thesis on glucosinolate metabolism by gut bacteria!

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Lab rockstar, Marissa Kinney, successfully defended her master’s thesis today!!! After a well-earned holiday break, Master Kinney is pursuing a career in biomedical/microbiological research.

Marissa Kinney

Marissa was Master of Science student in Microbiology, and a researcher in the One Health and the Environment program, both of which are prestigious graduate programs at UMaine, from Jan 2023 – Dec 2024. She loves learning and bench microbiology, and she employed these passions on multiple lab projects investigating the bacteria which transform glucoraphanin in broccoli sprouts into the anti-inflammatory sulforaphane in the gut. The focus of her time has been to develop new lab protocols, refine existing ones and make them easier for new lab members to learn, and to share her expertise by teaching other students in the lab. She’s excelled at these objectives so well, that in the past two years many people assumed she was a Lab Manager rather than a student.

Marissa has been extremely productive in the last two years: in her first three months she contributed lab work to two publications on broccoli sprout diets in mouse models of Inflammation Bowel Disease in 2023, and has since contributed to another manuscript currently in review on glucoraphanin supplements and gut microbiome changes in people, and two more manuscripts in preparation on culturing gut microbiota, and a broccoli sprout diet in people. It’s no surprise that Marissa has been an author on so many papers in so little time — she led a publication when she was an undergraduate! You can check her Google Scholar page for more info on these papers. Marissa has also presented this work on campus at the UMaine Student Research Symposium twice, as well as attended conferences for the American Society for Nutrition and the American Society for Microbiology for professional development.

  • Marissa Kinney presenting research.
  • The Ishaq Lab at Boda Borg in Boston, summer 2023. We are showing how many quests we completed.
  • Lab lunch with Mira Talalay, Sue, and Marissa Kinney

Previous to being in the lab, Marissa 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. After 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 felt a big pull towards laboratory work and academic research, and her graduate work enforced this passion. Marissa has been a core member of the lab, and we’ll miss her!! She plans to pursue a research career here in Maine after defending and enjoying a well-earned vacation.

USING BROCCOLI SPROUT DIETS TO UNDERSTAND GUT BACTERIAL GLUCOSINOLATE METABOLISM TO RESOLVE INFLAMMATORY BOWEL DISEASE

Abstract

Globally, millions of people have been diagnosed with a type of inflammatory bowel disease (IBD). These diseases cause dysfunction of the gastrointestinal (GI) tract, resulting in a wide range of symptoms that create a disruption in overall health. Research has suggested that diet and the microbial community composition of the gut microbiome play a significant role in regulating gastrointestinal inflammation. Specifically, studies have shown that diets high in cruciferous vegetables, such as broccoli, are associated with a reduction in gastrointestinal inflammation. Glucoraphanin is a compound present in broccoli that can be metabolized by gut bacteria to become an anti-inflammatory compound known as sulforaphane. Our initial research showed that the administration of a broccoli sprout diet to mouse models for Crohn’s disease and ulcerative colitis, two major types of IBD, yields inflammation reduction and symptom resolution. For these trials, fecal samples obtained from different sections of the mouse bowel were tested for presence of glucoraphanin-metabolizing genes present in a common gut bacteria, Bacteroides thetaiotaomicron (B. theta). Glucoraphanin conversion is higher and more reliable in mice than in people, however mouse models are not perfect representatives of humans. Hoping to understand the impacts of broccoli sprouts on the human gut microbiome, fecal samples were obtained from healthy individuals who consumed broccoli sprouts for 28 consecutive days, as long-term diet interventions are needed to meaningfully change gut microbial communities. In a separate trial conducted by the scientists at Brassica Protections Product, fecal samples were collected from people who were administered a single dietary supplement containing a high dose of glucoraphanin with and without plant-sourced myrosinase, as a means of evaluating the effectiveness of glucoraphanin conversation which was or was not reliant on gut microbiota, respectively. These samples were analyzed for glucoraphanin metabolizing genes from B. theta and other commensal gut bacteria. Data collected from these human trial experiments aided in understanding the impacts of a whole food broccoli sprout diet and supplementation of glucoraphanin on the bacterial community composition of the gut microbiota. Additionally, this work will help grow and strengthen the current knowledge on broccoli as an anti-inflammatory and the variabilities present in the gut microbiomes of humans.

Alice Hotopp prepares for her dissertation defense on feather melanism, adapation, and feather microbes!

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Alice Hotopp will defend her PhD dissertation this Thursday! The presentation is open to the public, and the zoom link is here. Alice is in the Ecology and Environmental Sciences program, and she is advised by Drs. Kristina Cammen and Brian Olsen. She has been an affiliate of the Ishaq Lab for several years, as some of her work investigated the bacterial and fungal communities on feathers of several species of salt marsh sparrows, and she performed much of the data analysis on a study identifying bacteria that can be transferred by nemotodes to ants.

Hotopp-Defense-FlyerDownload
Alice Hotopp

Alice Hotopp, M.S.

Alice is a PhD candidate in Ecology and Environmental Sciences, co-advised by Drs. Kristina Cammen and Brian Olsen. Alice is part of the Genomic Ecology of Coastal Organisms (GECO) research group, which studies the genomic basis of adaptation in sparrow species inhabiting tidal salt marshes along the Atlantic coast of North America. Alice’s research focuses on understanding potential evolutionary drivers of plumage coloration, such as plumage microbial communities, in tidal marsh sparrows. 

Papers published with the Ishaq Lab:

Hotopp AM, Olsen BJ, Ishaq SL, Frey SD, Kovach AI, Kinnison MT, Gigliotti FN, Roeder MR, Cammen KM (2024) Tidal marsh sparrow plumage microorganism communities. iScience. 27: 108668.

Ishaq SL, Hotopp A, Silverbrand S, Dumont JE, Michaud A, MacRae JD, Stock SP, Groden E. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal Maine. iScience. 2021 May 29;24(6):102663.

Lola Holcomb won a student research award from the Bioscience Association of Maine!!

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Congratulations to Lola Holcomb, PhD candidate in the Graduate School for Biomedical Sciences and Engineering program, for winning a graduate student research award from the Bioscience Association of Maine!!

Over the next few months, she’ll focus on characterizing candidate anti-inflammatory bacterial species and genes of the gut microbiome, using whole genome sequence data from bacteria we previously isolated during a broccoli sprout diet study. This is part of Lola’s larger PhD project investigating which bacteria produce sulforphane in the gut, how they do it, and under which circumstances. It complements the collective lab research on how broccoli sprouts and gut microbes can be used to resolve Inflammatory Bowel Disease.

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

Lola Holcomb, B.S.

Doctorate of Philosophy candidate, Biomedical Science

Lola entered as a rotating first-year GSBSE student in March 2022, and declared the Ishaq Lab her dissertation lab soon after.  Troubled with indecisiveness and the desire to research, well, everything, she quickly found that using bioinformatics and big data as a lens to study microbial ecology (and in time, its relation to social equity) allowed her to do the kind of meaningful interdisciplinary research she’s always wanted to do.  Lola is currently working on 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 is currently doing 16S data analysis for ongoing lab projects and developing a metagenomic analysis workflow to compare gut microbiomes of mouse models of Inflammatory Bowel Disease with broccoli as a dietary treatment. In addition to research, she instructs a graduate-level Genetics course, tutors several Biology undergraduate students, and serves as a GSBSE senator in the Graduate Student Government here at UMaine. 

Google Scholar page.

MSE seminar this Friday on “Advancing Queer and Transgender Equity in Science (AQTES)”

sueishaqlabLeave a comment
The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

Events will be hosted January – December, 2024, once a month on a Friday, 12:00 – 14:00 pm ET. Presented over Zoom.

After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine and the UMaine Cultural Affairs/Distinguished Lecture Committee.

Register here for free!

“Advancing Queer and Transgender Equity in Science (AQTES)“

Presented by Dr. JL Weissman and other members of the Advancing Queer and Transgender Equity in Science (AQTES) working group

Dec 20, 2024 12:00 PM Eastern Standard Time

Jackie Lee “JL” Weissman (they/she) is an Assistant Professor at Stony Brook University starting Fall 2024. Her research examines how microbes survive and thrive across diverse environments. She develops new tools to infer what microbes are doing and can do from DNA sequences captured directly from the environment (“metagenomes”), aiming to improve the representation of microbially-mediated biogeochemical cycles in global climate models. She also has a special interest in using a combination of comparative genomics, population genetics, and mathematical models to understand the ancient and ongoing battle between microbes and their viruses. She believes all students, with supportive training and mentorship, can become highly-capable computational biologists, and loves to show students how a little coding can go a long way.

The newly-formed group, Advancing Queer and Trans Equity in Science (AQTES), wants to improve the field of research by making the hiring process fair and welcoming for everyone. No matter what your personal identity is, we can all agree that fair and unbiased job searches are critical to hiring the best talent. But, sometimes a poorly-organized job search prevents the people with the best talent from applying at all.

In our white paper, we give suggestions on how to host a job search that is better for everyone. We provide examples and advice on how to write job adverts, create the agenda and atmosphere for the job search, how to make the interview process more accessible for everyone by remembering that we are humans and not robots, and how to support your new faculty.

Citation for the paper: Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES). 2024. Running a queer- and trans-inclusive faculty hiring process. EcoEvoRvix repository 6791.

Perspective piece introducing the paper:  Weissman JL, Chappell CR, Francesco Rodrigues de Oliveira B, Evans N, Fagre AC, Forsythe D, et al. (2024) Queer- and trans-inclusive faculty hiring—A call for change. PLoS Biol 22(11): e3002919.

Logo designed by Alex Guillen

Alexis Kirkendall won a student research award from the Bioscience Association of Maine!!

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Congratulations to Alexis Kirkendall, PhD student in the Microbiology Program, for winning a graduate student research award from the Bioscience Association of Maine!!

Over the next year, she’ll focus on culturing bacteria that we previously isolated from mice consuming a steamed broccoli sprout diet, to test their capacity to grow amongst the gut pathogen Helicobacter pylori and produce the anti-inflammatory sulforphane under different conditions. This will be part of Alexis’ larger PhD project investigating which bacteria produce sulforaphane in the gut, how they do it, and under which circumstances. It complements the collective lab research on how broccoli sprouts and gut microbes can be used to resolve Inflammatory Bowel Disease.

Alexis Kirkendall

Doctor of Philosophy student, Microbiology

Alexis is from Ohio and initially joined the lab in 2022 when she was majoring in Biology at Heidelberg University, through the Summer 2022 REU, during which she divided her time researching Cryptosporidium in cows, helping in the MSE Symposium, and aiding in the Camel Rumen Microbiome Project. Alexis 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. Her research interests are in genetics and she has a love for the fascinating world of microbes.

She returned in January 2024 as a graduate student in the Microbiology program!

 

MSE seminar today: “Building multifunctional agricultural landscapes – from microbes to people.”

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Events will be hosted January – December, 2024, once a month on a Friday, 12:00 – 14:00 pm ET. Presented over Zoom.

After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine and the UMaine Cultural Affairs/Distinguished Lecture Committee.

Register here for one or all speakers for free!

“Building multifunctional agricultural landscapes – from microbes to people”

Dr. Aidee Guzman, PhD.

Dec 6, 2024 12:00 PM Eastern Standard Time. This event has passed, watching the recording here.

Dr. Aidee Guzman is an assistant professor at Stanford University in the Department of Biology in the Ecology and Environmental Science group. Her research group examines agroecological approaches that could harness biodiversity and ecosystem functioning for improved agricultural resilience. Specifically, they investigate how agricultural management impacts biotic interactions (e.g. between plants, insects, and soil microbes) across scales (e.g. shifts in community structure, cascading changes in ecosystem functioning). The overarching goal of her research program is to support farmers, especially those who are historically underserved, through research, education, and outreach that builds on their innovations and demonstrates ecological pathways to agricultural resilience. 

Lab website here.

Logo designed by Alex Guillen

Marissa Kinney set to defend her master’s thesis on glucosinolate metabolism by gut bacteria!

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Lab rockstar, Marissa Kinney, is set to defend her Master’s of Science thesis in Microbiology on Wednesday, December 18th!! The thesis abstract is below.

You can register here for the publicly available seminar portion from 1 – 2 pm ET on Zoom

Marissa Kinney

Marissa has been a Master of Science student in Microbiology, and a researcher in the One Health and the Environment program, both of which are prestigious graduate programs at UMaine, for the last two years. She loves learning and bench microbiology, and she employed these passions on multiple lab projects investigating the bacteria which transform glucoraphanin in broccoli sprouts into the anti-inflammatory sulforaphane in the gut. The focus of her time has been to develop new lab protocols, refine existing ones and make them easier for new lab members to learn, and to share her expertise by teaching other students in the lab. She’s excelled at these objectives so well, that in the past two years many people assumed she was a Lab Manager rather than a student.

Marissa has been extremely productive in the last two years: in her first three months she contributed lab work to two publications on broccoli sprout diets in mouse models of Inflammation Bowel Disease in 2023, and has since contributed to another manuscript currently in review on glucoraphanin supplements and gut microbiome changes in people, and two more manuscripts in preparation on culturing gut microbiota, and a broccoli sprout diet in people. It’s no surprise that Marissa has been an author on so many papers in so little time — she led a publication when she was an undergraduate! You can check her Google Scholar page for more info on these papers. Marissa has also presented this work on campus at the UMaine Student Research Symposium twice, as well as attended conferences for the American Society for Nutrition and the American Society for Microbiology for professional development.

  • Marissa Kinney presenting research.
  • The Ishaq Lab at Boda Borg in Boston, summer 2023. We are showing how many quests we completed.
  • Lab lunch with Mira Talalay, Sue, and Marissa Kinney

Previous to being in the lab, Marissa 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. After 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 felt a big pull towards laboratory work and academic research, and her graduate work enforced this passion. Marissa has been a core member of the lab, and we’ll miss her!! She plans to pursue a research career here in Maine after defending and enjoying a well-earned vacation.

USING BROCCOLI SPROUT DIETS TO UNDERSTAND GUT BACTERIAL GLUCOSINOLATE METABOLISM TO RESOLVE INFLAMMATORY BOWEL DISEASE

Abstract

Globally, millions of people have been diagnosed with a type of inflammatory bowel disease (IBD). These diseases cause dysfunction of the gastrointestinal (GI) tract, resulting in a wide range of symptoms that create a disruption in overall health. Research has suggested that diet and the microbial community composition of the gut microbiome play a significant role in regulating gastrointestinal inflammation. Specifically, studies have shown that diets high in cruciferous vegetables, such as broccoli, are associated with a reduction in gastrointestinal inflammation. Glucoraphanin is a compound present in broccoli that can be metabolized by gut bacteria to become an anti-inflammatory compound known as sulforaphane. Our initial research showed that the administration of a broccoli sprout diet to mouse models for Crohn’s disease and ulcerative colitis, two major types of IBD, yields inflammation reduction and symptom resolution. For these trials, fecal samples obtained from different sections of the mouse bowel were tested for presence of glucoraphanin-metabolizing genes present in a common gut bacteria, Bacteroides thetaiotaomicron (B. theta). Glucoraphanin conversion is higher and more reliable in mice than in people, however mouse models are not perfect representatives of humans. Hoping to understand the impacts of broccoli sprouts on the human gut microbiome, fecal samples were obtained from healthy individuals who consumed broccoli sprouts for 28 consecutive days, as long-term diet interventions are needed to meaningfully change gut microbial communities. In a separate trial conducted by the scientists at Brassica Protections Product, fecal samples were collected from people who were administered a single dietary supplement containing a high dose of glucoraphanin with and without plant-sourced myrosinase, as a means of evaluating the effectiveness of glucoraphanin conversation which was or was not reliant on gut microbiota, respectively. These samples were analyzed for glucoraphanin metabolizing genes from B. theta and other commensal gut bacteria. Data collected from these human trial experiments aided in understanding the impacts of a whole food broccoli sprout diet and supplementation of glucoraphanin on the bacterial community composition of the gut microbiota. Additionally, this work will help grow and strengthen the current knowledge on broccoli as an anti-inflammatory and the variabilities present in the gut microbiomes of humans.

Dr. Alaba begins a postdoc position in the Michelsen Lab at Cedars-Sinai!

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The Ishaq Lab congratulates Dr. Tolu Alaba on accepting a postition as Postdoctoral Researcher at Cedars-Sinai!!! Tolu will be working in Dr. Michelsen’s Lab which focuses on exploring immune pathways contributing to Inflammatory Bowel Disease-related fibrosis, and Cedars-Sinai is a non-profit organization for healthcare research, education, and services. This position is in line with Tolu’s career goals of using nutrition to influence health.

Tolu presenting at a Functional Food Conference in 2024.
Tolu performing metabolomics at UC Irvine during her PhD.
Tolu Esther Alaba is standing in front of a science conference poster, smiling, and holding her infant.
Tolu Esther Alaba at her 2024 CIMM poster.
Tolu performing metabolomics at UC Irvine during her PhD.

MSE seminar this Friday, “Building multifunctional agricultural landscapes – from microbes to people”

sueishaqlabLeave a comment

Events will be hosted January – December, 2024, one a month on a Friday 12:00 – 14:00 pm ET. Presented over Zoom.

After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine and the UMaine Cultural Affairs/Distinguished Lecture Committee.

Register here for one or all speakers for free!

“Building multifunctional agricultural landscapes – from microbes to people”

Dr. Aidee Guzman, PhD.

Dec 6, 2024 12:00 PM Eastern Standard Time. This event has passed, watching the recording here.

Dr. Aidee Guzman is an assistant professor at Stanford University in the Department of Biology in the Ecology and Environmental Science group. Her research group examines agroecological approaches that could harness biodiversity and ecosystem functioning for improved agricultural resilience. Specifically, they investigate how agricultural management impacts biotic interactions (e.g. between plants, insects, and soil microbes) across scales (e.g. shifts in community structure, cascading changes in ecosystem functioning). The overarching goal of her research program is to support farmers, especially those who are historically underserved, through research, education, and outreach that builds on their innovations and demonstrates ecological pathways to agricultural resilience. 

Lab website here.

Logo designed by Alex Guillen