Author: Kat Milligan-Myhre

Summer 2019 lab update

Oh wow, it only took me a couple of years to get bad at updating information about our lab. I have reasons, but let’s focus here on an update of our lab over the last year.

In the past year we had a ton of people leave, and some new people come and go. I will never get used to this in academia. Several of these fine folks are looking for graduate school (see Cooper Danner) or permanent positions (Drs. Amber Nashoba, Lucas Kirshman, and Emily Lescak; Dr. Lescak is also doing consulting work). Please take a look at their information on the “Former members” part of the “People” page for contact information!

It has been a rough year. In addition to losing several fantastic people, our lab survived a huge earthquake in November, fought for funding in the spring and summer as the legislature and Governor fought over the budget for the University of Alaska, survived smoke and high temperatures that almost threatened our fish in our vivarium this summer, and are now facing the uncertainty of the future of the University of Alaska Anchorage as the University of Alaska has declared financial exigency and is debating becoming one accredited University rather than maintaining three separate accredited Universities.

However, we were also able to overcome some big hurdles. After several years, we now have a good protocol for sequencing the 16S gene from adult fish, and are in the process of analyzing gut microbiota from at least 6 different large experiments. Our former technician Katie D’Amelio (now with NOAA) was instrumental in getting an efficient labeling protocol going, and former technician Rachael Kramp (now a PhD student at the University of Pittsburgh) was able to improve on the protocol and together they were able to get several libraries sequenced this spring. Our grad students Ryan Lucas and Levi Wegner have been working diligently to get these analyzed in Qiime, while I have been attempting to get these working in Mothur. Hopefully we’ll have established pipelines by the end of this month in both.

Our former postdocs Dr. Emily Lescak and Dr. Lucas Kirschman are both very close on finishing manuscripts from their work in the lab. Keep an eye out for both!

Master’s student (and former undergraduate) Kelly Ireland started a new project identifying gut microbes that can degrade crude oil for potential bio-remediation during oil spills. This earned her a fellowship with ADAC, which comes with funding and more research experience related to Arctic issues. See a story about her research here.

Master’s student Levi Wegner earned funding from the Sloan foundation, which will help him complete a project examining the relationship between MHCII diversity and gut microbiota diversity in several stickleback populations. Congratulations!

Finally, we are part of a huge evolution project headed by Dr. Andrew Hendry and Dr. Michael Bell. Under their leadership, over 10 labs from across the world are working together to study the evolution of fish in several lakes. Look for a story from Dr. Hendry on this topic soon.

 

 

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Old news

I am going to remove the lab news part of this page and just use posts from now on. For archiving purposes, here is the old “Lab News!” portion of our website.

 

July 2017

Dr. Kat attended the Summer Internship for Indigenous Peoples in Genomics (SING) in Tucson, Arizona.

June 2017

Emily Lescak and Kenneth Sparks presented at the Evolution meeting in Portland Oregon. Emily gave a talk titled:  Gene-By-Environment Interactions Drive Developmental Responses to Antibiotic Exposure in Threespine Stickleback Fish. Kenneth presented a poster: Effects of Antibiotic Exposure on Growth of Bacterial Strains Isolated from Threespine Stickleback Guts.

Dr. Kat gave a talk at the Fish Microbiota meeting in Trondheim, Norway: Gene-by-environment interactions drive microbiota variation and response to antibiotics.

Dr. Kat also presented a poster at the ASM Microbe 2017 meeting in New Orleans, LA: Fishing for Contributions of Host Genetic Background to Host-Microbe Interactions.

May 2017

Kelly Ireland, Kenneth Sparks, and Jeremiah Lewis received the OURS/Aalska INBRE undergraduate research assistantship awards! Congratulations to all three! Kelly used hers to create a qRTPCR protocol to measure immune response genes in stickleback raise in different microbial environments; Kenneth created two mock stickleback gut communities and compared their ability to withstand antibiotic challenge in vitro vs in vivo. Jeremiah designed a survey to gather information about Kombucha brewing so that he could collect samples from various sources and characterize the microbes associated with kombucha.

Ruth Isenberg presented a poster at the UABRC in Fairbanks titled: The Effect of a Host’s Environment on the Composition of Their Gut Microbiota.

April 2017

Emily Lescak gave a talk at the Pacific Northwest SETAC meeting in Anchorage, Alaska: Gene-By-Environment Interactions Drive Developmental Responses to Environmentally Relevant Levels of Antibiotic Exposure in Threespine Stickleback Fish

March 2017

Master’s student Ryan Lucas presented a poster at the American Fisheries Society meeting in Fairbanks Alaska: Effects of tetracycline on somatic development in threespine stickleback fish.

February 2017

Undergraduate Kenny Sparks received a UAA Honors College Undergraduate Research Award for his work determining how the microbiota of fish respond to exposure to antibiotics. As part of this project, Kenny will be creating a stickleback artificial gut microbiota community that we hope to use in future studies as well.

Kat gave a talk at the Oceans and Atmosphere Colloquium at Stony Brook University.

January 2017

Kat was featured in an article about her participation in the National Research Mentoring Network program, highlighting her experience learning how to write grant proposals with their GUMSHOE (Grantwriting Uncovered: Maximizing Strategies, Help, Opportunities, Experiences) group.

December 2016

Research in the Milligan-Myhre lab was highlighted in the Green and Gold paper. It included a video with interviews from several lab members!

Fall 2016

September 2016: Kat gave a talk at the UAF Institute of Arctic Biology.

Undergraduate Kelly Ireland has received a UAA Honors College Undergraduate Research Award and the American Fisheries Society Alaska Chapter Molly Ahlgren Award for her work validating qPCR assays to measure immune response in stickleback. This protocol will be used in many aspects in the lab, including the ability to measure the immune response in fish from different populations that are exposed to microbes isolated from stickleback guts.

Summer 2016

We are excited to have been chosen as mentors for the American Fisheries Society’s Hutton Program. An Anchorage high school student will be working with us this summer on metagenomic data analysis.

Masters student Ryan Lucas has received an Alaska INBRE graduate student fellowship to study the effects of clinical levels of antibiotics on microbial community composition and immune response in stickleback.

Postdoc Emily Lescak has received an NSF Broadening Participation postdoctoral fellowship to study the effects of environmentally-relevent levels of antibiotics on microbial community composition and development in stickleback.

Lab Members on the Road!

Kat gave a talk at the Evolution Meeting in June.

Emily attended ECOGEO in July 2017.

Foster attended the Research Institute at MIT summer of 2016.

Fish Tech position opening

The Milligan-Myhre and Weber Labs at the University of Alaska Anchorage are hiring a full-time technician to oversee fish-care and help with a diversity of research projects.

Links to lab websites:
Dr. Milligan-Myhre and Dr. Weber

Your duties (among other things):

Help lab mates (undergraduates, graduate students, postdocs) with their projects, including research on microbiomes, immunology, genetics, parasite infections, field studies, etc. See our lab webpages for full descriptions of people and ongoing research. All of these projects are united around their focus on a powerful model organism–the threespine stickleback fish.

Maintain and breed several populations of fish from both Alaska and BC in the lab

Experiment with freezing and recovering fish sperm and eggs

Maintain and expand microbe and parasite stocks

Maintain a copepod colony, which will be used for experimental parasite infections

Play with (or, formally, experiment with) microbes and parasites in our collection

Order supplies/help keep things orderly

Opportunities:

Gain experience in animal husbandry, sterile technique, high-throughput DNA sequencing and analysis, and flow cytometry

Conduct field-sampling expeditions for fish, microbes, and parasites throughout Alaska

Opportunities to do outreach in the STEM fields throughout the year

Contribute to data collection, analyses, and writing, with the possibility of authorship on lab publications

Minimum Qualifications:

Bachelor’s degree, preferably in Biology-related field

Enthusiasm to learn new techniques, organizational skills, detailed oriented, record keeping, ability to work well with others required

Currently reside in, or willingness to move to, Anchorage, Alaska

Preferred Qualifications:

1-4 years research experience involving fish care and husbandry

Other details:

40 hours/week

Research Tech level 2-4 (see descriptions below)

Funding for position through Dec 2019.

How to apply:

The position is listed as temporary. For UAA, this means 18 months, after which you will need to take 120 days off.  We may be able to extend that, depending on funding.

Please send Kat an email (see “Contact us”) with your CV, 3 references, and a cover letter, and apply to the link below.

http://careers.alaska.edu/cw/en-us/job/506368/cas-research-20172018-research-technician-14-pool

Research tech levels

Research Technician 2: One year college coursework in relevant field and one year experience in a field relevant to the research or an equivalent combination of training and experience.

Research Technician 3: Two years experience in relevant field, or acceptable combination of education and experience.

Research Technician 4: Bachelor’s degree in a field relevant to the research and four years experience in a field relevant to the research, or an equivalent combination of training and experience.

Additional descriptions of each job level can be found here.

Minimum Hourly Wage/Salary: Varies according to project requirements and level of position to be filled.

Research Technician 2: Grade 76, Step 1, $18.18/hour

Research Technician 3: Grade 77, Step 1, $20.47/hour​

Research Technician 4: Grade 78, Step 1, $22.36/hour

Notice of Nondiscrimination:

Equal opportunity employer. We encourage women and minorities to apply.

The University of Alaska is an affirmative action/equal opportunity employer and educational institution.  The University of Alaska does not discriminate on the basis of race, religion, color, national origin, citizenship, age, sex, physical or mental disability, status as a protected veteran, marital status, changes in marital status, pregnancy, childbirth or related medical conditions, parenthood, sexual orientation, gender identity, political affiliation or belief, genetic information, or other legally protected status. The University’s commitment to nondiscrimination, including against sex discrimination, applies to students, employees, and applicants for admission and employment. Contact information, applicable laws, and complaint procedures are included on UA’s statement of nondiscrimination available at www.alaska.edu/nondiscrimination

#NewPIAdvice/#NewPI

As I prepare for my 4th year review, I have time to reflect on my first 3 years in a tenure track position at a primarily undergraduate university. For those of you just joining the ranks of TT, I thought I’d pass on advice that helped me the most these first two years. As an under-representative minority (URM) and woman, much of this advice will be shaped by those experiences.

Research:

  1. Your first semester will be spent ordering things. If you have funding in your start-up, hire a good lab manager to handle ordering and negotiating deals from reps.
  2. Go to conferences and make the most of them. Call/email your funding org (NIH or NSF) ahead of time and find out if your PO will be there. If they are, set up a meeting time, and have questions ready to ask. Set up meetings with potential collaborators and potential mentors. I have gotten a lot of great advice from both. If you aren’t great at meeting people for the first time, ask a mentor or outgoing friend to introduce you to people. Don’t be afraid to talk to folks in your field with more experience or expertise than you. The good ones will be open to talking; the ones that blow you off are folks to cross off your list of potential collaborators.
  3. Find collaborators who will be supportive and who value your expertise. Steer clear of those that want you on their grant because they believe it will improve their chances of getting funding if they include an URM or PI with early investigator status.
  4. If your University has a heavy research requirement for tenure, make sure you protect your research time. This means learning how to say no.
  5. If offered, attend grant writing and/or manuscript writing workshops. I attended GUMSHOE through the National Research Mentoring Network (NRMN; https://nrmnet.net/) and found it extremely helpful.

Teaching:

  1. If your University offers teaching assistance, use it. My University provides workshops in effective teaching styles, student assessment, etc. I wish I had spent more time my first two years attending those workshops.
  2. If you are teaching a class that was previously taught at your university, get as many of the previous year’s resources as possible. You should design your own syllabus/lectures/exams/etc, but it helps to have a starting point. If you are designing a class that has never been taught, talk to people who have taught a similar class at other Universities.
  3. If you are URM, be prepared with a response for students that question your qualifications to teach. I run through my qualifications my first class (almost 20 years’ experience in microbiology, classes I’ve taken, quick rundown of my studies) in a 2 minute summary, and restate that summary when challenged by students. My qualifications were challenged my first four semesters.
  4. Have a teaching mentor. Have them come to one of your classes to watch you teach, and get feedback from them in person and in writing. The written comments should go in your tenure track portfolio.
  5. Get advice on how to best use teaching evaluations. Few students (5 out of a class with 130 students) responded to the on-line evaluations my university uses, so I get feedback from students during class. I used Google Surveys these last two classes and feedback went down again. It’s more laborious to get in-class comments, but you get higher quality comments that way.

Mentoring:

  1. Figure out how many people you can handle. I have ~15 people in my lab currently. I started with one postdoc my first year and that was about all I could handle at that time. My second year I added a tech, master’s student, and 5 undergrads. I think that was too many undergrads. I added two postdocs this year, who will help mentor the undergrads, and two part-time techs.
  2. Have weekly meetings with the people in your labs. I have a group meeting weekly and one-on-one meetings weekly for people in my lab 40 hours a week, and every other week for the undergrads.
  3. Get feedback from your mentees. Remember that each person is different; some will require more supervision than others. Be upfront with your mentees about how much time you can offer, but also be generous with these folks.
  4. If your University offers mentoring for you, take advantage of it. I have a mentoring committee that meets with me yearly to give me feedback. More importantly, those are three people that I can contact with questions almost any time.
  5. Keep track of who has been in your lab and what their major accomplishments were for letters of recommendation and for grants. I started a spreadsheet with every person who has ever worked in my lab, when they started, what they worked on, what their major accomplishments were, and where they went after their time in my lab.

Service:

  1. Be protective of your time. This is especially true for URM, LGBTIQ, and women. Figure out which activities are going to make the most impact, both in terms of encouraging up and coming scientists, and in giving you satisfaction and do those.
  2. Choose your university service wisely. Find out which are related to your research and passions and serve on those committees.
  3. Learn to let others lead. You likely became a PI because you have exhibited leadership ability. It’s easy to want to lead the committees you’ll be on, but that can be time consuming during a time when you should be focused on teaching and research.
  4. Learn to say no. I said it before, and I’ll say it again because it is so. Very. Important. Also, learn when to say yes.
  5. Put all your outreach/service/leadership activities in a master CV so that when you are writing your annual report and/or your workload, you are given credit for all the service you do. It’s also a good way to look back on your year and figure out if you have spent your time wisely.

Organization:

  1. Keep a master CV with ALL the things you do. This will be used for activity reports, updating NIH biosketches and NSF CVs, completing just-in-time documents for grants, etc. Mine has a table of contents so that I can find each section easily.
  2. Keep a folder for every academic year that breaks down the tenure requirements. For example, I have a master folder called “Tenure Track” with subfolders for each year; within each of those are the subfolders “Teaching” “Research” “Service” “Other”. Teaching has evaluations and syllabus for each class; research includes the submission and acceptance letters for each grant; service includes letters for each committee; other includes mentee information etc.
  3. Figure out what calendar/to-do list system works best for you.
  4. Keep notes of the weekly meetings with your mentees (if you have weekly meetings) or updates on their projects.
  5. Find a communication tool that works best for your lab. We use WhatsApp for day-to-day conversations, email for formal things, and online shared folders for documents.
  6. Read an email but didn’t do the thing that was asked of you? Mark it unread and keep an unread folder or to-do folder in your email box.
  7. Find a way to organize your other stuff. I use spreadsheets galore. I have spreadsheets for everything we’ve ever ordered in the lab, every collection we’ve done, every sample we’ve processed.

Self-care:

It’s so easy to lose yourself in the first year or two. Make sure you maintain good self-care. These are some steps I took; you’ll need to find what works best for you.

  1. Exercise! For me that was running. I have a running buddy who makes sure I prioritize a long Sunday run. Releases tension, clears my head, and gives me an outlet. My running partner my first year was also another first year TT in the department, so we used that time to support each other as well.
  2. Prioritize family. I have a standing lunch date with my spouse and keep (or try to) 6-9pm for my kids.
  3. Don’t let health issues slide. I didn’t get a sore shoulder checked out and ended up with over 1.5 years of physical therapy trying to get a frozen shoulder back in working order.
  4. Reward yourself. It’s easy to not celebrate an accomplishment. They can be few and far between…make sure you acknowledge when you and your mentees have done well!
  5. Find what work/life balance works best for you. I take each Saturday off, for example.

Keep in mind this is not an exhaustive list, just a quick jot-down of the things that I’ve found helpful. There are SO many great resources out there for new PIs. Take advantage of the Slack NewPI channel, twitter, read books on teaching and mentoring, and remember to take all the advice (even mine!) with a grain of salt. Find what works for you, and reevaluate once in a while. Remember to breathe, not to take it all TOO seriously, and realize that this is a job, but it’s also a part of your life. If you aren’t enjoying it, find a way to make it enjoyable.

New Kat MM lab members!

I am very excited to announce that we have several new members of the Milligan-Myhre lab. In alphabetical order:

Katie D’Amelio, research technician, completed her M.S. at Drexel University in Philadelphia, PA where she studied the gut microbiome of army ants. Her research focused on identifying how different factors such as host genetics, transmission mode, and host natural history may shape the diversity of microbes found within the army ant gut. She has switched from insects to vertebrates and now studies the gut microbiota of stickleback fish in the Kat Lab.  She will focus on sequencing bacterial communities of stickleback guts and creating whole genomes of bacterial isolates.

Lucas J. Kirschman, postdoc, is a physiological ecologist who studies how life history trade-offs affect animal development, immune function and how these interactions can scale up to ecosystem level processes. He recently received his Ph.D. from Southern Illinois University Carbondale where he studied the pleiotropic effects of neuroendocrine stress on during a critical window of development in larval amphibians. Dr. Kirschman will initially focus on host selection and shaping of gut microbial communities, including both developmental tradeoffs and immune response genes.

Amber R. Nashoba, postdoc and research professional, is interested in the application of evolutionary theory to understand and address environmental change. Her dissertation research studied population-level adaptation, natural selection, and the response to selection of a native prairie legume (Chamaecrista fasciculata). This project focused on the empirical application of Fisher’s Fundamental Theorem of Natural Selection and among-year environmental variation in the form of trait relationships, adaptive capacity, and fitness landscapes. She recently completed a Future Faculty Fellowship at the Northeastern University; during this time, she examined allele frequency change in drought and salinity associated genes in newly restored Spartina alterniflora in a Rhode Island salt marsh. In our lab, Dr. Nashoba will focus on phenotypic changes in a population of stickleback that is undergoing rapid selection and adaption to a novel microbial environment. Dr. Nashoba has been a member of the American Indian Science and Engineering Society since 2011.

Kat O’Brien, fish technician, previously worked at Northeastern University modeling Atlantic cod (Gadus morhua) Essential Fish Habitat (EFH) in the Gulf of Maine. With the rising ocean temperature and cod stocks declining, EFH is a good indicator where the few remaining cod could be. This information enables researchers and managers to make cogent decisions on fishing area designations. O’Brien now works as a husbandry technician at UAA, working in both the vivarium and in the Milligan-Myhre labs. She will focus on creating a vivarium for our recently funded stickleback stock center. O’Brien enjoys fly fishing, beach combing for sea glass, walking her dog, and SCUBA diving (not in Alaska).

I’m very excited about our newest members!  Now, back to the science.

Pros and cons of traveling as an assistant professor

I (Dr. Kat) have had an incredibly busy summer in terms of traveling. I have been trying to determine whether this amount of travel was appropriate/worthwhile for an assistant professor ending the 2nd year on the tenure track. Rather than just turn it over in my tiny brain, I thought I would write a post on it, to give others insight as well. Time permitting (ha!) I’d like to write a blog post for each of the work-related trips to summarize what I learned from each.

My Summer Travel:

ASM Microbe 2017 meeting in New Orleans May 31-June 5

Field work various days

Fish Microbiota workshop in Trondheim Norway June 17-25

SING workshop in Tucson Arizona July 9-15

Talkeetna trapping trip a weekend in July

Family trip end of August for two weeks

Wedding for close friends a weekend in August

Camping mid-week for two nights

 

Other obligations:

Teaching ANSEP high school students Microbiology 3 afternoons per week for two weeks

Hiring research tech/post docs

Committees (students and departmental)

 

Pros:

Networking. I met several people in person that I follow on twitter/studied their work/used their assays/etc. I’ve gained a new perspective on their work, received great advice for how to proceed down the tenure track, and received valuable advice for my work/TT path/balancing work-life/becoming a better mentor/giving back to my tribe. There are a couple of possible collaborations that may come from meeting various folks, including a chat with a person I sat next to on the plane who happens to work in my field. That networking is much harder to do over email/twitter/phone calls/skyping.

Visiting new places to gain a bigger perspective of the world. This is true in terms of place, people, research, mentoring, and insight into how I can become a better contributor to both my scientific and personal networks.

Exposure for my lab. This overlaps with networking quite a bit. Although I didn’t get much traffic at my poster at ASM, I was able to talk to quite a few people about the work our lab is doing and get feedback during one-on-one meetings. My students/postdoc also presented at Evolution and came back with some great ideas for their own projects. I gave a talk at the Fish Microbiota workshop that was well received, and may result in some collaborations.

Insight into what others are doing in my field. As a PI, I have almost no time during the day to catch up on the latest in publications. While I read abstracts/peruse papers from links via twitter, or take a quick look through the latest titles/abstracts that come to my email from pubmed and google scholar updates, listening to a talk provides more information in a short period of time. At meetings I also tend to learn more about things happening outside my field, or studies that are only tangentially related to my studies but that could have a big impact in the way we proceed. Not to mention the papers online are summaries of work that was done years ago, and typically don’t include the negative data or failed assays that are presented at posters/talks/gleamed from talking to people at a meeting.

 

Cons:

Time away from my family. This was especially hard as I have two daughters who are asking questions like “Do you love your work more than you love me?” (seriously folks, this was asked between trips 2 and 3.)

Time away from mentoring. While I feel like my lab handled my time away from the lab OK, this summer I didn’t feel like I was being a good mentor. In my mind, that includes weekly meetings, having time in the lab to help trouble shoot assays, handling my own project, etc. I obviously wasn’t in the lab or field as much this summer, and my disconnect from my mentees reflects that.

Time away from data collecting/processing. I need to publish papers from my own lab, and yet I collected very little data myself this summer. Since I teach during the spring and fall semester, this means I won’t have as much data for the year as I would like. This is weighing heavily on my mind as I enter my third year on the tenure track.

Time away from teaching prep. My teaching load is heavier than some and lighter than others. Theoretically I don’t need much teaching prep time, but I still would like more time to process the feedback I got back from my students last year, and to develop new classes.

Less time for subsistence and no time in Kotzebue. Summer is prime time in Alaska for fishing and berry collecting. Due to my travels this year I made the hard decision to not go home to Kotzebue to help my dad with fishing or my folks with berry picking and hunting. My parents are getting older, and my chances to camp/fish/hunt/pick with them is getting smaller with each season. One of the reasons I moved to Alaska was to be closer to my folks and home so that I could regain a connection with my family. The professional travel and decision to use vacation time in the Lower ’48 is stripping away my chances to do so.

I am so so so so far behind in administrative duties. As in my inbox is overflowing, and a student is waiting for me to finish my IRB training so that he can proceed with his work. (which also means it’s time to wrap up this post)

 

Conclusion:

While the networking and perspectives gained this summer were valuable, next summer I am going to prioritize time in Kotzebue, writing, and in the lab. I will send more of my students/mentees to conferences rather than attending myself. As a new PI, this summer was a good time to travel in that I was able to make valuable connections and get exposure to our work just as we’re prepping manuscripts. Strategically, although it was time well spent overall professionally, I think I could have shortened a couple of the trips and still gotten as much out of the conferences. I arrived a day early for each trip (traveling from Alaska means that most of my trips took an entire day for flights) and left either the last or next day for each trip. I will shorten that for future trips and lose a day or two on either end.

I am going to push to have my family join me on more of my trips next year to minimize my time away from them. This will cut back dramatically on my networking (many of the connections I made were over drinks, meals, or hikes).  I will also likely only attend a few days of a conference, rather than spend a week away at a time.

One final thought: There are pros and cons to attending big general meetings (ASM microbe) vs small meetings (Fish microbiota and SING). I was able to get a broader look into research that is only tangentially related to my work at ASM microbe and I met some great potential collaborators at ASM who didn’t attend the smaller meetings. However, the connections I made at the Fish Microbiota and SING meetings were deeper because we spent so much more time together (hiking trips, several dinners, social hours) and single sessions (as opposed to the multiples sessions in different rooms in large buildings at ASM) meant that I gave my full attention to each talk at the smaller meetings. I like the balance of a large meeting and a small meeting. Because the work in our lab is so interdisciplinary (microbiology, immunology, ecology, evolution), I think I will send my mentees to more meetings next year and only attend one small and one large meeting myself next summer.

One more final-final thought: I have some personal travel time at the end of the summer. This is the first real vacation with my entire family in three years. While it comes at a tricky time (just before classes start!) due to a family event, I am hoping it provides a desperately needed break just before I dive into year three. I also hope to incorporate real vacations in future summers.

May 2017: Awards and travel

Both Kelly Ireland and Kenneth Sparks were awarded the OURS-INBRE undergraduate research award! Congratulations to both. This funding will allow Kenneth to create a Stickleback mock community from bacteria isolated from stickleback guts in Oregon and two Alaskan populations, and allow Kelly to use the qRT-PCR assay she has been developing to determine the immune response to microbes in several different stickleback populations. Well done to both students.

Curious about what we do? Chat with one of us at the following meetings!

May 18/19 – Fairbanks, Alaska – Research technician and soon-to-be graduate student Ruth Isenberg will present a poster at the University of Alaska Biomedical Research Conference: “The Effect of a Host’s Environment on the Composition of Their Gut Microbiota”

June 1-5 – New Orleans, LA – Dr. Kat will present a poster and give a poster talk at the ASM Microbe meeting: “Fishing for Contributions of Host Genetic Background to Host-Microbe Interactions”
Poster talk:  6/2/2017 1:45:00 PM – 6/2/2017 2:35:00 PM
Poster: Poster Presentation Date/Time: Sunday Jun 4, 2017 12:15 PM – 2:15 PM
(For a meeting of this size, we are not able to consider special scheduling concerns)
Poster Board Number: SUNDAY – 887

June 19-23 – Trondheim, Norway – Dr. Kat will present a talk at the Fish Microbiota Workshop titled: Gene-by-environment interactions drive microbiota variation and response to antibiotics

June 23-27 – Portland, OR – Postdoctoral fellow Emily Lescak will give a talk titled: Gene-By-Environment Interactions Drive Developmental Responses to Antibiotic Exposure in Threespine Stickleback Fish

Other recent presentations:

Emily Lescak gave a talk at the Pacific Northwest regional Chapter of the Society of Environmental Toxicology and Chemistry meeting in Anchorage Alaska in April 2017 titled: Gene-By-Environment Interactions Drive Developmental Responses to Environmentally Relevant Levels of Antibiotic Exposure in Threespine Stickleback Fish

Graduate student Ryan Lucas presented a poster at the American Fisheries Society Alaska meeting in March 2017 in Fairbanks titled: Effects of tetracycline on somatic development in threespine stickleback fish

Postdoctoral Fellowship in Microbiology and/or Immunology

Update: We have hired a postdoctoral fellow. More details will follow in an updated post.

We are hiring! A postdoctoral position is available immediately at the University of Alaska Anchorage Biological Sciences Department in the laboratory of Dr. Kat Milligan-Myhre. We are interested in someone who has strengths in microbiology and/or immunology, and who is interested in using threespine stickleback fish as a model to study host-microbe interactions. You will study the contribution of the host genetic background on the interactions between the host and the microbiota, with a focus on the ability of the host to resist developmental delays due to the disruption of the microbiota and/or immune system.

Qualifications:

  • PhD in Biological Sciences, with an emphasis in microbiology, immunology or evolution preferred
  • Enthusiasm to learn new techniques; good organizational skills; detailed oriented record keeping; ability to work well with others
  • Willingness to move to Anchorage, Alaska

Opportunities:

  • Grant-writing experience
  • Mentor undergraduate/graduate students
  • Outreach opportunities throughout the year
  • Teaching opportunities available, but not required
  • Experiment with freezing and recovering fish sperm and eggs
  • Play with (I mean experiment with) microbes in our collection
  • Learn lab management skills through duties shared among lab members (fish husbandry, microbe stock maintenance, ordering supplies, etc)

Other details:

Full-time position

Funding for position through Dec 2018, possibly through Dec 2019

How to apply:

Equal opportunity employer. We encourage women and minorities to apply.

Please send Dr. Kat Milligan-Myhre (kat.mm at alaska dot edu) your cover letter, CV, three references, a statement of research interests and career goals (not restricted to academia), and favorite winter activity.

Research Technician wanted!

Update: We have hired a research technician. Updated post will follow soon. Thank you to everyone who applied!

We are hiring! Our research technician will be heading off to grad school mid-summer 2017. We need a new research technician to start in June 2017.

Your duties (among other things):

Help lab mates (undergraduates, graduate students, postdoc; see “People” to learn who you will work with) with their projects, including microbiome studies, immunology studies, field studies, etc (see the “About” section for a full description of what our lab works on)

Maintain fish in the lab

Experiment with freezing and recovering fish sperm and eggs

Maintain and expand microbe stocks

Play with (I mean experiment with) microbes in our collection

Order supplies/help keep things orderly

Opportunities to do outreach in the STEM fields throughout the year

Qualifications:

Bachelor’s degree, preferably in Biology-related field

0-4 years experience

Enthusiasm to learn new techniques, organizational skills, detailed oriented, record keeping, ability to work well with others required

Willingness to move to Anchorage, Alaska

Other details:

40 hours/week

Research Tech level 2-3

Funding for position through Dec 2018, possibly through Dec 2019

How to apply:

The position is listed as temporary. For UAA, this means 18 months, after which you will need to take 120 days off.  We may be able to extend that, depending on funding.

Please send Kat an email (see “Contact us”) with your CV, 3 references, and a cover letter, and apply to the link below.

http://careers.alaska.edu/cw/en-us/job/501227/20162017-cas-research-research-technician-14-pool

Equal opportunity employer. We encourage women and minorities to apply.

 

Mid summer accomplishments

I like to take a moment once in a while and think about what we’ve accomplished. It’s important to do that, because the day to day grind of doing science often involved lots of small jobs that don’t seem to contribute to the overall picture. Today’s thoughts:

It’s been almost a year since I started at the University of Alaska Anchorage. I started with a completely empty space to house my fish, and an almost completely empty bench. I was very fortunate to hire my postdoc, Dr. Emily Lescak, who started shortly after I did. Together we stuffed my bench with everything we would need to look at microbes, measure the development and isolate DNA from fish, and analyze the host immune responses to microbes.  Our very first undergraduate student, Brianna Triplett from my hometown (hopefully I’ll be able to talk about what it means to me to be able to have students from Alaska work with me), helped us clean, organize, and collect our first bits of data while taking a challenging course load.

In addition to building up a lab, we built a working fish facility from scratch. We were extremely lucky to be able to use a pre-fab rack from a generous PI at UAA, Dr. Tim Hinterberger, for raising fish from embryos through the juvenile stage; however, we needed larger tanks for adults. We haggled with makers of fish racks until we realized there was no way we were going to be able to afford to purchase enough racks for two rooms and decided to build our own. This wouldn’t have been possible without the help of Mark Currey, who works with Dr. Bill Cresko at the University of Oregon, and the countless phone calls and emails that he answered and photos he shared. We were also fortunate to have a tech in the vivarium, Joyce, who had experience putting together pipes and working with fish. Soon-to-be graduate student, Ryan Lucas, and patient and hard-working undergraduates, Koral Campbell, Kenneth Sparks, and Kelly Ireland, worked with Joyce, myself and Emily to put the shelves together, design piping and filtration systems, and glue and cut countless pipes. We are almost done with 4 racks, and are starting to work on our second fish facility room. Our large tanks for recirculating water just arrived today and are awaiting cleaning and assembly in the facility.

Spring brought our first germ free fish experiments in the lab, which is very important for a lab that studies host-microbe interactions! It was our first big experiment that was done almost completely in our lab (huge thanks to Mark and Bill for sharing their fish!). Our undergraduate student Keagan Whitcomb has been diligently taking measurements from various images we have from the fish, and we hope to present that data soon.

IMAG1806

Making our first germ free fish!

In Alaska, spring and summer are prime times for harvesting food to last through the winter. In the lab this year, spring and early summer were prime times for collecting the data and materials we will analyze through the rest of the summer, fall and winter. We were able to collect fish and water samples from 4 different populations, and produce eggs for experiments from three different populations. Our collaborator, Dr. Brandon Briggs from UAA, will help us isolate DNA and characterize the microbes in the water, which we can then compare to the microbes in the guts of our stickleback. So many comparisons ahead!

IMAG3121 Gary and Koral take notes and pictures as Emily collects fishIMAG3436

A busy day in the lab! From left to right, Ryan examines colonies isolated on plates, Koral puts away new plates she poured, high school Hutton awardee Gary characterizes colonies from stickleback guts, and Kenneth examines microbial colonies under the microscope. (BTW, I put together that microscope!)

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From top to bottom: Gary, Koral, Ryan and Emily isolate microbes from water and gut samples on a packed bench

In June we sadly watched Dr. Frank von Hippel pack his lab and ship it to it’s new home at Northern Arizona University. Dr. von Hippel has been an important mentor my first year here, as he was the only other stickleback researcher on campus and one of the few researchers in the state of Alaska to have a highly coveted RO1 grant from NIH. He was also a wonderful graduate mentor to Emily and undergraduate mentor to Ryan. He was very kind to introduce me to several stickleback researchers from other universities, as my lab will be the new Alaska contact for several researchers who study Alaskan stickleback populations. We started a collaborative research project with Dr. von Hippel before he left. We hope will turn into a productive and interesting project in the years to come.

It’s been a productive and busy year. A huge thank you to all everyone in our lab for their hard work, our collaborators at UAA and UO, and future collaborators who have been helping me put together ideas!