Category Archives: Uncategorized

Friesen Lab is Trying sciNote, an Open Source Electronic Lab Notebook

We are trying sciNote, a promising new electronic lab notebook that was a Kickstarter Project in fall 2015. One of the coolest things about it is that it is open-source — and it is being actively developed. Maren spoke with the folks there about the future and they’re working on integrating with Office (so that you can edit files directly inside the platform) and on developing a real database for samples. We’d love to see the Chado schema for stocks and natural diversity integrated…

http://gmod.org/wiki/Chado_Natural_Diversity_Module

http://database.oxfordjournals.org/content/2011/bar051.full

In the meantime, several labmembers are trying this out before we decide whether to switch entirely from paper!

Check out sciNote for yourself here (the 1Gb plan is free): sciNote Open source Electronic Lab Notebook

Note: Through their PIs program, by posting this link we are getting the upgraded storage (100Gb) for free.

An exciting new project let by Sarah Evans (KBS) with Lisa Tiemann, Maren Friesen, and Jim Cole was just announced! Check out the MSU press release here.

Evans, Tiemann, Friesen, and Cole in front of ornamental switchgrass on MSU campus.

Postdoctoral Opening: Plant-microbe community genomics

Postdoc in Ecological Plant Transcriptomics and Microbiome Analysis

The Friesen Lab in the Department of Plant Biology at Michigan State University is seeking highly motivated individuals to contribute to data analysis and manuscript preparation for two funded projects investigating the transcriptomic connections linking plant-plant competition and plant-microbiome interactions in legumes (collaborative with Sharon Strauss at UC Davis) and grasses (collaborative with Sarah Evans, Lisa Tiemann, and Jim Cole at MSU). The legume project is focused on questions related to niche evolution and species coexistence, while the grass project aims to understand plant-microbe resource exchange and nutrient cycling across diversity and fertility gradients.

Key qualifications include a strong statistical and computational background with the ability to ask creative questions. Familiarity with Illumina data and bioinformatics is desired but not essential–this could be a great opportunity for the right person to develop genomics expertise. Excellent communication and organizational skills are required along with a track record of timely publications.

Funding is initially available for one year with renewal based upon performance. The successful applicant would be encouraged to develop independent lines of research in accordance with an individualized mentoring plan. The Friesen lab is located in the Molecular Plant Sciences building which is designed to foster collaboration. Start date is flexible, ideally spring 2016 but earlier or later would be considered.

Please send a ~1 page statement of interest, CV, and contact info for 3 references to mfriesen@msu.edu .  Applications will be reviewed until the position is filled.

Undergraduate Opening: Computational Biology

The Friesen lab is seeking a motivated undergraduate student with an interest in computational biology to assist on a series of projects investigating ecological genomics and transcriptomics in non-model species of clover and their nitrogen-fixing bacterial symbionts. Applicants should be comfortable with a command line and preferably a computer cluster; knowledge of at least one programming language and the willingness to use multiple languages will be required. These positions will be primarily computational, but there may be opportunities to participate in data generation if desired. This paid position will require a minimum of 10 hours of work a week; work times can be set to accommodate academic schedules. Candidates will be encouraged to design and implement side research projects that complement larger project goals.

Please apply through http://friesen.plantbiology.msu.edu/?page_id=352

Undergraduate Opening: Microbiology

The Friesen lab is seeking motivated undergraduate students with an interest in microbiology to assist on a project culturing novel microorganisms with the ability to fix nitrogen. The position will require a minimum of 10 hours of lab work a week; work times can be set to accommodate academic schedules. Main duties will include culturing bacteria from environmental samples, glassware washing, preparation and sterilization of solid and liquid media, decontamination and disposal of used culturing materials. Candidates will be trained in sterile technique and exposed to culturing techniques for a variety of organisms with diverse metabolic demands along with basic molecular biology (e.g., PCR) and microscopy techniques. Furthermore, candidates will be encouraged to design and implement side research projects that complement larger project goals. These positions are currently available on a volunteer or for-credit basis.

Please apply through http://friesen.plantbiology.msu.edu/?page_id=352

Can you explain your research using only the ten hundred most used words?

Check out Colleen’s award-winning attempt!

We study big green things that use sun light as food and littler things that use some parts of the air as food and live in the ground that the big green things live in. The big green things give the littler things food made from sun light, and the littler things give the big green things food they made from the air. This makes both the big green things and littler things happier. We want to know how the big green things and the littler things talk to each other and decide how much food to give and take.  

Maren, Prateek, and Colleen took on the challenge at the Science Communication Workshop hosted by Danielle Whittaker at BEACON Congress 2015. Here is Maren’s description:

I study how tiny cells make friends with big green things to share good things with each other. The tiny cells make food out of air and the bigger things make another kind of food. When they live together, they are both better off than when they are alone because they are good at different things. A lot of people think that tiny cells that don’t make food are mean and bad for the big green thing, but it turns out that these tiny cells aren’t happy either.

If you want to try this on your own, head over to http://splasho.com/upgoer5/ and type your text in the box. It will alert you if you use a word that isn’t in the ten hundred most used words. This was a fun and silly exercise that illustrates how difficult it can be to explain your research simply, without the jargon and buzzwords scientists take for granted. Admittedly, I would not recommend using this level of language to actually explain your research to anyone-that might be a bit insulting! But it will definitely improve your creativity. On a side note, can we talk about how alarming it is that “plant” is not among the ten hundred most commonly used words? We need to work on changing that.

We also learned about writing great Twitter “hooks” to promote an article you would like your followers to read. It’s important to make it something exciting and intriguing that will leave your reader interested enough to actually click on the link you posted. You can see the tweet that won the contest at the workshop below, plus Maren and Colleen’s entries.

Prateek was also terribly brave and tackled explaining his thesis in three minutes or less, with a single slide. Prateek did a great job explaining how he is exploring how plants make friends with their microbial partners and how many friends plant actually need to be happy. This exercise taught us how important it is to translate your research into succinct, easy to understand sound bites to effectively communicate your research in a short period of time. Check out his slide below!

Untitled

Plant Biology 2015 Conference

26 July 2015-30 July 2015

This past week Dr. Friesen, Colleen and I attended the Plant Biology conference through the American Society of Plant Biologists (ASPB) in Minneapolis, MN. The conference highlighted plant research in areas such as development, plant-microbe interactions, plant-insect interactions, biochemistry, abiotic & biotic factors, and genetics. We each presented a poster of our recent work and interacted with other scientists. I received a Bio-Research Experience for Undergraduates (REU) travel stipend from the NSF to attend this conference—it was for former students of REUs to display their work at a conference of their choice.

View of Minneapolis from our plane.

View of Minneapolis from our plane.

Maren's poster.

Maren’s poster.

Colleen Friel's poster.

Colleen Friel’s poster.

Katie Wozniak's poster.

Katie Wozniak’s poster.

Minneapolis is beautiful and surprisingly clean. They have an efficient rail system for long distance transportation (and it’s only $1.75/ride), electric buses, and recycling at every turn. Most of the buildings downtown are connected via a skyway, which is unique to Minneapolis. Without ever going outside, you can walk across town and visit a series of shops and restaurants. I can imagine this is a huge perk during the brutal Minnesota winters.

A beautiful day in MN!

"mini Polis" city in a park near the convention center.

“mini Polis” city in a park near the convention center.

We listened to the major symposia speakers and had choices of mini symposia with different featured disciplines in plant research. They even had a symposium on space biology! On the first day of the conference, we were asked “What do you want to learn at this meeting?” and Colleen and I wrote “Take legumes (with rhizobia) to space.” Someone from the Space Biology program actually tweeted a picture of our response! P.S. I now have a Twitter handle thanks to Dr. Friesen, so follow me @OKmicrobe.

Tweet

Dr. Friesen, Colleen & Katie before the first major symposium.

Dr. Friesen, Colleen & Katie before the first major symposium.

The most rewarding part of the conference for me was networking. Coffee breaks and poster sessions allowed me to speak to my peers at the conference about my research, and my graduate school interests. I gained advice on new contacts, how to apply to graduate school, where to apply, and what life is like as a graduate student at some of the schools I’m interested in. I also got to meet several professors, including one from the University of Minnesota! On the last night of the conference, there was a party in Minneapolis’ Orchestra Hall—I never knew plant biologists loved to dance.

Colleen & Katie at the farewell party.

Colleen & Katie at the farewell party.

Dr. Friesen and Dr. Harcombe as "Drago" at the farewell party.

Dr. Friesen and Dr. Harcombe (as “Drago”) at the farewell party.

Overall, the conference was a learning experience for me and I am thankful to have attended. Now, back to work…

Summer Update

This summer at the Friesen Lab we have all been extremely busy! Dr. Friesen was in Europe until last week collecting Medicago polymorpha so it was up to the rest of us to keep the laboratory productive in her absence. We have a few new summer interns, which makes the lab a full house but we are happy to have them! From the Plant Genomics REU program, Nayeli is working with Colleen on characterizing novel bacterial isolates from various Trifolium species collected at the Bodega Bay ecological research site in California. From the Summer Research Opportunity (SROP) program, Carla is working with Dr. Chandra Jack to determine the effects of herbivory on native and invasive Medicago polymorpha. We also have two new high school students from HSHSP: Matt, who is mentored by Colleen, is researching the potential benefits of mixed nodules in Medicago plants that are inoculated with a fixing and a non-fixing variety of the same strain of rhizobia and Amy, who is being mentored by Dr. Jack, is using Medicago polymorphaEnsifer medicae, and Chrysodeixis includens to test the Novel Weapons Hypothesis.

In addition to mentoring students this summer, Colleen is working to parameterize a mathematical model of the carbon/nitrogen trade between legumes and rhizobia. She is growing plants over a carbon and nitrogen gradient and examining how their allocation to acquiring resources and the symbiosis changes across the gradient. Prateek is conducting a study to understand gene expression profiles of plants under different competition regimes—it will also be extrapolated to see if rhizobacterial members are affected by changes in exudation and gene expression profiles. He is also trying to identify how changes in resource complexity and abundance impact digital microbiomes using Avida. *Ellie has not submitted a statement*

As for the undergraduates, I am here full time; we also have Duncan and Megan who are working on maintaining our greenhouses, seed stock and Medicago experiment. Starting soon, we will have a new laboratory technician starting on DNA extractions from our various harvests. We have a new rotating graduate student, Shawna, who was a member of SROP in our lab last summer. Dr. Chandra Jack is away at the evolution conference in Brazil and will travel to Europe after that for another conference. Dr. Jeff Norman is continuing his work culturing oxygen-tolerant free-living N fixers from a diverse array of environments in line with the goals of the Nitrogenase project.  He is also currently using stable isotope probing to identify the organisms that fix nitrogen in natural systems and will soon be starting work to investigate biogeochemical controls over free-living nitrogen fixation as well.

Our large greenhouse is now fully functional and is equipped with an automatic misting system and catchment apparatus for easy runoff decontamination. The misting system is modeled after a system set up by our collaborator, Stephanie Porter, at University of California-Riverside. We have been tweaking it for our own use since January 2015. Now that we have it set up, we won’t have to worry about introducing contamination to our plants because they will be watered by the system. The misting runoff that could contain foreign rhizobial strains is now being funneled into a tank under the benches where it can then be bleached and safely disposed of.

One of the three benches in our new greenhouse; complete with automatic misting system!

One of the three benches in our new greenhouse; complete with automatic misting system!

One of the largest experiments we currently have in the greenhouse consists of 800 pots of Medicago polymorpha and lupulina. The goal of this experiment is to collect phenotype data, and perform Restriction site Associated DNA (RAD) sequencing to determine the community structure of native and invasive genotypes. Strains from nodule contents of the Bodega harvest are still being grown up and put into freezer stocks. After PCR confirmation of rhizobial strains, these strains of wild invasive region (CA) rhizobia will be useful for our lab’s future experiments.

In late-July, I will be traveling to Minneapolis, MN for the American Society of Plant Biology (ASPB) conference with Colleen and Dr. Friesen. This trip is funded by a Bio-REU travel grant from the National Science Foundation. I will be presenting a poster titled “Assessing rhizobial dependence of Medicago polymorpha as it evolves in non-native regions,” which was a project from spring semester. I recently set up another experiment to further investigate how native and invasive genotypes interact with different sets of soil microbes for the greatest growth benefit.

Dean’s Research Scholars Program

I, Katie Wozniak, have been selected to serve as a Dean’s Research Scholar for the College of Natural Science here at MSU for the 2015-2016 school year. The Dean’s scholars are a group of undergraduate students who do research in math and science and are able to effectively communicate their research to a broad range of alumni. Scholars travel to speaking engagements and attend special events where they interact one-on-one with alumni of Michigan State University.

Each of the scholars have a biography and Q&A posted online. They also maintain a blog about their experiences speaking to alumni. Since I am new to the program, the College of Natural Science’s photographer, Harley Seeley, came to take pictures of me in our lab’s greenhouse!  Harley brought his lighting,  computer, and a top of the line camera along with him. After exploring different poses that took into account the lighting, he began shooting. Harley was able to capture ~60 unique images.

The photos will be reviewed and sent to me for my critiques soon. I will be sure to post a link to my Dean’s Research Scholar webpage as soon as it is available!

Harley J. Seeley sets up photography equipment in one of the Friesen Lab's greenhouses.

Harley J. Seeley sets up photography equipment in one of the Friesen Lab’s greenhouses.

For more information about MSU’s Dean’s Research Scholars, please visit: https://natsci.msu.edu/students/undergraduate/deans-research-scholars/

Paul Helling

IMGP1096

Paul is currently a third year undergraduate and a first year graduate student in the plant biology masters program at Michigan State University. He joined the lab in spring 2013 and works off and on a cophylogeny project to better understand the relationships between  Medicago and their rhizobial symbionts, except he’s still trying to figure out how to grow all 20 species he wants to study and how to get them to produce nodules. After he graduates, he hopes to continue his graduate studies in orchid systematics.

When he’s not working, studying, or thinking about research, Paul enjoys eating frozen yogurt, fantasizing about all the rare orchids he hopes to grow someday, and writing short stories about characters with really cool lives and psychic powers. However, Paul spends too much time obsessing over his favorite TV shows and the lives of their protagonists to have a life of his own.

The picture above was taken in Antarctica and has Adélie penguins (Pygoscelis adeliae) in the background.