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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.

Software Carpentry Workshop

Maren, Roxanne, & Ellie attended the hpcc swc bootcamp. Thanks instructors!

Maren’s notes from the bootcamp are posted here.

From the organizers:
We hope you enjoyed the Software Carpentry bootcamp this week and picked up a few new skills to speed up your research workflow.
If you’re still unsure how to integrate any of these tools or skills into your workflow, we’d be happy to meet with you to discuss your specific needs and help you get started. (Note: The longer you wait to integrate these skills into your workflow, the less likely you are to do it, so it’s best to start now.)
Respond to this email if you’d like to schedule consultation with us. As always, the only cost is your time and effort.
MSU’s ICER department also offers weekly office hours and can provide similar consultation on a weekly basis.
We’d also like you point out that Software Carpentry has free online materials (video lectures and notes) for all of the material we covered in the workshop (and much more).
Finally, if you’d like to get involved with Software Carpentry (or know someone that might want to), take a look at SWC’s Get Involved page. We’re always looking for more helpers and instructors at bootcamps, new places to run bootcamps, and new contributors to help us improve our teaching material.
Cheers,
MSU Software Carpentry team

Evolution favours nice guys…

“We found evolution will punish you if you’re selfish and mean,” said lead author Christoph Adami, MSU professor of microbiology and molecular genetics. – See more at: http://msutoday.msu.edu/news/2013/evolution-will-punish-you-if-youre-selfish-and-mean/#sthash.bsFC1Gr4.dpuf

Perhaps this is why there are so many examples of cooperation in the biological world. In a meta-analysis published last year (Friesen 2012) I found strong positive fitness correlations between legumes and rhizobia that I term “fitness alignment”.

In a NCEAS working group “When is a mutualist a cheater?” that I am co-leading with Emily Jones, we are compiling fitness correlations for other mutualisms to determine if this pattern generalizes to other systems such as plant-fungal and plant-insect interactions.

Code for boxplot

> setwd(‘C:/Users/Nikhil/Desktop’)
>
> getwd()
[1] “C:/Users/Nikhil/Desktop”
>
> dir()
[1] “~$ stuff.docx”
[2] “~$y Does Medicine Need Explanation.docx”
[3] “burk_final_harvest.txt”
[4] “Class Schedule.docx”
[5] “desktop.ini”
[6] “Dropbox.lnk”
[7] “Ebooks & TV”
[8] “Fall Semester 2011”
[9] “GoldWave.lnk”
[10] “Google Chrome.lnk”
[11] “image.png”
[12] “iRinger.exe”
[13] “LB 332”
[14] “MCAT PREP”
[15] “nodulecfu.txt”
[16] “P90x.zip”
[17] “PHY 232”
[18] “Plant Research”
[19] “R stuff.docx”
[20] “R x64 2.15.2.lnk”
[21] “Research Projects”
[22] “Resumes”
[23] “Spybot.lnk”
[24] “Wallpaper”
>
> read.delim(‘nodulecfu.txt’)->dat
> dat
plantID burk.strain rhiz density date rep1 rep2 rep3
1 17 0 R med 20112 2126250.0 245714.3 111666.7
2 21 0 R med 12412 123333.3 20000.0 NA
3 49 0 R med 12612 1920000.0 758571.4 801428.6
4 50 0 R med 20912 8336250.0 9855000.0 11760000.0
5 72 0 R med 20412 2880000.0 1061250.0 9416250.0
6 79 0 R med 12712 NA NA NA
7 22 B1 R med 20112 3363750.0 1755000.0 9510000.0
8 46 B1 R med 21412 25287187.5 18908437.5 15946875.0
9 53 B1 R med 12612 28188000.0 1319000.0 7984285.7
10 61 B1 R med 12712 5454000.0 13473000.0 76000.0
11 63 B1 R med 21412 21748500.0 15868125.0 8656875.0
12 83 B1 R med 20912 7080000.0 12352500.0 25818750.0
13 4 B2 R med 20412 39285000.0 5512500.0 474444.4
14 25 B2 R med 21012 25211250.0 21566250.0 26122500.0
15 26 B2 R med 21012 26426250.0 23085000.0 26426250.0
16 31 B2 R med 21012 8100000.0 38576250.0 28552500.0
17 41 B2 R med 21012 40550625.0 71077500.0 9618750.0
18 42 B2 R med 21412 23814000.0 19819687.5 24603750.0
19 52 B2 R med 21412 325500.0 315000.0 7492500.0
rep4
1 417500.00
2 26666.67
3 1178181.82
4 11016000.00
5 11070000.00
6 982125.00
7 495000.00
8 12757500.00
9 210000.00
10 46980000.00
11 12605625.00
12 14700000.00
13 45360000.00
14 12622500.00
15 28248750.00
16 33108750.00
17 9618750.00
18 5163750.00
19 4741875.00
> dim(dat)
[1] 19 9
> names(dat)
[1] “plantID” “burk.strain” “rhiz” “density” “date”
[6] “rep1” “rep2” “rep3” “rep4”
> summary(dat)
plantID burk.strain rhiz density date
Min. : 4.00 0 :6 R:19 med:19 Min. :12412
1st Qu.:25.50 B1:6 1st Qu.:16412
Median :46.00 B2:7 Median :20912
Mean :44.05 Mean :18717
3rd Qu.:57.00 3rd Qu.:21012
Max. :83.00 Max. :21412

rep1 rep2 rep3 rep4
Min. : 123333 Min. : 20000 Min. : 76000 Min. : 26667
1st Qu.: 3000938 1st Qu.: 1125688 1st Qu.: 7492500 1st Qu.: 1080153
Median : 8218125 Median :11103750 Median : 9510000 Median :11016000
Mean :15012216 Mean :14198266 Mean :12551343 Mean :13226472
3rd Qu.:25268203 3rd Qu.:19591875 3rd Qu.:24603750 3rd Qu.:13728750
Max. :40550625 Max. :71077500 Max. :28552500 Max. :46980000
NA’s :1 NA’s :1 NA’s :2
> [,1:9]
Error: unexpected ‘[‘ in “[”
> dat[,1:9}
Error: unexpected ‘}’ in “dat[,1:9}”
> dat[,1:9]
plantID burk.strain rhiz density date rep1 rep2 rep3
1 17 0 R med 20112 2126250.0 245714.3 111666.7
2 21 0 R med 12412 123333.3 20000.0 NA
3 49 0 R med 12612 1920000.0 758571.4 801428.6
4 50 0 R med 20912 8336250.0 9855000.0 11760000.0
5 72 0 R med 20412 2880000.0 1061250.0 9416250.0
6 79 0 R med 12712 NA NA NA
7 22 B1 R med 20112 3363750.0 1755000.0 9510000.0
8 46 B1 R med 21412 25287187.5 18908437.5 15946875.0
9 53 B1 R med 12612 28188000.0 1319000.0 7984285.7
10 61 B1 R med 12712 5454000.0 13473000.0 76000.0
11 63 B1 R med 21412 21748500.0 15868125.0 8656875.0
12 83 B1 R med 20912 7080000.0 12352500.0 25818750.0
13 4 B2 R med 20412 39285000.0 5512500.0 474444.4
14 25 B2 R med 21012 25211250.0 21566250.0 26122500.0
15 26 B2 R med 21012 26426250.0 23085000.0 26426250.0
16 31 B2 R med 21012 8100000.0 38576250.0 28552500.0
17 41 B2 R med 21012 40550625.0 71077500.0 9618750.0
18 42 B2 R med 21412 23814000.0 19819687.5 24603750.0
19 52 B2 R med 21412 325500.0 315000.0 7492500.0
rep4
1 417500.00
2 26666.67
3 1178181.82
4 11016000.00
5 11070000.00
6 982125.00
7 495000.00
8 12757500.00
9 210000.00
10 46980000.00
11 12605625.00
12 14700000.00
13 45360000.00
14 12622500.00
15 28248750.00
16 33108750.00
17 9618750.00
18 5163750.00
19 4741875.00
> dat[,6:9]
rep1 rep2 rep3 rep4
1 2126250.0 245714.3 111666.7 417500.00
2 123333.3 20000.0 NA 26666.67
3 1920000.0 758571.4 801428.6 1178181.82
4 8336250.0 9855000.0 11760000.0 11016000.00
5 2880000.0 1061250.0 9416250.0 11070000.00
6 NA NA NA 982125.00
7 3363750.0 1755000.0 9510000.0 495000.00
8 25287187.5 18908437.5 15946875.0 12757500.00
9 28188000.0 1319000.0 7984285.7 210000.00
10 5454000.0 13473000.0 76000.0 46980000.00
11 21748500.0 15868125.0 8656875.0 12605625.00
12 7080000.0 12352500.0 25818750.0 14700000.00
13 39285000.0 5512500.0 474444.4 45360000.00
14 25211250.0 21566250.0 26122500.0 12622500.00
15 26426250.0 23085000.0 26426250.0 28248750.00
16 8100000.0 38576250.0 28552500.0 33108750.00
17 40550625.0 71077500.0 9618750.0 9618750.00
18 23814000.0 19819687.5 24603750.0 5163750.00
19 325500.0 315000.0 7492500.0 4741875.00
> boxplot(rhiz~rep1,data=dat)
Error in boxplot.default(split(mf[[response]], mf[-response]), …) :
adding class “factor” to an invalid object
> boxplot(rep1~rhiz,data=dat)
> boxplot(rep1:rep4~rhiz,data=dat)
Error in model.frame.default(formula = rep1:rep4 ~ rhiz, data = dat) :
variable lengths differ (found for ‘rhiz’)
In addition: Warning messages:
1: In rep1:rep4 :
numerical expression has 19 elements: only the first used
2: In rep1:rep4 :
numerical expression has 19 elements: only the first used
> boxplot(rep1~rhiz, data=dat) boxplot(rep2~rhiz, data=dat)
Error: unexpected symbol in “boxplot(rep1~rhiz, data=dat) boxplot”
> boxplot(rep1~rhiz, data=dat)
> boxplot(rep2~rhiz, data=dat)
> boxplot(rep2~rhiz, main=”Plant Number vs. Mass”, xlab=”Plant Number”, ylab=”Mass”, data=dat)
> boxplot(rep2~rhiz, main=”Plant Number vs. Mass”, xlab=”Plant”, ylab=”Mass”, data=dat)
> boxplot(rep2~rhiz, main=”Plant Number vs. Mass”, col=(c(“gold”,”darkgreen”)), xlab=”Plant”, ylab=”Mass”, data=dat)
> boxplot(rep2~rhiz, main=”Plant Number vs. Mass”, col=(c(“blue”,”darkgreen”)), xlab=”Plant”, ylab=”Mass”, data=dat)
> boxplot(rep2~rhiz, main=”Plant Number vs. Mass”, col=(c(“blue”,”red”)), xlab=”Plant”, ylab=”Mass”, data=dat)
> boxplot(rep2~rhiz, main=”Plant Number vs. Mass”, col=(c(“blue”,”red”)), xlab=”Plant 1″, ylab=”Mass”, data=dat)

> >

Welcome to the Friesen Lab Website

Our research interests lie at the interface of ecology and evolution. How do the molecular and physiological pathways of organisms shape their ecology, and how does selection imposed by interactions with other organisms and the environment ultimately shape their genomes?

We are moving to Washington State University Fall 2017! If you are interested in joining us as a postdoc or graduate student, please get in touch with Maren by email.