NEWS
January 2024
Brook and Anais are headed to AbSciCon in Rhode Island May 5-10 2024. Anais Gentilhomme hopes to present her recent work on Cp34H, a marine psychrophile, living at subzero temperatures in perchlorate rich media. The work was a collaboration with the Junge Lab here at UW in the Applied Physics Department Polar Division. Kusum Dhakar, a postdoc from the Nunn lab, was interested in how a cold active organism would survive perchlorate stress so she worked in the Junge lab to grow them at several subzero temperatures. Anais has been completing the data analysis and finalizing a paper for submission!
Brook and Anais are headed to AbSciCon in Rhode Island May 5-10 2024. Anais Gentilhomme hopes to present her recent work on Cp34H, a marine psychrophile, living at subzero temperatures in perchlorate rich media. The work was a collaboration with the Junge Lab here at UW in the Applied Physics Department Polar Division. Kusum Dhakar, a postdoc from the Nunn lab, was interested in how a cold active organism would survive perchlorate stress so she worked in the Junge lab to grow them at several subzero temperatures. Anais has been completing the data analysis and finalizing a paper for submission!
October -December 2024
Emma Timmins Schiffman is in Antarctica! She is completing the first snow microbiome! Together with the Junge lab, we are working to determine if the bacteria in Antarctic snow and ice are contributing to the ozone hole by degrading brominated hydrocarbons released from algae. The degradation of the brominated hydrocarbons could increase the rate at which bromine enters the atmosphere, negatively affecting ozone (our protection against UV).
Follow her BLOG here
Emma Timmins Schiffman is in Antarctica! She is completing the first snow microbiome! Together with the Junge lab, we are working to determine if the bacteria in Antarctic snow and ice are contributing to the ozone hole by degrading brominated hydrocarbons released from algae. The degradation of the brominated hydrocarbons could increase the rate at which bromine enters the atmosphere, negatively affecting ozone (our protection against UV).
Follow her BLOG here
August 2023
Dr. Brook Nunn was invited to present the lab's research at the National Academy of Sciences Panel on Continental Scale Biology. BELOW is a link to the video of the talk and the following panel discussion where they discuss the future of global scale biology research.
Dr. Brook Nunn was invited to present the lab's research at the National Academy of Sciences Panel on Continental Scale Biology. BELOW is a link to the video of the talk and the following panel discussion where they discuss the future of global scale biology research.
To see the Video click here!
At minute 34:00 the panel discussion starts - The discussion is about how we integrate biology across large scales and disciplines to develop better models and an improved understanding of our world!
At minute 34:00 the panel discussion starts - The discussion is about how we integrate biology across large scales and disciplines to develop better models and an improved understanding of our world!
April - May 2023
We would love for you to join us for Engage’s 2023 Science Now series!
These talks feature graduate students from a variety of STEM fields, who will be sharing their amazing dissertation research at Town Hall Seattle this April and May. These students have all completed training in science communication through Engage, so their talks are sure to be exciting and geared toward a broad audience!
You can find more information about each night's speakers and topics, as well as purchase tickets here. If you are a UW student, contact [email protected] for a discount code.
Come join us for exciting stories about science happening at UW right now! Snacks and drinks are available for purchase at Town Hall Seattle as well.
We hope to see you there!
These talks feature graduate students from a variety of STEM fields, who will be sharing their amazing dissertation research at Town Hall Seattle this April and May. These students have all completed training in science communication through Engage, so their talks are sure to be exciting and geared toward a broad audience!
You can find more information about each night's speakers and topics, as well as purchase tickets here. If you are a UW student, contact [email protected] for a discount code.
Come join us for exciting stories about science happening at UW right now! Snacks and drinks are available for purchase at Town Hall Seattle as well.
We hope to see you there!
September 2019
We examined metaproteome profiles from two Arctic microbiomes during 10-day shipboard incubations to directly track early functional and taxonomic responses to a simulated algal bloom and an oligotrophic control. Taxonomic assignments revealed that the core microbiome collectively responded to algal substrates by assimilating carbon before select taxa utilize and metabolize nitrogen intracellularly. Incubations of Chukchi Sea bottom water microbiomes showed similar, but delayed functional responses to identical treatments. Although 24 functional terms were shared between experimental treatments, the timing, and degree of the remaining responses were highly variable, showing that organic matter perturbation directs community functionality prior to alterations to the taxonomic distribution at the microbiome class level.
Cartoon drawing was completed by Julia Robbins, our in-house scientific artist. [email protected]
March 2019
Analyzing Differences Between Taxonomic Distributions of Arctic Ocean Microbiomes Determined by Using Metagenomic Sequencing as Compared to 16S rRNA Sequencing
High School Student Jenna Everard Wins 1st Place in BioExpo Research!
Over the past few months,PhD Candidate Andy Lin and Dr.s Nunn and Timmins-Schiffman mentored a high school student through an investigation of the use of metagenomic reads and metaproteomic peptide assignments for the purpose of identifying the bacterial taxonomic composition in an ocean microbiome
Jenna Everard entered the Research Division competition at the The Washington State Bio Expo. Jenna Everard is from Juanita High School in Kirkland Washington.
Over the past few months,PhD Candidate Andy Lin and Dr.s Nunn and Timmins-Schiffman mentored a high school student through an investigation of the use of metagenomic reads and metaproteomic peptide assignments for the purpose of identifying the bacterial taxonomic composition in an ocean microbiome
Jenna Everard entered the Research Division competition at the The Washington State Bio Expo. Jenna Everard is from Juanita High School in Kirkland Washington.
The Genome Science Symposium is coming up: Nov 2nd!
SEQUENCING, UNDERSTANDING AND EDITING THE GENOME TO IMPROVE HUMAN HEALTH7 PM FRIDAY, NOVEMBER 2, 2018 | FOEGE AUDITORIUM & KANE HALLDr. Eric Dishman, Director All of Us, NIH, will be giving the evening keynote lecture:
"Accelerating Precision Health for All of Us: The All of Us Research Program"
RSVP
SEQUENCING, UNDERSTANDING AND EDITING THE GENOME TO IMPROVE HUMAN HEALTH7 PM FRIDAY, NOVEMBER 2, 2018 | FOEGE AUDITORIUM & KANE HALLDr. Eric Dishman, Director All of Us, NIH, will be giving the evening keynote lecture:
"Accelerating Precision Health for All of Us: The All of Us Research Program"
RSVP
March 2018
Over the past few months, Dr.s Nunn and Timmins-Schiffman mentored 2 high school students through a proteomic examination of coral skeletal organic matrix. These 2 students prepared samples from corals, digested them for proteomics, analyzed the samples on a mass spectrometer, and analyzed the resulting data. Their findings were ground breaking!
They then continued on to take this research to the Washington State Science and Engineering Fair in Bremerton WA in March of 2018. They won several awards (see below).
Great job Christina Le and Hana Abay!
Over the past few months, Dr.s Nunn and Timmins-Schiffman mentored 2 high school students through a proteomic examination of coral skeletal organic matrix. These 2 students prepared samples from corals, digested them for proteomics, analyzed the samples on a mass spectrometer, and analyzed the resulting data. Their findings were ground breaking!
They then continued on to take this research to the Washington State Science and Engineering Fair in Bremerton WA in March of 2018. They won several awards (see below).
Great job Christina Le and Hana Abay!
- WSSEF finalists (top 15 out of over 300 projects!)
- 1st in senior division and 1st in category
- Best in category
- Wolfram Alpha special award
- Ohio University scholarship special award
February 26-March 3, 2017
Join us in Honolulu, HI and learn more about marine meta-omics at the ASLO conference. We are chairing a session on Friday, March 3, titled "Advances in Aquatic Meta-Omics: Creating Tools for More Accurate Characterization of Microbial Communities". We have some great talks and posters that address emerging bioinformatic and biological problems and solutions.
Join us in Honolulu, HI and learn more about marine meta-omics at the ASLO conference. We are chairing a session on Friday, March 3, titled "Advances in Aquatic Meta-Omics: Creating Tools for More Accurate Characterization of Microbial Communities". We have some great talks and posters that address emerging bioinformatic and biological problems and solutions.
November, 2016
Coming soon! Skyler Nunn's paper on diatom organelle proteomics is accepted and in final stages of review at the Journal of Emerging Investigators. Great work, Skyler!!
Coming soon! Skyler Nunn's paper on diatom organelle proteomics is accepted and in final stages of review at the Journal of Emerging Investigators. Great work, Skyler!!
JULY 11, 2016
ISME Journal accepted post doctoral fellow Emma Timmins-Schiffman's paper that clearly demonstrates that metaproteomic analyses require site and time specific metagenomes for accurate assessments. GREAT JOB EMMA!! Thanks to everyone who contributed to the work!!
Damon May (UW Genome Science graduate student), Molly Mikan (Old Dominion Univ. graduate student), Chris Frazar (UW), Mike Riffle (UW), Bill Noble (UW), Rodger Harvey (ODU).
ISME Journal accepted post doctoral fellow Emma Timmins-Schiffman's paper that clearly demonstrates that metaproteomic analyses require site and time specific metagenomes for accurate assessments. GREAT JOB EMMA!! Thanks to everyone who contributed to the work!!
Damon May (UW Genome Science graduate student), Molly Mikan (Old Dominion Univ. graduate student), Chris Frazar (UW), Mike Riffle (UW), Bill Noble (UW), Rodger Harvey (ODU).
Critical decisions in metaproteomics: Achieving high confidence protein annotations in a sea of unknowns
Emma Timmins-Schiffman*, Damon H. May, Molly Mikan, Michael Riffle, Chris Frazar,
H. Rodger Harvey, William S. Noble, Brook L. Nunn*
Emma Timmins-Schiffman*, Damon H. May, Molly Mikan, Michael Riffle, Chris Frazar,
H. Rodger Harvey, William S. Noble, Brook L. Nunn*
February 22-26th, 2016
The International Ocean Sciences Meeting in New Orleans will host thousands of the world's leaders in ocean physics, chemistry and biology. Monday, February 24th our lab will be presenting a tutorial on how to use Skyline, a software ecosystem developed in the MacCoss lab where we reside. Additionally, we have multiple talks and posters being presented.
T002. An Open Source Proteomics and Metabolomics Visualization and Development tool for Quantitative Mass Spectrometry Experiments
Brook Nunn and Emma Timmins Schiffman
Monday, February 22, 2016 02:00 PM - 02:30 PM Room R03
AH51A Physiological diagnosis of a Southern Ocean Diatom's Resonses to Future Complex Ocean Circulation
Philip Boyd, Brook Nunn, Emma Timmins Schiffman, Evelyn Armstrong, Peter Dillingham
Friday, February 26, 2016 09:15 AM - 09:30 AM room 206
MM41A-02: Proteomic Assessment of Polar Bacteria Phylogeny and Functional Shifts During POM Degradation at 0°C
Molly Mikan, Emma Timmins Schiffman, Damon May, Brook Nunn, Rodger Harvey
Thursday, February 25, 2016 08:15 AM - 08:30 AM R04
MM44C-0507: The peptide equivalent of the 16SrRNA assay: Revealing Phylogeny and Function
Damon May, Emma Timmins Schiffman, Bill Noble, Brook Nunn
Actual poster Title:
Thursday, February 25, 2016 04:00 PM - 06:00 PM Poster
Poster Download
MM44C-0510: Achieving high confidence protein annotations in a sea of unknowns
Emma Timmins Schiffman, Damon May, Molly Mikan, Rodger Harvey, Brook Nunn
Thursday, February 25, 2016 04:00 PM - 06:00 PM Poster
MM44C-0511: Plastid proteomics for elucidating iron limited remodeling of plastid physiology in diatoms
Kristopher Gomes, Brook Nunn, Bethany Jenkins
Thursday, February 25, 2016 04:00 PM - 06:00 PM Poster
The International Ocean Sciences Meeting in New Orleans will host thousands of the world's leaders in ocean physics, chemistry and biology. Monday, February 24th our lab will be presenting a tutorial on how to use Skyline, a software ecosystem developed in the MacCoss lab where we reside. Additionally, we have multiple talks and posters being presented.
T002. An Open Source Proteomics and Metabolomics Visualization and Development tool for Quantitative Mass Spectrometry Experiments
Brook Nunn and Emma Timmins Schiffman
Monday, February 22, 2016 02:00 PM - 02:30 PM Room R03
AH51A Physiological diagnosis of a Southern Ocean Diatom's Resonses to Future Complex Ocean Circulation
Philip Boyd, Brook Nunn, Emma Timmins Schiffman, Evelyn Armstrong, Peter Dillingham
Friday, February 26, 2016 09:15 AM - 09:30 AM room 206
MM41A-02: Proteomic Assessment of Polar Bacteria Phylogeny and Functional Shifts During POM Degradation at 0°C
Molly Mikan, Emma Timmins Schiffman, Damon May, Brook Nunn, Rodger Harvey
Thursday, February 25, 2016 08:15 AM - 08:30 AM R04
MM44C-0507: The peptide equivalent of the 16SrRNA assay: Revealing Phylogeny and Function
Damon May, Emma Timmins Schiffman, Bill Noble, Brook Nunn
Actual poster Title:
Thursday, February 25, 2016 04:00 PM - 06:00 PM Poster
Poster Download
MM44C-0510: Achieving high confidence protein annotations in a sea of unknowns
Emma Timmins Schiffman, Damon May, Molly Mikan, Rodger Harvey, Brook Nunn
Thursday, February 25, 2016 04:00 PM - 06:00 PM Poster
MM44C-0511: Plastid proteomics for elucidating iron limited remodeling of plastid physiology in diatoms
Kristopher Gomes, Brook Nunn, Bethany Jenkins
Thursday, February 25, 2016 04:00 PM - 06:00 PM Poster
JUNE 3, 2015
Emma Timmins Schiffman will present at Combi seminar in the Department of Genome Sciences at the University of Washington. Emma will be presenting some of her latest research on metagenomics and metaprotemics in the Arctic Ocean and mass spectrometry detection limits of bacterial proteins within Eukaryotic matrices.
Emma Timmins Schiffman will present at Combi seminar in the Department of Genome Sciences at the University of Washington. Emma will be presenting some of her latest research on metagenomics and metaprotemics in the Arctic Ocean and mass spectrometry detection limits of bacterial proteins within Eukaryotic matrices.
AUGUST 1, 2014
Brook L. Nunn was hired by the Department of Genome Sciences at the University of Washington as a Research Assistant Professor. She will continue her research using proteomics to reveal adaptation strategies of ocean organisms and decipher trophic-level relationships in our changing climate.
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JUNE 18, 2014
A great example of a successful scientific collaboration. Through tremendous teamwork, graduate students and professors from Georgia Institute of Technology, University of Washington, and University of Birmingham completed the first metabolomic and proteomic survey of a diatom's response to alleopathic chemicals released by the red tide competitor Karenia brevis. The study required expertise in culturing multiple species of microscopic plankton living in the presence of the red-tide forming dinoflagellate, NMR and MS-based metabolomics, and MS-based proteomics. Our manuscript "Metabolomics and proteomics reveal metabolic impacts of chemically mediated competition on marine plankton" is published in the Proceedings of the National Academy of Sciences (PNAS). Authors of the work: Kelsey L. Poulson-Ellestad, Christina M. Jones, Jessie Roy, Mark R. Viant, Facundo M. Fernández, Julia Kubaneka, and Brook L. Nunn. The cover image was created by Yuval Boss- a fabulous intern in the MacCoss lab! |
OUR COVER !!
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SIGNIFICANCE: Microscopic marine algae (phytoplankton) are responsible for much of Earth's photosynthesis, serving as the base of a massive food web supporting fisheries. Phytoplankton compete for limiting resources, with some species producing noxious compounds that kill competitors or inhibit their growth. The red-tide dinoflagellate Karenia brevis is one such allelopathic species, causing growth suppression of other phytoplankton and negatively impacting coastal ecosystems. Metabolomic and proteomic approaches were used to characterize the sublethal physiological impacts of K. brevis allelopathy on two competing phytoplankton, providing insights into the physiological mechanisms by which allelopathy occurs and the metabolic pathways that enable resistance in co-occurring competitors.
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Cover image: Pictured are SEM images of two phytoplankton species, the cylindrical diatom Thalassiosira pseudonana and the heart-shaped dinoflagellate Karenia brevis, composed on a false background. Kelsey L. Poulson-Ellestad et al. investigated the effects of K. brevis, the causative agent of red tides, on two phytoplankton species. Energy metabolism remained robust in one species, but was disrupted in the other, suggesting that co-occurring phytoplankton species may evolve resistance to allelopathy, the suppression of growth and reproduction of one organism resulting from the release of chemicals by another. See the article by Poulson-Ellestad et al. on pages 9009–9014. Image courtesy of Brook L. Nunn (University of Washington, Seattle), Yuval Boss (University of Washington, Seattle), Nils Kroger (B CUBE Center for Molecular Bioengineering, Dresden, Germany), and Florida Fish and Wildlife Conservation Commission.
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MAY 22, 2014
Our manuscript "Metabolomics and proteomics reveal metabolic impacts of chemically mediated competition on marine plankton" is coming out in the Proceedings of the National Academy of Sciences (PNAS) June 2nd, 2014 journal edition. This is the first time, to our knowledge, that Metabolomic and proteomic approaches have been used to characterize the sub-lethal physiological impacts of allelopathy on two competing phytoplankton. Our study provides insights into the physiological mechanisms by which allelopathy occurs and the metabolic pathways that enable resistance in co-occurring competitors. Authors of the work: Kelsey L. Poulson-Ellestad, Christina M. Jones, Jessie Roy, Mark R. Viant, Facundo M. Fernández, Julia Kubaneka, and Brook L. Nunn.
APRIL 30, 2014
Dr. Brook Nunn is presenting some of her research to The Department of Genome Sciences Wednesday April 30th in the Foege Auditorium. "Using proteomics to understand the fate of carbon and nitrogen in the ocean: from blooms to Burial"
FEBRUARY 23-28, 2014
We had a spectacular 'omics' specific session at the ASLO International Ocean Sciences Meeting! Three independent investigator teams each submitted abstracts for the meeting that were all related to the latest and greatest proteomic, transcriptomic and metabolomic approaches being applied to the the ocean. As a result, these abstracts were merged, thereby creating a spectacular team of scientists with specialties ranging from global modeling to organism-specific quantitative proteomics. The great line-up of talks can be found at the link below.
Session 062 Linking Molecular ‘Omics’ Measurements to Develop Conceptual and Computational Models of Ocean Microbial Ecology, Diversity and Biogeochemistry
NOVEMBER 1-3, 2013
In collaboration with the MacCoss and Kolker labs will be presenting a hands-on-demonstration of chemical separations frequently used by our lab. We have a 5 foot tall chromatography column to experiment with and a super-magnetic race track mass spectrometer to test out! Come check us out at the Life Sciences Research Weekend.
SEPTEMBER 5, 2013
A short article on our collaborative work with Bob Morris' group about hydrothermal vent bacterial activity can be found here: Deep-ocean carbon sinks
Deep-ocean carbon sinks: Study involves basic research on dark ocean microorganisms
FEBRUARY 1, 2013
After searching for a long time, Brook Nunn joins Mike MacCoss's lab group in the Department of Genomic Sciences. Brook's official title will remain with UW Medicinal Chemistry since this is one of the few departments at UW that will allow her to be a Principal Investigator while not having to be a faculty member. This is exciting for Brook as she advances her proteomic work towards more targeted approaches such as SRM and MRM.
OCTOBER 1, 2013
Dr. Goodlett, director of the mass spectrometry lab in Medicinal Chemistry Department, announces his move to the University of Maryland. There, he will make big advances in lipidomics with his lab group.
Our manuscript "Metabolomics and proteomics reveal metabolic impacts of chemically mediated competition on marine plankton" is coming out in the Proceedings of the National Academy of Sciences (PNAS) June 2nd, 2014 journal edition. This is the first time, to our knowledge, that Metabolomic and proteomic approaches have been used to characterize the sub-lethal physiological impacts of allelopathy on two competing phytoplankton. Our study provides insights into the physiological mechanisms by which allelopathy occurs and the metabolic pathways that enable resistance in co-occurring competitors. Authors of the work: Kelsey L. Poulson-Ellestad, Christina M. Jones, Jessie Roy, Mark R. Viant, Facundo M. Fernández, Julia Kubaneka, and Brook L. Nunn.
APRIL 30, 2014
Dr. Brook Nunn is presenting some of her research to The Department of Genome Sciences Wednesday April 30th in the Foege Auditorium. "Using proteomics to understand the fate of carbon and nitrogen in the ocean: from blooms to Burial"
FEBRUARY 23-28, 2014
We had a spectacular 'omics' specific session at the ASLO International Ocean Sciences Meeting! Three independent investigator teams each submitted abstracts for the meeting that were all related to the latest and greatest proteomic, transcriptomic and metabolomic approaches being applied to the the ocean. As a result, these abstracts were merged, thereby creating a spectacular team of scientists with specialties ranging from global modeling to organism-specific quantitative proteomics. The great line-up of talks can be found at the link below.
Session 062 Linking Molecular ‘Omics’ Measurements to Develop Conceptual and Computational Models of Ocean Microbial Ecology, Diversity and Biogeochemistry
NOVEMBER 1-3, 2013
In collaboration with the MacCoss and Kolker labs will be presenting a hands-on-demonstration of chemical separations frequently used by our lab. We have a 5 foot tall chromatography column to experiment with and a super-magnetic race track mass spectrometer to test out! Come check us out at the Life Sciences Research Weekend.
SEPTEMBER 5, 2013
A short article on our collaborative work with Bob Morris' group about hydrothermal vent bacterial activity can be found here: Deep-ocean carbon sinks
Deep-ocean carbon sinks: Study involves basic research on dark ocean microorganisms
FEBRUARY 1, 2013
After searching for a long time, Brook Nunn joins Mike MacCoss's lab group in the Department of Genomic Sciences. Brook's official title will remain with UW Medicinal Chemistry since this is one of the few departments at UW that will allow her to be a Principal Investigator while not having to be a faculty member. This is exciting for Brook as she advances her proteomic work towards more targeted approaches such as SRM and MRM.
OCTOBER 1, 2013
Dr. Goodlett, director of the mass spectrometry lab in Medicinal Chemistry Department, announces his move to the University of Maryland. There, he will make big advances in lipidomics with his lab group.