21
16 January 2009 COBRE Retreat Steinke, 1 Proteomic & Metabolic Studies of a Microbial Community Laurey Steinke, PhD Department of Biochemistry & Molecular Biology UNMC
| Date post: | 22-Dec-2015 |
| Category: |
Documents |
| View: | 213 times |
| Download: | 0 times |
16 January 2009 COBRE Retreat Steinke, 1
Proteomic & Metabolic Studies of a Microbial
Community
Proteomic & Metabolic Studies of a Microbial
Community
Laurey Steinke, PhD
Department of Biochemistry & Molecular Biology
UNMC
Laurey Steinke, PhD
Department of Biochemistry & Molecular Biology
UNMC
16 January 2009 COBRE Retreat Steinke, 2
The Importance of Microbial CommunitiesThe Importance of Microbial Communities In the human body, microbial cells are
estimated to outnumber human cells by ten to one
Gut flora perform a portion of human metabolism
Identity of microbial species change aspects of human health.
Particular communities of microbes are associated with obesity and cardiovascular disease
In the human body, microbial cells are estimated to outnumber human cells by ten to one
Gut flora perform a portion of human metabolism
Identity of microbial species change aspects of human health.
Particular communities of microbes are associated with obesity and cardiovascular disease
16 January 2009 COBRE Retreat Steinke, 3
NIH Roadmap for medical researchNIH Roadmap for medical research Mapping the human microbiome Metagenomics
Mapping the human microbiome Metagenomics
16 January 2009 COBRE Retreat Steinke, 4
Steps after the metagenome Steps after the metagenome
Transcriptomics--mRNA has only a 30% correlation with increases in protein levels.
Meta-proteomics Meta-metabolomics Why so many omics?
Transcriptomics--mRNA has only a 30% correlation with increases in protein levels.
Meta-proteomics Meta-metabolomics Why so many omics?
16 January 2009 COBRE Retreat Steinke, 5
State of MetaproteomicsState of Metaproteomics
Jillian Banfield mapped the proteome of a microbial community in an acid mine drainage system.
Environmental Proteomics The community consisted of 5 species Metagenome was sequenced.
Jillian Banfield mapped the proteome of a microbial community in an acid mine drainage system.
Environmental Proteomics The community consisted of 5 species Metagenome was sequenced.
16 January 2009 COBRE Retreat Steinke, 6
Long-term goalLong-term goal
Contribute to understanding of the evolutionary, environmental and community forces that shape microbial communities.
Contribute to understanding of the evolutionary, environmental and community forces that shape microbial communities.
16 January 2009 COBRE Retreat Steinke, 7
Objective of this applicationObjective of this application
Improve or develop bioanalytical methods that will allow more rapid and effective studies of the proteome and the metabolome of microbial communities.
Improve or develop bioanalytical methods that will allow more rapid and effective studies of the proteome and the metabolome of microbial communities.
16 January 2009 COBRE Retreat Steinke, 8
Model systemModel system
Microbial mat community of Octopus hot spring, Yellowstone National Park
Microbial mat community of Octopus hot spring, Yellowstone National Park
16 January 2009 COBRE Retreat Steinke, 9
RationaleRationale
Intermediate complexity of species Metagenomic map available Chemistry and major organisms are
well-characterized.
Intermediate complexity of species Metagenomic map available Chemistry and major organisms are
well-characterized.
16 January 2009 COBRE Retreat Steinke, 10
Specific aimsSpecific aims
Develop a rapid mass spectrometric method that will provide increased coverage of the proteome of this microbial community.
Develop robust methods to determine key microbial metabolites.
Develop a rapid mass spectrometric method that will provide increased coverage of the proteome of this microbial community.
Develop robust methods to determine key microbial metabolites.
16 January 2009 COBRE Retreat Steinke, 11
Goal of this workGoal of this work
The methods developed will ultimately be applicable to the more complex human microbiome and to research involving the microbiome
The methods developed will ultimately be applicable to the more complex human microbiome and to research involving the microbiome
16 January 2009 COBRE Retreat Steinke, 12
Critique of ProposalCritique of Proposal
Needs a more thorough discussion and evaluation of technological literature
Level of technological innovation is moderate
Needs a more complete analysis of the bioinformatics issues.
Needs a more thorough discussion and evaluation of technological literature
Level of technological innovation is moderate
Needs a more complete analysis of the bioinformatics issues.
16 January 2009 COBRE Retreat Steinke, 13
LiteratureLiterature
Analytical Chemistry & Journal of the American Society for Mass Spectrometry contain much of the technological innovation. Read them.
Attend ASMS this year Attend Metabolomics course at ASMS
taught by Gary Siuzdiak.
Analytical Chemistry & Journal of the American Society for Mass Spectrometry contain much of the technological innovation. Read them.
Attend ASMS this year Attend Metabolomics course at ASMS
taught by Gary Siuzdiak.
16 January 2009 COBRE Retreat Steinke, 14
Higher level of Technological innovationHigher level of Technological innovation Use literature review to spark new
ideas. Brainstorm Discuss possibilities with mentors and
other mass spectrometrists on campus.
Use literature review to spark new ideas.
Brainstorm Discuss possibilities with mentors and
other mass spectrometrists on campus.
16 January 2009 COBRE Retreat Steinke, 15
More complete analysis of Bioinformatics issuesMore complete analysis of Bioinformatics issues Mark Pauley, UNO, is working on the
direct question posed about tryptic peptides.
Dr. Pauley is performing analysis on chaperonin tryptic peptides to identify markers in an MRM study for proof of principle.
Mark Pauley, UNO, is working on the direct question posed about tryptic peptides.
Dr. Pauley is performing analysis on chaperonin tryptic peptides to identify markers in an MRM study for proof of principle.
16 January 2009 COBRE Retreat Steinke, 16
Recent Progress: MRMRecent Progress: MRM
Have started a collaboration with an investigator interested in the production of chaperonins in an isolated hyperthermophile.
Will use MIDAS software from Applied Biosystems to predict MRM transitions.
Will move to quantification of chaperonins in a mat community.
Have started a collaboration with an investigator interested in the production of chaperonins in an isolated hyperthermophile.
Will use MIDAS software from Applied Biosystems to predict MRM transitions.
Will move to quantification of chaperonins in a mat community.
16 January 2009 COBRE Retreat Steinke, 17
Recent progress: Sample preparationRecent progress: Sample preparation Developed a protocol for utilization of a
“bead beater” at UNO. Tested protocol on two sets of microbial
mat samples. Greater coverage of proteins achieved.
(150 vs.. 25) More equal coverage of Roseiflexus
and Synnechococcus.
Developed a protocol for utilization of a “bead beater” at UNO.
Tested protocol on two sets of microbial mat samples.
Greater coverage of proteins achieved. (150 vs.. 25)
More equal coverage of Roseiflexus and Synnechococcus.
16 January 2009 COBRE Retreat Steinke, 18
Recent Progress: Roseiflexus RS-1 isolationRecent Progress: Roseiflexus RS-1 isolation Originally described strain was lost A strain has been brought into culture
from 2008 collections from Octopus hot spring microbial mat.
A sample is in preparation for 16S rRNA confirmation of species.
Originally described strain was lost A strain has been brought into culture
from 2008 collections from Octopus hot spring microbial mat.
A sample is in preparation for 16S rRNA confirmation of species.
16 January 2009 COBRE Retreat Steinke, 19
Recent Progress: PublicationRecent Progress: Publication
Two publications through the Protein Structure Core Facility
A manuscript in preparation describing the preliminary data from the funded NSF proposal.
Two publications through the Protein Structure Core Facility
A manuscript in preparation describing the preliminary data from the funded NSF proposal.
16 January 2009 COBRE Retreat Steinke, 20
Next stepsNext steps
Survey available mass spectrometers with test samples to determine best machine to use for proteomic coverage.
Develop an MRM method to quantify chaperonin from test organism.
Survey available mass spectrometers with test samples to determine best machine to use for proteomic coverage.
Develop an MRM method to quantify chaperonin from test organism.
16 January 2009 COBRE Retreat Steinke, 21
FundingFunding
Department of Biochemistry & Molecular Biology
Office of the Vice Chancellor of Research, UNMC
Related work: National Science Foundation
Department of Biochemistry & Molecular Biology
Office of the Vice Chancellor of Research, UNMC
Related work: National Science Foundation
