MBARI - 2008 Potential Intern Projects

Application procedure:

Applications for 2008 are now being solicited. Applications should include a cover letter, a curriculum vitae, three letters of recommendation, and we would also like you to complete an online form. The cover letter should include a statement of your research interests (with specific mention of one of the following potential projects or areas), relevant coursework and grades, and complete contact details (home and work phone numbers and email address, if available). MBARI is an equal opportunity employer.

Below you will find a list of some potential projects and mentors (this list will be updated, so please bookmark and check this page from time to time). Clearly identifying a specific research interest/area is an important part of your application and is essential in the application process. Please contact George Matsumoto if you have any questions. I have provided links to the mentors home pages (if available) so that you can learn more about the various mentors, please DO NOT contact the mentor directly.

Application materials (including letters) can be sent to MBARI via fax (831 775 1620), regular post, or by email. If you opt for an email application, please send your materials to both George and to Alta Anzalone as George will be out of town for a few weeks.

Jim Barry

Climate change and ocean acidification: The goals of this project are to evaluate the response of deep-sea organisms to environmental perturbations expected in association with large-scale deep-sea CO2 releases, under consideration as a method to reduce atmospheric levels of CO2. We are conducting studies of faunal tolerance to CO2 / pH plumes and physiological studies of pH compensation and metabolic depression for deep-sea organisms. This subproject is coupled closely to Dr. Peter Brewer’s studies of CO2 chemistry and physics.

Lisa Borok and Kim Fulton-Bennett

Science communication: The MBARI Communications group is looking for an intern to create one or more "podcasts" (audio interviews/stories for the web) about selected MBARI research projects. The intern would be responsible for all aspects of production, including story outline, scripting, interviews, audio recording (equipment will be provided), voiceover (if appropriate), and audio editing. This would be a pilot project, so as a final paper, we would like the intern to report on the feasibility of creating podcasts on a regular basis. We are looking for an applicant with a science background and experience in journalism (especially radio journalism). Please include samples of writing and/or audio projects (or links to such samples on the web) with your application.

Peter Brewer and Ed Peltzer

Ocean Chemistry: Become a part of an energetic laboratory team investigating the geochemistry of methane hydrates, and breakthroughs in identifying the future of a high CO2 ocean as climate change and greenhouse gases evolve. We have deployed novel tools, including a laser Raman spectrometer at 3.6 km depth, for the measurement of hydrates and hydrothermal vents. We are also carrying out studies of the effects of CO2 enriched seawater released on the ocean floor, and investigating techniques for simulating the biogeochemistry of the mid-21st century ocean. With this in mind, long-term CO2-enrichment experiments are being designed which are powered and controlled through the Monterey Accelerated Research System (MARS - www.mbari.org/mars) undersea cabled observatory. For more information you can look at the following websites: Ocean Chemistry of Greenhouse Gases and Laser Raman Spectroscopy.

Dave Clague

Submarine Volcanism: Multibeam bathymetric, sidescan, and sub-bottom chirp seismic data to be collected during the MBARI expedition to the Gulf of California in spring 2008 should allow a detailed analysis of mid-ocean ridge structure and volcanic history for the Alarcon Rise, the northernmost segment of the East Pacific Rise. Preliminary processing and analysis of these data will be completed to help us define ROV dive targets during the expedition. However, the detailed final processing of these data, analysis and synthesis of the different datasets, and incorporation of the dive observations open up numerous opportunities for projects to be defined and completed by a summer intern. We should have nearly 15 days of AUV data and projects could address the structure of ridge-transform intersections, the structure of the small non-transform discontinuity in the segment, mapping of individual lava flows along the ridge with age estimates based on visual dive observations, analysis of the apparent asymmetry of spreading on this segment, or sediment distribution on and near the ridge in this high-sedimentation rate region. The intern will utilize the processing program MB-System and work in GIS to be able to overlay different data sets. Knowledge of one or both software packages is a plus, but is not a requirement.

Craig Dawe and Steve Etchemendy

Monterey Accelerated Research System (MARS): Update and upgrade the MARS web pages on MBARI's system. Tasks to include a users guide for researchers and would include all relevant documentation for a user to build or rework existing equipment for deployment on MARS and contact information for possible funding and deployment scenarios. Compile and create an interface to engineering documentation along with an Operators manual. Perhaps also write articles on MARS for popular magazines.

Duane Edgington and Danelle Cline

Automated visual event detection: Our project involves implementing a computer vision system that analyzes video collected by observatory cameras or underwater vehicles to detect, classify, and identify organisms visible in the video. We are collaborating with labs at Caltech and University of Southern California to adapt and extend computer vision systems modeled after the human visual system. The internship involves working with a small team, participating in development, analyzing videos from Eye-in-the-Sea, Neptune Canada, or ROV midwater or benthic dives and comparing the analysis with processing performed by the computer vision system, and mining the MBARI database of annotated video to collect representative sample video clips for analysis. We welcome applicants with a background in computer science, machine vision, or marine biology.

Kevin Gomes

Developing Ocean Observing Technologies on an Enterprise Service Bus (ESB): MBARI is collaborating with the National Center for Supercomputing Applications (NCSA) to prototype ocean observing technologies on the industrial software technology known as an Enterprise Service Bus (http://www.mulesource.com). The intern will work with a team of MBARI software engineers to bring oceanographic instrumentation and its interactions onto the ESB. Development will be done in the Java programming language with potential tasks ranging from ESB component development to implementing an instrument control interface on an embedded controller. The end result of this work will provide MBARI and our collaborators with an interface to oceanographic instrumentation on an ESB to inform the international efforts developing software infrastructures for environmental science.

Steve Haddock

Zooplankton and Bioluminescence: Intern will work on a self-directed project involving bioluminescence, fluorescence, or phylogenetics of gelatinous zooplankton (ctenophores, siphonophores, or medusae). Molecular, chemical, or ecological projects may be possible. One high-priority project involves setting up a web site for monitoring coastal observations of jellyfish (and other animals). The site would accept data entry from "citizen scientists". This would require programming to interact with the Google Maps API.

Judith Kildow

Economic Impacts from Climate Change Effects on California’s Coast: Project 1: Using the latest data available on sea level rise for sections of California’s coast, describe the infrastructure that is at risk and create several scenarios of rise with the estimated economic losses they represent. Project 2: Working with a local community on the central coast such as the City of Monterey, create a template for how it might add climate change impacts into its Local Coastal Plan and describe what it might look like for planning purposes.

Bill Kirkwood with collaborators Dr. Chris Kitts (Univ. Santa Clara) and Dr. Geoff Wheat (NOAA/OER)

Improving and Verifying Performance of Near Shore Science Operations using an Autonomous SWATH Platform: This project builds upon the existing prototype Small Water-plane Area Twin Hull (SWATH) autonomous surface craft called SeaWASP. The tasks for a candidate intern will be to integrate further instrumentation for remote command and control, further test selected science instrumentation, and operate a designated mission in autonomous mode as part of a science field campaign. The science mission will include remote operations from shore as a primary goal including the successful collection of science instrument data. The candidate will be required to do data analysis and produce science publication quality data products. The project will conclude with a science data set and an engineering report correlating science data quality to system performance being delivered. Key output from this project will be recommendations for the next phase of upgrades to improve functionality for science. Candidates must be willing to participate on a science mission involving time at sea and travel to a remote location for several weeks.

Zbigniew Kolber and Denis Klimov

Effect of Ocean Acidification on the Upper Ocean Ecology: By absorbing excess of anthropogenically-produced CO2, the pH in the upper ocean will decrease by up to 0.6 units within the next 200 years, possibly affecting a variety of biologically important processes such as calcification, metal speciation, and silica solubility. Changes in ocean’s pH will also modify the redox potential of photosynthetic and respiratory electron carriers, directly affecting a range of biophysical processes involved in photosynthesis, carbon assimilation, and respiration. To investigate these effects you will operate a cluster of sea-going pH-stats to manipulate the pCO2 level, pH, temperature, light, and nutrient status of phytoplankton in continuous cultures. You will grow selected species of phytoplankton and the natural phytoplankton assemblages under conditions of CO2, pH, and temperature resembling that of the anticipated conditions in the upper ocean within the next 100-300 years. Using a suite of fluorescence-based techniques developed at MBARI, you will measure corresponding changes in the efficiency of photosynthetic light utilization, the yield of photosynthesis, and the kinetics of the photosynthetic electron transport. You will analyze these data to assess the potential effect of the anticipated pH shift on the ocean photosynthesis, primary production, and the phytoplankton growth rates.

George Matsumoto

Intern Logistical Coordinator: This intern will be assisting with the MBARI intern program. This assistance will likely include assisting the interns with travel logistics during the program as well as coordinating some educational activities on the weekends. It is expected that this intern will also be working on their own independent research project. The successful applicant will be an alumna/alumnus of the MBARI intern program and will stay in the same housing as the interns. Letters of recommendation are not required, but please elaborate on what your research project will entail in your application letter.

Kanna Rajan and Conor McGann

Onboard Autonomy: MBARI's Autonomous Systems group is engaged in research efforts to use advanced Artificial Intelligence (AI) techniques to enable Autonomous Underwater Vehicles (AUV) to be more adaptive and self aware of their resource and goal commitments. Our onboard deliberative system T-REX (http://www.mbari.org/autonomy/TREX/ ) being used on AUV platform (http://www.mbari.org/auv/ ), is based on the sense-deliberate-act paradigm synthesizing new mission plans in response to environmental conditions. T-REX uses a state-of-the-art temporal constraint-based planner (EUROPA) developed originally at NASA and flown on a number of space missions. Potential projects include:

1. PlanWorks debugging tool for EUROPA which allows us to leverage work done in visualization of constraint networks, token networks and timelines. The internship primarily be focused on developing PlanWorks to provide diagnostic information for T-REX.

2. Expanding the simulation capability currently available within T-REX, including monte-carlo simulation for model and and agent validation. The internship will focus on augmenting and adding new features for shore-side T-REX validation.

3. Extend the NDDL domain modeling language within the EUROPA planner to natively support arithmetic constraints and propagate them efficiently.

Highly motivated graduate or undergraduate students with substantial + Java programming skills + Limited C or C++ programming skills + AI Planning and a background in Constraint Satisfaction would be a plus are encouraged to apply.

Steve Ramp

Ocean Physics - Internal Waves: It is now commonly appreciated that waves supported by density stratification within the ocean (internal waves) are just as ubiquitous as surface waves on the air/sea interface. Internal waves are most commonly generated by tides impinging on abrupt topography, such as the continental shelf edge, sills, or island arcs. Two data sets from field experiments designed expressly to study internal waves are in hand and ready for analysis. These include the Monterey Bay, typically shelf edge phenomena, and the South China Sea, where the world’s largest internal waves are generated in the Luzon Strait and propagate WNW across the sea. We seek an intern to study all aspects of internal wave generation, propagation, growth, transformation, and dissipation.

Steve Ramp and Heather Kerkering

Products, Education, and Outreach: The Central and Northern California Ocean Observing System (CeNCOOS) is one of eleven Regional Associations (RAs) charged with implementing the national Integrated Ocean Observing System. CeNCOOS (see www.cencoos.org) is an end-to-end system including sensors, data management and communications, numerical modeling and prediction, and product development for the region spanning Pt. Conception to the Oregon border. The difference between CeNCOOS and other basic research grants is that we are charged with delivering information products that meet end-user needs such as evaluating climate change, water quality, harmful algal blooms, ecosystem-based management, and ocean education. We seek an intern with a marine policy and/or education interest to help develop and deliver such products.

John Ryan and Erich Rienecker

Coastal Plankton Ecology: In this project, the intern will have the opportunity to study the lives and times of plankton and their Monterey Bay home, viewed through the lens of multi-platform, multi-scale, multi-disciplinary observations. These observations come from satellites, aircraft, moorings, drifters, autonomous underwater vehicles, towed vehicles, and ships. The project will include time at sea and time at the computer, analyzing the vast data gathered from the sea. The focus will be a systems view of how the abundantly productive Monterey Bay works.

Chris Scholin and Christina Preston

Environmental Sample Processor: Molecular diagnostic procedures for identifying microbes, their genes and gene products typically require the return of discrete samples to a laboratory for analysis. As a step towards overcoming this limitation, we are exploring use of the Environmental Sample Processor (ESP), a novel instrument that can be used to detect water borne microorganisms remotely, subsurface, in near real-time. The ESP automates application of custom DNA probe arrays to detect particular species and transmits results of those assays via radio modem. The ESP also archives samples for microscopy and nucleic acid analyses. To date, assays for several bacterioplankton groups, harmful algal species and invertebrate larvae have been tested and deployed on the instrument. We are interested in developing several other assays to target other bacterioplankton groups that can be used in conjunction with the ESP.

Bob Vrijenhoek

Molecular ecology: We use molecular tools to study evolutionary and ecological relationships between populations and species of deep-sea animals. Our current interests focus on the use of DNA sequences to study how marine animals disperse and the rates of gene flow between populations. We also study polychaete worms that eat the sunken bones from marine mammals. The work focuses on evolutionary relationships among the worms, their development, and on the peculiar dwarf males that appear to be an arrested larval stage

Alexandra WordenAlexandra Worden

Carbon Cycling in Marine Ecosystems: We study marine phytoplankton and how they interact with their environment. This involves work at sea as well as lab work, including flow cytometry and microscopy as well as whole genome sequencing, metagenomics and transcriptomics. Most of our work focuses on the smallest of the eukaryotic algae (less than 2 microns in size), but we also consider other microbial populations. In the long term we hope to gain a mechanistic understanding of how populations are controlled, both from the perspective of growth (nutrients, competition etc.) and predation. This internship opportunity is flexible in that we have a range of projects to be involved in, from purely computer based to "wet lab" work.

Bill Ussler

Methanogen Incubation Experiment: A lab-oriented project exists with a marine geology/geochemistry group studying the sources and sinks of methane carbon in marine sediments and the role of microorganisms. The specific task involves developing a hydrogen delivery system for a sediment chemostat that will be used to study the growth of methanogens in marine sediments. The intern will assist with designing and building a prototype system, and performing chemical analyses to document growth of microbial communities. We desire a person who enjoys hands-on laboratory work and who has analytical chemistry laboratory skills, an understanding of basic electronics and physical chemistry, and an interest in building systems to simulate natural biogeochemical processes.

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Application procedure: Applications for 2008 are now being solicited. Applications should include a cover letter, a curriculum vitae, three letters of recommendation, and we would also like you to complete an online form. The cover letter should include a statement of your research interests (with specific mention of one of the following potential projects or areas), relevant coursework and grades, and complete contact details (home and work phone numbers and email address, if available). MBARI is an equal opportunity employer. Below you will find a list of some potential projects and mentors (this list will be updated, so please bookmark and check this page from time to time). Clearly identifying a specific research interest/area is an important part of your application and is essential in the application process. Please contact George Matsumoto if you have any questions. I have provided links to the mentors home pages (if available) so that you can learn more about the various mentors, please DO NOT contact the mentor directly. Application materials (including letters) can be sent to MBARI via fax (831 775 1620), regular post, or by email. If you opt for an email application, please send your materials to both George and to Alta Anzalone as George will be out of town for a few weeks. Jim Barry Climate change and ocean acidification: The goals of this project are to evaluate the response of deep-sea organisms to environmental perturbations expected in association with large-scale deep-sea CO2 releases, under consideration as a method to reduce atmospheric levels of CO2. We are conducting studies of faunal tolerance to CO2 / pH plumes and physiological studies of pH compensation and metabolic depression for deep-sea organisms. This subproject is coupled closely to Dr. Peter Brewer’s studies of CO2 chemistry and physics. Lisa Borok and Kim Fulton-Bennett Science communication: The MBARI Communications group is looking for an intern to create one or more "podcasts" (audio interviews/stories for the web) about selected MBARI research projects. The intern would be responsible for all aspects of production, including story outline, scripting, interviews, audio recording (equipment will be provided), voiceover (if appropriate), and audio editing. This would be a pilot project, so as a final paper, we would like the intern to report on the feasibility of creating podcasts on a regular basis. We are looking for an applicant with a science background and experience in journalism (especially radio journalism). Please include samples of writing and/or audio projects (or links to such samples on the web) with your application. Peter Brewer and Ed Peltzer Ocean Chemistry: Become a part of an energetic laboratory team investigating the geochemistry of methane hydrates, and breakthroughs in identifying the future of a high CO2 ocean as climate change and greenhouse gases evolve. We have deployed novel tools, including a laser Raman spectrometer at 3.6 km depth, for the measurement of hydrates and hydrothermal vents. We are also carrying out studies of the effects of CO2 enriched seawater released on the ocean floor, and investigating techniques for simulating the biogeochemistry of the mid-21st century ocean. With this in mind, long-term CO2-enrichment experiments are being designed which are powered and controlled through the Monterey Accelerated Research System (MARS - www.mbari.org/mars) undersea cabled observatory. For more information you can look at the following websites: Ocean Chemistry of Greenhouse Gases and Laser Raman Spectroscopy. Dave Clague Submarine Volcanism: Multibeam bathymetric, sidescan, and sub-bottom chirp seismic data to be collected during the MBARI expedition to the Gulf of California in spring 2008 should allow a detailed analysis of mid-ocean ridge structure and volcanic history for the Alarcon Rise, the northernmost segment of the East Pacific Rise. Preliminary processing and analysis of these data will be completed to help us define ROV dive targets during the expedition. However, the detailed final processing of these data, analysis and synthesis of the different datasets, and incorporation of the dive observations open up numerous opportunities for projects to be defined and completed by a summer intern. We should have nearly 15 days of AUV data and projects could address the structure of ridge-transform intersections, the structure of the small non-transform discontinuity in the segment, mapping of individual lava flows along the ridge with age estimates based on visual dive observations, analysis of the apparent asymmetry of spreading on this segment, or sediment distribution on and near the ridge in this high-sedimentation rate region. The intern will utilize the processing program MB-System and work in GIS to be able to overlay different data sets. Knowledge of one or both software packages is a plus, but is not a requirement. Craig Dawe and Steve Etchemendy Monterey Accelerated Research System (MARS): Update and upgrade the MARS web pages on MBARI's system. Tasks to include a users guide for researchers and would include all relevant documentation for a user to build or rework existing equipment for deployment on MARS and contact information for possible funding and deployment scenarios. Compile and create an interface to engineering documentation along with an Operators manual. Perhaps also write articles on MARS for popular magazines. Duane Edgington and Danelle Cline Automated visual event detection: Our project involves implementing a computer vision system that analyzes video collected by observatory cameras or underwater vehicles to detect, classify, and identify organisms visible in the video. We are collaborating with labs at Caltech and University of Southern California to adapt and extend computer vision systems modeled after the human visual system. The internship involves working with a small team, participating in development, analyzing videos from Eye-in-the-Sea, Neptune Canada, or ROV midwater or benthic dives and comparing the analysis with processing performed by the computer vision system, and mining the MBARI database of annotated video to collect representative sample video clips for analysis. We welcome applicants with a background in computer science, machine vision, or marine biology. Kevin Gomes Developing Ocean Observing Technologies on an Enterprise Service Bus (ESB): MBARI is collaborating with the National Center for Supercomputing Applications (NCSA) to prototype ocean observing technologies on the industrial software technology known as an Enterprise Service Bus (http://www.mulesource.com). The intern will work with a team of MBARI software engineers to bring oceanographic instrumentation and its interactions onto the ESB. Development will be done in the Java programming language with potential tasks ranging from ESB component development to implementing an instrument control interface on an embedded controller. The end result of this work will provide MBARI and our collaborators with an interface to oceanographic instrumentation on an ESB to inform the international efforts developing software infrastructures for environmental science. Steve Haddock Zooplankton and Bioluminescence: Intern will work on a self-directed project involving bioluminescence, fluorescence, or phylogenetics of gelatinous zooplankton (ctenophores, siphonophores, or medusae). Molecular, chemical, or ecological projects may be possible. One high-priority project involves setting up a web site for monitoring coastal observations of jellyfish (and other animals). The site would accept data entry from "citizen scientists". This would require programming to interact with the Google Maps API. Judith Kildow Economic Impacts from Climate Change Effects on California’s Coast: Project 1: Using the latest data available on sea level rise for sections of California’s coast, describe the infrastructure that is at risk and create several scenarios of rise with the estimated economic losses they represent. Project 2: Working with a local community on the central coast such as the City of Monterey, create a template for how it might add climate change impacts into its Local Coastal Plan and describe what it might look like for planning purposes. Bill Kirkwood with collaborators Dr. Chris Kitts (Univ. Santa Clara) and Dr. Geoff Wheat (NOAA/OER) Improving and Verifying Performance of Near Shore Science Operations using an Autonomous SWATH Platform: This project builds upon the existing prototype Small Water-plane Area Twin Hull (SWATH) autonomous surface craft called SeaWASP. The tasks for a candidate intern will be to integrate further instrumentation for remote command and control, further test selected science instrumentation, and operate a designated mission in autonomous mode as part of a science field campaign. The science mission will include remote operations from shore as a primary goal including the successful collection of science instrument data. The candidate will be required to do data analysis and produce science publication quality data products. The project will conclude with a science data set and an engineering report correlating science data quality to system performance being delivered. Key output from this project will be recommendations for the next phase of upgrades to improve functionality for science. Candidates must be willing to participate on a science mission involving time at sea and travel to a remote location for several weeks. Zbigniew Kolber and Denis Klimov Effect of Ocean Acidification on the Upper Ocean Ecology: By absorbing excess of anthropogenically-produced CO2, the pH in the upper ocean will decrease by up to 0.6 units within the next 200 years, possibly affecting a variety of biologically important processes such as calcification, metal speciation, and silica solubility. Changes in ocean’s pH will also modify the redox potential of photosynthetic and respiratory electron carriers, directly affecting a range of biophysical processes involved in photosynthesis, carbon assimilation, and respiration. To investigate these effects you will operate a cluster of sea-going pH-stats to manipulate the pCO2 level, pH, temperature, light, and nutrient status of phytoplankton in continuous cultures. You will grow selected species of phytoplankton and the natural phytoplankton assemblages under conditions of CO2, pH, and temperature resembling that of the anticipated conditions in the upper ocean within the next 100-300 years. Using a suite of fluorescence-based techniques developed at MBARI, you will measure corresponding changes in the efficiency of photosynthetic light utilization, the yield of photosynthesis, and the kinetics of the photosynthetic electron transport. You will analyze these data to assess the potential effect of the anticipated pH shift on the ocean photosynthesis, primary production, and the phytoplankton growth rates. George Matsumoto Intern Logistical Coordinator: This intern will be assisting with the MBARI intern program. This assistance will likely include assisting the interns with travel logistics during the program as well as coordinating some educational activities on the weekends. It is expected that this intern will also be working on their own independent research project. The successful applicant will be an alumna/alumnus of the MBARI intern program and will stay in the same housing as the interns. Letters of recommendation are not required, but please elaborate on what your research project will entail in your application letter. Kanna Rajan and Conor McGann Onboard Autonomy: MBARI's Autonomous Systems group is engaged in research efforts to use advanced Artificial Intelligence (AI) techniques to enable Autonomous Underwater Vehicles (AUV) to be more adaptive and self aware of their resource and goal commitments. Our onboard deliberative system T-REX (http://www.mbari.org/autonomy/TREX/ ) being used on AUV platform (http://www.mbari.org/auv/ ), is based on the sense-deliberate-act paradigm synthesizing new mission plans in response to environmental conditions. T-REX uses a state-of-the-art temporal constraint-based planner (EUROPA) developed originally at NASA and flown on a number of space missions. Potential projects include: 1. PlanWorks debugging tool for EUROPA which allows us to leverage work done in visualization of constraint networks, token networks and timelines. The internship primarily be focused on developing PlanWorks to provide diagnostic information for T-REX. 2. Expanding the simulation capability currently available within T-REX, including monte-carlo simulation for model and and agent validation. The internship will focus on augmenting and adding new features for shore-side T-REX validation. 3. Extend the NDDL domain modeling language within the EUROPA planner to natively support arithmetic constraints and propagate them efficiently. Highly motivated graduate or undergraduate students with substantial + Java programming skills + Limited C or C++ programming skills + AI Planning and a background in Constraint Satisfaction would be a plus are encouraged to apply. Steve Ramp Ocean Physics - Internal Waves: It is now commonly appreciated that waves supported by density stratification within the ocean (internal waves) are just as ubiquitous as surface waves on the air/sea interface. Internal waves are most commonly generated by tides impinging on abrupt topography, such as the continental shelf edge, sills, or island arcs. Two data sets from field experiments designed expressly to study internal waves are in hand and ready for analysis. These include the Monterey Bay, typically shelf edge phenomena, and the South China Sea, where the world’s largest internal waves are generated in the Luzon Strait and propagate WNW across the sea. We seek an intern to study all aspects of internal wave generation, propagation, growth, transformation, and dissipation. Steve Ramp and Heather Kerkering Products, Education, and Outreach: The Central and Northern California Ocean Observing System (CeNCOOS) is one of eleven Regional Associations (RAs) charged with implementing the national Integrated Ocean Observing System. CeNCOOS (see www.cencoos.org) is an end-to-end system including sensors, data management and communications, numerical modeling and prediction, and product development for the region spanning Pt. Conception to the Oregon border. The difference between CeNCOOS and other basic research grants is that we are charged with delivering information products that meet end-user needs such as evaluating climate change, water quality, harmful algal blooms, ecosystem-based management, and ocean education. We seek an intern with a marine policy and/or education interest to help develop and deliver such products. John Ryan and Erich Rienecker Coastal Plankton Ecology: In this project, the intern will have the opportunity to study the lives and times of plankton and their Monterey Bay home, viewed through the lens of multi-platform, multi-scale, multi-disciplinary observations. These observations come from satellites, aircraft, moorings, drifters, autonomous underwater vehicles, towed vehicles, and ships. The project will include time at sea and time at the computer, analyzing the vast data gathered from the sea. The focus will be a systems view of how the abundantly productive Monterey Bay works. Chris Scholin and Christina Preston Environmental Sample Processor: Molecular diagnostic procedures for identifying microbes, their genes and gene products typically require the return of discrete samples to a laboratory for analysis. As a step towards overcoming this limitation, we are exploring use of the Environmental Sample Processor (ESP), a novel instrument that can be used to detect water borne microorganisms remotely, subsurface, in near real-time. The ESP automates application of custom DNA probe arrays to detect particular species and transmits results of those assays via radio modem. The ESP also archives samples for microscopy and nucleic acid analyses. To date, assays for several bacterioplankton groups, harmful algal species and invertebrate larvae have been tested and deployed on the instrument. We are interested in developing several other assays to target other bacterioplankton groups that can be used in conjunction with the ESP. Bob Vrijenhoek Molecular ecology: We use molecular tools to study evolutionary and ecological relationships between populations and species of deep-sea animals. Our current interests focus on the use of DNA sequences to study how marine animals disperse and the rates of gene flow between populations. We also study polychaete worms that eat the sunken bones from marine mammals. The work focuses on evolutionary relationships among the worms, their development, and on the peculiar dwarf males that appear to be an arrested larval stage Alexandra WordenAlexandra Worden Carbon Cycling in Marine Ecosystems: We study marine phytoplankton and how they interact with their environment. This involves work at sea as well as lab work, including flow cytometry and microscopy as well as whole genome sequencing, metagenomics and transcriptomics. Most of our work focuses on the smallest of the eukaryotic algae (less than 2 microns in size), but we also consider other microbial populations. In the long term we hope to gain a mechanistic understanding of how populations are controlled, both from the perspective of growth (nutrients, competition etc.) and predation. This internship opportunity is flexible in that we have a range of projects to be involved in, from purely computer based to "wet lab" work. Bill Ussler Methanogen Incubation Experiment: A lab-oriented project exists with a marine geology/geochemistry group studying the sources and sinks of methane carbon in marine sediments and the role of microorganisms. The specific task involves developing a hydrogen delivery system for a sediment chemostat that will be used to study the growth of methanogens in marine sediments. The intern will assist with designing and building a prototype system, and performing chemical analyses to document growth of microbial communities. We desire a person who enjoys hands-on laboratory work and who has analytical chemistry laboratory skills, an understanding of basic electronics and physical chemistry, and an interest in building systems to simulate natural biogeochemical processes. BACK to 2008 Internship advertisement Last updated: Jan. 31, 2008
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