Aerobic Bioremediation of Hazardous Compounds
The Hazen Lab is a diverse group scientific engineering associates, post doctoral fellows, research associates, technicians, and students in microbial ecology and environmental engineering that are led by Dr. Terry C. Hazen. The primary research emphasis of the lab is basic and applied field microbial ecology, especially as it relates to bioremediation of metals/radionuclides, petroleum, and chlorinated solvents. The overarching vision for the lab is understanding the fundamental concepts of environmental stress response pathways from the molecular to the ecosystem level to improve our knowledge of biogeochemistry.
The student will work on specific experiments on aerobic landfill bioremediation and/or PAH, TCE, PCB and UXO biodegradation in soil. S/he will have a specific project dealing with one aspect of the work in elucidating principles that will allow us to better cleanup these contaminants in soil and groundwater. This will include making media, counting bacteria, taking lab and field measurement for carbon dioxide, methane, oxygen, pH, moisture, and contaminant concentrations. S/he will experience all aspects of the experimental project (cradle to grave) and have opportunities to gain addtional experience from other students and post-docs working in the lab and field. The student can expect to learn field and laboratory experimental design, sampling, data analysis and reporting for bioremdiation experiments in lab simulations and at field sites at LBNL and locally.
Students interested in this position should have one or more of the following: microbiology, ecology, analytical chemistry, and the position requires computer literacy (word processing, spreadsheets, internet), general biology and chemistry.
Majors: Biology, Biochemistry, Environmental Engineering
Mentors: Terry C. Hazen
Division: Earth Sciences
Group: Center for Environmental Biotechnology
Mail Stop: 70A-3317
Phone: 510.486.6223
email: TCHazen@lbl.gov
Student Research Abstract; Summer, 2005
For more information, you can check the group's website
Reposted: 30 January 2008

Automating Data Analysis for DNA Microarray Experiments
This position is for a student to develop software for data analysis and web-accessible databases. The data will be generated from high-density microarrays used to detect bacteria from a variety of settings. The person also may help with data analysis.
The student will assist in writing software for automating data analysis of DNA microarray experiments and help develop a database for the integration of analytical results. The student also will create functions for web- based browsing of data from the database mentioned. Secondary responsibilities will be preparing figures for scientific presentations and publications.
To be successful, a student in this position should have programming ability in Perl, Java, CGI, or RDBMS; familiarity with Excel spreadsheets and basic Statistics is also helpful.
Majors: Computer Science, Bioinformatics
Mentor: Todd DeSantis
Mail Stop: 70A-3317
Phone: 510-761-6720
email: tdesantis@lbl.gov
Posted: February 11, 2007

Ecological Engineering & Biokinetics
There will be two or more openings for undergraduate researchers interested in studying water quality issues related to non-point source pollution and ecosystem restoration.
The undergraduate students will participate in an on-going study of algal growth kinetics in the San Joaquin River in the Central Valley of California. The students will learn how to take water quality samples, measure hydraulic parameters important to executing river ecosystem studies, analyze chemical and biological parameters important to understanding and modeling algal biokinetics, and otherwise participate in a full-scale ecosystem study.
These experiments require that the student develop skills in both field sampling and analytical chemistry. The student can expect to learn the scientific method, become familiar with basic laboratory techniques of analytical chemistry, and gain experience in environmental science.
Completed course work in chemistry, biology, and microbiology would be useful. Laboratory classes or field experience a plus. Requires interest in a scientific career in the environmental sciences.
Majors: Chemistry, engineering, environmental science, geology, microbiology, biology.
Mentor: William Stringfellow
[Mentor has requested no prior contact]
Student Research Abstract; Summer, 2005
Revised: February, 2005

Materials Chemistry
This researcher is currently working in materials chemistry related to materials that serve a dual function, that of both radiation detection materials and solar cell-active materials. The student will do laboratory work, including minimal synthesis work coupled with a lot of instrumentation. There are plans for the student to work at the ALS on some of their instrumentation. The student will learn to use techniques that are applicable to a wide range of materials chemistry problems, some of them being societal-related such as the solar cell issue.
Majors: chemistry, chemical engineering
Mentor: Dale Perry
Mail stop: 70A-3317
Phone: 510.486.4819
email: DLPerry@lbl.gov
Posted: February 12, 2007

Molecular Microbial Ecology
The Molecular Microbial Ecology group uses molecular approaches for the study of a variety of natural microbial communities. This includes the development of new techniques to dissect the microbial diversity of complex ecosystems. The long-term goal of this research is to integrate different fields of biology (i.e., genomics, ecology, molecular biology, proteomics, bioinformatics, medicine, and metagenomics) to provide insight into the survival of microorganisms under stressful or favorable conditions. Current research in the lab focuses on the microbial ecology of a number of environments including the air, water, soil, deep subsurface, and the human lung. Several studies emphasize the natural distribution of pathogens in the environment. By understanding processes that allow specific bacteria to exploit unique environments, they hope to better understand critical mechanisms for survival.
A student in this group may be assigned to one of two areas:
1) technical: student will prepare samples for molecular analyses, such as real-time PCR or high-density DNA microarray analysis. In particular, plant soils and/or tissues will be extracted for nucleic acids that are then amplified using PCR.
2) bioinformatics: student will be writing software for automating data analysis of DNA microarray experiments and helping to develop a database for the integration of analytical results; also create functions for web-based browsing of data from the database.
A student in the technical position can expect to become proficient in doing several molecular techniques useful in a variety of academic and industrial work environments. Students may have an opportunity to troubleshoot techniques applied to new samples, providing valuable experience in working through common lab procedures.
A bioinformatics student will learn about designing programs to process large quantities of data, increasingly important with the ever-expanding data-rich methods being developed to further science in many arenas.
To be successful in this position it is useful for the technical student to have basic knowledge in chemistry (measuring, weighing, mixing solutions) and biology
To be successful in bioinformatics a student would have familiarity with Excel and basic statistics and ability to program in at least one of Perl, Java, CGI, RDBMS, or AJAX
Majors: biology, microbiology, medicine, bioinformatics, or computer science
Mentor: Gary Andersen
Mail stop: 70A-3317
Phone: 510.495.2795
email: GLAndersen@lbl.gov
Posted: February 1, 2007

Terrestrial Biogeochemistry Lab
The Torn Lab studies the links between the carbon cycle and climate change. Fire is an important management tool in prairie ecosystems, with effects on the carbon cycle that are not well understood. In addition, global warming may increase the frequency of wildfires. Increased fire frequency can, in turn, amplify climate change by releasing more carbon (CO2) to the atmosphere. They are studying the carbon cycle (soil carbon stocks, plant growth, and CO2 fluxes) in two prairie fields using a burning experiment in which one field was burned and the other maintained as a control. This project uses a variety of measurements to understand the effects of increased fire on the carbon cycle of prairie ecosystem (Southern Great Plains).
The student will participate in the experiment by doing lab work to help determine the amount of carbon stored in burned and unburned prairie soil and plants. The student will process soil and vegetation samples from the field site in Oklahoma, and learn about ecosystem science measurements, basic lab techniques, data analysis, and presentation of results.
Students should have an interest in global change and the environment. Some laboratory experience (through a class, project, or job) such as using a balance and keeping good lab notes, is essential. Course work in environmental science, biology, chemistry or an agricultural science are useful.
Students who are planning to teach at the K-12 level can also work on a project to design a curriculum based on classroom litter decomposition experiments.
Majors: Biology, Chemistry, Environmental Science
Mentor:Margaret S. Torn
Mail stop: 90R1116
phone: 510.495.2223
email: mstorn@lbl.gov
Posted: February 1, 2007

Wetland Habitat Assessment and Salinity Management
This position involves monitoring of saline drainage from seasonally managed wetlands in the San Joaquin Valley of California using state-of-the-art water quality and flow measurement equipment and techniques. The position will involve both laboratory and field work and travel into the San Joaquin Valley. Student will become part of a study team which is using geophysical methods (electromagnetic sensors) to map wetland soil salinity to assess long term impact of innovative wetland drainage management techniques. A Bowen ratio weather station collects atmospheric data in an allied experiment to measure wetland evapotranspiration. Student will help in field data acquisition and in the development of a mathematical model of seasonal wetland hydrology and working up weather station data into a completion report. This project works closely with water managers in local water districts, the department of Water Resources and US Bureau of Reclamation and wetland biologists in the California Department of Fish and Game. Success with this project depends on someone who is self-motivated with an interest in field-level experimentation; an intern is likely to be left on her/his own for some of the time. A current driver's license will be essential.
Majors: Environmental engineering, Ecology, Environmental management
Mentor: Nigel W.T. Quinn
Division: Earth Sciences
Mail Stop: 70A-3317K
Phone: (510) 486-7056
email: nwquinn@lbl.gov
Student Research Abstract; Summer, 2005
Revised: 6 February 2008