Frontiers in Biological Sciences
The seminar series features nationally/internationally known researchers from industry, government, and academia discussing novel ideas and advancements related to biological sciences. The hour-long seminars will feature a 45-minute talk by the featured speaker followed by 15 minutes of discussion with the audience members.
Lance C. Seefeldt, Ph.D.
Professor of Chemistry and Biochemistry
Utah State University
Wednesday, July 18, 2012
CO2 Reduction and Coupling to Hydrocarbons Catalyzed by Nitrogenase
The enzyme nitrogenase catalyzes the six electron/proton reduction of N2 to form 2 NH3. In addition, the enzyme also catalyzes the reduction of protons to make H2. Professor Seefeldt's lab has discovered that when amino acids close to the active metal cluster FeMo-cofactor are substituted to remodel the active site, nitrogenase can reduce CO2 to CH4. He will further demonstrate that CO2 reduction can be coupled with acetylene reduction to give the olefin propene, thereby providing a pathway for conversion of CO2 into valuable hydrocarbons with a single catalyst. Recent evidence indicates the importance of metal-hydrides in the nitrogenase mechanism. Professor Seefeldt will discuss the possible involvement of metal-hydrides in CO2 reduction and present a draft mechanism for N2 reduction.
Lauren J. Webb, Ph.D.
Department of Chemistry and Biochemistry
University of Texas at Austin
Tuesday, July 17, 2012
Electrostatic Fields at Biological Interfaces
In the post-genomic era, enhanced understanding of the cooperation between biological molecules is necessary to explore the complexity of living cells. The affinity and specificity of macromolecular interactions in biological systems are the result of both structural and electrostatic driving forces, but while the field of structural biology has made great advances, much less is understood about electrostatic influences.
Professor Webb will describe how vibrational spectroscopy can be used to measure electrostatic fields in two complex biomolecular systems: 1) stable protein-protein interfaces and 2) peptides intercalated in free-standing lipid bilayer membranes. Her laboratory is developing computational models that accurately predict these interactions using vibrational Stark effect (VSE) spectroscopy, in which spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment.
Wuhan Center for Magnetic Resonance
Wuhan Institute of Physics and Mathematics
Chinese Academy of Sciences
Research at the Wuhan Center for Magnetic Resonance
Monday, April 23, 2012
Each professor will describe research at the Wuhan Institute's Center for Magnetic Resonance, including:
Solid-state NMR spectroscopy and theoretical DFT calculations studies of solid acid catalysts and catalytic reactions. With the increasingly intense demands for environmentally friendly processes in the chemical and petroleum industries, solid acid catalysts (zeolites, heteropoly acids, complex metal oxides) offer new alternatives to the highly corrosive, hazardous and polluting liquid acids (HF, H2SO4). The acidity of solid acid catalysts is closely related to their catalytic activities. In this presentation, recent work at the Wuhan Center on characterization of the acidity of solid acid catalysts and related catalytic reactions by solid-state NMR spectroscopy and DFT calculations will be introduced.
- NMR approaches for bio-analysis. Approaches developed recently in at the Center for analysis of biological samples include:
- Solvent signal suppression using WATERGATE
- Selective detection of choline contained metabolites in tissue using 1H-14N HSQC
- GFFT for processing non-linear acquired nD NMR data and NASR for suppression noise and artifacts
- An effective approach to characterize individual variation of human blood plasma and application to protein-drug interaction.
Jennifer DuBois, Ph.D.
Associate Professor of Chemistry and Biochemistry
University of Notre Dame
Monday, February 20, 2012
From O-O bond formation to Fe metabolism: the story of a new bacterial protein superfamily
Bacteria have a remarkable capacity for change. Several genera of bacteria have been discovered that have evolved the ability to respire and thereby detoxify oxochlorates: biocides and oxidants of recent anthropogenic origin that are a particular problem at DOE sites. The respiratory pathway concludes with a biologically unusual and chemically challenging reaction: the conversion of chlorite (ClO2-) into Cl- and O2. This heme-dependent reaction provides a remarkably efficient model for catalyzing O-O bond formation, a reaction of current interest for clean energy research. At the same time, the protein is one of a quarter of the approximately 5700 unicellular clusters of orthologs (COGs) that still lacks any defined biological function.
Our research into understanding the proteins at the forefront of this COG's evolution has now led us back into an exploration of their origins, and the broader biological relevance of the family from which the O2-generating proteins evolved. Specific functional links of the COG to heme and nitrogen metabolism have been discovered through genetic and biochemical means. Structural and informatics analyses have further shown that these proteins are part of a previously unrecognized structural superfamily of proteins, called the CDE superfamily.
Patrick S. Chain, Ph.D.
Patrick S. Chain, Ph.D.
Metagenomics and Next Generation Sequencing (NGS) Applications Team Leader
Los Alamos National Laboratory
Wednesday, February 1, 2012
Sequencing microbial communities: progress and challenges
The increased throughput of next-generation sequencing platforms has opened the door to a number of sequencing applications that were not fathomable even a few years ago. While the increased sequencing capacity has enabled the interrogation of microbial consortia of varying diversities, the tremendous amount of data generated has required new data management practices and the development of novel algorithms and tools to adequately analyze the resulting sequences. The constantly changing landscape in sequencing throughput and platforms continues to challenge our ability to process the data (including common practices such as assembly and annotation). In this presentation, some of these challenges will be discussed, along with novel methods adapted for large datasets derived from microbial communities. In particular, the challenge of metagenome assembly will be presented, along with the use of reference genomes, and efforts to improve single cell genomics methods to more adequately obtain near-complete references for a target environment.
Trent R. Northen, Ph.D.
Principal Investigator, Molecular Cartography Project
Lawrence Berkeley National Laboratory
Friday, November 4, 2011
Mass spectrometry-based metabolite profiling and imaging
Metabolite profiling using mass spectrometry provides an attractive approach for the interrogation of metabolic capabilities from complex biological systems. Untargeted metabolite profiling using electrospray ionization has the potential to improve functional genome annotations, characterize uptake and release of metabolites, and study the effects of low-dose ionizing radiation. However, conventional methods are slow, and de novo identification of metabolites from spectral features remains a challenge given the large number of experimental artifacts.
In this talk, Dr. Northen will present an integrated workflow for metabolite identification, characterization of uptake/release, fate, and metabolite/activity screening. This was done using uniform stable isotope labeling for chemical formula determination, structural analysis using MS/MS spectra vs. spectral database records, and systematic screening of consumed or excreted metabolites using metabolite profiling of growth media from microbial cultures (referred to as metabolic footprinting).
They have performed systematic evaluation of intracellular and extracellular metabolites on the model cyanobacterium Synechococcus sp. PCC 7002. It was found that 102 out of 202 detected metabolites were exchanged significantly and the fate of uptake several metabolites were determined using stable isotopic labeling. He will also present applications of nanostructure-initiator mass spectrometry (NIMS) technologies for imaging and screening glucoside hydrolase activities.
Jian Xu, Ph.D.
Professor and Director, BioEnergy Genome Center
Chinese Academy of Sciences
Qingdao Inst of BioEnergy and Bioprocess Technology
Tuesday, September 13, 2011
BSF Darwin Room
Genetic Foundation for Robust Production of Oil in Microalgae
Microalgae are considered one promising feedstock for photosynthetic biofuels. However, the genetic diversity and genomic evolution of microalgal traits relevant to oil production remain elusive. Nannochloropsis is a genus of planktonic unicellular microalgae that lack chlorophyll b and c. Many strains of this genus are capable of growing rapidly and producing large amounts of neutral lipids mainly in a form of triacylglycerol (TAG). We have developed a Phylo- Genomics approach to investigate the genetic diversity and genomic evolution of oleaginous microalgae using Nannochloropsis as a model. First, a high-quality draft genome sequence of Nannochloropsis oceanica has been generated using a hybrid sequencing and assembly strategy that combines the powers of pairended reads from 454 and Solexa. Second, transcript sequencing was applied to reconstruct the global diversity and dynamics of gene expression under various pivotal environmental conditions that lead to robust accumulation of TAG in N. oceanica. Third, draft genome sequences of representatives of other known Nannochloropsis species, including N. salina CCMP537, N. gaditana CCMP527, N. sp. CCMP531, N.oculata CCMP525, N.limnetica CCMP505 and N.granulata CCMP529 were obtained. Together, these Nannochloropsis genomes decoded span a wide phylogenetic range. The genome sizes are all between 20Mb to 35Mb; however, the sequence diversity and genome-structure divergence of these species/strains vary widely. In this presentation, the conservation and divergence of genes, regulatory elements and metabolic pathways in Nannochloropsi, particularly those for oil production, will be described. Furthermore, the implications of the high-throughput functional genomics approach for developing new-generation algal feedstocks will be discussed.
Claudia Schmidt-Dannert, Ph.D.
Department of Biochemistry, Molecular Biology and Biophysics
BioTechnology Institute, University of Minnesota
August 8, 2011
BSF Darwin Room
Building Better Microorganisms for Biotechnology
Advances in 'omics and genetic engineering have led to the emergence of the field of synthetic biology, which aims to reengineer and synthesize biological systems at much larger scales than manipulating one gene at a time. Reprogramming and rewiring biological systems by introducing new functionalities offers great promise for the design of cells to produce new chemicals, bioenergy, and biofuels.
Dr. Schmidt-Dannert will discuss and show examples of efforts on engineering new complex properties into microbial cells. She and her colleagues are studying the possibility of engineering non-photosynthetic cells for the conversion of light energy into useful chemical energy or electricity. She will present their efforts to engineer light-driven electricity generation into Shewanella oneidensis. Concentration and sequestration of toxic metabolites inside bacterial cells is another highly desirable feature to be introduced into microbial workhorses. Being able to compartmentalize metabolic reactions would, for example, enable efficient CO2 capture and corsion, increase flux through engineered pathways, and prevent accumulation of toxic pathway intermediates.
Her lab has recently engineered micro-compartments in E. coli for targeted enzyme localization, and she will present some of their results on the creation of such in vivo nano-bioreactors. She will also provide a look at current work in the area of synthetic ecology where she and her colleagues aim to design microbial communities for task sharing in the production of metabolites such as biofuels.
Leigh Anderson, Ph.D.
CEO, Plasma Proteome Institute
and Applied Chemistry
Friday, July 15, 2011
The current clinical plasma proteome consists of 109 proteins measured by FDA-cleared or approved assays and 96 proteins measured using widely available laboratory developed tests, ~1% of the baseline human proteome. However the rate at which new protein analytes achieve FDA approval has remained essentially constant over the past 15 years at 1.5 proteins per year, insufficient to meet medical needs. The striking shortfall in new protein diagnostics emerging from proteomics research reflects a lack of critical biomarker verification capacity.
To bridge the gap between biomarker discovery and clinical use, a new approach to verification is described: multiplexed panels of specific candidate assays based on hybrid immuno-mass spectrometric (SISCAPA) detection. By combining high sensitivity, high throughput, and precision with use of small plasma samples, a platform for systematic verification of hundreds of candidates in thousands of samples can be implemented. In the clinical laboratory, affinity enrichment with MS quantitation can provide absolute specificity, true internal standardization, and facile multiplexing—thus transcending the limitations of conventional immunoassays. An extension of this approach, the hPDQ project providing a library of specific tests for all 21,300 human proteins, could provide the larger biomedical research community with direct quantitative access to the entire human proteome.
Terry C. Hazen
Terry C. Hazen, Ph.D.
DOE BER Distinguished Scientist
Head, Ecology Department
Head, Center for Environmental Biotechnology
Director, Microbial Communities, Joint BioEnergy Institute
Co-Director, Virtual Institute Microbial Stress and Survival
Earth Sciences Division, Lawrence Berkeley National Laboratory
June 13, 2011
11:15 a.m.- 12:15 p.m.
A Systems Biology approach to the Deepwater Horizon Oil Spill—An example of team science for ecological disasters
The explosion on April 20, 2010, at the British Petroleum-leased Deepwater Horizon drilling rig in the Gulf of Mexico off the coast of Louisiana resulted in oil and gas rising to the surface and oil coming ashore in many parts of the Gulf. It also resulted in an immense oil plume 4,000 feet deep. Despite spanning more than 600 feet in the water column and extending more than 10 miles from the wellhead, the dispersed oil plume was gone within weeks after the wellhead was capped—degraded and diluted to undetectable levels.
Ecogenomics enabled discovery of new and unclassified species of oil-eating bacteria that apparently lives in the deep Gulf where oil seeps are common. Using 16s microarrays, functional gene arrays, clone libraries, lipid analysis, phenotypic microarrays, metagenomes, metatranscriptomes, single cell sequencing, and stable isotope analysis in combination with a variety of hydrocarbon and micronutrient analyses, scientists were able to characterize the deep-sea microbial ecosystem and the effect of the oil spill. This team-science approach suggests a great potential for intrinsic bioremediation of oil plumes in the deep-sea and other environs in the Gulf of Mexico.
Caroline M Ajo-Franklin
Caroline M Ajo-Franklin, PhD
Staff Scientist, The Molecular Foundry
Lawrence Berkeley National Laboratory
June 6, 2011
CSF Mural Room (1508)
1:30 - 2:30 p.m.
Interfacing Living Cells and Inorganic Materials at the Nanoscale
Dr. Ajo-Franklin's research group uses synthetic biology, biophysics, and nanoscience to engineer and understand the functional interface between living cells and inorganic materials at the nanoscale. By directly interfacing living organisms with synthetic materials, scientists can harness the vast capabilities of life in photo- and chemical energy conversion, chemical and material synthesis, and self-assembly and repair.
She will describe their efforts to engineer electronic communication between biological cells and inorganic materials and our efforts to understand how living cells can influence mineralization of inorganic materials. These efforts illustrate how scientists seek to understand and control nanoscale processes at the cellular-inorganic surface so to engineer cells to become self-replicating, programmable "living materials."
Eleftherios (Terry) Papoutsakis
Eleftherios (Terry) Papoutsakis, PhD
Department of Chemical Engineering, Department of Biology
Delaware Biotechnology Institute
University of Delaware, Newark, DE
June 1, 2011
1:15 - 2:15 p.m.
Systems Analysis and Metabolic Engineering of Solventogenic Clostridia
Clostridia are anaerobic, endospore-forming prokaryotes of major importance to cellulose degradation, human and animal health, and acidogenesis, with several applications in biotechnology and advance bioremediation. Clostridial genetics and biotechnology have been frequently misunderstood or ignored. In the last 5 years, however, there has been enormous growth in clostridial-based industrial processes. For example, solventogenic clostridia can produce a large array of metabolites, while metabolic engineering could enhance these native capabilities for production of additional chemicals. Such chemicals can serve as biofuels directly or indirectly.
Dr. Papoutsakis will review the origin and successes in metabolically engineering and some of the systems biology work on solventogenic clostridia, and will highlight recent developments in his lab in modifying their sporulation program. The goal of these "differentiation engineering" efforts is to generate solventogenic but non-sporulating strains suitable for intensive, continuous or semi-continuous bioprocessing. Dr. Papoutsakis will also highlight recent work in his lab to understand core regulons and the stress response system in these organisms.
Dr. Krishna Mahadevan
Department of Chemical Engineering
and Applied Chemistry
University of Toronto
Thursday, May 12, 2011
BSF Darwin (1007)
Recent advances in experimental and computational technologies have enabled the detailed characterization of biological systems. In particular, the molecular components of these systems, including the list of genes, proteins they encode, and compounds that interact with these proteins, can be determined. This availability of tools to analyze system-wide changes at the gene, protein, and metabolite level has created significant opportunities to understand cellular functions resulting in the emergence of systems biology. Specifically, constraint-based modeling approach has proven successful in predicting the physiology of well-studied and poorly characterized microorganisms.
Dr. Mahadevan will give an overview of a constraint-based modeling approach and recent developments in this area, including limitations, and discuss the development of metabolic models for environmentally relevant bacteria and their use in optimizing practical applications in electricity generation and bioremediation. Finally, he will present extensions of this approach for analyzing microbial ecology in the subsurface; specifically, using genome-based approaches to study the competition dynamics between different species of iron-reducing bacteria critical for uranium bioremediation. Results provide an improved understanding of factors controlling growth and respiration of the microbial population and their impact on bioremediation in heterogeneous environments.
Director, Center for Spatial Systems
Oregon Health & Science University
Monday, April 18, 2011
EMSL Auditorium, Richland, WA
Dr. Gray's laboratory explores mechanisms by which genomic, transcriptional, and proteomic abnormalities occur in selected cancers; elucidates how these abnormalities contribute to cancer pathophysiology; and assesses the ways in which these abnormalities influence responses to gene-targeted therapies. Current studies focus on developing (a) genome-wide analyses of the spectrum of recurrent abnormalities that influence cancer behavior, (b) systems biology approaches to elucidate mechanisms by which cancer-associated molecular abnormalities influence individual responses to therapeutic inhibitors, (c) siRNA approaches to treat breast or ovarian cancer subpopulations that do not respond well to current chemotherapy, and (d) strategies for early detection of metastasis-prone breast cancer.
Monday, April 19, 2010
EMSL Auditorium, Richland, WA
Dr. Larabell's lab is at the forefront of developing soft x-ray tomography as a new tool for visualizing the location of proteins in cells and for imaging sub-cellular architecture with a spatial resolution of 40 nanometers or better. This new imaging technique combines many of the advantages of both light and electron microcopies, with characteristics unique to x-ray imaging. Her lab has designed and built the world's first soft x-ray microscope for biomedical imaging at the Advanced Light Source at Lawrence Berkeley National Laboratory.
Highlight: Modeling Microbes and Minerals
Friday, March 19, 2010
EMSL Auditorium, Richland, WA
Dr. Banfield's research group studies interactions between microorganisms and minerals, especially the impact of microorganisms on mineral weathering and crystal growth, biomineralization, and geochemical cycling. In this seminar, she will describe a highly productive ecosystem in an extreme natural environment that is supported by air, water, and iron sulfide minerals. Through integrating cultivation-independent molecular ('omic, 3-D electron tomography, and other) methods with geochemical approaches, it has been possible to begin to determine how these communities are structured and to unravel complex interdependencies, spatial organization, and evolutionary pathways.
Highlight: Building Better Biofuels
Tuesday, November 10, 2009
EMSL Auditorium, Richland, WA
Dr. Timothy Donohue, Professor of Bacteriology, University of Wisconsin-Madison
Professor Donohue has been a member of the UW-Madison Bacteriology Department for more than 20 years. His research program studies solar energy use by photosynthetic bacteria; specifically, how cells divert the energy captured from sunlight into different pathways. He has been a member of various federal research panels, served on several editorial boards and advisory committees in microbiology, and helped author reports for the Department of Energy on solar energy generation and the conversion of plant biomass into biofuels. He has decades of experience in leading cross-disciplinary research programs, including the NIGMS Biotechnology Training Program.
In 2007, Dr. Donohue was named director of the new Department of Energy-sponsored Great Lakes Bioenergy Research Center (GLBRC). The Center conducts basic, genomics-based research to design the microbial and plant systems needed to realize the potential of biofuels. In particular, GLBRC programs are focused on the sustainable conversion of cellulosic and other plant biomass into ethanol or other next-generation biofuels.
Combining innovative science, a critical mass of natural assets, and the corporate horsepower to build and advance a new bioenergy economy, Great Lakes Bioenergy is position to become a worldwide center of excellence for R&D of cellulosic ethanol and other bioenergy products. In support of this vision, GLBRC activities are being led by academic, national lab, and industry experts in plant biology, microbiology, molecular or cell biology, biochemistry, protein design, engineering, computer sciences, systems analysis, and ecology.
Monday, March 23, 2009
EMSL Auditorium, Richland, WA
Dr. Birgitte Ahring, Director of the Center for Bioproducts and Bioenergy and Battelle Distinguished Professor, based at WSU Tri-Cities, was the presenter.
Dr. Ahring has been Director of the Center for Bioproducts and Bioenergy at WSU-Tri-Cities' Bioproducts, Sciences, and Engineering Laboratory (BSEL) since August 2008. Previously, she was professor at The Technical University of Denmark in Lyngby. She is an internationally recognized authority in using anaerobic bacteria—bacteria that exists in an oxygen-free environment—to biodegrade waste.
Dr. Ahring's diverse background includes public-private partnerships, academic and industrial collaboration, high-level research, and a passion for educating others. She received her Ph.D. in microbiology in 1986 from the University of Copenhagen.
She also is founder and Chief Executive Officer of BioGasol, an engineering and technology company that designs and develops technologies for second-generation bioethanol production. Her company is a partner in the Pacific Northwest's first ethanol plant, which is funded with $24 million by the U.S. Department of Energy. This plant is being built in Boardman, Ore., about 70 miles southwest of WSU Tri-Cities.