Bio Workshop Abstracts

Biofuels Session: Thursday May 9th AM

The Developing Biofuels Program in New Mexico

Jose Olivares, Ph.D.

Bioscience Division Leader
Los Alamos National Laboratory

The formation of public-private partnerships has been lauded as a model for big endeavors, where industry and government can come together and advance science and technology towards  industrial processes. In this presentation the example of the National Alliance for Biofuels and Bioproducts (NAABB), will be reviewed. The success of this program in bringing new activities to the state of New Mexico through partnerships with industry, academia and national laboratory participation is a model that we hope to continue grow through close partnership with the New Mexico Consortium.

Algae and the Water, Energy, and Environment Nexus

Peter J Lammers, Professor

Director, Algal Bioenergy Program
New Mexico State University
The case for microalgae as a third generation biofuel producer has been widely discussed, driven by the knowledge that microalgae can accumulate large quantities of extractable fuel precursors and have the potential to achieve 5- to 6-fold higher yields than the best terrestrial crops (1).  Algae are responsible for nearly 50% of global photosynthesis and unlike terrestrial cellulose, algal biomass is readily convertible into a wide variety of different fuel, chemical and nutritional feedstocks (2-4). The diversity of microalgae that could be exploited for biotechnology applications is enormous spanning the earth’s oceans, freshwater streams and lakes, ice sheets, desert crusts, even acidic hot springs. However, technical and logistical uncertainties continue to constrain government and private investments necessary for growth of a large-scale algal biofuel industry. Barriers to be navigated include water and nutrient resource availability, potential resource competition with food-based agriculture, and most particularly the absence of demonstrated large-scale (>1,000 acre) systems for stable cultivation of aquatic microorganisms. Thus, current techno-economics strongly favor fossil fuel production, despite well-documented linkage to greenhouse gas-based climate change and ocean acidification.  Nevertheless, opportunities for creating disruptive new microalgal technologies abound, particularly at the interface between waste water remediation and production of renewable fuel and chemical feedstocks. New Mexico is well-positioned for global leadership in this area with expertise and state-of-the-art facilities for algal molecular biology, large scale cultivation and biomass process engineering.  A resource-optimized test case will be presented for the use of heat-tolerant algae from acidic hot springs (5) for municipal waste water processing coupled to scalable algal cultivation for fuel production without evaporative water loss.  
1. R. H. Wijffels, M. J. Barbosa, An Outlook on Microalgal Biofuels. Science 329, 796 (Aug 13, 2010).
2. R. H. Wijffels, M. J. Barbosa, M. H. M. Eppink, Microalgae for the production of bulk chemicals and biofuels. Biofuels Bioproducts & Biorefining-Biofpr 4, 287 (May-Jun, 2010).
3. K. M. Weyer, D. R. Bush, A. Darzins, B. D. Willson, Theoretical Maximum Algal Oil Production. BioEnergy Research 3, 204 (Jun, 2010).
4. J. Fabregas, C. Herrero, Marine microalgae as a potential source of single cell protein (SCP). Applied Microbiology and Biotechnology 23, 110 (1985).
5. G. Schonknecht et al., Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science (New York, N.Y.) 339, 1207 (2013).

Setting the Stage for the Next Generation of Biofuels

David T. Hanson, Associate Professor

Associate Professor of Biology
Associate Herbarium Curator: Museun of Southwestern Biology
University of New Mexico

Alcohols from sugars and starches as well as biodiesel from oil crops, ligno-cellulosic ethanol, and oils from microalgae are often considered the first three generations of biofuels while a range of technologies are competing to be called fourth and fifth generations. The developmental stages of each generation are vastly different with the microalgal generation in still in its infancy, but each has provided important lessons for understanding the sustainability of large-scale biofuel production. What is emerging is recognition that an interdisciplinary approach between engineers and biologists will be required for next generation sustainable and scalable productivity that is energy-positive and carbon-negative. We are embarking on the process of cross-training engineering and biology students through ground-up engineering of microalgal culturing and processing systems where custom designed organisms with specific metabolically engineering can be studied in situ. Our goal is to break through the divide between low-investment open raceways and high-investment conventional closed bioreactors. This presentation will cover how ecological and evolutionary principles along with an understanding of basic cellular biology will guide the development of next generation biofuel production systems.

Development of Algal 'Omics Technologies

Shawn Starkenburg

Postdoctoral Research Associate
Bioenergy and Biome Sciences Group
Los Alamos National Laboratory

Biological innovation is a critical component to the commercial success of algal and bacterial based biofuels.  Our ability to engineer strains that grow fast and accumulate large amounts of oil is heavily dependent on a detailed knowledge of the biochemical and molecular basis of these physiological processes.  To this end, algal biologists have generated a significant amount of ‘omics’ data (genomics, transcriptomics, proteomics, metabolomics, lipidomics, and phenomics) to gain insight into the physiological and biochemical basis of growth and oil accumulation in algae that show promise for deployment in cultivation systems.  The recent advances in technologies, including next-generation sequencing have contributed substantial volumes of information toward this, and other, applications. Unfortunately, effective integration of complimentary -omics data sets remains a challenge and requires the development of new tools to analyze and mine the information.  Harnessing the expertise found within New Mexico institutions, we have a unique opportunity build a “Center of Excellence” that can generate, receive, analyze, and integrate all varied types of -omics data to streamline biological innovation and strain optimization.  In this presentation, I will highlight several technological capabilities and strengths at LANL that can be linked to form an integrated ‘omics’ platform that would serve academic, governmental, and industrial stakeholders.

Plant Biotechnology: New Routes to Biofuels, Polymer Building Blocks and Specialty Chemicals

Norman G. Lewis

Institute of Biological Chemistry,
Washington State University and Ealasid Inc., Pullman, WA
There is an urgent need to develop game-changing strategies (scientifically and technologically) to meet the growing expectations for the sustainable production of “man-made“ biofuels, polymer building blocks (e.g. styrene, substituted styrenes, propene, etc.) and specialty chemicals (e.g. phenyl ethanol, ethyl benzene, eugenol, etc.) from sustainable and renewable resources.  Many such chemicals have hitherto largely been petroleum-derived at scale and cost needed, and there is now the expectation of attaining alternative sustainable sources for their supply.  Our recently developed and successful biotechnological platforms in generating fast growing designer woody hybrid poplar affording such substances offer an exciting opportunity to meet society’s growing needs over the long term.  In this presentation, platforms now enabling production of key specialty/commodity/biofuel chemicals from modified poplar plant lines via development and application of short rotation, multiple harvesting, regimens are described, together with their long term potential. These new approaches give an excellent, and hitherto unprecedented, means to generate renewable, sustainable, sources of these commodity chemicals. 

Biomedical Session: Thursday May 9th PM

Flow Cytometry in New Mexico: Past, Present, and Future

Steven Graves, Ph.D.

Director, Biomedical Engineering Graduate Program
Center for Biomedical Engineering
Associate Professor, Chemical and Nuclear Engineering

A flow cytometer is capable of multiparameter analysis and sorting of cells, particles, and chromosomes on a one-by-one basis at rates of greater than 50,000 cells/second.  This has made it a powerful tool with many clinical and research applications including CD4+ cell counting for HIV progression analysis, complete blood counts (CBCs), chromosome sorting, and rare cell sorting. The extreme utility of flow cytometry has made it a billion dollar industry worldwide and its applications are now extending into point of care, industrial, environmental, and energy application spaces. Many of the foundations for modern flow cytometry were laid in New Mexico in the 1960’s with key technologies developed at Los Alamos, which have blossomed throughout the state with critical technology centers developing at Los Alamos, the University of New Mexico, and elsewhere in the state. This talk will provide a historical background of flow cytometry in the state, discuss the many current flow cytometry efforts across the state (both commercial and academic), and explore potential paths forward for this critical technology area. 

Dynamic Transition Ttates of ErbB1 Phosphorylation Predicted by Spatial-stochastic Modeling

Meghan M. McCabe

Doctoral Candidate
Edwards Research Lab
University of New Mexico

ErbB1 overexpression is strongly linked to carcinogenesis, motivating better understanding of erbB1 dimerization and activation. Recent single particle tracking data have provided improved measures of dimer lifetimes and strong evidence that transient receptor co-confinement promotes repeated interactions between erbB1 monomers. Here, spatial stochastic simulations explore the potential impact of these parameters on erbB1 phosphorylation kinetics. This rulebased mathematical model incorporates structural evidence for conformational flux of the erbB1 extracellular domains, as well as asymmetrical orientation of erbB1 cytoplasmic domains during dimerization. The asymmetrical orientation model considers the theoretical consequences of restricted transactivation of erbB1 receptors within a dimer, where N-lobe of one monomer docks with the C-lobe of the second monomer and activates its catalytic activity. The dynamic nature of erbB1 phosphorylation state is shown by tracking activation states of individual monomers as they diffuse, bind and rebind after ligand addition. The model reveals the complex interplay between interacting liganded and non-liganded species and the influence of their distribution and abundance within features of the membrane landscape.

Overview of NMCIM ~ Highlighting Interactions in the Past and Looking at Future Opportunities

Scott W. Burchiel, Ph.D.

The New Mexico Center for Isotopes in Medicine (NMCIM)
UNM  Health Sciences Center - College of Pharmacy

The mission of NMCIM is to develop unique medically-useful radioisotopes, in collaboration with the Los Alamos National Laboratory (LANL) Isotope Production Facility (IPF).  The IPF is a beam spur off of the LANL linear accelerator (LINAC) that produces unique gamma emitting and positron emitting (PET) isotopes that have not historically been available in sufficient quantities for product development.  The IPF represents a $30M investment in infrastructure. While LANL has unique capabilities in the production of novel isotopes, it does not have the ability to formulate or test potentially useful medical products. This, NMCIM was established to develop medically useful radioisotope formulations for cancer imaging and therapy, and eventually for the detection of other diseases. The UNM Radiopharmaceutical Sciences Program (RSP) brings its longstanding expertise in handling, formulation, research and development of medical isotopes to establish medically useful radiopharmaceuticals.  The UNM RSP will work with renowned scientists and commercial sponsors to develop products and markets for the radioisotopes from LANL IPF.  UNM RSP will develop radiochemical procedures and formulations, will test these novel radiopharmaceuticals in appropriate in vitro and in vivo models leading to clinical trials for diagnostic and therapeutic agents. It is anticipated that the NMCIM will contribute to the interdisciplinary research and education programs of the UNM HSC and UNM main campus and will strongly support the Cancer Center imaging and therapy program in product development and future Neuroscience imaging approaches. 

Diffusion Properties Limit Effectiveness of Chemotherapy in Cancer

Vittorio Cristini, Ph.D.

The Victor & Ruby Hansen Surface Professor of Pathology, Chemical and Biomedical Engineering
The University of New Mexico

Biobarriers pose a multitude of challenges for the penetration of drugs into tumors, yet a comprehensive understanding of these challenges remains elusive, hindering the development of more effective, efficient treatment options and better patient outcomes. Here, we retrospectively study the diffusion of chemotherapeutic drugs into liver metastases from colorectal cancer (CRC) by comparing measurements from histopathological human patient samples and predictions from a new mathematical model of diffusion. The model predicts the fraction of dead tumor cells based on various physical, measurable patient-specific parameters (fractional are occupied by tumor vessels and their average diameter), and agrees well with the fraction of tumor killed measured in the patient tissue (coefficient of determination R2 = 0.94 in regression analysis). We then test the model by directly measuring the model parameters from 4 archival patient samples of glioma after chemotherapy, and demonstrate reliable predictions of individual patient responses (R2 = 0.74, 0.86, 0.89 and 0.91). Clinical translation of this model should help in the rational design of individualized treatment strategies such as amount, frequency and duration of drug regimen and the need for ancillary non-drug based treatment.

Structure and Dynamics of Functional Polyampholytes 

Eva Y. Chi, Ph.D.

Assistant Professor, Department of Chemical and Nuclear Engineering
Center for Biomedical Engineering
University of New Mexico
Polyampholytes are amphiphilic macromolecules with mixed charge characters. Understanding the structural dynamics and molecular interactions of polyampholytes with soft biological materials represents a fundamental scientific challenge and has the potential to impact a number of fields. In this talk, I will summarize our work in understanding the behaviors of two classes of polyampholytes, naturally occurring amyloid proteins linked to neurodegenerative diseases and synthetic biocidal polyelectrolyte polymers and oligomers that hold the potential to combat the global threat of antibiotic resistance.
Amyloid proteins are a diverse class of proteins whose misfolding and aggregation into fibrils are implicated to cause neurodegeneration in over 20 diseases, including Alzheimer’s and Parkinson’s diseases. There are currently no cures for these disorders due to, at least in part, a lack of understanding of the mechanisms by which amyloid proteins aggregate and exert neurotoxicity. We show that the lipid membrane plays duel roles in the pathogenesis of neurodegenerative diseases by: 1. catalyzing the misfolding and assembly of proteins into toxic aggregates and 2. serving as a target for protein aggregates to exert toxicity via membrane permeabilization. Our work sheds light on the molecular basis of amyloid protein aggregation, particularly the early structural fluctuations that trigger protein misfolding and aggregation. 

A novel class of phenylene ethynylene-(PPE) based polyelectrolyte polymer and oligomers, synthesized my collaborator David Whitten at UNM, has been shown to exhibit significant light-activated biocidal activity and efficient killing efficacy in the dark against a broad spectrum of pathogens, including bacteria, viruses, and spores. Importantly, we show that the cationic and amphiphilic nature of the PPE-based polymers and oligomers provides them the ability to interact with and disrupt the structures, and thereby functions, of multiple cellular targets, including the cell membrane, proteins and protein assemblies, and nucleic acids. These non-specific intermolecular interactions give rise to the compounds’ broad-spectrum biocidal activity. A fundamental understanding of the structure-function relationship of these compounds will guide the rational design of novel compounds with optimal toxicity and selectivity.

Detection of Shiga-toxin Carrying E. coli in the Beef-chain

Harshina Mukundan, Ph.D.

Bioscience Business Development Executive
Los Alamos National Laboratory

The USDA has initiated a multi-institutional inter-disciplinary CAP Grant effort, lead by the University of Nebraska, to combat the increasing risk of Shiga-toxin carrying E. coli in the beef chain. The effort encompasses a study of the genetic, physiological, epidemiological and culture-based characteristics of the pathogen, and the development of detection strategies for the same. LANL is the primary institution for the bio-detection component of this effort, with investigators developing both nucleic-acid based (Alina Deshpande) and biomarker-based (Harshini Mukundan) assays. This presentation will summarize some of the key objectives of this grant and interesting findings thus far in this effort.

Thursday Dinner 5pm - 8pm

Addressing the Global Challenges in Renewable Energy Production, Food Security, and Climate Change

Richard T. Sayre, Ph.D.

Senior Scientist, Los Alamos National Laboratory & NMC
New Mexico Consortium

Among the greatest grand challenges facing humanity are; 1) providing sufficient food for a growing population while using reduced land and water resources, 2) providing adequate, low-cost biomass feedstocks for domestic energy production, and 3) reducing greenhouse gas emissions for a sustainable environment. Understanding and improving the biological conversion of solar energy into high-energy organic molecules is a central theme common to each of these challenges. Photosynthetic carbon reduction and oxygen evolution is the largest biochemical process on earth. Photosynthesis is also the base of virtually all food chains, and accounts for more than half of the global carbon flux from the atmosphere to terrestrial and aquatic environments. Yet photosynthesis and the downstream processes leading to biomass accumulation convert less than 5% of the solar radiation energy impingent on the earth’s surface into the chemical energy of carbohydrates (starch and cellulose), proteins, and oils. The challenges facing the research teams at the new Entrada facility are how to use the diverse technologies and human talent available in our community of science to improve the efficiency of carbon capture and accumulation by photosynthetic organisms so as to produce food, green chemicals and energy feedstocks more efficiently in the most sustainable way. By bringing together a diverse group of scientists from the Los Alamos National Laboratories and our state university partners in New Mexico, we will foster innovation at the interfaces of biology, chemistry, physics, and theory to address the grand challenges of renewable energy production, food security, and global climate change.

Food Security Session: Friday May 10th AM

Tapping the Molecular Potential of Microalgae to Produce Biomass

Richard T. Sayre, Ph.D.

Senior Scientist, Los Alamos National Laboratory & NMC
New Mexico Consortium

One of the more environmentally sustainable ways to produce energy is the conversion of solar energy into biomass. Plants and algae use solar energy to reduce carbon dioxide to carbohydrates and oils. Biomass conversion to fuels has undergone substantial improvements in the last 20 years. The first-generation biofuels (alcohol and diesel) were/are produced from only a few crop systems. Typically, only a fraction of the solar energy captured and converted into chemical energy (biomass) is harvestable. Inefficiencies in feedstock harvesting and processing further reduce the recoverable energy and reduce net carbon capture. Second-generation biofuel systems including cellulosics are now being developed. Conversion of cellulosics to sugars using advanced enzyme catalysts promises to increase the available reduced carbon resources for fuel production and reduce the land area required for biofuel production. Many second generation biofuel systems do not directly compete with food production, require fewer inputs, and potentially have lower environmental impacts than first-generation biofuels. The third generation of biofuel production systems will be expected to have even lower impact on the environment, greater productivity, greater energy return on investment, and will be directly compatible with the existing energy infra-structure. One of the more attractive third generation biofuel systems under development is algae. Algae grow rapidly, have high oil content (up to 55% oil), and are capable of producing 2-10 times more biomass per unit land area than any terrestrial crop system. In addition, algae can potentially capture CO2 as bicarbonate in ponds as well as utilize nutrient-rich waste water. Significantly, the single celled algae are also one of the more evolutionary diverse groups of organisms whose biodiversity represents a rich resource for bioprospecting. We will report on progress to optimize biomass productivity from algae using transgenic strategies informed from “omics” and biodiversity surveys.

We Don't Need Agricultural Research; Wal-Mart Always has Enough Food to Feed my Family

David C. Thompson, Ph.D.

Associate Dean & Director, Agricultural Experiment Station System
New Mexico State University

Support for Agricultural Research in the United States is actually suffering because our industries have been so successful.  The average citizen in the US spends 6.4% of their income on food.  This is the lowest in the World; in fact, much of the world pays over 30% of their income on food.  As drought conditions persist and as food security becomes more of a concern in 2013 we are hearing predictions of wide scale famine and suffering.  The agricultural community is being asked to produce more to feed the increased demands of the human population – the US population and the world population are expected to increase 25 to 40% by the year 2050 – with no increase in land and with decreased water.   Preparing to meet these needs is a passion of many of the faculty and staff associated with the New Mexico State University Agricultural Experiment Station System, whose mission is to conduct research that will provide information to improve the success – yield, profits, health, and satisfaction – of the citizens of New Mexico.   We have 12 Agricultural Science Centers, in addition to our main campus lands and laboratories in Las Cruces, encompassing over 95,000 acres.  In these times of ever diminishing resources it is critical to partner with other state, federal, or private industries to find solutions to the inevitable food insecurity problems that WILL plague the world without serious intervention in the near future.  Although much of New Mexico is not ideal agricultural land, in terms of water availability and soil health, it is representative of over 50% of the land available for potential agricultural production on our planet.  This leaves us in a position to be a leader in the sustainable, productive use of marginal lands for agriculture. 

Drought, Climate Change, and Global Vegetation Mortality

Nathan G. McDowell, Technical Staff Member

Los Alamos National Laboratory
Earth and Environmental Sciences

The rate of vegetation mortality is currently accelerating in concert with the Earth's rising surface temperature, with all biomes showing similar trends.  We currently cannnot predict where, when, or what type of plant will die in the future due to limitations associated with 1) our fundamental understanding of how plants die, 2) basic observations of where, when, and what dies during drought, and 3) the current modeling structure.  I will review the basic science problems, the state of international knowledge, and review key future research directions.  

Plant and Ecosystem Responses to Climate Change

William Pockman, Ph.D. 

Professor & Associate Chair Biology
University of New Mexico

Plants exhibit physiological adaptations that are important determinants of the physical conditions where they occur.  Climate anomalies and directional climate change can present a challenge for established plant populations with consequences for growth, productivity, and survival of individual species as well as plant community composition and ecosystem function.  Understanding the underlying mechanisms of these responses is critical for predicting plant and ecosystem responses to anthropogenic climate change.  I will discuss the critical research needs in this area using examples from studies of grassland, shrubland and woodland ecosystems in New Mexico.

Soil Fungal Communities in Forest and Arid Shrubland Ecosystems

Cheryl Kuske, Ph.D. Technical Staff Member

Los Alamos National Laboratory
Bioscience Division

Fungi dominate soil biomass in forest systems and carry out essential biogeochemical processes. Saprotrophic fungi are prolific degraders of plant material deposited to surface soils as litter and root biomass. Mycorrhizal fungi participate in decomposition of organic matter and transfer nitrogen and phosphorus to their plant partners. In contrast to forest systems, arid shrublands harbor a very different community of soil fungi and the ecological roles of this fungal community are not understood. In both ecosystems, understanding the interactions between soil fungal processes and living plants and/or dead plant biomass is important to determine rates of soil C and N cycling. Representing this component of forest and arid shrubland ecosystems is needed to accurately describe the responses to, and feedbacks derived from, altered inputs of C and N through anthropogenic activities. Our current studies use molecular tools and metagenomic sequencing to map responses in the soil fungal community in forest and arid land ecosystems under elevated CO2 and/or N deposition scenarios.

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