Scott Boyken to postdoc with David Baker

Upon graduation, Scott will join the lab of David Baker at the University of Washington. Baker is one of the premier researchers in the area of protein folding. Scott will take part in protein design research in his lab.

Scott's mentor, Amy Andreotti, is a BCB faculty member in the Biochemistry, Biophysics and Molecular Biology Department. His other co-major professors are Robert Jernigan, BBMB and Drena Dobbs, GDCB.

Congratulations, Scott !!

From the Baker lab research page:

From prediction of structure to design of function

The primary goals of the research in the Baker group over the past several years have been to predict the structures of naturally occurring biomolecules and interactions and to design new molecules with new and useful functions. These prediction and design challenges have direct relevance for biomedicine and provide stringent and objective tests of our understanding of the fundamental underpinnings of molecular biology.

Design of New Protein Functions

Several years ago, we developed a general computational strategy for designing new protein structures that incorporates full backbone flexibility into rotamer-based sequence optimization. This was accomplished by integrating ab initio protein structure prediction, atomic-level energy refinement, and sequence design in Rosetta. The procedure was used to design Top7, a 93-residue protein with a novel sequence and topology. Top7 was found to be folded and highly stable, and the x-ray crystal structure of Top7 is virtually identical  to the design model (Kuhlman et al, 2003). Since the validation of our protein design methodology provided by Top7, we have focused on designing proteins with new and useful functions. We are concentrating on four challenges: (1) the design of new protein-protein interactions, (2) the design of new enzymes catalyzing reactions not catalyzed by naturally occurring enzymes, (3) the design of novel endonucleases with any specified cleavage specificity, and (4) the design of a vaccine for HIV.

Plans for the Future

We will continue to work to improve the physical model and the sampling methodology underlying the prediction and design calculations in Rosetta. On the structure calculation side, we will strive for consistent near-atomic resolution ab initio structure prediction for small proteins, and work towards atomic level structure determination for proteins greater than 200 amino acids using limited experimental data such as backbone only NMR data and 5-7Å electron density data. We will focus in particular on membrane proteins and other systems for which obtaining high resolution experimental data is difficult--this is where our approach are likely to contribute the most. We will also extend data guided structure determination to biological assemblies where SAXS, crosslinking and other types of data often can be collected.

On the design side, we will extend our methodology to non natural amino acids and cofactors to try to leapfrog over the limitations nature has faced with the limited set of twenty amino acids. We are aiming to design a complete pathway for fuel production from CO2 using solar generated reducing equivalents. We will also develop and test methods for designing high affinity binders/inhibitors for any specified surface patch on a protein of known structure. More generally, we hope to develop new biomolecules with new functions--inhibitors, enzymes, endonucleases, and vaccines--that can have a positive impact on the world.

Jonathan Wendel, BCB faculty member in EEOB

Recent Nature publication

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Andrew H. Paterson, Jonathan F. Wendel, Heidrun Gundlach, Hui Guo, Jerry Jenkins, Dianchuan Jin, Danny Llewellyn, Kurtis C. Showmaker, Shengqiang Shu, Joshua Udall, Mi-jeong Yoo, Robert Byers, Wei Chen, Adi Doron-Faigenboim, Mary V. Duke, Lei Gong, Jane Grimwood, Corrinne Grover, Kara Grupp, Guanjing Hu, Tae-ho Lee, Jingping Li, Lifeng Lin, Tao Liu, Barry S. Marler et al.

Nature 492, 423-427 (20 December 2012) doi:10.1038/nature11798

Received 17 August 2012 Accepted 21 November 2012 Published online 19 December 2012

Abstract: Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments1. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago2, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica3 among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum AtDt (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.

9th International Symposium on

Bioinformatics Research Applications

Charlotte, North Carolina

May 20-22, 2013

Advancing One Community Award recipients announced

By Paula Van Brocklin
January 24, 2013

Recipients of this year's Advancing One Community Awards will be honored Jan. 24 (4 p.m., Memorial Union Sun Room) during the Martin Luther King Jr. Legacy Convocation. All are invited to attend.

Since 2006, Iowa State has honored students, groups and faculty or staff members who demonstrate a commitment to King's principles and goals to create an inclusive multicultural community, and to reduce injustice and inequity at Iowa State. Winners receive a $500 stipend and a plaque. This year's recipients are:

Student: Arun Sethuraman, a graduate student in the department of ecology, evolution and organismal biology, has served as president of the Indian Student Association. He promotes an understanding and knowledge of the Indian culture, and has created a support network for Indian students. He also educates members of the Indian community about homophobia and xenophobia

.
Faculty/staff member: Joel Geske, associate professor, Greenlee School of Journalism and Communication, is a consistent advocate for community members who identify as LGBT. Through his scholarship, teaching, service and initiatives, he consistently shows a commitment to diversity, inclusion and institutional self-awareness.

Group: Alpha Sigma Kappa, a sorority for women in technical studies, encourages young women and girls to consider STEM careers. The organization also has developed a support structure for women in technical fields.

Group: Lambda Theta Phi fraternity has worked to improve Iowa State's community for Latino students since its founding in November 2011. The group helped develop the Latino Leadership Retreat and supports Latino Heritage Month activities. The group also is active in community service and voter registration on campus.

Nominations for the 2014 Advancing One Community Award recipients will be accepted later this fall. More information about the awards, including eligibility requirements and past winners, is available online.

Upcoming Conference to be Chaired by Srinivas Aluru

The 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) which will take place June 12-14, 2013, in New Orleans, LA will be chaired by Srinivas Aluru, BCB faculty member in ECPE. More details are here: http://www.iccabs.org/

Steering Committee

Srinivas Aluru - Iowa State U.
Reda A. Ammar - U. of Connecticut
Tao Jiang - U.C. Riverside
Vipin Kumar - U. of Minnesota
Ming Li - U. of Waterloo
S. Rajasekaran (Chair) - U. of Connecticut
John Reif - Duke University
Sartaj Sahni - U. of Florida

General Chairs

Srinivas Aluru - Iowa State University
S. Rajasekaran - U. of Connecticut

Advances in high-throughput technologies such as DNA sequencing and mass spectrometry are profoundly transforming life sciences, resulting in the collection of unprecedented amounts of biological and medical data. Using this data to advance our knowledge about fundamental biological processes and improve human health requires novel computational models and advanced analysis algorithms. IEEE ICCABS aims to bring together leading academic and industry researchers to discuss the latest advances in computational methods for bio and medical sciences.

Topics of interest include but are not limited to: Biological modeling and simulation, Biomedical image processing, Biomedical data and literature mining, Computational genetic epidemiology, Computational metabolomics, Computational proteomics, Databases and ontologies, Gene regulation, Genome analysis, Health Informatics, High-performance bio-computing, Immunoinformatics, Molecular evolution, Population genomics, Sequence analysis, Structural bioinformatics, Systems biology, Transcriptomics.

Two special issues of journals (BMC Bioinformatics and BMC Genomics) on selected extended abstracts will be published. A limited number of student travel awards will be made (conditional upon NSF support). This year we also plan to have review sessions where researchers get to present their results (possibly published in other venues). These results will not appear in the proceedings.

Travel Grant Information

ICCABS 2013 plans to support some number of student travel grants (conditional upon NSF support) up to $1200 per student. In particular, this money can be used for the following items:
• Registration fee
• Hotel accommodation
• Airfare
• Food and other expenses
The applicants should submit the following materials to Sanguthevar Rajasekaran (rajasek@engr.uconn.edu). Preference will be given to students presenting their works in the conference (including the CANGS workshop) who apply by February 6th.
• Number and title of a paper or poster that has been accepted (if any) to ICCABS
• A brief summary of the research interests of the student together with an explanation of how this conference will help her/his research efforts.
• A support letter from the student's supervisor/advisor that indicates that the student is in good academic standing and how the student will benefit from attending this conference.
• An estimate on the total expenses and availability of other sources of funding

BCB Alums - Outstanding Opportunities realized ...

The impressive outcomes of BCB alums continues to create national prominence for our BCB program. Of our 90 alums, 12 hold positions as professors. Others hold research positions as follows: 36 in academia, 40 in industry, and 2 in government. Here are recent examples of the quality outcomes for our students:

• Preeti Bais, mentors, Julie Dickerson, ECPE, and Basil Nikolau, BBMB, joined a start-up with Stemina in Madison, WI, which perfectly matched her dissertation research topic;
• Nick Larson, mentors, Dan Nettleton, Statistics, and Jack Dekkers, Animal Science, joined the Mayo Clinic in Rochester, MN as did Michael Zimmermann, mentors, Bob Jernigan, BBMB, and Edward Yu, Physics;
• Fadi Towfic, mentors, Vasant Honavar, Computer Science, and Heather Greenlee, Biomedical Sciences, moved from the Broad Institute, which collaborates with Harvard and MIT, to a position as V.P. of Biocomputing for Immuneering, Boston, MA, a small start up which uses data from clinical trials to help increase drug efficacy for patients with chronic conditions.
• Pan Du, mentors, Julie Dickerson, ECPE, Eve Wurtele, GDCB, moved from Northwestern Univ. in Chicago to a position with Robert Gentleman's group at Genentech in San Francisco, CA. Genentech works with genetic engineering techniques to develop new medicines. Pan Du joins Michael Lawrence, another BCB alum, who has worked with Gentleman for a number of years. His mentor was Di Cook, Statistics.
• Olga Nikolova competed with 100 PhD's nationwide, and won a position with Sage Bionetworks in Seattle, WA. Olga's mentor's are Srinivas Aluru, ECPE, and Pat Schnable, Agronomy. Sage creates disease predictive models from clinical datasets to improve the speed and efficiency of drug development.
• Tieming Ji, mentors, Dan Nettleton, Statistics, and Pat Schnable, Agronomy, has accepted a tenure-track faculty position at the University of Missouri, Columbia, in the Statistics Department.

BCB Student Achievements ...

Exceptional students are the foundation for a robust and dynamic graduate program. Students find a culture of high achievement in research outcomes in the BCB Graduate Program which reflects the mission and goals of Iowa State University:

• Three BCB students have won the prestigious Zaffarano Prize for Graduate Research award – the last recipient was Michael Zimmermann, mentor, Bob Jernigan, BBMB Department, who received an Honorable Mention.
• 14 Research Excellence awards have been awarded to BCB students from our 90 program graduates.
• Seven students have received the BCB Program’s James Cornette Research Fellowship award. Scott Boyken, mentors, Amy Andreotti and Bob Jernigan, BBMB, received this award for a high-profile publication in the prestigious journal Nature, (Long et al., 2010 Nature 467:484), along with an interdisciplinary team that includes another BCB student, Mike Zimmermann, and two faculty, Bob Jernigan, BBMB, and Ed Yu, Physics, who is senior author on the study.

In this context of excellence, BCB students seek out and take full advantage of opportunities for growth:

• Our student-led BCBLab organized an invited-speaker seminar series, from identifying and inviting speakers, to hosting visiting scientists: Reinhard Laubenbacher (Virginia Tech), Martin Krzywinski, (British Columbia Cancer Agency), Paul Hohenlohe (Univ of Idaho), and Pierre Baldi (UC Irvine). Prior to each visit, BCBLab students organized discussion sessions in which local experts provided an overview of the field, and students discussed recently published work of visiting scientists. This outstanding achievement provided exceptional professional development opportunities.

• Participation in conferences showcases research being done at Iowa State and in our program, which is the foundation for successful recruitment efforts. And, our students make important contacts for post-graduate opportunities. Li Xue, mentors: Vasant Honavar, ComSci and Drena Dobbs, GDCB, won the top poster award at the 2011 ACM-BCB international conference on Bioinformatics, Computational Biology and Biomedicine held in Chicago demonstrating how machine learning methods can be used to improve ranking scores for models of protein-protein complexes generated by computational docking. An extended version of her paper was invited for publication in a special issue of BMC Bioinformatics.

Chris Tuggle and Max Rothschild published in Nature recently

Analyses of pig genomes provide insight into porcine demography and evolution

Nature, 491, 393-398, (15 November 2012), doi:10.1038/nature11622

Authors: Martien A. M. Groenen, Alan L. Archibald, Hirohide Uenishi, Christopher K. Tuggle, Yasuhiro Takeuchi, Max F. Rothschild, Claire Rogel-Gaillard, Chankyu Park, Denis Milan, Hendrik-Jan Megens, Shengting Li, Denis M. Larkin, Heebal Kim, Laurent A. F. Frantz, Mario Caccamo, Hyeonju Ahn, Bronwen L. Aken, Anna Anselmo, Christian Anthon, Loretta Auvil, Bouabid Badaoui, Craig W. Beattie, Christian Bendixen, Daniel Berman, Frank Blecha et al.

Abstract: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

AMES, Iowa - Engineers and scientists are working together in new ways to invent catalysts that lead to industrial chemicals from biorenewable resources. Industrial partnerships are expanding. Startup companies are launching. Education partnerships are reaching teachers and students. And an international reputation is growing.

By Mike Krapfl, ISU News Service, 515-294-4917, mkrapfl@iastate.edu

They're all steps the National Science Foundation (NSF) Engineering Research Center for Biorenewable Chemicals based at Iowa State University has made over its initial four years. That progress has led to the NSF augmenting the center (known as CBiRC, "See-burk") with three additional years and $12 million.

That brings the total federal investment in the center through the NSF's Engineering Research Center program up to $30.5 million over eight years. The center can still be renewed for an additional two years, potentially bringing the NSF's total support to 10 years and $34.9 million. After 10 years, CBiRC will transition to a self-supporting research center. In addition to the center's base funding, it has so far garnered more than $14 million in other support.

"In four years we've certainly come together as a center and we have a shared vision across all the researchers," said Brent Shanks, the center's director and the Mike and Jean Steffenson Professor of Chemical and Biological Engineering at Iowa State. "We are accomplishing what the NSF wanted - interdisciplinary research."

The center's vision is to transform the industrial chemical industry - a $400 billion-a-year business in the United States - from one based on petroleum to one based on biorenewable resources. To do that, the center has asked researchers who study chemical or biological catalysts to start working together to develop new and sustainable technologies that produce the industrial chemicals used in everything from building materials to personal-care products.

Basil Nikolau, the center's deputy director and the Frances M. Craig Professor of Biochemistry, Biophysics and Molecular Biology at Iowa State, said the center's interdisciplinary approach is attracting the attention of industry.

"We are making progress and a measure of that is the companies that have joined us," Nikolau said. "We're setting a new paradigm for this research. We're doing basic research that companies are buying into."

When the center was established, it had six industrial partners. The center now has 27 (including Ashland, Chevron Phillips Chemical Co., DuPont, Grain Processing Corp., Michelin Americas Research Co., and POET) and is discussing additional partnerships. The center is also spinning off four companies in Iowa and three from partner institutions. The Iowa startups include Glucan Biorenewables LLC, originally established by Shanks; Peter Keeling, the center's industrial collaboration and innovation consultant; and James Dumesic, the Steenbock Professor and Michel Boudart Professor of Chemical and Biological Engineering at the University of Wisconsin-Madison.

The center has also attracted attention from funding agencies and the science media:

Earlier this year, Nikolau, Keeling and Shivani Garg - a graduate student in biochemistry, biophysics and molecular biology - won an Innovation Corps grant from the NSF. The grant will support their work to develop bio-based chemical feedstocks.

And, the CBiRC way - combining chemical and biological technologies to produce biorenewable chemicals - was recently featured in Chemical & Engineering News. The story by Mitch Jacoby notes that "coupling chemical and biological processing offers advantages over either one on its own."

In addition to those developments, the leaders of the center's three research thrusts said they're seeing many signs of technical progress:

Thrust one, new biocatalysts for pathway engineering

Joseph Noel - professor and director of the Jack H. Skirball Center for Chemical Biology and Proteomics at the Salk Institute for Biological Studies in La Jolla, Calif., and an investigator with the Howard Hughes Medical Institute based in Chevy Chase, Md. - said the program has identified pyrones as molecules for the center's testbed research across disciplines. He said researchers have developed protein engineering techniques to improve the production of biorenewable molecules from sugar by common baker's yeast. Chemical catalysts then convert the molecules to commodity chemicals. Noel said the research program has also successfully integrated high school and undergraduate students in its laboratories.

Thrust two, microbial metabolic engineering

Jackie Shanks, the Manley Hoppe Professor of Chemical and Biological Engineering at Iowa State, said researchers have used E. coli to produce carboxylic acids at the highest level reported to date. Carboxylic acids can be used to produce many industrial chemicals. She said researchers have also improved E. coli's ability to resist the toxicity of the acids.

Thrust three, chemical catalyst design

Robert Davis, the Earnest Jackson Oglesby Professor of Chemical Engineering at the University of Virginia in Charlottesville, said researchers have made significant progress converting pyrones from research thrusts one and two to high-value chemicals. He said researchers have also developed technologies that convert carboxylic acids to alpha olefins that are used to make detergents and other chemicals.

Brent Shanks said the center has established several education initiatives, including a graduate minor in biorenewable chemicals at Iowa State, research internships at the center's European partners, a summer research program for undergraduates, research experiences and workshops for school teachers and a program that places graduate students in middle school science classrooms.

All in all, Shanks said the center's work is getting noticed and its researchers are taking calls from industry, technical conferences and the biorenewable research community.

"It is our driving goal," he said, "to be considered the place in the world to do biorenewable chemicals."

The NSF Engineering Research Center for Biorenewable Chemicals is based at Iowa State and is working with academic partners at the Salk Institute for Biological Studies in San Diego; the University of Michigan in Ann Arbor; Rice University in Houston; the University of California, Irvine; Penn State University in University Park; the University of New Mexico in Albuquerque; the University of Virginia in Charlottesville; and the University of Wisconsin-Madison. International partners are the Fritz-Haber-Institute of the Max-Planck-Society in Berlin, Germany; the Technical University of Denmark in Lyngby; the Eindhoven University of Technology in Eindhoven, the Netherlands; and the Abo Akademi University in Turku, Finland. The center is also developing pre-college programs with Des Moines Public Schools.

Suraj Kothari - Regents Award for Faculty Excellence recipient

Professor of electrical and computer engineering and of computer science

Kothari has provided outstanding teaching, research and service to Iowa State for 28 years, bringing in nearly $6 million in external funding, publishing 70 scientific articles, obtaining four patents and supervising 56 master's and doctoral students. He was the catalyst behind the new software engineering degree program launched in 2007. Kothari has also been a member of the BCB faculty.

Iowa State researchers developing 'BIGDATA'

toolbox to help genome researchers

Iowa State University's Patrick Schnable, left, and Srinivas Aluru are developing a toolbox to help life sciences researchers analyze all of the data produced by today's DNA sequencing instruments. Photo by Bob Elbert.

AMES, Iowa - Today's life scientists are producing genomes galore.

But there's a problem: The latest DNA sequencing instruments are burying researchers in trillions of bytes of data and overwhelming existing tools in biological computing. It doesn't help that there's a variety of sequencing instruments feeding a diverse set of applications.

Iowa State University's Srinivas Aluru is leading a research team that's developing a set of solutions using high performance computing. The researchers want to develop core techniques, parallel algorithms and software libraries to help researchers adapt parallel computing techniques to high-throughput DNA sequencing, the next generation of sequencing technologies.

Those technologies are now ubiquitous, "enabling single investigators with limited budgets to carry out what could only be accomplished by an international network of major sequencing centers just a decade ago," said Aluru, the Ross Martin Mehl and Marylyne Munas Mehl Professor of Computer Engineering at Iowa State.

"Seven years ago we were able to sequence DNA one fragment at a time," he said. "Now researchers can read up to 6 billion DNA sequences in one experiment.

"How do we address these big data issues?"

A three-year, $2 million grant from the BIGDATA program of the National Science Foundation and the National Institutes of Health will support the search for a solution by Aluru and researchers from Iowa State, Stanford University, Virginia Tech and the University of Michigan. In addition to Aluru, the project's leaders at Iowa State are Patrick Schnable, Iowa State's Baker Professor of Agronomy and director of the centers for Plant Genomics and Carbon Capturing Crops, and Jaroslaw Zola, a former research assistant professor in electrical and computer engineering who recently moved to Rutgers University.

The majority of the grant - $1.3 million - will support research at Iowa State. And Aluru is quick to say that none of the grant will support hardware development.

Researchers will start by identifying a large set of building blocks frequently used in genomic studies. They'll develop the parallel algorithms and high performance implementations needed to do the necessary data analysis. And they'll wrap all of those technologies in software libraries researchers can access for help. On top of all that, they'll design a domain specific language that automatically generates computing codes for researchers.

Aluru said that should be much more effective than asking high performance computing specialists to develop parallel approaches to each and every application.

"The goal is to empower the broader community to benefit from clever parallel algorithms, highly tuned implementations and specialized high performance computing hardware, without requiring expertise in any of these," says a summary of the research project.

Aluru said the resulting software libraries will be fully open-sourced. Researchers will be free to use the libraries while developing, editing and modifying them as needed.

"We're hoping this approach can be the most cost-effective and fastest way to gain adoption in the research community," Aluru said. "We want to get everybody up to speed using high performance computing."

Quick look   A research team led by Iowa State University's Laura Jarboe is working to develop hungry, robust microbes that can ferment biofuels from the bio-oil produced by rapidly heating biomass such as corn stalks and sawdust. It's all part of Iowa State's efforts to combine two conversion paths -- thermochemical and biochemical -- to produce the next generation of biofuels.   Quote   "The goal is to produce biorenewable fuels and chemicals in a manner that's economically competitive with petroleum-based processes." "At the end of the process, we want to say, 'Hey, I've got a great bug.'"   Laura Jarboe, an Iowa State assistant professor of chemical and biological engineering

Evolving microbes help Iowa State engineers turn bio-oil into advanced biofuels

By Mike Krapfl, ISU News Service, 515-294-4917, mkrapfl@iastate.edu

AMES, Iowa - Microbes are working away in an Iowa State University laboratory to ferment biofuels from the sugar and acetate produced by rapidly heating biomass such as corn stalks and sawdust.

But it's not an easy job for E. coli and C. reinhardtii.

The bacteria and microalgae, respectively, don't like something in the bio-oil produced by fast pyrolysis - the rapid heating of biomass without oxygen and with catalysts. The result of the thermochemical process is a thick, brown oil that smells like molasses.

A research team led by Laura Jarboe, an Iowa State assistant professor of chemical and biological engineering, and BCB faculty member, is feeding the bio-oil (also known as "pyrolytic sugars") to the microbes. The E. coli are supposed to turn the levoglucosan in the sugar-rich fraction of bio-oil into ethanol and lactic acid; the C. reinhardtii are supposed to turn acetate-rich fractions into lipids for biodiesel.

It's part of the hybrid approach Iowa State researchers are using to produce the next generation of biofuels. They're combining two conversion paths - thermochemical and biochemical - to find efficient ways to produce renewable fuels and chemicals.

"The goal is to produce biorenewable fuels and chemicals in a manner that's economically competitive with petroleum-based processes," Jarboe said.

There are, however, contaminants and toxins in the bio-oil that are getting in the way of the fuel production. Jarboe and a research team are experimenting with pre-treatments of the bio-oil that could reduce the toxicity. And they're working to develop microbes that can tolerate the contaminants.

In addition to Jarboe, the research team includes Robert C. Brown, the Iowa Farm Bureau Director of Iowa State's Bioeconomy Institute, an Anson Marston Distinguished Professor in Engineering and the Gary and Donna Hoover Chair in Mechanical Engineering; Zhiyou Wen, an associate professor of food science and human nutrition; Zhanyou Chi, a post-doctoral research associate for Iowa State's Center for Sustainable Environmental Technologies; Tao Jin, a doctoral student in chemical and biological engineering; and Yi Liang, a doctoral student in food science and human nutrition. The project is supported by a three-year, $300,000 grant from the National Science Foundation and a three-year, $315,020 grant from the Iowa Energy Center.

The researchers are using a technique called directed evolution to produce microbes that are more tolerant of the contaminants in bio-oil. The microbes are grown with higher and higher concentrations of bio-oil and as they divide, they replicate their DNA. Sometimes there are replication mistakes that lead to mutations.

"It could be a mistake that's immediately lethal," Jarboe said. "Or it could be a mistake that helps the microbe tolerate the problematic compounds and it grows faster."

"At the end of the process, we want to say, 'Hey, I've got a great bug.'"

Every day researchers check the experiments for signs of progress. So far, Jarboe said the evolving bacteria and microalgae have been able to tolerate slightly higher concentrations of bio-oil.

When mutations eventually produce a better breed of microbe, the researchers will analyze genomic data to learn and understand the important mutations. That will allow researchers to duplicate the microbes for better biofuel production.

Jarboe said development of those hungry, robust microbes could lead to important advancements in biofuel production: a hybrid process that's biorenewable, fast, cheap and doesn't depend on food crops as a source of biomass.

Recent research from BCB faculty member,

Gustavo MacIntosh and graduate student, Matt

Studham

Quick look   Aphids possess a unique ability to block the genetic defense response of soybeans and may open the door for other pests to do even more damage to crops, according to a recent study by researchers at Iowa State University. The paper found that aphids essentially can short-circuit the hormonal defense mechanism in soybeans meant to combat insect infestations, making it easier for other pests, such as the soybean cyst nematode, to colonize the plant as well.   Quote   "After about seven days, a successful aphid infestation can hijack the plant's defense response. The soybean plant initially puts up a defense, but that response is gone after about a week." Gustavo MacIntosh, ISU associate professor of biochemistry, biophysics and molecular biology

ISU study: Aphid attacks weaken genetic defenses in soybeans, may open door for other pests

A recently published study co-authored by Gustavo MacIntosh, and BCB graduate student, Matthew Studham, found that prolonged aphid attacks weaken genetic defenses in soybeans. Photo by Robert Elbert.

AMES, Iowa - Aphids, the tiny insects that have become a primary threat to Iowa soybeans in recent years, possess a unique ability to block the genetic defense response of soybeans and may open the door for other pests to do even more damage to crops, according to a recent study by researchers at Iowa State University.

The study, published recently in the journal Molecular Plant-Microbe Interactions and made possible through grants from the Iowa Soybean Association and the ISU Plant Sciences Institute, found that aphids essentially can short-circuit the hormonal defense mechanism in soybeans meant to combat insect infestations.  The change may make it easier for other pests, such as the soybean cyst nematode, to colonize the plant as well, according to the study.

"After about seven days, a successful aphid infestation can hijack the plant's defense response. The soybean plant initially puts up a defense, but that response is gone after about a week," said Gustavo MacIntosh, co-author of the paper and an ISU associate professor in the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology. MacIntosh co-wrote the paper with Matthew Studham, a graduate student in the ISU Bioinformatics and Computational Biology program.

Aphids emerged as a serious threat to Iowa soybeans around 2000. The insects are native to Asia and most likely came to the United States on international travelers or plants brought into the country.  In the years since, aphids have caused soybean farmers major headaches, reducing yields in affected fields by up to 40 percent, MacIntosh said. Their presence in a field may require farmers to have insecticides applied, which increases the costs of crop production.

The study focused on the effect aphids have on soybeans after prolonged infestation, MacIntosh said. The presence of aphids initially activates a biological defense mechanism in soybeans, but a successful aphid infestation blocks the soybean plant's natural defenses in about a week by making the plant 'think' that it's experiencing environmental stress, he said.

When that happens, the soybean plant goes through a number of changes, from its leaves all the way to its roots. These changes explain why aphids make plants more susceptible to soybean cyst nematode infection, as shown previously in research MacIntosh conducted with the laboratories of Matt O'Neal, an ISU associate professor of entomology, and Greg Tylka, an ISU professor of plant pathology and microbiology. That work was published in January and was supported by soybean checkoff funds from the Iowa Soybean Association.

The increased susceptibility to nematodes after an aphid infestation even occurred in soybean varieties that are genetically resistant to the soybean cyst nematode, Tylka said.

"The nematodes reproduce better if there is a successful aphid infestation. On the other hand, nematodes have a negative effect on aphid populations," Macintosh said. "This seems to be a rare relationship between different species of pests."

Macintosh said he hopes that his research will lead to soybean varieties that will be more resistant to aphids and other pests. Tylka added that MacIntosh's work may also help to predict the response of soybeans when new pests arise in the future. Such advances ultimately will lead to more consistent production and make soybeans more profitable for farmers, Tylka said.