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Student Staff 9
IGB Fellows 8
Visiting Researchers 21
Postdoctoral Researchers 73
Research Staff 103
Graduate Students 194
2 Patents Issued in FY19
Production of Xylitol from a Mixture of Hemicellulosic Sugars; Huimin Zhao
Procaspase-Activating Compounds and Methods; Paul Hergenrother
Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field
South, P. F., Cavanagh, A. P., Liu, H. W. & Ort, D. R., Jan 4 2019, Science. 363, 6422, eaat9077.
Early human dispersals within the Americas
Víctor Moreno-Mayar, J., Vinner, L., De Barros Damgaard, P., De La Fuente, C., Chan, J., Spence, J. P., Allentoft, M. E., Vimala, T., Racimo, F., Pinotti, T., Rasmussen, S., Margaryan, A., Orbegozo, M. I., Mylopotamitaki, D., Wooller, M., Bataille, C., Becerra-Valdivia, L., Chivall, D., Comeskey, D., Devièse, T., Grayson, D. K., George, L., Harry, H., Alexandersen, V., Primeau, C., Erlandson, J., Rodrigues-Carvalho, C., Reis, S., Bastos, M. Q. R., Cybulski, J., Vullo, C., Morello, F., Vilar, M., Wells, S., Gregersen, K., Hansen, K. L., Lynnerup, N., Lahr, M. M., Kjær, K., Strauss, A., Alfonso-Durruty, M., Salas, A., Schroeder, H., Higham, T., Malhi, R. S., Rasic, J. T., Souza, L., Santos, F. R., Malaspinas, A. S., Sikora, M., Nielsen, R., Song, Y. S., Meltzer, D. J. & Willerslev, E., Dec 7 2018, Science. 362, 6419, eaav2621.
A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme
Mirts, E. N., Petrik, I. D., Hosseinzadeh, P., Nilges, M. J. & Lu, Y., Sep 14 2018, Science. 361, 6407, p. 1098-1101
The evolutionary history of dogs in the Americas
Leathlobhair, M. N., Perri, A. R., Irving-Pease, E. K., Witt, K. E., Linderholm, A., Haile, J., Lebrasseur, O., Ameen, C., Blick, J., Boyko, A. R., Brace, S., Cortes, Y. N., Crockford, S. J., Devault, A., Dimopoulos, E. A., Eldridge, M., Enk, J., Gopalakrishnan, S., Gori, K., Grimes, V., Guiry, E., Hansen, A. J., Hulme-Beaman, A., Johnson, J., Kitchen, A., Kasparov, A. K., Kwon, Y. M., Nikolskiy, P. A., Lope, C. P., Manin, A., Martin, T., Meyer, M., Myers, K. N., Omura, M., Rouillard, J. M., Pavlova, E. Y., Sciulli, P., Sinding, M. H. S., Strakova, A., Ivanova, V. V., Widga, C., Willerslev, E., Pitulko, V. V., Barnes, I., Gilbert, M. T. P., Dobney, K. M., Malhi, R. S., Murchison, E. P., Larson, G. & Frantz, L. A. F., Jul 6 2018, Science. 361, 6397, p. 81-85
Ancient human parallel lineages within North America contributed to a coastal expansion
Scheib, C. L., Li, H., Desai, T., Link, V., Kendall, C., Dewar, G., Griffith, P. W., Mörseburg, A., Johnson, J. R., Potter, A., Kerr, S. L., Endicott, P., Lindo, J., Haber, M., Xue, Y., Tyler-Smith, C., Sandhu, M. S., Lorenz, J. G., Randall, T. D., Faltyskova, Z., Pagani, L., Danecek, P., O’Connell, T. C., Martz, P., Boraas, A. S., Byrd, B. F., Leventhal, A., Cambra, R., Williamson, R., Lesage, L., Holguin, B., Soto, E. Y. D., Rosas, J. T., Metspalu, M., Stock, J. T., Manica, A., Scally, A., Wegmann, D., Malhi, R. S. & Kivisild, T., Jun 1 2018, Science. 360, 6392, p. 1024-1027
Darwinian bee-keeping: lessons from the wild
Robinson, G., Jul 1 2019, Nature. 571, 7763, p. 34-35
The population history of northeastern Siberia since the Pleistocene
Sikora, Martin; Pitulko, Vladimir V.; Sousa, Vitor C.; Allentoft, Morten E.; Vinner, Lasse; Rasmussen, Simon; Margaryan, Ashot; de Barros Damgaard, Peter; de la Fuente, Constanza; Renaud, Gabriel; Yang, Melinda A.; Fu, Qiaomei; Dupanloup, Isabelle; Giampoudakis, Konstantinos; Nogués-Bravo, David; Rahbek, Carsten; Kroonen, Guus; Peyrot, Michaël; McColl, Hugh; Vasilyev, Sergey V.; Veselovskaya, Elizaveta; Gerasimova, Margarita; Pavlova, Elena Y.; Chasnyk, Vyacheslav G.; Nikolskiy, Pavel A.; Gromov, Andrei V.; Khartanovich, Valeriy I.; Moiseyev, Vyacheslav; Grebenyuk, Pavel S.; Fedorchenko, Alexander Yu; Lebedintsev, Alexander I.; Slobodin, Sergey B.; Malyarchuk, Boris A.; Martiniano, Rui; Meldgaard, Morten; Arppe, Laura; Palo, Jukka U.; Sundell, Tarja; Mannermaa, Kristiina; Putkonen, Mikko; Alexandersen, Verner; Primeau, Charlotte; Baimukhanov, Nurbol; Malhi, Ripan S.; Sjögren, Karl Göran; Kristiansen, Kristian; Wessman, Anna; Sajantila, Antti; Lahr, Marta Mirazon; Durbin, Richard; Nielsen, Rasmus; Meltzer, David J.; Excoffier, Laurent; Willerslev, Eske. Nature, Vol. 570, No. 7760, 13.06.2019, p. 182-188.
Small-molecule ion channels increase host defences in cystic fibrosis airway epithelia
Muraglia, K. A., Chorghade, R. S., Kim, B. R., Tang, X. X., Shah, V. S., Grillo, A. S., Daniels, P. N., Cioffi, A. G., Karp, P. H., Zhu, L., Welsh, M. J. & Burke, M. D., Mar 21 2019, Nature. 567, 7748, p. 405-408
Improved reference genome of Aedes aegypti informs arbovirus vector control
Matthews, B. J., Dudchenko, O., Kingan, S. B., Koren, S., Antoshechkin, I., Crawford, J. E., Glassford, W. J., Herre, M., Redmond, S. N., Rose, N. H., Weedall, G. D., Wu, Y., Batra, S. S., Brito-Sierra, C. A., Buckingham, S. D., Campbell, C. L., Chan, S., Cox, E., Evans, B. R., Fansiri, T., Filipović, I., Fontaine, A., Gloria-Soria, A., Hall, R., Joardar, V. S., Jones, A. K., Kay, R. G. G., Kodali, V. K., Lee, J., Lycett, G. J., Mitchell, S. N., Muehling, J., Murphy, M. R., Omer, A. D., Partridge, F. A., Peluso, P., Aiden, A. P., Ramasamy, V., Rašić, G., Roy, S., Saavedra-Rodriguez, K., Sharan, S., Sharma, A., Smith, M. L., Turner, J., Weakley, A. M., Zhao, Z., Akbari, O. S., Black, W. C., Cao, H., Darby, A. C., Hill, C. A., Johnston, J. S., Murphy, T. D., Raikhel, A. S., Sattelle, D. B., Sharakhov, I. V., White, B. J., Zhao, L., Aiden, E. L., Mann, R. S., Lambrechts, L., Powell, J. R., Sharakhova, M. V., Tu, Z., Robertson, H. M., McBride, C. S., Hastie, A. R., Korlach, J., Neafsey, D. E., Phillippy, A. M. & Vosshall, L. B., Nov 22 2018, Nature. 563, 7732, p. 501-507
Ancient herders enriched and restructured African grasslands
Marshall, F., Reid, R. E. B., Goldstein, S., Storozum, M., Wreschnig, A., Hu, L., Kiura, P., Shahack-Gross, R. & Ambrose, S. H., Sep 20 2018, Nature. 561, 7723, p. 387-39
Cooperative asymmetric reactions combining photocatalysis and enzymatic catalysis
Litman, Z. C., Wang, Y., Zhao, H. & Hartwig, J. F., Aug 16 2018, Nature. 560, 7718, p. 355-35
With Groups at the
University of Illinois
With Community Organizations
Science Volunteer Time
Of Outreach Activities
Of Outreach Events
Department of Energy $29,568,564
National Institutes of Health $8,394,726
National Science Foundation $1,261,594
EBI/BP & Shell Oil $2,045,749
Bill & Melinda Gates Foundation $11,213,630
Other (plus USDA) $3,726,179
Total (FY19): $56,210,442
IGB Faculty Awards
Lisa Ainsworth, USDA Agricultural Research Service Scientist (GEGC) received 2019 NAS Prize in Food and Agriculture Sciences; elected Fellow of American Association for the Advancement of Science.
Brian Allan, Associate Professor of Entomology (CGRH/IGOH) named University Scholar.
Andrew Alleyne, Professor of Mechanical Science and Engineering (BSD) elected Fellow of the American Association for the Advancement of Science.
Stephen Boppart, Professor of Engineering (RBTE) named Fellow of the National Academy of Inventors (NAI).
Martin Burke, Professor of Chemistry (MMG), received Mukaiyama Award from the Society of Synthetic Organic Chemistry, Japan; named 2019 iCON Honoree.
Ximing Cai, Professor of Civil and Environmental Engineering (CABBI) named Fellow of the American Geophysical Union.
Nigel Goldenfeld, Professor of Physics (BCXT leader/CGRH/GNDP) awarded Leo P. Kadanoff Award from the American Physical Society.
Jiawei Han, Professor of Engineering (GNDP) named Michael Aiken Chair.
Brendan Harley, Professor of Chemical and Biomolecular Engineering (RBTE Theme Leader) named Robert W. Schaefer Professor; inducted into American Institute for Medical and Biological Engineering (AIMBE) College of Fellows.
Paul Hergenrother, Professor of Chemistry (ACPP Leader/MMG) elected Fellow of the American Association for the Advancement of Science; received George and Christine Sosnovsky Award for Cancer Research from the American Chemical Society.
Joseph Irudayaraj, Professor of Bioengineering (ONC-PM) elected Fellow of the Biomedical Engineering Society (BMES).
Paul Kenis, Professor of Chemical and Biomolecular Engineering (RBTE) named Fellow of the Electrochemical Society.
Hyunjoon Kong, Professor of Chemical and Biomolecular Engineering (RBTE) named Robert W. Schaefer Professor.
David Kranz, Professor of Biochemistry (ACPP) named Fellow of the National Academy of Inventors (NAI).
Stephen Long, Professor of Crop Sciences and Plant Biology (BSD/CABBI/GEGC) elected to National Academy of Sciences.
Ting Lu, Associate Professor of Bioengineering (BSD/BCXT/CABBI/MME) received Maximizing Investigators' Research Award (MIRA) from NIH.
Zan Luthey-Schulten, Professor of Chemistry (BCXT) invested as Murchison-Mallory Endowed Chair in Chemistry.
Ruby Mendenhall, Associate Professor of Sociology (CGRH/GNDP) selected for inaugural cohort of Public Voices Fellowship.
Jeffrey Moore, Professor of Chemistry (BSD) received American Chemical Society Award in Polymer Chemistry.
Pablo Perez-Pinera, Assistant Professor of Bioengineering (ACPP) received 2019 Impact Award from Parkinson's Foundation.
Bruce Schatz, Professor of Computer Science (CGRH) named Associate Editor of Nature Digital Medicine.
Saurabh Sinha, Professor of Computer Science (BSD/CABBI/GNDP/GSP) received Maximizing Investigators' Research Award (MIRA) from NIH.
Jonathan Sweedler, Professor of Chemistry (BSD/CABBI/MMG) named to top spot on Analytical Scientist’s 2019 Power List.
Amy Wagoner Johnson, Professor of Mechanical Science and Engineering (CGRH/RBTE) selected for inaugural cohort of Public Voices Fellowship.
Rachel Whitaker, Professor of Microbiology (IGOH leader/BCXT) elected American Academy of Microbiology Fellow.
Huimin Zhao, Professor of Chemical and Biomolecular Engineering (BSD lead/CABBI/MMG) received Enzyme Engineering Award.
Alisa King, Claudia Lutz
Alan Flurry (University of Georgia, Athens), Ananya Sen, April Wendling, Christine Herman, Claire Benjamin, CSL Communications, Dave Evensen, Diana Yates, Emily Scott, Institute for Sustainability, Energy, and Environment, Katie Willis (University of Alberta, Edmonton Canada), Kim Gudeman, Laura Schmitt, Lauren Quinn, Liz Ahlberg Touchstone, Lois Yoksoulian, MDOT SHA Communications, Rensselaer Polytechnic Institute, Sharita Forrest, Siv Schwink, Stephanie Henry
Andrew Smith, Beckman Institute, Bruce Fouke, C. Young, Carl Zimmer, Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Chi P. Ting, Coordinated Science Lab, Claire Benjamin, Department of Bioengineering, Erik Sacks, Fred Zwicky, Gustavo Caetano-Anollés, Janet Sinn-Hanlon, Jordan Goebig, Julia Pollack, Justin McGrath, Kathryn Faith, L. Brian Stauffer, Lauren Quinn, Leslie Vosshall, M. Read, Maria Alejandra Bautista, Mary F. Calvert for The Washington Post, Mayandi Sivaguru, Michael Melkonian, Monika Ziogaite, Nanotechnology Lab, Nathan Schroeder, Nicholas Vasi, Nick Holonyak Mico, Ray Ming, Rebecca Schultz, Rene Begay, Rhodes College Digital Archives, Yong-Su Jin, Walter S. Judd, Xing Wang
Our microbial foes are also our allies; for far longer than we have been fighting the bacteria and other pathogens that make us ill, they have been fighting each other. A medical revolution occurred when we learned that we could borrow the products microbes use to protect themselves, like penicillin, and use them to protect ourselves--a strategy that has been greatly accelerated by genomics. Explore a doctor’s office to spot other ways that genomics is revolutionizing medicine once again.
For CRISPR, tweaking DNA fragments yields highest efficiency rates yet
Researchers set a new high for reported rates of gene insertion into human cells with the CRISPR-Cas9 gene-editing system, a necessary step toward harnessing CRISPR for clinical gene-therapy applications.
Led by Steven L. Miller Chair Professor of Chemical and Biomolecular Engineering Huimin Zhao (BSD leader/CABBI/MMG), the researchers published their work in the journal Nature Chemical Biology. The NIH supported this work. Zhao also is affiliated with the Carle Illinois College of Medicine.
Researchers have found CRISPR to be an efficient tool to turn off, or “knock out,” a gene. However, in human cells, it has not been a very efficient way to insert or “knock in” a gene.
Thanks to chemical tweaks to the ends of the DNA to be inserted, the new technique is up to five times more efficient than current approaches.
The researchers saw improvements at various genetic locations tested in a human kidney cell line, even seeing 65% insertion at one site where the previous high had been 15%.
“A good knock-in method is important for both gene-therapy applications and for basic biological research to study gene function,” said Zhao. “With a knock-in method, we can add a label to any gene, study its function and see how gene expression is affected by cancer or changes in chromosome structure. Or for gene-therapy applications, if someone has a disease caused by a missing gene, we want to be able to insert it.”
Structurally designed 'DNA star' enables ultrasensitive test for dengue virus
By folding snippets of DNA into the shape of a five-pointed star using structural DNA nanotechnology, researchers have created a trap that captures dengue virus as it floats in the bloodstream. Once sprung, the trap—which is nontoxic and is naturally cleared from the body—lights up. It’s the most sensitive test yet for the mosquito-borne disease.
Published in the journal Nature Chemistry, this detection technique could be expanded to other viruses and adapted to kill the viruses it snares. The work was supported with funding from both the NIH and the NSF.
“This is more sensitive than any other way of detecting dengue, beating the clinical test by more than 100-fold,” said chemist and corresponding author Xing Wang (ONC-PM). “The binding is tight and the specificity is high, enabling us to distinguish the presence of dengue on the first day of infection.”
The spherical surface of dengue, like the closely related Zika virus, is studded with multiple latch points to catch a cell surface. The team settled on a five-pointed star as the best match between points on the DNA shape and latch points on the virus. Wang’s team attached specific aptamers, molecules the viral latches will bind to, precisely to the tips and vertices of the star so they would align with the distribution of the latches on the virus. Once bound to the virus, the DNA star starts to fluoresce, making it easily visible in a blood test.
Dozens of potential new antibiotics discovered with free online app
A new web tool speeds the discovery of drugs to kill Gram-negative bacteria, which are responsible for the vast majority of antibiotic-resistant infections and deaths. The tool also offers insights into discrete chemical changes that can convert drugs that kill other bacteria into drugs to fight Gram-negative infections. The team proved the system works by modifying a Gram-positive drug and testing it against three different Gram-negative bacterial culprits in mouse sepsis. The drug was successful against each.
Researchers report their findings in the journal Nature Microbiology.
“It’s really hard to find new antibiotics for Gram-negative pathogens, because these bacteria have an extra membrane, an outer membrane, that’s very good at keeping antibiotics out,” said Kenneth L. Rinehart Jr. Endowed Chair in Natural Products Chemistry and Professor of Chemistry Paul Hergenrother (ACPP leader/MMG), who led the NIH-funded research.
The new app, called eNTRyway, can quickly evaluate potential drug compounds to determine if they have the necessary molecular characteristics to cross the membrane and accumulate inside Gram-negative bacteria.
Developed by graduate student Bryon Drown, the app can also point to ways of modifying existing drugs to convert them into potent killers of Gram-negative pathogens.
Hergenrother and his colleagues have so far identified more than 60 antibiotics that are effective only against Gram-positive bacteria but can be converted into drugs to fight Gram-negative infections.
Artificial intelligence to run the chemical factories of the future
A new proof-of-concept study details how an automated system driven by artificial intelligence can design, build, test and learn complex biochemical pathways to efficiently produce lycopene, a red pigment found in tomatoes and commonly used as a food coloring, opening the door to a wide range of biosynthetic applications, researchers report.
The results of the study, which combined a fully automated robotic platform called the Illinois Biological Foundry for Advanced Biomanufacturing with AI to achieve biomanufacturing, are published in the journal Nature Communications. The work was funded by the DOE via CABBI.
“Biofoundries are factories that mimic the foundries that build semiconductors, but are designed for biological systems instead of electrical systems,” said study leader Huimin Zhao (BSD leader/CABBI/MMG), Steven L. Miller Chair Professor of Chemical and Biomolecular Engineering. Zhao and his group leverage the Illinois Biological Foundry for Advanced Biomanufacturing, or iBioFAB, in much of their work.
The new AI system tested in the present study, dubbed BioAutomata, completed two rounds of fully automated construction and optimization of the lycopene-production pathway, which includes the design and construction of the lycopene pathways, transfer of the DNA-encoding pathways into host cells, growth of the cells, and extraction and measurement of the lycopene production.
Zhao envisions fully automated biofoundries being a future revolution in smart manufacturing, not unlike what automation did for the automobile industry.
Study tracks evolutionary history of metabolic networks
By analyzing how metabolic enzymes are built and organized, researchers have reconstructed the evolutionary history of metabolism. Their study shows how metabolic networks, which drive every cellular process from protein building to DNA repair, became less random, more modular and more hierarchical over time, the researchers say.
Their study, published in the journal PLOS ONE, shines a light on the patchwork process that allowed cells to shape metabolic pathways into what they are today. The USDA and Illinois’ NCSA supported this research.
“If you’re going to choose a network in biology, metabolism is the most important one,” said Professor of Crop Sciences Gustavo Caetano-Anollés, (GEGC) who led the study with graduate student Fizza Mughal. “This network is responsible for negotiating not just matter but also energy—the two elements that are the most fundamental for an organism to work.”
To understand how cells assembled their metabolic networks, the researchers focused on the enzymatic machinery that lies at the heart of these networks. When the researchers examined how the metabolic pathways had evolved, they saw that early metabolic networks were more random, and probably less efficient, than present-day networks, which gained a more modular and hierarchical configuration. This modular hierarchy is a feature of other advanced networks, like the internet or neural networks of the brain, Caetano-Anollés said.
Genome mining reveals novel production pathway for promising malaria treatment
Microbes are well-known among biologists as master engineers of useful small molecules, and there are many tricks of their trade. When researchers at the University of Illinois took a closer look at how a known microbe makes a known so-called natural product, they were rewarded with the discovery of a completely unknown biochemical trick.
G. William Arends Professor of Molecular and Cellular Biology William Metcalf (MMG leader) led the study with then-postdoctoral researcher Elizabeth (Betsy) Parkinson. Parkinson is now an assistant professor of chemistry at Purdue University. Metcalf, Parkinson and coauthors reported their work, which was supported by NIH, in Nature Chemical Biology.
The researchers explored how their microbe of interest, Streptomyces lavendulae, creates a chemical called dehydrofosmidomycin. The team was interested in how this compound is created in part because it’s an antimicrobial that is effective against malaria, a mosquito-borne illness that kills hundreds of thousands of people each year. The team found that the genes that S. lavendulae was using to make dehydrofosmidomycin were completely unlike those seen in other microbes; one gene in particular encoded an enzyme that facilitates a complex chemical reaction not previously observed in nature.
“So why do you care about how molecules like this are made? . . . A really good bioengineered pathway, it's the cheapest way to make anything,” Metcalf said. “This offers another route to the same molecule, which might be a more efficient route, might be a cheaper route, that has yet to be explored.”
Biosynthetic pathway in bacteria a recipe for drug discovery and production
Microbes are master chefs of the biomolecular world; collectively, they harbor the ability to produce a vast array of unknown substances, some of which may have therapeutic or other useful properties. In searching for useful products, a team of chemists have discovered a whole new class of microbial recipes.
“The kind of reactions that these enzymes are doing are mind-boggling . . . when we first saw them, we were scratching our heads,” said HHMI Investigator Wilfred van der Donk (MMG), who led the study. “Then we had to painstakingly prove that the reactions we thought the enzymes were doing, are indeed carried out.”
Van der Donk, who is also the Richard E. Heckert Endowed Chair in Chemistry, and his colleagues at Illinois collaborated with the laboratory of HHMI Investigator and University of California, Los Angeles Professor of Biological Chemistry and Physiology Tamir Gonen to confirm their findings, which were published in Science. The work was supported by HHMI and the NIH.
The researchers made their unexpected discovery while examining a cluster of genes found in the bacterium Pseudomonas syringae, which infects plants. They had found that their cluster of genes included one that held the information for a peptide made by a ribosome, while another coded for an enzyme that could independently extend the peptide chain. That extension is modified in a series of steps and then broken off to create a desired product, leaving the peptide free to be extended once more. The researchers are excited about finding ways to put this completely novel pathway to use.
Scientists develop fast, efficient way to build amino acid chains
Scientists often build new protein molecules by stringing groups of amino acids together to make polypeptides, which are needed in drug development and the creation of new biomaterials.
Researchers have developed a streamlined process that purifies the amino acid precursors and builds the polypeptides at the same time, unlike previous methods in which the processes were separate, laborious and time-consuming. They reported their findings in the Proceedings of the National Academy of Sciences.
Traditionally, making polypeptide chains has been a very complicated process, said Materials Science and Engineering Professor Jianjun Cheng (RBTE), who led the new research. Synthesizing and purifying the amino acid precursors, namely N-carboxyanhydride, or NCA, requires days of tedious effort, and building the polypeptide chains takes hours to days. Cheng and his colleagues drew inspiration from ribozymes, which excel at making amino acid chains quickly while isolating them from the cellular environment. The team developed a system that mimics the ribozyme function, building the amino acid chains quickly while removing any molecules that could contaminate the system.
“Previously, the field required specialized chemists like us to make these building blocks,” Cheng said. “Our new protocol allows anyone with basic chemistry skills to build the desired polypeptides in a few hours.”
The researchers are investigating how to scale up the process and explore the full range of chemical and biological applications the new approach allows.
The NSF and NIH supported this work.
Project aims to revive natural product discovery
The mid-20th century was the golden age of natural product discovery where scientists discovered groundbreaking drugs, like penicillin and tetracycline, from natural sources.
At the same time, the emergence of genomics allowed scientists to use genetic information to understand how natural products were made. This brought success in discovering new natural products, but only on a very small scale. However, a new project aims to discover new natural products on a larger scale by using synthetic biology and automation.
The project, funded by the NIH, will be led by Steven L. Miller Chair Professor of Chemical and Biomolecular Engineering Huimin Zhao (BSD theme leader/CABBI/MMG) and chemistry professors Wilfred van der Donk (MMG) and Doug Mitchell (MMG).
This interdisciplinary effort will allow them to unlock the potential of a specific class of natural products known as ribosomally synthesized and post-translationally modified peptides, or RiPPs.
The researchers will leverage a robotic system called the Illinois Biological Foundry or iBioFAB, which will not only allow them to identify new RiPPs and create new molecules, but also determine — to some extent — whether they have medical value.
While they may be able to determine the medical value of these compounds, their main goal is to discover new natural products and see what’s out there.
The lifesaving drugs that the pharmaceutical industry developed from natural products have added more than a decade to the human lifespan. And this industry, according to Mitchell, is built on just one percent of the chemical bounty of the microbial world.
Low-calorie sweetener gets manufacturing boost from yeast
The quest to satisfy the sweet tooth without adding to the waistline has a new weapon in its arsenal: a strain of yeast that can metabolize lactose, the sugar in dairy products, into tagatose, a natural sweetener with less than half the calories of table sugar.
Yong-Su Jin, Professor of Food Science and Human Nutrition (BSD/CABBI/MME), led the research team that engineered the yeast strain, which produces tagatose in much larger quantities than traditional enzymatic manufacturing techniques, making tagatose a cost-effective alternative to sugar or high-fructose corn syrup.
The researchers published their work in the journal Nature Communications.
In spite of its benefits, tagatose has a high manufacturing cost that has kept it from wide commercial use, Jin said. Although it is naturally present in fruits and dairy products, the concentrations are too low to isolate tagatose effectively.
The researchers engineered a strain of yeast that produces tagatose from lactose by making two genetic tweaks. Thus, when the yeast is fed lactose, its own metabolism drives it to produce a solution that is 90 percent tagatose—much higher than the 30 percent yield from traditional manufacturing.
“We showed that lactose can be efficiently and rapidly utilized by engineered yeast. With further metabolic engineering, we can produce other valuable products from the lactose abundant in whey, using our engineered yeast strain,” Jin said.
The EBI and the DOE supported this work.
Cystic fibrosis treatment uses 'molecular prosthetic' for lung protein
An approved drug normally used to treat fungal infections could perform the role of a protein channel that is missing or defective in the lungs of people with cystic fibrosis, operating as a prosthesis on the molecular scale, says new research from Illinois and the University of Iowa.
Cystic fibrosis is a lifelong disease that makes patients vulnerable to lung infections. There are treatments for some patients but no cure. The approved drug has potential to become the first treatment to address all types of cystic fibrosis, regardless of the genetic mutation that causes the protein deficiency. The researchers published their findings in the journal Nature.
“Instead of trying gene therapy—which is not yet effective in the lung—or to correct the protein, our approach is different. We use a small molecule surrogate that can perform the channel function of the missing protein, which we call a molecular prosthetic,” said Martin D. Burke (MMG), Professor of Chemistry and Associate Dean for Research at the Carle Illinois College of Medicine and leader of the study.
Burke’s group has long investigated the channel-forming properties of a drug used to treat fungal infections, amphotericin (am-foe-TARE-is-in). They found that amphotericin can form channels in the surface membrane of lung tissue donated by people with cystic fibrosis that was caused by various mutations in the CFTR gene.
This work was funded in part by Emily’s Entourage and the NIH.
Researchers study bacterial immunity to understand infectious disease
Hospital patients with cystic fibrosis are often infected by Pseudomonas aeruginosa, a bacterium that infects the lungs and prevents breathing, often causing death. P. aeruginosa itself can also be infected by viruses, which can affect the clinical outcomes of cystic fibrosis patients.
Professor of Microbiology Rachel Whitaker (IGOH theme leader/BXCT) and PhD students Whitney England and Ted Kim had the idea to use P. aeruginosa as a “model system” for understanding how bacteria’s interactions with viruses may affect human health.
Their findings, published in mSystems, provide insight into this bacterium’s diversity and immune system called the CRISPR/Cas system, which prevents viral infection. This work was supported in part by the Cystic Fibrosis Foundation.
The researchers analyzed the CRISPR/Cas system within P. aeruginosa in a group of cystic fibrosis patients in Copenhagen, Denmark and found that the bacterial immune profiles were diverse. They then compared the bacterial population to known viruses of P. aeruginosa, and found that some viruses were highly targeted by the bacteria’s immune system.
Cystic fibrosis patients will often use phage therapy - which utilizes viruses to kill bacteria - to target P. aeruginosa. On a larger scale, this research provides foundation for other researchers who study bacterial infections, whether they’re looking to stop antibiotic resistance or prevent epidemics.
“We don’t really want to prevent epidemics in this case—we want to promote epidemics of the viruses that kill the bacteria,” Whitaker said. “I think that this is a big step in that direction.”
Unlocking silent gene clusters leads to discovery of new natural products
By enticing away the repressors dampening unexpressed, silent genes in Streptomyces bacteria, researchers have unlocked several gene clusters for new natural products, according to a study published in the journal Nature Chemical Biology.
The NIH supported this work.
Since many antibiotics, anti-cancer agents and other drugs have been derived from genes expressed in Streptomyces, the researchers hope that unsilencing genes will yield additional candidates in the search for new antimicrobial drugs, says study leader and Chemical and Biomolecular Engineering Professor Huimin Zhao (BSD leader/CABBI/MMG).
“There are so many undiscovered natural products lying unexpressed in genomes. We think of them as the dark matter of the cell,” Zhao said.
To unlock the large gene clusters, Zhao’s group created clones of the DNA fragments of interest and injected them into the bacteria to sequester the repressors. Of the eight new molecules produced, the researchers purified and determined the structure of two molecules, one being a novel type of oxazole, a class of molecules often used in drugs. This technique will be used to explore additional silent biosynthetic gene clusters in Streptomyces and other bacteria and fungi to find more undiscovered natural products.
Cell size determines reactivation of HIV-infected T-cells
Thanks to the development of antiretroviral drugs, human immunodeficiency virus (HIV) is considered a manageable chronic disease today. However, if left undiagnosed or untreated, HIV can develop into AIDS (acquired immune deficiency syndrome).
According to Assistant Professor of Bioengineering Roy Dar BCXT/GNDP), researchers have focused on eradicating the latent reservoir because it can reactivate spontaneously, evade drug therapy, or be a source for viral rebound, which can occur if a patient does not strictly adhere to the antiretroviral therapy treatment regimen.
In a recent study, Dar and his research group investigated the reactivation of T-cells that were latently infected with HIV. They used a viral construct that contained a gene for a green fluorescent protein (GFP) that gets expressed when a cell reactivates to quantify T-cell behavior.
The full paper, "Cell size-based decision-making of a viral gene circuit," was published in the journal Cell Reports, with Bioengineering postdoctoral researcher Kathrin Bohn-Wippert as lead author. This work was funded by the NIH and the Cancer Center at Illinois through its Cancer Scholars program.
They discovered that within a latent population, only larger host cells reactivated, providing a natural cellular mechanism for enhancing burst size of viral expression while destabilizing the latent state and biasing viral decision making. These findings may be useful in guiding stochastic design strategies for drug therapies, have applications in synthetic biology, and play a role in advancing HIV diagnostics and treatments.
For many people, the natural world provides opportunities for exploration, escape, exercise, or all of the above. For scientists, it is also an endless source of fundamental questions. How did life first appear on Earth, and in what form? How did such a beautiful diversity of living things arise? Genomics is a lens that allows us to see the history and the potential future of our living world with new clarity--take a look.
Online tool speeds response to elephant poaching by tracing ivory to source
A new tool uses an interactive database of geographic and genetic information to help authorities quickly identify where the confiscated tusks of African elephants were originally poached. Developed by an international team of researchers, the Loxodonta Localizer, described in a publication in the Journal of Heredity, matches genetic sequences from poached ivory to those stored in the database.
Between 2006 and 2016, the number of African elephants declined by about 110,000, and the rate of poaching has been increasing since 2008. Today, about 415,000 African elephants remain.
Designed to help address these losses, the Loxodonta Localizer relies on genetic information from a small, highly variable region of mitochondrial DNA from African elephants. Mitochondrial DNA is passed only from females to their offspring. This makes mitochondrial DNA especially useful for tracking elephants, since the herds are matrilineal and females do not disperse, said Professor of Animal Sciences Alfred Roca (CGRH/GNDP), who led development of the new tool.
"Right now, I believe we have about one out of every 200 elephants in Africa included in the database," Roca said. "What we really need are more samples from more locations, so that the database holds as many of the rare but geographically informative sequences as possible."
The U.S. Fish and Wildlife Service African Elephant Conservation Fund, the conservation group known as TRAFFIC, the U.S. Department of State and the U.S. Agency for International Development supported this work.
Goldenfeld co-leads initiative tackling 'last great problem of classical physics'
The rich complexity of turbulence—with its wide range of length and time scales—poses a major challenge to the development of predictive models based on fluid dynamics. Now, four leading physicists will co-lead an international effort to develop a statistical theory of turbulence. If successful, a statistical theory of turbulence would have broad applications, including in aeronautics, geophysics and astrophysics, medicine, and in the efficient transport of fluids through pipelines.
Funded by the Simons Foundation, the research project titled “Revisiting the Turbulence Problem Using Statistical Mechanics” will bring together an international team from the U.S., U.K., France, Austria, and Israel to apply novel techniques in non-equilibrium statistical physics to the unresolved problem. Swanlund Professor of Physics Nigel Goldenfeld (BCXT leader/CGRH/GNDP) is a lead PI on the project.
“This is the last great problem from classical physics,” notes Goldenfeld. “It has eluded a theoretical description since it was first scientifically studied in the 18th century. Turbulence has major significance for everyday life.
For example, the speed of every flowing river is determined by turbulence. The drag experienced by an airplane or car is determined by turbulence. If we could understand how to control this, it could save billions of dollars every year in fuel costs.”
The grant will support two graduate students conducting original research in the Goldenfeld group, on topics emanating from the project.
Woese Undergraduate Scholars experience a summer of science
Two of the most basic motivations that drive scientific research—exploration of the unknown and the desire to solve a pressing problem—were represented by this year’s Carl R. Woese undergraduate research scholars. Allison Narlock spent her summer investigating the mechanics of archaeal cell division; Monika Ziogaite worked to identify genetic variants that contribute to the metastatic potential of breast cancers.
Both Narlock, a sophomore majoring in molecular and cellular biology, and Ziogaite, a senior majoring in interdisciplinary health sciences, were awarded support for 10 weeks of independent research at the IGB.
“There are many diverse genes that are involved in the metastasis of breast cancer such as the BRCA1 and BRCA2 genes,” Ziogaite said. “My findings suggested a tissue-specific dependent interaction which could be further used to understand the proteins’ contribution to metastasis.” Ziogaite is planning on taking a gap year after graduation where she will volunteer and gain clinical experiences before applying to medical school.
Narlock joined the laboratory of Professor of Microbiology Rachel Whitaker (IGOH leader/BCXT) after a description of the lab’s work on microbial ecology piqued her interest. She has spent the spring learning to use imaging techniques that will help her examine a mechanism of cell division in the archaeon Sulfolobus islandicus.
Great Barrier Reef coral provides correction factor to global climate
For over 500 million years, corals have been used to keep track of changing sea-surface temperature by recording the ratio of calcium to strontium and oxygen isotopes within their skeletons. Newly developed geological techniques helped uncover the most accurate and high-resolution climate records to date, according to a new study.
Their findings were reported in the journal Frontiers in Marine Science.
“We can ground true coral-based sea-surface temperature records against records made using temperature probes,” Professor of Geology and Microbiology Bruce Fouke (BCXT) said. “Remarkably, the coral records are accurate most of the time, but there are instances where measurements have been off by as much as nine degrees Celsius, and this needs to be rectified.”
As seawater flows through the coral structure, it deposits newly crystalized aragonite on top of skeletons, which may record a different sea-surface temperature. To test this, the team collected drill cores from the skeletons of living Porites coral heads at 10 to 100 feet water depth on the Great Barrier Reef off the coast of Australia.
Using an array of microscopy techniques, the team uncovered a multitude of different aragonite crystallization histories, ranging from seasonal variations in skeletal growth to smaller-scale processes that could be occurring on daily—even hourly—cycles.
Sea-surface temperature records derived from coral skeleton chemistry are the gold standard for accurate climate reconstructions and future predictions, thus making this new insight.
The NASA Astrobiology Institute, Office of Naval Research and the Australian Research Council supported this study
'Fettuccine' may be most obvious sign of life on Mars
A rover scanning the surface of Mars for evidence of life might want to check for rocks that resemble pasta, researchers report in the journal Astrobiology.
The bacterium that controls the formation of such rocks on Earth is ancient and thrives in harsh environments that are similar to conditions on Mars, said Geology and Microbiology Professor Bruce Fouke (BCXT), who led the new, NASA-funded study.
The bacterium Sulfurihydrogenibium yellowstonense or ‘Sulfuri’ belongs to a lineage that evolved prior to the oxygenation of Earth roughly 2.35 billion years ago.
It can survive in extremely hot, fast-flowing water bubbling up from underground hot springs and withstand exposure to ultraviolet light. Sulfuri survives only in environments with extremely low oxygen levels, using sulfur and carbon dioxide as energy sources.
The team looked at Sulfuri’s rock-building capabilities, finding that proteins on the bacterial surface speed up the rate at which calcium carbonate, also called travertine, crystallizes in and around the cables. The result is the deposition of broad swaths of hardened rock with an undulating, filamentous texture.
“If we see the deposition of this kind of extensive filamentous rock on other planets, we would know it’s a fingerprint of life,” Fouke said. “It’s big and it’s unique. No other rocks look like this. It would be definitive evidence of the presence of alien microbes.”
Illinois study identifies key to soybean cyst nematode growth
The soybean cyst nematode, one of the crop’s most destructive pests, isn’t like most of its wormy relatives.
Whereas the vast majority of nematodes look like microscopic worms, the female soybean cyst nematode shape-shifts into a lemon-shaped body after feeding on soybean roots.
These findings were published in the journal EvoDevo; Assistant Professor of Crop Sciences Nathan Schroeder (GNDP) was corresponding author of the publication.
The round shape allows female soybean cyst nematodes to retain about two-thirds of their fertilized eggs inside their bodies. Schroeder says these adaptations have allowed the soybean cyst nematode to become as successful as it is.
From previous research with a different species, the scientists suspected stem cells were responsible for governing the shift in body shape. The research team also investigated the division pattern in other plant-parasitic nematodes and found similar stem cell proliferation in several others, despite not being closely related to soybean cyst nematodes.
“From my perspective, it’s a combination of interesting biology and practical implications with an economically important pest causing yield loss throughout the Midwest,” Schroeder said. “If we can find some new target strategies that will affect it but not the other thousands of beneficial nematode species in the soil, that would be a game-changer.”
The research was supported by the Schlumberger Foundation, the USDA NIFA Hatch program, and the NIH.
Archaeologists find 200-year-old African DNA on tobacco pipe
DNA found on tobacco pipe stems uncovered by archaeologists from the Maryland Department of Transportation State Highway Administration (MDOT SHA) and Anne Arundel County from a 200-year-old stone slave quarter at Belvoir along MD 178 has been determined to be most closely related to Mende in Sierra Leone.
The slave quarter was discovered as part of an MDOT SHA Transportation Enhancement Program project to learn more about the history along MD 178 (General’s Highway). The program is partially funded by the Federal Highway Administration.
From the slave quarter excavation, four tobacco pipe stems were sent to Illinois for DNA analysis. MDOT SHA Chief Archaeologist Julie Schablitsky conferred with Associate Professor of Anthropology Ripan Malhi (CGRH/GSP/GNDP/IGOH/RBTE), who leads an ancient DNA (aDNA) laboratory at Illinois. The recovery of aDNA from tobacco pipes represented a unique challenge to Malhi, who hoped to link the aDNA from the pipe stems with the living descendants of Belvoir’s ancestors.
Together with Associate Professor of Evolutionary Genomics Hannes Schroeder at the University of Copenhagen, the researchers linked recovered aDNA from one woman to be most closely related to Mende living in present day Sierra Leone in West Africa. This was the first time human DNA from an ancient artifact has been connected with a person’s ancestry. Their findings were published in the Journal of Archaeological Science.
“When Africans stepped on those slave ships, they lost not only their freedom but their identity,” said Schablitsky. “This is one way archaeologists can help descendants reclaim their heritage.”
Study of archaeal cells could teach us more about ourselves
Forty-two years after Carl Woese defined Archaea as the third domain of life, scientists are still learning about these ancient organisms in ways that could help us learn more about eukaryotes. Professor of Microbiology Rachel Whitaker (IGOH theme leader/BXCT) and research scientist Changyi Zhang wanted to better understand the archaeal cell by studying Sulfolobus islandicus, an archaeal microorganism that is found in geothermal hot springs.
Their results, published in Nature Communications, gave insight into archaea’s potential shared ancestry with eukaryotes and the evolutionary history of cells. Funding for this work was mainly provided by the NASA Astrobiology Institute.
The researchers determined the essential genes—those that are critical for an organism’s growth and survival—of S. islandicus and compared them to eukaryotic genes, providing insight into the origin of eukaryotes. The study revealed a set of genes that are both unique and essential to archaea.
A better understanding of archaeal cells could help the scientific community learn more about functions of eukaryotic cells, many of which are not well understood. These functions can affect our cells’ health, and unhealthy cells can experience mutations and genome instability, which can cause cancer.
“Our hope is that, in better understanding the core pieces of those functions, we might be able to better understand those systems, and in doing that, better understand our own selves,” Whitaker said.
Whether it’s the inability to digest gluten or having susceptibility to certain diseases, these individual variations are what make humans unique. Inside our bodies, microbial communities also contribute to our uniqueness. Researchers can use genomics to understand causes for individual variation to create personalized treatment options that provide better care for individuals. Have a look inside this gym to learn how genomics contributes to a workout routine.
Single-molecule detection of cancer markers brings liquid biopsy closer to clinic
A fast, inexpensive yet sensitive technique to detect cancer markers is bringing researchers closer to a “liquid biopsy"—a test using a small sample of blood or serum to detect cancer, rather than the invasive tissue sampling routinely used for diagnosis.
Researchers led by Donald Biggar Willett Professor of Engineering Brian Cunningham (ONC-PM leader/MMG) have now developed a method to capture and count cancer-associated microRNAs, or small non-coding messenger RNA molecules that are exuded from cells and detectable in blood or serum, with single-molecule resolution. The team published its results in the Proceedings of the National Academy of Sciences.
“Cancer cells contain gene mutations that enable them to proliferate out of control and to evade the immune system, and some of those mutations turn up in microRNAs,” Cunningham said.
“There are specific microRNA molecules whose presence and concentration is known to be related to the presence and aggressiveness of specific types of cancer, so they are known as biomarkers that can be the target molecule for a diagnostic test.”
Cunningham’s group developed a technique named Photonic Resonator Absorption Microscopy to capture and count microRNA biomarkers. The IGB and the NIH supported this work. Jay and Ann Schenck Professor of Chemistry Yi Lu (BSD/CABBI/ONC-PM) and Associate Professor of Bioengineering Andrew Smith (ONC-PM) were collaborators and coauthors.
MAGIC system allows researchers to modulate activity of genes acting in concert
Genomic research has unlocked the capability to edit the genomes of living cells; yet so far, the effects of such changes must be examined in isolation. In contrast, the complex traits that are of interest in both fundamental and applied research, such as those related to microbial biofuel production, involve many genes acting in concert. A newly developed system will now allow researchers to fine-tune the activity of multiple genes simultaneously.
Huimin Zhao (BSD leader/CABBI/MMG), Steven L. Miller Chair Professor of Chemical and Biomolecular Engineering, led the study. Zhao and his research team described their new functional genomics system, which they named multi-functional genome-wide CRISPR (MAGIC), in a recent publication in Nature Communications.
Researchers design their own DNA sequences that work within CRISPR systems to precisely edit the genomes of living things, either increasing, decreasing, or completely eliminating gene activity, according to the way that cuts in the genome are made and repaired. Until now, though, there has been no easy way to use more than one of these editing modes simultaneously.
“We have developed the tri-functional CRISPR system which can be used to engineer the expression of specific genes to various expression levels,” Zhao said. “Using MAGIC, we can modulate almost all ~6000 genes in the entire yeast genome individually or in combination to various expression levels.”
The work was supported by the DOE, the Natural Science Foundation of China, the Fundamental Research Funds for the Central Universities and Zhejiang Provincial Universities, and the University of Illinois.
Mathematical models provide snapshot of human gut microbial community
Microbial communities can be found everywhere—from lakes to the soil on the ground, they are omnipresent yet invisible to the naked eye. Within those environments there exist dynamic communities that fluctuate in response to environmental changes. One such example is the human gut microbiome, which is composed of microbes that influence the overall landscape of the gut.
Sergei Maslov (BCXT/CABBI), Professor of Bioengineering and Bliss faculty scholar, and collaborators have recently published multiple findings on microscopic ecosystems. A study examining how such communities are organized and how they are shaped by various environmental factors, such as nutrient viability, competition for nutrients, and bacteriophage predators, was reported in PLOS Computational Biology. The work was funded by the European Research Council.
In a related eLife study, the researchers harnessed mathematical models to examine the factors that contribute to regime shifts or abrupt, persistent transitions within these microbial communities and ultimately, the survival of an individual species. After modeling all possible stable compositions within a community, they could then predict the amount of nutrients necessary for each stable composition and likewise, what triggered regime shifts. Another study, reported in mSystems, examined bacteriophages as another external factor that can induce regime shifts within these communities.
“Microbial ecosystems are absolutely everywhere so not just the gut but the soil, bioreactors, and all of the biogeochemical cycles impacting climate, which all have a very significant contribution from microbial communities,” Maslov said. “Being able to somehow manipulate them in a robust and predictable manner is very important.”
Smartphone diagnostics kit for infectious diseases
Infectious diseases such as Zika and dengue remain a top contributor to death and disability across the globe. Diagnosing and treating these diseases, which often have similar symptoms, is especially difficult in developing countries, where access to health care and laboratories is often limited.
A four-year grant from the NIH is allowing a research group led by Donald Biggar Willett Professor in Engineering Brian Cunningham (ONC-PM leader/MMG) to develop a lab-on-a-smartphone system that will enable healthcare professionals to detect disease at the point of care. They aim to give healthcare providers the capability to detect and report the presence of pathogens in less than 30 minutes using a single drop of blood—all with a smartphone clip-on instrument that costs less than $10.
The planned device will also include a microfluidic cartridge loaded with short nucleic acid sequences that specifically recognize and amplify DNA from the pathogen targets. When the clip-on instrument interfaces with the cartridge, the instrument will use LED illumination to excite fluorescent dyes in the sample. The phone’s camera will detect light from the dyes, enabling the phone to quantify the presence of DNA that is specific to each virus. The phone will then link to a cloud-based system to interpret the results and forward them to an offsite medical professional.
"Even in the United States, where we enjoy good access to diagnostic testing laboratories, it can take hours or days to have results from lab work," Cunningham said. "We believe this can provide affordable access and fast results to patients around the globe."
Injections and exercise promote muscle regrowth after atrophy in mice
By injecting cells that support blood vessel growth into muscles depleted by inactivity, researchers say they are able to help restore muscle mass lost as a result of immobility.
The research, conducted in adult mice, involved injections of cells called pericytes (PERRY-sites), which are known to promote blood vessel growth and dilation in tissues throughout the body. The mice that received the injections had significantly better improvement than those that regained mobility without the injections.
Their findings were reported in The FASEB Journal, with support from NIH.
“We’re excited by the new findings because we hope to one day use these cells or biomaterials derived from these cells to help restore lost muscle mass, particularly in elderly or disabled adults who are most likely to see a decline in their overall health as a result of the decline in muscle viability,” said Kinesiology and Community Health Professor Marni Boppart (RBTE), who led the research. Boppart is also affiliated with the Beckman Institute for Advanced Science and Technology and the Carle Illinois College of Medicine.
Fatty acids rewire cells to promote obesity-related breast cancer
Scientists have discovered that free fatty acids in the blood appear to boost proliferation and growth of breast cancer cells. The finding could help explain obese women’s elevated risk of developing breast cancer after menopause.
Professor of Food Science and Human Nutrition and Director of Women’s Health, Hormones and Nutrition Lab Zeynep Madak-Erdogan (GSP/ONC-PM) led the study in which blood samples from healthy women and women with breast cancer were obtained from the Susan G. Komen Tissue Bank and compared, looking for the presence of various metabolites, biomarkers of inflammation and cancer-related proteins. Their findings were published in the journal Cancer Research.
To explore the impact that obesity has on ER-positive cancer cells, the researchers treated several lines of primary tumor and metastatic cancer cells with the blood of obese women. They found that the cancer cells became more viable and multiplied—effects that increased as the fatty acid levels in the women’s blood samples increased.
“Our clinical data provide a more complete understanding of the mechanisms that connect obesity with breast cancer, and provide an opportunity to assess the ability of pathway-preferential estrogens to decrease breast cancer risk in obese postmenopausal women,” said Madak-Erdogan.
Support from the Office of the Vice Chancellor for Research and Innovation, the Beckman Institute for Advanced Science and Technology, the College of Agricultural, Consumer and Environmental Sciences, and the USDA funded this research.
Smart antioxidant-containing polymer responds to oxidant levels
Oxidants found within living organisms are byproducts of metabolism and are essential to wound-healing and immunity. However, at higher concentrations, inflammation and tissue damage can occur.
Engineers, led by Robert W. Schaefer Professor of Chemical and Biomolecular Engineering Hyunjoon Kong (RBTE), have developed and tested a new drug-delivery system that senses high oxidant levels and responds by administering just the right amount of antioxidant to restore this delicate balance.
Their findings were published in the journal Small.
Kong and his team found a way to assemble crystals of catechin—the bright green antioxidant found in green tea—using a polymer that can sense when oxidant concentrations become too high. The researchers tested the responsiveness of the resulting catechin crystal-containing polymer in the common freshwater planktonic crustacean Daphnia magna, also known as the water flea.
The researchers exposed the daphnids to water contaminated with sublethal concentrations of the natural oxidant hydrogen peroxide and observed increased heart rates. When the team added the new catechin crystal assembled with polymer to the experiment, the water fleas recovered a close-to-normal heart rate.
“Hydrogen peroxide is often used to clean water fouled by excessive algae, and this raises concern about how the oxidant may be affecting living organisms in water,” he said. “We think this new antioxidant-delivery system could be used to address the problem of over-oxidized natural waters.”
The Korea Institute of Science and Technology-Europe, Department of Defense, NSF and NIH supported this research.
Microbes overcome human tissue boundaries to swap genes
Bacteria in different parts of the human body are undergoing horizontal gene transfer or the direct sharing of genes at a higher rate than is typically seen in nature, researchers report in the journal Scientific Reports.
The findings are the result of a molecular data-mining method initially conceptualized by Kyung Mo Kim, Senior Research Scientist at the Korea Polar Research Institute. Crop sciences professor Gustavo Caetano-Anollés (GEGC) developed the approach with former student Arshan Nasir.
“Horizontal gene transfer is a major force of exchange of genetic information on Earth,” Caetano-Anollés said. “These exchanges allow microorganisms to adapt and thrive, but they are likely also important for human health. There are some bacteria that cannot live outside our bodies and some without which we cannot live.”
In all cases, gene transfer was most common among closely related organisms, with gene sharing across different body sites occurring at a higher rate than gene sharing among distantly related bacteria living at the same sites.
The researchers say other scientists can use the tool they developed for this work, HGTree, to more accurately predict which genes were inherited “vertically,” through the process of reproduction, and which were picked up from other microbes through horizontal gene transfer. This will lead to an improved understanding of microbial—and human—evolution, the researchers said.
The NSF supported the international collaboration that made this work possible.
Drugs reprogram genes in breast tumors to prevent endocrine resistance
Treating breast tumors with two cancer drugs simultaneously may prevent endocrine resistance by attacking the disease along two separate gene pathways, scientists found in a new study. Their findings were reported in the journal Cancers.
The two drugs used in the study, selinexor and 4-OHT, caused the cancer cells to die and tumors to regress for prolonged periods, said Director of Women’s Health, Hormones and Nutrition Lab and Food Science and Human Nutrition Professor Zeynep Madak-Erdogan (GSP/ONC-PM).
While endocrine therapy is the most effective form of treatment for hormone-responsive breast cancer, some patients will either not respond or develop resistance to the drugs over time. This condition, called endocrine resistance, causes metastases and is responsible for a majority of women’s deaths from hormone-responsive breast cancer.
When they tested the three treatments on human breast tumor cells implanted in mice, they found that the combination of 4-OHT and selinexor caused the tumors to regress faster and more completely than either drug alone, effects that continued for several weeks after treatment ended.
“By decreasing the expression of certain genes, the 4-OHT and selinexor combination prevented tumor cells from activating these survival pathways, which were prominent when the tumors were treated with either drug alone,” said Madak-Erdogan.
Funding from the USDA, a Karyopharm Investigator grant, the Office of the Vice Chancellor for Research and Innovation, an Arnold O. Beckman Award, and private donors supported this work.
Illinois researchers become first to count growth factors in single cells
Whether healthy or diseased, human cells exhibit behaviors and processes that are largely dictated by growth factor molecules, which bind to receptors on the cells. When growth factor levels are too high or too low, or when cells respond irregularly to their directions, many diseases can result, including cancer.
In a recent paper published in Nature Communications, Associate Professor of Bioengineering Andrew Smith (ONC-PM) reported the invention of a new technology platform that digitally counts, for the first time ever, the number of growth factor molecules entering an individual cell.
This work was funded by the NIH and Illinois.
Smith's technology platform tags each growth factor molecule with a single engineered (10 nanometer) infrared fluorescent quantum dot, which can then be visualized using a three-dimensional microscope. In their study, they counted how many epidermal growth factor (EGF) molecules bound to human triple-negative breast cancer cells that were pre-patterned on island-like surfaces. EGF molecules typically signal cell division and lead to tissue growth; numerous cancer cell types have mutations in their EGF receptors.
"We showed the first direct cause-and-effect relationships of growth factors in single cells," Smith said. "We expect the outcomes to lead to a new understanding of cell signaling, how cells respond to drugs, and why cell populations become resistant to drugs, particularly toward improved treatments for cancer."
You have your grandmother's knack for this game! This recipe has been handed down in our family for generations. Our genomes and the environments we create and share with one another influence our behaviors, our personalities, and our wellbeing. Research that discovers exactly how this works can help us understand ourselves and become part of our strategy for staying happy and healthy. Join this family game night to see the different ways genomics might play a part.
Study tracks genomic changes that reinforce darter speciation
When they share habitat, orangethroat and rainbow darters tend to avoid one another, even though they are closely related and can produce “hybrid” offspring. A new study offers an analysis of the genomic changes that occur when these fish hybridize, granting insight into the accumulation of incompatible traits that likely drives them to diverge. The researchers reported their findings in the journal Molecular Biology and Evolution.
Becky Fuller (GNDP), a professor of evolution, ecology and behavior, led the research with first author Rachel Moran. Now a postdoctoral researcher at the University of Minnesota, Moran conducted the research as a graduate student in Fuller’s lab. The NSF, the NIH and Illinois supported the research.
To understand how genomic factors influence this process, the researchers mated orangethroat and rainbow darters in the lab and analyzed the genomes of the few hybrid offspring that survived past hatching. They sequenced the genome of the orangethroat darter and conducted a series of analyses to determine which regions of the two species were misaligned.
“We found that areas of the genome that had a lot of genetic divergence between the two species likely contributed to their reproductive incompatibility,” Moran said.
“How species that exchange genetic material through hybridization are able to coexist and remain distinct from one another has puzzled evolutionary biologists for decades; the insights we’ve gained from this study have hopefully gotten us a little closer to answering that big question.”
Signature call in cowbirds is the password that unlocks song learning
Cowbirds, like cuckoos and a few others, stealthily lay their eggs in the nests of other birds and leave their young to be raised by parents of another species. Mark Hauber (GNDP), Harley Jones Van Cleave Professor of Host-Parasite Interactions in the Department of Evolution, Ecology and Behavior, has studied these brood parasitic birds throughout his career.
In a report in Current Biology, he and his coauthors shared the culmination of a decades-long effort to work out how cowbirds learn the courtship song that enables males to attract mates, and females to recognize them.
The cowbird’s password, as Hauber and other songbird researchers refer to it, is a sound called the chatter call that reaches into their brain and whispers, hey friend! This is the cowbird song. It’s your song too, so pay attention.
Hauber wanted to confirm that this hypothesized message yields tangible results—do cowbirds actually learn better after hearing the chatter call? To answer this question, the team of researchers hand-raised young male cowbirds, playing the juveniles pre-recorded calls: either a canary song paired with a cowbird chatter call, or the same canary song paired with a mourning dove coo.
Although the cowbirds never became fluent in the canary song, it was immediately apparent that male birds who heard the chatter learned to produce a more canary-like song. Other findings from the NSF-funded study, including analyses of brain gene activity in response to the chatter-paired sounds, reinforced the call’s effectiveness at promoting song learning.
Fish fathers exhibit signatures of “baby brain” that may aid parental behavior
Many new parents are familiar with terms like “baby brain” or “mommy brain” that hint at an unavoidable decline in cognitive function associated with the hormonal changes of pregnancy, childbirth, and maternal caregiving. A new study of parental care in stickleback fish is a reminder that such parenting-induced changes in the brain and associated shifts in cognition and behavior are not just for females—and they’re not just for mammals either.
Work led by Alison Bell (GNDP), a professor of evolution, ecology and behavior, found that transition to fatherhood is accompanied by a host of changes in gene activity in the brain. The study, published in Nature Communications, focused on male sticklebacks because they, rather than female sticklebacks, provide parental care to eggs and fry. Graduate student Abbas Bukhari was first author of the study.
To characterize the fish brain’s response to fatherhood, the researchers measured gene expression—that is, they quantified which genes in the genome were being used to make the proteins they encoded, and how often. Bukhari designed a method to meaningfully compare the neural responses of the relatively disparate stickleback and mouse genomes. The team was surprised by what this analysis revealed.
“There was overlap . . . between these stickleback paternal care genes and the mouse maternal care genes,” Bell said. “It's surprising to think that the same molecular mechanisms could be involved in parental care in a fathering fish and in a mothering mammal.”
The research was supported by the Simons Foundation, NSF, NIH, and Illinois.
New IGB research theme takes closer look at protection of genomic data
Genomic technologies have the power to transform individual healthcare for the better. But with that power comes the responsibility to protect the privacy of the individual and to make ethical choices that respect the rights of communities and populations.
A newly established research theme at the IGB is addressing these and related issues. The theme, Genomic Security and Privacy (GSP), is led by Professor of Computer Science Carl Gunter. Assistant Professor of Political Science Aleksander Ksiazkiewicz will lead policy-based work within the theme.
“As the methods get cheaper to produce sequencing data . . . people are going to be a lot more concerned,” Gunter said. “Going back ten years ago when it cost hundreds of millions of dollars to sequence something, it wasn't really that much of a concern . . . but now, it seems like every time you turn around, there's some new security- or privacy-related concern.”
Gunter and Ksiazkiewicz represent the two-pronged approach that the theme will take, simultaneously pursuing the identification of privacy concerns and development of strategies in the arenas of technology and policy. For example, unique formats for genomic data storage could lend themselves to unique, optimal data security solutions. Similarly, well-designed policy surrounding genomic data privacy should take into account the unique societal implications of such data, including genomic information that is shared across related individuals. The theme’s work will be strengthened by the interdisciplinarity of its research team, which already includes researchers with backgrounds in computational genomics, electrical and computer engineering, nutrition, anthropology, business, and law.
Illinois, NIH host workshop on equity and diversity in genomic data science
The study of human genomics is inextricably linked to larger societal practices: how well diversity is represented in those who direct and conduct scientific research, how we balance data access with individual privacy, and the ways we group and describe both healthy and ill people. This September, the IGB had the privilege of collaborating with the National Human Genome Research Institute (NHGRI) to host a workshop examining these issues.
“Equity, Diversity, and Genomic Data Science” was a three-day workshop featuring presentations and discussions offered by Illinois faculty and invited experts from institutions across the U.S. Attendees were drawn from academia, industry, government, professional societies, advocacy groups, community-based organizations, and education groups. During the workshop, participants worked together to draft recommendations for the NHGRI’s 2020 strategic plan, which is currently under development.
“Genomics research is conducted in a very rigid manner that does not allow for community feedback or what community members feel are their problems (health, justice or otherwise),” said Ripan Malhi (CGRH/GNDP/IGOH/RBTE), an associate professor of anthropology who presented at the workshop. “Genomic research is conducted using concepts that trace back to colonial ideas that are not representative of human diversity we see in the world today.”
Conclusions from the workshop will be reflected in the NHGRI’s updated strategic plan, anticipated to be published in October 2020 to coincide with the 30th anniversary of the inception of the Human Genome Project.
For anemonefish, male-to-female sex change happens first in brain
The anemonefish is a gender-bending marvel. It starts out as a male, but can switch to female when circumstances favor a change, for example, when the only female present dies or disappears. In a new study, researchers found that the male-to-female sex-change occurs first in the fish’s brain and only later involves the gonads—sometimes after a delay of months or years.
The findings, reported in the journal Hormones and Behavior, describe the first known example of an animal undergoing a sex change in the brain before it occurs in the sex organs, the researchers said. The work was funded by private donations.
Professor of Psychology Justin Rhodes (GNDP) and his colleagues wanted to know whether the transition from male to reproductively viable female began first in the brain or gonads. They set up experiments in the laboratory where they paired male anemonefish together and tracked their development. In all, they followed 17 pairs of male anemonefish. Within minutes or hours of being put together in a tank, one of the two males emerged as dominant, and began to behave as a female would.
“We thought that once the fish figured out it was dominant, then immediately its gonads would start changing,” Rhodes said. “In fact, that’s not what happened. The gonads stayed male while the brain was changing.”
Illinois teams up with Anheuser-Busch for bee research
An unlikely partnership between Illinois and St. Louis-based Anheuser-Busch, LLC was formed in the hopes of raising money for bee research at Illinois. Anheuser-Busch has pledged $5,000 to The Healthy Bee Fund at Illinois along with donating $1 to the fund for every case sold of b, an alcoholic honey beverage that went on sale in the Northeast U.S. in March 2019.
Research on the plight of the western honey bee is as important as ever, with a variety of stress factors endangering the industrious pollinators. Gene Robinson (GNDP), Swanlund Professor of Entomology and Director of the IGB, spearheaded the honey bee genome sequencing project completed in 2006, just prior to the first reports of colony collapse disorder.
In 2018, Illinois was named a Bee Campus USA and is widely known for its educational outreach programs regarding bees and other pollinators. In 2009, the university opened the Pollinatarium, created by Robinson and head of entomology and Professor of Plant Biology May Berenbaum (GEGC/IGOH) as the first free-standing science center in the nation devoted to pollinators.
“We have a long track record in trying to figure out what the problems are that bees face and how to fix them,” Berenbaum said. “So this is a wonderful partnership.”
An apple a day keeps the doctor away—even so with apples that never brown. For several years, scientists have harnessed genomic technology to improve crop yield and quality through genetic modification of plant genomes, meeting the constant demand for food and fuel. Take a look inside a grocery store trip to learn how genomics plays a role in the food industry.
Illinois iGEM team aims to clean up crops
Herbicides are an integral component of modern farming. However, glyphosate, the most widely used herbicide in the United States and the main ingredient in formulations like Roundup™, was classified in 2015 as a probable carcinogen by the International Agency for Research on Cancer (IARC). Although scientific bodies still disagree on whether this substance poses a hazard, discovering pathways to facilitate its breakdown is an area of interest.
Enter Illinois’ International Genetically Engineered Machine (iGEM) team. A group of five undergraduate students, guided by several researchers at CABBI and the IGB, made this area the focus of their research project for the iGEM worldwide synthetic biology competition. Competitors design their own summer research projects and present their work in the fall at the “iGEM Jamboree” conference in Boston; Illinois’ team was awarded a silver medal for their achievements this year.
The team based their project around the degradation pathway found in Pseudomonas pseudomallei 22, a bacterium naturally found in the soil. The students inserted the relevant genes into E. coli, allowing these water-tolerant bacteria to degrade glyphosate into AMPA. The iGEM team decided to name their modified E. coli “Rounddown”. The freedom to design a project like this afforded learning opportunities for the team’s undergraduate members.
“I learned a lot of things that I wouldn’t have learned if I was in a normal lab,” said Sachin Jajoo, a member of the iGEM team and a junior in molecular and cellular biology. “In most labs, you’re just focused on doing one part of a project, but here, we did a whole experiment.”
Study provides framework for 1 billion years of green plant evolution
Gene sequences for more than 1100 plant species have been released by an international consortium of nearly 200 plant scientists, the culmination of a nine-year research project.
The findings, published in Nature, reveal the timing of whole genome duplications and the origins, expansions and contractions of gene families contributing to fundamental genetic innovations enabling the evolution of green algae, mosses, ferns, conifer trees, flowering plants and all other green plant lineages. The history of how and when plants secured the ability to grow tall, and make seeds, flowers and fruits provides a framework for understanding plant diversity around the planet including annual crops and long-lived forest tree species.
The study was authored by the One Thousand Plant Transcriptomes Initiative (1KP), a global collaboration examining the diversification of plant species, genes and genomes across the more than one-billion-year history of green plants dating back to the ancestors of flowering plants and green algae.
The study inspired a community effort to gather and sequence diverse plant lineages derived from terrestrial and aquatic habitats on a global scale. Over 100 taxonomic specialists contributed material from field and living collections around the globe. Founder Professor of Computer Science Tandy Warnow (BCXT/CGRH/IGOH) helped to develop new algorithms for inferring evolutionary relationships from hundreds of gene sequences for over 1000 species, addressing substantial heterogeneity in evolutionary histories across the genomes.
Illinois announces Center for Digital Agriculture
Illinois has announced the creation of the Center for Digital Agriculture (CDA), a new center that brings together agricultural producers, researchers, and industries to innovate on the technology that is transforming agriculture to feed and support a growing global population. The center seeks to develop digital solutions to agricultural roadblocks.
The CDA, which is a collaboration between the Grainger College of Engineering, the College of ACES, the NCSA, and the IGB, seeks to leverage Illinois’ historic land-grant pillars of agriculture and engineering and position both to work in tandem towards a digital future.
The new center will combine campus’ areas of expertise in engineering and agriculture to cement Illinois’ position as an innovator in this emerging field of agricultural technology, and develop solutions to agricultural problems that use digital technology.
“The CDA is a broad, interdisciplinary center founded to identify digital solutions for agricultural problems,” said Matt Hudson (CABBI/CGRH/GNDP), co-director of the CDA and professor in the Department of Crop Sciences. “This includes research, education and outreach activities. I am very excited about the potential of our new center for researchers, farmers, students and industry in Illinois and beyond.”
Study finds rising ozone a hidden threat to corn
Like atmospheric methane and carbon dioxide, ground-level ozone is on the rise. But ozone, a noxious chemical byproduct of fossil fuel combustion, has received relatively little attention as a potential threat to corn agriculture.
A recent study began to address this lapse by exposing a genetically diverse group of corn plants in the field to future ozone levels.
The study, reported in the journal Global Change Biology, found that some members of the corn family tree are more susceptible than others to yield losses under high ozone air pollution. Discovering the genetic underpinnings of those differences could help plant scientists develop ozone-resistant corn, the researchers said.
The NSF supported this work.
“Ozone enters plants the same way carbon dioxide does: It diffuses from the atmosphere into the leaf,” said Lisa Ainsworth (CABBI/GEGC), a USDA Agricultural Research Service scientist who led the research with Professor of Plant Biology Andrew Leakey (CABBI/GEGC); University of Florida Professor of Molecular Genetics and Microbiology Lauren McIntyre; and University of California, Davis Professor of Plant Sciences Patrick Brown.
The researchers used the Free Air Concentration Enrichment facility at Illinois to track the real-world consequences of higher atmospheric ozone levels in an agricultural field. They planted 45 hybrid corn plants representing all the major types of corn to look for variation in their responses to high ozone levels. They found that some hybrids were more sensitive to ozone stress than others.
Pineapple genome sequences hint at plant domestication in single step
As their Latin name indicates, pineapples are truly “excellent fruits”—and thanks to a recently completed genome sequencing project, researchers have gained a new understanding of how human agriculture has shaped the evolution of this and other crops.
An international team led by Professor of Plant Biology Ray Ming (GEGC) published their analysis of the genome of the red pineapple, a plant grown for fiber production and as an ornamental, in Nature Genetics. They also examined new sequence data for other key cultivars of pineapple grown for fruit, leading to new insights into the genetic responses of the plant to centuries of domestication and cultivation.
In particular, the work supported the hypothesis that domestication of crops that are propagated without using seeds, through cuttings or other means, can be domesticated in a single step.
“We have chosen major pineapple cultivars worldwide . . . to test our hypothesis of ‘one-step operation’ in domestication of clonally propagated crops,” Ming said. He highlighted this aspect of the researchers’ work as one of the primary goals of the study. “The co-existence of punctuated sexual reproduction and “one-step operation” in domestication of clonally propagated crops implies rapid domestication of clonally propagated crops is possible,” he said.
The work was supported by the Department of Science and Technology of Fujian Province, the National Natural Science Foundation of China, the Fuzhou Science and Technology, Fujian Agriculture and Forestry University, the Swiss National Science Foundation, and the NSF.
Scientists find ways to improve ‘crop of inequality’ cassava
Cassava is a “crop of inequality:” its starchy, tuberous roots sustain more than 500 million people in sub-Saharan Africa, yet cassava has been largely neglected by research and development compared to the staple crops of wealthier regions. Recently, Amanda De Souza and a team from Realizing Increased Photosynthetic Efficiency (RIPE) published a study in New Phytologist that identified opportunities to improve cassava yields, which have not increased for more than 50 years in Africa.
"For smallholder farmers who depend on tiny plots of land to feed and support their families, cassava is a 'backup' crop when other crops fail," De Souza said, explaining her use of the term ‘crop of inequality.’ "Especially for women, who represent a majority of smallholder farmers, cassava is a savings account. It is a resource they can harvest all year to pay for things like medical treatments and their children's school fees."
The recent study, led by Ikenberry Endowed University Chair of Crop Sciences and Plant Biology Stephen Long (BSD/CABBI/GEGC), examined factors that limit photosynthesis in 11 popular, or farmer-preferred, African varieties of cassava with the goal to eventually help cassava overcome photosynthetic limitations to boost yields. The researchers found that if they could improve the rate at which cassava leaves respond to changes in light levels throughout the day, its photosynthetic efficiency and thus crop yield could be significantly increased.
The RIPE project is an international effort to develop more productive crops by improving photosynthesis—the natural, sunlight-powered process that all plants use to fix carbon dioxide into carbohydrates that fuel growth, development, and ultimately yields. RIPE is supported by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government's Department for International Development (DFID).
Summer heats up with a week of science at IGB’s Pollen Power camp
Pollen Power camp, offered in July for the seventh consecutive year by the IGB, offers a quirky blend of plant science, technological exploration, and summer fun. The camp aims to introduce middle school girls to the world of plant biology research and provide strong female role models in STEM fields; this year’s attendees appreciated the full breadth of the camp’s offerings.
“What I for real liked about it was, you made new friends,” said eighth grader Janae Hall. “I really liked that part, getting to know people.”
Seventh grader Lauren Payton, a fellow camper, also enjoyed making new friends. “But I like succulents a lot, I love them so much, especially cacti. So when we went to the greenhouse earlier and we went into the room with all the succulents, I was in love,” she said.
The camp is co-organized by USDA Agricultural Research Service scientist Lisa Ainsworth (CABBI/GEGC) and Professor of Plant Biology Andrew Leakey (CABBI/GEGC), working with IGB Core Facilities and Outreach staff. Funding is provided in part by the NSF and the IGB. Outreach and Communication Specialist Adrienne Gulley directs the week-long camp, and female researchers in plant sciences, entomology, crop sciences, and related fields are recruited as counselors.
Highlights of the camp’s activities include imaging, modeling, and 3D printing representations of individual grains of pollen; pollinating research plants in the field; and constructing an evolutionary timeline of Earth’s flora. Campers also script, plan, and film newscasts on the past, present, and future climate.
Improved model better predicts crop yield, climate change effects
A new computer model incorporates how microscopic pores on leaves may open in response to light—an advance that could help scientists create virtual plants to predict how higher temperatures and rising levels of carbon dioxide will affect food crops, according to a study published in a special issue of the journal Photosynthesis Research.
“This is an exciting new computer model that could help us make much more accurate predictions across a wide range of conditions,” said Johannes Kromdijk (GEGC), who led the work as part of RIPE, which is supported by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research, and the U.K. Government’s Department for International Development. Kromdijk is a University Lecturer at the University of Cambridge.
The current work focused on simulating the behavior of what are known as stomata—microscopic pores in leaves that, in response to light, open to allow water, carbon dioxide, and oxygen to enter and exit the plant.
“We’ve known for decades that photosynthesis and stomatal opening are closely coordinated, but just how this works has remained uncertain,” said Stephen Long (BSD/CABBI/GEGC), Ikenberry Endowed University Chair of Crop Sciences and Plant Biology. “With this new computer model, we have a much better tool for calculating stomatal movements in response to light.”
Yield-boosting stay-green gene identified from 118-year-old corn
A corn gene identified from a 118-year-old crop experiment on the Illinois campus could boost yields of today’s elite hybrids with no added inputs. The gene, identified in a recent Plant Biotechnology Journal study, controls a critical piece of senescence, or seasonal die-back, in corn. When the gene is turned off, field-grown elite hybrids yielded 4.6 bushels more per acre on average than standard plants.
Dating back to 1896, the Illinois experiment was designed to test whether corn grain composition could be changed through artificial selection, then a relatively new concept.
“One of the things that was noted as early as the 1930s was that the low-protein line stays greener longer than the high-protein line. It’s really obvious,” says Stephen Moose (BSD/CABBI/GEGC), professor of crop sciences and co-author of the study.
Staying green longer into the season can mean greater yield since the plant continues photosynthesizing and putting energy toward developing grain. But until now, no one knew the specific genes responsible for the stay-green trait in corn. The present work to identify these genes was performed in collaboration with DuPont Pioneer, which is now part of Corteva Agriscience™.
"The stay-green trait is like a ‘fountain of youth’ for plants because it prolongs photosynthesis and improves yield,” says Anne Sylvester, a program director at the NSF, which provided additional funding for this research. “This is a great basic discovery with practical impact."
Scientists transform tobacco into factory for high-value proteins
For thousands of years, plants have produced food for humans; with genetic tweaks, they can also manufacture useful proteins, including antibodies and vaccine components. Now, plants are also being used to produce cellulase, an enzyme that is used in food processing and biofuel production from waste.
A team of researchers from Cornell University and Illinois announced in Nature Plants that crops can cheaply manufacture proteins inside their cellular power plants called chloroplasts—allowing the crops to be grown widely in fields rather than restrictive greenhouses, with no cost to yield.
Typically, these proteins are produced using cell cultures of yeast or other microbes. In this study, the team engineered tobacco to produce cellulase enzymes in the crop’s chloroplasts, intracellular structures that convert sunlight and carbon dioxide into sugar via photosynthesis. Chloroplasts naturally contain many copies of a vestigial genome that can produce an enormous amount of protein.
“Tobacco—as a crop bred to produce large quantities of leaves—could be a factory for good,” said Stephen Long (BSD/CABBI/GEGC), Ikenberry Endowed University Chair of Crop Sciences who co-led the USDA-funded study.
“Chloroplasts are not present in pollen, making it possible to cultivate this engineered tobacco in fields and transform land once used for cigarette and cigar production into protein factories that can improve our health and industrial efficiency.”
A warming Midwest increases likelihood that farmers will need to irrigate
If current climate and crop-improvement trends continue into the future, Midwestern corn growers who rely on rainfall to water their crops will need to irrigate their fields, a new study finds.
The study, reported in the journal Ecosphere, calculated the extent to which hotter conditions expected by mid century will draw more moisture out of corn plants, said Evan DeLucia (CABBI director/GEGC), G. William Arends Professor of Integrative Biology, and Baum Family Director of the Institute for Sustainability, Energy, and Environment (iSEE), who led the study.
“If you add to this the decades-old trend toward bigger, more productive corn plants, you see an overall increase in water use and water loss through plant leaves—without comparable increases in rainfall to counter the deficit,” DeLucia said.
Precipitation is not expected to increase enough in the Midwest to compensate for the drying conditions of the warmer atmosphere.
Strategies include minimum tillage and mulches which can reduce the rate of water loss from the soil and genetically modifying plants to sequester more chlorophyll in their lower leaves and less in the top. A research effort to do this is underway in the laboratory of Donald Ort (GEGC theme leader/BSD/CABBI), Robert Emerson Professor of Plant Biology and Crop Sciences.
The DOE and NASA supported this research.
Scientists stack algorithms to improve predictions of yield-boosting crop traits
Hyperspectral data comprises the full light spectrum; this dataset of continuous spectral information has many applications from understanding the health of the Great Barrier Reef to picking out more productive crop cultivars. To help researchers better predict high-yielding crop traits, a team of researchers have stacked together six high-powered, machine learning algorithms that are used to interpret hyperspectral data; they demonstrated that this technique improved the predictive power of a recent study by up to 15 percent, compared to using just one algorithm.
In this new study, published in Frontiers in Plant Science, the team improved previous predictions of photosynthetic capacity by as much as 15 percent using machine learning, where computers automatically applied these six algorithms to their dataset without human help.
“By applying the expertise of data analysts to address the needs of plant physiologists like myself, we ended up refining a technique that is relevant to other hyperspectral datasets,” said Professor of Plant Biology Carl Bernacchi (CABBI/GEGC), RIPE research leader and scientist with the USDA Agricultural Research Service.“The next step is to test more stacked machine learning algorithms on datasets from many more crop species and explore the utility of this technique to estimate other parameters, such as abiotic stresses from drought or disease.”
RIPE is supported by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID).
High-throughput method helps measure photosynthetic improvements for production boost
An international team is using advanced tools to develop crops that give farmers more options for sustainably producing more food on less land. In a special issue of the journal Remote Sensing of Environment, scientists have described a new technology that can quickly scan an entire field of plants to capture improvements in their natural capacity to harvest energy from the sun.
A faster, or “higher-throughput” method, called spectral analysis, analyzes the light that is reflected back from leaves to predict photosynthetic capacity in as little as 10 seconds.
“While there are still hurdles ahead, spectral analysis is a game-changing technique that can be used to assess a variety of photosynthetic improvements to single out the changes that are most likely to substantially and sustainably increase crop yields,” said RIPE executive committee member Christine Raines, Professor of Plant Molecular Physiology at the University of Essex. “These tools can help us speed up our efforts to develop high-yielding crops for farmers working to help feed the world.”
RIPE, which is led by Illinois, is engineering crops to be more productive by improving photosynthesis, the natural process all plants use to convert sunlight into energy and yield. RIPE is supported by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID).
Reducing the energy requirement for carbon dioxide waste conversion into resources
Surplus industrial carbon dioxide creates an opportunity to convert waste into a valuable commodity. Engineers have assessed the technical and economic feasibility of a new electrolysis technology that uses a cheap biofuel byproduct to reduce the energy consumption of the waste-to-value process by 53 percent.
The new findings were published in the journal Nature Energy.
Conversion of carbon dioxide to chemicals like ethylene for plastics is possible through a process called electrochemical reduction. Typically, a stream of carbon dioxide gas and a fluid electrolyte move through an electrolysis cell that breaks the carbon dioxide down into molecules like ethylene and oxygen from water on the anode.
“About 90 percent of the energy required in conventional carbon dioxide reduction is used up by the oxygen-producing, anode side of an electrolysis cell,” said Paul Kenis (RBTE), Professor of Chemical and Biomolecular Engineering. “But there is no big market for the excess oxygen, so 90 percent of the energy is essentially wasted.”
To test carbon dioxide conversion to a carbon neutral or negative budget, the researchers examined the cost and energy consumption for the production cycle of the waste-to-value process. The analysis concluded that the prospects of carbon dioxide reduction, in terms of carbon dioxide emissions and economics, can drastically improve by looking beyond conventional anode reactions.
The International Institute for Carbon Neutral Energy Research; Japanese Ministry of Education, Culture, Sports, Science and Technology; Dow Chemical Company; and the Glenn E. and Barbara R. Ullyot graduate fellowship supported this research.
Extension of Crops in silico project
The Crops in silico (Cis) project has received a $5 million grant from the Foundation for Food and Agriculture Research (FFAR) to continue building a computational platform that integrates multiple models to study a whole plant virtually.
With the global population increasing and the climate continuing to change, understanding how crops respond and adapt to environmental changes is needed to address current and future food insecurity. Developing crops using traditional methods is research, labor and cost intensive. However, Cis allows researchers to quickly determine and test characteristics that help crops thrive in specific environments. This modeling allows researchers to conduct more experiments than can be realistically achieved in a field.
Researchers have extensive knowledge about models depicting individual processes that drive plant growth and development, and how plants use resources. Until now, researchers have yet to combine this knowledge into whole plant models that mimic biology. This project integrates diverse computational models that allow researchers to determine how crops respond to environmental changes at all biological levels, from cellular to ecosystem-level interactions.
“The Cis approach has already identified opportunities that resulted in successful field trials by optimizing single processes like photosynthesis or single organs like root architecture,” said Amy Marshall-Colón (CABBI/GEGC), Assistant Professor of Plant Biology and the Principal Investigator for the new four-year grant. “By scaling up our work to whole plants and fields, we can move years ahead in optimizing plants for different growing conditions.”
Siberian Miscanthus plants surpass main bioenergy variety in cold conditions
Photosynthesis drives yields but in cold conditions, the process takes a hit. Miscanthus is a popular, sustainable, perennial feedstock for bioenergy production that thrives on marginal land in temperate regions.
A new study in GCB Bioenergy from Illinois and Aarhus University assessed Miscanthus collected on a Siberian expedition to identify three new accessions with exceptional photosynthetic performance in chilling temperatures that outstrip the industry favorite.
Today, a sterile clone of the hybrid of Miscanthus sacchariflorus and Miscanthus sinensis called Miscanthus x giganteus ‘Illinois’ is considered one of the best bioenergy feedstocks available due to its ability to thrive on marginal land, withstand chilling temperatures, and produce 59 percent more biomass than corn.
Scientists from Illinois, the USDA, and Russia’s N.I. Vavilov Research Institute of Plant Industry (VIR) led an expedition to Eastern Siberia - the coldest region where Miscanthus grows - to find wild populations of M. sacchariflorus that could be used to breed improved M. x giganteus hybrids.
“Now I am working on breeding these highly cold-tolerant accessions with other forms of Miscanthus in order to form new hybrid cultivars that hopefully will be more effective, productive, and resilient in the field,” said Erik Sacks, Associate Professor of Crop Sciences at Illinois. “But the ultimate goal of our work is to provide consumers with a sustainable, plant-derived source of energy.”
This work was funded in part by the USDA Agricultural Research Service and the Office of Biological and Environmental Research.
Rising temperatures may safeguard crop nutrition as climate changes
Recent research has shown that rising carbon dioxide levels will likely boost crop yields, but at the cost of nutrition. A new study in Plant Journal from Illinois, the USDA Agricultural Research Service (ARS), and Donald Danforth Plant Science Center suggests that this is an incomplete picture of the complex environmental interactions that will affect crops in the future—and rising temperatures may actually boost nutrition but at the expense of lower yields.
The study was led by Ivan Baxter, principal investigator at the Danforth Center, and co-led by Assistant Professor of Plant Biology and Crop Sciences Carl Bernacchi (CABBI/GEGC), also a scientist at the USDA-ARS. Funding from the USDA supported this work.
The team tested the soybeans in real-world field conditions at the Soybean Free-Air Concentration Experiment (SoyFACE), an agricultural research facility at Illinois that is equipped to artificially increase carbon dioxide and temperature to futuristic levels.
Two years of field trials showed that increasing temperatures by 3 degrees Celcius may help preserve seed quality, offsetting the effects of carbon dioxide that make food less nutritious. In soybeans, elevated carbon dioxide levels decreased the amount of iron and zinc in the seed by about 8 to 9 percent, whereas increased temperatures had the opposite effect.
“This study shows that a trade-off between optimizing yields for global change and seed nutritional quality may exist,” said Bernacchi.
Engineered shortcut to photosynthetic glitch leads to enhanced crop growth
Plants convert sunlight into energy through photosynthesis; however, most crops on the planet are plagued by a photosynthetic glitch. To deal with the glitch, plants have evolved an energy-expensive process called photorespiration that drastically suppresses their yield potential. Researchers from Illinois and USDA Agricultural Research Service reported in the journal Science that crops engineered with a photorespiratory shortcut are 40 percent more productive in real-world agronomic conditions.
Scientists have engineered alternate routes to replace the circuitous and complicated photorespiration pathway, drastically shortening the trip and saving enough resources to boost plant growth by 40 percent. The team tested their hypotheses in tobacco and are now translating these findings to boost the yield of soybean, cowpea, rice, potato, tomato, and eggplant.
“Much like the Panama Canal was a feat of engineering that increased the efficiency of trade, these photorespiratory shortcuts are a feat of plant engineering that prove a unique means to greatly increase the efficiency of photosynthesis,” said RIPE Director Stephen Long (BSD/CABBI/GEGC), Ikenberry Endowed University Chair of Crop Sciences and Plant Biology at Illinois.
This landmark study is part of Realizing Increased Photosynthetic Efficiency (RIPE), an international research project that is engineering crops to photosynthesize more efficiently to sustainably increase worldwide food productivity with support from the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID).
The Carl R. Woese Institute for Genomic Biology (IGB) was founded in 2007 with the intention of facilitating genomic research across the campus. IGB members are drawn from many schools and departments, including biology, chemistry, physics, engineering, sociology, and business. What unites them is a shared vision of what a genomics-based approach can achieve: a healthier global population, increased food and fuel security, a toolbox of genomic technologies to meet future societal challenges, and a deep knowledge of the diversity of life on our planet.
Kleinmuntz Center off to a strong start in inaugural year
In its inaugural year of operation, the Catherine and Don Kleinmuntz Center for Genomics in Business and Society significantly enhanced and accelerated the broader impact of the IGB’s research and innovation by providing unique opportunities for public engagement and social impact.
The Kleinmuntz' generous support allowed IGB members to share their research and its implications with professional groups and the broader public, reaching roughly 3,500 people with educational events. Events made possible by the Center this year included a World of Genomics, IGB’s most heavily attended public program, offered in partnership with the National Academy of Sciences; a yearlong professional development workshop offered to IGB graduate students and postdoctoral researchers; and Genomics For™ events offered to several professional groups.
The Center also launched the Mikashi Awards, a proof-of-concept program supporting IGB faculty innovations during their pre-commercialization phase. Donald Biggar Willett Professor of Engineering Brian Cunningham (ONC-PM leader/MMG) and Kenneth L. Rinehart Jr. Endowed Chair in Natural Products Chemistry Paul Hergenrother (ACPP leader/MMG), were each awarded a $50,000 award in the first year. Their proposals focus on aspects of cancer research, one by developing a new liquid biopsy technology called activate capture + digital counting (AC+DC) Assay Technology, and the other a novel therapeutic strategy for treating cancerous liver lesions, respectively.
The IGB is extremely grateful to have partnered with the Kleinmuntz Center. The support, guidance, and leadership of Catherine and Don Kleinmuntz have made possible these and other impactful professional and community activities.
IGB forms external advisory Leadership Council
The IGB undergoes regular, external review from leaders in academia, industry, and government to assess all aspects of the institute. The External Advisory Board that has previously been in place has been divided into two separate boards to better evaluate and advise on the scientific and business facets of the IGB. The Science Advisory Board reviews the research portfolio, while the Leadership Council advises on IGB’s other endeavors.
Composed of prominent individuals with expertise in the business world, the Leadership Council will review and guide our efforts to encourage business development, commercialization, and philanthropy, in support of the IGB’s community engagement goals. The IGB is grateful to the members of the council for devoting their time and expertise towards the betterment of our efforts in these areas.
Scientists partnering with indigenous communities for genomics research
Scientists are interested in studying the DNA of Indigenous populations because it can lead to discoveries such as when their ancestors first arrived on the continent and where they originally came from. Genomics research can also shed light on the genetic basis of disease.
But early in his career, anthropologist Ripan Malhi (CGRH/GNDP/IGOH/RBTE) said he recognized there was a lack of trust between scientists and Indigenous communities. In 2011, he launched the SING (Summer Internship for Indigenous People in Genomics) program in an effort to change that. The program brings together 15 to 20 Indigenous scientists and members of their communities every year for a week of hands-on training in genomics.
Since SING launched, Malhi said more than 120 participants have received hands-on training in genomics. SING alumni and faculty have also worked to publish ethical guidelines for scientists on how to approach genomics research in a way that is sensitive to the interests of Indigenous people and can benefit their communities. Other countries, including Canada and New Zealand, have now launched SING programs as well.
Ethics Center working to develop leadership curriculum for HHMI
Researchers from Illinois’ National Center for Professional & Research Ethics (NCPRE) are developing a new curriculum for the HHMI, a nonprofit research organization that employs scientists at more than 60 universities, hospitals, and other research institutions nationwide. The curriculum will support HHMI scientists in creating a culture that encourages the highest levels of excellence and productivity, by coaching them in specific strategies and behaviors for dealing with ethical challenges. The $2.6 million initiative is called “Labs That Work … For Everyone.”
“The work of science is team-based, yet when faculty are given responsibility for managing laboratories and developing the careers of their students, they are given limited support or preparation for those roles and responsibilities,” said Professor Emerita of Business C.K. Gunsalus, director of the NCPRE.
“This initiative will address that void by supporting leadership development for lab leaders—and for their lab members, who are the research leaders of the future. It will cover ethical laboratory and scientific practices, improving cultural competence, and helping researchers to work together effectively, including dealing with conflicts, difficult decisions, and interpersonal problems.”
NCPRE plans to pilot two modules in 2021 for HHMI, using the IGB as a parallel testbed. The innovative structure of the IGB, which leverages interdisciplinary team science strategies in life science research to tackle grand societal challenges, makes the institute an ideal participant. Pending the outcome of this early work, a full curriculum for HHMI scientists could follow.
World of Genomics arrives at the National Academy of Sciences Building
The IGB partnered with the National Academies of Sciences, Engineering, and Medicine (NASEM) to bring Family Science Day at the NAS Building: DecisionTown in the World of Genomics in April 2019, combining the largest outreach event World of Genomics with NASEM's engaging DecisionTown interactive public experience.
Held in Washington, D.C., DecisionTown in the World of Genomics invited families to visit and see how the decisions they make every day are influenced by science, engineering, and medicine.
More than 17 interactive spaces offered activities centered on issues facing DecisionTown as it planned for the future. Visitors participated in fun, creative, and engaging hands-on activities for kids and adults, including a health-themed food court, an interactive weather station, a courtroom where they learned about eyewitness identification, and a medical center explaining DNA sequencing and personalized health.
The event was supported by NASEM and the IGB.
Neurobiologist Leslie Vosshall gives IGB Distinguished Public Lecture
Leslie Vosshall, Robin Chemers Neustein Professor, Head of the Laboratory of Neurogenetics and Behavior, and Director of the Kavli Neural Systems Institute at The Rockefeller University, spoke as part of the IGB's Genomics and Society Distinguished Public Lecture series on April 2019 at the Alice Campbell Alumni Center. Her talk was entitled "Thirst for Blood: Mosquito Neurobiology and Behavior."
Working with the dengue and Zika vector mosquito, Aedes aegypti, and human subjects, Vosshall’s research has yielded new knowledge about how sensory stimuli are perceived and processed.
Vosshall’s lab identified the genes that mediate odor and carbon dioxide perception in insects, including orco, a member of the odorant receptor gene family. The researchers pinpointed Orco as a potential target for chemical inhibitors, which could potentially be used to fight mosquito-transmitted infectious diseases.
The Vosshall lab has also developed genome-editing techniques for targeted mutagenesis in Ae. aegypti using the CRISPR-Cas9 system to enable the tracing of neural pathways and functional imaging of circuits activated by sensory cues.
Mosquitoes transmit deadly infectious diseases to humans both in the United States and around the world, and understanding the rules by which these animals target human hosts will enable the development of tools to reduce their capacity to spread disease.
IGB and SciLine team up for Genomics for Journalists workshop
Imagined as a sort of science “boot camp” for reporters, Genomics for Journalists, a multi-day workshop designed to arm journalists with the knowledge and context they need to cover newsworthy science, health, and environment issues with confidence, was offered this spring by the IGB in collaboration with the American Association for the Advancement of Science.
Genomics is becoming increasingly central to advances in health, agriculture, and environmental science, as well as law enforcement and criminal justice.
Genomics for Journalists was designed for working reporters and covered the basic science of genomics, including exploration of advances in the field that are changing the way diseases are diagnosed and treated, novel crop varieties are developed, forensic evidence is interpreted, and new materials and fuels are being produced. The workshop was open to science journalists nationwide with any level of experience, including those without deep backgrounds in science.
The workshop included faculty presentations, panel discussions, networking opportunities, and hands-on scientific laboratory experiences. Topics covered include genomics, genealogy, and criminal justice; genomic editing in health, medicine, and agriculture; direct-to-consumer genetic testing; diet, microbiome, and health; ecosystems and environmental genomics; and the ethical, legal, and social issues raised by genomic advances. The workshop also held lab exercises featuring hands-on experience with editing bacterial genomes.
Genomics for Journalists was jointly offered by SciLine, an independent, nonpartisan, philanthropically supported service hosted by the nonprofit American Association for the Advancement of Science, and the IGB.
Donovan named to 2020 dietary guidelines advisory committee
Sharon Donovan (MME), Professor of Food Science and Human Nutrition and the Melissa M. Noel Endowed Chair in Nutrition and Health, has been appointed to the USDA’s 2020 Dietary Guidelines Advisory Committee. U.S. Secretary of Agriculture Sonny Perdue and U.S. Health and Human Services (HHS) Secretary Alex Azar announced the appointment of 20 nationally recognized scientists to serve on the committee to ensure America’s dietary guidance reflects the latest science.
Their review, along with public and agency comments, will help inform the USDA and HHS’ development of the 2020-2025 Dietary Guidelines for Americans (DGAs), which are updated every five years.
Donovan, a registered dietician, conducts basic and translational research in the area of pediatric nutrition. Ongoing work in Donovan’s lab focuses on optimizing intestinal and cognitive development of neonates, development of the gut microbiome, and prevention of childhood obesity and picky eating habits of children.
“Sharon Donovan’s contribution to pediatric nutrition research is advancing our understanding of some of the most pressing health issues for children and families, including promoting a healthy gut, brain, and microbiome through diet, and preventing childhood obesity,” said Kim Kidwell, dean of the College of ACES at Illinois. “I am thrilled that she has been appointed to this committee and I know that her participation in informing dietary guidelines for Americans will help to improve lives.”
Award-winning author and columnist Carl Zimmer speaks on new book
New York Times columnist and renowned author Carl Zimmer gave a lecture on his newest book, titled She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity, in March 2019. The book was named a Notable Book of the Year by the New York Times Book Review. It was also selected for Publisher’s Weekly Best Ten Books of 2018, the 2018 shortlist for Baillie-Gifford Prize for Nonfiction, and named best science book of 2018 by The Guardian. The event, sponsored by the Department of History and the IGB, was followed by a reception and book signing.
In his lecture, Carl Zimmer redefined heredity, weaving together historical and current scientific research, exemplary original reporting, and his own experience as a parent of two daughters.
Introducing audiences to the not-too-distant future, Zimmer explored ways in which DNA editing with the powerful new CRISPR tool may change our world—and ourselves. He fearlessly examined controversial topics (Do races actually exist? Is success inherited?) in light of current advances in DNA analysis, and discussed the ways in which heredity has historically been used to justify racism and social inequality.
As we go about our daily lives, we are faced with endless decisions, both large and small. The choices we make are influenced by a multitude of factors. But how often are we aware of the science that lies behind the options we are presented with and the thought processes we use to weigh them?
In this year’s Annual Report, you will be transported into everyday scenarios that reveal the interconnectivity between genomics and the world around us. From an ordinary trip to the grocery store to a hike in the park, you will uncover the science behind familiar objects and discover that science permeates everyday lives.