IGB_AR_PDF

A
2014 ANNUAL REPORT
CARL R. WOESE INSTITUTE FOR GENOMIC BIOLOGY

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Director's message
1-2
1
People
73
Giving and donor roll
77
About
3-5
Mining
Microbial
Genomes
Genomic
Ecology of
Global
Change
Center for
Nutrition,
Learning, and
Memory
Themes and partnerships
5
Numbers in 2014
74-76
TABLE OF CONTENTS
Stories from 2014
8-71
December 8-15
November 16-20
October 21-23
September 24-29
August 30-33
July 34-40
June 41-47
May 48-51
April 52-58
March 58-62
February 62-67
January 68-71

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“Knowing this, society will come to see that
biology is here to understand the world . . .
Biology's primary job is to teach us. In that
realization lies our hope of learning to live
in harmony with our planet.”– Carl R. Woese,
“A New Biology for a New Century,”
Microbiology and Molecular Biology Reviews
These were the closing words of a review written by renowned Illinois microbiologist
Carl R. Woese and published in 2004, eight years before his death. Around the same
time that Woese wrote these words, he also wrote to university administration in
support of an initiative to form a new institute, one that united scientists across
campus in the dawning era of genomic research. In 2006, this initiative culminated
in the Institute for Genomic Biology (IGB). This year, to recognize Woese’s paradigm-
altering achievements in biology, we have renamed our institute in his honor.
Since its foundation, the IGB has been committed to great science, and to addressing
societal challenges—two aspects of a single comprehensive mission. The world of
research and the world at large are inextricably linked, and they mirror each other
in the changes they experience over time. In scientific research and in society, new
technologies have allowed us to break down geographical barriers and increase
connectedness; they have led to a shift toward Big Data and bigger goals.
This year, we have seen these trends reflected in the accomplishments of the IGB’s
academic partnerships. A partnership between researchers at the Mayo Clinic and at
Illinois, including many IGB members, is poised for great achievements; a $9.34M grant
from the NIH to establish a Center of Excellence will support them as they create a
MORE
DIRECTOR'S MESSAGE
Gene E. Robinson

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revolutionary computing analytical tool. Other joint undertakings in genomic Big Data
came to full fruition, including the efforts of two international consortia that used
datasets of an unprecedented scale to clarify the evolutionary origins of modern bird
and flowering plant species.
The collaborations that make our work possible extend beyond the traditional
boundaries of academia. Citizen scientists working in the labs of IGB members, as
well as many others across campus, are making important contributions to research.
Many of these individuals participate through the Osher Lifelong Learning Institute,
a learning community for people over the age of 50. Involvement in science brings
new passion and interest to the lives of those who volunteer in these roles, and their
presence adds to the diverse skill sets and depth of knowledge being applied to
important research challenges.
Established programs like this one help us maintain our strong ties to the community.
As the ways in which our society shares and receives information continue to evolve,
we also continue to explore new forms of public engagement. This summer, IGB
members and their collaborators released a popular new massively open online
course, or MOOC. Other IGB members shared their work and ideas via the blogs and
websites of national-level organizations. They also engaged public interest through
diverse media forms including videos, images, and music.
We are proud that our members bring energy, ingenuity, and dedication to every
aspect of our institute’s mission. Those qualities have resulted in findings and
innovations that have great potential to positively impact our society’s welfare. Our
work this year included the development of new ways to discover antibiotics, and
to understand their actions; new understanding of how the genome controls the
incredible healing potential of stem cells; and new models to understand how the
environment is impacted by human activities, and how we can protect it.
In the spirit of connectedness, of investigating novel ideas and forms of
communication, we are also including an extra facet to this year’s annual report. In
the pages that follow, we have included some stories of events that brought our
global society together—in sadness, in triumph, or in exploration. The connections
between these stories and our own research help us reflect on what we have
accomplished, and where we need to go from here. This year brought us a new name,
new avenues of research, and a renewed sense of purpose.
MORE
Gene E. Robinson
DIREC TOR, CARL R. WOESE INSTITUTE FOR GENOMIC BIOLOGY

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Seven years ago, the University of Illinois
founded the Carl R. Woese Institute for
Genomic Biology (IGB), a visionary facility
that brought together the university’s
diverse expertise to address formidable
challenges. Today, this experiment
in transdisciplinary research forms
collaborations that yield many discoveries
and scientific advancements, continuing to
support the hypothesis that the whole is
greater than the sum of its parts.
IGB members are drawn from a broad range of disciplines, including life sciences, social
sciences, engineering, law and business. IGB faculty and affiliate members remain an
integral part of home departments while pursuing collaborative research projects at the
IGB. Theme leaders help coalesce members into thematic research groups.
The IGB research portfolio is diversified, but its goal is singular: advance life sciences
research to benefit society. One theme is seeking the origin of life, another is
solving the global energy crisis, while others are developing regenerative therapies,
personalizing cancer treatments, and investigating how the brain influences behavior.
These groups are housed in large shared laboratories, enabling the sharing of
equipment and ideas.
IGB research themes are not permanent; they are expected to evolve. Every five years,
an external advisory board reviews the relevance and progress of IGB themes. Anyone
can propose new themes to explore developments in biological research and emerging
problems in health, agriculture, and the environment.
ABOUT THE IGB
MORE
Integrating Diverse
Backgrounds
Problem-oriented
Research
Dynamic Research Focus

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Through innovative outreach and education programs, the IGB invites people of
all ages to learn about and participate in transdisciplinary research. The IGB hosts
accessible, hands-on educational activities for children and their families, as well as
workshops and events designed to engage specific groups in meaningful and relevant
genomic research.
The mission of the IGB is to advance life science research at the University of Illinois at
Urbana-Champaign and to stimulate bio-economic development in the state of Illinois.
MORE
IGB Research Themes
IGB Strategic Partnerships
Biocomplexity
(BCXT)
Biosystems Design
(BSD)
Business, Economics and Law
of Genomic Biology (BIOBEL)
Cellular Decision Making in
Cancer (CDMC)
Genomic Ecology of Global
Change (GEGC)
Gene Networks in Neural &
Developmental Plasticity
(GNDP)
Mining Microbial Genomes
(MMG)
Regenerative Biology & Tissue
Engineering (RBTE)
Center for Nutrition, Learning,
and Memory (CNLM)
Energy Biosciences
Institute (EBI)
Explores the origin of life and the behavior of
biological systems.
Uses engineering concepts to guide the study,
design and construction of biological systems.
Examines the financial and legal issues related
to genomic technology.
Works to better understand how cancer alters
the inner workings of cells.
Studies the intersection of genomics and global
climate change.
Investigates how biological diversity is
affected by the structure and function of gene
regulatory networks.
Discovers small molecules that might provide
new medical solutions.
Studies the replacement or regeneration of
tissues and organs.
Determines the impacts of nutrition on
learning and memory in the human brain. In
addition to the IGB, the Center partners with
Abbott Nutrition and the Beckman Institute for
Advanced Science and Technology.
Addresses the global energy challenge through
a unique public-private collaboration, originally
funded by a 10-year, $500 million grant from
BP. The partnership includes the University of
California, Berkeley; the University of Illinois
at Urbana-Champaign; the Lawrence Berkeley
National Laboratory; and BP.
Where Science
Meets Society

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CONCEPTUAL CONNECTIONS ACROSS IGB THEMES AND PARTNERSHIPS
Mining
Microbial
Genomes
Cellular
Decision
Making in
Cancer
Biocomplexity
Regenerative
Biology
& Tissue
Engineering
Business,
Economics
and Law
of Genomic
Biology
Gene Networks
in Neural &
Developmental
Plasticity
Center for
Nutrition,
Learning, and
Memory
Energy
Biosciences
Institute
TRANSLATIONAL MEDICINE COMPLEX NET WORKS ENGINEERING SOLUTIONS
ENVIRONMENT AND ECOSYSTEMS NUTRITIONAL HEALTH AND FOOD SECURITY
MENTAL AND EMOTIONAL HEALTH
Genomic
Ecology of
Global
Change
Biosystems
Design

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The IGB believes that education is the most powerful
tool to inspire progress. Providing and participating
in educational opportunities is key to achieving the
Institute’s mission.
With visionary researchers and state-of-the-art
technology, the IGB has the potential to feed a growing
population, treat terrible diseases, provide sustainable
fuel, and address other societal challenges.
The IGB strives not only to benefit the community through
research, but to engage it through outreach and education
initiatives. These programs invite people to connect with
the research that may one day impact their lives.
The IGB is a part of the global community; work at the
Institute affects, and is affected by, circumstances and
events around the world.
IGB faculty are united by their determination to
improve the status quo. Their collaborations with each
other, as well as other researchers from across the
world, drive innovation and discovery.
PARTNERSHIPS
EDUCATION
RESEARCH
COMMUNITY
WORLD NEWS
This annual report is a chronicle of news and events
in 2014. The IGB news stories feature the four pillars
of the Institute’s mission, denoted by the icons
below. Interspersed with these stories are world
news items that highlight connections between
ongoing IGB research and current global issues.
Combined, these stories illustrate that the IGB is the
vertex where science meets society.

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A year is defined by the passing of
days, the changing of seasons. But
each year is punctuated by events
that break our routines, inspiring
us to consider our roles in society.
The Carl R. Woese Institute for
Genomic Biology is where science
meets society, where we employ
genomics to realize our vision of a
healthier, more prosperous world
in the coming years.

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18 December 2014
Carl R. Woese:
An indivisible
part of our
history
go.illinois.edu/IGBrenamed
Image: Jason Lindsey
go.illinois.edu/Lindsey
On December 18, 2014, the Institute for
Genomic Biology was renamed in honor of
Carl R. Woese, a microbiology professor
who changed the course of science with
his discovery of a third major branch of the
tree of life.
“We are now the Carl R. Woese Institute for Genomic Biology,” said Swanlund Chair of
Entomology and IGB Director Gene Robinson. “By changing our name, we honor an
individual who has made legendary contributions to science, who served as an Illinois
microbiology faculty member for nearly 50 years and who, as a founding member of
the IGB, paved the way for us to emerge as a leader in advancing life sciences.”
In 1977, Woese and his colleagues overturned a universally held assumption about
the basic structure of the tree of life. They discovered that there were three distinct
branches, or “domains,” of life—not two, as had been previously thought. The new
class of organisms they discovered looked superficially like bacteria, but their
12

9
evolutionary history was completely different. These microbes are now known as
archaea (are-KEY-uh), and are genetically and evolutionarily as distinct from bacteria
as plants and animals are.
Woese made his discovery by comparing the molecular sequences associated with
the cellular machinery that translates the genes of individual organisms into proteins.
In doing so, he pioneered the practice of using molecular sequences to gain insights
into biology, an approach that has now become standard in biology and is the
precursor of today’s genomics. Woese passed away in late 2012.
“Carl Woese’s discoveries in evolutionary biology have had revolutionary implications
for all branches of biology, and no more so than in the emerging science of genomics,
which owes its foundation to Carl’s work,“ said Nigel Goldenfeld (BCXT Theme Leader),
a Swanlund Endowed Chair Professor of Physics and longtime colleague, collaborator
and friend of Woese. “It is very fitting indeed that the IGB will forever be associated
with his name, and it will be an inspiration to all who work here.”
“Since our dedication in 2007, this Institute has carried on the spirit of discovery,
dedication and determination so well-embodied by Carl,” Robinson said. “His legacy is
now an indivisible part of our history.”
DECEMBER

10
NASA’s Curiosity rover recorded a burst of
methane lasting more than two months, an
indication that the Red Planet may support
life after all. The discovery of carbon-based
organic molecules is more evidence that
Mars may support life.
“There are two possible explanations for this methane,” said Nigel Goldenfeld (BCXT
Theme Leader) (see June 9), a Swanlund Endowed Chair Professor of Physics. “One is
life itself. The other is a geological process known as serpentinization. In fact, they
are connected.”
16 December 2014
Methane
suggests that
Mars may
harbor life
astrobiology.illinois.edu
Image: NASA, ESA, and
the Hubble Heritage Team
(STScI/AURA)
Congratulations to Rashid Bashir (RBTE),
elected to be a Fellow of the International
Academy of Medical and Biological
Engineering. The honor goes to researchers
from across the world who have made
"outstanding contributions to the profession
of medical and biological engineering."
December 2014
Department of
Bioengineering, College
of Engineering
17 December 2014 Nigel Goldenfeld
@NigelGoldenfeld
#CuriosityRover finds methane on #Mars! Life or serpentinization? Or both?
http://nyti.ms/1A6D4Bu http://bit.ly/1zsp6Kg #astrobiology

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The Institute for Universal Biology (IUB), a NASA Astrobiology Institute housed
within the Biocomplexity (BCXT) research theme, is characterizing the fundamental
principles governing the origin and evolution of life (see July 7). IUB member Elbert
Branscomb, working closely with Michael Russell at the Jet Propulsion Laboratory
in Pasadena, has shown how serpentinizing environments, such as Earth’s alkali
hydrothermal vents under the ocean, might be natural locations for life as we know it to
emerge. The pH of these vents explains the strange way all known cells on Earth have
evolved to produce and use energy.
This process, quite bizarrely, involves constantly filling up and depleting a kind of
chemical reservoir that is created by pushing a lot more protons onto one side of a
membrane than the other—just like pumping water uphill to fill a lake behind a dam.
This reserve of protons can later be released to produce a form of energy called ATP.
Every day our bodies produce and consume their weight in ATP. Within minutes, the
human body’s entire ATP energy reserve is consumed and regenerated.
“That’s why you can’t stand to be without oxygen for more than a few minutes,” said
physicist Elbert Branscomb (BCXT), an affiliate faculty member at the IGB. “We live on
a thin, desperate edge to keep our metabolic motors running full blast. Yet in spite of
this desperation, the process isn’t carried out by using our energy sources directly, but
by using the indirect, proton reservoir method. It’s an arrestingly strange way of doing
business that has made many scientists question why it is this way.”
Curiosity’s discovery is evidence of serpentinization and therefore evidence that life
may be evolving on Mars right now, just as IUB scientists speculate it did on Earth four
billion years ago. That is, if life hasn’t evolved already. Scientists also speculate that the
methane is a waste product of living microbes.
While the jury is still out, the IUB seeks to find out if early life forms are still being
created on Earth by serpentinization, and if so, how to detect them. "We have a
sample of only one planet known to harbor life,” Goldenfeld said. “Thus it is critical
that we be creative in extracting the most information from Earthly life as possible,
if we are to ever understand the existence, likelihood, and nature of life elsewhere in
the Universe.”
Ongoing work to understand serpentinization is done in collaboration with Russell
and postdoctoral researcher Tommaso Biancalani (BCXT).
Marni Boppart (RBTE) was elected
a fellow in the American College of
Sports Medicine. Among other things,
the fellowship recognizes “professional
achievement and competence in the
related disciplines of sports medicine via
education, published works, professional
practice and a demonstrated interest
in and/or contribution to the goals of
sports medicine.”
December 2014
Department of
Kinesiology and
Community Health,
College of Applied
Health Sciences
Beautiful images from
@IGBIllinois in a display at Chicago's
O'Hare. This one is
of colorectal cancer cells.
15 December 2014 ElizabethWhittington
@eyoste

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Hey @IGBIllinois would you be the ones that I need to talk to to clone Malcolm Hill or
is that someone else?
.@IlliniJohnGroce Unfortunately, you can only clone cells. You can’t clone things like
dedication, talent, and commitment.
10 December 2014 Fake John Groce
@IlliniJohnGroce
Genomic Biology
@IGBIllinois
Looks like something new is coming to the IGB Gatehouse ...10 December 2014
I just got my honey from Entomology!
@Illinois_Alma @IGBIllinois @MayBerenbaum via @BuzzFeed http://www.buzzfeed.com/
igbillinois/13-things-only-igbillinois-understands-16hfl …
12 December 2014 Mayor Don Gerard
@DonFerard
An international effort involving more than
100 researchers, nine supercomputers and
about 400 years of CPU time has yielded the
most reliable avian tree of life yet produced,
researchers report in Science. The tree
reflects the evolutionary relationships of 48
species of birds.
The computational effort, led by Founder Professor of Bioengineering and Computer
Science Tandy Warnow (BCXT) and University of Texas at Austin graduate student
Siavash Mirarab, took more than four years to complete. They were funded by the NSF,
the Howard Hughes Medical Institute and the Guggenheim Foundation.
12 December 2014
Birds find their
place in the
avian tree of life
go.illinois.edu/
BirdFamilyTree

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4 December 2014
EBI:
Addressing one
of the grand
challenges of
our time
energybiosciencesinstitute.org
On Dec 4, 2014, BP announced that the
EBI will no longer continue with the
development of the lignocellulosic (LC)
biofuels technology and business. As the
historic grant (to date the largest university-
industry partnership known) winds down,
EBI Deputy Director Isaac Cann (EBI/BCXT)
reflects on past accomplishments and looks
to the grant’s future.
“The fact that the EBI is coming to an end doesn't mean that the production of
cellulosic fuel has come to an end,” said Cann, a professor of microbiology and
animal sciences. “Two or three companies just started on a commercial scale, and the
students whom we trained are going to work for them. We trained a lot of manpower
for the field.”
Congratulations to the six Illinois faculty elected 2014
fellows of the American Association for the Advancement
of Science, including IGB members Brendan A. Harley,
professor of chemical and biomolecular engineering, and Phillip A. Newmark,
professor of cell and developmental biology.
December 2014
Harley: Department of
Chemical and Biomolecular
Engineering, College
of Engineering
Newmark: Department of
Cell and Developmental
Biology, College of Liberal
Arts and Sciences
MORE

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3 December 2014
@RIPEresearch Director, Steve Long, named one of the World's Most Influential
Scientific Minds: 2014 @TR_ScienceWatch http://bit.ly/1sx4uyM
RIPE Research
@RIPEresearch
In 2007, BP hosted an international competition for universities looking to solve the
global energy challenge. The resulting EBI partnership, originally funded by a $500
million grant for 10 years, includes researchers from the University of California,
Berkeley (also the EBI headquarters); the University of Illinois at Urbana-Champaign
(where research is housed within the IGB); the Lawrence Berkeley National Laboratory;
and BP.
The EBI should be very proud of all that it has accomplished to date, Cann said (see
July 28 and September 2). Before this partnership, microbes would convert one type
of sugar into biofuel, then convert a second type of sugar, an inefficient process
that took a long time. EBI researchers engineered microbes that use the two sugars
simultaneously, a landmark achievement that dramatically sped up the fermentation
process. Researchers also developed an “ingenious” way to produce jet fuel and
biodiesel that is compatible with current engines.
Over the last seven years, the EBI was issued 1 patent and released 2,488 public
disclosures, including disclosure forms, abstracts, manuscripts, posters, presentations,
etc. The extraordinary individuals who devoted their talent, time and energy to the
EBI made these achievements possible. In 2014, the Institute included 91 principal
investigators and faculty, 200 postdoctoral researchers/staff scientists, 202 graduate
and undergraduate students, 73 specialists, technicians and assistants, as well as 30
people in administrative support.
To Cann, the students are one of the EBI’s most important investments and greatest
achievements. As the EBI winds down, BP will continue to invest in the future of bioenergy
research by supporting the partnership's students and postdoctoral researchers.
“As a university professor, my main job is to train the next generation of scientists,”
Cann said. “The EBI offered me the opportunity to give the best training that I can to
these students. Every student who had a chance to work at this place, both here and
at Berkeley, had the opportunity of a lifetime.”
For many, the EBI was an unparalleled opportunity to work together, with top-notch
resources and support, toward a common goal. By opting not to delegate specific
funds to the partner institutions, but instead grant funds to exceptional applications
regardless of their affiliation, the EBI fueled academic competition that led to
impactful discoveries. This partnership will no doubt serve as a model for future
collaborations between industries and universities.
“It wasn't that everybody who applied succeeded in getting a grant. If your grant
was deemed excellent, then you got funded,” Cann said. “This approach to funding
enforced trust that led to collaboration, ensuring a truly multidisciplinary approach to
doing research to address one of the grand challenges of our time.”
MORE
EBI: Addressing one of
the grand challenges of
our time
2 December 2014 US Rep Rodney Davis
@RodneyDavis
Congratulations to Dr. Berenbaum, a world class @Illinois_Alma entomologist, on
receiving the National Medal of Science! youtube.com/watch?v=yz5W05...

15
Gene Robinson (Director) was conferred the degree of Doctor Philosophiae
Honoris Causa of the Hebrew University of Jerusalem.
December 2014
Department of
Entomology, College of
Liberal Arts and Sciences
1 December 2014
Study shows
different
species share
a "genetic
toolkit" for
behavioral
traits
go.illinois.edu/
GeneticToolkit
Image: Alexander Francis
Lydon,1879
The house mouse, stickleback fish and
honey bee appear to have little in common,
but at the genomic level these creatures
respond in strikingly similar ways to danger,
researchers report. A study led by Cell and
Developmental Biology Professor Lisa Stubbs
(GNDP Theme Leader) found that when
these animals confront an intruder, many of
the same genes and brain gene networks
tune up or down in response.
Animal biologist Alison Bell (GNDP), Swanlund Chair Professor of Entomology and
IGB Director Gene Robinson, and computer scientist Saurabh Sinha (BSD/GNDP) also
made important contributions to the work, which was reported in the Proceedings of
the National Academy of Sciences.
The team used comparative genomics to look at changes in brain gene expression in
each species in response to intrusion by another member the same species. All three
species exhibited changes in the expression of genes that regulate hormones and
neurotransmitters known to influence behavior. Other shared responses were seen in
the expression of genes that contribute to brain growth and plasticity; metabolic genes;
and genes related to muscle function. The Simons Foundation supported this research.

16
20 November 2014
Entomology
professor May
Berenbaum
awarded
National Medal
of Science
go.illinois.edu/
MedalofScience
Swanlund Professor of Entomology
May Berenbaum (GEGC) has been awarded
the National Medal of Science, the
nation's highest honor for achievement
and leadership in advancing the fields of
science and technology, according to an
announcement from the White House
Press Office.
Berenbaum, also the head of the Department of Entomology, has been a faculty member
since 1980. Her research, which studies the chemical mechanisms underlying interactions
between insects and their host plants, including the detoxification of natural and
synthetic chemicals, has produced hundreds of peer-reviewed scientific publications and
35 book chapters.
21 November 2014 May Berenbaum
@MayBerenbaum
Yesterday at White House, Obama said to me "I do care about the bees and we'll fix
'em!" Too bad about term limits!
11
NOVEMBER
Image: National
Science and Technology
Medals Foundation

17
"Professor Berenbaum's work has fundamentally changed what we know, how we
study and how the public understands the role of insects in nearly every aspect of
human life and development," said Chancellor Phyllis M. Wise.
Devoted to teaching and fostering scientific literacy through formal and informal
education, Berenbaum has also authored numerous magazine articles and six books
about insects for the general public. She created the Insect Fear Film Festival, a local fixture
for over thirty years, to engage and entertain members of the public with feature-length
films and shorts, commentary on the films, an insect petting zoo and an insect art contest.
21-20 November 2014
Genomics for
everyone
go.illinois.edu/
GenomicsforJudges
Genomic research has an ever-growing
impact on areas such as health and
agriculture, yet members of the public have
limited access to educational opportunities
in genomics—resources that would help
them relate new findings to everyday life.
The IGB created the Genomics for™ program, a series of workshops for the public and
for professional groups, to address this need. Each workshop is tailored to a particular
demographic, with content that relates advances in genomics to the needs and
interests of that group.
Project NEURON, a curriculum development group at Illinois, partnered with the IGB
in July to offer Genomics for™ Teachers. Attendees of the week-long Genomics for™
November 2014 May Berenbaum
(GEGC) received the
National Medal of
Science, the nation's
highest honor for
achievement and
leadership in advancing the fields of
science and technology, administered
by the NSF and bestowed by the
President of the United States.
MORE
Image: Project NEURON
Department of
Entomology, College of

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6 November 2014
Team discovers
how microbes
build a
powerful
antibiotic
go.illinois.edu/
BuildingAntibiotics
Researchers report in Nature that they have
made a breakthrough in understanding
how a powerful antibiotic agent is made by
microbes. Their discovery solves a decades-
old mystery and opens up new avenues
of research into thousands of similar
molecules, many of which are likely to be
medically useful.
Richard E. Heckert Endowed Chair in Chemistry Wilfred van der Donk (MMG),
Biochemistry Professor Satish Nair (MMG) and group focused on a class of compounds
that includes dozens with antibiotic properties. The most famous of these is nisin, a
natural product in milk that can be synthesized in the lab and is added to foods as a
preservative. An enzyme involved in the creation of nisin removes water to help give
the antibiotic its final, three-dimensional shape. This is the first step in converting the
spaghetti-like peptide into a five-ringed structure.
The rings are essential to nisin's antibiotic function: two of them disrupt the
construction of bacterial cell walls, while the other three punch holes in bacterial
membranes. This dual action is especially effective, making it much more difficult
for microbes to evolve resistance to the antibiotic. The NIH and the Ford Foundation
supported this work.
Team led by chemistry professor and IGB faculty Wilfred van der Donk discovers how
microbes build a powerful antibiotic in a recent paper in Nature. http://bit.ly/1EVMG1f
18 November 2014
Teachers workshop engaged in and critiqued hands-on curriculum activities related to
genomics, heard presentations from Illinois faculty on the societal impacts of genomic
biology, and received guidance and peer feedback on independent curriculum
development projects.
In November 2014, the Illinois Office of the State's Attorney Appellate Prosecutor
and the IGB held another workshop, Genomics for™ Prosecutors. The two-day event
explored the relationship between genome activity and criminal behavior, and the
accuracy and admissibility of DNA evidence.
MORE
Genomics for everyone

19
4 November 2014 Rory Sacks
@RorySacks
the @IGBIllinois MOOC is one of the best and most engaging MOOCs out there right
now. Setting the bar for sure #Illinoisemergenceoflife
More than 300 children, parents, and
friends of the IGB gathered at the Orpheum
Children’s Science Museum in Champaign
for an afternoon of fun with DNA, cells, and
the tree of life. Genome Day, an open-house
event for community members of all ages,
was organized this year by Animal Biology
Professor Karen Sears (GNDP/RBTE) and IGB
Fellow Farhan Chowdhury (CDMC), and held
on November 1.
1 November 2014
Kids and
parents explore
a molecular
world at
Genome Day
go.illinois.edu/GenomeDay
1 November 2014 ssmirhee
First time going to #GenomeDay hosted by #IGBIllinois. Idk if my 3yo understood
much but she was ranting about #cells and #DNE (or DNA, lol). And she had a lot
of fun!!
MORE

20
November 2014
Communications Office,
Carl R. Woese Institute for
Genomic Biology
Nicholas Vasi
(ADMIN) received
the 2014
Communicator
of the Year Award for
Communications & Marketing
Excellence from the office of
Public Affairs. This award is
presented to an individual
who exemplifies the qualities
of service, innovation, and
advancement.
1 November 2014
@IGBIllinois Genome Day was a great success! @stubbslab taught about alleles
causing variations in taste and smell.
Stubbs Lab
@stubbslab
Genomic Biology retweeted:
Genome Day features hands-on, child-friendly activities related to genomics. This year,
attendees used beads, tonic water, and a black light to model the spread of infection;
built models of genes, cells and viruses; and reconstructed animal skeletons. For
the second consecutive year, volunteers from SACNAS (Society for Advancement of
Chicanos and Native Americans in Science) provided language assistance for Spanish-
speaking attendees.
As part of the outreach mission of the IGB, events such as Genome Day make
genomics research engaging and relatable. Participants this year commented on their
enjoyment of the wide variety of scientific topics covered by the many activities. Next
year’s Genome Day is already on the calendar for November 14, 2015.
MORE
Kids and parents explore
a molecular world at
Genome Day

21
29 October 2014
New study
uses DNA
sequences to
look back in
time at plant
evolution
go.illinois.edu/
PlantEvolution
Image: Susan Sprunt
go.illinois.edu/Sprunt
Scientists from North America, Europe and
China published a paper in the Proceedings
of the National Academy of Sciences that
provided strong evidence for a major
revision of the evolutionary tree of plant life.
The research team used next-generation DNA sequencing technologies and
analytical tools to gather and interpret an unprecedented amount of genomic data
from a diverse set of plant species, resulting in an improved understanding of the
evolutionary history of land plants.
As part of the 1000 Plants (1KP) initiative, the researchers generated millions of gene
sequences from plant species sampled from across the tree of life. By resolving these
relationships, the study illuminated the complex processes that allowed ancient algae to
evolve into land plants, with adaptations to compete for light, water and soil nutrients.
Computer scientist Tandy Warnow (BCXT) and her student Siavash Mirarab developed
new methods for analyzing the massive datasets used in the project, with support
from the NSF. “The datasets we were analyzing in this study were too big and too
challenging for existing statistical methods to handle, so we developed approaches
with better accuracy,”Warnow said.
OCTOBER
10

22
15 October 2014
Join @IGBIllinois Director Gene Robinson
and donate at our blood drive in 612
IGB; accepting donations until 1 pm.
Genomic Biology
@IGBIllinois
Today’s researchers, working with the
advantages of new, sophisticated laboratory
technology, have unleashed a river of
valuable biomedical data—much more, in
fact, than many of them have the tools to
properly analyze, or the capacity to store.
In 2012, the NIH created the Big Data to
Knowledge (BD2K) initiative to enable efforts
to harness the potential of this flood of
information. In September 2014, as part of
the first wave of BD2K funding, Mayo Clinic
and Illinois received a $9.34M, 4-year award
to create one of several new Centers of
Excellence for Big Data Computing.
The goals of the Illinois-Mayo Center, which is hosted by the IGB’s Gene Networks
of Neural and Developmental Plasticity (GNDP) research theme, are focused on the
9 October 2014
Illinois,
Mayo Clinic
collaborate to
revolutionize
genomic data
analysis
go.illinois.edu/KnowEnG

23
Paul Hergenrother (CDMC) and Sandra Rodriguez-Zas (GNDP) were
named University Scholars; this program was created to recognize the
university’s most talented teachers, scholars and researchers.
Ever wonder about the trillions of microbes that live on your skin, in your muscles and
organs, even inside your brain? Watch our helpful animation, produced by the IGB, to
learn a little bit more about microbiota and your own microbiome.
October 2014
7 October 2014
Microbes:
The residents
living on and
inside you
www.youtube.com/
IGBIllinois
analytical challenges posed by the rapidly growing body of genomic and transcriptomic
data produced by genome-wide, high-throughput experimental technologies.
Abel Bliss Professor of Computer Science Jiawei Han (GNDP) is the Center’s Program
Director. Other Principal Investigators are Professor of Computer Science Saurabh
Sinha (BSD/GNDP); Founder Professor of Bioengineering and Physics Jun Song
(CDMC); and Richard Weinshilboum, M.D., Interim Director of the Mayo Clinic
Center for Individualized Medicine and Director of the Center’s Pharmacogenomics
Translational Program. NCSA and IGB Director of Bioinformatics and Director of the
HPCBio Group C. Victor Jongeneel (GNDP) is Executive Director of the new Center.
Together, the team is developing an analytical tool called KnowEnG, which will
integrate many disparate sources of gene-related data into one enormous network, a
comprehensive guide against which a researcher’s specific results can be compared.
KnowEnG will accommodate future growth in size and scope of the network, as the
scientific community continues to learn about the relationships among genes. In
addition, the Center is creating a training framework that empowers researchers to
use the new tool and engage in bioinformatics research, regardless of their prior
computational knowledge.
Hergenrother: Department
of Chemistry, College of
Rodriguez-Zas: Department
of Animal Sciences, College
of Agricultural, Consumer
and Environmental Sciences

24
28 September 2014
Novel roadmap
through
bacterial
genomes leads
to new drug
discovery
go.illinois.edu/
NaturalProductGenomics
For millennia, bacteria and other microbes
have engaged each other in intense battles
of chemical warfare. Doctors fight diseases
with antibiotics co-opted from these
microbial wars, but their efforts are frustrated
by the development of drug resistance that
outpaces drug discovery.
Microbiologist and molecular and cellular biologist Bill Metcalf (EBI/MMG Theme
Leader), IGB Fellow James Doroghazi (MMG), and colleagues have now created an
9
SEPTEMBER

25
26 September 2014
New research
may help
doctors
personalize
cancer
treatments
go.illinois.edu/
CombatCancer
Image:
Doroghazi, Albright et al.
Most types of tumors, including cancer,
require a supply of blood to grow larger than
a few millimeters. Scientists have made great
progress in combating cancer by finding
effective ways to stop the formation of new
blood vessels, called angiogenesis.
The NIH, Merck, American Cancer Society, Illinois Division Basic Research Grant, United
Negro College Fund, and the Federation of American Societies for Experimental
Biology support this work.
In a paper in PLOS ONE, Assistant Professor of Bioengineering Princess Imoukhuede
(RBTE) and co-authors used optical approaches that can be further developed to
trap cancer cells. In another paper, published in the Journal of Materials Chemistry B,
Imoukhuede and other researchers began setting the calibration standards needed
to quantitatively profile cancer cells. In two articles in Cancer Medicine and PLOS ONE
on profiling and modeling, Imoukhuede and her colleagues reported that they have
begun collecting data and creating computational models.
algorithm to analyze microbial genomic data and speed discovery of new therapeutic
drugs. Their work, supported by the NIH and the IGB, was published in Nature
Chemical Biology.
Metcalf and Doroghazi combined multiple comparative metrics in an algorithm that
sorted data from 830 bacterial genomes into an orderly, searchable reference. An
experiment performed in collaboration with a group of chemists at Northwestern
University, led by former Illinois faculty member Neil Kelleher, then used a high-
precision analytical technique to infer the chemical composition of unknown
compounds isolated from bacterial strains in the study. The researchers were able to
match the presence of these compounds with specific groups of genes.
23 September 2014
@nytimes report on our efforts to develop crops tolerant of pollution and climate
change nyti.ms/1ri59lI @IGBIllinois @Illinois_Alma
The New York Times
Testing Future Conditions for the Food Chain
Researchers are trying to mimic the growing
conditions expected to arise decades in the future
as the air fills with heat-trapping gases and other
pollutants from human activity, with some worrisome...
Andrew Leakey
@leakey77

26
23 September 2014 markwilliamholmes
Out at the farm this morning
.@MarkWHolmes, is this a picture of South Farms at @Illinois_Alma? Beautiful.
Genomic Biology
@IGBIllinois
@IGBIllinois @Illinois_Alma Yup. I was out at SoyFACE at dawn for some measurements.
Mark Holmes
@MarkWHolmes
Bruce Fouke (BCXT/EBI) has been
chosen to serve as the 2014-2015
American Association of Petroleum
Geologists Roy Huffington
Distinguished Lecturer in the Asia/
Pacific Region. His formal AAPG lecture
tour will include New Zealand, Australia,
Thailand, Vietnam and Japan, and cover
topics such as field geobiology, coral
reef ecosystems, and his work with the
Yellowstone Hot Springs.
October 2014
Department of Geology
and Department of
Microbiology, College of

27
Eight percent of your genome derives from
retroviruses that inserted themselves into
human sex cells millions of years ago. Right now
the koala retrovirus (KoRV) is invading koala
genomes, a process that can help us understand
our own viral lineage and make decisions
about managing this vulnerable species.
“It may be a very long, slow, painful process for the host species, one which human
ancestors have gone through and overcome many times in the distant past,” said
animal scientist Alfred Roca (GNDP).
In a recent study, published in Molecular Biology and Evolution, Roca and co-authors
discovered that 39 different KoRVs in one koala’s genome were all endogenous, which
means passed down to the koala from one parent or the other; one KoRV was found
in both parents. The San Diego Zoo, Columbus Zoo, San Francisco Zoo, and Riverbanks
Zoo provided koala samples for the study, which was supported by the NIH.
23 September 2014
Koala study
reveals clues
about origins
of the human
genome
go.illinois.edu/KoRV
Image: Norbert Potensky and
the Vienna Zoo
Researchers reported that attentive
stickleback fish fathers influence their
offspring to behave in a way that makes
them less susceptible to predators. The
offspring of these fathers also show changes
in brain gene expression.
17 September 2014
Male stickleback
fish influence
offspring
behavior, gene
expression
go.illinois.edu/
SticklebackDads
MORE

28
Stephen Long (GEGC) was named a Thomson
Reuters Highly Cited Researcher in recognition
of ranking among the top one percent of
researchers for most cited documents in their
specific field. He was also named by Thomson
Reuters as one of the World's Most Influential
Scientific Minds for 2014.
October 2014
10 September 2014
Where will
science take us
in 20 years? Blog
provides 2034
predictions
go.illinois.edu/MentalHealth
The Science Coalition, a nonprofit
organization that promotes the importance
of federal investment in research, unveiled
a new blog featuring predictions of what
science and innovation will yield for the
future. The blog—SCIENCE 2034—is intended
to call attention to the need for strong and
sustained federal funding for basic scientific
research by highlighting the exciting
possibilities of the future.
“In the year 2034, we will have solved a fundamental mystery of the brain: how past
experience affects future behavior,” wrote Swanlund Chair of Entomology and IGB
Director Gene Robinson in his contribution to the blog.
This discovery could help reduce instances of mental illness and help more Americans
live healthier, more productive lives. Why does this matter? Too many people struggle
with debilitating conditions like depression, schizophrenia, and post-traumatic stress
disorder. Once we better understand the connections between our past experiences
and the changes in gene activity that cause these diseases, we will be better able to
treat specific brain ailments.
Animal biologist Alison Bell (GNDP) and postdoctoral researcher Katie McGhee
evaluated fatherly influence on fry behavior by separating half of the fry from their
dads before they hatched. When a predator fish was near, the orphaned sticklebacks
made frantic attempts to escape, making them easier targets for the predator. Their
attentive father-reared sibling exhibited less of this frantic behavior. In contrast,
there were no behavioral differences between orphaned or parented fry of less
attentive fathers.
These findings suggest that fathers can help to compensate for inherent
vulnerabilities by changing their behavior in ways that affect offspring behavior, Bell
said. This work, supported by the NSF and NIH, was published in the Proceedings of the
Royal Society B: Biological Sciences.
MORE
Male stickleback fish
influence offspring
behavior, gene expression
Department of Plant
Biology, College of
Liberal Arts and Sciences;
Department of Crop
Sciences, College of
Agricultural, Consumer and
Environmental Sciences

29
Scientists have scoured cow rumens
and termite guts for microbes that can
efficiently break down plant cell walls for the
production of next-generation biofuels, but
some of the best microbial candidates may
actually reside in the human lower intestine.
Reported in the Proceedings of the National Academy of Sciences, these findings have
significance for human health, but also for biofuels production, since the same sugars can
be fed to yeast to generate ethanol and other liquid fuels. The human microbes appear
to be endowed with enzymes that break down a complex plant fiber component more
efficiently than the most efficient microbes found in the cow rumen, said animal scientist
Isaac Cann (BCXT/EBI Deputy Director), whose work was funded by the EBI and USDA.
2 September 2014
Search for
better biofuels
microbes
leads to the
human gut
go.illinois.edu/
BetterBiofuels
8 September 2014 laurawennstrom
#Drawing class field trip to #IGB to draw #TonyTasset #DarwinsPlayground #uiuc
#publicart

30
In the collective memory of several
generations, Robin Williams’ acting persona
is the archetypal mentor. His vivid portrayals
of the unconventional English teacher John
Keating in Dead Poets Society and the frank
yet gentle therapist Sean Maguire in Good
Will Hunting leave viewers with an impression
of kind sincerity, an impression that is only
reinforced by Williams’ more light-hearted
roles. Williams used his incredible comedic
talent to positively impact the lives of his
audiences through the parts he played and
his philanthropic efforts.
8
AUGUST
11 August 2014
Robin Williams’
life and death
inspire others
to help those
in need
go.illinois.edu/MentalHealth
Image: Peggy Sirota
go.illinois.edu/Sirota

31
His legacy makes the manner of his death this August all the more poignant. Williams
took his own life; his doctors reported that his recent depression and death were likely
caused by Lewy body dementia, a Parkinson’s-like neurological disease.
William’s death shook the world because of his unique personality and talent.
Tragically, the mental illnesses that led to his death are quite common. Millions
of people suffer from debilitating disorders of mood and aging-related dementia
each year, yet researchers are still struggling to understand the neurological and
developmental origins of these diseases.
Recent and ongoing advances in research technology offer hope that a genomic
approach to mental disorders may prove fruitful (see September 10). For example,
work by researchers like Associate Professor of Psychology and IGB affiliate Monica
Uddin explores how the genome integrates the influences of nature and nurture on
mental health.
“We have not had as much success in identifying the genetic basis for stress-
related mental disorders such as major depressive disorder (MDD) or post-traumatic
stress—in part because the environment plays a larger role in the development of
these disorders,” said Uddin. “There has been a growing appreciation for the role of
epigenetics—molecular factors such as DNA methylation and histone modifications
that help to regulate gene function without changing the underlying DNA
sequence—in shaping risk for mental disorders.”
Uddin is currently engaged in a collaboration with Professor of Psychiatry and
Psychology Susannah Tye, a clinical researcher at Mayo Clinic, to examine epigenetic
predictors of antidepressant resistance in rats. The insights from this work may
eventually enable better diagnostics and treatment for MDD. Other work at the IGB
also examines the interplay between brain gene regulation, behavior, and well-being
(see September 17).
Perhaps this can be part of the legacy of Williams and countless others who have lost
their lives to neurological disorders: a renewed dedication to discover effective means
of treatment, and ultimately to predict and prevent illnesses before they begin.
11 August 2014 Nicholas Rabchenuk
@rabbitnutz
Memorial at good will hunting bench. @7News @NESN @fox25news @GregHillWAAF
@rabbitnutz We have lost a favorite son, when will researchers solve mental illness
puzzle? We know more about universe than the human mind
rcs
@guzmania

32
Stephen Boppart (RBTE) and Martha Gillette (GNDP) were
among 36 researchers to receive Early Concept Grants for
Exploratory Research from the NSF. These grants enable the
development of new technologies to better understand how
complex behaviors emerge from the activity of brain circuits.
Cancer cells that break away from tumors
to go looking for a new home may prefer
to settle into a soft bed, according to work
published in Nature Communications. In a
process called metastasis, cancer cells can
spread to other organs, evading treatment
and causing relapse. Leonard C. and Mary
Lou Hoeft Professor in Engineering Ning
Wang (RBTE) and colleagues found that
these so-called tumor-repopulating cells
may lurk quietly in some environments, but
thrive in others.
Cancer cells placed in very soft gels grew and multiplied, as expected. The cells placed
on stiffer gels became dormant, but “woke up” and began to multiply and spread
when later moved to softer environments.
Wang said these findings may explain why soft tissues, such as the brain or lungs, are
most vulnerable to metastasis. This work was supported by the NIH.
6 August 2014
Cell mechanics
may hold key
to how cancer
spreads and
recurs
go.illinois.edu/
CancerCellMechanics
August 2014
Boppart: Department of
Electrical and Computer
Engineering, College of
Engineering
Gillette: Department of
Cell and Developmental
Biology, College of Liberal
Arts and Sciences
Image: Jason Lindsey
go.illinois.edu/Lindsey

33
llinois scientists have discovered that they
can crank up insect aggression through a
surprising method—interfering with a basic
metabolic pathway in the insect brain. Their
study of fruit flies and honey bees showed a
direct, causal link between brain metabolism
and aggression.
In a new study reported in the Proceedings of the National Academy of Sciences,
postdoctoral researcher Clare Rittschof, Swanlund Chair Professor of Entomology
and IGB Director Gene Robinson, and colleagues saw that increased aggression was
dose-dependent in drugged bees. However, the drugs had no effect on chronically
stressed bees.
The findings offer insight into the immediate and longer-term changes that occur in
response to threats, Robinson said. The NSF supported this work.
August 2014
4 August 2014
Researchers
boost insect
aggression by
altering brain
metabolism
go.illinois.edu/
BrainMetabolism
Brian T. Cunningham (MMG) received a
Technical Achievement Award from the
Institute of Electrical and Electronics
Engineers’ Engineering in Medicine and
Biology Society. Cunningham received
the award “for development and
commercialization of optics-based biosensors
and detection instruments for applications in
drug discovery, diagnostics, environmental
monitoring and life science research.”
Deborah Leckband (RBTE) was
elected a 2014 fellow of the
Biomedical Engineering Society
for her research, which includes
the investigation of how
mechanical and biochemical
signals are transduced across
cell membranes to regulate cell
and tissue functions.
August 2014
Department of Electrical
and Computer Engineering,
College of Engineering
Department of Chemical
and Biomolecular
Engineering

34
JULY
28 July 2014
Earth can
sustain more
terrestrial plant
growth than
previously
thought
go.illinois.edu/PlantGrowth
Image: NASA/Apollo 17 crew;
taken by either Harrison
Schmitt or Ron Evans
A new analysis suggests the planet can
produce much more land-plant biomass—
the total material in leaves, stems, roots,
fruits, grains and other terrestrial plant
parts—than previously thought. The study,
reported in Environmental Science and
Technology, found current estimates do
not consider human efforts to boost plant
productivity through genetic engineering,
plant breeding and land management, said
Evan DeLucia (EBI/GEGC), the G. William
Arends Professor of Biology.
To estimate a new theoretical limit, Delucia and his team used a model of light-
use efficiency and the theoretical maximum efficiency with which plant canopies
convert solar radiation to biomass. This limit is “roughly two orders of magnitude
higher than the productivity of most current managed or natural ecosystems,” the
authors wrote. The EBI funded this research.
7

35
A study that used radio-frequency
identification (RFID) tags to track the flight
activity of hundreds of individual honey bees
has yielded two discoveries: some foraging
bees are much busier than others; and if
those busy bees disappear, others will take
their place.
“We found that some bees are working very, very hard—as we would have expected,”
said Swanlund Chair Professor of Entomology and IGB Director Gene Robinson, who
led the research. Data from the tags revealed that about 20 percent of the foraging
bees in a hive brought home more than half of the nectar and pollen supply.
Surprisingly, when elite honey bees were removed from the colony, previously low-
activity bees were able to dramatically increase their foraging rate to compensate.
Citizen scientist Paul Tenczar developed the technique to attach RFID tags to bees
and to track their flight activity with monitors. He worked with Robinson’s laboratory
group to measure the foraging behavior of bees. Swanlund Professor of Physics Nigel
Goldenfeld (BCXT Theme Leader) and graduate student Vikyath Rao analyzed the data.
The study was funded by NSF and the Christopher Family Foundation and reported in
the journal Animal Behaviour.
19 July 2014
Radio
frequency ID
tags on honey
bees reveal
hive dynamics
go.illinois.edu/
HiveDynamics
17 July 2014
To bees and
humans, all
sugar sources
are not created
equal
go.illinois.edu/SugarSources
Many beekeepers feed their honey bees
sucrose or high-fructose corn syrup when
times are lean inside the hive. This practice
has come under scrutiny; some bee health
experts suspect that inadequate nutrition
plays a role in honey bee declines.
In a new study described in Scientific Reports, researchers examined the effect
of bees’ diet on gene activity in a tissue called the fat body, which combines the
functions of the liver and fat tissues in vertebrates. Hundreds of genes related to
protein metabolism, brain signaling and immune defense showed differences in
activity depending on whether bees were fed corn syrup or sucrose versus honey.
“It seems that in both bees and humans, sugar is not sugar—different carbohydrate
sources can act differently in the body,” said Swanlund Chair Professor of
Entomology and IGB Director Gene Robinson, who performed the new analysis
together with entomology graduate student Marsha Wheeler. Funds for the study
were provided by the North Central Region Integrated Pest Management Center.

36
17 July 2014
Identifying
barriers to stem
cell production
go.illinois.edu/
ReprogrammingCells
Pluripotent stem cells, naturally occurring
stem cells that develop into any one of the
many cell types, have enormous implications
for regenerative medicine, but they are
rare in adults and difficult to grow in the
laboratory. The recent discovery that human
somatic cells can be reprogrammed in the
laboratory to generate pluripotent stem cells
could lead to revolutionary treatments for
many chronic diseases, including cancer.
These laboratory-modified cells, called induced pluripotent stem cells (iPSCs),
appear to be equivalent in every way to naturally occurring stem cells.
Unfortunately, cells inherently resist the reprogramming of gene expression
researchers use to create iPSCs. For the first time, Founder Professor of Physics and
of Bioengineering Jun Song (CDMC) and other researchers have systematically
catalogued the barriers to reprogramming somatic cells to generate iPSCs.
This work, reported in Cell, was supported by grants from the NIH; Netherlands
Organization for Scientific Research; California Institute for Regenerative Medicine;
University of California, San Francisco Program for Breakthrough Biomedical
Research; and a Sontag Foundation Distinguished Scientist Award.
Royal Society Fellow Stephen
Long (GEGC) was invited
to serve as a Sectional
Committee Chair for the
Royal Society. The Sectional
Committees select a short list
of candidates for election as
Royal Society Fellows from
the hundreds of nominations
received each year.
July 2014
Department of Plant
Biology, College of
Liberal Arts and Sciences;
Department of Crop
Associate professor of anthropology Ripan Malhi featured on the Day of Archaeology
website with great new article Molecular Archeology Puts Artifacts in Perspective.
Read it at http://bit.ly/1oOvrJQ
16 July 2014

37
15 July 2014
Turning
the tide for
rare disease
research
http://mayoillinois.org
Image: Wilfred van der Donk
ice bucket challenge UIUC.
go.illinois.edu/DonkALS
This summer, a pop culture craze for internet
charity swept the nation—carried along by a
two million-bucket wave of ice water.
The “Ice Bucket Challenge” emerged as a way to raise awareness of amyotrophic
lateral sclerosis (ALS), sometimes called Lou Gehrig’s Disease, and to raise funds for
ALS research. ALS, a fatal disorder, is characterized by the progressive death of nerve
cells that control muscle movement, resulting in decreasing motor control and the
eventual loss of ability to move, swallow, or breathe. There is currently no cure.
Participants in the Ice Bucket Challenge created videos in which they doused
themselves with freezing water, sometimes in elaborate or unexpected ways. They
referenced ALS and nominated others to create their own videos, donate to research
through a nonprofit organization, or both. Although initially not focused on a
particular charity, the phenomenon went viral after several high-profile individuals
related their participation to the need for ALS research funding. Eventually, the
trend generated enthusiasm for charitable giving to support research for a variety of
disorders, along with other philanthropic endeavors.
Part of the inspiration for the ALS Ice Bucket Challenge came from the difficult
circumstances that surround ALS research. The disease is complex, rare, and deadly.
For those who suffer from uncommon and intractable disorders, and for those close to
them, the need for effective treatments and cures is overwhelming. However, each of
these disorders presents a unique and daunting scientific challenge, while their rarity
makes it difficult for research efforts to get enough attention and funding.
Research at academic institutions like Illinois is an important component of the
solution to this societal problem. Partnerships with medical institutions, such as
the Mayo-Illinois Alliance (see October 9 and March 17), facilitate the type of broad,
interdisciplinary clinical research projects that are needed to tackle complex disorders.
14 July 2014
Have you heard about the ICE BUCKET CHALLENGE for ALS? Danny the Intern survived
it this weekend... http://fb.me/1jROiF8i8
ALS Cycle of Hope
@CycleofHope4ALS

38
11 July 2014
Ripan Malhi
featured on ‘Day
of Archaeology’
website
go.illinois.edu/
DayofArchaeology
Where archeologists exhume secrets,
lost histories from the soil, “molecular
archeologists” uncover secrets lying inside
human remains. By piecing together ancient
DNA, molecular archeologists can more
definitively answer questions about our past.
For the “Day of Archaeology,” a project that provides a window into the daily lives
of archeologists from all over the world, anthropologist Ripan Malhi (BIOBEL/RBTE)
described what it’s like to be a molecular archeologist.
“Some people in my field consider themselves to be molecular archeologists as we tend
to work with archeological remains and use an archeological context to help infer the
genetic patterns we see,”he said.
8 July 2014
The Emergence of Life #MOOC by @IGBIllinois @coursera sounds truly
fascinating. Can't wait to learn more! https://www.coursera.org/course/
emergenceoflife …
Coursera
Emergence of Life - University of Illinois at Urbana-
Champaign...
Emergence of Life from University of Illinois at Urbana-
Champaign. Take free online classes from 115+ top
universities and educational organizations. We partner
with schools like Stanford, Yale,...
Ritu Raman
@raman_ritu
Patricia Blair (MMG) was selected to receive an
American Chemical Society Division of Medicinal
Chemistry Predoctoral Fellowship, a prestigious award
given annually since 1991. The award recognizes
superior achievement as a graduate student.
July 2014
Department
of Chemistry,
College of Liberal
Arts and Sciences

39
7-11 July 2014
Another
successful year
for the IGB
summer camp,
Pollen Power!
go.illinois.edu/
PollenPower2014
For many people, the word “pollen” evokes
only the idea of a springtime allergenic
nuisance. For one group of middle school
girls, though, pollen is now a symbol of
summertime fun and learning. Twenty-six
girls from around East Central Illinois came
to participate in Pollen Power!, a week-long
science day camp hosted July 7-11 by the
IGB on the Urbana-Champaign campus.
Campers investigated the function and microscopic structure of pollen, and
discovered connections between the biology of pollen and larger ideas: how
plants grow and reproduce, the environmental impacts of climate change, and the
importance of insect and vertebrate pollinators.
The camp was designed to give girls a kaleidoscopic picture of what it means to
be a plant biologist. Activities included using the IGB Core Facilities’ high-powered
microscopes; learning to identify different types of pollen and pollinate corn; and
hearing guest talks from IGB researchers on the science of pollen and the crucial role
that women play in STEM fields. The camp, which will be offered again July 6-10, 2015,
is supported in part by the NSF.
How did life emerge on Earth? How have life
and Earth co-evolved through geological
time? Is life elsewhere in the universe?
7 July 2014
Thousands
united through
a new online
course to
explore the
origins of life
go.illinois.edu/
EmergenceofLife
www.youtube.com/
IGBIllinois
MORE

40
While hiking through the Ozarks’characteristic
oak and hickory forests as a teenager,
ecologist and IGB Fellow Scott Woolbright
(GEGC) discovered something decidedly
uncharacteristic for the region: prickly pear
cacti growing on an exposed, rocky ledge.
In a recent paper published in Trends in Ecology and Evolution, Woolbright describes
how populations and communities like these, known as climate relicts, can help
scientists understand how ecological communities are affected by climate change.
The IGB supported this work.
1 July 2014
Climate relicts
may help
researchers
understand
climate change
go.illinois.edu/
ClimateRelicts
Image: Victor Korniyenko
© Victor Korniyenko, used
under a CC BY-SA 3.0 license.
go.illinois.edu/Korniyenko
1 July 2014 Genomic Biology
@IGBIllinois
Check out Francis Collins @NIHDirector perform our @NIH_CommonFund song by
@neurobeegirl! http://bit.ly/1sUbVQY #doublehelixguitar
The College of Liberal Arts and Sciences, the IUB, and the IGB have partnered to create
an online course that explores these and other enticing questions. The course, called
Emergence of Life, has attracted thousands of participants since it was offered on
Coursera for the first time this summer. Course material covers the entire history of life
on Earth within the context of the Tree of Life, from ancient primordial life before the
first cell to the evolution of modern species.
The pioneering work of Carl R. Woese, Stanley O. Ikenberry Endowed Chair of
Microbiology at the time of his death, has revolutionized our understanding of the
fundamental structure and evolutionary relatedness of all living entities on Earth.
Although concepts from Woese's work are central to transdisciplinary genomic
research, the new course is among the first to include his work in its curricula.
The course, which was offered a second time this fall, was made possible with the
contributions of scientific experts from around the world, including Karl Stetter at
the University of Regensburg; Norm Pace at the University of Colorado Boulder; Jan
Sapp at York University; and Mike Russell at the California Institute of Technology.
Two Illinois faculty members, Professor of Geology and Carver Biotechnology Center
Director Bruce Fouke (BCXT/EBI) and Swanlund Professor of Physics Nigel Goldenfeld
(BCXT Theme Leader), also played major roles in the course.
MORE
Thousands united through
a new online course to
explore the origins of life

41
JUNE
6
Throughout the spring of 2014, a
deadly epidemic was gradually building
momentum in West Africa. By midsummer,
the humanitarian aid organization
Médecins Sans Frontières (Doctors Without
Borders) announced that the scale of the
growing outbreak of Ebola virus disease
had exceeded their ability to respond. Just
a few days later, the number of reported
cases totaled 779, and the number of
reported deaths reached 481—more than
any previous outbreak, yet only a small
fraction of the 20,000 cases and 7,800
deaths confirmed by the end of 2014.
The outbreak had a dramatic global impact. International health organizations, as well
as the aid organizations of individual nations, worked together to help Guinea, Sierra
Leone and Liberia, the three countries most devastatingly affected by the disease.
30 June 2014
Ebola outbreak
focuses global
attention on
African health
needs
hpcbio.illinois.edu
Image: ©Crown copyright 2012
go.illinois.edu/CrownCopyright
MORE

42
The health crisis created by the Ebola outbreak brought attention to the challenges
faced by medical workers in many regions of Africa: the need for better public health
education; lack of personnel, infrastructure, and equipment; and many other serious,
ongoing health issues.
A source of hope throughout the Ebola outbreak has been the dedicated efforts of
many different groups and organizations to combat the disease. One such group is
the Human Heredity and Health in Africa Consortium (H3Africa). H3Africa is a large-
scale project funded by the NIH and Wellcome Trust to enable African researchers
to apply the power of genomic research to health challenges that affect their
geographical region. Computational and bioinformatics support for the consortium is
supported by H3ABioNet, a multi-institutional project.
NCSA and IGB Director of Bioinformatics and Director of the HPCBio Group C. Victor
Jongeneel (GNDP), as well as other HPCBio group members (see October 9), are key
participants in H3ABioNet. The training and consultation provided by H3ABioNet
have already expanded the genomic research capabilities of H3Africa projects across
the continent. These research efforts are addressing not only the acute challenge of
Ebola, but also the chronic and severe health concerns that these areas face, including
hemorrhagic fevers, malaria, tuberculosis, and HIV.
Ebola outbreak focuses
global attention on African
health needs
Gutgsell Endowed Professor of Crop
Sciences and Plant Biology Stephen
Long (BSD/EBI/GEGC) was inspired by his
participation this June in the Gatsby Plant
Science Summer School for undergraduate
students, held near York, England. The
annual week-long intensive course
addresses a growing need to promote
student interest in plant sciences. Long
delivered a plenary lecture, conducted a
QA, and met with small groups. He also
advised on the design and execution of
laboratory activities for high schools.
“The success of this course in exciting that interest was palpable,”Long said. He believes
that plant biology is no longer emphasized in U.S. and U.K. high schools in part because
plant sciences are seen as uninteresting and unimportant. In actuality, he said, “plants
are fundamental to our existence, and we're running out of what they provide.”
29-30 June 2014
Securing
tomorrow’s
food supply
by engaging
today’s
students
go.illinois.edu/
PlantBioResearch
MORE

43
Illinois researchers established the university's
first rice paddy to test rice performance in
Illinois and at Kyoto University in Japan. The
two plots, which were planted on the same
date, should reveal clues about what factors
help the plants more efficiently convert the
sun’s energy into food, a metric known as
photosynthetic performance.
This experiment is part of the Realizing Increased Photosynthetic Efficiency (RIPE)
project, a five-year effort led by Gutgsell Endowed Professor of Plant Biology and
Crop Sciences Stephen Long (BSD/EBI/GEGC), which is funded by a $25 million grant
from the Bill Melinda Gates Foundation to substantially improve the productivity of
worldwide staple food crops.
25 June 2014
Illinois
study may
improve rice
productivity
go.illinois.edu/RicePaddy
Biosphere is an ongoing video series that showcases IGB research. In our debut video,
IGB Fellow and microbe maven Melissa Cregger discusses about her adventures in
microbiome research and starting a family.
26 June 2014
Biosphere
features IGB
Fellow Melissa
Cregger
www.youtube.com/
IGBIllinois
Jeffrey Moore (BSD) was named an HHMI
Professor. This distinction honors respected
researchers who also are transforming education
within their fields.
June 2014
Department of Chemistry,
College of Liberal Arts
and Sciences

44
Antibiotic resistance is depleting our arsenal
against deadly pathogens, including those that
cause tuberculosis and Staph infections. In an
ACS Chemical Biology study, Assistant Professor
of Chemistry Doug Mitchell (MMG) with his
lab members developed a new technique to
quickly uncover novel products (including
potential antibiotics) produced by bacteria.
Using genomics, researchers are now able to screen soil bacteria that are likely to
produce novel antibiotic products. During the screening process, a chemical tag is added
to the compounds of interest. The addition of these tags adds mass to the product so
researchers can easily detect the reactive products using mass spectrometry.
This study was supported by the David and Lucile Packard Fellowship for Science and
Engineering, Robert C. and Carolyn J. Springborn Endowment, American Society for
Biochemistry and Molecular Biology Undergraduate Research Award, National Center
for Research Resources, NIH, and the IGB.
17 June 2014
Innovative
technique
transforms
hunt for
antibiotics
go.illinois.edu/
NaturalProductDiscovery
June 2014
Department of Sociology,
and Sciences
Image: Tiffany Jolley,
WILL Illinois Public Media
Ruby Mendenhall (GNDP)
was named a Richard and
Margaret Romano Professorial
Scholar. The three-year
appointment is based upon
recognition of outstanding
achievements in research and
leadership on campus.
23 June 2014 Claire Sturgeon
@ClaireSturg
Had a behind the scenes look at
@leakey77 on @WICD w/ @JHarrisWICD
talking about #pollenpower. http://Bit.
ly/1m4UCCX

45
Inspired by the Red Queen in Lewis Carroll’s
Through the Looking Glass, plant biologist
James O’Dwyer (BCXT) improved a 35-year-
old ecology model to better understand how
species evolve over decades to millions of years.
The new model, called a mean field model for competition, builds on the “Red Queen
Effect,” an evolutionary theory introduced by Leigh Van Valen in the 1970s, which
suggests that organisms must constantly undergo evolutionary adaptation in response
to changes in other ever-evolving organisms and an ever-changing environment.
The mean field model assumes that new species have competitive advantages that
allow them to multiply, but over time new species with even better competitive
advantages will evolve and outcompete current species, like a conveyor belt
constantly moving backwards. Ecologists can use models to predict what happens
next and diagnose sick ecosystems. The Templeton World Charity Foundation
supported this work, which was published in Ecology Letters.
13 June 2014
Classic
Lewis Carroll
character
inspires new
ecological
model
go.illinois.edu/
EcologyModel
Rashid Bashir (RBTE) was selected as
Chair of the Nanotechnology Study
Section (NANO) in the
Center for Scientific Review of the NIH.
NANO reviews applications focused
on research in bioengineering and
technology development relating to the
unique properties of nanomaterials.
June 2014
Department of
Bioengineering, College of
Engineering
12 June 2014 NASA
@NASA
In 1 hr: @AstroIllini talks living working
in space at @NASAGoddard. Watch:
http://www.ustream.tv/channel/nasa-
educational … #askNASA Q's

46
The Huffington Post’s Susan Mazur
interviewed Swanlund Professor of Physics
Nigel Goldenfeld (BCXT Theme Leader)
about evolution, Carl R. Woese, and the need
for a theory of life:
As a condensed matter physicist, Goldenfeld's main interest is pattern formation and
the processes involved in pattern formation. He researches everything from snowflakes
to geological formations to the stock market. He and his team have captured gorgeous
images of some of these formations in progress at Yellowstone National Park.
In response to a question from Mazur about whether any common themes united his
diverse research interests, Goldenfeld said during the interview:
One thing is that systems that are out of equilibrium are much more interesting than
systems that are in equilibrium. Systems in equilibrium lapse into perfect states like
crystals, etc. Systems that are out of equilibrium are messy and produce turbulence and
swirly clouds and human beings and galaxies and strange patterns in space and time .
. . it's my main intellectual interest.
9 June 2014
Nigel
Goldenfeld
interviewed in
Huffington Post
go.illinois.edu/
HuffingtonPost
The Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB) is a fully
integrated computational and physical infrastructure that supports rapid design,
fabrication, validation/quality control, and analysis of genetic constructs and
organisms. As the first living foundry in the world, the iBioFAB provides a new
manufacturing paradigm for chemicals, materials, and biologics.
5 June 2014
iBioFAB at
University of
Illinois
www.youtube.com/
IGBIllinois
3 June 2014 NCSAatIllinois
@NCSAatIllinois
@IGBIllinois recently hosted @NASA Astrobiology Institute Executive Council. Thx for
taking time to tour #BlueWaters http://t.co/gxTXiwzy9S

47
Researchers have some bad news for future
farmers and consumers: as carbon dioxide
levels rise this century, some grains and
legumes will become significantly less
nutritious than they are today.
Associate Professor of Plant Biology Andrew Leakey (EBI/GEGC) and colleagues from
eight institutions in Australia, Israel, Japan and the United States simulated high
carbon dioxide levels in open-air fields and reported in Nature that the nutritional
quality of some of the world’s most important crops dropped in response to elevated
carbon dioxide. This research was supported by the USDA; Illinois Council for Food
and Agricultural Research; and the National Institute for Climatic Change Research.
Congratulations to Bioenergy Connection, the
EBI magazine, which received a bronze award
from the Council for the Advancement and
Support of Education (CASE) for its latest issue
“Forest Bioenergy: Is It Sustainable?”
Read the issue online at
www.bioenergyconnection.org/.
June 2014
3 June 2014 Laura McLay
@lauramclay
Univ. of Illinois
@Illinois_Alma
Neat @Illinois_Alma exhibit at
@fly2ohare #yeahscience
@lauramclay @fly2ohare Where science art meet. Thanks for sharing your photo of
the @IGBIllinois display.
3 June 2014
As carbon
dioxide levels
rise, crop
nutritional
value will
decline
go.illinois.edu/CO2Effects

48
MAY
30 May 2014
New technique
first step to
stem cell
specialization
go.illinois.edu/StemCells
Image: Poh, Y.-C. et al.
go.illinois.edu/Poh
The gap between stem cell research and
regenerative medicine just became a
lot narrower. A new technique coaxes
stem cells to begin differentiating into
specific cell types, a process known as
specialization. It is the first time this critical
step has been demonstrated in a laboratory.
Mechanical Science and Engineering Professor Ning Wang (RBTE) demonstrated that
not only is it possible to induce mouse embryonic stem cells to differentiate into
developmental tissue categories in the lab, but also that this manipulation requires a
careful combination of correct timing, chemical factors and physical environment. The
team used genetically expressed fluorescent dyes to monitor the process in real time.
Illinois researchers, in collaboration with scientists at Notre Dame University and the
Huazhong University of Science and Technology (HUST) in China, published their
results in Nature Communications. This work was supported by the NIH and HUST.
5
Wilfred A. van der Donk (MMG) was
elected to the American Academy of
Arts and Sciences, one of the longest-
standing honorary societies in the
nation. In addition, for his “creative
work on the chemistry, biosynthesis
and mechanistic enzymology of the
cyclic peptide and phosphonate classes
of antibiotics,” he was awarded the
Royal Society of Chemistry’s Bioorganic
Chemistry Award for 2014.
May 2014
Department of
Chemistry, College of

49
16 May 2014
Collaborative
learning: The
OLLI Citizen
Scientist
Program
go.illinois.edu/
OLLIscientists
Albert Himoe stands in front of a cluttered
lab bench and holds a plastic tube up to
the light, looking for the small mass of DNA
16 May 2014
Genetic study
resolves
speculation
about first
people in
Americas
go.illinois.edu/
FirstInhabitants
Image: The Iconographic
Encyclopaedia of Science,
Literature and Art, 1851
go.illinois.edu/
IconographicEncyclopaedia
Numerous genetic analyses support the
widely accepted view that the original
American immigrants crossed over a land
bridge that once connected northeast Asia
to present-day Alaska. However, ancient
remains with narrower skulls and other
features distinct from most Native Americans
led to hypotheses that these individuals
came to the Americas from as far away as
Australia or Southeast Asia.
Associate Professor of Anthropology Ripan Malhi (BIOBEL/RBTE) and coauthors
reported in Science that genetic information extracted from the tooth of an
adolescent girl who fell into a sinkhole in the Yucatan 12,000 to 13,000 years ago is
unique to Native Americans, despite her unusually shaped skull.
This research was an international effort involving scientists, divers and technicians
from more than a dozen institutions. Funding was provided by the NSF, Expeditions
Council of the National Geographic Society, Archaeological Institute of America, Waitt
Institute, Pennsylvania State University, University of New Mexico, University of Texas
at Austin, DirectAMS, and Instituto Nacional de Antropología e Historia.
MORE

50
16 May 2014 U of I News Bureau
@NewsAtIllinois
Honey bees did better this winter, but it's not clear why. @IGBIllinois prof Gene
Robinson explains in @NatGeo: http://ow.ly/wVFJ3
National Geographic
U.S. Honey bee Losses Not as Severe
This Year | Nat Geo Food
By National Geographic @NatGeo
Harvard study says pesticides play a role
in the die-off of U.S. honey bees, essential
plant pollinators.
clinging to the side of the tube. It looks
like a dry wad of mucus. Himoe has spent
the last four days preparing this seemingly
insignificant speck of genetic material.
It contains a special gene that will play an integral role in genetic research on Fragile
X Syndrome (FXS), the most common cause of inherited cognitive impairment, with
20 to 30 percent being diagnosed with autism. Professor of Cell and Developmental
Biology Stephanie Ceman (GNDP) has been studying this condition since 1997.
Himoe joined Ceman’s lab in 2011 as a citizen scientist through the Osher Lifelong
Learning Institute (OLLI), a member-driven learning community for people over the
age of 50. OLLI citizen scientists are matched with scientists at Illinois based on their
knowledge, skills, and interests. They volunteer in a lab for several hours every week,
often being assigned their own task to manage for the lab.
The Citizen Scientist Program was conceived by Swanlund Chair and Professor of
Psychology and Neuroscience and Beckman Institute Director Art Kramer, Swanlund
Chair Professor of Entomology and IGB Director Gene Robinson, and former OLLI
Director Kathleen Holden in 2009. Today the program has about 15 citizen scientists
who are involved in a variety of disciplines and subject areas, from entomology to
neuroscience. Past participants include retired school teachers, bankers, gardeners,
scientists, and others.
MORE
Collaborative learning:
The OLLI Citizen
Scientist Program
Jonathan Sweedler (MMG) received the
Council for Chemical Research 2014
Malcolm E. Pruitt Award. The award
recognizes outstanding individual
contributions to the progress of chemistry
and chemical engineering through
promotion of mutually beneficial
interactions among universities, the
chemical industry, and government.
Sweedler is the first Illinois faculty
member to win the award.
May 2014
and Sciences

51
May 2014
and Sciences
Kyle Dunbar (MMG) was
chosen for the 2014
Knowles Award by the
American Chemical
Society Division of
Biological Chemistry.
Robert Emerson Professor of Plant Biology
Don Ort (BSD/GEGC Theme Leader) and
Gutgsell Endowed Professor of Crop
Sciences and Plant Biology Stephen Long
(BSD/EBI/GEGC), discuss corn belt yield limits
in a recent perspective entitled “Limits on
Yields in the Corn Belt” in Science:
In total global production, corn (maize, Zea mays L.) is the most important food and
feed crop. Of the 967 million metric tons produced in 2013, 36.5% were produced
in the United States, mostly in the Midwest Corn Belt. The United States is by far
the world's largest corn exporter, accounting for 50% of corn exports globally. Until
recently, breeding and management have allowed farmers to increase the number of
plants per acre without loss of yield per plant. On page 516 of this issue [of Science],
Lobell et al. use a detailed data set for farms across the Corn Belt, to show that
increasing yields have been accompanied by rising drought sensitivity, with important
implications for future crop yields.
The data set contains yields, environmental variables, and management variables
for Midwest corn fields in each year from 1995 to 2012. Lobell et al.'s analysis reveals
that while corn yield has increased, drought sensitivity has also increased. This may be
explained by the fact that with more plants per acre, less soil water is available to each
plant. Yield was most sensitive to water vapor pressure deficit (VPD), a factor that has
rarely been included in past analyses but that has major implications for yields as
climate change progresses in the Corn Belt.
2 May 2014
Yield limits
in the corn
belt topic of
latest science
perspective
go.illinois.edu/YieldLimits

52
APRIL
4
Antibiotic resistance is now a major global
threat to public health, according to a report
by the World Health Organization (WHO),
which said resistance is now in every region
of the world.”The report, based on data from
114 countries, focused on seven bacteria that
cause serious diseases, including pneumonia,
diarrhea and blood infections.
“Without urgent, coordinated action by many stakeholders, the world is headed for a
post-antibiotic era, in which common infections and minor injuries which have been
treatable for decades can once again kill,” said Keiji Fukuda, WHO’s Assistant Director-
General for Health Security, in a news release.
Practices such as over-prescribing, failing to finish courses of antibiotics, and reliance
on too few products are depleting our cache. The pharmaceutical industry currently
runs on less than 10 percent of the synthetic potential of the microbial world, says
Bill Metcalf (EBI/MMG Theme Leader), the G. William Arends Professor in Molecular
and Cellular Biology. That is, while the most prolific bacteria can produce 30 or 40
antibiotic compounds, scientists know of less than 10 percent of all natural products
produced by bacteria.
However, there is hope, said Doug Mitchell (MMG), an assistant professor of chemistry.
The Mining Microbial Genomes (MMG) research theme is interested in pathways and
genes that can be mined to discover novel products that are medically useful. One
goal is to generate a catalog of potential antibiotics and partner with industry to get
them to patients.
30 April 2014
A race against
evolutionary
time to
discover new
cures
go.illinois.edu/MMG
Image: Bernard Walker
© Bernard Walker, used under
a CC BY-NC 2.0 license.
go.illinois.edu/Walker

53
Animal biologist Karen Sears (GNDP/RBTE)
held a gray short-tailed opossum in front of
the camera. Special lighting had transformed
this evolutionary researcher’s everyday
laboratory into a television set for Your Inner
Fish, a three-part PBS series based on a book
by Neil Shubin (also the show’s host) that
traces 350 million years of human evolution.
During the second episode called ”Your Inner Reptile,”which aired on April 16, Sears
showed the television audience that some of the opossums’developmental processes
resemble the evolution of mammals’middle ear bones from reptile jawbones. She
described how, as embryonic opossums mature into adults, two tiny bones disconnect
from their jawbone, shrink, and move up to become their middle ear bones.
16 April 2014
IGB researcher
stars in national
TV series
go.illinois.edu/
YourInnerReptile
“We use modern techniques to discover antibiotics and other naturally occurring
products that might be anticancer agents or immunosuppressants, all of which are
complex molecules from nature that have medicinal value,” Mitchell said. “We can do
this with technologies that weren’t available to us even just a few years ago.”
MMG is already unlocking the innate potential of bacteria. Mitchell’s group developed
a novel way to screen antibiotic-producing bacteria and identify natural products that
are produced in extremely small quantities (see June 17). Metcalf created an algorithm
to analyze microbial genomic data and speed discovery of new therapeutic drugs
(see September 28). Richard E. Heckert Endowed Chair in Chemistry Wilfred van der
Donk (MMG) and Biochemistry Professor Satish Nair (MMG) made a breakthrough in
understanding how microbes build some of the powerful antibiotic agents in nature
(see November 6).
“If you look at our ancestors, who did not benefit from modern antimicrobial
chemotherapies, you can envision a future where our descendants are not going to
live lives as full and healthy as ours,” Mitchell said. “If resources aren't earmarked for
this problem, if we stay on the present course, we are in big trouble.”
22 April 2014 Genomic Biology
@IGBIllinois
The IGB Art of Science wall installation
is complete! Stop by @IGBIllinois to see
these breathtaking images.

54
“We’ve recently discovered a new species of
cockroach in the genus Xestoblatta. It’s dirty,
it’s ugly, it’s smelly, and it needs a name,”
wrote Dominic Evangelista, a Ph.D. candidate
at Rutgers University, in a blog post for
Entomology Today on March 20.
In an effort to fund a research project about tropical landscapes driving evolution,
Evangelista turned to Experiment.com, a crowdfunding site for scientific endeavors.
He offered the privilege to name the new cockroach to the highest bidder.
Swanlund Professor of Entomology May Berenbaum (GEGC), also head of the
Department of Entomology, read about the new insect’s biology and was sold. The
species, now named Xestoblatta berenbaumae, represented a quarter of the cockroach
specimens Evangelista collected in Guyana.
Evangelista presented Berenbaum with specimens of Xestoblatta berenbaumae at
Entomology 2014, ESA’s annual meeting in Portland, Oregon. “There’s no greater
honor, and no better form of immortality in science,” she said.
“What an incredibly good illustration of how little we know,” Berenbaum said. “A
quarter of the specimens collected were undescribed species!”
13 April 2014
May Berenbaum
receives a
namesake
go.illinois.edu/Cockroach
Image: Kayla Kaplan and
Dominic A. Evangelista
go.illinois.edu/
KaplanEvangelista
Don't miss Episode 2 of Your Inner Fish on PBS tonight at 9pm, featuring Karen Sears,
assistant professor at the School of Integrative Biology. Tonight's episode is entitled
Your Inner Reptile, and will showcase among other things some of the major
transitions in our ancestor's evolution. http://www.pbs.org/your-inner-fish/about/
episode-guide/
16 April 2014
9 April 2014 Genomic BIology
@IGBIllinois
Via @nprnews: What To Do Now That The Heartbleed Bug Exposed The Internet
http://n.pr/1qrIJdn

55
April 2014
April 2014
Department of Crop
Department of Animal
Agricultural, Consumer
and Environmental
Sciences; Department of
Microbiology, College of
Isaac Cann (BCXT/EBI) was awarded the Paul
A. Funk Recognition Award by the College of
Agricultural, Consumer and Environmental
Sciences, presented to faculty and academic
professionals for outstanding achievement
and major contributions to the betterment
of agriculture, natural resources, and
human systems.
Art of Science 4.0 (22 photos)
The‘Art of Science: Images from the Institute for Genomic Biology,’now in its fourth year, is
a meeting place between the University and our community as a whole, and a celebration
of common ground between science and art. — at indi go Artist Co-Op
10 April 2014
Stephen Moose (EBI/BSD/GEGC)
received a Faculty Award for Excellence
from the College of Agricultural,
Consumer and Environmental Sciences,
recognizing outstanding professional
achievement and demonstrated
excellence in the areas of teaching,
research, and extension.

56
Artists and scientists have unique ways of
discovering the mysteries of nature, yet they
share a common language—the language
of images—to communicate with the world.
The IGB’s Art of Science series, now in its
fourth year, is a celebration of common
ground between science and art. This year’s
exhibit, held April 3-7, included images of
microchannels used to sort single cells, laser
dissections of developing root tips, and honey
bees identified with colorful paint marks.
As in the past, the exhibit was displayed at the indi go Artist Co-op in Champaign,
Illinois. Art of Science images from previous years can also be seen at several locations
throughout the state: Champaign Willard Airport, Chicago Midway International
Airport, and, since February 2014, O’Hare International Airport in Chicago.
The Art of Science would not exist without the assistance of a Champaign
businessman, Doug Nelson from BodyWork Associates, who envisioned the exhibit as
a way to engage the public by showcasing the beauty of scientific research.
Array Cafe has good food down to a science
The first time I visited Array Cafe was last year, when I was lured in by a sign outside of
the Institute for Genomic Biology that read something along the lines of...
SMILEPOLITELY.COM
Of course we know how great our Array Cafe is - but it's nice to see others discovering
it as well! Check out a recent article from Smile Politely ...
2 April 2014
go.illinois.edu/SmilePolitely
3-7 April 2014
Cells to societies:
Images span
scales of
measurement,
and the border
of art and
science
go.illinois.edu/OHareAoS

57
Many popular web servers use OpenSSL to
encrypt usernames, passwords and and other
information so it cannot be accessed by a third
party when these data are transferred from
a personal computer to a website. The 1.0.1
version of OpenSSL, an open-source project,
included a mistake that allowed hackers to
retrieve information from the web server’s
memory without leaving any evidence.
Here’s how it works: when a computer is connected to the Internet, it uses a call and
response, called a heartbeat, to ensure that the website is actively waiting for its
requests. The computer sends a set of data, and the website echoes back those same
data. With Heartbleed, a hacker could request extra data from the server’s memory,
including requests made by other users such as login credentials, cookies and other
exploitable information.
The Computer Network and Resource Group (CNRG) at the IGB ran a command to see
which machines were vulnerable to Heartbleed and later installed a patch to secure
them, said CNRG Director Dan Davidson. To protect IGB users and their data, CNRG
uses firewalls and automatically locks out users for five minutes after three incorrect
attempts to log in. They also use a security monitoring systems to oversee attempts to
hack the IGB, of which there are thousands each day.
These hackers want personal information, like user names, passwords and emails, that
they can use for money-making scams. “Few are interested in stealing genomic data
because they lack the expertise to understand and exploit it,” Davidson said. “They
are trying to find a way to break into systems, so that they can send out more spam,
that gets out through more systems, so more people get duped into giving them
important information.”
1 April 2014
Heartbleed
leaves 17% of
the Internet's
web servers
vulnerable to
data theft
go.illinois.edu/CNRG
MORE

58
Medical data, including genomes, are often tied to personal information, said
C. Victor Jongeneel (GNDP), NCSA and IGB Director of Bioinformatics and Director
of HPCBio. Healthcare providers, like Mayo Clinic, and researchers are interested
in how to share medical information while also protecting it. “Clearly those are
contradictory imperatives,” Jongeneel said. “But you cannot do large scale human
genetics and find genetic causes of diseases without sharing information.”
With few human genome projects in the IGB research portfolio, the Institute is able to
focus more of its efforts on data preservation. In the meantime, Jongeneel said, “We are
trying to make sure that if we do get data that are private and sensitive, we don’t do
stupid stuff with it, and we comply with all regulatory requirements including HIPAA
[Health Insurance Portability and Accountability Act].”
Heartbleed leaves 17% of
the Internet's web servers
vulnerable to data theft
MARCH
19 March 2014
New research
seeks beneficial
qualities of
viruses
go.illinois.edu/VirusDynamics
3
Viruses are responsible for much more than
sore throats and stuffy noses. Researchers
now believe that some viruses may protect
hosts from competitors and help them
survive. Despite the fact that viruses are
practically everywhere and affect every living
thing, scientists know very little about their
positive impact on their hosts.
MORE

59
Image: Graham Beards
© Graham Beards, used
go.illinois.edu/Beards
Chemical and biomolecular engineer
Hyunjoon Kong (RBTE) and colleagues have
improved MRI (a noninvasive test that allows
doctors to see detailed pictures of tissues
and organs). To do so, they turned current
contrast agent technology on its head—or
rather, they turned it inside out. The new
compound they designed in collaboration
with Roger Adams Professor of Chemistry
Steven C. Zimmerman is not only more
effective, but also self-assembling.
When doctors perform an MRI, they administer a contrast agent: a chemical that
improves the clarity of the resulting image. In a recent ACS Nano article, the team
reported their creation of a contrast agent in the form of a nanoparticle, whose
components naturally join together in solution. The nanoparticle produced clear
diagnostic images in comparison with other contrast agents. In a second study
published in Langmuir, Kong and Smith developed a process for chemically cross-
linking the components of the nanoparticle that made the nanoparticles more stable.
The work reported in ACS Nano was a collaboration among Kong, Zimmerman, and
others at Illinois, as well as Dr. Sanjay Misra and researchers at the Mayo Clinic. Both
studies were supported by funding from the NIH and Illinois Center for Advanced Study.
17 March 2014
Combining weak
chemical forces
to strengthen a
novel imaging
technology
go.illinois.edu/ContrastAgent
The NSF awarded a five-year, $2-million grant to microbiologist Rachel Whitaker
(BCXT) and an interdisciplinary, multi-institutional team to explore the idea of viruses
and their hosts coevolving in a laboratory model system of hot springs in Yellowstone
National Park.
Sua Myong (CDMC) received
the Rose Award for Teaching
Excellence, created to foster
and reward excellence in
undergraduate teaching in the
College of Engineering.
March 2014
Department of
Engineering

60
13 March 2014
Mammoth
discovery
highlights
ancient DNA
sib.illinois.edu/malhi
Image: Mauricio Antón
© 2008 Public Library of Science,
used under a CC BY 2.5 license.
go.illinois.edu/Anton
Scientists recently unearthed one of the
world’s best-preserved wooly mammoth
specimens. Scientists hope the 43,000-year-
old specimen has intact DNA that can be
used to recreate the extinct species’ genome.
Some want to use this genetic code to clone the mammoth, nicknamed Buttercup, a
goal that presents both scientific hurdles and ethical considerations. So far, the team
has not found a complete copy of Buttercup's genome. However, they may be able to
recreate it by piecing together long fragments of DNA.
Associate Professor of Anthropology Ripan Malhi (BioBEL/RBTE) said this type of
ancient DNA research is accelerating right now, due to recent advances. “We can
do things now that we haven’t been able to do before,” Malhi said. “I like to say that
ancient DNA is in a golden era. When I was a graduate student working on ancient
DNA, it probably would’ve taken me years to sequence one complete mitochondrial
genome, and now we can do that in a week or so.”
Malhi studies the ancient history of humans (some more than 10,000 years old) in
North and South America (see July 11). While some specimens are found in arctic
conditions, similar to Buttercup, others come from shell middens, ancient trash
heaps that preserve DNA remarkably well. Malhi has found that while cultural
artifacts (like pottery) diffused over thousands of years, DNA evidence suggests that
Native American families generally remained in the same geographic region (see
May 16).
“Many North American indigenous communities lost a strong connection with their
past because of the effects of European contact and colonization,” Malhi said. “Due
to the large amount of death that happened at that time, the oral histories that may
have been passed down were limited or nonexistent. In the way of revitalizing these
communities and learning about their past, indigenous peoples can do it through
archeology, oral histories, and the use of DNA as a way of understanding their
ancestral influence.”

61
5 March 2014 Mirhee Lee
@Meeds80
A dessert fit for @IGBIllinois Scared and
excited to eat it! Hope it doesn't taste like
a mouse!
Scientists discovered the largest known
virus, buried 100 feet within the Siberian
permafrost, where it has been hidden for
30,000 years. In a laboratory, they reactivated
the ancient virus and found that it infects
single-celled amoebas.
This discovery has raised concerns that other viruses, including smallpox found in
frozen corpses, may be released as the planet warms. “But think about what they did,”
said Maria Bautista, a graduate student in the lab of Microbiology Professor Rachel
Whitaker (BCXT). “They took the samples to a lab and put the viruses on a plate of
cells that were just waiting to be infected. The chances are slim that this virus would
just aerosolize where a live, active amoeba is hanging out on the frozen tundra.”
Instead of the arctic tundra, Whitaker’s lab is hunting for new viruses in acidic hot
springs at Yellowstone National Park and Kamchatka, Russia (see March 19). “Obviously
they are completely different environments, but the strategies we use are very similar,”
Bautista said. “We are both looking for novel, different viruses.”
3 March 2014
Scientists
‘resurrect’
30,000-year-old
giant virus
life.illinois.edu/whitaker/
Image:
Brocken Inaglory
© Brocken Inaglory, used
go.illinois.edu/Inaglory
MORE

62
FEBRUARY
Whitaker is a member of the Biocomplexity (BCXT) research theme, which uses
genomics to explore the interplay between evolution and ecology, especially in
extreme environments. Other IGB research explores how viruses integrate themselves
into an organism’s genome (see September 23). To date, scientists estimate that they
have only explored one percent of existing viral diversity.
“We really don't understand how host-virus interactions are shaping the evolution of
natural populations,” Bautista said. “To do so, we need to go find these viruses, find out
if they can confer any benefit to their hosts, or if they make them sick. If we don't find
them, and we don't study these interactions, we are always going to be missing part
of the equation.”
Scientists ‘resurrect’
30,000-year-old giant virus
MORE
2

63
25 February 2014
Team converts
sugarcane to a
cold-tolerant, oil-
producing crop
go.illinois.edu/PETROSS
A multi-institutional team reports that it
can increase sugarcane’s geographic range,
boost its photosynthetic rate by 30 percent
and turn it into an oil-producing crop for
biodiesel production.
Stephen Long (BSD/EBI/GEGC), Gutgsell Endowed Professor of Crop Sciences and Plant
Biology, and his team have an ambitious goal: to enable growers to meet 69 percent of
the U.S. mandate for renewable fuels by growing the modified sugarcane on abandoned
land in the southeastern United States. The team presented its latest findings on
February 25 at the DOE’s Advanced Research Projects Agency-Energy (ARPA-E) Energy
Innovation Summit in Washington, D.C. ARPA-E supported this research.
February 2014
and Biomolecular
Engineering
Brendan Harley (RBTE) received the
Everitt Award for Teaching Excellence
from the College of Engineering for
development of an innovative elective
course on tissue engineering. The
winner of this award is selected by
students from the Engineering Council.
24 February 2014 Genomic Biology
@IGBIllinois
Genomic Biology
@IGBIllinois
@zeiss_micro Key Account Manager Sam
Byerly sent us an @ohare Art of Science
exhibit #scienceselfie. #IGB #ILLINOIS
@zeiss_micro Love this #scienceselfie and
your cutting-edge #microscopes that
made this @Sci_Art exhibit possible. pic.
twitter.com/XVdGnQGVMZ
ZEISS Microscopy
@zeiss_micro
@IGBIllinois and we love your #sciart exhibit! best wishes from the whole team ;)

64
February 2014
and Biomolecular
Engineering
Christopher Rao (BSD/
EBI) received the
Excellence in Research
Award from the College
of Engineering for his
research accomplishments
in the area of biomolecular
engineering, on topics
such as infectious disease,
bioenergy production, and
synthetic biology.
24 February 2014 Genomic Biology
@IGBIllinois
Still haven't found an outfit to debut on the @TheEllenShow? We've got the #science
grad students covered. #Ellenois pic.twitter.com/iMSU23PmFC
Caroline
@c_cvetkovic
@IGBIllinois or these outfits? :) #scienceselfie @TheEllenShow
Genomic Biology
@IGBIllinois
@c_cvetkovic LOVE IT! Can't believe these didn't make the cut. Maybe there will be a
next time, @TheEllenShow? #ILLINOISlove #SCIENCElove

65
12 February 2014
Advanced
techniques
yield new
insights into
ribosome self-
assembly
go.illinois.edu/
RibosomeAssembly
The Art of Yellowstone Science: Mammoth Hot Springs as a Window on
Evolutionary Processes
Friday, 14 February 2014 at 12:00
Carl R. Woese Institute for Genomic Biology in Urbana, Illinois
Don't miss our upcoming talk this Friday with geologist Bruce Fouke as he discusses
the Art of Yellowstone Science - part of the NASA Astrobiology Institute Seminar
Lecture Series.
10 February 2014
Ribosomes, the cellular machines that build
proteins, are themselves made up of dozens
of proteins and a few looping strands of
RNA. A study reported in Nature offered new
clues about how the ribosome, the master
assembler of proteins, also assembles itself.
Better understanding of how the ribosome
is put together may suggest new possible
antibiotic targets. The NSF and HHMI funded
this project.
“The ribosome has more than 50 different parts—it has the complexity of a sewing
machine in terms of the number of parts,” said Gutgsell Professor of Physics Taekjip
Ha (CDMC Theme Leader). “A sewing machine assembles other things, but it cannot
assemble itself if you have the parts lying around. The ribosome, however, can do that.
It’s quite amazing.”
Ha, who led the research, worked with William and Janet Lycan Professor of Chemistry
Zaida Luthey-Schulten (BCXT) and Johns Hopkins University Biophysics Professor
Sarah Woodson. Together, they discovered that as a ribosome comes together, the
first component protein to be added tends to bind to RNA when the RNA takes on
an unusual conformation—one not seen in the fully assembled ribosome. Shape and
flexibility of the RNA may help subsequent proteins to incorporate themselves into
the ribosome as it forms.

66
The sports of the Winter Olympics are
filled with a sparkling, daredevil charm that
distinguishes the Games from their summer
counterpart. Several first-time American
Olympians returned from the 2014 Winter
Games, held February 7-23 in Sochi, Russia,
with gold medals in snowboard and ski
events. However, two stellar and popular
skiers, Bode Miller and Lindsey Vonn, were
forced to miss events by another ubiquitous
aspect of these winter sports: serious and
recurring injury.
Both Miller and Vonn have undergone knee surgeries in the past few years, followed
by lengthy recovery processes. A recent study of elite winter athletes suggested that
more severe injuries are more frequent than milder ones, in contrast to high-risk
summer sports, in which injury frequency typically drops as severity increases. The
majority of the severe injuries seen in many winter sports are knee ligament injuries.
Connective tissue damage is difficult to heal; scar tissue forms readily, and current
treatments rely on reconstructing or transplanting tissue, strategies that leave the
joint less stable and more vulnerable to relapse.
What if injured tendons or ligaments could be coaxed to recover by using some of the
same growth processes that formed them in the first place? Researchers, including
many in the Regenerative Biology Tissue Engineering (RBTE) research theme, are
working to create medical technologies that would actively promote regrowth of
damaged bone, muscle, and connective tissues. Brendan Harley (RBTE), an assistant
professor in the Department of Chemical and Biomolecular Engineering, and his lab
are engaged in a particularly complex challenge: how to regenerate the interfaces
between multiple tissues, such as tendon and bone.
7 February 2014
Winter
Olympics
highlight
sports’
triumphs and
pitfalls
go.illinois.edu/RBTEtheme
Image:
© Misha Tenetko, used under
a CC BY-NC 2.0 license.
go.illinois.edu/Tenetko

67
February 2014
Department of
Engineering
Jun S. Song (CDMC) was named
the first Founder Professor of the
Department of Bioengineering as
part of the Grainger Engineering
Breakthroughs Initiative established
in 2013 to support big data and
bioengineering by enhancing facilities,
funding student scholarships, and
bringing senior faculty to Illinois.
“The tissues in our body are not uniform. Instead they contain patterns and gradients
essential to their function. What I'm most excited about is how you develop
biomaterials that replicate these heterogeneities in order to promote regeneration,”
Harley said. One technology his lab is developing: a porous “collagen foam, like a
kitchen sponge,” that could be taken from storage in an operating room, loaded with
a patient’s own cells (see July 17 and May 30) , and implanted in the body to actively
promote regeneration of the tendon-bone interface. This collagen scaffold contains
structural, mechanical, and biochemical signals that aid and guide tissue growth.
Part of Harley’s research is to consider how the collagen scaffold can be designed
so that the rate of tissue formation is synchronized with the rate at which the
scaffold naturally degrades inside the body. Another critical engineering challenge
is to balance competing concerns between the porosity of the scaffold required to
promote healing and the strength of the scaffold required for it to remain intact in
the patient.
“You can make scaffolds stronger by making them less porous, but that impairs both
the cells' ability to get in, and the ability for nutrients to diffuse in,” Harley said. “In
our group, we've been inspired by design principles you see in porcupine quills and
sunflower stalks. In these bioinspired structures, we’re integrating reinforcing elements
such as high-density membrane shells or fiber reinforcement structures to create a
composite scaffold that has the requisite strength and porosity.” In a few more years,
this technology and others like it may restore the physical fitness of orthopedic
patients, whether their arena is an Olympic slope or their own back yard.
2014 Summer Internship for Native Americans in Genomics
University of Illinois and University of Texas partner to host the Summer Intership for
Native Americans in Genomics (SING) Workshop.
IGB.ILLINOIS.EDU
We've partnered with the Department of Anthropology, and the Native American
and Indigenous Studies Program at the University of Texas at Austin, to host the next
Summer Internship for Native Americans in Genomics (SING) Workshop.
4 February 2014

68
January 2014
2014 winter
defined by
polar vortex
The winter of 2014 was marked by heavy
snowfall and record low temperatures. On
January 6, 2014, Central Illinois was colder
than Anchorage, Alaska. Non-essential
Illinois employees were encouraged to stay
home when temperatures plummeted to -6
degrees Fahrenheit, with a wind chill of -40.
Meteorologists partly credited this unusually cold weather to the polar vortex,
a pocket of extremely cold air that usually circulates around the Earth’s poles. A
recent study established a link between the effects of climate change, i.e. warming
oceans and melting ice, and the distorted polar vortex bringing arctic weather more
frequently into the Midwest.
This isn’t the first time that America’s Heartland will experience the ill effects of climate
change, nor will it be the last. The summer of 2012 was characterized by record heat
JANUARY
1

69
and widespread drought. This increasing variability is just as concerning as the warming
trend, said Jim Angel, the Illinois State Climatologist. The Genomic Ecology of Global
Change (GEGC) research theme predicts what these changes will mean for ecosystems
and develops ways to overcome these challenges to meet humanity’s needs.
Using novel technologies, researchers in the GEGC theme are able to simulate rising
temperatures and levels of carbon dioxide and ozone to study how agronomic
ecosystems will respond to climate change.
GEGC experts reported that as carbon dioxide levels rise, crops become less nutritious
(see June 3). “When we take all of the FACE [Free Air Concentration Enrichment]
experiments we’ve got around the world, we see that an awful lot of our key crops
have lower concentrations of zinc and iron in them at high CO2,“ said Andrew Leakey
(EBI/GEGC), associate professor of plant biology. “And zinc and iron deficiency is a big
global health problem already for at least 2 billion people.”
Fellow GEGC members Stephen Long (BSD/EBI/GEGC) and Don Ort (GEGC/BSD),
both professors in plant biology and crop sciences, are engineering plants that
photosynthesize more efficiently and therefore produce more. It’s not a silver bullet,
but this increase in yield can help meet growing demands and compensate for yield
hits from climate change (see June 25).

70
7 January 2014 Lindsey Vonn
I am devastated to announce that I will not be able to compete in Sochi. I did
everything I possibly could to somehow get strong enough to overcome having no
ACL but the reality has sunk in that my knee is just too unstable to compete at this level.
I'm having surgery soon so that I can be ready for the World Championships at home
in Vail next February. On a positive note, this means there will be an additional spot so
that one of my teammates can go for gold. Thank you all so much for all of the love and
support. I will be cheering for all of the Olympians and especially team USA! XO Lindsey
Through DNA analysis, Animal Sciences
Professor Alfred Roca (GNDP) has disproved
years of rumors and hearsay surrounding
the ancient Battle of Raphia, the only
known battle between Asian and African
elephants. This work was supported by the
United States Fish and Wildlife Service and
published in the Journal of Heredity.
The battle took place in 217 B.C. between Ptolemy IV, the King of Egypt, and
Antiochus III the Great, the King of the Seleucid kingdom that reached from modern-
day Turkey to Pakistan. In 1948, Sir William Gowers reasoned that Ptolemy must have
fought with forest elephants that fled from larger Asian elephants, as Greek historian
Polybius described 100 years after the battle. Until now, the question remained: Did
Ptolemy employ African savanna elephants (Loxodonta africana) or African forest
elephants (Loxodonta cyclotis) in the Battle of Raphia?
“Using three different markers, we established that the Eritrean elephants are
actually savanna elephants,” said Adam Brandt, a doctoral candidate in Roca’s lab.
“Their DNA was very similar to neighboring populations of East African savanna
elephants, but with very low genetic diversity, which was expected for such a small,
isolated population.”
9 January 2014
War elephant
myths debunked
by DNA
go.illinois.edu/WarElephant
January 2014 Amy Wagoner Johnson (RBTE) was awarded a Chair of
Excellence by the NanoSciences Foundation. This award
program attracts talented researchers to collaborate
with laboratories on progressive research projects in
Grenoble, France. (Department of Mechanical Science
and Engineering, College of Engineering)

71
Kingman Arts PhotoBlog
Happy New Year!
via the-science-llama
1 January 2014
31 December 2013
January 2014 Brian T. Cunningham (MMG) was elected
as a 2013 Charter Fellow of the National
Academy of Inventors (NAI). According to
the NAI, election is a “high professional
distinction accorded to academic inventors
who have demonstrated a highly prolific
spirit of innovation in creating or facilitating
outstanding inventions that have made a
tangible impact on quality of life, economic
development, and the welfare of society.
Ed Yong
@edyong209
If you had a [lousy] 2013, regression to the mean is your friend in 2014. If you had a
good 2013, ignore this tweet, what do I know?
Department of Electrical
and Computer Engineering,
College of Engineering

72
IGB NUMBERS IN 2014
Just as a year is made of months,
made of days, our Institute is made
of transdisciplinary themes, made of
faculty, who believe that collaboration
is the linchpin of discovery. Their
breakthroughs, detailed in publications
that include Science and Nature, are
made possible by the generous support
of funding agencies and donors.

73
Agricultural
Engineering
Sciences
Building
Plant Sciences Lab
Large Animal Clinic
Small Animal Clinic
College of Education
Building
Animal Sciences Lab
Mumford Hall
Burrill Hall
Morrill Hall
Davenport Hall
Chemical and Life
Sciences Laboratory
Carl R. Woese IGB
Turner Hall
Edward R. Madigan Laboratory
National Soybean
Research Center
Beckman Institute
Micro Nanotechnology Lab
Computing Applications Building
Digital Computer Lab
NCSA
Newmark
Lab
Transportation
Building
Siebel Center for
Computer Science
Mechanical Engineering Building
Loomis
Altgeld
Noyes
Lab
Materials
Science
Engineering
Computing Applications Building
Shelford
Vivarium
Illini Hall
Psychology Building
Medical Sciences Building
Everitt Lab
Henry Administration Building
Lincoln Hall
Faculty: 69
Affiliates: 69
Administration: 43
IGB Fellows: 6
Visiting Researchers: 20
Student Staff: 38
Research Staff: 141
Post Docs: 144
Undergraduates: 245
Graduate Students: 376
PEOPLE
IGB faculty span
7 colleges and
32 departments
TOTAL: 1151
NCSA Petascale Computing
College of Law
Building
College of Business Building
Freer Hall
Roger Adams Lab

74
Chemla,Y.R., Ha,T. ”Ultraslow relaxation of confined DNA.” Science. 2014, 345:380-381.
Kennett DJ, Asmerom Y, Kemp BM, Polyak V, Bolnick DA, Malhi RS, Culleton BJ. Early
Americans: misstated results. Science. 2014, 345:390.
Watanabe J, Hattori M, Berriman M, Lehane MJ, Hall N, Solano P, Aksoy S, Hide W, Touré
Y, Attardo GM, Darby AC, Toyoda A, Hertz-Fowler C, Larkin DM, Cotton JA, Sanders MJ,
Swain MT, Quail MA, Inoue N, Ravel S, Taylor TD, Srivastava TP, Sharma V, Warren W,
Wilson RK, Suzuki Y, Lawson D, Hughes DST, Megy K, Masiga DK, Mireji PO, Hansen IA,
Van Den Abbeele J, Benoit JB, Bourtzis K, Obiero GFO, Robertson HM, Jones JW, Zhou
J-J, Field LM, Friedrich M, Nyanjom SRG, Telleria EL, Caljon G, Ribeiro JMC, Acosta-
Serrano A, Ooi C-P, Rose C, Price DP, Haines LR, Christoffels A, Sim C, Pham DQD,
Denlinger DL, Geiser DL, Omedo IA, Winzerling JJ, Peyton JT, Marucha KK, Jonas M,
Meuti ME, Rawlings ND, Zhang Q, Macharia RW, Michalkova V, Dashti ZJS, Baumann
AA, Gäde G, Marco HG, Caers J, Schoofs L, Riehle MA, Hu W, Tu Z, Tarone AM, Malacrida
AR, Kibet CK, Scolari F, Koekemoer JJO, Willis J, Gomulski LM, Falchetto M, Scott MJ,
Fu S, Sze S-H, Luiz T, Weiss B, Walshe DP, Wang J, Wamalwa M, Mwangi S, Ramphul UN,
Snyder AK, Brelsfoard CL, Thomas GH, Tsiamis G, Arensburger P, Rio RVM, Macdonald
SJ, Panji S, Kruger A, Benkahla A, Balyeidhusa ASP, Msangi A, Okoro CK, Stephens D,
Stanley EJ, Mpondo F, Wamwiri F, Mramba F, Siwo G, Githinji G, Harkins G, Murilla G,
Lehväslaiho H, Malele I, Auma JE, Kinyua JK, Ouma J, Okedi L, Manga L, Aslett M, Koffi
M, Gaunt MW, Makgamathe M, Mulder N, Manangwa O, Abila PP, Wincker P, Gregory R,
Bateta R, Sakate R, Ommeh S, Lehane S, Imanishi T, Osamor VC, Kawahara Y. Genome
sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
Science. 2014, 344:380-386.
Chatters JC, Kennett DJ, Asmerom Y, Kemp BM, Polyak V, Blank AN, Beddows PA,
Reinhardt E, Arroyo-Cabrales J, Bolnick DA, Malhi RS, Culleton BJ, Erreguerena PL,
Rissolo D, Morell-Hart S, Stafford TW Jr. Late Pleistocene human skeleton and mtDNA
link Paleoamericans and modern Native Americans. Science. 2014, 344:750-754.
Cooper KL, Sears KE, Uygur A, Maier J, Baczkowski KS, Brosnahan M, Antczak D,
Skidmore JA, Tabin CJ. Patterning and post-patterning modes of evolutionary digit
loss in mammals. Nature. 2014, 511:41-45.
Moroz LL, Kocot KM, Citarella MR, Dosung S, Norekian TP, Povolotskaya IS, Grigorenko
AP, Dailey C, Berezikov E, Buckley KM, Ptitsyn A, Reshetov D, Mukherjee K, Moroz TP,
Bobkova Y, Yu F, Kapitonov VV, Jurka J, Bobkov YV, Swore JJ, Girardo DO, Fodor A, Gusev
F, Sanford R, Bruders R, Kittler E, Mills CE, Rast JP, Derelle R, Solovyev VV, Kondrashov FA,
Swalla BJ, Sweedler JV, Rogaev EI, Halanych KM, Kohn AB. The ctenophore genome
and the evolutionary origins of neural systems. Nature. 2014, 510:109-114.
Myers SS, Zanobetti A, Kloog I, Huybers P, Leakey AD, Bloom AJ, Carlisle E, Dietterich
LH, Fitzgerald G, Hasegawa T, Holbrook NM, Nelson RL, Ottman MJ, Raboy V, Sakai H,
Sartor KA, Schwartz J, Seneweera S, Tausz M, Usui Y. Increasing CO2 threatens human
nutrition. Nature. 2014, 510:139-142.
IGB FY14 PUBLICATIONS
268 papers published, 9 in Science or Nature
SCIENCE
NATURE
Highlighted authors are
IGB members or affiliates.

75
“High Resolution Sensing and Control of Electrohydrodynamic Jet Printing”
Andrew Alleyne, John Rogers, Kira Barton, Placid Ferreira, Sandipan Mishra
“Compositions and Methods Including Cell Death Inducers and Procaspase Activation”
Karson Putt, Paul Hergenrother, Quinn Peterson, Valerie Fako
“Materials and Methods for Autonomous Restoration of Electrical Conductivity”
Aaron Finke, Aaron Jackson, Benjamin Blaiszik, Jeffrey Moore, Joshua Ritchey, Khalil
Amine, Marta Baginska, Mary Caruso, Nancy Sottos, Paul Braun, Scott White, Susan Odom
“Therapeutic Methods and Agents for Treating Myotonic Dystrophy”
Chun-Ho Wong, Jessie Peh, Paul Hergenrother, Steven Zimmerman
ECONOMIC DEVELOPMENT
By the end of FY14 the IGB had 101 total disclosures, including 33 from the EBI, and
58 patent applications, of which 17 were from the EBI.
101 TotalFY14: 15
11 58
9
134
3
Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Jr.,
Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R,
Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman
PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM,
Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux
F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E.
The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
Nature. 2014, 506:225-229.
Kim H, Abeysirigunawarden SC, Chen K, Mayerle M, Ragunathan K, Luthey-Schulten Z,
Ha T, Woodson SA. Protein-guided RNA dynamics during early ribosome assembly.
Nature. 2014, 506:334-338.
MORE
DISCLOSURES
PATENT APPLICATIONS
LICENSES OPTIONED
PATENTS ISSUED
Patents Issued
IGB CORE FACILITIES USAGE
FY14 Users – 109 Research Groups, 293 active users

76
IGB GRANT FUNDING
MORE
Economic
Development
FY
14
FY
05
FY
06
FY
07
FY
08
FY
09
FY
10
FY
11
FY
12
FY
13
$5M$0M $10M $15M $20M $25M $30M
NSF
$961,202
NSF
$1,627,806
NSF
$1,480,541
NSF
$1,370,637
NSF
$1,180,535
NSF
$1,467,853
NSF
$1,652,255
NSF
$488,046
NSF
$558,646
NSF
$1,837,319
NIH
$7,613,918
NIH
$9,008,327
NIH
$1,497,047
NIH
$1,469,892
NIH
$1,671,720
NIH
$208,788
NIH
$9,477,991
NIH
$10,972,645
NIH
$10,180,004
USDA
$36,736
USDA
$1,160,155
USDA
$2,825,589
USDA
$5,480,164
USDA
$5,493,000
EBI
$11,926,813
EBI
$14,098,112
EBI
$14,064,422
EBI
$18,810,366
EBI
$15,831,720
EBI
$14,775,498
EBI
$14,484,742
Other
$7,275,794
Other
$11,712,818
Other
$652,156
Other
$191,033
Other
$1,222,500
Other
$15,263
Other
$227,664
Other
$60,013
DOE
$2,949,350
DOE
$779,089
DOE
$355,000
DOE
$198,429
DOE
$1,300,320
DOE
$399,545
DOE
$1,982,384
DOE
$3,907,214
DOE
$362,855
DOE
$140,000
FY14 Total: $30,763,813
Department of Energy
(DOE)
National Institutes of Health
(NIH)
National Science Foundation
(NSF)
United States Department of
Agriculture (USDA)
Energy Biosciences Institute
(EBI)
Other

77
GIVING AND DONOR ROLL
Thank you to all the individuals, foundations, corporations, and organizations that
have supported the Carl R. Woese Institute for Genomic Biology. All gifts to the IGB
from July 1, 2013 to June 30, 2014 are included in the Honor Roll. Gifts may include
any of the following: cash, stock, matching gifts, grants, bequests, planned gifts, gifts-
in-kind, real estate, and paid life insurance.
Great care was taken to ensure the accuracy of the Honor Roll listings. We would
appreciate you alerting us to any errors or omissions. Please direct your inquiries to
Melissa McKillip, IGB Development and Outreach Director, at mmckilli@illinois.edu or
(217) 333-4619.
American Society of Plant Biologists
Anonymous
Bill Melinda Gates Foundation
BodyWork Associates
Donald Danforth Plant Science Center
Sharon M. Donovan
Carol and Francis Egan
ExxonMobil Foundation
Karl Fogel
Howard O. Grundy
Insomnia Cookies
Irene L. Lange
George Lewin
Martha Loustaunau
Melissa J. McKillip
Microsoft Corporation
Monsanto Company
Robert E. Morgan
Sara and Donald Ort
Renaissance Charitable Foundation, Inc.
Julia and Gene Robinson
Roy J. Carver Charitable Trust
Mirian A. Schaup
Jeffrey A. Shular
Sandra Perry Sigman
Simons Foundation
The Burroughs Wellcome Fund
Daniel J. Wolf

Image: JD Maloney
go.illinois.edu/Maloney

Managing Editor
Printing
Design
Images
Writing
Nicholas Vasi
Original Smith Printing
Mirhee Lee
Kathryn Coulter
Contributing photographers and illustrators: Haley Ahlers, Mauricio Antón, Graham
Beards, Dominic Evangelista, Ron Evans, Alexander Francis, Don Hamerman, Barbara
Hug, Brocken Inaglory, Tiffany Jolley, Kayla Kaplan, Victor Korniyenko, Jason Lindsey, JD
Maloney, Carl Osmond, Norbert Potensky, Harrison Schmitt, Peggy Sirota, Susan Sprunt,
Brian Stauffer, Claire Sturgeon, Misha Tenetko, John Tenniel, Bernard Walker
Claudia Lutz and Claire Sturgeon
Contributing writers: Liz Ahlberg, Phil Ciciora, Dusty Rhodes, Siv Schwink, Diana Yates

UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
CARL R. WOESE INSTITUTE FOR GENOMIC BIOLOGY
Where science meets society • igb.illinois.edu

WHAT DO THESE ICONS MEAN?
This annual report is a chronicle of news and events in 2014. The IGB news stories feature the four
pillars of the Institute’s mission, denoted by the icons below. Interspersed with these stories are
world news items that highlight connections between ongoing IGB research and current global
issues. Combined, these stories illustrate that the IGB is the vertex where science meets society.
EDUCATIONRESEARCH WORLD NEWSCOMMUNITYPARTNERSHIPS
T WIT TER
FACEBOOK
INSTAGRAM RECOGNITIONS
YOUTUBE
BCXT Biocomplexity
BSD Biosystems Design
BIOBEL Business, Economics and Law of Genomic Biology
CDMC Cellular Decision Making in Cancer
GEGC Genomic Ecology of Global Change
GNDP Gene Networks in Neural Developmental Plasticity
MMG Mining Microbial Genomes
RBTE Regenerative Biology Tissue Engineering
EBI Energy Biosciences Institute
CNLM Center for Nutrition, Learning, and Memory
AAAS American Association for the Advancement of Science
ARS Agricultural Research Service
IGB Carl R. Woese Institute for Genomic Biology
DOE Department of Energy
HHMI Howard Hughes Medical Institute
IUB NASA Astrobiology Institute for Universal Biology
NIH National Institutes of Health
NSF National Science Foundation
USDA United States Department of Agriculture
ABBREVIATIONS AND ACRONYMS
IGB RESEARCH
THEMES
OTHER
ABBREVIATIONS
AND
ACRONYMS
IGB STRATEGIC
INDUSTRY
PARTNERSHIPS

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