Humans will soon embark on a detailed characterization of habitable planets beyond the solar system. Space-based telescopes probing the atmospheres of small planets around nearby stars will shortly be joined by ground-based observatories. What should these instruments be looking for?
Christopher Reinhard, an assistant professor in the School of Earth and Atmospheric Sciences, aims to define the atmospheric chemistries that provide strong evidence for the presence of life at a planet’s surface – or atmospheric biosignatures. He recently received a three-year grant from NASA’s Exobiology Program to develop a model of Earth’s early atmosphere and ocean, about 4 billion years ago, when the planet was devoid of oxygen.
Joining Reinhard on this research is a multi-institutional team, including co-principal investigators Shawn Domagal-Goldman of NASA Goddard Space Flight Center and Andrew Ridgwell of the University of California, Riverside, as well as collaborators Kazumi Ozaki of the University of Tokyo and Giada Arney of NASA Goddard Space Flight Center.
“Our ultimate aim is to develop robust atmospheric biosignatures for future analysis of extrasolar worlds, while providing computational tools for understanding the deep past and forecasting the long-term future of Earth’s biosphere. We’re fortunate to have support from NASA to take a big step in that direction.”
In looking for life beyond our solar system, Earth “provides a powerful natural lab for examining the processes that promote the emergence and maintenance of atmospheric biosignatures,” Reinhard says. However, Earth’s current atmospheric biosignatures come from eons of interactions between microbes, the oceans, and the Earth’s evolving geology. Reinhard’s team believes the most relevant atmospheric biosignatures in the search for extraterrestrial may be those from Earth’s very early age, before photosynthesis blanketed the planet with oxygen.
Using the NASA grant, Reinhard’s team will examine the metabolic networks that would have controlled atmospheric biosignatures on the primitive Earth. The research will be aimed at developing an “ecophysiological module” that links microbial metabolism with ocean chemistry. The module will be embedded within an ensemble of computational models of atmospheric chemistry, climate, and 3-D ocean chemistry.
“We think this research will provide significant steps forward in our predictive understanding of the links between microbial metabolism and atmospheric chemistry, and will refine our understanding of the early evolution of Earth’s biosphere,” Reinhard says. “Our ultimate aim is to develop robust atmospheric biosignatures for future analysis of extrasolar worlds, while providing computational tools for understanding the deep past and forecasting the long-term future of Earth’s biosphere. We’re fortunate to have support from NASA to take a big step in that direction.”
The Georgia Tech Algorithms, Combinatorics, and Optimization Program (ACO) has selected Chun-Hung Liu to receive the 2018 ACO Outstanding Student Prize. The award recognizes academic excellence in the areas represented by ACO.
Liu’s selection is based on two major accomplishments. First, he did breakthrough research as a Ph.D. student by resolving the Robertson conjecture for topological minors, namely that graphs that do not have a Robertson chain of fixed length as a topological minor are well-quasi-ordered.
Second, Liu developed and refined parts of the classical Robertson-Seymour theory, discovering entirely new methods alongside. In addition, he is honored for displaying an exemplary attitude toward research and scholarship.
Liu received B.S. and M.S. degrees in mathematics from the National Taiwan University, in Taiwan. After completing the Georgia Tech Ph.D. program in Algorithms, Combinatorics, and Optimization in 2014, he joined Princeton University as an instructor. In 2018, he moved to Texas A&M University as an assistant professor of mathematics.
“I am very grateful to Prof. Thomas for his constant support and encouragement during my life at Georgia Tech. His professionalism, passion, and leadership undoubtedly shaped my development.”
School of Mathematics Professor Robin Thomas was Liu’s supervisor at Georgia Tech. Thomas recalls Liu as “a very strong student,” passing the comprehensive examination early and then writing four strong papers in quick succession. This achievement earned Liu the school’s Top Graduate Student Award while only in his second year. “I expect he will become a regular invitee to Graph Theory meetings in Oberwolfach, Banff, and elsewhere,” Thomas says.
Liu says he “deeply benefited” from ACO, which he describes as a “wonderful multidisciplinary program that integrates three fascinating and active directions in an amazingly terrific way.”
Liu adds: “I am very grateful to Prof. Thomas for his constant support and encouragement during my life at Georgia Tech. His professionalism, passion, and leadership undoubtedly shaped my development.”
Scientists share the scoop on how your cat’s sandpapery tongue deep cleans
Albuquerque Journal, Nov. 30, 2018
Cat lovers know when kitties groom, their tongues are pretty scratchy. Using high-tech scans and some other tricks, scientists are learning how those sandpapery tongues help cats get clean and stay cool. The secret: Tiny hooks that spring up on the tongue – with scoops built in to carry saliva deep into all that fur.
That's the finding of research in the lab of David Hu, an associate professor in the Schools of Mechanical Engineering and of Biological Sciences. Hu is also an adjunct professor in the School of Physics.
Hu's Ph.D. student Alexis Noel, who conducted the study, is seeking a patent for a 3D-printed, tongue-inspired brush.
Fifteen Georgia Tech scientists have made the 2018 Highly Cited Researchers list; nine of them are affiliated with the College of Sciences:
- Claire Berger, Physics
- Jean-Luc Brédas, Cross-Field
- Edward Conrad, Physics
- Mostafa El-Sayed, Chemistry
- Walter de Heer, Physics
- Nga Lee (Sally) Ng, Geosciences
- Arthur Ragauskas, Cross-Field
- Zhong Lin Wang, Chemistry, Materials Science, Physics
- Younan Xia, Chemistry, Materials Science, Physics
Clarivate Analytics Web of Science compiled the list, which is based on citations of papers published from 2006 to 2016. It features at least 6,000 unique authors who amassed sufficient citations to place them among the top 1% most cited in at least one of 21 subject fields.
The 2018 list is the first to identify researchers with Cross-Field impact. These researchers had substantial impact over several fields during 2006-16.
Claire Berger is a professor of the practice in the School of Physics. Her scientific interests center on nanoscience and electronic properties of graphene-based systems.
Edward Conrad is a professor in the School of Physics. He specializes in the study of surface order, thermal stability of surfaces to the formation of extended defects, and two-dimensional growth.
Jean-Luc Brédas is Regents Professor in the School of Chemistry and Biochemistry. His group studies organic materials with promising characteristics for electronics, photonics, and information technology. Brédas is among researchers identified with Cross-Field impact.
Mostafa El-Sayed is Regents Professor in the School of Chemistry and Biochemistry. Currently his research focuses on the use of nanoparticles in treating cancer.
Walter de Heer is Regents Professor in the School of Physics. He is renowned for research on nano-patterned epitaxial graphene and nanoclusters in beams.
Nga Lee “Sally” Ng is an associate professor with joint appointments in the School of Earth and Atmospheric Sciences and the School of Chemical and Biomolecular Engineering. She studies aerosols, including their formation, life cycle, and health effects of aerosols.
Arthur Ragauskas is a professor in the School of Chemistry and Biochemistry. His research focuses on the green chemistry of biopolymers including cellulose, hemicellulose, and lignin. Ragauskas is among scientists identified with Cross-Field impact.
Zhong Lin Wang is Regents Professor in the School of Materials Science and Engineering and an adjunct professor in the School of Chemistry and Biochemistry. Wang is one of several authors cited in three subject fields.
Younan Xia is a professor with joint appointments in the Wallace H. Coulter Department of Biomedical Engineering, School of Chemistry and Biochemistry, and the School of Chemical and Biomolecular Engineering. Xia is widely known for seminal contributions to shape-controlled synthesis of metal nanocrystals with major impact on catalysis, plasmonics, and biomedicine. Xia is one of several authors cited in three subject fields.
Berger, El-Sayed, de Heer, Ng, Wang, and Xia were also in the 2017 list of highly cited researchers.
Other Georgia Tech researchers on the 2017 list of highly cited researchers are:
- Ian Akyildiz, Computer Science
- Yong Ding, Cross-Field
- Geoffrey Ye Li, Computer Science
- Zhiqun Lin, Cross-Field
- Meilin Liu, Cross-Field
- Gleb Yushin, Materials Science
What The National Climate Assessment Means For Rural, Coastal Georgia
On Second Thought, GPB
November 27, 2018
While many Americans scanned websites and superstore aisles for deals on Black Friday, and others recovered from Thanksgiving food comas, the Trump administration released a major new report on climate change.
The 1,600-page National Climate Assessment was published by the U.S. Global Change Research Program, a group of 13 federal agencies including the Department of Defense, the Environmental Protection Agency and NASA. The news inside that report is not good for a number of Georgia industries, including agriculture.
Kim Cobb, a climate scientist and director of the Global Change Project at Georgia Tech, spoke about the major takeaways from this report as well as efforts to fight climate change on Georgia's coast. Cobb is a professor in the School of Earth and Atmospheric Sciences.
Listen to the broadcast here.
Perfect stir-fried rice recipe is all a matter of maths, say scientists
MSN
November 19, 2018
The beauty of our universe is that it can be described by elegant mathematical formulas and patterns. That beauty, it seems, extends to stir-fried rice. David Hu and his team tracked the movements of the chef when stirring the rice. They called these oscillations. Based on those oscillations, they created a mathematical model that would, theoretically, make the perfect stir-fried rice. And a robot chef to program it into may not be far away. Now, who's hungry?
Hu is an associate professor in the Schools of Mechanical Engineering and of Biological Sciences and an adjunct associate professor in the School of Physics.
What an unprecedented study found about 3D printing's dangers.
Fast Company
November 19, 2018
There is no such thing as a 3D printer that doesn't emit concerning microparticles into the air, according to Rodney Weber's groundbreaking study about the dangers of 3D printing. Even industrial models that appear sealed put out measurable particles.
But Weber warns us not to be too alarmed. The true danger is that the industry is currently unregulated, but the particles from 3D printer's aren't any different from the ones already floating around in the air.
Weber is a professor in the School of Earth and Atmospheric Sciences.
High-Speed Video of Cat Tongues Yields Another Reason Why They're Superior
Inverse
November 25, 2018
David Hu is at it again, this time diving deep into cat grooming Using videos captured by high-speed cameras (about 500 frames per second), he showed that cats have a four-phase grooming regimen aided by tiny keratin spikes on their tongues, called filiform papillae.
Hu is an associate professor in the Schools of Mechanical Engineering and of Biological Sciences and an adjunct associate professor in the School of Physics.
Call it instinct, but something, perhaps programs in their genes, compels some animals to behave in striking ways. Take boy fish who tirelessly build sand structures to attract girl fish: Researchers have now connected gene activity with this instinctive behavior.
The scientists at the Georgia Institute of Technology and Stanford University who led the new study hope in the future to see if some behaviors are indeed genetic programs and if gene regulation is clicking off neuronal firing patterns in real time to create behavior.
“We’re not there yet, but we’re beginning to get a handle on gene regulation patterns that drive the neuronal patterns,” said Todd Streelman, professor and chair of Georgia Tech’s School of Biological Sciences and also its chair, and a researcher in the Petit Institute for Bioengineering and Bioscience. “We were able to see that there’s a clear connection between gene expression and behavior.”
Better understanding autism
The research also may contribute to a better understanding of autism because the genes behind the fish behavior have human cousins that are implicated in autism spectrum disorder. And some typical autism behaviors like “stacking,” in which a child compulsively arranges objects into neat rows or towers, have parallels in how the fish, called cichlids, repetitively pile up sand to make symmetrical formations.
But for now, the researchers explored male cichlids trying to attract a mate in Lake Malawi in Africa and found that the regulation of specific genes and associated repetitive behavior occurred nearly hand-in-glove, a novel discovery.
They published their results in the journal Proceedings of the National Academy of Sciences. The research was funded by the National Institute of Neurological Disorders and Stroke, the National Institute on Aging, and the National Institute of General Medicine, all part of the National Institutes of Health.
Dig my castle
Let’s start with the behavior then go to the matching gene regulation:
Boy cichlids knock themselves out building stuff out of sand to impress girl fish ready to mate. Most of the cichlid species’ guys build a pit, or crater, and other species build a castle.
Both pits and castles are known as “bowers” and require the male fish to swim in the same circular way, scooping up sand in one place and spitting it out somewhere else.
The difference is that the pit builders scoop up the sand from inside their swimming pattern and deposit it outside, leaving a hole in the middle of the bower with a raised rim surrounding it that makes the bower resemble a crater. Castle builders scoop the sand from outside the circle and deposit it inside. That creates a raised structure in the middle of the bower, making it resemble a volcano.
Turning him on
“A switch goes on once the females become reproductively active. Suddenly, the males begin scooping and spitting thousands of times to build their structure,” said Zachary Johnson, a postdoctoral researcher in Streelman’s Lab. Johnson was a co-author on the new study and Streelman a co-principal investigator.
Scooping and spitting are so incessant that two-inch fish shovel up two-foot-wide structures: pit bowers for some species, castle bowers for others. The difference serves in attracting the right mate.
“Various species make their pits and castles in a common area, and structures have to be very specific, so the right female species can see, ‘This is the guy that I want’ compared to the other guys from other species that build the other thing. And she then has to pick the specific guy she wants from her own species,” said Chinar Patil, a co-first author of the study and a graduate research assistant in Streelman’s lab.
Cross-breeding cichlids
Now for the gene regulation part:
To observe the genes connected to either of these building behaviors, researchers have cross-mated pit-building species with castle-building species to make hybrid cichlids that have both sets of genes. These hybrids have delivered a lucky surprise.
The hybrid fish performed both behaviors neatly in sequence: first the pit making, then the castle making, always in that order.
“That’s amazing,” Johnson said. “You might expect hybrid behavior to be jumbled, or take on some intermediate form. Instead, they perform one species-specific behavior and then transition to performing the other species-specific behavior.”
Bower genes power up
This is useful to research because the hybrids have one full copy of genes from the pit parent and one from the castle parent. The cleanly separated behaviors have allowed for matching each behavior with increased and decreased activation in either set of genes in the fish’s brains.
The Georgia Tech and Stanford researchers were able to clearly match pit gene activation with pit behavioral mode as well as castle gene activation with castle behavioral mode.
“A lot of genes in the pit copy got up-regulated while the fish was in pit-making mode and the castle copy got up-regulated during castle-making mode,” Patil said. The genes and the behavior got visibly “turned on” and “tuned in” in tandem.
The difference in expression of either pit vs. castle genes was less of an absolute click-clack-on-off switch and more like inching one set of levers down on an audio mixer while tuning up the other set to a dominant level.
Gene-behavior evolution
This was the study’s big achievement, which almost sounds like genes directly creating behavior, but that’s unconfirmed as of yet and could be the topic of future studies.
The study also brought new insights into genetic evolution in tandem with behavioral evolution, about which little is known. The genetic component may center around gene regulation in response to what’s going on in the animal’s environment in this case when females are ready to mate.
Pit making appears to be the evolutionarily older and better-established bower building behavior, and castle making is widely accepted as being the newer evolutionary development. But pit and castle species have very similar genomes, so where’s the evolutionary change?
When the team sequenced the DNA of pit and castle species, it was differences in regulatory genes that stuck out, and many up-regulated specific other genes connected to the respective bower building behaviors when mating time hit. It appeared the evolution of the regulatory genes was linked to the evolution of the behavior.
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Read MORE: On genetics of neuroscience and behavior
The following researchers also co-authored this study: Ryan York, Hunter Fraser and Russel Fernald of Stanford University; Kawther Abdilleh and Patrick McGrath of Georgia Tech; Mathew Conte of the University of Maryland; and Martin Genner of the University of Bristol. The research was funded by the National Institutes of Health’s National Institute of Neurological Disorders and Stroke (grant R01NINDS034950), the National Institute on Aging (grant R21AG050304), and National Institute of General Medicine (grants R01GM101095, 2R01GM097171-05A1, R01GM114170). Findings, conclusions, opinions, and recommendations in the material are those of the authors and not necessarily of the funding agencies.
Research News
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Ribonucleotide monophosphates (rNMPs) and deoxyribonucleotide monophosphates are the basic building blocks of RNA and DNA. The difference between them is that rNMPs contain ribose instead of deoxyribose as their sugar component. During processes like DNA replication and repair, rNMPs become embedded in genomic DNA, influencing DNA fragility, mutability, and ultimately the stability of the genome.
Because rNMPs alter the way DNA works in both structure and function, it’s important to be able to identify them and their sites of genomic incorporation. Recent advances in high-throughput sequencing techniques now make it possible to tag rNMPs embedded in genomic DNA. Simultaneously with three other methods to capture rNMPs in DNA, a unique and robust technique called ribose-seq was developed by the lab of Francesca Storici, professor in the School of Biological Sciences at the Georgia Institute of Technology, and her collaborators.
They published a description of the technique and the discoveries it yielded a few years ago in the journal Nature Methods. While their method is applicable to DNA from virtually any source and organism (including humans), allowing the researchers to determine the full profile of rNMPs embedded in genomic DNA, it essentially generates large, complex datasets like the other three approaches to study ribonucleotides in DNA.
“But there is no standardized system to analyzing the data from ribose-seq or the three other techniques,” notes Alli Gombolay, a fourth-year PhD student in Storici’s lab. “We wanted to create a bioinformatics toolkit that could rapidly and effectively analyze the data from any of those techniques to study all types of data and gather as much information as possible.”
Standard computational pipelines designed to map embedded rNMPs are customized for data generated using only one kind of sequencing technique. So Gombolay and her co-advisors – Storici and Fred Vannberg, researchers in the Petit Institute for Bioengineering and Bioscience – developed Ribose-Map.
They recently published their research in the journal Nucleic Acids Research. In their paper, entitled “Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in DNA,” they describe how to transform raw sequencing data into summary datasets and publication-ready results, which would allow researchers to identify sites of embedded rNMPs, study the nucleotide sequence context of these rNMPs, and explore their genome-wide distribution.
“Ribose-Map increases reproducibility and allows us to directly compare the data, and ultimately gather more information.” says Gombolay.
Other labs are already interested in making those comparisons. This became abundantly clear to Gombolay in September when she attended the 15th RNase H meeting in Warsaw, Poland, a biennial international gathering.
For researchers who want to know more about Ribose-Map and how to use it, Gombolay has created a GitHub page, where she describes how to set-up, install, and run the toolkit.
“It’s a simpler approach to mapping ribose in DNA or other modifications,” she says. “It’s particularly helpful for people with limited bioinformatics skillsets, or for people who are new to the relatively small field of ribonucleotide mapping. But since we can now map ribonucleotides in DNA, we think the field could grow faster.”
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