Wednesday, July 11, 2018

Evidence reveals our fractured African roots

A range of ancient cultural artifacts found in different regions of Africa. Clear regionally distinctive material cultural styles, typically involving complex stone tools, first emerged within the Middle Stone Age.

Anthropologists are challenging the long-held view that humans evolved from a single ancestral population in one region of Africa. Instead, a scientific consortium has found that human ancestors were diverse in form and culture and scattered across the continent. These populations were subdivided by different habitats and shifting environmental boundaries, such as forests and deserts.

The journal Trends in Ecology and Evolution published the findings, which drew from studies of bones (anthropology), stones (archaeology) and genes (population genomics), along with new and more detailed reconstructions of Africa’s climates and habitats over the last 300,000 years.

Emory University anthropologist Jessica Thompson was one of 23 authors on the paper. The research was led by the Max Planck Institute for the Science of Human History in Germany and the University of Oxford in England. In the following Q&A, Thompson explains the paper and its significance.

Can you provide some background on our understanding of human evolution? 

Jessica Thompson: Even as early as 20 years ago, fossils were the main material we had to try to answer the question of where humans originated. A multi-regionalist theory hypothesized that Homo sapiens emerged in different places at the same time, evolving at the same rate across the Old World. This would mean that there was extensive gene exchange across ancient Asia, Europe and Africa, and that groups such as Neanderthals would not be a separate species but just a localized form of Homo sapiens. But it is difficult to get that level of resolution from bones alone.

By the 1990s, mitochondrial DNA analyses provided growing genetic evidence for the competing theory — that all modern humans originated in Africa and then dispersed from there around the globe. The implication of this is that groups such as the Neanderthals would actually have been different species, and that they were replaced by modern human groups dispersing from Africa.

Intense debate continued over the two theories but, by the early 2000s, it was clear that the out-of-Africa group had won. Only a small percentage of modern humans from the total population living in Africa actually left the continent, creating a genetic bottleneck in populations outside of Africa. So there is more diversity within the genomes of some living peoples in Africa today than there is, say, between an Australian aboriginal person and a Norwegian person.

As a final twist, whole-genome DNA now shows that there was some gene flow with Neanderthals as those first modern populations emerged from Africa. This could have happened several times over many thousands of years, and so a “leaky out-of-Africa” model seems to be the best fit for the data.

Jessica Thompson in the field in Malawi, where her archaeological sites are at a crossroads between southern and eastern Africa. "There, we find a long, but relatively unexplored cultural record of human behavior that goes back into the last Ice Age," she says.

How does the current paper fit into this model?

JT: While it was well established that modern humans originated in Africa, there was still the question of where in Africa. East Africa and South Africa have been strong candidates, but that could be due to the long historical bias of where fossils were being found.

Our paper takes the global idea of multi-regionalism and shrinks it down to the boundaries of Africa. The answer to where humans originated appears to be lots of places within the continent, often separated for long periods, but again with leaky boundaries. Essentially, there is not a single ancestral human population. Who we are today probably evolved as a mosaic of populations of very near modern humans who were separated by geographic and cultural boundaries but were also all interacting with one another at different points in time. Our origin story is one of lots and lots of different humans that came together and then separated and later came together again in this really confusing manner. There’s a lot of moving parts. Humans, for a very long time, have been a culturally and phenotypically diverse bunch.

What new questions does this paradigm shift bring up?

JT: Instead of seeking the origin of humans in one spot, we need to look for pieces of the puzzle in many different places. Then we can ask, what adaptations did different populations have that contributed to who we are today? How did they come to be present in the single species we are now? And, perhaps more philosophically, what are the unifying characteristics that bind us together as that species, in spite of our differences?

While we need more data from places like East Africa and South Africa, it’s apparent now that West Africa and Central Africa are also key players in the story. They’re at the crossroads for much of the continent and yet we know very little about ancient populations from those regions. I’m hoping I can contribute to that effort with my current work in Malawi, which is positioned between southern and eastern Africa. There, we find a long, but relatively unexplored cultural record of human behavior that goes back into the last Ice Age.

We also recently recovered some of the oldest DNA in Africa from a site in Malawi, which we published last year. This helped to actually show some of those ancient interactions between populations at least over the last 10,000 years or so — as well as some of the differences between them. The implications are that this kind of structure went back even farther in time, to our origins as a species.

Malawi yields oldest-known DNA from Africa
Bonding over bones, stones and beads
Have skull drill, will travel

Monday, July 9, 2018

Science on stage: Atlanta playwrights explore the human microbiome

Learning about the microbiome "is shifting my perspective of what it means to be human and an individual," says playwright Margaret Baldwin. "What bacteria are driving our dreams?"

Four Atlanta playwrights + 48 hours = four new plays at the forefront of art and science.

That’s the premise of Theater Emory’s “ 4:48,” a frenetic yet focused showcase of new works inspired by the human microbiome that will be performed July 14 at the Schwartz Center for Performing Arts.

The annual speed-writing challenge always yields compelling results, as talented local playwrights come together at Emory to quickly produce plays based on common source material. But this year, for the first time, the Playwriting Center of Theater Emory is teaming up with the Emory Center for the Study of Human Health for “4:48” — an innovative, interdisciplinary collaboration that promises to push the boundaries of both fields.

“Theater offers an exciting communication mechanism to convey cutting edge-research findings to a wide audience, while simultaneously encouraging curiosity and imagination,” says Amanda Freeman, instructor in the Center for the Study of Human Health.

The collaborators hope that this project will introduce the human microbiome — the trillions of microorganisms that live in us and on us — to a whole new audience, providing a spotlight for research that is being done right here on campus.

“I have found very few venues where new science and new art can emerge from a single exercise, so ‘4:48’ is special,” says David Lynn, Asa Griggs Candler Professor of Chemistry and Biology, one of several Emory science faculty offering support as resources for the writers.

Readings of the work developed during "4:48" begin at 4 pm on Saturday, July 14, in the Theater Lab of Schwartz Center. All readings are free and open to the public. For the schedule of readings and play titles, visit the Theater Emory website.

Click here to learn more.

Learning to love our bugs: Meet the microorganisms that help keep us healthy
Environment, the microbiome and preterm birth

Tuesday, July 3, 2018

A grave tale: The case of the corpse-eating flies

Dozens of ceramic vessels from West Mexico, part of the collection of Emory's Michael C. Carlos Museum, were believed to be "grave goods," traditionally placed near bodies in underground burial chambers almost 1,500 years before the Aztecs. The compact figures depict humans and animals engaged in everyday activities, vividly capturing a place and time. Residue and wear patterns suggested that the vessels had once been filled with food and drink, perhaps to accompany the departed along their journey.

But were the figures authentic?

Seeking answers, the museum invited forensic anthropologist Robert Pickering — who uses entomology, among other techniques – to examine the vessels with the help of Emory scholars.

His quest? Locate telltale insect casings likely left by coffin flies, corpse-eating insects that fed on decomposing bodies interred in the ancient underground shaft tombs of Western Mexico.

"Not to be impolite, but where you have dead people, you have bugs," Pickering explains.

Read more about the project here.

Monday, July 2, 2018

New Atlanta NMR Consortium links resources of Emory, Georgia Tech and Georgia State

The Atlanta Nuclear Magnetic Resonance Consortium "lowers the activation energy to take advantage of partners’ expertise," says Emory chemist David Lynn.

NMR – nuclear magnetic resonance – is a powerful tool to investigate matter. It is based on measuring the interaction between the nuclei of atoms in molecules in the presence of an external magnetic field; the higher the field strength, the more sensitive the instrument.

For example, high magnetic fields enable measurement of analytes at low concentrations, such as the compounds in the urine of blue crabs, opening doors to understanding how chemicals invisibly regulate marine life. High-field NMR also allows scientists to “see” the structure and dynamics of complex molecules, such as proteins, nucleic acids, and their complexes.

NMR is used widely in many fields, from biochemistry, biology, chemistry, and physics, to geology, engineering, pharmaceutical sciences, medicine, food science, and many others.
David Lynn

NMR instruments, however, are a major investment. The most advanced units can cost up to up to millions of dollars per piece. Maintenance can cost tens of thousands of dollars a year. The investment in people is also significant. It can take years of training before a user can perform some of the most advanced techniques.

For these and other reasons, Emory University, Georgia Institute of Technology, and Georgia State University have formed the Atlanta NMR Consortium. The aim is to maximize use of institutional NMR equipment by sharing facilities and expertise with consortium partners.

Through the consortium, students, faculty, and staff of a consortium member can use the NMR facilities of their partners. The cost to a consortium member is the same as what the facility charges its own constituents.

“NMR continues to grow and develop because of technological advances,” says David Lynn, a chemistry professor at Emory University. To keep up, institutions need to keep buying new, improved instruments. Such a never-ending commitment is becoming untenable and redundant across Atlanta, Lynn says. Combining forces is the way to go.

Immediately, the consortium offers access to the most sensitive instruments now in Atlanta – the 700- and 800-MHz units at Georgia Tech. Georgia Tech invested more than $5 million to install the two high-field units, as well as special capabilities, in 2016.

Partners can gain access to Georgia State’s large variety of NMR probes. Solid-state capability, which is well established in Emory and advancing at Georgia Tech, will be available to partners.

Needless to say, the consortium offers alternatives when an instrument at a member institution malfunctions.

Beyond maximizing use of facilities, the consortium offers other potential benefits.

Anant Paravastu
“The biggest benefit is community,” says Anant Paravastu. Paravastu is an associate professor in the Georgia Tech School of Chemical and Biomolecular Engineering. He is also a member of the Parker H. Petit Institute for Bioengineering and Bioscience (IBB).

“Each of us specializes the hardware and software for our experiments,” Paravastu says. “As we go in different directions, we will benefit from a cohesive community of people who know how to use NMR for a wide range of problems.”

Paravastu previously worked at the National High Magnetic Field Laboratory, in Florida State University. That national facility sustains a large community of NMR researchers who help each other build expertise, he says. “We Atlanta researchers would benefit from a similar community, and not only for the scientific advantage.”

Both Lynn and Paravastu believe the consortium will help the partners jointly compete for federal grants for instrumentation. “A large user group will make us more competitive,” Lynn says. “The federal government would much rather pay for an instrument that will benefit many scientists rather than just one research group in one university,” Paravastu says.

“The most important goal for us is the sharing of our expertise,” says Markus Germann, a professor of chemistry at Georgia State. A particular expertise there is the study of nucleic acids. More broadly, Georgia State has wide experience in solution NMR. Researchers there have developed NMR applications to study complex structures of biological and clinical importance.

Germann offers some examples:
Structure and dynamics of damaged and unusual DNA
Structure and dynamics of protein—DNA and protein—RNA complexes
Structural integrity of protein mutants
Small ligand-DNA and -RNA binding for gene control
Protein-based contrast agents for magnetic resonance imaging

“For me, there’s a direct benefit in learning from people at Georgia State about soluble-protein structure,” Paravastu says. He studies the structures of peptides; of particular interest are certain water-soluble states of beta-amyloid peptide, in Alzheimer’s disease. These forms, Paravastu says, have special toxicity to neurons.
Markus Germann

Paravastu also studies proteins that self-assemble. “People at Emory have a different approach to studying self-assembling proteins,” he says. “We have a lot of incentive to strengthen our relationships with other groups.”

“Different labs do different things and have different expertise,” Lynn says. “The consortium lowers the activation energy to take advantage of partners’ expertise.”

Even before the consortium, Germann notes, his lab has worked with Georgia Tech’s Francesca Storici on studies of the impact of ribonucleotides on DNA structure and properties. Storici is a professor in the School of Biological Sciences and a member of IBB.

Germann has also worked with Georgia Tech’s Nicholas Hud on the binding of small molecules to duplex DNA. Hud is a professor in the School of Chemistry and Biochemistry and a member of IBB.

“While collaborations between researchers in Atlanta universities is not new,” Paravastu says, “the consortium will help facilitate ongoing and new collaborations."

What will now be tested is whether the students, faculty, and staff of the partners will take advantage of the consortium.

Travel from one institution to another is a barrier, Lynn says. “Are people going to travel, or will they find another way to solve the problem? How do you know that the expertise over there will really help you?” he asks.

“The intellectual barrier is very critical,” Lynn says. “We address that through the web portal.”

The website defines the capabilities, terms of use, training for access, and institutional fees, among others. Eventually, Lynn says, it will be a place to share papers from the consortium partners.

“Like many things in life, the consortium is about breaking barriers,” Paravastu says. It’s about students meeting and working with students and professors outside their home institutions.

Already some partners share a graduate-level NMR course. For the long-term, Paravastu suggests, the partners could work together on training users to harmonize best practices and ease the certification to gain access to facilities.

“We can think of students being trained by the consortium rather than just by Georgia Tech, or Emory, or Georgia State,” Paravastu says. “By teaming up, we can create things that are bigger than the sum of the parts.”

Written by by Maureen Rouhi, Georgia Tech

How protein misfolding may kickstart chemical evolution
Peptides may hold 'missing link' to life

Tuesday, June 5, 2018

Physicists devise method to reveal how light affects materials

"Our finding may pave the way for improvements in devices such as optical sensors and photovoltaic cells," says Emory physicist Hayk Harutyunyan. (Stock photo)

By Carol Clark

Physicists developed a way to determine the electronic properties of thin gold films after they interact with light. Nature Communications published the new method, which adds to the understanding of the fundamental laws that govern the interaction of electrons and light.

“Surprisingly, up to now there have been very limited ways of determining what exactly happens with materials after we shine light on them,” says Hayk Harutyunyan, an assistant professor of physics at Emory University and lead author of the research. “Our finding may pave the way for improvements in devices such as optical sensors and photovoltaic cells.”

From solar panels to cameras and cell phones — to seeing with our eyes — the interaction of photons of light with atoms and electrons is ubiquitous. “Optical phenomenon is such a fundamental process that we take it for granted, and yet it’s not fully understood how light interacts with materials,” Harutyunyan says.

One obstacle to understanding the details of these interactions is their complexity. When the energy of a light photon is transferred to an electron in a light-absorbing material, the photon is destroyed and the electron is excited from one level to another. But so many photons, atoms and electrons are involved — and the process happens so quickly — that laboratory modeling of the process is computationally challenging.

For the Nature Communications paper, the physicists started with a relatively simple material system — ultra-thin gold layers — and conducted experiments on it.

“We did not use brute computational power,” Harutyunyan says. “We started with experimental data and developed an analytical and theoretical model that allowed us to use pen and paper to decode the data.”

Harutyunyan and Manoj Manjare, a post-doctoral fellow in his lab, designed and conducted the experiments. Stephen Gray, Gary Wiederrecht and Tal Heilpern — from the Argonne National Laboratory — came up with the mathematical tools needed. The Argonne physicists also worked on the theoretical model, along with Alexander Govorov from Ohio University.

For the experiments, the nanolayers of gold were positioned at particular angles. Light was then shined on the gold in two, sequential pulses. “These laser light pulses were very short in time — thousands of billions of times shorter than a second,” Harutyunyan says. “The first pulse was absorbed by the gold. The second pulse of light measured the results of that absorption, showing how the electrons changed from a ground to excited state.”

Typically, gold absorbs light at green frequencies, reflecting all the other colors of the spectrum, which makes the metal appear yellow. In the form of nanolayers, however, gold can absorb light at longer wave lengths, in the infrared part of the spectrum.

“At a certain excitation angle, we were able to induce electronic transitions that were not just a different frequency but a different physical process,” Harutyunyan says. “We were able to track the evolution of that process over time and demonstrate why and how those transitions happen.”

Using the method to better understand the interactions underlying light absorption by a material may lead to ways to tune and manage these interactions.

Photovoltaic solar energy cells, for instance, are currently only capable of absorbing a small percentage of the light that hits them. Optical sensors used in biomedicine and photo catalysts used in chemistry are other examples of devices that could potentially be improved by the new method. 

While the Nature Communications paper offers proof of concept, the researchers plan to continue to refine the method’s use with gold while also experimenting with a range of other materials. 

“Ultimately, we want to demonstrate that this is a broad method that could be applied to many useful materials,” Harutyunyan says.

$2 million NSF grant funds physicists' quest for optical transistors