2020

Detecting Molecules of Exoplanet Life

Nick Konidaris of the Observatories, Johanna Teske of the Earth and Planets Laboratory, and Jason Williams, a USC graduate student, will undertake a project to develop an instrument for detecting life-indicating molecules in exoplanet atmospheres. The team will develop a prototype, dubbed the Henrietta, to develop a new technique aimed at the challenge of measuring the small signals of exoplanet atmospheres from the ground. One challenge for detecting and analyzing light from an exoplanet is that Earth’s atmosphere absorbs some of it. In order to remove the effect of absorption, the team will work with a tool called a holographic diffuser, which spreads the star’s very bright signal over 100s of pixels—instead of the typical handful—to improve the measurement’s precision, as well as the range of stars available for study.

This diffuser technique has never been demonstrated with a spectrograph in the lab or on the sky. The team will build a spectrograph and atmospheric simulator in the lab and then install it on the Swope telescope at Carnegie’s Las Campanas Observatory, to conduct a small survey of exoplanet atmospheres. The lessons learned will be used by applied to the Magellan Infrared Multi-Object Spectrograph (MIRMOS), currently under design for the Magellan telescopes, and then the Giant Magellan Telescope when it is completed later this decade, to study thousands of exo-atmospheres.

Determining Genetics for Coral Adaptation to Heat and Bleaching  

Moises Exposito-Alonso of Plant Biology and Phillip A. Cleves of Embryology propose using CRISPR/Cas9 gene editing to conduct a genome-wide association study that will identify and test the genes that may control heat and bleaching tolerance in coral. The team will take a multidisciplinary approach to find the locations on chromosomes—loci—that control heat tolerance and bleaching susceptibility in wild coral. In a preliminary analysis by graduate student Veronica Pagowski, they have found several genomic regions in two different species that are associated with historical warming events.

The team will use existing datasets to conduct a genome-wide association study (GWAS) to identify candidate loci that may control heat and bleaching tolerance. They will then use CRISPR/Cas9 gene editing in corals to engineer replacement methods for specific alleles—alternative versions of the same gene—to functionally test these loci in heat stress and bleaching conditions. Their strategy combines the unique expertise from the two departments to develop a new field of evolutionary functional genomics in corals. This work could generate critical multi-scale insights into corals and their ecosystems. Using genetics to identify resistant corals will be powerful in efforts to help rebuild degraded reefs.

2019

Carbon-rich Super-Earths: Constraining Internal Structure from Dynamic Compression Experiments

The Peter Driscoll/Sally June Tracy project is an interdisciplinary opportunity for an early career materials physicist, Tracy, to work with an early career geodynamicist, Driscoll, and for a postdoc to gain expertise in both fields using novel high-pressure techniques that inform new models.

The explosion of extrasolar planet discoveries has raised new questions about the formation, evolution and the habitability of planets. The mantles of carbon-rich super-Earths, exoplanets up to about 10 Earth-masses, are thought to be rich in silicon carbide (SiC), while the cores are believed to be rich in iron/iron-carbide.  However, there are obstacles in modeling the internal structure and thermal evolution of such planets because of poor constraints on material properties at the extreme pressure-temperature conditions of planetary interiors. The duo, with a postdoc, seeks to overcome this problem with new high-pressure experiments that will inform new models. Peter Driscoll and Sally June Tracy are shown in the lab.

Thermo-adaptation of Photosynthesis in Extremophilic Desert Plants

The Sue Rhee/Joe Berry/Jen Johnson project brings together ecophysiology, genomics, systems biology, biochemistry, and modeling to provide new insights into the high temperature limits of photosynthesis, which is particularly critical as we face a changing climate.

Photosynthesis is exquisitely sensitive to temperature. Across the range from 10° to 50°C (50°F to 122°F), all higher plants exhibit a distinctive thermal optimum for photosynthesis. As the warming of the climate intensifies, photosynthesis will be pushed toward the inhibitory part of the temperature response. However, it is a mystery what chain of molecular events causes the high temperature inhibition. In this project, the team aims to understand the molecular basis of photosynthetic performance at high temperatures using comparative studies of Tidestromia oblongifolia, a heat-tolerant plant native to the Mojave Desert, and Amaranthus hypochondriacus, a closely related but heat-sensitive cereal crop native to cooler climates. Team members Karine Prado, a postdoc in Plant Biology and Global Ecology is shown left, while Jen Johnson, research associate in Global Ecology is in the middle image, and Sue Rhee’s mother, Soon Sup Rhee near the Salton Sea is at right.

2018

Deciphering Life Functions in Extreme Environments

The Geophysical Laboratory’s Dionysis Foustoukos and Sue Rhee of the Department of Plant Biology, with colleague Costantino Vetriani of Rutgers have teamed up to integrate microbial physiology, genomics, and metabolic network modeling with high pressure and temperature experimentation to understand gene regulation in response to changing environmental conditions. Their objective is to unravel how microorganisms interact with each other and the environment. They will use a high-pressure adapted (piezophilic) chemolithoautotrophic bacterium that Foustoukos and Vetriani recently isolated from an active deep-sea vent at the East Pacific Rise. This is the only autotrophic organism that has been characterized among the piezophilic organisms isolated to date.

The scientists will look at the adaptation mechanisms of the microorganisms’ metabolism in response to different pressures up to 680 times atmospheric pressure and temperatures up to 175º F (80 º C) in different nutrients using a novel bioreactor used by Foustoukos and Vetriani. Experimental results will be compared to genomic studies and genome databases from the Rhee lab to reconstruct the metabolic network models of piezophilic microorganisms. The team hopes to better understand how environmental factors and physiology of these organisms shape the evolution of the deep biosphere.

2017-B

Astronomer Andrew McWilliam of the Observatories has teamed up with Hubble Postdoctoral Fellow Johanna Teske of Terrestrial Magnetism to detect molecules important to the emergence of life on Earth-sized exoplanets. A priority target is TRAPPIST-1 system, with seven Earth-sized planets. They will analyze light transmitted through these exoplanet atmospheres as the planets move in front of their host stars, searching for the faint molecular fingerprints of species like water, carbon dioxide, and methane. The researchers will work with the world-class instrumentation team at Observatories to adapt a new, high-resolution near-infrared spectrograph, from the University of Tokyo, to be deployed on the Magellan-Clay telescope, and develop custom reduction and analysis tools for exo-atmospheric detection. 

A priority target for detecting molecules essential to life is the TRAPPIST-1 system (left, artist’s concept). It has seven Earth-sized planets, and three of them are in the habitable zone, where temperatures permit liquid water to occur on the surface. Image courtesy NASA/JPL-Caltech/R. Hurt, T. Pyle (IPAC)

Measuring Photosynthesis At Large Scales

A second grant was awarded to a collaboration among instrument designer Nick Konidaris of the Observatories and global ecologists Greg Asner, Joe Berry and Ari Kornfeld, to disentangle the faint light emitted by chlorophyll during photosynthesis from the much brighter sunlight reflected off the plant surface. This remote sensing technique, called Solar Induced Chlorophyll Fluorescence (SIF), can be used in ​applications​ ​from​ ​precision​ ​farming,​ ​to​ ​forestry,​ ​to​ ​ understanding and​ ​predicting​ ​global​ ​climate​ ​change.​ These methods can also be used to study low-surface-brightness features in nearby galaxies thereby advancing both ecological and astronomical studies. As a first step in advancing these two fields, a SIF instrument will be incorporated into the Carnegie Airborne Observatory to allow measurements of photosynthesis to be coupled with structural characteristics in unprecedented detail.

The image at left shows chlorophyll fluorescence from photosynthesis at the molecular level. The Carnegie Airborne Observatory (CAO) can render height maps of forests, as in the image at right. Red in this image indicates the tallest plants. The team will use the remote sensing technique called Solar Induced Chlorophyll Fluorescence (SIF) to measure photosynthesis, coupled with structural characteristics from the CAO in unprecedented detail at large scales.

A "Gene Gun" for Genetic Manipulation

A third Venture Grant was awarded to a project planned by plant biologists Zhiyong Wang and global ecologists Joe Berry and Jennifer Johnson, with Karlheinz Merkle of Stanford University to develop a new “gene gun” that can deliver biomolecules deep into plant cells that then participate in reproduction for the purpose of genetic manipulation. The new tool would be much quicker and more effective than current methods and could break a time-consuming bottleneck in plant research and biotechnology.

The researchers will use the maize plant, shown at left under greenhouse lighting, to inject biomolecules deep into plant cells with their new “gene gun” for genetic manipulation.

Materials Science Applied to Biological Protein Folding 

A fourth grant will go to a team that includes materials physicists at the Geophysical Laboratory Tim Strobel, Ron Cohen and Li Zhu, in collaboration with Plant Biology’s Proteomics Facility Director Shouling Xu. The team will apply their new computational method designed to understand materials synthesis to the biological problem of understanding the mechanisms of protein folding, which is vital to life. Misfolded proteins are believed to lead to many diseases. The team hopes to help bridge the gap between known protein sequences and protein structures.

This image is an example of a modeled biological protein fold using techniques from materials science. Like an activated phase transition—such as graphite to diamond—in any solid-state material, proteins fold by changing configuration with associated energy penalties and benefits.

2017-A

2016-B

Direct Shock Compression of Pre-synthesized Mantle Mineral to Super-Earth Interior Conditions

Yingwei Fei, a high-pressure experimentalist at the Geophysical Laboratory, and Peter Driscoll, theoretical geophysicist in the Department of Terrestrial Magnetism, have been awarded a Carnegie Science Venture Grant for their project “Direct Shock Compression of Pre-synthesized Mantle Mineral to Super-Earth Interior Conditions.”The project is an entirely new approach to investigate the properties and dynamics of super-Earths—extrasolar planets with masses between one and 10 times that of Earth. They will use the world’s most powerful magnetic, pulsed-power radiation source, called the Z Machine at Sandia National Laboratory, to generate shock waves that can simulate the intense pressure conditions of these enormous bodies. Reaching such high pressures has not been possible before with conventional techniques. The results will be used to develop models and predictions of super-Earth interiors.  Below, Fei and Driscoll are in the lab. The Z Machine is at right. Z Machine Image courtesy Sandia Lab

2016-A

Coral calcification and the future of reefs—Art Grossman of Plant Biology is teaming up with Global Ecology’s Rebecca Albright, Ken Caldeira and others to develop a new model for understanding how coral calcification works at the cellular/molecular and community levels. This blends fieldwork with understanding the molecular mechanisms that coral use to remove calcium and inorganic carbon from the seawater for calcification.  The objective is to create a model to understand how the system is affected by climate change in the face of the growing global coral reef demise. The team will collaborate with the California Academy of Sciences to build a laboratory-based coral model system and focus on the critical larval and metamorphosis period to look at the DNA, RNA and proteins involved when cells begin to calcify. There is also the potential for a biomedical spin-off including the generation of bone material for grafting.  

Far left image below: Healthy coral reefs like this example in the Great Barrier Reef are under severe attack worldwide. The Grossman,/Albright/Caldeira  team will develop a new model for understanding how coral calcification works at the cellular/molecular and community level to understand how the system is affected by climate change. Image courtesy David Kline

How do plants sense temperature and time their flowering?—This team will investigate the molecular mechanisms that control how plants sense temperature changes. Temperature changes affect carbon fixation, development, the timing of flowering, and more. The timing of flowering is particularly important with global temperature rise. Embryology’s Yixian Zheng’s lab recently looked at how a protein whose transition into a liquid state at physiological temperature promoted a cell division process. That protein, BuGZ, belongs to a protein class called intrinsically disordered proteins and is similar to a protein called SUF4 involved in regulating flowering in plants. She is teaming up with David Ehrhardt’s lab in Plant Biology lab to determine if a similar temperature-dependent “phase transition” of SUF4 is required to regulate the flowering process. The Zheng and Ehrhardt labs will tag the protein to observe SUF4 behavior. It is uses temperature-dependent phase transition to regulate the flowering process, it would establish a new paradigm for temperature sensing in biological systems.

Middle two images below: Embryology’s Yixian Zheng’s lab recently looked at how a protein, whose temperature-dependent transition into a liquid droplet state promoted a cell division process. That protein, BuGZ is shown in droplet form (second from left). She is teaming up with Dave Ehrhardt at Plant Biology to see if this transition to a liquid droplet state in a similar protein, SUF4, is involved in the flowering process in the model plant Arabidopsis ( third image from left) .

C-MOOR: The Carnegie Massive Open Online Research Platform—This grant will establish C-MOOR (pronounced “See More!”), an internet resource that allows select Carnegie data sets to be easily accessed and analyzed by citizen scientists. Frederick Tan and Zehra Nizami of Embryology are teaming up with Terrestrial Magnetism’s Alan Boss, Sergio Dieterich and Johanna Teske (also with the Observatories) to combine Carnegie’s experience in cell, molecular, and computational biology expertise with astronomical and astrophysical observations and programming experience. Other like-minded Carnegie researchers are invited to help establish a community website with tutorials, discussion forums, an “Ask a Scientist” query portal, and other engaging features. This platform targets users seeking course credit, scouting, or merit badges as well as those driven by sheer curiosity. 

Top right image below: Most astronomical objects are known only as coordinate and brightness entries in astronomical catalogs. These catalogs have hundreds of millions of entries and the vast majority of them remain unstudied or even unnoticed by scientists. By partnering with citizen scientists to sift through these data we hope to learn more about stars both as individual objects and as a population. This image exemplifies the fact that for every star we study closely, in this case Luhman 16 at the center of the image (number 42), there are countless others that remain as mere numbers in a catalog. Could astronomical secrets be hiding in plain sight in images such as this one? C-MOOR will address this and other questions with the help of citizen scientists.

Bottom right image below: Many of the modifications that occur in our genome are biased towards specific subsets of the 3 billion basepairs that form the fundamental building block of DNA. In this image, red regions represent changes in one type of modification, DNA methylation, that may alter the activity of nearby genes and transposable elements—segments of DNA that jump around—during mouse sperm development.  Carnegie scientists are interested in understanding what predisposes particular regions of the genome to these and other changes. This vast array of information and more can be sifted through by the citizen scientists participating in C-MOOR. Image courtesy of Valeriya Gaysinskaya and Alex Bortvin.

2015

SWEET Transporters in Zebrafish
Steven Farber (Dept. of Embryology), Wolf Frommer (Dept. of Plant Biology)
Sugar homeostasis is critical for health – both under- and oversupply cause cellular and organismal damage. The Farber Lab from Carnegie’s Embryology and the Frommer lab from Carnegie’s Plant Biology have joined forces to better understand the regulation of sugar transport in the vertebrate intestine.  A novel sugar transporter discovered in plants (SLC50A; SWEET1) influences plant sugar transport, including plant vein loading, seed filling, gametophyte nutrition and nectar secretion.  Interestingly, SWEET1 is also present in vertebrates and has been shown to transport glucose although we know very little about its specific roles in digestive organs like the intestine.  Here we intend to establish the basis for understanding the role of SWEETs in humans by exploring the role and function of the single zebrafish version of SWEET1. Why are we performing this study in zebrafish?  Because the larval zebrafish is optically clear, so we can deploy fluorescent biosensors, developed in the Frommer lab, that measure sugar levels by changing their fluorescent properties.  The Farber lab has perfected ways of imaging the transport of another key nutrient (lipids) in single zebrafish intestinal cells so with these Frommer lab sensors they can more easily apply these same methods to the study of sugar transport. Currently, it is not possible to study subcellular nutrient transport inside a live digestive organ in a mammal like a mouse or human. We will use state-of-the-art genomic editing to create zebrafish with broken SWEET1 transporters (mutants) and study their phenotype and physiology with the help of theses glucose biosensors. It is our belief that the data from our studies will be relevant in the context of human nutrition, as well as diseases states such as Diabetes.

Carbon Isotope Ratio of Earth's Mantle
Erik Hauri (Dept. of Terrestrial Magnetism), Anat Shahar (Geophysical Laboratory), Stephen Elardo (Geophysical Laboratory)
Traditionally, carbon isotopes have been used to trace the movement and cycling of carbon between the atmosphere, oceans, and shallow subsurface environments. As high temperatures cause a decrease in equilibrium stable isotope fractionation, it was assumed for decades that carbon isotope fractionation in deep Earth conditions would be negligible. However, this may not be true.The silicate Earth has a carbon isotope signature that is quite different from those of meteorites, and other planetary and asteroidal bodies. However, it is thought that Earth, Mars, and the asteroids all received their volatiles, including carbon, from a similar source. So why is Earth’s carbon isotope ratio so different? Is it plausible that core formation, the single largest physical and chemical event in Earth’s history, could change the carbon isotopic signature of the entire planet? And if so, what would that mean for the composition of the core?We will try to understand this paradox by testing whether the differentiation of Earth’s core from mantle could have been accompanied by a significant shift in the carbon isotopic signature of the mantle by: 1. Determining the carbon isotopic fractionation factor between metal and silicate at high pressure and temperature for the first time, and 2. Placing an independent constraint on the amount of carbon in the Earth’s core.

Mapping Coral Bleaching
Greg Asner, Ken Caldeira, Rebecca Albright, Robin Martin (Dept. of Global Ecology)
Despite covering less than 0.1% of the world’s oceans, coral reefs harbor one of the most diverse ecosystems on the planet and are valued at ~$30 billion per year. Coral bleaching, a phenomenon whereby warmer-than-normal ocean temperatures stress corals causing them to expel the symbiotic algae living in their tissues, is one of the largest and most pervasive threats to coral reefs. In October, the National Oceanic and Atmospheric Association (NOAA) declared the third ever global bleaching event; the epicenter of this event is Hawaii, which is currently experiencing record-breaking bleaching due to ocean warming associated with El Niño conditions. To document the extent of this bleaching event, the Asner and Caldeira labs are joining forces in an exciting new project to apply cutting edge remote sensing techniques to the marine environment. Asner is an expert in ecological remote sensing and has been conducting research in Hawaii for over 20 years. Caldeira is a climate scientist who has been researching the impacts of climate change on coral reefs for nearly two decades. This partnership represents an exciting new direction that promises to unfold relationships between ocean warming and coral stress, providing scientifically robust information to inform decision-makers and guide conservation-management. 

Guidelines