Revolutionary progress in understanding plant biology is being driven through advances in DNA sequencing technology. Carnegie plant scientists have played a key role in the sequencing and genome annotation efforts of the model plant Arabidopsis thaliana and the soil alga Chlamydomonas reinhardtii. Now that many genomes from algae to mosses and trees are publicly available, this information can be mined using bioinformatics to build models to understand gene function and ultimately for designing plants for a wide spectrum of applications.

 Carnegie researchers have pioneered a genome-wide gene association network Aranet that can assign functions to genes for which no function had previously been assigned (to date about 50% of the plant genome) by their associations with genes of known function. They are also building protein interaction and metabolic pathway networks in plants to systematically identify signaling and metabolic pathways and relationships among these pathways.

Investigators also develop and apply mining methods to capture biological knowledge about the function of plant genes and maintain and improve the Arabidopsis genome annotation and provide online bioinformatics tools for use by plant biologists worldwide.Other researchers use algal genomes to identify genes that are specific to the green lineage, the so-called Greencut, to uncover the yet unknown regulatory systems critical for photosynthesis.

The objective of this computational work is to understand the evolution of multicellularity and sexual reproduction in the plant lineage, and the evolution of plant- specific characters, and the interactions between plants and other organisms.

Scientific Area: 
Plant Science
Reference to Person: 
Sue Rhee

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A bright field image of the anemone Aiptasia populated with its symbiotic algae.
Could algae that are “poor-providers” help corals come back after bleaching?
December 6, 2018

Stanford, CA—How much of the ability of a coral reef to withstand stressful conditions is influenced by the type of algae that the corals hosts?

Corals are marine invertebrates from the phylum called cnidarians that build large exoskeletons from which colorful reefs are constructed. But this reef-building is only possible because of a mutually beneficial relationship between the coral and various species of single-celled algae called dinoflagellates that live inside the cells of coral polyps.

The algae are photosynthetic—meaning capable of converting the Sun’s energy into chemical energy for food, just like plants. And the exchange of nutrients between the

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Devaki Bhaya
Carnegie’s Devaki Bhaya named California Academy of Sciences Fellow
October 5, 2018

Palo Alto, CA—Carnegie’s Devaki Bhaya has been named a Fellow of the California Academy of Sciences. She is one of 14 new members selected as “partners and collaborators in the pursuit of the Academy mission to explore, explain, and sustain life.”

At Carnegie’s Department of Plant Biology Bhaya studies how photosynthetic microorganisms are affected by environmental stressors such as light, low nutrient availability, and viruses. Her research on speciation in the microbial mats of Yellowstone National Park is providing insights into how microbial populations communicate, evolve, and share resources. These findings offered a first glimpse into the

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Carnegie’s Arthur Grossman Receives Human Frontier Science Program Grant
April 9, 2018

Palo Alto, CA—Senior scientist Arthur Grossman of Carnegie’s Department of Plant Biology was part of a team* awarded a three-year grant, with $100,000 for each year, from the International Human Frontier Science Program (HFSP) Organization. The team will use an integrated approach to investigate how light and metabolic signals control photosynthetic processes in algae.  

HFSP’s collaborative research grants are given for endeavors that address “complex mechanisms of living organisms.” The program only supports “cutting-edge, risky projects” conducted by globally distributed teams.

Grossman has been studying algae for years.

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Walls, toxicity and explosions: How plant cells protect themselves from salinity in soil
February 16, 2018

Stanford, CA—Roots face many challenges in the soil in order to supply the plant with the necessary water and nutrients.  New work from Carnegie and Stanford University’s José Dinneny shows that one of these challenges, salinity, can cause root cells to explode if the risk is not properly sensed. The findings, published by Current Biology, could help scientists improve agricultural productivity in saline soils, which occur across the globe and reduce crop yields.

Salts build up in soils from natural causes, such as sea spray, or can be introduced as a consequence of irrigation and poor land management. Salinity has deleterious effects on plant health and

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The fight on rice blight

Carnegie will receive Phase II funding through Grand Challenges Explorations, an initiative created by the Bill & Melinda Gates Foundation that enables individuals worldwide to test bold ideas to address persistent health and development challenges. Department of Plant Biology Director Wolf Frommer,  with a team of researchers from the International Rice Research Institute, Kansas State University, and Iowa State University, will continue to pursue an innovative global health research project, titled “Transformative Strategy for Controlling Rice Blight.”

Rice bacterial blight is one of the major challenges to food security, and this project aims to

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A family of metabolite sensors

Carnegie researchers recently constructed genetically encoded FRET sensors for a variety of important molecules such as glucose and glutamate. The centerpiece of these sensors is a recognition element derived from the superfamily of bacterial binding protiens called periplasmic binding protein (PBPs), proteins that are primary receptors for moving chemicals  for hundreds of different small molecules. PBPs are ideally suited for sensor construction. The scientists fusie individual PBPs with a pair of variants and produced a large set of sensors, e.g. for sugars like maltose, ribose and glucose or for the neurotransmitter glutamate. These sensors have been adopted for measurement of

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Understanding "hydropatterning" in roots

Fresh water constitutes less than 1% of the surface water on earth, yet the importance of this simple molecule to all life forms is immeasurable. Water represents the most vital reagent for chemical reactions occurring in a cell. In plants, water provides the structural support necessary for plant growth. It acts as the carrier for nutrients absorbed from the soil and transported to the shoot. It also provides the chemical components necessary to generate sugar and biomass from light and carbon dioxide during photosynthesis. While the importance of water to plants is clear, an understanding as to how plants perceive water is limited. Most studies have focused on environmental conditions

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Salinity and plants

Today, humanity is increasingly aware of the impact it has on the environment and the difficulties caused when the environment impacts our communities. Environmental change can be particularly harsh when the plants we use for food, fuel, feed and fiber are affected by this change. High salinity is an agricultural contaminant of increasing significance. Not only does this limit the land available for use in agriculture, but in land that has been used for generations, the combination of irrigation and evaporation gradually leads to increasing soil salinity.

The Dinneny lab focuses on understanding how developmental processes such as cell-type specification regulate responses to

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William Ludington

The Ludington lab investigates complex ecological dynamics from microbial community interactions using the fruit fly  Drosophila melanogaster. The fruit fly gut carries numerous microbial species, which can be cultured in the lab. The goal is to understand the gut ecology and how it relates to host health, among other questions, by taking advantage of the fast time-scale and ease of studying the fruit fly in controlled experiments. 
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Nick Konidaris

Nick Konidaris is a staff scientist at the Carnegie Observatories and Instrument Lead for the SDSS-V Local Volume Mapper (LVM). He works on a broad range of new optical instrumentation projects in astronomy and remote sensing. Nick's projects range from experimental to large workhorse facilities. On the experimental side, he recently began working on a new development platform for the 40-inch Swope telescope at Carnegie's Las Campanas Observatory that will be used to explore and understand the explosive universe.

 Nick and his colleagues at the Department of Global Ecology are leveraging the work on Swope to develop a new airborne spectrograph that will be

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Michael Walter, Director

Experimental petrologist Michael Walter became director of the Geophysical Laboratory beginning April 1, 2018. His recent research has focused on the period early in Earth’s history, shortly after the planet accreted from the cloud of gas and dust surrounding our young Sun, when the mantle and the core first separated into distinct layers. Current topics of investigation also include the structure and properties of various compounds under the extreme pressures and temperatures found deep inside the planet, and information about the pressure, temperature, and chemical conditions of the mantle that can be gleaned from mineral impurities preserved inside diamonds.

Walter

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Leopoldo Infante, Director

Leopoldo Infante became the director of the Las Campanas Observatory on July 31, 2017.

Since 2009, Infante has been the founder and director of the Centre for Astro-Engineering at the Chilean university. He joined PUC as an assistant professor in 1990 and has been a full professor since 2006. He was one of the creators of PUC’s Department of Astronomy and Astrophysics, and served as its director from 2000 to 2006. He also established the Chilean Astronomical Society (SOCHIAS) and served as its president from 2009 to 2010.

Infante received his B.Sc. in physics at PUC. He then acquired a MSc. and Ph.D. in physics and astronomy from the University of Victoria in

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