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  • richardmitnick 10:45 am on December 10, 2018 Permalink | Reply
    Tags: , , Calditol, Geobiology, Stanford researchers show that a protein in a microbe’s membrane helps it survive extreme environments, , Sulfolobus acidocaldarius   

    From Stanford University: “Stanford researchers show that a protein in a microbe’s membrane helps it survive extreme environments” 

    Stanford University Name
    From Stanford University

    December 5, 2018
    Danielle Torrent Tucker
    (650) 497-9541
    dttucker@stanford.edu

    Scientists discovered a protein that modifies a microbe’s membrane and helps it survive in hot, acidic environments, proving a long-standing hypothesis that these structures have a protective effect.

    1
    The microorganism Sulfolobus acidocaldarius lives in extreme environments, such as Emerald Hot Spring in Yellowstone National Park. (Image credit: Rennett Stowe / flickr)

    Within harsh environments like hot springs, volcanic craters and deep-sea hydrothermal vents – uninhabitable by most life forms – microscopic organisms are thriving. How? It’s all in how they wrap themselves.

    Stanford University researchers have identified a protein that helps these organisms form a protective, lipid-linked cellular membrane – a key to withstanding extremely highly acidic habitats.

    Scientists had known that this group of microbes – called archaea – were surrounded by a membrane made of different chemical components than those of bacteria, plants or animals. They had long hypothesized that it could be what provides protection in extreme habitats. The team directly proved this idea by identifying the protein that creates the unusual membrane structure in the species Sulfolobus acidocaldarius.

    The structures of some organisms’ membranes are retained in the fossil record and can serve as molecular fossils or biomarkers, leaving hints of what lived in the environment long ago. Finding preserved membrane lipids, for example, could suggest when an organism evolved and how that may have been the circumstance of its environment. Being able to show how this protective membrane is created could help researchers understand other molecular fossils in the future, offering new evidence about the evolution of life on Earth. The results appeared the week of Dec. 3 in Proceedings of the National Academy of Sciences.

    “Our model is that this organism evolved the ability to make these membranes because it lives in an environment where the acidity changes,” said co-author Paula Welander, an assistant professor of Earth system science at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth). “This is the first time we’ve actually linked some part of a lipid to an environmental condition in archaea.”

    Rare chemistry

    The hot springs where S. acidocaldarius is found, such as those in Yellowstone National Park that are over 200 degrees Fahrenheit, can experience fluctuating acidity. This organism is also found in volcanic craters, deep-sea hydrothermal vents and other acidic environments with both moderate and cold temperatures.

    Welander became interested in studying this microbe because of its rare chemistry, including its unusual lipid membranes. Unlike plants and fungi, archaeal organisms do not produce protective outer walls of cellulose and their membranes do not contain the same chemicals as bacteria. Scientists had explored how the species produced its unusual membrane for about 10 years before experimentation stopped in 2006, she said.

    “I think we forget that some things just haven’t been done yet – I’ve been finding that a lot ever since I stepped into the geobiology world,” Welander said. “There are so many questions out there that we just need the basic knowledge of, such as, ‘What is the protein that’s doing this? Does this membrane structure really do what we’re saying it does?’”

    From previous research in archaea, Welander and her team knew that the organisms produce a membrane containing a ringed molecule called a calditol. The group thought this molecule might underlie the species’ ability to withstand environments where other organisms perish.

    To find out, they first went through the genome of S. acidocaldarius and identified three genes likely to be involved in making a calditol. They then mutated those genes one-by-one, eliminating any proteins the genes made. The experiments revealed one gene that, when mutated, produced S. acidocaldarius that lacked calditol in the membrane. That mutated organism was able to grow at high temperatures but withered in a highly acidic environment, suggesting that the protein is necessary to both make the unusual membrane and withstand acidity.

    The work was particularly challenging because Welander’s lab had to replicate those high temperature, acidic conditions in which the microbes thrive. Most of the incubators in her lab could only reach body temperature, so lead author Zhirui Zeng, a postdoctoral researcher in Welander’s lab, figured out how to imitate the organism’s home using a special small oven, she said.

    “That was really cool,” Welander said. “We did a lot of experimenting to try to figure out the chemistry.”

    Third domain of life

    This work is about more than just finding one protein, Welander said. Her research explores lipids found in present-day microbes with the goal of understanding Earth’s history, including ancient climatic events, mass extinctions and evolutionary transitions. But before scientists can interpret evolutionary characteristics, they need to understand the basics, like how novel lipids are created.

    Archaea are sometimes called the “third domain of life,” with one domain being bacteria and the other being a group that includes plants and animals – collectively known as eukaryotes. Archaea includes some of the oldest, most abundant lifeforms on the planet, without which the ecosystem would collapse. Archaea are particularly anomalous microbes, confused with bacteria one day and likened to plants or animals the next because of their unique molecular structures.

    The research is particularly interesting because the classification for archaea is still debated by taxonomists. They were only separated from the bacteria and eukaryote domains in the past two decades, following the development of genetic sequencing in the 1970s.

    “There are certain things about archaea that are different, like the lipids,” Welander said. “Archaea are a big area of research now because they are this different domain that we want to study, and understand – and they’re really cool.”

    See the full article here .


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  • richardmitnick 9:16 am on August 21, 2018 Permalink | Reply
    Tags: , Building phylogenetic trees, Chronograms, , , Geobiology, , Investigating Earth’s earliest life, Kelsey Moore, , ,   

    From MIT News: Women in STEM- “Investigating Earth’s earliest life” Kelsey Moore 

    MIT News
    MIT Widget

    From MIT News

    August 18, 2018
    Fatima Husain

    1
    Kelsey Moore. Image: Ian MacLellan

    Graduate student Kelsey Moore uses genetic and fossil evidence to study the first stages of evolution on our planet.

    In the second grade, Kelsey Moore became acquainted with geologic time. Her teachers instructed the class to unroll a giant strip of felt down a long hallway in the school. Most of the felt was solid black, but at the very end, the students caught a glimpse of red.

    That tiny red strip represented the time on Earth in which humans have lived, the teachers said. The lesson sparked Moore’s curiosity. What happened on Earth before there were humans? How could she find out?

    A little over a decade later, Moore enrolled in her first geoscience class at Smith College and discovered she now had the tools to begin to answer those very questions.

    Moore zeroed in on geobiology, the study of how the physical Earth and biosphere interact. During the first semester of her sophomore year of college, she took a class that she says “totally blew my mind.”

    “I knew I wanted to learn about Earth history. But then I took this invertebrate paleontology class and realized how much we can learn about life and how life has evolved,” Moore says. A few lectures into the semester, she mustered the courage to ask her professor, Sara Pruss in Smith’s Department of Geosciences, for a research position in the lab.

    Now a fourth-year graduate student at MIT, Moore works in the geobiology lab of Associate Professor Tanja Bosak in MIT’s Department of Earth, Atmospheric, and Planetary Sciences. In addition to carrying out her own research, Moore, who is also a Graduate Resident Tutor in the Simmons Hall undergraduate dorm, makes it a priority to help guide the lab’s undergraduate researchers and teach them the techniques they need to know.

    Time travel

    “We have a natural curiosity about how we got here, and how the Earth became what it is. There’s so much unknown about the early biosphere on Earth when you go back 2 billion, 3 billion, 4 billion years,” Moore says.

    Moore studies early life on Earth by focusing on ancient microbes from the Proterozoic, the period of Earth’s history that spans 2.5 billion to 542 million years ago — between the time when oxygen began to appear in the atmosphere up until the advent and proliferation of complex life. Early in her graduate studies, Moore and Bosak collaborated with Greg Fournier, the Cecil and Ida Green Assistant Professor of Geobiology, on research tracking cyanobacterial evolution. Their research is supported by the Simons Collaboration on the Origins of Life.

    An image of Cyanobacteria, Tolypothrix

    The question of when cyanobacteria gained the ability to perform oxygenic photosynthesis, which produces oxygen and is how many plants on Earth today get their energy, is still under debate. To track cyanobacterial evolution, MIT researchers draw from genetics and micropaleontology. Moore works on molecular clock models, which track genetic mutations over time to measure evolutionary divergence in organisms.

    Clad with a white lab coat, lab glasses, and bright purple gloves, Moore sifts through multiple cyanobacteria under a microscope to find modern analogs to ancient cyanobacterial fossils. The process can be time-consuming.

    “I do a lot of microscopy,” Moore says with a laugh. Once she’s identified an analog, Moore cultures that particular type of cyanobacteria, a process which can sometimes take months. After the strain is enriched and cultured, Moore extracts DNA from the cyanobacteria. “We sequence modern organisms to get their genomes, reconstruct them, and build phylogenetic trees,” Moore says.

    By tying information together from ancient fossils and modern analogs using molecular clocks, Moore hopes to build a chronogram — a type of phylogenetic tree with a time component that eventually traces back to when cyanobacteria evolved the ability to split water and produce oxygen.

    Moore also studies the process of fossilization, on Earth and potentially other planets. She is collaborating with researchers at NASA’s Jet Propulsion Laboratory to help them prepare for the upcoming Mars 2020 rover mission.

    “We’re trying to analyze fossils on Earth to get an idea for how we’re going to look at whatever samples get brought back from Mars, and then to also understand how we can learn from other planets and potentially other life,” Moore says.

    After MIT, Moore hopes to continue research, pursue postdoctoral fellowships, and eventually teach.

    “I really love research. So why stop? I’m going to keep going,” Moore says. She says she wants to teach in an institution that emphasizes giving research opportunities to undergraduate students.

    “Undergrads can be overlooked, but they’re really intelligent people and they’re budding scientists,” Moore says. “So being able to foster that and to see them grow and trust that they are capable in doing research, I think, is my calling.”

    Geology up close

    To study ancient organisms and find fossils, Moore has traveled across the world, to Shark Bay in Australia, Death Valley in the United States, and Bermuda.

    “In order to understand the rocks, you really have to get your nose on the rocks. Go and look at them, and be there. You have to go and stand in the tidal pools and see what’s happening — watch the air bubbles from the cyanobacteria and see them make oxygen,” Moore says. “Those kinds of things are really important in order to understand and fully wrap your brain around how important those interactions are.”

    And in the field, Moore says, researchers have to “roll with the punches.”

    “You don’t have a nice, beautiful, pristine lab set up with all the tools and equipment that you need. You just can’t account for everything,” Moore says. “You have to do what you can with the tools that you have.”

    Mentorship

    As a Graduate Resident Tutor, Moore helps to create supporting living environments for the undergraduate residents of Simmons Hall.

    Each week, she hosts a study break in her apartment in Simmons for her cohort of students — complete with freshly baked treats. “[Baking] is really relaxing for me,” Moore says. “It’s therapeutic.”

    “I think part of the reason I love baking so much is that it’s my creative outlet,” she says. “I know that a lot of people describe baking as like chemistry. But I think you have the opportunity to be more creative and have more fun with it. The creative side of it is something that I love, that I crave outside of research.”

    Part of Moore’s determination to research, trek out in the field, and mentor undergraduates draws from her “biggest science inspiration” — her mother, Michele Moore, a physics professor at Spokane Falls Community College in Spokane, Washington.

    “She was a stay-at-home mom my entire childhood. And then when I was in middle school, she decided to go and get a college degree,” Moore says. When Moore started high school, her mother earned her bachelor’s degree in physics. Then, when Moore started college, her mother earned her PhD. “She was sort of one step ahead of me all the time, and she was a big inspiration for me and gave me the confidence to be a woman in science.”

    See the full article here .


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