13 items with the tag “evolution

  • SMACK: A New Algorithm for Modeling Collisions and Dynamics of Planetesimals in Debris Disks
    NAI 2013 NASA Goddard Space Flight Center Annual Report

    Finding habitable planets and understanding the delivery of volatiles to their surfaces requires understanding the disks of rocky and icy debris that these planets orbit within. But modeling the physics of these disks is complicated because of the challenge of tracking collisions among trillions of trillions of colliding bodies. We developed a new technique and a new code for modeling the collisions and dynamics of debris disks, called “SMACK” which will help us interpret images of planetary systems to better understand how planetesimals transport material within young planetary systems.

    ROADMAP OBJECTIVES: 1.1 1.2 3.1
  • Molecular Biosignatures: Reconstructing Events by Comparative Genomics
    NAI 2013 Massachusetts Institute of Technology Annual Report

    Reconstructing ancient events in genome evolution provides a valuable narrative for planetary history. Phylogenetic analysis of protein families within microbial lineages can be used to detect horizontal gene transfers and the evolution of new metabolic pathways and physiologies, many of which are significant in reconstructing ancient ecologies and biogeochemical events. These gene transfers can also be used to constrain molecular clock models for early life evolution, applying principles of stratigraphy and date calibration. A better understanding of gene evolution, including partial horizontal gene transfer, is needed to improve these inferences and avoid systematic errors.

    ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 4.3 5.1 5.2 6.1
  • Early Animals: The Genomic Origins of Morphological Complexity
    NAI 2013 Massachusetts Institute of Technology Annual Report

    Understanding the origins of life’s complexity here on Earth is paramount to finding it elsewhere in the universe. The fossil record indicates that complexity on Earth arose in a near geological moment—the famous Cambrian explosion—about 525 million years ago. However, molecular sequence analyses indicate that complex animals actually arose nearly 200 million years before they make their first appearance in the fossil record (Erwin et al. 2011). This disparity between the advent of morphological complexity and its appearance in the fossil record motivates an interesting question: why is it that we cannot detect complex life here on Earth for nearly 200 million years? And if we cannot detect it on Earth, what hope would we have on another distant Earth-like planet? Our research is focused on addressing this question by trying to obtain a better understanding of what encodes morphological complexity in the genome. Our research (Heimberg et al. 2008; Philippe et al. 2001; Tarver et al. 2013) suggests that a group of non-coding RNA genes—microRNAs—might be instrumental for the advent and maintenance of complexity in animals, and therefore sequencing the genomes and the transcriptomes (the expressed component of the genome) from carefully chosen taxa might allow us to better understand the biology of animals that predated the Cambrian explosion.

  • Life and Environments: Fossils of the Late Meso- and Early Neoproterozoic
    NAI 2013 Massachusetts Institute of Technology Annual Report

    Any understanding of the major biological, biogeochemical and climatic events that characterized the late Neoproterozoic Era (ca. 750-541 million years ago) requires that we understand the state of Earth biota and environment as the critical interval began. Members of the Knoll lab have discovered and analyzed a series of fossil assemblages deposited between 1100 and 800 million years ago and continued to show the relationship between evolution and environmental change on the early Earth.

  • Ribosome Palentology
    NAI 2013 Georgia Institute of Technology Annual Report

    The origins of the translation machinery remain imprinted in the extant ribosome. The conformations of ribosomal RNA and protein components can be seen to change over time indicating clear molecular fossils. We are establishing methodology to determine chronologies of ancient ribosomal evolution. It is hypothesized that substantial, though necessarily incomplete evidence, relating to the origins and early development of the translation machinery and its relation to other core cellular processes continues to exist in the primary sequences, three-dimensional folding and functional interactions of the various macromolecules involved in the modern versions of these processes. To this end, we are using ribosomal paleontology to determine the relative age of various ribosomal components and subsystems and thereby develop timelines for the history of the ribosome as a whole as well as various sub processes such as initiation, termination, translocation etc. The results of these studies will interface ribosomal history with other key relating to the origin of life including the emergence of the genetic code, the origin of chirality, and the nature of the last common ancestor. We have also been developing new tools of ribosomal paleontology, to visualize the changes, and to determine timelines for ribosomal origins.

  • Culturing Microbial Communities in Controlled Stress Micro-Environments
    NAI 2013 University of Illinois at Urbana-Champaign Annual Report

    In NAI Theme 4B, our goal in Year 1 has been to initiate our understanding of how cells structure their genomes in response to specific environmental stresses and to determine whether or not such mechanisms have been a major force in directing the evolution of cells in natural environments over evolutionary time. Natural environments are typically rather heterogeneous at small scales, as established by sampling from geothermal hot spring communities, and so it is important to understand the generic impact on the evolution and structure of microbial communities. Our first step towards probing this phenomenon has been to culture living bacterial populations within a small specially constructed microfluidic device (called the GeoBioCell), where strong physical, chemical and biological gradients can be imposed under carefully controlled conditions.

    ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 5.2 5.3 6.1
  • The Nature of the Last Archaeal and Eukaryal Ancestor
    NAI 2013 University of Illinois at Urbana-Champaign Annual Report

    The evolutionary history of the eukaryotic cell is intimately linked evolution of atmospheric oxygen and with the endosymbiosis of bacterial symbionts to become the mitochondrial organelles. This project seeks to understand the evolutionary history of the eukaryotic cell using contemporary analogs of ancestral anaerobic eukaryotes (rumen ciliates), which are often associated with endosymbiotic archaea and bacteria in tightly associated communities. We study the evolution of this association using state-of-the-art metagenomic and ecological methods to gain a better understanding of the evolution of these types of associations and thus of eukaryotic evolutionary history.

    ROADMAP OBJECTIVES: 3.4 4.1 4.2 5.2 6.1
  • Thermodynamics of Life
    NAI 2013 University of Illinois at Urbana-Champaign Annual Report

    Although thermodynamics dictates that all spontaneous processes must be purely dissipative and “destructive” (the notoriously ungenerous face of the “2nd law”), under particular circumstances a spontaneous process can be a compound of two mechanistically coupled sub-processes only one of which (necessarily the larger one), is dissipative while its coupled, lesser partner is literally “driven” to be creative and generative – that is, a process that can “do work”, “build stuff”, and “make things happen”. A system functioning in this way is technically an engine and all living systems are necessarily, examples of such thermodynamically compound and creative “engine” systems – while at the same time operating internally via a complex, interlinked clockwork of such engines.
    Moreover, living systems inherently belong to a special thermodynamic subclass of such engines, namely those that are “autocatalytic” (self-growing and self-stabilizing) in their operation. Arguably, in fact, it is the property of being autocatalytic thermodynamic engines which at root underlies the potency and magic of living systems and which at the same time constitutes life’s most assuredly universal, fundamental, and primitive property. However, as of yet, we understand the implications of these thermodynamic facts quite poorly – notwithstanding that they seem certain to materially impact questions regarding the origin of life, evolutionary dynamics, and community, trophic, and ecology-level organization.
    The present project undertakes to redress this situation to some extent by investigating the formal dynamical behavior of model systems made up of interacting, thermodynamically driven, autocatalytic engines.

    ROADMAP OBJECTIVES: 3.3 3.4 4.2 5.1 5.2
  • Deconstruction of the Ribosome
    NAI 2013 Georgia Institute of Technology Annual Report

    In this Project we are investigating the folding and interactions of a fragment of rRNA with a fragment of a ribosomal protein (rProtein), both derived from T. thermophilus. The goal is to examine the granularity of rRNA-rProtein recognition, to determine if small RNA and protein components of the ribosome can recapitulate interactions observed in the native ribosome. We have assayed the in vitro and in vivo folding and interactions of an isolated subdomain of rRNA with an rProtein and with a peptide fragment of the rProtein. Chemical mapping shows that a 199-nucleotide fragment of Domain III of the 23S rRNA (defined here as Domain IIIcore) folds to a near-native state. This rRNA fragment binds to ribosomal protein L23 in a yeast three-hybrid assay, as predicted from interactions in the native ribosome. A peptide was designed based on the segment of the rProtein that penetrates deep into the core of the native ribosome and associates primarily with Domain IIIcore. A spectroscopic assay shows that the peptide forms a 1:1 complex with both Domain III and Domain IIIcore. The results indicate that rRNA-rProtein recognition is fine-grained, and can be directed by specific interactions between small rRNA and rProtein fragments.

    ROADMAP OBJECTIVES: 3.2 4.1 4.2
  • Developing New Biosignatures
    NAI 2013 Pennsylvania State University Annual Report

    The development and experimental testing of potential indicators of life is essential for providing a critical scientific basis for the exploration of life in the cosmos. In microbial cultures, potential new biosignatures can be found among isotopic ratios, elemental compositions, and chemical changes to the growth media. Additionally, life can be detected and investigated in natural systems by directing cutting-edge instrumentation towards the investigation of microbial cells, microbial fossils, and microbial geochemical products. Over the next five years, we will combine our geomicrobiological expertise and on-going field-based environmental investigations with a new generation of instruments capable of revealing diagnostic biosignatures. Our efforts will focus on creating innovative approaches for the analyses of cells and other organic material, finding ways in which metal abundances and isotope systems reflect life, and developing creative approaches for using environmental DNA to study present and past life.

    ROADMAP OBJECTIVES: 2.1 3.1 4.1 5.1 7.1
  • Biosignatures in Relevant Microbial Ecosystems
    NAI 2013 Pennsylvania State University Annual Report

    PSARC is investigating microbial life in some of Earth’s most mission-relevant modern ecosystems. These environments include the Dead Sea, the Chesapeake Bay impact structure, methane seeps, ice sheets, and redox-stratified Precambrian ocean analogs. We target environments that, when studied, provide fundamental information that can serve as the basis for future solar system exploration. Combining our expertise in molecular biology, geochemistry, microbiology, and metagenomics, and in collaboration with some of the planet’s most extreme explorers, we are deciphering the microbiology, fossilization processes, and recoverable biosignatures from these mission-relevant environments.

    PSARC Ph.D. (now postdoctoral researcher at Caltech) Katherine Dawson published a new paper documenting the anaerobic biodegradation of organic biosignature compounds pristane and phytane. PSARC Ph.D. Daniel Jones (now postdoctoral researcher at U. Minnesota) published a new paper that uses metagenomic data to show how sulfur oxidation in the deep subsurface environments may contribute to the formation of caves and the maintenence of deep subsurface microbial ecosystems. PSARC Ph.D. student Khadouja Harouaka published a new paper that represents some of the first available information about possible Ca isotope biosignatures. Lastly, the Macalady group published a paper showing how ecological models based on available energy resources can be used to predict the distribution of microbial populations in space and time.

    ROADMAP OBJECTIVES: 4.1 4.3 5.1 5.2 5.3 6.1 7.1 7.2
  • Biosignatures in Ancient Rocks - Kasting Group
    NAI 2013 Pennsylvania State University Annual Report

    The work by Ramirez concerned updating the absorption coefficients in our 1-D climate model. Harman’s work consisted of developing a 1-D code for modeling hydrodynamic escape of hydrogen from rocky planets.

    ROADMAP OBJECTIVES: 1.1 3.2 4.1 4.2 4.3 5.1 5.2 5.3 6.1 6.2 7.1 7.2
  • Understanding Past Earth Environments
    NAI 2013 VPL at University of Washington Annual Report

    For much of the history Earth, life on the planet existed in an environment very different than that of modern-day Earth. Thus, the ancient Earth represents a planet with a biosphere that is both dramatically different than the one in which we live, but that is also accessible to detailed study. As such, it serves as a model for what types of biospheres we may find on other planets. A particular focus of our work was on the “Early Earth” (formation through to about 500 million years ago), a timeframe poorly represented in the geological and fossil records but comprises the majority of Earth’s history. We have studied the composition, pressure and climate of the ancient atmosphere; the delivery of biologically available phosphorus; studied the sulfur, oxygen and nitrogen cycles; and explored atmospheric formation of molecules that were likely important to the origins of life on Earth.

    ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 5.1 5.2 6.1