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Project Reports

• AIRFrame Technical Infrastructure and Visualization Software Evaluation

  We have analyzed over four thousand astrobiology articles from the scientific press, published over ten years to search for clues about their underlying connections. This information can be used to build tools and technologies that guide scientists quickly across vast, interdisciplinary libraries towards the diverse works of most relevance to them.

  ROADMAP OBJECTIVES: 1.1 1.2 2.1 2.2 3.1 3.2 3.3 3.4 4.1 4.2 4.3 5.1 5.2 5.3 6.1 6.2 7.1 7.2

• Atmospheric Oxygen and Complex Life

  The biosynthesis of sterols requires oxygen but only in vanishingly low concentrations. Oxygen could be used by algae to make sterols in the surface ocean and, yet, at the same time, it would not be in sufficient concentration to destroy the mass-independent sulfur isotope signal for atmospheric oxygenation.

  Large sulfur isotope fractionations have been observed in sulfate reducing bacteria grown in a 'starvation’ regime, much as most natural populations experience. This casts doubt on the hypothesis that the large sulfur isotope fractionations seen in the Neoproterozoic rock record herald an increase in atmospheric oxygen and the inception of a new form of oxidative sulfur cycling.

  ROADMAP OBJECTIVES: 4.1 4.2 6.1

• Ecology of Extreme Environments: Characterization of Energy Flow, Bioenergetics, and Biodiversity in Early Earth Analog Ecosystems

  The distribution of organisms and their metabolic functions on Earth is rooted, at least in part, to the numerous adaptive radiations that have resulted in the ability to occupy new ecological niches through evolutionary time. Such responses are recorded in extant organismal geographic distribution patterns (e.g., habitat range), as well as in the genetic record of organisms. The extreme variation in the geochemical composition of present day hydrothermal environments is likely to encompass many of those that were present on early Earth, when key metabolic processes are thought to have evolved. Environments such Yellowstone National Park (YNP), Wyoming harbor >12,000 geothermal features that vary widely in temperature and geochemical composition. Such environments provide a field laboratory for examining the tendency for guilds of organisms to inhabit particular ecological niches and to define the range of geochemical conditions tolerated by that functional guild (i.e., habitat range or zone of habitability). In this aim, we are examining the distribution and diversity of genes that encode for target metalloproteins in YNP environments that harbor geochemical properties that are thought to be similar to those that characterize early Earth. Using a number of newly developed computational approaches, we have been able to deduce the primary environmental parameters that constrain the distribution of a number of functional processes and which underpin their diversity. Such information is central to constraining the parameter space of environment types that are likely to have facilitated the emergence of these metal-based biocatalysts.

  ROADMAP OBJECTIVES: 3.2 3.3 3.4 4.1 4.2 5.1 5.2 5.3

• Amino Acid Alphabet Evolution

  We study the question why did life on this planet “choose” a set of 20 standard building blocks (amino acids) for converting genetic instructions into living organisms? The evolutionary step has since been used to evolve organisms of such diversity and adaptability that modern biologists struggle to discover the limits to life-as-we-know-it. Yet the standard amino acid alphabet has remained more or less unchanged for 3 billion years.
  During the past year, we have found that the sub-set of amino acids used by biology exhibits some surprisingly simple, strikingly non-random properties. We are now building on this finding to solidify a new insight into the emergence of life here, and what it can reveal about the distribution and characteristics of life elsewhere in the universe.

  ROADMAP OBJECTIVES: 3.1 3.2 4.1 4.2 4.3 5.2 5.3 6.2 7.1

• Biomechanics of the Rangeomorph Fauna

  The oldest communities of fossil eukaryotes are found in the sedimentary rocks of Mistaken Point Newfoundland. These sediments were deposited in deep, slow-moving waters, at depths where light could not penetrate. Communities of fossil fronds preserved here reached up off the bottom, much like plants, but are thought to have lived by absorbing reduced compounds through their large surface area. In our work we show that growth off the seafloor provides an opportunity to reach higher flow velocity in this low flow environment. This exposure to flow breaks down diffusional limits, permitting more rapid uptake and growth. This opportunity is only available to larger-sized organisms, and this size advantage is exclusive to multicellular eucaryotes – not to competing bacteria with their smaller cell-size, and minimal multicellularity. Thus these communities and this advantage to multicellular form represents an important step in the evolution of complex multicellular life.

  ROADMAP OBJECTIVES: 4.2 5.2 6.1

• Assessing the Role of Chance vs. Necessity in Evolution: Experimental Evolution of Ancient Proteins in E.coli

  The goal of our current work is to create a “Bacterial Jurassic Park” in the laboratory. Our system combines synthetic biology (paleogenetics) with experimental evolution whereby we insert ancient genes into a modern bacterial genome. Replacing an essential bacterial gene with its ancient counterpart allows me to initiate a struggle for existence in these microbial populations since the ancient gene is maladapted to modern environments. Observing the real-time evolution of these resurrected genes as they adapt to the conditions of modern bacteria therefore allows me to monitor evolution in action (1-6).

  ROADMAP OBJECTIVES: 4.2

• Biosignatures in Ancient Rocks

  The Earth’s Archean and Proterozoic eons offer the best opportunity for investigating a microbial world, such as might be found elsewhere in the cosmos. The ancient record on Earth provides an opportunity to see what geochemical signatures are produced by microbial life and how these signatures are preserved over geologic time. As part of our integrated plan, we will study geochemical, isotopic, and sedimentary signatures of life in order to understand the context in which these biosignatures formed.

  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

• Evolution and Development of Sensory and Nervous Systems in the Basal Branches of the Animal Tree

  Animals interact with the world through complex sensory structures (eyes, ears, antennas, etc.), which are coordinated by collections of neurons. While the nervous and sensory systems of animals are incredibly diverse, a growing body of evidence suggests that many of these systems are controlled by similar sets of genes. We are looking at early branching and understudied lineages of the animal family tree (using the jellyfish Aurelia and the worm Neanthes respectively) to see if these animals use similar genes during neurosensory development as the better-studied fruit fly and mouse. This research is critical for determining which structures are shared between animals because of common ancestry (known as homologous structures) and those that evolved independently in different lineages. Ultimately, such research informs how morphologically and behaviorally complex animals evolve.

  ROADMAP OBJECTIVES: 4.1 4.2

• Geochemical Signatures of Multicellular Life

  We continued our studies of the sterol complements of basal metazoa and their closest unicellular relatives and discerned what appears to be an evolutionary trend toward the universal use of cholesterol by higher animals. Inverse carbon isotope patterns of lipids and kerogen, that are a distinctive characteristic of organic matter found in Neoproterozoic sediments, record heterogeneous primary biomass comprising a dominant input from bacteria.

  ROADMAP OBJECTIVES: 3.2 4.2

• Domain III of the 23S rRNA: An Independent Domain

  The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain that can fold to a near-native state in the absence of the remainder of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2’-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.

  ROADMAP OBJECTIVES: 3.2 4.2

• Metabolic Networks From Single Cells to Ecosystems

  Members of the Segre’ group use systems biology approaches to study the complex network of metabolic reactions that allow microbial cells to survive and reproduce under varying environmental conditions. The resource allocation problem that underlies these fundamental processes changes dramatically when multiple cells can compete or cooperate with each other, for example through metabolic cross-feeding. Through mathematical models of microbial ecosystems and computer simulations of spatially structured cell populations, the Segre’ team aims at understanding the environmental conditions and evolutionary processes that favor the emergence of multicellular organization in living systems.

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 5.2 6.1

• Modelling Planetary Albedo & Biomarkers in Rocky Planets’/moons Spectra

  Using data from Kepler and new ground-based detections, Lisa Kaltenegger and Dimitar Sasselov have identified which confirmed and candidate planets orbit within the Habitable Zone and could provide environments for basic and complex life to develop. They have also developed atmosphere models for extrasolar planetary environments for different geological cycles and varied environments for the advent of complex life. The team modeled detectable spectral features that identify such planetary environments for future NASA missions like the James Webb Space Telescope.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 6.2 7.2

• Extremophile Ribosomes

  One of the biggest challenges facing eukaryote extremophiles is the loss of water leading to desiccation. Resistance to desiccation as adults, juveniles, seeds, or spores is found in species of five animal phyla and four divisions of plants. Little is understood about the biochemistry of desiccation tolerance in eukaryotes, but ribosomes are likely to figure prominently in this phenomenon. The model for our investigations are animals from the phylum Rotifera which are capable from going from completely desiccated to an active, swimming animal in minutes to hours. We are examining how their ribosomes are capable of tolerating near complete dehydration, then rehydrate and engage in translation within minutes. Our hypothesis is that specific proteins associate with ribosomes during desiccation, protecting them from damage and then dissociate upon rehydration. We want to enumerate these proteins and discover the underlying genes. In the future, this knowledge could be used to engineer desiccation tolerance into organisms that currently lack this ability.

  ROADMAP OBJECTIVES: 3.2 4.2 5.3

• Deep (Sediment-Buried Basement) Biosphere

  The ocean crust comprises the largest aquifer on earth. Deep sediment cover provides an environ-ment for a unique biosphere hosting microorganisms surviving under extreme conditions. Frac-tured rock provides abundant surfaces that can be colonized by diverse microbes and water-rock reactions promote chemical conditions that influence key geochemical cycles within the Earth’s crust and oceans. Team members participated in a 14-day research cruise to study the sediment-buried basement (basaltic crust) biosphere, to provide unprecedented and unique insight into the mobility and origin of microorganisms within this remote biosphere.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 5.3 6.1 6.2 7.1 7.2

• High Level Theory – the Role of Mg2+ in Ribosome Assembly

  Magnesium plays a special role in RNA function and folding. Although water is magnesium’s most common first-shell ligand, magnesium has significant affinity for the oxyanions of RNA phosphates. Here we provide a quantum mechanical (QM) description of first shell RNA-magnesium and DNA-magnesium interactions, demonstrating unique features that appear to be required for folding of large RNAs. Our work focuses on multidentate chelation of magnesium by RNA and DNA, where multiple phosphate oxyanions enter the first coordination shell of magnesium. The results suggest that magnesium, compared to calcium and sodium, has enhanced ability to form bidentate chelation complexes with RNA. Sodium complexes, in particular, are unstable and spontaneously open. A magnesium cation is closer to the oxyanions of RNA than the other cations, and is stabilized not only by electrostatic interaction with the oxyanions but also by charge transfer and polarization interactions. Those interactions are quite substantial at close distances. The quantum effects are less pronounced for calcium due to its larger size, and for sodium due to its smaller charge. Additionally, we find that magnesium complexes with RNA are more stable than those with DNA. The nature of the additional stability is twofold: it is due to a slightly greater energetic penalty of ring closure to form chelation complexes for DNA, and elevated electrostatic interactions between the RNA and cations. In sum it can be seen that even at high concentration, sodium and calcium cannot replicate the structures or energetics of RNA-magnesium complexes.

  ROADMAP OBJECTIVES: 3.2 4.2

• Molecular and Isotopic Investigations Across the Neoproterozoic

  We gathered new data on molecular and isotopic stratigraphic trends from Cryogenian and Ediacaran sequences from Canada, Oman and Mongolia. These continue to show that the biogeochemical carbon cycle was anomalous, and unlike any other period in Earth history, prior to the advent of complex animal life. While difficult to interpret in a robust way these data are reproducible, reflect real trends and are not the result of 'diagenetic alteration’ as some have proposed.

  ROADMAP OBJECTIVES: 4.2 5.2 6.1

• In Vivo Deconstruction and Restoration of Ribosomal

  We are employing the yeast-three hybrid system to investigate in vivo interactions between a-RNA and ribosomal proteins. Our results demonstrate that a-RNA-γ binds in vivo to L2, L3, L4, L15, and L22. L2 is an initial protein in ribosomal assembly and binds to the intact 23S rRNA independently of other r-proteins. We are currently examining the potential for greater binding in vivo of L3, L4, L15, and L22 to the a-RNA-γ with co-expression of L2 in a yeast hybrid system.

  ROADMAP OBJECTIVES: 3.2 4.2

• Neoproterozoic Carbon Cycle

  The rock record late Neoproterozoic (540-800 Ma) appears to exhibit strong
  perturbations to Earth’s carbon cycle. This project seeks an understanding
  of the mechanisms that drive such events and their biogeochemical significance.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.2 6.1

• Origins of Multicellularity

  By comparing animal genomes with genomes from their closest living relatives, the choanoflagellates, we can reconstruct the genome composition of the last common ancestor of animals.

  ROADMAP OBJECTIVES: 4.2

• Ironing Out the RNA World

  Life originated during the early Archean, which was characterized by a non-oxidative atmosphere and abundant soluble Fe²⁺. Current theories on the origin of life focus on RNA-based genetic and metabolic systems. Here we show, by theory and experiment, that critical roles of Mg²⁺ in extant RNA folding and function can be better served by Fe²⁺ in the absence of oxygen. The results of our high-level quantum mechanical calculations show that the geometry of coordination of Fe²⁺ by RNA phosphates is similar to that of Mg²⁺. The conformation of Tetrahymena Group I intron P4-P6 domain is conserved between complexes of Fe²⁺ and Mg²⁺. Additionally, a ribozyme obtained previously by in vitro selection in the presence of Mg²⁺ and a natural ribozyme both have significantly greater catalytic competence in the presence of Fe²⁺ than in Mg²⁺. The combined biochemical and paleogeological data are consistent with an RNA-Fe²⁺ world that could have supported an array of RNA structures and catalytic functions far more diverse that of an RNA-Mg²⁺ world.

  ROADMAP OBJECTIVES: 4.1 4.2

• Project 3B: In Situ Sulfur Isotope Studies in Archean-Proterozoic Sulfides

  Using new protocols developed at WiscSIMS, we made in situ measurements of three stable isotopes of sulfur (32S, 33S and 34S) in pyrite from the Meteorite Bore Member with unprecedented small spot sizes and accuracy (Williford et al. 2011). We have found a moderate range of S-MIF (> 1‰) in authigenic pyrite before, during and after the Early Proterozoic glaciation as well as a 90‰ range of mass dependent sulfur isotope fractionation (δ34S) larger than any observed in sediments older than 700 Ma. Furthermore, abundant detrital pyrite preserved in one glacial sandstone unit from the Meteorite Bore Member exhibits a range of mass-independent sulfur isotope fractionation slightly larger than the largest published range, from 2.5 Ga sediments of the Hamersley and Transvaal Basins (> 15‰), suggesting that these detrital grains may have originated in rocks of similar age. Taken together, these data imply that the Meteorite Bore Member was deposited during the transitional interval when atmospheric oxygen had risen sufficiently for enhanced continental weathering and ocean sulfate to occur, yet remained low enough to permit the preservation of detrital pyrite and moderate S-MIF.

  ROADMAP OBJECTIVES: 1.1 4.1 4.2 7.1

• Stromatolites in the Desert: Analogs to Other Worlds

  In this task biologists go to field sites in Mexico to better understand the environmental effects on growth rates for freshwater stromatolites. Stromatolites are microbial mat communities that have the ability to calcify under certain conditions. They are believed to be an ancient form of life, that may have dominated the planet’s biosphere more than 2 billion years ago. Our work focuses on understanding these communities as a means of characterizing their metabolisms and gas outputs, for use in planetary models of ancient environments.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 5.3 6.1 6.2

• Paleontological Investigations of the Advent and Maintenance of Multicellular Life

  Understanding the origins and maintenance of complex life requires a two pronged approach: detailed investigations of the ecological and environmental context of the advent of complex life, as revealed by the fossil record, and exploration of the molecular underpinnings of how life becomes complex, how it is maintained, and how it is lost. The appearance of complex life that begins in the Ediacaran period around 580 million years ago and truly blossoms in the Cambrian Period about 530 million years ago reveals that ecological interactions – specifically predation – was a necessary component, and was depended upon the continuing oxygenation of the world’s oceans. Molecular investigations have revealed the genes and gene interactions that appear to be necessary for the advent of complex life, and what needs to be lost in order for complex life to become secondarily simplified. Together the fossil record and the molecular record indicate that evolving complex life involves both new genes and new ecologies within the context of permissive environmental circumstances.

  ROADMAP OBJECTIVES: 4.2

• Resurrection of an Ancestral Peptidyl Transferase

  We have created and test both in silico and in vitro models of an ancestral pepidyl transerase center (PTC). Our most recent in silico and in vitro models contain a significantly reduced 23S rRNA (called a-rRNA-γ, Figure 1), retraining the rRNA that forms and surrounds the PTC. To complete the in silico and in vitro models of the ancestral PTC (a-PTC-γ in silico and a-PTC-γ in vitro), we have combined a-rRNA-γ with peptides derived from the ribosomal proteins. The results here indicate that the ribosome and its components are highly robust in folding and assembly. We have shaved around 2500 nucleotides from the 23S rRNA and the vast majority of amino acids from the protein components, excising the globular domains in toto. Yet, the remaining rRNA and peptides retain the ability to fold and specifically assemble.

  ROADMAP OBJECTIVES: 3.2 4.2

• Protists of the Neoproterozoic

  T. Bosak (MIT), S. Pruss (Smith College), F. Macdonald (Harvard U.) and D. Lahr (U. Sao Paolo) discovered fossils of microscopic eukaryotes in limestone and dolostone strata deposited between the two Neoproterozoic low-latitude glaciations (between ~ 716 and 635 million years ago). These fossils include amoeba-like organisms that incorporated mineral-rich particles from the environment into their shells, mineral-rich shells of the oldest putative foraminiferans, and thick flask-shaped organic envelopes of the first putative ciliates, representatives of a major group of modern eukaryotes. These fossils demonstrate a previously unrecognized record of body fossils during the ~ 70 million years between the two “Snowball Earth” episodes and document the increasing diversity of morphologically and compositionally modern eukaryotes before the rise of complex animals.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• The Long Wavelength Limit for Oxygenic Photosynthesis

  Photosynthesis is process where plants and bacteria use solar energy to produce sugar and oxygen. It is also the only known process that produces signs of life (biosignatures) on a planetary scale. And, because starlight (or solar energy) is one of the most common sources of energy, it is expected that photosynthesis will be successful on habitable extrasolar planets. Our team is studying how photosynthetic pigments – the molecules that make photosynthesis possible – might function in unique or extreme environments on other planets. In our experiments, we use a bacteria called Acaryochloris marina to study how different photosynthetic pigments work. This bacterium is useful for our research because it uses a pigment known as chlorophyll d instead of chlorophyll a, which is more common on our planet. Chrolophyll a works well in Earth’s environment but, by studying chlorophyll d, we can begin to understand how photosynthesis might work on planets with different environments than Earth. So far, our research is revealing that photosynthesis can occur quite efficiently in environments that are very different from our planet.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 7.2

• Ribosome Paleontology

  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 time 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.

  ROADMAP OBJECTIVES: 3.2 4.2

• Proxies for Ocean Anoxia

  Episodes of widespread anoxia in past oceans are known as “Ocean Anoxic Events”. The ecosystem consequences of these events are actively debated. In this project, we are examining the chemical and isotopic signatures of the photosynthetic pigment, chlorophyll, to understand changes in ecosystems and the nutrients that fueled them. The seasonal oxygen minimum zone (OMZ) offshore Chile is being used as a modern analog.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 5.3 6.1

• Understanding Past Earth Environments

  For much of the history Earth, life on the planet existed in an environment dramatically 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 and is accessible to detailed study. As such, is 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 of the ancient atmosphere, modeled the effects of clouds on such a planet, studied the sulfur, oxygen and nitrogen cycles, and the 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

• Stoichiometry of Life, Task 3a: Ancient Records – Geologic

  We have generated and are interpreting a wide range of geochemical data from rocks that are over 1.5 billion years old. The data indicate that the ancient ocean was very different than today and had regions that were full of toxic hydrogen sulfide. These extreme conditions in the ocean were the backdrop against which early organisms appeared and evolved—and perhaps struggled.

  ROADMAP OBJECTIVES: 4.1 4.2

• Stoichiometry of Life, Task 4: Biogeochemical Impacts on Planetary Atmospheres

  Oxygenation of Earth’s early atmosphere must have involved an efficient mode of carbon burial. In the modern ocean, carbon export of primary production is dominated by fecal pellets and aggregates produced by the animal grazer community. But during most of Earth history the oceans were dominated by unicellular, bacteria-like organisms (prokaryotes) causing a substantially altered biogeochemistry. In this task we experiment with the marine cyanobacterium Synechococcus sp. as a model organism and test its aggregation and sinking speed as a function of nutrient (nitrogen, phosphorus, iron) limitation. We have found so far that aggregation and sinking of these minute cyanobacteria is influenced by the concentration of nutrients in the growth medium.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1 7.2