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NASA NTRS2003

Mammalian development in space

Life on Earth, and thus the reproductive and ontogenetic processes of all extant species and their ancestors, evolved under the constant influence of the Earth's l g gravitational field. These considerations raise important questions about the ability of mammals to reproduce and develop in space. In this chapter, I review the current state of our knowledge of spaceflight effects on developing mammals. Recent studies are revealing the first insights into how the space environment affects critical phases of mammalian reproduction and development, viz., those events surrounding fertilization, embryogenesis, pregnancy, birth, postnatal maturation and parental care. This review emphasizes fetal and early postnatal life, the developmental epochs for which the greatest amounts of mammalian spaceflight data have been amassed. The maternal-offspring system, the coordinated aggregate of mother and young comprising mammalian development, is of primary importance during these early, formative developmental phases. The existing research supports the view that biologically meaningful interactions between mothers and offspring are changed in the weightlessness of space. These changes may, in turn, cloud interpretations of spaceflight effects on developing offspring. Whereas studies of mid-pregnant rats in space have been extraordinarily successful, studies of young rat litters launched at 9 days of postnatal age or earlier, have been encumbered with problems related to the design of in-flight caging and compromised maternal-offspring interactions. Possibilities for mammalian birth in space, an event that has not yet transpired, are considered. In the aggregate, the results indicate a strong need for new studies of mammalian reproduction and development in space. Habitat development and systematic ground-based testing are important prerequisites to future research with young postnatal rodents in space. Together, the findings support the view that the environment within which young mammals develop, comprised of its mother and siblings, is of paramount importance in interpreting spaceflight effects.

Review↗

NASA NTRS1995

The Origin of Life--Did It Occur at High Temperatures

A high-temperature origin of life has been proposed, largely for the reason that the hyperthermophiles are claimed to be the last common ancestor of modern organisms. Even if they are the oldest extant organisms, which is in dispute, their existence can say nothing about the temperatures of the origin of life, the RNA world, and organisms preceding the hyperthermophiles. There is no geological evidence for the physical setting of the origin of life because there are no unmetamorphosed rocks from that period. Prebiotic chemistry points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100 C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine). Hyperthermophiles may appear at the base of some phylogenetic trees because they outcompeted the mesophiles when they adapted to lower temperatures, possibly due to enhanced production of heat-shock proteins.

Miller, Stanley L.↗

DOE OSTI2021

Cellular remains in a ~3.42-billion-year-old subseafloor hydrothermal environment

Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth’s earliest microbial habitats. Though the site of life’s emergence continues to be debated, evidence of early life provides insights into its early evolution1. Here we present our discovery of exceptionally well-preserved ~3.40-billion-years-old carbonaceous filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt (BGB) in South Africa. The distribution of the microfossils in growth position on the walls of the initial conduits created by low- temperature hydrothermal fluid and their morphological and chemical characteristics as investigated over a range of scales, are consistent with an assemblage of methanogens that thrived in an ultramafic volcanic substrate.

Cavalazzi, Barbara↗

NASA NTRS1983

Planetary biology and microbial ecology. Biochemistry of carbon and early life

Experiments made with cyanobacteria, phototrophic bacteria, and methanogenic bacteria are detailed. Significant carbon isotope fractionation data is included. Taken from well documented extant microbial communities, this data provides a basis of comparison for isotope fractionation values measured in Archean and Proterozoic (preCambrian) rocks. Media, methods, and techniques used to acquire data are also described.

Margulis, L.↗

DOE OSTI2020

Whole-proteome tree of life suggests a deep burst of organism diversity

An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an “alignment-free” method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a “deep burst” at the very beginning period near the root of the ToL—an explosive birth of life’s diversity.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2000

Models of the Protocellular Structures, Functions and Evolution

In the absence of extinct or extant record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids: First, a very large population of candidate molecules is generated using a random synthetic approach. Next, the small numbers of molecules that can accomplish the desired task are selected. These molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. To date, we have obtained "a proof of concept" by evolving simple, novel proteins capable of selectively binding adenosine tri-phosphate (ATP). Our next goal is to create an enzyme that can phosphorylate amino acids and another to catalyze the formation of peptide bonds in the absence of nucleic acid templates. This latter reaction does not take place in contemporary cells. once developed, these enzymes will be encapsulated in liposomes so that they will function in a simulated cellular environment. To provide a continuous energy supply, usually needed to activate the substrates, an energy transduction complex which generates ATP from adenosine diphosphate, inorganic phosphate and light will be used. This system, consisting of two modern proteins, ATP synthase and bacteriorhodopsin, has already been built and shown to work efficiently. By coupling chemical synthesis to such a system, it will be possible to drive chemical reactions by light if only the substrates for these reactions are supplied.

Pohorille, Andrew↗

NASA NTRS1991

Paleobiomarkers and defining exobiology experiments for future Mars experiments

Mars is a cold, dry planet with an oxidizing surface bombarded by ultraviolet and ionizing radiation, making prospects for an extant Mars biota bleak. Yet, it is suggested that early Earth and early Mars were similar enought that life may have evoled on Mars. If life did evolve on Mars, what evidence for its existence might we find? What constitutes a Martian paleobiomarker, and how can we distinguish such a marker from abiotically produced substances? The topics studied to answer this question include carbon and nitrogen cycling, as well as the stability and relative abundance of their intermediates in microbially dominated ecosystems. The microbially dominated ecosystems studied are the crytoendolithic microbial community living within sand rocks, the endoevaporite microbial community living inside salt crystals, and the microbial communities living beneath perennially ice-covered lakes and hypersaline ponds. The nitrogen cycle of these communities ranges from simple, where only assimilation occurs, to the more complex, where a complete cycle occurs. The carbon cycle of these communities appears to be complete.

Mancinelli, R. L.↗

NASA NTRS1974

The development and diversification of Precambrian life

The temporal relationships among various prominent events occurring in the evolution of life are considered. It is seen that the Precambrian encompasses an enormous segment of geologic time and includes more than 80% of the history of life on this planet. As a result of the studies of the past decade it appears that living systems were probably extant as early as 3300 m.y. ago. Photoautotrophs, apparently including blue-green algae, originated earlier than 3000 m.y. ago. Blue-green algae were the dominant components of earth's biota for the period extending from about 3000 to 1000 m.y. ago. The nucleated, eukaryotic cell type had become established at least as early as 900, and possibly prior to 1300 m.y. ago.

Schopf, J. W.↗

NASA NTRS1986

Research Opportunities in Nutrition and Metabolism in Space

The objectives of the Life Sciences Research Office (LSRO) study on nutrient requirements for meeting metabolic needs in manned space flights are as follows: review extant knowledge on the subject; identify significant gaps in knowledge; formulate suggestions for possible research; and produce a documented report of the foregoing items that can be used for program planning. In accordance with NASA's request for this study, the report focuses on issues of nutrition and metabolism that relate primarily to the contemplated United States Space Station, secondarily to the Shuttle Program as an orbital test bed for operational studies, and incidentally to scenarios for future long-term space flights. Members of the LSRO ad hoc Working Group on Nutrition and Metabolism were provided with pertinent articles and summaries on the subject. At the meeting of the Working Group, presentations were made by NASA Headquarters program staff on past experiences relative to space-flight nutrition and metabolism, as well as scenarios for future flights. The discussions of the ad hoc Working Group focused on the following: (1) metabolic needs related to work and exercise; (2) nutrients required to meet such needs; (3) food types, management, and records; and (4) nutritional amelioration or prevention of space-related physiological and behavioral changes.

Altman, Philip L.↗

NASA NTRS2018

Modeling Venus-Like Worlds Through Time: What Can They Tell Us About the the Liquid Water Habitable Zone, the Evolution of Venus' Atmosphere & Conditions Amenable to Life

Using a modern three-dimensional general circulation coupled atmosphere/ocean model [1] we recently demonstrated [2] that climatic conditions may have permitted liquid water on Venus' surface for ~2 billion years in its early history. Similar such conditions on Earth are believed amenable to the rise of life. Several assumptions were made based on what little data we have for early Venus such as; the type of solar spectrum extant at that time, orbital parameters, estimates of a shallow ocean from Pioneer Venus D/H ratios, and topography from the Magellan Mission. We also assumed that it would have had an atmosphere similar to modern day Earth: 1 bar N2, 400 ppmv CO2, 1 ppmv CH4. I will discuss the motivations behind these assumptions and additional parameter space studies with direct relevance to hypothetical exoplanetary Venus-like worlds found at the inner edge of the liquid water habitable zone. Finally, I will show how our studies demonstrate that the reason for Venus' present climatic state is unlikely to be related to the gradual warming of our sun over the past 4Gyr as is commonly believed.

Way, Michael↗

NASA NTRS2007

Preservation of Reduced Carbon on Mars: Implications for Understanding Habitability

Upcoming Mars missions (e.g., Mars Science Laboratory, ExoMars, Astrobiology Field Laboratory, and Mars Sample Return) will search for evidence of extant and fossil microbial habitats and the potential for future habitation. Understanding the distribution and composition of reduced carbon (or organic carbon) is critical for unraveling the Martian carbon cycle, potential for life, and possible biosignature record. Reduced carbon may be produced from biological, geochemical, or interstellar processes; however, evidence for reduced carbon on Mars is lacking with the exception of parts per billion of atmospheric methane. In contrast, abundant atmospheric carbon dioxide may reflect surface oxidation of reduced carbon and accumulation over geological timescales. This suggests that there is an undetected or lost pool of reduced carbon - a pool that may host molecular biosignatures, a characteristic of extant or extinct habitability. In this presentation, we will evaluate factors influencing the preservation potential for organic molecules in rocks on Earth and Martian. We,draw examples from organic molecules in sulfates, basalts, and ancient shales from Mars-analog settings to show how the distribution of organics and their structural patterns will aid Mars habitability studies.

Conrad, Pamela↗

NASA NTRS2000

Computer Modeling of the Earliest Cellular Structures and Functions

In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

Pohorille, Andrew↗

NASA NTRS1982

Working in space

The capabilities of the NASA Neutral Buoyancy Simulator (NBS) water tank test facility are described, with reference to the proving of crew-operated mechanisms incorporated by the Space Telescope (ST). There are 24 Orbital Replaceable Units which are subject to handling in space by suited crewmen of the Space Shuttle, the largest of which is comparable to a telephone booth and weighs over 700 lb. The water volume of the simulator is sufficient to accept a full-size mockup of the Space Shuttle cargo bay, in which all ST operations will be conducted. Early ST simulations tested the mechanisms which astronauts would operate during contingency operations. More recently, the simulation tasks have reflected maintenance objectives of ST orbital life prolongation. With the recent addition of a fully functional Remote Manipulator System and the Manned Maneuvering Unit, the simulator constitutes the most complete training ground for extravehicular activities extant.

Sanders, F. G.↗

NASA NTRS1993

Microfossils of the Early Archean Apex chert - New evidence of the antiquity of life

Eleven taxa (including eight heretofore undescribed species) of cellularly preserved filamentous microbes, among the oldest fossils known, have been discovered in a bedded chert unit of the Early Archean Apex Basalt of northwestern Western Australia. This prokaryotic assemblage establishes that trichomic cyanobacteriumlike microorganisms were extant and morphologically diverse at least as early as about 3465 million years ago and suggests that oxygen-producing photoautotrophy may have already evolved by this early stage in biotic history.

Schopf, J. W.↗

DOE OSTI2020

Toward a Fully Resolved Fungal Tree of Life

In this review, we discuss the current status and future challenges for fully elucidating the fungal tree of life. In the last 15 years, advances in genomic technologies have revolutionized fungal systematics, ushering the field into the phylogenomic era. This has made the unthinkable possible, namely access to the entire genetic record of all known extant taxa. Here, we first review the current status of the fungal tree and highlight areas where additional effort will be required. We then review the analytical challenges imposed by the volume of data and discuss methods to recover the most accurate species tree given the sea of gene trees. Highly resolved and deeply sampled trees are being leveraged in novel ways to study fungal radiations, species delimitation, and metabolic evolution. Finally, we discuss the critical issue of incorporating the unnamed and uncultured dark matter taxa that represent the vast majority of fungal diversity.

systematics↗

NASA NTRS2017

Exploring the Evolutionary Accident Hypothesis: Are Extant Protein Folds the Fittest or the Luckiest?

Considering the range of functions proteins perform, it is surprising they fold into a relatively small set of structures or "folds" that facilitate such function. One explanation is that only a minority were fit enough to emerge from Darwinian selection during the early evolution of life. Alternatively, perhaps only a fraction of all possible folds were trialed. Understanding proto-catalyst selection will aid understanding of the origins and early evolution of life. To investigate which explanation is correct, we study a protein evolved in vitro to bind ATP by Jack Szostak (Fig. 1). This protein adopts a fold which is absent from nature. We are testing whether this fold would have possessed the capability to evolve that would have been essential to survive natural selection on early Earth. Folds that couldn't improve their fitness and evolve to perform new functions would have been replaced by rivals that could. To determine whether the fold is evolvable, we are attempting to change the function of the protein by rationally redesigning to bind GTP. Two design strategies in the region of the nucleobase have been implemented to provide hydrogen bonding partners for the ligand i) an insertion ii) a MET to ASN mutation. Redesigns are being studied computationally at Ames Research Center including free energy of binding calculations. Binding affinities of promising redesigns are to be validated by experimental collaborators at ForteBio using Super Streptavidin Biosensors. If the fold is found to be non-evolvable, this may suggest that many structures were trialed, but the majority were pruned on the basis of their evolvability. Alternatively, if the fold is demonstrated to be evolvable, it would be difficult to explain its absence from nature without considering the possibility that the fold simply wasn't sampled on early Earth. This would not only further our understanding of the origins of life on Earth but also suggest a common phe-nomenon of proto-catalyst evolution.

Shannon, G.↗

DOE OSTI2024

ZW sex chromosome structure in Amborella trichopoda

Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromosome evolution. Amborella trichopoda, the sole species of a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly contiguous assemblies of the Z and W chromosomes. We identify a ~3-megabase sex-determination region (SDR) captured in two strata that includes a ~300-kilobase inversion that is enriched with repetitive sequences and contains a homologue of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, such as repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Sizing battery energy storage and PV system in an extreme fast charging station considering uncertainties and battery degradation

In this paper, we present mixed integer linear programming (MILP) formulations to obtain optimal sizing for a battery energy storage system (BESS) and solar generation system in an extreme fast charging station (XFCS) to reduce the annualized total cost. The proposed model characterizes a typical year with eight representative scenarios and obtains the optimal energy management for the station and BESS operation to exploit the energy arbitrage for each scenario. Contrasting extant literature, this paper proposes a constant power constant voltage (CPCV) based improved probabilistic approach to model the XFCS charging demand for weekdays and weekends. This paper also accounts for the monthly and annual demand charges based on realistic utility tariffs. Furthermore, BESS life degradation is considered in the model to ensure no replacement is needed during the considered planning horizon. Different from the literature, this paper offers pragmatic MILP formulations to tally BESS charge/discharge cycles using the cumulative charge/discharge energy concept. McCormick relaxations and the Big-M method are utilized to relax the bi-linear terms in the BESS operational constraints. Finally, a robust optimization-based MILP model is proposed and leveraged to account for uncertainties in electricity price, solar generation, and XFCS demand. Case studies were performed to signify the efficacy of the proposed formulations.

24 POWER TRANSMISSION AND DISTRIBUTION↗