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Synthetic Biological Membrane

The ultimate goal of the Synthetic Biological Membrane project is to develop a new type of membrane (using FOST - Forward Osmosis Secondary Treatment) that will enable the waste water treatment system required on exploration missions to operate for extended periods while requiring no maintenance, and using only available resources. Because current water treatment systems have a lifetime of less than 1 year, extending membrane life will benefit exploration missions by reducing upmass and crew time requirements associated with maintenance and resupply/replacement of membranes. The project will use synthetic biology to engineer organisms that protect and replenish the membrane, and this new technology can be easily adapted for use in terrestrial waste water treatment plants.

Biomimetic membrane↗

Space Biology and Medicine: Space and Its Exploration - Volume I

Perhaps one of the greatest gifts that has been given to the people of the world in the last few hundred years has been an emerging sense of the place of our planet and its inhabitants within the context of the vast universe. Our knowledge of the rest of the universe has not come quickly, nor was the process of attaining it only recently begun; however, the unprecedented acceleration of that process has benefitted from a fundamental new aspect of our species that has only manifested itself in the last 30 years or so, the ability to travel in space. Before the space age, the Universe was studied only through observations from the Earth. All that has changed with the beginning of the space age. Machines built by humans have flown to all but one of the nine planets that revolve around our Sun, have ventured billions of miles from the Earth and looked back, and have landed on three other worlds. Spacecraft in orbit around the Earth have viewed the sky at a vast number of electromagnetic wavelengths, detecting the shape of the galaxy and the universe, and even measuring the remnants of the universe's beginning. Human explorers have ventured forth, first for short stays in orbit, then, later, walking upon the Moon and living for long periods in space. As they did so, billions of people on the Earth came to view the Earth in a fundamentally different way, not just as the familiar day to- day backdrop for their lives, but as a small oasis suspended in the night sky above an alien landscape. It is this new view of the Earth that is the true gift of space exploration. Space exploration has at once given us a new perspective on the value of our world, and a new perspective from which to understand how it operates. It has shown us that the Earth is by far the most precious place in the solar system in terms of supporting human life, while revealing that other destinations may still be compelling. The exploration of space has at once become a challenge for humanity to overcome and a path to our common future. But for humanity to embark on this path, we need to understand ourselves in a new environment. As such, an understanding of the biological consequences of and opportunities in space flight is essential. In this, the first volume of a joint U.S./Russian series on space biology and medicine, we describe the current status of our understanding of space and present general information that will prove useful when reading subsequent volumes. Since we are witnesses to the beginning of a new era of interplanetary travel, a significant portion of the first volume will concentrate on the physical and ecological conditions that exist in near and outer space, as well as heavenly bodies from the smallest ones to the giant planets and stars. While space exploration is a comparatively recent endeavor, its foundations were laid much more than 30 years ago, and its history has been an eventful one. In the first part of this volume, Rauschenbach, Sokolskiy, and Gurjian address the "Historical Aspects of Space Exploration" from its beginnings to a present-day view of the events of the space age. The nature of space itself and its features is the focus of the second section of the volume. In the first chapter of the part, "Stars and Interstellar Space," the origin and evolution of stars, and the nature of the portions of space most distant from Earth are described by Galeev and Marochnik. In Chapter 2, Pisarenko, Logachev, and Kurt in "The Sun and Interplanetary Space" bring us to the vicinity of our own solar system and provide a description and discussion of the nearest star and its influence on the space environment that our Earth and the other planets inhabit. In our solar system there are many fascinating objects, remnants of the formation of a rather ordinary star in a rather obscure portion of the galaxy. Historical accident has caused us to be much more curious (and knowledgeable) about "The Inner Planets of the Solar System" than about any of these other objects. In Chapter 3, Marov describes the planets Mercury, Venus, Earth, and Mars, their history and origin, and their environmental conditions, and in Chapter 4 Owen provides similar information about Jupiter, Saturn, Uranus, Neptune, and Pluto, "The Outer Planets of the Solar System." Morrison provides a thorough discussion of "Asteroids, Comets, and Other Small Bodies" in Chapter 5. The understanding of these relics of the formation of the solar system may form the center of our ability to understand the origin of solar systems in general, and of the critical role that the beginning of the solar system had on the prospects for the origin of life and its continued survival and evolution in the face of their recurrent impacts on Earth. In Chapter 6, the first chapter of the third part, Rummel describes the area of "Exobiology," the study of the origin, evolution, and distribution of life in the context of the origin and evolution of the universe. The same processes that have given rise to life on Earth may have given rise to life elsewhere. In Chapter 7, the "Earth and the Biosphere," the nature and function of the Earth are discussed as a specific instance of planetary and biological evolution. The effects of biological processes on the Earth under the influence of human activities are also addressed by Moore and Bartlett in Chapter 7. The final chapter in this section concerns the prospects that life in the universe may be widespread; "SETI," the Search for Extraterrestrial Intelligence, by Billingham and Tarter, presents the arguments for conducting a search for evidence of life elsewhere in the galaxy, and describes the various methods proposed for conducting such a search. While SETI has a distinctly exploration al character, more direct means are available for exploring the solar system around us. The fourth part of the volume addresses this subject of space exploration. Considering the prospects for research on space biology and medicine, the means of providing "Access to Space" are described by Feoktistov and Briggs in Chapter 9. This chapter addresses carriers and launch systems, the unmanned and manned spacecraft that they loft into space, and the task of mission operations by which these precious vessels are monitored, navigated, and controlled. Despite the successes of the past and the capabilities of the present, it is clear that the study of space biology and medicine will be even more rewarding in the future than it has been to date. The work of the next few years that will be undertaken by the U.S. and Russia, both independently and jointly, will focus first on enabling greater capabilities in the exploration of space, and then on using the unique characteristics of the space environment to provide insight and greater understanding into biological systems, their behavior, development, and origin. The chapters of the first volume were written by leaders in their fields from the U.S. and Russia. The material presented summarizes our current understanding of space and its exploration. We understand that the first volume will be of interest not only to medical personnel and biologists, but also to general readers who want information about space beyond their own particular fields of expertise.

Nicogossian, Arnauld E.↗

New developments in space radiation research at NASA: Annotating data using a novel radiation biology ontology

Like many interdisciplinary sciences, data producers and consumers in the field of radiation biology often use a wide variety of terminology to describe their experiments and data. Furthermore, space systems and technologies are rapidly evolving, and a shared understanding and common terminology for these is also lacking. The efficiency of research organizations can be enhanced by standardizing metadata through the use of knowledge resources like ontologies. Employing a sophisticated model such as a formal ontology to standardize metadata enables automated data acquisition processes and supports more complete, accurate meta-analysis through more efficient and complete data discovery and retrieval, particularly when using multiple data sources. Thus, we developed the Radiation Biology Ontology (RBO) in order to improved radiation biology metadata uniformity and transparency. We used open-source software (the Ontology Development Kit, Protégé and WebProtégé) and worked within the OBO Foundry framework, which includes a set of ontology development principles and practices for ontology consistency, uniformity, and accountability. The RBO has now been incorporated into two radiation research data repositories, NASA’s GeneLab omics database (https://genelab.nasa.gov), and the European Commission STORE database (https://www.storedb.org/). Continuous build integration tools allowed our international RBO collaboration to be more efficient and focus its efforts on semantic model design. Currently, the RBO contains over 300 annotated classes and individuals specific to the study of radiation on biological systems, as well as imports of many additional classes from other OBO Foundry ontologies that relate to and/or provide context for these RBO entities. We publish the RBO through the OBO Foundry, so that it is available for browsing, download, and querying through NCBI Bioportal web site and application programming interface. The NASA Ames Life Science Data Archive (ALSDA) is also in the process of adopting use of the RBO, taking NASA one step closer to a knowledge-based system for space biology data. It is our hope that the global communities of radiation research Investigators, data curators and data analysts can similarly leverage the RBO and will contribute to its further development.

radiation↗

GeneLab: A Systems Biology Platform for Omics Analysis

NASA's GeneLab includes an open-access repository of some 200+ omics datasets generated by biological experiments relevant to spaceflight (including simulated cosmic radiation and microgravity). In order to maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab is now transforming the data in the repository into actual biological and physiological knowledge of the genetic and proteomic signatures found in these samples. This processed data is being derived by establishing standard data analysis workflows vetted by 114 scientists who are members of the four GeneLab Analysis Working Groups (Animal AWG, Plant AWG, Microbe AWG, Multi-Omics AWG). AWG members from institutes spanning the U.S. and four other countries participate on a voluntary basis. The AWGs meet monthly to discuss data mining, compare results and interpretations, and test forthcoming releases of the GeneLab Data Systems (GLDS). GLDS version 3.0 has been available to the general public since October 1st 2018, and has been providing a professional state-of-the-art bioinformatics platform for everyone in the space biology community to upload their data into a space biology omics data commons, to process their data with vetted standard workflows and to compare to existing analyses. The user interface for the platform is being designed to be accessible to a broad variety of users including those with limited bioinformatics experience, including high school and college students who can use it to learn about omics data analysis and space biology. As such, Genelab will constitute a powerful general public outreach capability of NASA and the Space Biology community at large. Data mining of the GeneLab database by the AWG has already started generating very interesting findings, including reports linking specific spaceflight conditions such as radiation, microgravity or carbon dioxide levels to molecular changes seen across various species. In this presentation, we will report on the current and future objectives for GeneLab, and review recent studies reported by the various AWGs relating molecular changes observed in various animal models and tissue with microgravity, radiation, circadian rhythm, hydration and carbon dioxide conditions.

Omics↗

GeneLab: A Systems Biology Platform for Omics Analysis: Disseminate and Reuse Data, Tools, and Samples Post-Project

NASA's GeneLab includes an open-access repository of some 200 plus omics datasets generated by biological experiments relevant to spaceflight (including simulated cosmic radiation and microgravity). In order to maximize the intelligibility of these data, particularly for users with limited bioinformatics knowledge, GeneLab is now transforming the data in the repository into actual biological and physiological knowledge of the genetic and proteomic signatures found in these samples. This processed data is being derived by establishing standard data analysis workflows vetted by 114 scientists who are members of the four GeneLab Analysis Working Groups (Animal AWG, Plant AWG, Microbe AWG, Multi-Omics AWG). AWG members from institutes spanning the U.S. and four other countries participate on a voluntary basis. The AWGs meet monthly to discuss data mining, compare results and interpretations, and test forthcoming releases of the GeneLab Data Systems (GLDS). GLDS version 3.0 has been available to the general public since October 1st 2018, and has been providing a professional state-of-the-art bioinformatics platform for everyone in the space biology community to upload their data into a space biology omics data commons, to process their data with vetted standard workflows and to compare to existing analyses. The user interface for the platform is being designed to be accessible to a broad variety of users including those with limited bioinformatics experience, including high school and college students who can use it to learn about omics data analysis and space biology. As such, Genelab will constitute a powerful general public outreach capability of NASA and the Space Biology community at large. Data mining of the GeneLab database by the AWG has already started generating very interesting findings, including reports linking specific spaceflight conditions such as radiation, microgravity or carbon dioxide levels to molecular changes seen across various species. In this presentation, we will report on the current and future objectives for GeneLab, and review recent studies reported by the various AWGs relating molecular changes observed in various animal models and tissue with microgravity, radiation, circadian rhythm, hydration and carbon dioxide conditions.

Omics↗

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields in the last two decades, in part thanks to an increasing culture of open data sharing and reuse. Due to its capability for identifying complex relationships and patterns, AI/ML methodology is particularly well suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are many key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Even with the positive culture of Open Science and data sharing, inexperienced researchers working quickly without proper checks can produce models that perform poorly outside of the immediate training dataset. Lessons learned from biological AI/ML research indicate that Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Andrew Casaletto↗

Preface

No abstract available

NASA Discipline Radiation Health↗

Nonselective enrichment for yeast adenine mutants by flow cytometry

The expression of certain adenine biosynthetic mutations in the yeast Saccharomyces cerevisiae results in a red colony color. This phenomenon has historically provided an ideal genetic marker for the study of mutation, recombination, and aneuploidy in lower eukaryotes by classical genetic analysis. In this paper, it is reported that cells carrying ade1 and/or ade2 mutations exhibit primary fluorescence. Based on this observation, the nonselective enrichment of yeast cultures for viable adenine mutants by using the fluorescence-activated cell sorter has been achieved. The advantages of this approach over conventional genetic analysis of mutation, recombination, and mitotic chromosomal stability include speed and accuracy in acquiring data for large numbers of clones. By using appropriate strains, the cell sorter has been used for the isolation of both forward mutations and chromosomal loss events in S. cerevisiae. The resolving power of this system and its noninvasiveness can easily be extended to more complex organisms, including mammalian cells, in which analogous metabolic mutants are available.

Non-NASA Center↗

How Do UTLS Jet and Tropopause Dynamics Influence Ozone Variability? Investigations Supporting the SPARC OCTAV-UTLS Activity

Understanding changes in UTLS ozone is exceptionally challenging because of large spatial and temporal variability and because of the difficulty of satellite measurements in the UTLS. It is also exceptionally important: for example, to understand climate impacts of radiatively active substances and to understand physical and biological effects of pollution transport and stratosphere-troposphere exchange (STE). Multi-decadal global observations of UTLS ozone are now available from numerous satellite platforms, as well as local and regional observations from aircraft, balloons, and lidar. The upper tropospheric (UT) jets and tropopauses are important drivers of composition variability in the UTLS, acting as transport barriers and controlling STE and long-range transport. We report here on investigations of relationships between extratropical UTLS ozone variability and dynamical diagnostics of mixing / transport barriers, Rossby Wave breaking, and stratosphere-troposphere exchange. We will view these relationships in the context of ozone mapped into dynamical coordinates with respect to the UTLS jets and / or the tropopause. This work will help provide direction for analyses within the Stratosphere-troposphere Processes And their Role in Climate (SPARC) Observed Composition Trends and Variability in the UTLS (OCTAV-UTLS) activity, which aims to use dynamical coordinate mapping to help detect and attribute observed UTLS composition trends, and to project future data needs to better quantify those trends. The work we report on here will focus on satellite ozone observations (primarily from the Aura Microwave Limb Sounder, additionally from ACE-FTS and OSIRIS) and assimilated ozone and dynamical fields (from multiple reanalyses); we will also provide some examples of comparisons with aircraft and balloon observations.

Manney, Gloria L.↗

Biomolecular Analysis Capability for Cellular and Omics Research on the International Space Station

International Space Station (ISS) assembly complete ushered a new era focused on utilization of this state-of-the-art orbiting laboratory to advance science and technology research in a wide array of disciplines, with benefits to Earth and space exploration. ISS enabling capability for research in cellular and molecular biology includes equipment for in situ, on-orbit analysis of biomolecules. Applications of this growing capability range from biomedicine and biotechnology to the emerging field of Omics. For example, Biomolecule Sequencer is a space-based miniature DNA sequencer that provides nucleotide sequence data for entire samples, which may be used for purposes such as microorganism identification and astrobiology. It complements the use of WetLab-2 SmartCycler"TradeMark", which extracts RNA and provides real-time quantitative gene expression data analysis from biospecimens sampled or cultured onboard the ISS, for downlink to ground investigators, with applications ranging from clinical tissue evaluation to multigenerational assessment of organismal alterations. And the Genes in Space-1 investigation, aimed at examining epigenetic changes, employs polymerase chain reaction to detect immune system alterations. In addition, an increasing assortment of tools to visualize the subcellular distribution of tagged macromolecules is becoming available onboard the ISS. For instance, the NASA LMM (Light Microscopy Module) is a flexible light microscopy imaging facility that enables imaging of physical and biological microscopic phenomena in microgravity. Another light microscopy system modified for use in space to image life sciences payloads is initially used by the Heart Cells investigation ("Effects of Microgravity on Stem Cell-Derived Cardiomyocytes for Human Cardiovascular Disease Modeling and Drug Discovery"). Also, the JAXA Microscope system can perform remotely controllable light, phase-contrast, and fluorescent observations. And upcoming confocal microscopy capability will allow for optical sectioning of biological tissues to determine microanatomical localization of biomarkers. Furthermore, NASA's geneLAB effort addresses integration of genomic, epigenomic, transcriptomic, proteomic and metabolomic datasets, by applying an innovative open source science platform for multi-investigator high throughput utilization of the ISS. In sum, the expanding ISS capability for analysis of biomolecules is enabling innovative research in a broad spectrum of areas such as cellular and molecular biology, biotechnology, tissue engineering, biomedicine, and Omics, providing manifold benefits for humanity.

Guinart-Ramirez, Y.↗

Temperature prediction of space flight experiments by computer thermal analysis

Life sciences experiments are especially sensitive to temperature. A small temperature difference between otherwise identical samples can cause various differences in biological reaction rates. Knowledge of experimental temperatures and temperature histories help to distinguish the effects of microgravity and temperature on spaceflight experiments compared to ground based studies, and allow appropriate controls and sensitivity tests. Up to the present time, the Orbiter (Space Shuttle) has not generally provided temperature measurement instrumentation inside ambient lockers located in the Mid-deck of the Orbiter, or inside similar facilities such as Spacehab and Spacelab, but many pieces of hardware do have temperature recording capability. Most of these temperatures, however, have only been roughly measured or estimated. Such reported experimental temperatures, while accurate within a range of several degrees Celsius, are of limited utility to biological researchers. The temperature controlled lockers used in spaceflight, such as Commerical-Refrigeration Incubation Modules (C-R/IMs), severely reduce the mass and volume available for test samples and do not necessarily provide uniform thermal environments. While these test carriers avoid some of the experimental temperature variations of the ambient lockers, the number of samples which can be accommodated in these temperature controlled units is limited. In the present work, improved models of thermal prediction and control were sought. Temperatures are predicted by thermal analysis software using empirical temperatures recorded during STS-57. These temperatures are compared to data recorded throughout the mission using Ambient Temperature Recorders (ATRs) located within several payload lockers. Additional test cases are undertaken using controlled ground experiments to more precisely determine the reliability of the thermal model. The approach presented should increase the utility of various spaceflight carriers in the support of biological and material science research and ground control studies done in preparation for flight.

Birdsong, M. B.↗