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NASA NTRS2016

The Search for Life in the Universe

Each recent report of liquid water existing elsewhere in the solar system has reverberated through the international press and excited the imagination of humankind. We have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. Dr. Lynn Rothschild, an evolutionary biologist known for her work on life in extreme environments and a founder of the field of astrobiology, tells us about intriguing new data. The prevalence of potential abodes for life in our solar system and beyond, the survival of microbes in the space environment, modeling of the potential for transfer of life between celestial bodies, and advances in synthetic biology suggest that life could be more common than previously thought. Are we truly "alone"?

Life in the Universe↗

NASA NTRS2016

An Invited Preface for the Following Book: Astrobiologia, Uma Ciencia Emergente

Since the dawn of civilization, we have beheld at the beauty and wonder of the natural world around us and wondered how it came to be. We have pondered the past, and have been intrigued about the future. For this we are unique. Our ancestors looked to the vastness of space and thought surely there are others out there. We are now at a new time in human history where we can address these age-old questions with a scientific approach and study rigorously the three big questions of astrobiology: Where do we come from? Where are we going? and Are we alone? These fundamental questions of astrobiology correspond to those of humanity, and arguably, what makes us human. And so we cannot help but be drawn to the field. Unlike other scientific disciplines, Astrobiology draws on the latest advances in a multitude of fields, from evolutionary and molecular biology, to prebiotic and interstellar chemistry, from astrophysics to astronomy, with a healthy dose of earth and planetary science. Astrobiology is in reality a "metadiscipline" drawing on useful science wherever it is to be found. From a practical point of view, this endeavor requires the interaction of scientists who might not normally meet each other, much less work on a common research project. And, unlike most other scientific disciplines, Astrobiology has implications for how we see ourselves, and how we interact with the earth and beyond. "Where do we come from" touches on the "why" questions that have intrigued not just scientists but philosophers and theologians. "Where are we going" adds to these an economic and political involvement that is currently being played out with discussions of climate change. "And are we alone" will someday force us to face the fact that we as living creatures are not unique, or perhaps that we are utterly alone in the universe, the result of a chemical history that was so improbable as to result in a sample size of one. Either result will force ethical considerations of either "the other" and their relationship to us, or our solitude and thus responsibility as the only life form in our cosmos. So what is Astrobiology? Let's start with the "Where do we come from?" A biologist will approach this looking at the evolution of life on earth, using such traditional tools as comparative anatomy and paleontology and newer tools such as molecular techniques. But this doesn't address why this happened the way it did without a comprehensive understanding of the environment. What was the temperature at such and such a time? Was the earth in a snowball phase or being bombarded by meteorites -- or even just a single large, well-placed one such as struck off the Yucatan peninsula 65 million years ago. This event could not have been predicted by population genetics alone, yet it had the most profound influence on our evolution as without it, we could still be in a world dominated by dinosaurs with the mammals cowering under cover. But it is not enough to go back to LUCA, the Last Universal Common Ancestor of all extant life. One must go back to the dawn of life. How did life arise? What was the environmental backdrop that allowed it to happen? How did we happen to end up with a habitable planet? Indeed, what is the origin and evolution of our solar system, galaxy, biogenic elements all the way back to the Big Bang. The "Where are we going?" tends to be ignored in many astrobiology programs, but in fact this is of the most immediate importance to us. Whereas the past was dominated by physical and chemical processes, and organismal interactions, the future has a new major player: us. While we probably don't have the power (yet) to stop our galaxy passing through another, or even reset the sun or stop the movement of the moon away from the earth, all of these things will influence the future of life on earth. We are already proving that we have the power to visit other bodies in our solar system, either with humans or our robotic surrogates. We are changing our atmospheric composition and thus our climate. We have the power to render species extinct, including our own. But we also have the power to use these tools for the common good, to extend our lifetimes and reclaim our rivers and forests. Which will it be? And then there is the question where science fiction becomes a reality: "Are we alone?" While many people are anxious to find signs of intelligent life out there, such a creature may not share either our curiosity or values. But what if there was a beneficent alien civilization that could communicate with us, perhaps forging a mutual understanding? More likely in the forseeable future is finding a small life, less evolved, life form. Note I did not use the word "simple" as there is nothing "simple" about life, ever. Which brings us back to the question: what is life? So where does Brazil come in? For nearly a decade there has been interest in a Brazilian astrobiology program, from a small side meeting held by the Brazilian Exobiology Program (BEP) of the Brazilian National Research Council, held in Rio de Janeiro, Brazil, on August 12, 2009, in association with the IAU Assembly to subsequent workshops held in several locations and membership of the Brazilian program in the NASA Astrobiology Institute (NAI). Each time I go to Brazil, I am impressed by the enthusiasm of the community, both scientific and student, the latter an excellent omen for the future of astrobiology in Brazil. Facilities are being built to supplement the natural laboratories that Brazil is blessed to have. In my own lab I have been privileged to have a wonderful Brazilian postdoctoral fellow, Dr. Ivan Paulino-Lima, resulting in a daily reminder of the program. I am honored to have been part of the development of astrobiology in Brazil, and hope that this relationship will continue to flourish. Clearly to advance astrobiology needs new knowledge, a reorganization of that which is known, and space missions. To help the reader join on this quest, what follows is a buffet of topics that will allow the reader to nibble on the richness that is Astrobiology. And, like a fabulous meal, it should make you want more. Welcome to Astrobiology.

Are we alone?↗

NASA NTRS2015

The Search for Life in the Universe

Each recent report of liquid water existing elsewhere in the solar system has reverberated through the international press and excited the imagination of humankind. We have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. Dr. Lynn Rothschild, an evolutionary biologist known for her work on life in extreme environments and a founder of the field of astrobiology, tells us about intriguing new data. At NASA's Ames Research Center in Moffett Field, CA, she leads a program in synthetic biology and works with researchers in industry, government agencies around the world and in academia, including at Brown and Stanford University. The prevalence of potential abodes for life in our solar system and beyond, the survival of microbes in the space environment, modeling of the potential for transfer of life between celestial bodies, and advances in synthetic biology suggest that life could be more common than previously thought. Are we truly "alone"?

Water↗

NASA NTRS2016

The Search for Life in the Universe

astrobiology↗

NASA NTRS2017

Are We Alone? The Search for Life in the Universe

Each report of liquid water existing elsewhere in the solar system has reverberated through the international press and excited the imagination of humankind. We have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. Dr. Lynn Rothschild, an evolutionary biologist known for her work on life in extreme environments and a founder of the field of astrobiology, tells us about intriguing new data. The prevalence of potential abodes for life in our solar system and beyond, the survival of microbes in the space environment, modeling of the potential for transfer of life between celestial bodies, and advances in synthetic biology suggest that life could be more common than previously thought. Are we truly alone?

solar system↗

NASA NTRS2017

Countdown to the Future

At the NASA Ames Research Center in California, the next generation of space biologists are working to understand the effects of long duration space flight on model organisms, and are developing ways to protect the health of future astronauts.

student researchers↗

NASA NTRS2018

Quantifying the Early Snowmelt Event of 2015 in the Cascade Mountains, USA by Developing and Validating MODIS-Based Snowmelt Timing Maps

Spring snowmelt serves as the major hydrological contribution to many watersheds of the US West. Since the 1970s the conterminous western USA has seen an earlier arrival of spring snowmelt. The extremely low snowpack and early melt of 2015 in the Cascade Mountains may be a harbinger of winters to come, underscoring the interest in advancements in spring snowmelt monitoring. Target-of-opportunity and point measurements of snowmelt using meteorological stations or stream gauges are common sources of these data, however, there have been few attempts to identify snowmelt timing using remote sensing. In this study, we describe the creation of snowmelt timing maps (STMs) which identify the day of year that each pixel of a remotely sensed image transitions from "snow-covered" to "no snow" during the spring melt season, controlling for cloud coverage and ephemeral spring snow storms. Derived from the 500 meter MODerate-resolution Imaging Spectroradiometer (MODIS) standard snow map, MOD10A2, this new dataset provides annual maps of snowmelt timing, with corresponding maps of cloud interference and interannual variability in snow coverage from 2001-2015. We first show that the STMs agree strongly with in-situ snow telemetry (SNOTEL) meteorological station measurements in terms of snowmelt timing. We then use the STMs to investigate the early snowmelt event of 2015 in the Cascade Mountains, USA, highlighting the protected areas of Mt. Rainier, Crater Lake, and Lassen Volcanic National Parks. In 2015 the Cascade Mountains experienced snowmelt 41 days earlier than the 2001-2015 average, with 25 percent of its land area melting more than 65 days earlier than average. The upper elevations of the Cascade Mountains experienced the greatest snowmelt anomaly. Our results are relevant to land managers and biologists as they plan adaptation strategies for mitigating the effects of climate change throughout temperate mountains.

snowmelt timing↗

NASA NTRS2016

Storage of Physical Sample Metadata in the Astrobiology Habitable Environments Database (AHED)

The National Aeronautics and Space Administration has begun an effort to store, curate, and publish information about physical samples collected and analyzed in conjunction with NASA-funded astrobiology research. Astrobiology is a multidisciplinary area of scientific research being conducted by collaborating teams of biologists, chemists, geologists, atmospheric scientists, oceanographers, astrophysicists, astronomers, and other specialists. Astrobiology studies the origin, evolution, and distribution of life in the Universe. NASA uses the results of astrobiology research to focus its future missions on targets of opportunity for the discovery of life off Earth. Astrobiology researchers conduct both field-based and laboratory-based research, during which physical samples are collected, processed, and catalogued. The cataloguing practices employed by different teams of astrobiologists vary widely, and there are no specific standards available to guide the collection and recording of astrobiology sample data. The disparity in data collection approaches and the lack of a centralized sample repository makes it difficult for astrobiology teams to share data and benefit from resultant synergies.To facilitate data sharing within the astrobiology community, NASA is developing a prototype database the Astrobiology Habitable Environments Database (AHED) and an associated set of data collection templates. The database will store information about samples, along with associated measurements and analyses, including information about biological cultures enriched or isolated from samples, and the results of analyses performed on the samples (e.g., via spectrography, microscopy, etc.). In addition, the system will store contextual information about field sites where samples were collected, the instruments or equipment used for analysis, and people and institutions involved in their collection. AHED is being implemented on top of Open Data Repository's Data Publisher [1], an open source software platform for the publication of scientific datasets. The data collection templates under development represent an initial attempt to propose a set of metadata for capture and storage within AHED. The design of these templates is being conducted by a consolidated group of astrobiologists from active research teams at NASA Ames Research Center, assisted by data science and software engineering specialists. These initial templates must be vetted with the broader astrobiology community through a defined process to ensure that they meet community needs. Each template captures a different type of data collection record. For each template, we are developing a list of fields to be captured, including a set of required entry fields, a set of recommended but optional fields, and a set of discretionary fields. A datatype selected from a variety of text and numeric types is specified for each field. Included is a 'choice' type that restricts user input to an enumerated list of values. Many of the fields and field values capture information of particular interest to the astrobiology community, and are intended to facilitate search and retrieval of relevant data across multiple datasets.

Keller, Rich↗

NASA NTRSDate not supplied

The Pheno-Evo Model: Evolution of Microbial Phenotypic Diversity in 2D Space

Biologists appreciate microbes for their simplicity and predictability: we assume that a population of genetically identical cells in a uniform environment will all behave the same way. While this assumption is often useful, it is also often wrong. Not only might microbes in a clonal population act differently from one another, the differences may be categorical (growing v. non-growing; toxin-sensitive v. tolerant), and this diversity might be an evolved trait conferring increased fitness on the population. How does such phenotypic heterogeneity evolve? And how does a population find the optimal distribution of phenotypes for a given environment? Efforts at modeling microbial phenotypic heterogeneity often focus on populations with two discrete phenotypic types; phenotypes in continuous distributions remain poorly explored. To address this gap and to explore the role of spatial relationships, we use agent-based modeling to simulate a phenotypically diverse population of microbial cells evolving in the presence of periodic toxic stress. Cells on patches in a 2D grid may degrade toxin, suffer damage from toxin, switch phenotype, and reproduce. An individual's phenotype its toxin degradation rate-- for which there is a tradeoff with reproduction-- and the genotype encodes the distribution of phenotypic values in the population. The rate of toxin diffusion determines how individuals influence their neighbors' environments. We examine the effects of toxin concentration, diffusion rate, and environmental predictability on the survival success of populations with different phenotype distributions, and populations' evolutionary trajectories when phenotype distribution is allowed to evolve. We conduct all simulations on the platform NetLogo, which provides a friendly interface allowing users of any experience level to tweak parameters and run their own simulations. We have also created custom tools in R for analyzing and visualizing the results of multiple runs.

microbial evolution↗

NASA NTRS2020

Chemical Reactivity of In-Situ Lunar Dust

Is in-situ lunar dust less, the same, or more chemically reactivity reactive than the Apollo samples currently stored in curation facilities here on Earth? This question has been debated extensively across the community of scientists that have focused on lunar dust biotoxicity. A definitive answer will further mitigate exploration risks to future human explorers on the Moon and will provide useful information for astrobiologists and space biologists as well.

Lunar Dust↗

NASA NTRS2021

Chemical Reactivity of In-Situ Lunar Dust for Biotoxicity Assessment

How does the chemical reactivity of in-situ lunar dust compare to Apollo samples currently stored in curation facilities here on Earth? Essential investigations of this question will help us to further mitigate exploration risks for future human explorers on the Moon and will also provide critical information for astrobiologists and space biologists using the Moon for scientific inquiry. Apollo 14 dust biotoxicity studies, carried out by the NASA Lunar Airborne Dust Toxicity Assessment Group (LADTAG), included numerous cellular and animal experiments. Intratracheal instillation and inhalation studies in rats both showed Apollo 14 dust to be intermediate in toxicity compared to low-tox titanium dusts and high-tox quartz dusts of similar particle sizes. The collective results were used in models to establish a safe exposure limit for astronauts. Although LADTAG took extensive steps to preserve what chemical reactivity may still have existed in the samples, it is simply unknown if they possessed true in-situ chemical reactivity or if that reactivity has decayed. Initial gas loss on collection and other alterations, and even intermittent exposure to Earth-normal conditions during subsequent decades of handling, obscure a forensic reconstruction of the initial state. Because a mineral dust’s chemical reactivity influences its biotoxicity, researchers have developed methods to “activate” lunar dust and simulants. Past studies that modeled impact processes and radiation in the lunar environment suggest that in-situ lunar dust is likely to be more chemically reactive than Earth-exposed samples. Because of these results, in-situ measurements are warranted. Since the lunar surface is heterogeneous, dust biotoxicity is expected to vary from site to site due to particle size, mineralogy, physical characteristics, degree of space weathering, and chemical reactivity. This circumstance dictates dust assessments at a suite of lunar sites enabled by CLPS opportunities. Dose, location, and duration of particle exposure will also affect biological responses. In-situ chemical reactivity measurements can inform cross-cutting collaborative research campaigns such as astrobiology studies examining regolith interactions with organisms and its ability to preserve chemical and structural biomarkers, as well as space biology investigations that examine regolith-microbe interactions relating to life support systems, plant growth, biomining, and development of regolith biocomposites.

Jon C Rask↗

NASA NTRSDate not supplied

Chemical Reactivity of In-Situ Lunar Dust for Biotoxicity Assessment

Introduction: How does the chemical reactivity of in-situ lunar dust compare to Apollo samples currently stored in curation facilities here on Earth? Essential investigations of this question will help us to further mitigate exploration risks for future human explorers on the Moon and will also provide critical information for astrobiologists and space biologists using the Moon for scientific inquiry. Discussion: Apollo 14 dust biotoxicity studies, carried out by the NASA Lunar Airborne Dust Toxici-ty Assessment Group (LADTAG), included numerous physiochemical studies[1] and cellular and animal ex-periments. Intratracheal instillation [2] and inhalation studies [3] in rats both showed Apollo 14 dust to be intermediate in toxicity compared to low-tox titanium dusts and high-tox quartz dusts of similar particle siz-es. The collective results were used in models [4] to establish a safe exposure limit for astronauts [5]. Alt-hough LADTAG took extensive steps to preserve what chemical reactivity may still have existed in the sam-ples, it is simply unknown if they possessed true in-situ chemical reactivity or if that reactivity has de-cayed. Initial gas loss on collection and other altera-tions, and even intermittent exposure to Earth-normal conditions during subsequent decades of handling, obscure a forensic reconstruction of the initial state. Because a mineral dust’s chemical reactivity influ-ences its biotoxicity [6], researchers have developed methods to “activate” lunar dust and simulants [7][8]. Past studies that modeled impact processes and radia-tion [9] in the lunar environment suggest that in-situ lunar dust is likely to be more chemically reactive than Earth-exposed samples. Because of these results, in-situ measurements are warranted [10]. Other studies have examined the hydroxyl generating capability of iron bearing mineral phases [11][12] and further em-phasize the role iron plays in chemical reactivity of lunar material, as well as decay of chemical reactivity in mineral dusts [12]. Recent observations of the lunar surface reveal the presence of hematite [13], a finding that further supports the hypothesis that in-situ lunar dust is reactive. Since the lunar surface is heterogene-ous, dust biotoxicity is expected to vary from site to site [14] due to particle size, mineralogy, physical characteristics, degree of space weathering, and chemi-cal reactivity (Figure 1). This circumstance dictates dust assessments at a suite of lunar sites enabled by upcoming NASA and commercial lunar payload ser-vices (CLPS) opportunities. Dose, location, and dura-tion of particle exposure will also affect biological responses. In-situ chemical reactivity measurements can inform cross-cutting collaborative research cam-paigns such as astrobiology studies examining regolith interactions with organisms and its ability to preserve chemical and structural biomarkers, as well as space biology investigations that examine regolith-microbe interactions relating to life support systems, plant growth, biomining, and development of regolith bio-composites. Figure 1: Environment conditions on the lunar surface that may alter regolith reactivity. Summary A series of in-situ measurements of lu-nar dust free radical chemistry at future Artemis and CLPS landing sites, combined with LADTAG-like studies of freshly collected lunar dust specimens, will reveal the true chemical reactivity of in-situ lunar dust and generate scientific data that can be compared to the chemical reactivity and biotoxicity of samples from Apollo landing sites. Furthermore, results from in situ measurements and biotoxicity studies of freshly col-lected specimens can also be used to validate, or re-quire revision of, the current astronaut permissible exposure limit [15]. References: [1] McKay D et al (2015), Acta As-tronaut 107:163–176. [2] Rask J et al (2013), LPSC, p 3062. [3] Lam CW et al (2013), Inhal Toxicol 25:661–678. [4] James JT, et. al. (2013) , Inhal Toxicol 25:243–256. [5] Scully RR, et.al. (2013), Inhal Toxi-col 25:785–793. [6] Porter, D. W., et.al., (2002), Tox-icology 175, 63–71. [7] Wallace WT, et.al., (2009), Meteorit Planet Sci 44:961–970. [8] Wallace WT, et.al., (2010), Earth Planet Sci Lett 295:571–577. [9] Loftus D, Rask J, et.al., (2010), Earth Moon Planet 107:95–105. [10] Rask J, et.al., (2009) LEAG p 57. [11] Turci F, et.a., (2015), Astrobiology. 2015;15(5):371-380. [12] Hendrix DA, et.al., (2019), Geohealth. 2019;3(1):28-42. [13] Li, S., et.al., (2020), Science advances, 6(36), p.eaba1940. [14] Rask J. (2018), In: Cudnik B. (eds) Encyclopedia of Lunar Science. Springer, Cham. [15] Rask, J, (2020), LPI, Artemis III Sci. def. paper 2120.

chemical reactivity↗

NASA NTRSDate not supplied

Spaceflight Autonomous Multigenerational Microbial Sequencer in Support of Plant-Growth Systems

The CubeSat platform has proven successful in obtaining meaningful life science information when biological payloads are incorporated. Examples include: 1) the first-ever CubeSat with a biological payload, GeneSat-1, which demonstrated decreased growth rates for flight samples of Escherichia coli in low Earth orbit (Parra et al. 2008); 2) PharmaSat, demonstrated that Saccharomyces cerevisiae in the microgravity environment exhibits a significant level of metabolic activity even at high doses of applied antifungal (Ricco et al. 2011); 3) O/OREOS, which used Bacillus subtilis(bacteria) to demonstrate for the first time that microorganisms can be loaded in a dried, dormant form and then rehydrated and grown in orbit months after launch (Nicholson et al. 2011; Ehrenfreund et al. 2014; 4) the SporeSat payload, which investigated Ceratopteris richardii(fern spores) using lab-on-a-chip devices (BioCDs) and minicentrifuges to produce artificial gravitational forces in ground studies (Park et al. 2017), with demonstration of the BioCD and minicentrifuge in space; 5) EcAMSat, the first CubeSat to be directly deployed from the ISS for an experiment assessing antibiotic resistance of E. coli in the microgravity environment (Padgen et al. 2020); 6) BioSentinel, exposed a culture of yeast to galactic cosmic radiation (GCR) and solar particle events while in heliocentric orbit to measure the rate of double-strand-break repair using DNA-repair-deficient mutants. This effort measures the metabolic parameters of yeast in a deep-space environment compared to Earth ambient conditions using a 3-color LED detection system (Ricco et al. 2020; Padgen et al. 2021). We aim to expand this list to include a Spaceflight Autonomous Multigenerational Microbial Sequencer (SAMMS). SAMMS will allow for the genome level understanding of changes in growth and metabolic activity for any organism. While microbes are suitable for early studies in our proposed platform because of their small size, small and relatively less-complicated genomes, fast generation times, and relevance to life support systems; multicellular organisms can similarly be evaluated for their genetic response to the spaceflight environment. The Spaceflight Autonomous Multigenerational Microbial Sequencer (SAMMS) will enable autonomous sequencing of biological samples in plant production units, cislunar orbit and on the lunar surface to examine spaceflight effects (ie. radiation, altered gravity, reduced pressures) on plant and microbial genomes.On this team a Kennedy Space Center (KSC) space crop production and water systems microbiologist/molecular biologist works with a Johnson Space Center (JSC) International Space Station (ISS) microbial sequencing expert and an Ames Research Center (ARC) CubeSat Engineering team to convert an automated Oxford Nanopore librarypreparation and sequencing method to a fluidic CubeSat payload system. The Oxford Nanopore MinION sequencing platform has proven successful in the spaceflight environment onboard the ISS (Stahl-Rommel et al. 2021). Further long-duration spaceflight and exposure to high levels of radiation will cause genotypic effects in biological organisms that may affect their function. Monitoring the adaption of a population to the spaceflight environment and any subsequent beneficial mutations will allow for the harnessing of organisms best suited for use in life support systems. This will ensure that the selected life support-essential microorganisms maintain their intended specified function over generations of culturing in the relevant spaceflight environment without becoming hazardous to crew or spacecraft systems.

Aubrie E Orourke↗

NASA NTRSDate not supplied

RadLab Platform: Investigating Space Radiation

The RadLab Project, initiated by the Open Science Data Repository (OSDR) for Space Biology at NASA Ames Research Center (osdr.nasa.gov), aims to be an ongoing compilation of radiation data relevant to human space flight. Sponsored by the NASA Human Research Program, RadLab serves as the latest database in this domain. RadLab is intended to serve the needs of both the space radiation detector and space radiation biology communities. The RadLab architecture is being designed to accommodate data both from low Earth orbit (LEO) and beyond low Earth orbit (BLEO). Our long-term vision entails the establishment of a sustainable database receiving continuous updates through APIs connecting to other databases, as well as individual investigator contributions via a RadLab submission portal, modeled on the OSDR (https://osdr.nasa.gov/bio/submission-sso-login.html). In addition to serving as a resource for space biologists and space radiation physicists, such a database would facilitate the deployment of AI algorithms to study the impact of location in space and within spacecraft on the ambient space radiation field. The ultimate goal is to develop predictive dosimetry algorithms for future BLEO missions.

Sylvain V Costes↗

NASA NTRS2023

How do tradeoffs in satellite spatial and temporal resolution impact snow water equivalent reconstruction?

Given the tradeoffs between spatial and temporal resolution, questions about resolution optimality are fundamental to the study of global snow. Answers to these questions will inform future scientific priorities and mission specifications. Heterogeneity of mountain snowpacks drives a need for daily snow cover mapping at the slope scale (≤30 m) that is unmet for a variety of scientific users, ranging from hydrologists to the military to wildlife biologists. But finer spatial resolution usually requires coarser temporal or spectral resolution. Thus, no single sensor can meet all these needs. Recently, constellations of satellites and fusion techniques have made noteworthy progress. The efficacy of two such recent advances is examined: (1) a fused MODIS–Landsat product with daily 30 m spatial resolution and (2) a harmonized Landsat 8 and Sentinel 2A and B (HLS) product with 3–4 d temporal and 30 m spatial resolution. State-of-the-art spectral unmixing techniques are applied to surface reflectance products from 1 and 2 to create snow cover and albedo maps. Then an energy balance model was run to reconstruct snow water equivalent (SWE). For validation, lidar-based Airborne Snow Observatory SWE estimates were used. Results show that reconstructed SWE forced with 30 m resolution snow cover has lower bias, a measure of basin-wide accuracy, than the baseline case using MODIS (463 m cell size) but greater mean absolute error, a measure of per-pixel accuracy. However, the differences in errors may be within uncertainties from scaling artifacts, e.g., basin boundary delineation. Other explanations are (1) the importance of daily acquisitions and (2) the limitations of downscaled forcings for reconstruction. Conclusions are as follows: (1) spectrally unmixed snow cover and snow albedo from MODIS continue to provide accurate forcings for snow models and (2) finer spatial and temporal resolution through sensor design, fusion techniques, and satellite constellations are the future for Earth observations, but existing moderate-resolution sensors still offer value.

Edward H. Bair↗

DOE OSTI2021

Flexible and Adaptive Malware Identification Using Techniques from Biology

The holy grail in cyber analytics is to find new ways to understand the information we already have access to. One way to do that is to characterize the data into reasonable sizes and then leverage any known information to generate new insights. Biologists have been using a similar process for decades. This paper introduces the MLSTONES tool set that was developed by leveraging biology and bioinformatics, high performance computing, and statistical algorithms applied to cyber data and specifically to malware. Furthermore, the paper discusses the tool suite, its applications, and how it compares or can work with other related tools.

Peterson, Elena S.↗

DOE OSTI2021

The Role of Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology: Proceedings of a Workshop

Quantum concepts hold the potential to enable significant advances in sensing and imaging technologies that could be vital to the study of biological systems. The workshop Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology, held online March 8–10, 2021, was organized to examine the research and development needs to advance biological applications of quantum technology. Hosted by the National Academies of Sciences, Engineering, and Medicine, the event brought together experts working on state-of-the-art, quantum-enabled technologies and scientists who are interested in applying these technologies to biological systems. Through talks, panels, and discussions, the workshop facilitated a better understanding of the current and future biological applications of quantum-enabled technologies in fields such as microbiology, molecular biology, cell biology, plant science, mycology, and many others. The workshop was organized around three main themes. The first, quantum in biology, examined quantum concepts that are hypothesized to be important for life processes and that researchers are working to observe through biological imaging and sensing. The second, quantum for biology, addressed ways to use quantum concepts to enhance technologies for biological imaging and sensing. The third, biology for quantum, offered a wider discussion of how the frontiers of biological imaging and sensing could enable future study using quantum concepts, tools, or technologies. Throughout the workshop, participants identified a wide range of emerging approaches and opportunities at the intersection of quantum physics and biological sensing and imaging. During the workshop, there were some differences in how each speaker defined the term quantum. During one of the panels, Prem Kumar offered thoughts on what phenomena are classical versus quantum, explaining that techniques get progressively more quantum as you move from just having superposition to having superposition with measurement and entanglement. Another explanation from Clarice Aiello delineates the definition into several levels. This includes a base level of “quantum-ness,” which reflects that all matter is made of atoms, and when these particles are isolated they behave based on quantum mechanical principles. A second level is related to quantum coherence, where a single quantum object might be found in a coherent superposition state. A final level, which she described as the quantum-entangled level, involves multiple quantum systems which are entangled among themselves. Overall, the workshop touched on concepts such as superposition, entanglement, and squeezing and their potential implications for communication, computing, and simulation, in addition to the workshop’s main focal area, biological sensing and imaging. At the opening of the workshop, Thorsten Ritz of the University of California, Irvine, identified two questions at the heart of quantum biology: Is the machinery of life quantum mechanical, and can quantum mechanics be used to study the machinery of life in new ways? Participants highlighted systems in which researchers have explored these questions, from the vast array of molecular interactions involved in biological processes such as photosynthesis, to the mechanics involved in cellular functions such as differentiation and aggregation, to the role of oscillating magnetic fields in flight orientation among birds. Sensing and imaging technologies are crucial to biological research; these technologies could both enhance the study of quantum effects and be enhanced by quantum concepts. A critical challenge in biological research is to develop imaging and sensing tools that do not damage or interfere with the often fragile and fleeting systems being studied. Attendees discussed a variety of established and emerging technologies that could enhance noninvasive biological imaging, including single- and two-photon spectroscopy, single-molecule spectroscopy, quantum illumination, ghost imaging, and cryo-electron microscopy. One example came from Marlan Scully who gave a keynote address on the first day of the workshop. Scully emphasized the use of different laser technologies, which exhibit coherence and other quantum properties, in moving toward real-world biological applications, such as the detection of SARS-CoV-2. Both tools and theory will play an important role in advancing quantum biology research and applications. Several participants suggested theorists and experimentalists should work in tandem to understand and model biological processes. While physics often reduces systems to their simplest forms for fundamental insights, participants also noted the value of observing and understanding biological systems in all their “messiness,” capturing both the inner workings of biological systems and the complex interactions that occur within and between organisms. In discussions among participants, several attendees stressed the need to match emerging tools with the right scientific questions. Rather than developing quantum technologies as “a hammer looking for a nail,” participants emphasized a focus on exploring the problems these technologies are best suited to address. For example, it is important to consider the size of the phenomenon being studied, the timescales that are important in answering the scientific question, and other relevant considerations. Every tool along the spectrum from classical to quantum involves its own set of trade-offs. For example, Ted Laurence of the Lawrence Livermore National Laboratory said that quantum measurements, such as single photon counting, fluorescence transitions, and lasers, can take longer to produce the same results as classical measurements. These quantum measurements, however, do not require calibration and can enable new research questions to be answered. Prem Kumar, Northwestern University, noted that, despite their promise, quantum approaches should not be used simply for the sake of using quantum, especially in situations where classical approaches better meet the needs of the researcher. Understanding and applying quantum concepts could enable advances in a wide range of application areas including energy, synthetic biology, medicine, and sustainability. For example, Michelle O’Malley, University of California, Santa Barbara, described how improved noninvasive imaging approaches could help capture the complex interactions and functions involved in the breakdown of organic matter by microbial communities and lead to new technologies for capturing valuable products from plant waste. Several other participants discussed needs in tracking the movement of metabolites and molecules in microbial communities for insights into nutrient cycling in environments such as soil. Margaret Ahmad, Sorbonne University, discussed potential opportunities to leverage the magnetic properties of cryptochromes to advance new treatment approaches for diseases such as COVID-19 and cancer. Looking toward the future development of the field, participants discussed challenges to advancing quantum biology that arise from disciplinary disconnects between physicists and biologists. The siloing of academic research disciplines represents a significant barrier to progress. Disconnects in terminology, motivations and priorities, and structural barriers to collaborative work underscore the need for concerted efforts to bridge these divides. Attendees and speakers offered suggestions for resolving these divergences, establishing a shared language, moving the field forward, and fostering meaningful feedback between disciplines. Overall, participants stressed a need for balance, open communication, collaboration, unity, and clear dialogue on trade-offs between quantum and classical approaches. Keiko Torii, The University of Texas at Austin, said that the best collaborations happen when the project provides mutual advantages that can show off everyone’s talents, each team finds the work interesting, and partners develop a camaraderie to pursue new knowledge. To enable near- and long-term opportunities in this space, participants suggested that exploratory, high-risk funding could improve existing instrumentation to explore quantum enhancement collaboratively. They also emphasized the need for collaboration between quantum physicists and sensing/imaging scientists, which could be advanced through a dedicated quantum biology investigator program. People, even more than technology, will be crucial to the future of quantum biology. Participants explored training, education, and workforce needs to further develop this burgeoning field and cultivate the next generation of scientists. While many programs are still in their nascent stages, participants highlighted examples of approaches and programs being developed at various types of institutions to engage students and professional scientists in quantum biology research. Several participants stressed the need for an inclusive approach, spanning disciplines as well as communities to foster a diverse field fueled by the intellectual contributions of a wide range of people, including historically under-resourced schools and students. To increase awareness and excitement about quantum physics and related areas of biology, attendees suggested capitalizing on the “buzz” around quantum. Several participants emphasized the need to start early, introducing students to quantum concepts and their appealing “weirdness” in K–12 education. Engaging students early—before they become entrenched in traditional disciplinary siloes as typically happens in graduate school—could help to galvanize interest in the area and foster a generation of scientists with the interdisciplinary mindset and skills needed to advance this interdisciplinary field. While these efforts could be advanced at many levels and across multiple sectors, several participants suggested a national quantum biology center could be a valuable hub to coordinate and support quantum biology education and workforce development across academia, industry, and government.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Lake Arrowhead Microbial Genomics Conference

The Lake Arrowhead Microbial Genomics Conference (formerly the E. coli and Small Genomes Conference, and the Microbial Genomes Conference) was held September 11-15, 2022, at the UCLA Conference Center at Lake Arrowhead, California. This conference is part of a yearly meeting initiated in 1991 to bring together genome sequencers, bioinformatics specialists, biologists, and geneticists, to forge interactions that would result in meaningful functional genomics. The goal of the meeting was to translate the influx of new genome sequencing information into useful biological studies. The Lake Arrowhead 2022 meeting had a major focus on microbial communities, the human microbiome, pathogens, phage therapy, bioinformatic methods of analysis, bioenergenics, and environmental microbiology. The field of genomics has reached the point where deriving the sequence of an organism’s entire genome is now seen as a beginning rather than an endpoint. Moreover, understanding the sequences of whole communities, and particularly those that make up different microbiomes, is now a central point of the field. The 2022 meeting covered microorganisms for which extensive analyses exist, and those for which new biological and technical strategies are being developed. The focus on biodiversity, the human microbiome, pathogenic organisms and methods of countering them, and bioenergetics added special significance to this meeting. This meeting was designed to have a mix of 36 invited presentations and poster sessions with more than 80 posters, and had 147 participants. This meeting has become established as a major annual microbial genomics conference during the last 29 years and has assured status and quality. It offers a major opportunity for young investigators and students to attend, present posters, and give talks. In fact, 50% of the invited speakers were early career stage scientists. An important impact of the conference was the forging of new collaborations between scientists and particularly young scientists with the array of multidisciplinary researchers at the meeting.

Miller, Jeffrey H.↗