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Consumption, supply and transport: self-organization without direct communication

Swimming bacteria of the species Bacillus subtilis require and consume oxygen. In static liquid cultures the cells' swimming behaviour leads them to accumulate up oxygen concentration gradients generated by consumption and supply. Since the density of bacterial cells exceeds that of the fluid in which they live, fluid regions where cells have accumulated are denser than depleted regions. These density variations cause convection. The fluid motion is dynamically maintained by the swimming of the cells toward regions of attraction: the air-fluid interface and the fluctuating advecting attractors, gradients of oxygen concentration that are embedded in the convecting fluid. Because of the fluid dynamical conservation laws, these complex physical and biological factors generate patterns ordered over distances > 10000 bacterial cell diameters. The convection enhances long-range transport and mixing of oxygen, cells and extracellular products by orders of magnitude. Thus, through the interplay of physical and biological factors, a population of undifferentiated selfish cells creates functional dynamic patterns. Populations of bacteria that have organised themselves into regularly patterned regions of vigorous convection and varying cell concentration interact with their environment as if they were one purposeful, coherent multicellular individual. The mathematical and experimental ingredients of these remarkable phenomena are presented here.

Non-NASA Center↗

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↗

Effects of Livestock Exclusion on Stream Habitat and Aquatic Biota: A Review and Recommendations for Implementation and Monitoring

Abstract To inform riparian restoration, research, and monitoring and to provide management recommendations, we reviewed published studies evaluating the physical and biological effectiveness of livestock exclusion and grazing reduction on various metrics in riparian and aquatic areas. We identified 95 North American studies that reported the effects of livestock grazing reduction on physical habitat (channel morphology, mesohabitats, substrate, and bank stability), biological assemblages (riparian vegetation, macroinvertebrates, fish, and birds), and water quality metrics (temperature, nitrates, phosphorus, and turbidity). Most studies reported that methods to reduce or exclude livestock decreased channel width, width-to-depth ratio, bank erosion, soil bulk density, bare ground, water temperature, nitrogen, and phosphorus and increased riparian vegetation (cover, height, productivity, biomass, and abundance), riparian bird abundance, and young-of-the-year fishes. Results for channel depth, instream substrate, mesohabitats, water depth, juvenile and adult fishes, and macroinvertebrates showed no consistent response to exclusion. Project success was influenced by the time since exclusion; whether there was complete exclusion or continued grazing; and local climate, geology, and soils. Apart from bank erosion and stability, most of the physical and biological metrics took more than a decade to respond to livestock exclusion. However, coupling exclusion with planting and other restoration measures decreased the recovery time. Complete exclusion of livestock produced more consistent improvements in riparian condition and other metrics than rest–rotation or other grazing management strategies. Understanding how physical and biological metrics respond to livestock exclusion will require (1) focused, long-term studies using before–after or before–after, control–impact designs; and (2) monitoring of metrics that most consistently respond to exclusion. Ultimately, the design of exclusions should be driven by local climate, geology, biophysical conditions, and management history. Our results highlight the need for watershed-scale approaches to excluding livestock from broad areas and the need for implementation monitoring to ensure that fencing and other exclusion measures continue to exclude livestock and produce the desired responses.

Krall, Michelle↗

Science & Technology Review March 2021

At Lawrence Livermore National Laboratory, we focus on science and technology research to ensure our nation’s security. We also apply that expertise to solve other important national problems in energy, bioscience, and the environment. Science & Technology Review is published eight times a year to communicate, to a broad audience, the Laboratory’s scientific and technological accomplishments in fulfilling its primary missions. The publication’s goal is to help readers understand these accomplishments and appreciate their value to the individual citizen, the nation, and the world.

08 HYDROGEN↗

Groundwater Inflows to the Columbia River Along the Hanford Reach and Associated Nitrate Concentrations

Healthy river ecosystems require the interaction of many physical and biological processes to maintain their status. One physical process supporting biogeochemical cycling is hydrologic exchange (i.e., hydrologic exchange flows, HEFs) between relatively fast-flowing channel waters and slower-flowing surface and subsurface waters (lateral and vertical). Land uses adjacent to rivers have the potential to alter the water quality of off-channel surface and subsurface waters, and HEFs therefore have the potential to deliver solutes associated with river-adjacent land uses to rivers. HEFs can be nonpoint, diffuse sources of pollution, making the ultimate pollution source difficult to identify, especially in large rivers. Here, we seek to identify HEFs in the Columbia River near Richland, WA by looking for anomalies in temperature and electrical conductivity (EC) along the bed of the river in February, June, July, August, and November 2018. These are ultimately the “ends” of HEFs as they are locations of subsurface inflow to the river. We found these anomalies to be a combination of warmer or colder and higher (but not lower) EC than river water. We identified a majority of warm anomalies in February and July 2018, and majority cold anomalies in June, August, and November 2018. High-EC anomalies were found mostly in February, August, and November. Combined, we observe a shift from warm, high EC anomalies dominating in February to equivalent EC, warm anomalies in June, to equivalent EC, cool anomalies dominating July. In August, we also measured dissolved nitrate ($NO^-_3$) in-situ to determine whether anomalies were associated with increased $NO^-_3$ loading to the river, especially along the eastern shoreline, which is dominated by agricultural land use. Inflows along the eastern shoreline have greater concentrations of nitrate than river water (up to 10 mg $N–NO^-_3$/L). This research demonstrates that HEFs are temporally and spatially dynamic transferring heat and solutes to rivers.

54 ENVIRONMENTAL SCIENCES↗

Subtropical Gyre Variability Observed by Ocean Color Satellites

The subtropical gyres of the world are extensive, coherent regions that occupy about 40% of the surface of the earth. Once thought to be homogeneous and static habitats, there is increasing evidence that mid-latitude gyres exhibit substantial physical and biological variability on a variety of time scales. While biological productivity within these oligotrophic regions may be relatively small, their immense size makes their total contribution significant. Global distributions of dynamic height derived from satellite altimeter data, and chlorophyll concentration derived from satellite ocean color data, show that the dynamic center of the gyres, the region of maximum dynamic height where the thermocline is deepest, does not coincide with the region of minimum chlorophyll concentration. The physical and biological processes by which this distribution of ocean properties is maintained, and the spatial and temporal scales of variability associated with these processes, are analyzed using global surface chlorophyll-a concentrations, sea surface height, sea surface temperature and surface winds from operational satellite and meteorological sources, and hydrographic data from climatologies and individual surveys. Seasonal and interannual variability in the areal extent of the subtropical gyres are examined using 8 months (November 1996 - June 1997) of OCTS and nearly 5 years (September 1997 - June 02) of SeaWiFS ocean color data and are interpreted in the context of climate variability and measured changes in other ocean properties (i.e., wind forcing, surface currents, Ekman pumping, and vertical mixing). The North Pacific and North Atlantic gyres are observed to be shrinking over this period, while the South Pacific, South Atlantic, and South Indian Ocean gyres appear to be expanding.

McClain, Charles R.↗

Deep-Learning Electron Diffractive Imaging

Here, we report the development of deep-learning coherent electron diffractive imaging at subangstrom resolution using convolutional neural networks (CNNs) trained with only simulated data. We experimentally demonstrate this method by applying the trained CNNs to recover the phase images from electron diffraction patterns of twisted hexagonal boron nitride, monolayer graphene, and a gold nanoparticle with comparable quality to those reconstructed by a conventional ptychographic algorithm. Fourier ring correlation between the CNN and ptychographic images indicates the achievement of a resolution in the range of 0.70 and 0.55 Å. We further develop CNNs to recover the probe function from the experimental data. The ability to replace iterative algorithms with CNNs and perform real-time atomic imaging from coherent diffraction patterns is expected to find applications in the physical and biological sciences.

47 OTHER INSTRUMENTATION↗

Enabling Space Biology Knowledge Discovery Through Biospecimen Sharing: The NASA Biological Institutional Scientific Collection and Space Microbial Culture Collection

NASA and international partners have conducted experiments in space to understand the biological impacts and address hazards to health. The resulting basic and applied science is imperative to enabling humanity to venture back to the Moon and then to Mars and beyond. Sending organisms into space is a costly endeavor. All biospecimens not required by spaceflight-relevant Principal Investigators are harvested, preserved, and archived in the NASA Biological Institutional Scientific Collection (NBISC) to maximize the scientific return. The NASA Biological and Physical Sciences (BPS) Division ‘Open Science’ endeavor includes NASA Genelab, the Space Biology Program’s Biospecimen Sharing Program, Physical Sciences Informatics, the Ames Life Sciences Data Archive, and NBISC to integrate extensive data and biospecimen resources from spaceflight and/or ground-based analog experiments. NBISC biospecimens are collected and preserved according to well-established standard operating procedures to maintain scientific quality and are available on-request by the international scientific community. NBISC currently stores over 32,000 biospecimens from Shuttle, International Space Station, and ground-based space analog investigations. Tissue sharing has resulted in at least 33 publications since 2011 and 48 requests since 2016. Many requests for NBISC biospecimen come from first-time investigators who subsequently submit grants as the port-of-entry into the field of space biology. Some NBISC biospecimens have been awarded to NASA Genelab, who then generate various ‘Open Science’ -omics data sets on their platform for bioinformatics. Other NBISC biospecimen awards have led to multiple studies such as fecal microbiome analysis, DNA damage analysis using single-cell DNA sequencing, enzymatic-pathway identification involved in spaceflight muscle atrophy, and characterization of ocular morphological changes. Of note, NBISC has expanded to include a new Space Microbial Culture Collection (SMCC) for the collection, identification, documentation, long-term preservation, and distribution of space-related microbial isolates.

biospecimens↗

Physical, resource supply, and biological controls on nutrient processing along the river continuum

Nutrient impairment has led to damages to US surface and groundwater systems in excess of 100 billion dollars per year. Therefore, there is a strong need to develop methods to predict the transport, uptake, and export of nutrients along fluvial networks. We present results that are based on a data-driven mechanistic understanding of three factors that largely control nutrient uptake and export: 1) interactions between transport-related processes (mass transfer to metabolically active zones), 2) resource supply dynamics (nutrient concentration, stoichiometric constraints, etc.), and 3) biological controls (microbial community structure and function). Our results were generated from column experiments conducted along the Jemez River-Rio Grande continuum, which spans four orders of magnitude in mean annual discharge, more than 2000 m in altitude, and more than 500 km of stream longitude. Two resource supply injections were performed on each of the columns, i.e., a nitrate only addition, followed by a stoichiometrically ‘balanced’ 106Carbon:16Nitrogen:1Phosphorus addition. We quantified NO3-N uptake kinetics while constraining three variables: stream order, sediment type and type of injection (N vs stoichiometrically ‘balanced’ C:N:P). Following the laboratory nutrient uptake experiments, the columns were destructively sampled and the contents were homogenized to collect subsamples for DNA sequencing. Amplicon analysis was carried out as described by the Earth Microbiome Protocol for 16s and ITS sequencing.

54 ENVIRONMENTAL SCIENCES↗

Physiological factors and optical parameters as bases of vegetation discrimination and stress analysis.

The successful application of photographic, optical-mechanical scanning, and other sensing techniques to vegetation must be based on an understanding of the biological and physical principles involved. The objective is to review the biological and optical characteristics of vegetation and to discuss how knowledge of them can support operational programs by aiding in wavelength selection, timing of missions, and discriminations between vegetation types as well as between healthy and stressed plants of the same type. Both laboratory situations, in which relatively pure spectral data are obtained, and field situations are considered. In the latter, sensor performance and background variables affect data quality.

Wiegand, C. L.↗

Radial Distribution of Electron Spectra from High-Energy Ions

The average track model describes the response of physical and biological systems using radial dose distribution as the key physical descriptor. We report on an extension of this model to describe the average distribution of electron spectra as a function of radial distance from an ion. We present calculations of these spectra for ions of identical linear energy transfer (LET), but dissimilar charge and velocity to evaluate the differences in electron spectra from these ions. To illustrate the usefulness of the radial electron spectra for describing effects that are not described by electron dose, we consider the evaluation of the indirect events in microdosimetric distributions for ions. We show that folding our average electron spectra model with experimentally determined frequency distributions for photons or electrons provides a good representation of radial event spectra from high-energy ions in 0.5-2 micrometer sites.

Cucinotta, Francis A.↗

NASA Microgravity Combustion Science Research Plans for the ISS

A peer-reviewed research program in Microgravity Combustion Science has been chartered by the Physical Sciences Research Division of the NASA Office of Biological and Physical Research. The scope of these investigations address both fundamental combustion phenomena and applied combustion research topics of interest to NASA. From this pool of research, flight investigations are selected which benefit from access to a microgravity environment. Fundamental research provides insights to develop accurate simulations of complex combustion processes and allows developers to improve the efficiency of combustion devices, to reduce the production of harmful emissions, and to reduce the incidence of accidental uncontrolled combustion (fires, explosions). Through its spacecraft fire safety program, applied research is conducted to decrease risks to humans living and working in space. The Microgravity Combustion Science program implements a structured flight research process utilizing the International Space Station (ISS) and two of its premier facilities- the Combustion Integrated Rack of the Fluids and Combustion Facility and the Microgravity Science Glovebox - to conduct space-based research investigations. This paper reviews the current plans for Microgravity Combustion Science research on the International Space Station from 2003 through 2012.

Sutliff, Thomas J.↗

GeneLab: Current and Future Omics Data Integration Between Space Biology and HRP

For the past five years, the Biological and Physical Sciences Division has pioneered Open Science in Space Biology by funding the NASA GeneLab project. Along with the Ames Life Sciences Data Archive, GeneLab has quickly become the world leader in archiving and scientifically curating spaceflight and spaceflight relevant multi-omics data. Specifically, the GeneLab Data System has become a full enterprise solution providing advanced mining capabilities, several application programming interfaces for data federation and machine learning approaches, and delivering to the world an analytical and visualization platform which has enabled collaboration within the scientific community. Over the past three years, large meta-analysis and modeling studies have been published by the GeneLab Analysis Working Groups (AWGs), which are comprised of ~200 volunteer scientists. One natural extension of GeneLab data reuse has recently turned towards linking animal data with human data, which is the next necessary step to further validate animal models for inferring biological risks to humans conducting LEO, lunar or Martian missions. As such, data from the Human Research Program are an essential component of GeneLab and ALSDA. At the moment, simulated space radiation experiments conducted at Brookhaven National Laboratory make the most of HRP GeneLab data, and the scientific community has been eager to also link their animal spaceflight results to actual Astronaut data and human analog data. We will discuss further the current status of knowledge and future approaches to accelerate our basics understanding of the impact of space stressors on humans using latest omics technology.

omics↗

Enabling Space Biology Knowledge Discovery Through Biospecimen Sharing: The NASA Biological Institutional Scientific Collection

NASA and international partners have conducted experiments in space to understand the biological impacts and address hazards to health. The resulting basic and applied science is imperative to enabling humanity to venture back to the Moon and then to Mars and beyond. Sending organisms into space is a costly endeavor. All biospecimens not required by spaceflight-relevant Principal Investigators are harvested, preserved, and archived in the NASA Biological Institutional Scientific Collection (NBISC) to maximize the scientific return. The NASA Biological and Physical Sciences (BPS) Division has an ‘Open Science’ endeavor which includes NASA Genelab, the Space Biology Program’s Biospecimen Sharing Program, Physical Sciences Informatics, the Ames Life Sciences Data Archive, and NBISC. Its purpose is to integrate extensive data and biospecimen resources from spaceflight and/or ground-based analog experiments. NBISC biospecimens are collected and preserved according to well-established standard operating procedures to maintain scientific quality and are available on-request by the international scientific community. NBISC currently stores over 32,000 biospecimens from Shuttle, International Space Station, and ground-based space analog investigations. Tissue sharing has resulted in at least 33 publications since 2011 and 48 requests since 2016. Many requests for NBISC biospecimen come from first-time investigators who subsequently submit grants as the port-of-entry into the field of space biology. Some NBISC biospecimens have been awarded to NASA Genelab, who then generate various ‘Open Science’ -omics data sets on their platform for bioinformatics. Other NBISC biospecimen awards have led to multiple studies such as fecal microbiome analysis, DNA damage analysis using single-cell DNA sequencing, enzymatic-pathway identification involved in spaceflight muscle atrophy, and characterization of ocular morphological changes. Of note, NBISC has expanded to include a new Space Microbial Culture Collection (SMCC) for the collection, identification, documentation, long-term preservation, and distribution of space-related microbial isolates.

Ryan T. Scott↗

Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

59 BASIC BIOLOGICAL SCIENCES↗