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1,623 records · Page 91

First Plant Cell Atlas symposium report

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

59 BASIC BIOLOGICAL SCIENCES↗

Unbalancing Symbiotic Nitrogen Fixation: Can We Make Effectiveness More Effective?

One of the most critical uses of carbon fuels is in generating nitrogen fertilizer. Atmospheric dinitrogen is too stable to be used directly by plants, so plants need other chemical forms of nitrogen. Nitrogen fertilizer production uses ~4% of the world’s natural gas. Making N fertilizers leverages methane’s energy content by enabling additional energy to be captured into food and fiber through increased photosynthesis. Manufacturing fertilizer is essential—without it there would only be enough combined nitrogen to feed ~3 billion of the world’s ~7 billion people. How to alter this addiction is not obvious, but the best chance to secure substantial and sustainable amounts of future N might be through symbiotic nitrogen fixation (SNF). SNF describes mutualistic interactions where nitrogen-fixing bacteria provide fixed nitrogen to their plant hosts, freeing them from the need for nitrogen fertilizers. SNF already occurs on a large scale; "biological nitrogen” contributes about 5 Tg N/yr to American agriculture, a quarter of the nitrogen needed. Improving SNF and replacing inorganic fertilizers are both important goals in establishing sustainable and more energy-efficient farming. SNF has been used in agriculture for millennia, largely by using legumes like beans or alfalfa in mixed cropping systems. Legume SNF occurs in root nodules, organs that develop after a growing root is infected by bacteria called rhizobia. In the plant cells of a legume nodule, specialized forms of rhizobia fix nitrogen and can produce enough ammonia to supply the growing plant. The exchange of photosynthetically derived plant carbon compounds for nitrogen reduced by the bacteria is the engine that drives the symbiosis. Important details about the organization of development and metabolism in SNF remain to be determined, such as how plant and bacterial metabolism are coordinated as nitrogen is being fixed and what governs the overall level of nitrogen fixation. Most bacterial mutations that affect SNF completely block fixation (e.g. are Fix – ), providing a limited window into the feedback interactions that must be part of the process. We have investigated an unusual mutant of Sinorhizobium meliloti, a symbiotic partner of alfalfa, that fixes dinitrogen at a normal rate (i.e., it is Fix + ) but is not effective in supporting plant growth (i.e., it is ineffective or Eff – ). We have shown that the mutant has a specific mutation in the glnD gene, which codes for a protein that regulates the bacterial response to nitrogen stress, among other key pathways. A Fix + Eff – phenotype contains an unavoidable puzzle—how is it possible for the bacteria to fix nitrogen at a normal rate and without benefiting the nitrogen starved plant host? After eliminating other possibilities, we proposed that the bacteria synthesize a nitrogen-containing compound that the plant can’t use so that acquiring this compound does not relieve plant nitrogen stress. Extracts of nodules made by glnD mutant strains have high concentrations of pyruvate canaline oxime (PCO), a derivative of the plant defensive compound canaline, a toxic analog of ornithine, an amino acid. Many legumes produce canaline and the related arginine mimic canavanine. For reasons we do not yet understand, the mutation in glnD appears to trigger significant overproduction of canaline in a defense response that leads to substantial synthesis of PCO. We expected the bacteria to be able to use PCO, but we have not been able to grow S. meliloti on PCO under several conditions. PCO thus appears to be a metabolic dead end for both the plant and bacteria. We also examined bacterial catabolic pathways that degrade arginine and canavanine and showed that mutation of these did not alter the symbiosis in an obvious way. In related experiments to examine the metabolic development of root nodules, we carried out an ambitious experiment to simultaneously measure metabolites and protein changes during nodule maturation. For these experiments we used a related symbiotic interaction between S. medicae and Medicago truncatula. M. truncatula has a simpler genome than alfalfa so we could identify plant proteins based on predictions from the DNA sequence. Nodules formed on Medicago grow linearly, with the least mature tissues at the tip. Because development of nitrogen fixation is accompanied by the production of the pigmented plant oxygen carrier protein leghemoglobin, we were able to locate and manually separate the tip, transitional, and mature nitrogen-fixing regions from each other. Advances in proteomic and metabolomic techniques allowed us to analyze these tissues from a pool of as few as 10 nodules. We observed correlated transitions of various enzymes in the plant and bacterial proteomes from those characteristic of free-living metabolism to the microaerobic metabolism of the nitrogen-fixing tissues. The metabolome could not be separated into plant and bacterial domains but was consistent with this overall transition. A subsequent paper examined proteolysis in nodule bacteria. Protein turnover in mature regions of the nodule is significant. We were able to show complexes between various proteins and important proteases, using precipitation capture techniques to isolate the proteases and sensitive proteomic analysis to reveal the associated proteins.

09 BIOMASS FUELS↗

Service Life Extension of the Propulsion System of Long-Term Manned Orbital Stations

One of the critical non-replaceable systems of a long-term manned orbital station is the propulsion system. Since the propulsion system operates beginning with the launch of station elements into orbit, its service life determines the service life of the station overall. Weighing almost a million pounds, the International Space Station (ISS) is about four times as large as the Russian space station Mir and about five times as large as the U.S. Skylab. Constructed over a span of more than a decade with the help of over 100 space flights, elements and modules of the ISS provide more research space than any spacecraft ever built. Originally envisaged for a service life of fifteen years, this Earth orbiting laboratory has been in orbit since 1998. Some elements that have been launched later in the assembly sequence were not yet built when the first elements were placed in orbit. Hence, some of the early modules that were launched at the inception of the program were already nearing the end of their design life when the ISS was finally ready and operational. To maximize the return on global investments on ISS, it is essential for the valuable research on ISS to continue as long as the station can be sustained safely in orbit. This paper describes the work performed to extend the service life of the ISS propulsion system. A system comprises of many components with varying failure rates. Reliability of a system is the probability that it will perform its intended function under encountered operating conditions, for a specified period of time. As we are interested in finding out how reliable a system would be in the future, reliability expressed as a function of time provides valuable insight. In a hypothetical bathtub shaped failure rate curve, the failure rate, defined as the number of failures per unit time that a currently healthy component will suffer in a given future time interval, decreases during infant-mortality period, stays nearly constant during the service life and increases at the end when the design service life ends and wear-out phase begins. However, the component failure rates do not remain constant over the entire cycle life. The failure rate depends on various factors such as design complexity, current age of the component, operating conditions, severity of environmental stress factors, etc. Development, qualification and acceptance test processes provide rigorous screening of components to weed out imperfections that might otherwise cause infant mortality failures. If sufficient samples are tested to failure, the failure time versus failure quantity can be analyzed statistically to develop a failure probability distribution function (PDF), a statistical model of the probability of failure versus time. Driven by cost and schedule constraints however, spacecraft components are generally not tested in large numbers. Uncertainties in failure rate and remaining life estimates increase when fewer units are tested. To account for this, spacecraft operators prefer to limit useful operations to a period shorter than the maximum demonstrated service life of the weakest component. Running each component to its failure to determine the maximum possible service life of a system can become overly expensive and impractical. Spacecraft operators therefore, specify the required service life and an acceptable factor of safety (FOS). The designers use these requirements to limit the life test duration. Midway through the design life, when benefits justify additional investments, supplementary life test may be performed to demonstrate the capability to safely extend the service life of the system. An innovative approach is required to evaluate the entire system, without having to go through an elaborate test program of propulsion system elements. Evaluating every component through a brute force test program would be a cost prohibitive and time consuming endeavor. ISS propulsion system components were designed and built decades ago. There are no representative ground test articles for some of the components. A 'test everything' approach would require manufacturing new test articles. The paper outlines some of the techniques used for selective testing, by way of cherry picking candidate components based on failure mode effects analysis, system level impacts, hazard analysis, etc. The type of testing required for extending the service life depends on the design and criticality of the component, failure modes and failure mechanisms, life cycle margin provided by the original certification, operational and environmental stresses encountered, etc. When specific failure mechanism being considered and the underlying relationship of that mode to the stresses provided in the test can be correlated by supporting analysis, time and effort required for conducting life extension testing can be significantly reduced. Exposure to corrosive propellants over long periods of time, for instance, lead to specific failure mechanisms in several components used in the propulsion system. Using Arrhenius model, which is tied to chemically dependent failure mechanisms such as corrosion or chemical reactions, it is possible to subject carefully selected test articles to accelerated life test. Arrhenius model reflects the proportional relationship between time to failure of a component and the exponential of the inverse of absolute temperature acting on the component. The acceleration factor is used to perform tests at higher stresses that allow direct correlation between the times to failure at a high test temperature to the temperatures to be expected in actual use. As long as the temperatures are such that new failure mechanisms are not introduced, this becomes a very useful method for testing to failure a relatively small sample of items for a much shorter amount of time. In this article, based on the example of the propulsion system of the first ISS module Zarya, theoretical approaches and practical activities of extending the service life of the propulsion system are reviewed with the goal of determining the maximum duration of its safe operation.

Kamath, Ulhas↗