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At least 235 records · Page 13

Strong inter-population cooperation leads to partner intermixing in microbial communities

Patterns of spatial positioning of individuals within microbial communities are often critical to community function. However, understanding patterning in natural communities is hampered by the multitude of cell–cell and cell–environment interactions as well as environmental variability. Here, through simulations and experiments on communities in defined environments, we examined how ecological interactions between two distinct partners impacted community patterning. We found that in strong cooperation with spatially localized large fitness benefits to both partners, a unique pattern is generated: partners spatially intermixed by appearing successively on top of each other, insensitive to initial conditions and interaction dynamics. Intermixing was experimentally observed in two obligatory cooperative systems: an engineered yeast community cooperating through metabolite-exchanges and a methane-producing community cooperating through redox-coupling. Even in simulated communities consisting of several species, most of the strongly-cooperating pairs appeared intermixed. Thus, when ecological interactions are the major patterning force, strong cooperation leads to partner intermixing.

59 BASIC BIOLOGICAL SCIENCES↗

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions

Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗

Triton: Igiugig Fish Video Analysis (Project Report)

This document summarizes the analysis of video data collected around the Ocean Renewable Power Company’s RivGen® device in the Kvichak River during July and August 2015. Human (manual) analysis of the data was undertaken and used to develop automated algorithms to detect fish in the frames and describe interaction behavior. In addition, a web application, EyeSea, was developed to combine manual and automated processing, so that ultimately the automated algorithms could be used to identify where human analysis was needed (i.e., when fish are present in video frames). The aim of the project was to develop algorithms that could identify video frames with fish present that could then be used to enable faster manual analysis. However, the project has also identified recommendations for future data collection, and research that could help analysis and interpretation. The manual analysis started to look at all data from the start of the deployment; this was to ensure rare events were seen, and initially focused on night-time data when more fish were present. This process highlighted the amount of time taken to identify fish, and ultimately only 42.33 hours of video were reviewed due to the time-consuming analysis. The data were classified as ‘Fish’, when the reviewer was confident it was a fish, and ‘Maybe’ fish, when it was difficult to distinguish. This was based on the movement, shape and color characteristics. ‘Fish’ were further classified as ‘adult’, ‘juvenile’, or ‘unidentifiable’. Behavioral attributes were noted, which were broadly divided into passive and avoidance activities. In over 42 hours data, there were only 20 potential contact interactions, of which 3 were ‘Maybe’ classifications, 12 were juveniles and 5 were adults; on only one occasion was an actual contact confirmed, and this was an adult fish with the camera, not the turbine itself. This also highlights the difficulties associated with confirming a strike or collision event as occurring or being a near-miss. More interactions were detected at night; this was probably biased by nighttime artificial light use, which may have attracted fish, but also could have increased detection probability as the light is reflected from the fish itself. For the algorithm development, background subtraction, optical flow, and deep learning techniques were considered. The deep learning approach was determined as needing too much training data for this application, and therefore was not continued. The optical flow analysis was considered promising, but did not give immediate results, so would need further investigation. Therefore, background subtraction was the main focus. Three methods of background subtraction were tried: Robust Principal Components Analysis (RPCA), Gaussian Mixture Model (GMM) and Video Background Extraction(ViBE). A classification technique was then applied to the foreground images to determine fish presence. Using this combination, it was found that fish could be accurately detected when occupying more pixels (>200 pixels, 98.2% correct; 100-200 pixels, 99.6% correct; 5-100 pixels, 85.4% correct; 2-5 pixels, 66.3% correct). In parallel, EyeSea was developed to convert the video data to a usable form and to enable manual and automated analysis of the data that would have a standardized output. Recommendations for further research, and standardized methods for data collection are given.

13 HYDRO ENERGY↗

A SYSTEMATIC SURVEY FOR BROADENED CO EMISSION TOWARD GALACTIC SUPERNOVA REMNANTS

We present molecular spectroscopy toward 50 Galactic supernova remnants (SNRs) taken at millimeter wavelengths in {sup 12}CO J = 2 − 1. These observations are part of a systematic survey for broad molecular line (BML) regions indicative of interactions with molecular clouds (MCs). We detected BML regions toward 19 SNRs, including 9 newly identified BML regions associated with SNRs (G08.3–0.0, G09.9–0.8, G11.2–0.3, G12.2+0.3, G18.6–0.2, G23.6+0.3, 4C–04.71, G29.6+0.1, and G32.4+0.1). The remaining 10 SNRs with BML regions confirm previous evidence for MC interaction in most cases (G16.7+0.1, Kes 75, 3C 391, Kes 79, 3C 396, 3C 397, W49B, Cas A, and IC 443), although we confirm that the BML region toward HB 3 is associated with the W3(OH) H ii region, not the SNR. Based on the systemic velocity of each MC, molecular line diagnostics, and cloud morphology, we test whether these detections represent SNR–MC interactions. One of the targets (G54.1+0.3) had previous indications of a BML region, but we did not detect broadened emission toward it. Although broadened {sup 12}CO J = 2 − 1 line emission should be detectable toward virtually all SNR–MC interactions, we find relatively few examples; therefore, the number of interactions is low. This result favors mechanisms other than supernova feedback as the basic trigger for star formation. In addition, we find no significant association between TeV gamma-ray sources and MC interactions, contrary to predictions that SNR–MC interfaces are the primary venues for cosmic ray acceleration.

79 ASTRONOMY AND ASTROPHYSICS↗

Programming Metabolite Exchange to Understand and Control Plant-Microbe Interactions

Many aspects of plant growth and survival are dependent upon beneficial interactions between plant tissues and bacterial species of the endophyte and rhizosphere. These associated microorganisms can contribute positively to plant growth, stress tolerance, metabolism and protection against plant pathogens. For example, an endosymbiotic bacterium Burkholderia phytofirmans PsJN was shown to colonize and promote growth of switchgrass under controlled conditions, suggesting it may be a promising candidate for improving bioenergy crop production (Kim et al., 2012). Despite the documented benefits of endophytic and rhizosphere microbes on plant fitness and photosynthetic productivity, there is still a gap in our understanding of specific molecular -and cellular-level processes that guide the development of beneficial plant-microbe interactions. As these interactions involve physical contact/metabolite exchange we also posit that directed co-localization of beneficial bacteria and plant cells will enhance these benefits. We propose to engineer bacterial species that co-localize with the plant tissue and then to measure cell growth as well as carry out –omics analysis to obtain information regarding the specifics of these beneficial interactions as well as their extent. This report describes our progress with these goals and the results.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis of tRNA recognition by the widespread OB fold

The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNA Ile , which reveals that Trbp recognizes tRNAs solely by capturing their 3' ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3' terminal location, and specific sequence of the 3' CA dinucleotide — a universal feature of mature tRNAs. Arc1p supplements its OB – tRNA 3' end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.

59 BASIC BIOLOGICAL SCIENCES↗

A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization

Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. In this paper we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an “L”-like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conserved basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Finally, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.

60 APPLIED LIFE SCIENCES↗

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗

Photoluminescence and Confinement of Excitons in Disordered Porous Films

The exciton confinement effect in quantum dots at the surface of SiO{sub 2} spheres and the percolation phase transition in films based on a mixture of pure SiO{sub 2} spheres and spheres covered by CdS quantum dots (SiO{sub 2}/CdS nanoparticles) are studied. It is found that, due to the high surface energy of spheres, the quantum dots deposited onto their surface are distorted, which modifies the exciton confinement effect: the effect is retained only in one direction, the direction normal to the surface of the spheres. As a result, the energy of the exciton ground state exhibits a complex dependence on both the quantum-dot radius and sphere size. In the optical spectra of films based on this mixture, the clustering of small-sized nanoparticles and then, at a critical concentration of nanoparticles of ~60%, the formation of a percolation cluster are detected for the first time. The critical concentration is twice higher than the corresponding quantity given by the model of geometrical “colored percolation”, which is a consequence of interaction between submicrometer nanoparticles. The relation between the basic parameters of the percolation transition, such as the film porosity, coordination number, and the quantity defining the number of particles in the percolation cluster, is obtained and analyzed.

36 MATERIALS SCIENCE↗

A Theory for the Response of Tropical Moist Convection to Mechanical Orographic Forcing

Abstract Spatial patterns of tropical rainfall are strongly influenced by mountains. Although theories for precipitation induced by convectively stable upslope ascent exist for the midlatitudes, these do not represent the interaction of moist convection with orographic forcing. Here, we present a theory for convective precipitation produced by the mechanical interaction of a tropical ridge with a basic-state horizontal wind. Deviations from this basic state are represented as the sum of a “dry” perturbation, due to the stationary orographic gravity wave, and a “moist” perturbation that carries the convective response. The moist component dynamics are subject to the weak temperature gradient approximation; they are forced by the dry mode’s influence on lower-tropospheric moisture and temperature. Analytical solutions provide estimates of the precipitation distribution, including peak precipitation, upstream extent, and rain shadow extent. The theory can be used with several degrees of complexity depending on the technique used to compute the dry mode, which can be drawn from linear mountain wave theory or full numerical simulations. To evaluate the theory, we use a set of convection-permitting simulations with a flow-perpendicular ridge in a long channel. The theory makes a good prediction for the cross-slope precipitation profile, indicating that the organization of convective rain by orography can be quantitatively understood by considering the effect of stationary orographic gravity waves on a lower-tropospheric convective quasi-equilibrium state.

54 ENVIRONMENTAL SCIENCES↗

Human-System Interface Design Review Guidelines

The U.S. Nuclear Regulatory Commission (NRC) staff reviews the human factors engineering (HFE) aspects of nuclear power plants in accordance with the Standard Review Plan (NUREG-0800, Standard Review Plan for the Review of Safety Analysis Reports for Nuclear Power Plants: LWR Edition). The Human Factors Engineering Program Review Model (NUREG-0711, Revision 3, issued November 2012) contains detailed design review procedures. As part of the review process, the interfaces between plant personnel and the plant's systems and components are evaluated for conformance with HFE guidelines. This document, Human-System Interface Design Review Guidelines (NUREG-0700, Revision 3), provides the guidelines necessary to perform this evaluation. The review guidelines address the physical and functional characteristics of human-system interfaces (HSIs). Because these guidelines only address the HFE aspects of design and not other related considerations, such as instrumentation and control and structural design, they are referred to as HFE guidelines. In addition to the review of actual HSIs, the NRC staff can use the NUREG-0700 guidelines to evaluate a design-specific HFE guidelines document or style guide. The HFE guidelines are organized into four basic parts, which are divided into sections. Part I contains guidelines for the basic HSI elements: information displays, user-interface interaction and management, and analog displays and controls. These elements are used as building blocks to develop HSI systems to serve specific functions. Part II contains the guidelines for reviewing the following HSI systems: alarm system, safety parameter display system, group-view display system, soft control system, computer-based procedure system, automation system, and communication system. Part III provides guidelines for the review of workstations and workplaces. Part IV provides guidelines for the review of HSI support (i.e., maintainability of digital systems and degraded HSI and instrumentation and control conditions).

42 ENGINEERING↗

Optimal Uses of Magnetic Fields for Indirect-Drive Inertial Fusion

This project explored how applied magnetic fields can improve inertial confinement fusion (ICF), specifically the indirect-drive approach that uses a hohlraum. This has been proposed for several decades as potentially beneficial, due to thermal insulation (reduced losses) from the imploded hotspot. We performed the most advanced radiation-magneto-hydrodynamic modeling to date of magnetized ICF designs in the ignition regime. We found that adding technologically feasible fields up to 60 – 70 Tesla could increase the fusion yield of current igniting designs for the National Ignition Facility (NIF) by up to 8x. Also, simulations show that in certain cases relatively small fields of 3 – 5 Tesla could double the yield, and be implemented at much lower cost. Early work on re-optimizing NIF designs with magnetic fields, namely by using a thicker ablator with more mass remaining, could increase the yield of a sub-ignition target by 18x and bring it into the ignition regime. A separate benefit of magnetization besides reduced thermal loss is reduced hydrodynamic instability. Modeling work under this project shows this could be significant, though early experiments at NIF and the Omega Laser proved inconclusive. We designed and proposed an improved NIF experiment on magnetized mix, based on a large-amplitude imposed perturbation. The project also supported basic physics research into magnetized laser-plasma interactions, namely cross-beam energy transfer, both with experiments at Omega and theory / modeling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

In Situ Loading and Delivery of Short Single- and Double-Stranded DNA by Supramolecular Organic Frameworks

Short DNA represents an important class of biomacromolecules that are widely applied in gene therapy, editing, and modulation. However, the development of simple and reliable methods for their intracellular delivery remains a challenge. Herein, we describe that seven water-soluble, homogeneous supramolecular organic frameworks (SOFs) with a well-defined pore size and high stability in water that can accomplish in situ inclusion of single-stranded (ss) and double-stranded (ds) DNA (21, 23, and 58 nt) and effective intracellular delivery (including two noncancerous and six cancerous cell lines). Fluorescence quenching experiments for single and double end-labeled ss- and ds-DNA support that the DNA sequences can be completely enveloped by the SOFs. Confocal laser scanning microscopy and flow cytometry reveal that five of the SOFs exhibit excellent delivery efficiencies that, in most of the studied cases, outperform the commercial standard Lipo2000, even at low SOF–nucleic acid ratios. In addition to high delivery efficiencies, the water-soluble, self-assembled SOF carriers have a variety of advantages, including convenient preparation, high stability, and in situ DNA inclusion, which are all critical for practical applications in nucleic acid delivery.

59 BASIC BIOLOGICAL SCIENCES↗

Ab-Initio Hamiltonian Approach to Light Nuclei And to Quantum Field Theory

Nuclear structure physics is on the threshold of confronting several long-standing problems such as the origin of shell structure from basic nucleon-nucleon and three-nucleon interactions. At the same time those interactions are being developed with increasing contact to QCD, the underlying theory of the strong interactions, using effective field theory. The motivation is clear - QCD offers the promise of great predictive power spanning phenomena on multiple scales from quarks and gluons to nuclear structure. However, new tools that involve non-perturbative methods are required to build bridges from one scale to the next. We present an overview of recent theoretical and computational progress with a Hamiltonian approach to build these bridges and provide illustrative results for the nuclear structure of light nuclei and quantum field theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Investigations of Bubbly Flows using Direct Numerical Simulations

Direct numerical simulations are used to examine the behavior of relatively high void fraction bubbly flows. The full Navier-Stokes equations are solved for both the bubbles and the ambient liquid and the flow near the moving and deforming phase boundaries is resolved fully. This yields detailed data for the evolution of the system that can be used to extract information about the basic bubble-bubble and bubble-flow interactions as well as about the averaged properties of the system. Such information are critical for the generation of averaged engineering models of industrial size systems as well as for novel applications of bubbly flows where experiments are difficult. The project has yielded detailed information about many aspects of bubbly flows. The results for flows in vertical channels are particularly significant and have yielded an essentially complete understanding of many aspects of the flows. The important insight is that the flow has a particularly simple structure, consisting of a homogeneous core in hydrostatic balance and a wall layer whose composition depends of whether the liquid is flowing upward or downward. These results hold for both laminar and turbulent flows and have allowed us to derive an analytical model to predict the flow. We have also shown that bubble deformability results in a completely different flow structure, but also giving rise to relatively simple predictive models. Preliminary studies of transient migration of a non-homogeneous bubble distribution and coalescence induced flow regime transitions in vertical channels were also done.

42 ENGINEERING↗

Electrostatics-Driven Hierarchical Buckling of Charged Flexible Ribbons

In this work, we investigate the rich morphologies of an electrically charged flexible ribbon, which is a prototype for many beltlike structures in biology and nanomaterials. Long-range electrostatic repulsion is found to govern the hierarchical buckling of the ribbon from its initially flat shape to its undulated and out-of-plane twisted conformations. In this process, the screening length is the key controlling parameter, suggesting that a convenient way to manipulate the ribbon morphology is simply to change the salt concentration. We find that these shapes originate from the geometric effect of the electrostatic interaction, which fundamentally changes the metric over the ribbon surface. We also identify the basic modes by which the ribbon reshapes itself in order to lower the energy. Finally, the geometric effect of the physical interaction revealed in this Letter has implications for the shape design of extensive ribbonlike materials in nano- and biomaterials.

36 MATERIALS SCIENCE↗

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria

Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.

59 BASIC BIOLOGICAL SCIENCES↗