Tryptophan mutations in G3BP1 tune the stability of a cellular signaling hub by weakening transient interactions with Caprin1 and USP10
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59 BASIC BIOLOGICAL SCIENCES↗
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Results for “BASIC INTERACTIONS”
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An Evaluation of Detect and Avoid (DAA) Displays for Unmanned Aircraft Systems: The Effect of Information Level and Display Location on Pilot Performance
A consortium of government, industry and academia is currently working to establish minimum operational performance standards for Detect and Avoid (DAA) and Control and Communications (C2) systems in order to enable broader integration of Unmanned Aircraft Systems (UAS) into the National Airspace System (NAS). One subset of these performance standards will need to address the DAA display requirements that support an acceptable level of pilot performance. From a pilot's perspective, the DAA task is the maintenance of self separation and collision avoidance from other aircraft, utilizing the available information and controls within the Ground Control Station (GCS), including the DAA display. The pilot-in-the-loop DAA task requires the pilot to carry out three major functions: 1) detect a potential threat, 2) determine an appropriate resolution maneuver, and 3) execute that resolution maneuver via the GCS control and navigation interface(s). The purpose of the present study was to examine two main questions with respect to DAA display considerations that could impact pilots' ability to maintain well clear from other aircraft. First, what is the effect of a minimum (or basic) information display compared to an advanced information display on pilot performance? Second, what is the effect of display location on UAS pilot performance? Two levels of information level (basic, advanced) were compared across two levels of display location (standalone, integrated), for a total of four displays. The authors propose an eight-stage pilot-DAA interaction timeline from which several pilot response time metrics can be extracted. These metrics were compared across the four display conditions. The results indicate that the advanced displays had faster overall response times compared to the basic displays, however, there were no significant differences between the standalone and integrated displays. Implications of the findings on understanding pilot performance on the DAA task, the development of DAA display performance standards, as well as the need for future research are discussed.
detect and avoid↗
Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors
Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.
59 BASIC BIOLOGICAL SCIENCES↗
Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
59 BASIC BIOLOGICAL SCIENCES↗
Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin Binding Domain and Single-Stranded DNA
The origin-binding domain (OBD) of simian virus 40 (SV40) large T-antigen (T-Ag) is essential for many of T-Ag's interactions with DNA. Nevertheless, many important issues related to DNA binding, for example, how single-stranded DNA (ssDNA) transits along the T-Ag OBD, have yet to be established. Therefore, X-ray crystallography was used to determine the costructure of the T-Ag OBD bound to DNA substrates such as the single-stranded region of a forked oligonucleotide. A second structure of the T-Ag OBD crystallized in the presence of poly(dT){sub 12} is also reported. To test the conclusions derived from these structures, residues identified as being involved in binding to ssDNA by crystallography or by an earlier nuclear magnetic resonance study were mutated, and their binding to DNA was characterized via fluorescence anisotropy. In addition, these mutations were introduced into full-length T-Ag, and these mutants were tested for their ability to support replication. When considered in terms of additional homology-based sequence alignments, our studies refine our understanding of how the T-Ag OBDs encoded by the polyomavirus family interact with ssDNA, a critical step during the initiation of DNA replication.
59 BASIC BIOLOGICAL SCIENCES↗
The RIT1 C-terminus associates with lipid bilayers via charge complementarity
RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. For this study, we used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.
59 BASIC BIOLOGICAL SCIENCES↗
Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity
Algal-bacterial interactions provide clues to algal physiology, but mutualistic interactions are complicated by dynamic exchange. In this study, we characterized the response of Chlamydomonas reinhardtii to the presence of a putative alga-benefitting commensal bacterium ( Arthrobacter strain ‘P2b’). Co-cultivation promoted chlorophyll content, biomass, average cell size, and number of dividing cells, relative to axenic cultures. Addition of bacterial spent medium (whole, size-fractionated and heat-treated) had similar effects, indicating P2b does not require algal interaction to promote growth. Nutrients and pH were excluded as putative effectors, collectively indicating a commensal interaction mediated by Arthrobacter -released small exometabolite(s). Proteogenomic comparison revealed similar response to co-cultivation and spent media, including differential cell cycle regulation, extensive downregulation of flagellar genes and histones, carbonic anhydrase and RubisCO downregulation, upregulation of some chlorophyll, amino acid and carbohydrate biosynthesis genes, and changes to redox and Fe homeostasis. Further, Arthrobacter protein expression indicated some highly expressed putative secondary metabolites. Together, these results revealed that low molecular weight bacterial metabolites can elicit major physiological changes in algal cell cycle regulation, perhaps through a more productive G1 phase, that lead to substantial increases in photosynthetically-produced biomass. This work illustrates that model commensal interactions can be used to shed light on algal response to stimulating bacteria.
59 BASIC BIOLOGICAL SCIENCES↗
Lectin Receptor-like Kinase Signaling during Engineered Ectomycorrhiza Colonization
Mutualistic association can improve a plant’s health and productivity. G-type lectin receptor-like kinase (PtLecRLK1) is a susceptibility factor in Populus trichocarpa that permits root colonization by a beneficial fungus, Laccaria bicolor. Engineering PtLecRLK1 also permits L. bicolor root colonization in non-host plants similar to Populus trichocarpa. The intracellular signaling reprogramed by PtLecRLK1 upon recognition of L. bicolor to allow for the development and maintenance of symbiosis is yet to be determined. In this study, phosphoproteomics was utilized to identify phosphorylation-based relevant signaling pathways associated with PtLecRLK1 recognition of L. bicolor in transgenic switchgrass roots. Our finding shows that PtLecRLK1 in transgenic plants modifies the chitin-triggered plant defense and MAPK signaling along with a significant adjustment in phytohormone signaling, ROS balance, endocytosis, cytoskeleton movement, and proteasomal degradation in order to facilitate the establishment and maintenance of L. bicolor colonization. Moreover, protein–protein interaction data implicate a cGMP-dependent protein kinase as a potential substrate of PtLecRLK1.
ectomycorrhiza colonization↗
Reversible Crosslinked Polymer Binder for Recyclable Lithium Sulfur Batteries with High Performance
Owing to the negative impact of the extensive utilization of batteries on the environment, sustainability of the cells needs to be included in the systemic research of batteries. In this work, a dissolvable ionic crosslinked polymer (DICP) is exploited as a binder for lithium–sulfur batteries by crosslinking the polyacrylic acid and polyethyleneimine through carboxy-amino ionic interaction. This interaction is pH-controlled, and therefore, the crosslinked binder network can be readily dissociated under basic conditions, providing a facile strategy enabling valuable components recycled through a convenient washing method. The sulfur cathode prepared using the recycled carbon–sulfur composite can deliver comparable capacity as that of fresh electrode. In addition, evidence from cell performance and characterizations, such as in situ X-ray absorption spectroscopy, in situ UV–visible spectroscopy, X-ray photoelectron spectroscopy, and density functional theory calculation, confirms that DICP is a more effective binder than its commercial counterpart on suppressing polysulfide dissolution in the electrolyte. Exploiting reversible crosslinked polymer binder for recyclable Li–S batteries with ameliorated electrochemical performance, this study illuminates sustainable development for large-scale energy storage systems.
36 MATERIALS SCIENCE↗
What is a particle-conserving Topological Superfluid? The fate of Majorana modes beyond mean-field theory
We investigate Majorana modes of number-conserving fermionic superfluids from both basic physics principles, and concrete models perspectives. After reviewing a criterion for establishing topological superfluidity in interacting systems, based on many-body fermionic parity switches, we reveal the emergence of zero-energy modes anticommuting with fermionic parity. Those many-body Majorana modes are constructed as coherent superpositions of states with different number of fermions. While realization of Majorana modes beyond mean field is plausible, we show that the challenge to quantum-control them is compounded by particle-conservation, and more realistic protocols will have to balance engineering needs with astringent constraints coming from superselection rules. Majorana modes in number-conserving systems are the result of a peculiar interplay between quantum statistics, fermionic parity, and an unusual form of spontaneous symmetry breaking. We test these ideas on the Richardson–Gaudin–Kitaev chain, a number-conserving model solvable by way of the algebraic Bethe ansatz, and equivalent in mean field to a long-range Kitaev chain.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Method development for comprehensive extraction and analysis of marine toxins: Liquid-liquid extraction and tandem liquid chromatography separations coupled to electrospray tandem mass spectrometry
Toxins from biological sources are recognized as potential chemical weapon threats, with saxitoxin and ricin listed by the chemical weapons convention (CWC) as schedule one agents (CWC reference). These two toxins represent a metabolite (saxitoxin) and protein (ricin) from algal and plant sources, respectively. An array of toxins have been listed as "select agents" by the Health and Human Services (HHS) select agent program, including ricin, abrin, saxitoxin, tetrodotoxin, specific paralytic alpha conotoxin peptides, T-2 toxin, diacetoxyscirpenols, botulinum toxins, and staphylococcal enterotoxins [1]. The quantities of these toxins dictate whether they are considered select agents with federal oversight of their storage and use. While this list captures some of the naturally occurring toxins that may pose a threat to the public, there are a number of other naturally occurring toxins that may also be a concern.
biodetection↗
Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N -Methyltransferase
Burkholderia glumae converts the guanine base of guanosine triphosphate into an azapteridine and methylates both the pyrimidine and triazine rings to make toxoflavin. Strains of Burkholderia thailandensis and Burkholderia pseudomallei have a gene cluster encoding seven putative biosynthetic enzymes that resembles the toxoflavin gene cluster. Four of the enzymes are similar in sequence to BgToxBCDE, which have been proposed to make 1,6-didesmethyltoxoflavin (1,6-DDMT). One of the remaining enzymes, BthII1283 in B. thailandensis E264, is a predicted S-adenosylmethionine (SAM)-dependent N-methyltransferase that shows a low level of sequence identity to BgToxA, which sequentially methylates N6 and N1 of 1,6-DDMT to form toxoflavin. Here we show that, unlike BgToxA, BthII1283 catalyzes a single methyl transfer to N1 of 1,6-DDMT in vitro. In addition, we investigated the differences in reactivity and regioselectivity by determining crystal structures of BthII1283 with bound S-adenosylhomocysteine (SAH) or 1,6-DDMT and SAH. BthII1283 contains a class I methyltransferase fold and three unique extensions used for 1,6-DDMT recognition. The active site structure suggests that 1,6-DDMT is bound in a reduced form. The plane of the azapteridine ring system is orthogonal to its orientation in BgToxA. In BthII1283, the modeled SAM methyl group is directed toward the p orbital of N1, whereas in BgToxA, it is first directed toward an sp 2 orbital of N6 and then toward an sp 2 orbital of N1 after planar rotation of the azapteridine ring system. As a result, in BthII1283, N1 is hydrogen bonded to a histidine residue whereas BgToxA does not supply an obvious basic residue for either N6 or N1 methylation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth Halophile Marinobacter subterrani
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99 GENERAL AND MISCELLANEOUS↗
Dark states of electrons in a quantum system with two pairs of sublattices
A quantum state of matter that is forbidden to interact with photons and is therefore undetectable by spectroscopic means is called a dark state. This basic concept can be applied to condensed matter where it suggests that a whole band of quantum states could be undetectable across a full Brillouin zone. Here we report the discovery of such condensed-matter dark states in palladium diselenide as a model system that has two pairs of sublattices in the primitive cell. By using angle-resolved photoemission spectroscopy, we find valence bands that are practically unobservable over the whole Brillouin zone at any photon energy, polarization and scattering plane. Our model shows that two pairs of sublattices located at half-translation positions and related by multiple glide-mirror symmetries make their relative quantum phases polarized into only four kinds, three of which become dark due to double destructive interference. This mechanism is generic to other systems with two pairs of sublattices, and we show how the phenomena observed in cuprates, lead halide perovskites and density wave systems can be resolved by the mechanism of dark states. Our results suggest that the sublattice degree of freedom, which has been overlooked so far, should be considered in the study of correlated phenomena and optoelectronic characteristics.
electronic properties and materials↗
The evolution of the magnetic phases of Sb-doped Mn{sub 5}Sn{sub 3} compounds
The structural and magnetic properties of Mn{sub 5}(Sn{sub 1-x}Sb{sub x}){sub 3} compounds (x = 0-0.4) were investigated by means of X-ray diffraction and magnetization measurements. All samples crystallize in Ni{sub 2}In-type structure (P6{sub 3}/mmc) with the lattice parameters changing anisotropically with the increase of Sb concentration. Sb doping leads to the merging of the ferrimagnetic transition temperature T{sub c} and the re-entrant spin-glass transition temperature T{sub f}, indicating a direct transition from spin-glass state to paramagnetic state. The M(H) curve at 5 K evolves with x from a soft-magnet type to a linear-like shape. We proposed a basic explanation for the evolution of the magnetic properties in terms of crystal structure and magnetic interactions, which can be applied to other related compounds.
36 MATERIALS SCIENCE↗
A plant-responsive bacterial-signaling system senses an ethanolamine derivative
Significance A number of plant-associated bacteria possess transcription factors homologous to LuxR that respond to compounds found in plant tissue. These LuxR homologs are known to regulate virulence or symbiosis. Although the first of these proteins were described more than a decade ago, the factors they respond to remain unknown. Here we identify a compound that functions with PipR, a plant-responsive LuxR homolog from a tree root endopytic Pseudomonas isolate. The inducer is an ethanolamine derivative. Ethanolamine is a building block for plant membrane phospholipids and signaling molecules. This discovery connects at least one of the plant-responsive LuxR homolog systems to a growing understanding of ethanolamine chemistry and responses of bacterial cells to ethanolamine and ethanolamine derivatives.
59 BASIC BIOLOGICAL SCIENCES↗
New asteroseismic scaling relations based on the Hayashi track relation applied to red giant branch stars in NGC 6791 and NGC 6819
Stellar mass M, radius R, and gravity g are important basic parameters in stellar physics. Accurate values for these parameters can be obtained from the gravitational interaction between stars in multiple systems or from asteroseismology. Stars in a cluster are thought to be formed coevally from the same interstellar cloud of gas and dust. The cluster members are therefore expected to have some properties in common. These common properties strengthen our ability to constrain stellar models and asteroseismically derived M, R, and g when tested against an ensemble of cluster stars. Here we derive new scaling relations based on a relation for stars on the Hayashi track (√(T{sub eff})∼g{sup p}R{sup q}) to determine the masses and metallicities of red giant branch stars in open clusters NGC 6791 and NGC 6819 from the global oscillation parameters Δν (the large frequency separation) and ν{sub max} (frequency of maximum oscillation power). The Δν and ν{sub max} values are derived from Kepler observations. From the analysis of these new relations we derive: (1) direct observational evidence that the masses of red giant branch stars in a cluster are the same within their uncertainties, (2) new methods to derive M and z of the cluster in a self-consistent way from Δν and ν{sub max}, with lower intrinsic uncertainties, and (3) the mass dependence in the Δν - ν{sub max} relation for red giant branch stars.
79 ASTRONOMY AND ASTROPHYSICS↗
Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship
The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant–microbe functioning, thus facilitating low-input, sustainable agricultural practices.
59 BASIC BIOLOGICAL SCIENCES↗