Activity and fidelity of human DNA polymerase α depend on primer structure
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59 BASIC BIOLOGICAL SCIENCES↗
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Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms
Abstract Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.
59 BASIC BIOLOGICAL SCIENCES↗
Quantum field theory of topological spin dynamics
Here, we develop a field theory of quantum magnets and magnetic (semi)metals, which is suitable for the analysis of their universal and topological properties. The systems of interest include collinear, coplanar, and general noncoplanar magnets. At the basic level, we describe the dynamics of magnetic moments using smooth vector fields in the continuum limit. Dzyaloshinskii-Moriya interaction is captured by a non-Abelian vector gauge field, and chiral spin couplings related to topological defects appear as higher-rank antisymmetric tensor gauge fields. We distinguish type-I and type-II magnets by their equilibrium response to the non-Abelian gauge flux, and characterize the resulting lattices of skyrmions and hedgehogs, the spectra of spin waves, and the chiral response to external perturbations. The general spin-orbit coupling of electrons is similarly described by non-Abelian gauge fields, including higher-rank tensors related to the electronic Berry flux. Itinerant electrons and local moments exchange their gauge fluxes through Kondo and Hund interactions. Hence, by utilizing gauge fields, this theory provides a unifying physical picture of “intrinsic” and “topological” anomalous Hall effects, spin-Hall effects, and other correlations between the topological properties of electrons and moments. We predict “topological” magnetoelectric effect in materials prone to hosting hedgehogs. Links to experiments and model calculations are provided by deriving the couplings and gauge fields from generic microscopic models, including the Hubbard model with spin-orbit interactions. Much of the formal analysis is generalized to d spatial dimensions in order to access the $π_{d–1}(S^{d–1})$ homotopy classification of the magnetic hedgehog topological defects, and establish the possibility of novel quantum spin liquids that exhibit a fractional magnetoelectric effect. However, we emphasize the form of all results in the physically relevant $\textit{d}$ = 3 dimensions, and discuss a few applications to topological magnetic conductors like Mn 3 Sn and Pr 2 Ir 2 O 7 .
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Holographic operator mapping in dS / CFT and cluster decomposition
The bulk-to-boundary mapping for massive scalar fields is constructed, providing a de Sitter analog of the Lehmann-Symanzik-Zimmermann reduction formula. The set of boundary correlators thus obtained defines a potentially new class of conformal field theories based on principal series representations of the global conformal group. Conversely, we show that bulk field operators in de Sitter may be reconstructed from boundary operators. While consistent at the level of the free field theory, the boundary conformal field theory does not satisfy cluster decomposition. Furthermore, the resulting conformal field theory does not satisfy the basic axioms of Euclidean quantum field theory due to Osterwalder and Schrader, so it is likely not well defined once interactions are included.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2
Replication of Vibrio cholerae chromosome 2 (Chr2) depends on molecular chaperone DnaK to facilitate binding of the initiator (RctB) to the replication origin. The binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. Here we show that DnaK employs different mechanisms to enhance the two kinds of binding. We found that mutations in rctB that reduce DnaK binding also reduce 12-mer binding and initiation. The initiation defect is suppressed by second-site mutations that increase 12-mer binding only marginally. Instead, they reduce replication inhibitory mechanisms: RctB dimerization and 39-mer binding. One suppressing change was in a dimerization domain which is folded similarly to the initiator of an iteron plasmid—the presumed progenitor of Chr2. In plasmids, DnaK promotes initiation by reducing dimerization. A different mutation was in the 39-mer binding domain of RctB and inactivated it, indicating an alternative suppression mechanism. Paradoxically, although DnaK increases 39-mer binding, the increase was also achieved by inactivating the DnaK binding site of RctB. This result suggests that the site inhibits the 39-mer binding domain (via autoinhibition) when prevented from binding DnaK. Taken together, our results reveal an important feature of the transition from plasmid to chromosome: the Chr2 initiator retains the plasmid-like dimerization domain and its control by chaperones but uses the chaperones in an unprecedented way to control the inhibitory 39-mer binding.
59 BASIC BIOLOGICAL SCIENCES↗
Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization
Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.
59 BASIC BIOLOGICAL SCIENCES↗
Nipah Virus-Like Particle Egress Is Modulated by Cytoskeletal and Vesicular Trafficking Pathways: a Validated Particle Proteomics Analysis
Classified as a biosafety level 4 (BSL4) select agent, Nipah virus (NiV) is a deadly henipavirus in the Paramyxoviridae family, with a nearly 75% mortality rate in humans, underscoring its global and animal health importance. Elucidating the process of viral particle production in host cells is imperative both for targeted drug design and viral particle-based vaccine development. However, little is understood concerning the functions of cellular machinery in paramyxoviral and henipaviral assembly and budding. Recent studies showed evidence for the involvement of multiple NiV proteins in viral particle formation, in contrast to the mechanisms understood for several paramyxoviruses as being reliant on the matrix (M) protein alone. Further, the levels and purposes of cellular factor incorporation into viral particles are largely unexplored for the paramyxoviruses. To better understand the involvement of cellular machinery and the major structural viral fusion (F), attachment (G), and matrix (M) proteins, we performed proteomics analyses on virus-like particles (VLPs) produced from several combinations of these NiV proteins. Our findings indicate that NiV VLPs incorporate vesicular trafficking and actin cytoskeletal factors. The involvement of these biological processes was validated by experiments indicating that the perturbation of key factors in these cellular processes substantially modulated viral particle formation. These effects were most impacted for NiV-F-modulated viral particle formation either autonomously or in combination with other NiV proteins, indicating that NiV-F budding relies heavily on these cellular processes. These findings indicate a significant involvement of the NiV fusion protein, vesicular trafficking, and actin cytoskeletal processes in efficient viral particle formation. Nipah virus is a zoonotic biosafety level 4 agent with high mortality rates in humans. The genus to which Nipah virus belongs, Henipavirus , includes five officially recognized pathogens; however, over 20 species have been identified in multiple continents within the last several years. As there are still no vaccines or treatments for NiV infection, elucidating its process of viral particle production is imperative both for targeted drug design as well as for particle-based vaccine development. Developments in high-throughput technologies make proteomic analysis of isolated viral particles a highly insightful approach to understanding the life cycle of pathogens such as Nipah virus.
59 BASIC BIOLOGICAL SCIENCES↗
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I
All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys). A comprehensive study was conducted, by taking advantage of the PS I 3D structures and the TSR-based algorithm, to answer three questions: (i) Are electron cofactors including P700, A -1 and A 0 , which are chemically identical chlorophylls, structurally different? (ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites? The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A -1 and A 0 ; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A -1 , A 0 and A 1 as well as their cofactor binding sites; (iv) the tryptophan residues close to A 0 and A 1 are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods. The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.
59 BASIC BIOLOGICAL SCIENCES↗
Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens
The COVID-19 pandemic demonstrated the insufficiency of a reactive approach to emerging zoonotic pathogens. With spillover increasing in frequency as environments change and the human footprint continues to grow, pandemic prevention will require predictive models that can identify (i) potential zoonoses with a high likelihood of emergence and (ii) environmental or other features that may trigger a shift in host, vector, or pathogen baselines associated with emergence and/or spillover. Artificial intelligence (AI), and particularly its machine learning and deep learning branches, holds enormous potential for detecting shifts in large-scale biodiversity and disease datasets (genomic, ecological, geospatial, etc.). Such algorithms can be trained to identify subtle patterns in large volumes of data to yield insights into complex phenomena for which we have limited knowledge of the true cause(s) or predictor(s), as is the case for emerging infectious diseases.
59 BASIC BIOLOGICAL SCIENCES↗
The Monkeys and Parrots of Gold Rush-era California
As immigrant gold miners migrated en masse to San Francisco and northern California during the Gold Rush-era (ca. 1849–1855), they experienced new animals. Stopping in ports throughout Central and South America, these argonauts saw, felt, smelled, heard, and occasionally consumed, mammals, birds, reptiles, and many more creatures, which were wholly exotic to those species found at home. Two types of animals that the Gold Rush populace encountered during this era include parrots and monkeys. Although found throughout tropical environments in areas far distant from northern California, these animals became quickly imported to San Francisco during the early 1850s. A wild, turbulent Gold Rush-era helped facilitate the importation of these exotic animal types, both for comfort and entertainment, as they helped provide a source of companionship for miners unaccustomed to the shock of 1850s northern California.
59 BASIC BIOLOGICAL SCIENCES↗
Demonstration of a Strict Molecular Oxygen Requirement of Yellow Latex Oxidation in the Central Amazon Canopy Tree Muiratinga ( Maquira sclerophylla (Ducke) C.C. Berg)
Plant-derived latex is widely used in rubber production and plays important roles in ecological processes in the tropics. Although it is known that latex oxidation from the commercially important tree Hevea brasiliensis , results in latex browning, little is known about latex oxidation in highly diverse tropical ecosystems. Here we show that upon physical trunk damage, yellow latex released from the canopy tree Muiratinga ( Maquira sclerophylla (Ducke) C.C. Berg) is rapidly and extensively oxidized to a black resin in the presence of air within 15-30 min. In a nitrogen atmosphere, latex oxidation was inhibited, but was immediately activated upon exposure to air. The results suggest the occurrence of O 2 -dependent oxidative enzymes including polyphenol oxidase (PPO) within the latex of Muiratinga and supports previous findings of a key role of oxidation during latex coagulation.
59 BASIC BIOLOGICAL SCIENCES↗
Fully Implict Magneto-hydrodynamics Simulations of Coaxial Plasma Accelerators
The resistive Magneto-Hydrodynamic (MHD) model describes the behavior of a strongly ionized plasma in the presence of external electric and magnetic fields. We developed a fully implicit MHD simulation tool to solve the resistive MHD governing equations in the context of a cell-centered finite-volume scheme. The primary objective of this study is to use the fully-implicit algorithm to obtain insights into the plasma acceleration and jet formation processes in Coaxial Plasma accelerators; electromagnetic acceleration devices that utilize self-induced magnetic fields to accelerate thermal plasmas to large velocities. We also carry out plasma-surface simulations in order to study the impact interactions when these high velocity plasma jets impinge on target material surfaces. Scaling studies are carried out to establish some basic functional relationships between the target-stagnation conditions and the current discharged between the coaxial electrodes.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
The lethal cargo of Myxococcus xanthus outer membrane vesicles
Myxococcus xanthus is a bacterial micro-predator known for hunting other microbes in a wolf pack-like manner. Outer membrane vesicles (OMVs) are produced in large quantities by M. xanthus and have a highly organized structure in the extracellular milieu, sometimes occurring in chains that link neighboring cells within a biofilm. OMVs may be a vehicle for mediating wolf pack activity by delivering hydrolytic enzymes and antibiotics aimed at killing prey microbes. Here, both the protein and small molecule cargo of the OMV and membrane fractions of M. xanthus were characterized and compared. Our analysis indicates a number of proteins that are OMV-specific or OMV-enriched, including several with putative hydrolytic function. Secondary metabolite profiling of OMVs identifies 16 molecules, many associated with antibiotic activities. Several hydrolytic enzyme homologs were identified, including the protein encoded by MXAN_3564 (mepA), an M36 protease homolog. Genetic disruption of mepA leads to a significant reduction in extracellular protease activity suggesting MepA is part of the long-predicted (yet to date undetermined) extracellular protease suite of M. xanthus.
59 BASIC BIOLOGICAL SCIENCES↗
Drought Drives Spatial Variation in the Millet Root Microbiome
Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize rootassociated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA ampliconbased sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.
59 BASIC BIOLOGICAL SCIENCES↗
Microscopic Derivation of Transition-state Theory for Complex Quantum Systems
The decay of quantum complex systems through a potential barrier is often described with transition-state theory, also known as RRKM theory in chemistry. Here we derive the basic formula for transition-state theory based on a generic Hamiltonian as might be constructed in a configuration-interaction basis. Two reservoirs of random Hamiltonians from Gaussian orthogonal ensembles are coupled to intermediate states representing the transition states at a barrier. Under the condition that the decay of the reservoirs to open channels is large, an analytic formula for reaction rates is derived. Here, the transition states act as independent Breit–Wigner resonances which contribute additively to the total transition probability, as is well known for electronic conductance through resonant tunneling states. It is also found that the transition probability is independent of the decay properties of the states in the second reservoir over a wide range of decay widths.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
A method for analyzing dynamic stall of helicopter rotor blades
A model for each of the basic flow elements involved in the unsteady stall of a two-dimensional airfoil in incompressible flow is presented. The interaction of these elements is analyzed using a digital computer. Computations of the loading during transient and sinusoidal pitching motions are in good qualitative agreement with measured loads. The method was used to confirm that large torsional response of helicopter blades detected in flight tests can be attributed to dynamic stall.
Crimi, P.↗
Pioneer Venus mission plan for atmospheric probes and an orbiter.
The mission concept is described for a spin-stabilized spacecraft being designed to deliver an array of aerodynamic probes over the surface of Venus, and, on a second flight mission, to inject the spacecraft into a Venusian orbit. Large and Small Probes and the instrumented 'Bus' structure will enter the Venusian atmosphere and directly measure its characteristics. An orbiting configuration of the same basic Bus spacecraft will serve as a platform from which to examine the planetary environment, the outer atmosphere and its interaction with the solar wind, as well as surface topography. The orbital mission will extend over a complete revolution of the planet around the sun and around its own axis. Requirements for cost effectiveness and firm adherence within early cost projections are emphatic program guidelines which affect every major element of the mission plan and conceptual design.
Dyer, J. W.↗
Exploitation of Seasat-A oceanographic measurements for Navy R and D applications
Basic research, exploratory development and operational demonstration potentials for exploitation of SEASAT-A data are discussed. Some of the interactions and tradeoffs in sensor design and measurement technology, and advanced development of environmental analysis and prediction products for operational fleet support are outlined.
Noble, V.↗