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Noether currents for Eulerian variational principles in non-barotropic magnetohydrodynamics and topological conservations laws
We derive a Noether current for the Eulerian variational principle of ideal non-barotropic magnetohydrodynamics (MHD). It was shown previously that ideal non-barotropic MHD is mathematically equivalent to a five function field theory with an induced geometrical structure in the case that field lines cover surfaces and this theory can be described using a variational principle. Here we use various symmetries of the flow to derive topological constants of motion through the derived Noether current and discuss their implication for non-barotropic MHD.
A moment-conserving discontinuous Galerkin representation of the relativistic Maxwellian distribution
Kinetic simulations of relativistic gases and plasmas are critical for understanding diverse astrophysical and terrestrial systems, but the accurate construction of the relativistic Maxwellian, the Maxwell–Jüttner distribution, on a discrete simulation grid is challenging. Difficulties arise from the finite velocity bounds of the domain, which may not capture the entire distribution function, as well as errors introduced by projecting the function onto a discrete grid. Here, we present a novel scheme for iteratively correcting the moments of the projected distribution applicable to all grid-based discretizations of the relativistic kinetic equation. In addition, we describe how to compute the needed nonlinear quantities, such as Lorentz boost factors, in a discontinuous Galerkin scheme through a combination of numerical quadrature and weak operations. The resulting method accurately captures the distribution function and ensures that the moments match the desired values to machine precision.
Conservation and Diversity in the Primary Reverse Photodynamics of the Canonical Red/Green Cyanobacteriochrome Family
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Ndr/Lats Kinases Bind Specific Mob-Family Coactivators through a Conserved and Modular Interface
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Catalytic Reactions and Energy Conservation in the Cytochrome bc 1 and b 6 f Complexes of Energy-Transducing Membranes
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Correction to Norm-conserving pseudopotentials and basis sets to explore Lanthanide chemistry in complex environments
Correction was made to the funding and acknowledgment: Funding V.-A.G. was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. R.R. and M.-T.N. were supported by the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL) CheMSR Agile Investment. PNNL is operated by DE-AC05-76RLO01830. J.-B.L. and J.L. were supported by the National Natural Science Foundation of China (Nos. 21433005, 91645203, and 21590792). D.C.C. was supported by Research and Innovation at the University of Nevada, Reno. ACKNOWLEDGMENTS The research was performed using resources available through Research Computing at Pacific Northwest National Laboratory (PNNL), Tsinghua National Laboratory for Information Science and Technology and the Computational Chemistry Laboratory under Tsinghua Xuetang Talents Program, and University of Nevada, Reno High Performance Computing. J.- B.L. and J.L. acknowledge discussions with Dr. Yang-Gang Wang (Southern University of Science and Technology).
Investigation of Indigoidine Synthetase Reveals a Conserved Active-Site Base Residue of Nonribosomal Peptide Synthetase Oxidases
Nonribosomal peptide synthetase (NRPS) oxidase (Ox) domains oxidize protein-bound intermediates to install crucial structural motifs in bioactive natural products. The mechanism of this domain remains elusive. Here, by studying indigoidine synthetase, a single-module NRPS involved in the biosynthesis of indigoidine and several other bacterial secondary metabolites, we demonstrate that its Ox domain utilizes an active-site base residue, tyrosine 665, to deprotonate a protein-bound l-glutaminyl residue. In this work, we further validate the generality of this active-site residue among NRPS Ox domains. These findings not only resolve the biosynthetic pathway mediated by indigoidine synthetase but enable mechanistic insight into NRPS Ox domains.
Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
A human monoclonal antibody blocks malaria transmission and defines a highly conserved neutralizing
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Conserved features of TERT promoter duplications reveal an activation mechanism that mimics hotspot mutations in cancer
Mutations in the TERT promoter represent the genetic underpinnings of tumor cell immortality. Beyond the two most common point mutations, which selectively recruit the ETS factor GABP to activate TERT, the significance of other variants is unknown. In seven cancer types, we identify duplications of wildtype sequence within the core promoter region of TERT that have strikingly similar features including an ETS motif, the duplication length and insertion site. The duplications recruit a GABP tetramer by virtue of the native ETS motif and its precisely spaced duplicated counterpart, activate the promoter and are clonal in a TERT expressing multifocal glioblastoma. We conclude that recurrent TERT promoter duplications are functionally and mechanistically equivalent to the hotspot mutations that confer tumor cell immortality. The shared mechanism of these divergent somatic genetic alterations suggests a strong selective pressure for recruitment of the GABP tetramer to activate TERT.
Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain
ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster . Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.
Structural insights into strigolactone catabolism by carboxylesterases reveal a conserved conformational regulation
Phytohormone levels are regulated through specialized enzymes, participating not only in their biosynthesis but also in post-signaling processes for signal inactivation and cue depletion. Arabidopsis thaliana (At) carboxylesterase 15 (CXE15) and carboxylesterase 20 (CXE20) have been shown to deplete strigolactones (SLs) that coordinate various growth and developmental processes and function as signaling molecules in the rhizosphere. Here, we elucidate the X-ray crystal structures of AtCXE15 (both apo and SL intermediate bound) and AtCXE20, revealing insights into the mechanisms of SL binding and catabolism. The N-terminal regions of CXE15 and CXE20 exhibit distinct secondary structures, with CXE15 characterized by an alpha helix and CXE20 by an alpha/beta fold. These structural differences play pivotal roles in regulating variable SL hydrolysis rates. Our findings, both in vitro and in planta, indicate that a transition of the N-terminal helix domain of CXE15 between open and closed forms facilitates robust SL hydrolysis. The results not only illuminate the distinctive process of phytohormone breakdown but also uncover a molecular architecture and mode of plasticity within a specific class of carboxylesterases.
Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota
Few aerobic hyperthermophilic microorganisms degrade polysaccharides. Here, we describe the genome-enabled enrichment and optical tweezer-based isolation of an aerobic polysaccharide-degrading hyperthermophile, Fervidibacter sacchari, previously ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides for growth at 65–87.5°C and expresses 191 carbohydrate-active enzymes (CAZymes) according to RNA-Seq and proteomics, including 31 with unusual glycoside hydrolase domains (GH109, GH177, GH179). Fluorescence in-situ hybridization and nanoscale secondary ion mass spectrometry confirmed rapid assimilation of 13 C-starch in spring sediments. Purified GHs were optimally active at 80–100°C on ten different polysaccharides. Finally, we propose reassigning Fervidibacteria as a class within phylum Armatimonadota, along with 18 other species, and show that a high number and diversity of CAZymes is a hallmark of the phylum, in both aerobic and anaerobic lineages. Our study establishes Fervidibacteria as hyperthermophilic polysaccharide degraders in terrestrial geothermal springs and suggests a broad role for Armatimonadota in polysaccharide catabolism.
Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity
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Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes
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