Transfer Events Research Articles

Spatio-temporal fluctuations of interscale and interspace energy transfer dynamics in homogeneous turbulence

We study fluctuations of all co-existing energy exchange/transfer/transport processes in stationary periodic turbulence including those that average to zero and are not present in average cascade theories. We use a Helmholtz decomposition of accelerations that leads to a decomposition of all terms in the Kármán–Howarth–Monin–Hill (KHMH) equation (scale-by-scale two-point energy balance) causing it to break into two energy balances, one resulting from the integrated two-point vorticity equation and the other from the integrated two-point pressure equation. The various two-point acceleration terms in the Navier–Stokes difference (NSD) equation for the dynamics of two-point velocity differences have similar alignment tendencies with the two-point velocity difference, implying similar characteristics for the NSD and KHMH equations. We introduce the two-point sweeping concept and show how it articulates with the fluctuating interscale energy transfer as the solenoidal part of the interscale transfer rate does not fluctuate with turbulence dissipation at any scale above the Taylor length but with the sum of the time derivative and the solenoidal interspace transport rate terms. The pressure fluctuations play an important role in the interscale and interspace turbulence transfer/transport dynamics as the irrotational part of the interscale transfer rate is equal to the irrotational part of the interspace transfer rate and is balanced by two-point fluctuating pressure work. We also study the homogeneous/inhomogeneous decomposition of interscale transfer. The statistics of the latter are skewed towards forward cascade events whereas the statistics of the former are not. We also report statistics conditioned on intense forward/backward interscale transfer events.

Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species

Rice is a vital staple food crop worldwide, providing nutrition and sustenance to a significant portion of the global population. The genetic diversity of cultivated rice species has been significantly reduced during domestication, resulting in the loss of favorable alleles. To overcome this limitation, wild rice species have been used in introgression breeding programs to introduce beneficial alleles. In this study, we performed syntenic and phylogenetic analyses for 10 Oryza species, comprising both cultivar and wild species. Pairwise syntenic analysis revealed 3885 synteny blocks containing 1,023,342 gene pairs among 10 species. O. nivara contained the most blocks that were syntenous with the other nine species. In total, 425 paralogous and orthologous genes were identified for 30 key genes involved in rice breeding. His1 (43), GS3 (28), and qSW5/GW5 (27) had the most paralogous and orthologous genes. For GS3 and qSW5/GW5, two gene transfer events were detected. These findings have implications for rice breeding strategies, particularly with respect to gene pyramiding and introgression breeding programs. This research will contribute to the development of elite cultivars with improved quality and yield to meet the growing global demand for high-quality rice.

Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.

The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.

The role of stellar expansion on the formation of gravitational wave sources

ABSTRACT Massive stars are the progenitors of black holes and neutron stars, the mergers of which can be detected with gravitational waves (GW). The expansion of massive stars is one of the key factors affecting their evolution in close binary systems, but it remains subject to large uncertainties in stellar astrophysics. For population studies and predictions of GW sources, the stellar expansion is often simulated with the analytic formulae from Hurley et al. (2000). These formulae need to be extrapolated and are often considered outdated. In this work, we present five different prescriptions developed from 1D stellar models to constrain the maximum expansion of massive stars. We adopt these prescriptions to investigate how stellar expansion affects mass transfer interactions and in turn the formation of GW sources. We show that limiting radial expansion with updated 1D stellar models, when compared to the use of Hurley et al. (2000) radial expansion formulae, does not significantly affect GW source properties (rates and masses). This is because most mass transfer events leading to GW sources are initialized in our models before the donor star reaches its maximum expansion. The only significant difference was found for the mass distribution of massive binary black hole mergers (Mtot > 50 M⊙) formed from stars that may evolve beyond the Humphreys–Davidson limit, whose radial expansion is the most uncertain. We conclude that understanding the expansion of massive stars and the origin of the Humphrey–Davidson limit is a key factor for the study of GW sources.

The frequency of referential patterns guides pronoun comprehension.

There is extensive evidence that people are sensitive to the statistical patterns of linguistic elements at the phonological, lexical, and syntactic levels. However, much less is known about how people classify referential events and whether they adapt to the most frequent types of references. Reference is particularly complex because referential tokens can be multiply categorized, raising questions about what can be learned through referential exposure. We test the role of linguistic exposure to referential patterns in five experiments on pronoun comprehension, examining linguistic contexts like "X is doing something with Y" (Experiments 1a, b, and c) and transfer events like "X gave something to Y" (Experiments 2a and b). We ask whether the interpretation of ambiguous he or she pronouns is influenced by recent exposure and find that indeed it is, supporting the hypothesis that adaptation affects discourse processing. In Experiment 1, we further ask whether adaptation persists across three types of referring expressions (he or she pronouns, I/you pronouns, and names) and find that it is limited to he or she pronouns. In Experiment 2, we test whether people can learn both syntactically conditioned and semantically conditioned frequency patterns with transfer verbs. Results showed that they learned both patterns. These results provide critical new evidence that discourse processing biases are informed by exposure to referential patterns. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Rapid Light Response of a Novel Bi‐Based Metal–Organic Framework for Bacterial Wound Infections Treatment

AbstractBismuth metal–organic frameworks (MOFs) as catalysts are scarce. Herein, the first MOF comprising meso‐ tetra(4‐carboxyphenyl) porphine (TCPP) as an organic ligand and Bi ion as a metal node, denoted as Bi‐TCPP, is synthesized by a convenient one‐step hydrothermal method. Compared to other 2D (Cu‐TCPP) or 3D (PCN‐222) MOFs with TCPP as a ligand, Bi‐TCPP has ultrafast singlet oxygen generation ability and a high photothermal conversion efficiency of 49.5% under the irradiation of 660 nm light. This is due to Bi‐TCPP's strong ligand‐to‐metal charge transfer (LMCT) events that form singlet oxygen (1O2). Further, when the electrons and holes above the bandgap relax to the band edge, the excess energy is converted into heat. In vitro and in vivo experiments show excellent antibacterial and repair effects. Hence, the synthesis of Bi‐TCPP provides new ideas for the study of rare bismuth‐based MOFs, and its excellent biocompatibility provides a possibility for further application.

Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?

The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.

The complexity of the day-side X-line during southward interplanetary magnetic field

High-resolution global magnetohydrodynamics (MHD) simulations include both meso- and global-scale processes occurring at the magnetopause, which interact to determine the time-dependent orientation of the day-side x-line (DXL). This study demonstrates that the global orientation of the DXL in GAMERA global MHD simulations varies on a time scale of minutes during steady southward interplanetary magnetic field conditions. This behavior manifests in observational data when reconnection outflows indicate that the direction to the x-line is opposite to the prediction from a steady-state model of the reconnection location. Because steady-state models of the DXL do not capture dynamics that are independent of solar wind variations, particularly surface waves and flux transfer events, they represent a time-averaged state of the system.

The Mechanism of the Photodimerization of [60]Fullerene Derivatives: It is Still a Charge Separation Followed by a Back Transfer!

AbstractHerein, we present a systematic study of the photochemical behavior of a set of fullerene compounds bearing various organic addends attached to the fullerene cage. It has been shown that the yield of photodimerization products strongly depends on the structure and electronic properties of the material, primarily the electron affinity (acceptor strength) of the modified fullerene core. This finding being inconsistent with the conventional [2+2]cycloaddition mechanism and pointed to an alternative pathway. This proposed pathway involves photoinduced charge separation followed by back charge transfer events leading to the efficient generation of triplet excitons, which are responsible for the formation of dimerized species. The light‐induced charge separation pathway was confirmed by electron spin resonance spectroscopy and was supported by theoretical calculations. The revealed mechanism allows one to control the photochemical behavior of the fullerene derivatives via rational structural engineering: some of the compounds were shown to be fully resistant to photodimerization, which makes them promising candidates in the development of stable organic photovoltaics. Furthermore, this approach could be used to suppress back charge transfer in donor‐acceptor blends and hinder the formation of triplet excitons which represents one a major energy loss channel in the current generation of organic solar cells.

Intermolecular electron transfer in radical SAM enzymes as a new paradigm for reductive activation

Radical S-adenosyl-L-methionine (rSAM) enzymes bind one or more Fe-S clusters and catalyze transformations that produce complex and structurally diverse natural products. One of the clusters, a 4Fe-4S cluster, binds and reductively cleaves SAM to generate the 5'-deoxyadenosyl radical, which initiates the catalytic cycle by H-atom transfer from the substrate. The role(s) of the additional auxiliary Fe-S clusters (ACs) remains largely enigmatic. The rSAM enzyme PapB catalyzes the formation of thioether cross-links between the β-carbon of an Asp and a Cys thiolate found in the PapA peptide. One of the twoACs in the protein binds to the substrate thiol where, upon formation of a thioether bond, one reducing equivalent is returned to the protein. However, for the next catalytic cycle to occur, the protein must undergo an electronic state isomerization, returning the electron to the SAM-binding cluster. Using a series of iron-sulfur cluster deletion mutants, our data support a model whereby the isomerization is an obligatorily intermolecular electron transfer event that can be mediated by redox active proteins or small molecules, likely via the second AC in PapB. Surprisingly, a mixture of FMN and NADPH is sufficient to support both the reductive and the isomerization steps. These findings lead to a new paradigm involving intermolecular electron transfer steps in the activation of rSAM enzymes that require multiple iron-sulfur clusters for turnover. The implications of these results for the biological activation of rSAM enzymes are discussed.

Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae).

Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.

Intramolecular proton transfer reaction dynamics using machine-learned ab initio potential energy surfaces

Hydrogen bonding interactions, which are central to various physicochemical processes, are investigated in the present study using ab initio-based machine learning potential energy surfaces. Abnormally strong intramolecular O–H⋯O hydrogen bonds, occurring in β-diketone enols of malonaldehyde and its derivatives, with substituents ranging from various electron-withdrawing to electron-donating functional groups, are studied. Machine learning force fields were constructed using a kernel-based force learning model employing ab initio molecular dynamics reference data. These models were used for molecular dynamics simulations at finite temperature, and dynamical properties were determined by computing proton transfer free-energy surfaces. The chemical systems studied here show progression toward barrier-less proton transfer events at an accuracy of correlated electronic structure methods. Markov state models of the conformational states indicate shorter intramolecular hydrogen bonds exhibiting higher proton transfer rates. We demonstrate how functional group substitution can modulate the strength of intramolecular hydrogen bonds by studying the thermodynamic and kinetic properties.

The Spatial-Temporal Effects of Bacterial Growth Substrates on Antibiotic Resistance Gene Spread in the Biofilm.

Biofilm is considered as the hotspot of antibiotic resistance gene (ARG) dissemination. Bacterial growth substrates are important factors for biofilm formation, but its spatial-temporal effects on ARG spread in biofilm is still unclear. In this study, microfluidics combined with microscopic observation were used to reveal spatial-temporal effects of bacterial growth substrates on ARG transfer at real time. The initial horizontal gene transfer events were found to be independent of substrate levels. However, subsequent transfer processes varied greatly depending on the availability of growth substrates. The proportion of transconjugants was much higher (~12%) when observed in substrate-rich regions (under the channel) at 24 h, followed by an exponential decline, with the distance far from the channel. Furthermore, three-dimensional observation revealed that vertical gene transfer influenced by the concentrations of bacterial growth substrates was important for ARG spread in biofilm. The transfer frequency was 8.2 times higher in the high substrate concentration (50×) compared to low concentration (0.5×) in simulated sewage, underscoring the substantial impact of bacterial growth substrate variability on ARG dissemination. This study is helpful for in-depth understanding of ARG dissemination through biofilms and indicates that reducing pollutant emission is important for ARG control in the environment.

The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)

Abstract The transfer of DNA among distantly related organisms is relatively common in bacteria but less prevalent in eukaryotes. Among fungi and plants, few of these events have been reported. Two segments of fungal mitochondrial DNA have been recently discovered in the mitogenome of orchids. Here, we build on that work to understand the timing of those transfer events, which orchids retain the fungal DNA and the fate of the foreign DNA during orchid evolution. We update the content of the large DNA fragment and establish that it was transferred to the most recent common ancestor of a highly diverse clade of epidendroid orchids that lived ~28–43 Mya. Also, we present hypotheses of the origin of the small transferred fragment. Our findings deepen the knowledge of these interesting DNA transfers among organelles and we formulate a probable mechanism for these horizontal gene transfer events.

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.

ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria-where there is less certainty about the root position-ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.

Gravitational wave spectral synthesis

ABSTRACT We study the Laser Interferometer Space Antenna (LISA) sources that arise from isolated binary evolution, and how these depend on age and metallicity, using model stellar populations from bpass. We model these as single-aged populations which are analogous to star clusters. We calculate the combined gravitational wave (GW) spectrum of all the binaries within these model clusters, including all types of compact binaries as well as those with living stars. These results allow us to evaluate the detectability of star clusters with LISA. We find at late times the dominant sources are WD–WD binaries by factors of 50–200, but at times between 108 and 109 yr we find a significant population of NS–WD and BH–WD binaries (2–40 per 106 M⊙), which is related to the treatment of mass transfer and common-envelope events in bpass, wherein mass transfer is relatively likely to be stable. Metallicity also has an effect on the GW spectrum and on the relative dominance of different types of binaries. Using the information about known star clusters will aid the identification of sky locations where one could expect LISA to find GW sources.

Factors contributing to mitogenome size variation and a recurrent intracellular DNA transfer in Melastoma

BackgroundMitogenome sizes of seed plants vary substantially even among closely related species, which are often related to horizontal or intracellular DNA transfer (HDT or IDT) events. However, the mechanisms of this size variation have not been well characterized.ResultsHere we assembled and characterized the mitogenomes of three species of Melastoma, a tropical shrub genus experiencing rapid speciation. The mitogenomes of M. candidum (Mc), M. sanguineum (Ms) and M. dodecandrum (Md) were assembled to a circular mapping chromosome of 391,595 bp, 395,542 bp and 412,026 bp, respectively. While the mitogenomes of Mc and Ms showed good collinearity except for a large inversion of ~ 150 kb, there were many rearrangements in the mitogenomes between Md and either Mc or Ms. Most non-alignable sequences (> 80%) between Mc and Ms are from gain or loss of mitochondrial sequences. Whereas, between Md and either Mc or Ms, non-alignable sequences in Md are mainly chloroplast derived sequences (> 30%) and from putative horizontal DNA transfers (> 30%), and those in both Mc and Ms are from gain or loss of mitochondrial sequences (> 80%). We also identified a recurrent IDT event in another congeneric species, M. penicillatum, which has not been fixed as it is only found in one of the three examined populations.ConclusionsBy characterizing mitochondrial genome sequences of Melastoma, our study not only helps understand mitogenome size evolution in closely related species, but also cautions different evolutionary histories of mitochondrial regions due to potential recurrent IDT events in some populations or species.

Jets and Mirror Mode Waves in Earth's Magnetosheath.

Magnetosheath jets are localized plasma structures with high dynamic pressure which are frequently observed downstream of the Earth's bow shock. In this work we analyze Magnetospheric MultiScale magnetic field and plasma data and show that jets can be found in the quasi-perpendicular magnetosheath in regions permeated by Mirror mode waves (MMWs). We show that structures identified as jets by their enhanced dynamic pressure can have very different internal structure, with variable signatures in magnetic field magnitude and components, velocity, and density and can be associated to ion distribution functions of various types. This suggests that jets observed in the quasi-perpendicular magnetosheath are generated by different mechanisms. We find that jets can be related to traveling foreshocks, flux transfer events, and some have MMWs inside them. Our results suggest that some jets have a local source and their formation does not depend on upstream structures. We find that different types of ion distributions can exist inside the jets, while in some cases anisotropic distributions are present, in others counterstreaming distributions exist. We also show that for jets with MMWs inside them, ion distributions can be modulated. This highlights the importance of using ion distributions to identify and classify different types of jets.

Origin and evolution of the main starch biosynthetic enzymes

Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.

Directly Imaging and Regulating the Nanoscale Inhomogeneity of S‐Vacancies in Molybdenum Disulfide Monolayer during Electrocatalytic Hydrogen Evolution

AbstractThe study of electron transfer event on two‐dimensional (2D) layered transition metal dichalcogenides has attracted tremendous attentions attributing to their promising applications in electrochemical devices. Herein, we demonstrate an opto‐electrochemical strategy to directly map and regulate electron transfer event on molybdenum disulfide (MoS2) monolayer by combining bright field (BF) imaging technique with electrochemical modulation. The heterogeneity of electrochemical activity on MoS2 monolayer down to nanoscale is resolved spatiotemporally. The thermodynamics of MoS2 monolayer is measured during electrocatalytic hydrogen evolution, and the Arrhenius correlations are obtained. We validate that the defect generation engineered by oxygen plasma bombardment dramatically enhances the local electrochemical activity of MoS2 monolayer, which can be attributed to point defects of S‐vacancies as evidenced. Furthermore, by comparing the difference of electron transfer event on MoS2 with various layers, the interlayer coupling effect is uncovered. This study represents a facile method to image the heterogeneity of electrochemical properties for nanomaterials with atomic thickness and regulate the local activity within the plane by extrinsic factors. It also has potential applications in the design and evaluation of high‐performance layered electrochemical systems down to nanoscale.