The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid-dependent stress responses in Arabidopsis.

N 6-methyladenosine (m6A) is a common epitranscriptional mRNA modification in eukaryotes. Thirteen putative m6A readers, mostly annotated as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins, have been identified in Arabidopsis (Arabidopsis thaliana), but few have been characterized. Here, we show that the Arabidopsis m6A reader ECT1 modulates salicylic acid (SA)-mediated plant stress responses. ECT1 undergoes liquid-liquid phase separation in vitro, and its N-terminal prion-like domain is critical for forming in vivo cytosolic biomolecular condensates in response to SA or bacterial pathogens. Fluorescence-activated particle sorting coupled with quantitative PCR analyses unveiled that ECT1 sequesters SA-induced m6A modification-prone mRNAs through its conserved aromatic cage to facilitate their decay in cytosolic condensates, thereby dampening SA-mediated stress responses. Consistent with this finding, ECT1 overexpression promotes bacterial multiplication in plants. Collectively, our findings unequivocally link ECT1-associated cytosolic condensates to SA-dependent plant stress responses, advancing the current understanding of m6A readers and the SA signaling network.

Cooperative role of AtRsmD and AtRimM proteins in modification and maturation of 16S rRNA in plastids.

Chloroplast pre-ribosomal RNA (rRNA) undergoes maturation, which is critical for ribosome assembly. While the central and auxiliary factors in rRNA maturation have been elucidated in bacteria, their mode of action remains largely unexplored in chloroplasts. We now reveal chloroplast-specific factors involved in 16S rRNA maturation, Arabidopsis thaliana orthologs of bacterial RsmD methyltransferase (AtRsmD) and ribosome maturation factor RimM (AtRimM). A forward genetic screen aimed to find suppressors of the Arabidopsis yellow variegated 2 (var2) mutant defective in photosystem II quality control found a causal nonsense mutation in AtRsmD. The substantially impaired 16S rRNA maturation and translation due to the mutation rescued the leaf variegation phenotype by lowering the levels of chloroplast-encoded proteins, including photosystem II core proteins, in var2. The subsequent co-immunoprecipitation coupled with mass spectrometry analyses and bimolecular fluorescence complementation assay found that AtRsmD interacts with AtRimM. Consistent with their interaction, loss of AtRimM also considerably impairs 16S rRNA maturation with decelerated m2 G915 modification in 16S rRNA catalyzed by AtRsmD. The atrimM mutation also rescued var2 mutant phenotypes, corroborating the functional interplay between AtRsmD and AtRimM towards modification and maturation of 16S rRNA and chloroplast proteostasis. The maturation and post-transcriptional modifications of rRNA are critical to assembling ribosomes responsible for protein translation. Here, we revealed that the cooperative regulation of 16S rRNA m2 G915 modifications by AtRsmD methyltransferase and ribosome assembly factor AtRimM contributes to 16S rRNA maturation, ribosome assembly, and proteostasis in chloroplasts.

Anisotropic Charge Migration on Perovskite Oxysulfide for Boosting Photocatalytic Overall Water Splitting.

The synthesis of photocatalysts with both broad light absorption and efficient charge separation is significant for a high solar energy conversion, which still remains to be a challenge. Herein, a narrow-bandgap Y2Ti2O5S2 (YTOS) oxysulfide nanosheet coexposed with defined {101} and {001} facets synthesized by a flux-assisted solid-state reaction was revealed to display the character of an anisotropic charge migration. The selective photodeposition of cocatalysts demonstrated that the {101} and {001} surfaces of YTOS nanosheets were the reduction and oxidation regions during photocatalysis, respectively. Density functional theory (DFT) calculations indicated a band energy level difference between the {101} and {001} facets of YTOS, which contributes to the anisotropic charge migration between them. The exposed Ti atoms on the {101} surface and S atoms on the {001} surface were identified, respectively, as reducing and oxidizing centers of YTOS nanosheets. This anisotropic charge migration generated a built-in electric field between these two facets, quantified by spatially resolved surface photovoltage microscopy, the intensity of which was found to be highly correlated with photocatalytic H2 production activity of YTOS, especially exhibiting a high apparent quantum yield of 18.2% (420 nm) after on-site modification of a Pt@Au cocatalyst assisted by Na2S-Na2SO3 hole scavengers. In conjunction with an oxygen-production photocatalyst and a [Co(bpy)3]2+/3+ redox shuttle, the YTOS nanosheets achieved a solar-to-hydrogen conversion efficiency of 0.15% via a Z-scheme overall water splitting. Our work is the first to confirm anisotropic charge migration in a perovskite oxysulfide photocatalyst, which is crucial for enhancing charge separation and surface catalytic efficiency in this material.

Hierarchical regulatory module GENOMES UNCOUPLED1-GOLDEN2-LIKE1/2-WRKY18/40 modulates salicylic acid signaling.

Chloroplast-to-nucleus retrograde signaling (RS) pathways are critical in modulating plant development and stress adaptation. Among chloroplast proteins mediating RS pathways, GENOMES UNCOUPLED1 (GUN1) represses the transcription of the nuclear transcription factors GOLDEN2-LIKE1 (GLK1) and GLK2 that positively regulate chloroplast biogenesis. Given the extensive exploration of the function of GUN1 in biogenic RS carried out in previous years, our understanding of its role in plant stress responses remains scarce. Here, we revealed that GUN1 contributes to the expression of salicylic acid (SA)-responsive genes (SARGs) through transcriptional repression of GLK1/2 in Arabidopsis (Arabidopsis thaliana). Loss of GUN1 significantly compromised the SA responsiveness in plants, concomitant with the upregulation of GLK1/2 transcripts. In contrast, knockout of GLK1/2 potentiated the expression of SARGs and led to enhanced stress responses. Chromatin immunoprecipitation, coupled with quantitative PCR and related reverse genetic approaches, unveiled that in gun1, GLK1/2 might modulate SA-triggered stress responses by stimulating the expression of WRKY18 and WRKY40, transcriptional repressors of SARGs. In summary, we demonstrate that a hierarchical regulatory module, consisting of GUN1-GLK1/2-WRKY18/40, modulates SA signaling, opening a research avenue regarding a latent GUN1 function in plant-environment interactions.

Emergence and Causality in Complex Systems: A Survey of Causal Emergence and Related Quantitative Studies.

Emergence and causality are two fundamental concepts for understanding complex systems. They are interconnected. On one hand, emergence refers to the phenomenon where macroscopic properties cannot be solely attributed to the cause of individual properties. On the other hand, causality can exhibit emergence, meaning that new causal laws may arise as we increase the level of abstraction. Causal emergence (CE) theory aims to bridge these two concepts and even employs measures of causality to quantify emergence. This paper provides a comprehensive review of recent advancements in quantitative theories and applications of CE. It focuses on two primary challenges: quantifying CE and identifying it from data. The latter task requires the integration of machine learning and neural network techniques, establishing a significant link between causal emergence and machine learning. We highlight two problem categories: CE with machine learning and CE for machine learning, both of which emphasize the crucial role of effective information (EI) as a measure of causal emergence. The final section of this review explores potential applications and provides insights into future perspectives.

PLANT NATRIURETIC PEPTIDE A and Its Putative Receptor PNP-R2 Antagonize Salicylic Acid-Mediated Signaling and Cell Death.

The plant stress hormone salicylic acid (SA) participates in local and systemic acquired resistance, which eventually leads to whole-plant resistance to bacterial pathogens. However, if SA-mediated signaling is not appropriately controlled, plants incur defense-associated fitness costs such as growth inhibition and cell death. Despite its importance, to date only a few components counteracting the SA-primed stress responses have been identified in Arabidopsis (Arabidopsis thaliana). These include other plant hormones such as jasmonic acid and abscisic acid, and proteins such as LESION SIMULATING DISEASE1, a transcription coregulator. Here, we describe PLANT NATRIURETIC PEPTIDE A (PNP-A), a functional analog to vertebrate atrial natriuretic peptides, that appears to antagonize the SA-mediated plant stress responses. While loss of PNP-A potentiates SA-mediated signaling, exogenous application of synthetic PNP-A or overexpression of PNP-A significantly compromises the SA-primed immune responses. Moreover, we identify a plasma membrane-localized receptor-like protein, PNP-R2, that interacts with PNP-A and is required to initiate the PNP-A-mediated intracellular signaling. In summary, our work identifies a peptide and its putative cognate receptor as counteracting both SA-mediated signaling and SA-primed cell death in Arabidopsis.

Correction: Zhang, J.; Liu, K. Neural Information Squeezer for Causal Emergence. Entropy 2023, 25, 26.

There was an error in the original publication [...].

Generating multiple optical vortices in orange beams induced by selectively pumped frequency-doubled solid-state Raman lasers with mode conversion.

We employ a selectively pumped solid-state laser with stimulated Raman scattering and second-harmonic generation to generate frequency-doubled lasing modes (FDLMs) at 588 nm. The FDLMs are transformed by using an external cylindrical mode converter to generate various structured beams with multiple optical vortices. Theoretical analyses clearly reveal the relationship between the mode components in the laser emission and the transverse displacement of the off-center pumping. We further verify that the experimental results for the transformed FDLMs can be numerically reconstructed with a theoretical model. By analyzing the phase structures of the converted beams, it can be demonstrated that the number of vortices rises from 2 to 19 with increasing off-center displacement.

Facet Engineering on WO3 Mono-Particle-Layer Electrode for Photoelectrochemical Water Splitting.

Photoelectrochemical (PEC) performance of WO3 photoanodes for water splitting is heavily influenced by the orientation of crystal facets. In this work, mono-particle-layer electrodes, assembled by particulate WO3 square plates with highly uniform alignment along the (002) facet, improved PEC water oxidation kinetics and stability. Photo-deposition of Au along the cracks formed on the surface of the plates, which are the edges of {110} facets, was found to further enhance electron collection efficiency. Combination of these two strategies allowed the facet-engineered WO3 electrode to produce significantly higher efficiencies in charge separation and transfer than the electrode prepared without facet orientation. This work has provided a facile route for fabricating a structurally designed WO3 photoelectrode, which is also applicable to other regularly shaped semiconductor photocatalysts with anisotropic charge migration.

Neural Information Squeezer for Causal Emergence.

Conventional studies of causal emergence have revealed that stronger causality can be obtained on the macro-level than the micro-level of the same Markovian dynamical systems if an appropriate coarse-graining strategy has been conducted on the micro-states. However, identifying this emergent causality from data is still a difficult problem that has not been solved because the appropriate coarse-graining strategy can not be found easily. This paper proposes a general machine learning framework called Neural Information Squeezer to automatically extract the effective coarse-graining strategy and the macro-level dynamics, as well as identify causal emergence directly from time series data. By using invertible neural network, we can decompose any coarse-graining strategy into two separate procedures: information conversion and information discarding. In this way, we can not only exactly control the width of the information channel, but also can derive some important properties analytically. We also show how our framework can extract the coarse-graining functions and the dynamics on different levels, as well as identify causal emergence from the data on several exampled systems.

Bayesian and E-Bayesian Estimations of Bathtub-Shaped Distribution under Generalized Type-I Hybrid Censoring.

For the purpose of improving the statistical efficiency of estimators in life-testing experiments, generalized Type-I hybrid censoring has lately been implemented by guaranteeing that experiments only terminate after a certain number of failures appear. With the wide applications of bathtub-shaped distribution in engineering areas and the recently introduced generalized Type-I hybrid censoring scheme, considering that there is no work coalescing this certain type of censoring model with a bathtub-shaped distribution, we consider the parameter inference under generalized Type-I hybrid censoring. First, estimations of the unknown scale parameter and the reliability function are obtained under the Bayesian method based on LINEX and squared error loss functions with a conjugate gamma prior. The comparison of estimations under the E-Bayesian method for different prior distributions and loss functions is analyzed. Additionally, Bayesian and E-Bayesian estimations with two unknown parameters are introduced. Furthermore, to verify the robustness of the estimations above, the Monte Carlo method is introduced for the simulation study. Finally, the application of the discussed inference in practice is illustrated by analyzing a real data set.

Impaired PSII Proteostasis Promotes Retrograde Signaling via Salicylic Acid.

Photodamage of the PSII reaction center (RC) is an inevitable process in an oxygen-rich environment. The damaged PSII RC proteins (Dam-PSII) undergo degradation via the thylakoid membrane-bound FtsH metalloprotease, followed by posttranslational assembly of PSII. While the effect of Dam-PSII on gene regulation is described for cyanobacteria, its role in land plants is largely unknown. In this study, we reveal an intriguing retrograde signaling pathway by using the Arabidopsis (Arabidopsis thaliana) yellow variegated2-9 mutant, which expresses a mutated FtsH2 (FtsH2G267D) metalloprotease, specifically impairing its substrate-unfolding activity. This lesion leads to the perturbation of PSII protein homeostasis (proteostasis) and the accumulation of Dam-PSII. Subsequently, this results in an up-regulation of salicylic acid (SA)-responsive genes, which is abrogated by inactivation of either an SA transporter in the chloroplast envelope membrane or extraplastidic SA signaling components as well as by removal of SA. These results suggest that the stress hormone SA, which is mainly synthesized via the chloroplast isochorismate pathway in response to the impaired PSII proteostasis, mediates the retrograde signaling. These findings reinforce the emerging view of chloroplast function toward plant stress responses and suggest SA as a potential plastid factor mediating retrograde signaling.

Characterizing α-helical peptide aggregation on supported lipid membranes using microcantilevers.

We report the use of lipid membrane-coated microcantilevers to probe the interactions between phospholipid membranes and membrane-active peptides. This sensing method integrates two well-developed techniques: solid-supported lipid bilayers (SLBs) and microcantilever sensors. SLBs are prepared on the silicon dioxide surface of the microcantilevers using a vesicle fusion method. As molecules adsorb onto the surface of the microcantilever, the microcantilever bends due to the induced compressive or tensile stresses, which result from the surface free energy change. Real-time surface stress changes in the SLB due to interactions with small molecules can be detected by monitoring the deflection of the microcantilever. We investigate the mechanism for the interaction between SLBs and PEP1, a synthetic amphipathic peptide resembling a segment of the nonstructural protein (NS5A) of the hepatitis C virus. Initially, the PEP1 peptides adsorb onto the lipid membranes, and then at a critical concentration, the peptides begin to aggregate and form pores; finally, the peptides destabilize and induce solubilization of the supported membranes. The membrane-coated microcantilever sensor is capable of characterizing the kinetics and dynamics of this process with great sensitivity.

A Visible Light-Responsive TiO2 Photocathode Achieved by a Rh Dopant.

Developing an efficient and stable photocathode material for photoelectrochemical solar water splitting remains challenging. Herein, we demonstrate the potential of rutile TiO2 as a photocathode by Rh doping with visible light absorption up to 640 nm and an onset potential of 0.9 V versus the reversible hydrogen electrode. The dopant transforms the rutile host from an n-type semiconductor to a p-type one, as confirmed by the Mott-Schottky curve and kelvin probe force microscopy. Physical and photoelectrochemical analyses further suggest that the doping mechanism is dependent on concentration. Lower levels of dopants generate localized Rh3+, while higher levels favor Rh4+ that interacts more strongly with the O 2p orbitals. The latter is found not only to extend the visible light absorption range but also to facilitate charge transport. This work elucidates the role of the Rh dopant in adjusting the photoelectrochemical behavior of TiO2, and it provides a promising photocathode material for solar energy conversion.

Conformal and conductive biofilm-bridged artificial Z-scheme system for visible light-driven overall water splitting.

Semi-artificial Z-scheme systems offer promising potential toward efficient solar-to-chemical conversion, yet sustainable and stable designs are currently lacking. Here, we developed a sustainable hybrid Z-scheme system capable for visible light-driven overall water splitting by integrating the durability of inorganic photocatalysts with the interfacial adhesion and regenerative property of bacterial biofilms. The Z-scheme configuration is fabricated by drop casting a mixture of photocatalysts onto a glass plate, followed by the growth of biofilms for conformal conductive paste through oxidative polymerization of pyrrole molecules. Notably, the system exhibited scalability indicated by consistent catalytic efficiency across various sheet areas, resistance observed by remarkable maintaining of photocatalytic efficiency across a range of background pressures, and high stability as evidenced by minimal decay of photocatalytic efficiency after 100-hour reaction. Our work thus provides a promising avenue toward sustainable and high-efficiency artificial photosynthesis, contributing to the broader goal of sustainable energy solutions.

De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae.

MOTIVATION: Gene regulation involves complicated mechanisms such as cooperativity between a set of transcription factors (TFs). Previous studies have used target genes shared by two TFs as a clue to infer TF-TF interactions. However, this task remains challenging because the target genes with low binding affinity are frequently omitted by experimental data, especially when a single strict threshold is employed. This article aims at improving the accuracy of inferring TF-TF interactions by incorporating motif discovery as a fundamental step when detecting overlapping targets of TFs based on ChIP-chip data. RESULTS: The proposed method, simTFBS, outperforms three naïve methods that adopt fixed thresholds when inferring TF-TF interactions based on ChIP-chip data. In addition, simTFBS is compared with two advanced methods and demonstrates its advantages in predicting TF-TF interactions. By comparing simTFBS with predictions based on the set of available annotated yeast TF binding motifs, we demonstrate that the good performance of simTFBS is indeed coming from the additional motifs found by the proposed procedures. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Stimuli-responsive color films of poly(4-vinylpyridine)-b-poly(ε-caprolactone) complexed with cyano-capped chromophores.

Here, we develop a method to fabricate stimuli-responsive color films using block copolymer, poly(4-vinylpyridine)-b-poly(ε-caprolactone) (P4VP-PCL), as a template complexed with functionalized chromophores. The P4VP block in the P4VP-PCL can be associated with a cyano end-capped chromophore via charge transfer, which is a noncovalent interaction that can be conveniently manipulated by external stimuli, giving a specific color. The color of the film can be switched by tuning the charge transfer interaction between the chromophore and P4VP with controlled environmental conditions, such as pH, temperature, and moisture, while maintaining high transmittance for visible light due to the formation of the nanostructure of chromophore/P4VP-PCL complex. However, the association/dissociation process between chromophore and P4VP is diffusion-dominated, which may limit the kinetic response time for color change. A way to create quick and reversible color switching can be achieved by a combination of stimuli. The contrasting color change of the responsive chromophore/P4VP-PCL thin films which exhibit RGB primary colors can provide a sensor film that is flexible, fast-responsive, and convenient.

Rhodium-Doped Barium Titanate Perovskite as a Stable p-Type Photocathode in Solar Water Splitting.

Solar water splitting from a p-n-conjugated photoelectrochemical (PEC) system is a promising way to produce hydrogen sustainably. At present, finding a compatible p-type photocathode material for the p-n system remains a great challenge in consideration of the photocurrent and stability. This paper highlighted a promising candidate, Rh/BaTiO3, by switching BaTiO3 from an n-type photoanode to a p-type photocathode upon Rh doping. The dopant activated visible light absorption up to 550 nm and an onset potential as high as 1.0 V (vs RHE). Using surface photovoltage spectroscopy as a powerful characterization tool, the n- to p-type transition of the semiconductor was studied and explained microscopically by which we quantitatively isolated the cathodic contribution caused by the Rh dopant. Unbiased overall solar water splitting was accomplished by serially connecting the Pt/Rh/BaTiO3 photocathode to a CoOx/Mo/BiVO4 photoanode, which produced a solar to hydrogen conversion efficiency of 0.1% and an excellent stability over 100 h of operation at ambient pressure. This work revealed the key role that the Rh dopant played in the n- to p-type adjustment of titanate semiconductors and demonstrated its great potential for application in PEC water splitting.

Proportioning Factors of Alkali-Activated Materials and Interaction Relationship Revealed by Response Surface Modeling.

Alkali-activated fly-ash-slag blending materials (AA-FASMs) are gradually being studied and applied more because of their good performance. There are many factors affecting the alkali-activated system, and the effect of single-factor variation on the performance of AA-FASM has been mostly reported; however, there is a lack of unified understanding of the mechanical properties and microstructure of AA-FASM under curing conditions and multiple-factor interaction. Therefore, this study investigated the compressive strength development and reaction products of alkali-activated AA-FASM under three curing conditions including seal (S), dry (D) and water saturation (W). Based on the response surface model, the relationship between the interaction of slag content (WSG), activator modulus (M) and activator dosage (RA) on its strength was established. The results showed that the maximum compressive strength of AA-FASM after 28 days of sealed curing was about 59 MPa, while the strengths of dry- and water-saturation-cured specimens decreased by 9.8% and 13.7%, respectively. The seal-cured samples also had the smallest mass change rate and linear shrinkage and the most compact pore structure. Due to the adverse effects from a too-high or too-low modulus and dosage of the activators, the shapes of upward convex, slope and inclined convex were under the interaction of WSG/M, WSG/RA and M/RA, respectively. The correlation coefficient R2 > 0.95 and p-value < 0.05 indicated that the proposed model could be used to predict strength development given the complex factors. Optimal proportioning and curing conditions were found to be WSG = 50%, M = 1.4, RA = 50% and sealed curing.

Matrix transformation of lunar regolith and its use as a feedstock for additive manufacturing.

Building a sustainable human habitat on the Moon requires advances in excavation, paving, and additive manufacturing to construct landing pads, surface transportation arteries, resilient shelters, and scientific outposts. Construction of infrastructure elements on the lunar surface necessitates exploration of the interfacial reactivity of locally sourced regolith and the adaptation of Earth-based construction techniques. Various crosslinking frameworks and sintering methods have been proposed as a means of consolidating lunar regolith into load-bearing structures but each have challenges related to incomplete understanding of reaction chemistry, excessive thermal budgets, and lack of universal applicability to different mineral components of regolith. We describe here a versatile experimental and computational study of the consolidation of a regolith simulant through formation of siloxane networks enmeshing mineral particles by surface dissolution-precipitation and polycondensation reactions. Furthermore, by tailoring the rheological properties of the formulation an additive manufacturing feedstock can be developed for the construction of lunar infrastructure.