Emergence of Memory in Equilibrium versus Nonequilibrium Systems.

Experiments often probe observables that correspond to low-dimensional projections of high-dimensional dynamics. In such situations distinct microscopic configurations become lumped into the same observable state. It is well known that correlations between the observable and the hidden degrees of freedom give rise to memory effects. However, how and under which conditions these correlations emerge remain poorly understood. Here we shed light on two fundamentally different scenarios of the emergence of memory in minimal stationary systems, where observed and hidden degrees of freedom either evolve cooperatively or are coupled by a hidden nonequilibrium current. In the reversible setting the strongest memory manifests when the timescales of hidden and observed dynamics overlap, whereas, strikingly, in the driven setting maximal memory emerges under a clear timescale separation. Our results hint at the possibility of fundamental differences in the way memory emerges in equilibrium versus driven systems that may be utilized as a "diagnostic" of the underlying hidden transport mechanism.

Obtaining a Low and Wide Atomic Layer Deposition Window (150-275 °C) for In2 O3 Films Using an InIII Amidinate and H2 O.

Indium oxide is a major component of many technologically important thin films, most notably the transparent conductor indium tin oxide (ITO). Despite being pyrophoric, homoleptic indium(III) alkyls do not allow atomic layer deposition (ALD) of In2 O3 using water as a co-precursor at substrate temperatures below 200 °C. Several alternative indium sources have been developed, but none allows ALD at lower temperatures except in the presence of oxidants such as O2 or O3 , which are not compatible with some substrates or alloying processes. We have synthesized a new indium precursor, tris(N,N'-diisopropylformamidinato)indium(III), compound 1, which allows ALD of pure, carbon-free In2 O3 films using H2 O as the only co-reactant, on substrates in the temperature range 150-275 °C. In contrast, replacing just the H of the anionic iPrNC(H)NiPr ligand with a methyl group (affording the known tris(N,N'-diisopropylacetamidinato)indium(III), compound 2) results in a considerably higher and narrower ALD window in the analogous reaction with H2 O (225-300 °C). Kinetic studies demonstrate that a higher rate of surface reactions in both parts of the ALD cycle gives rise to this difference in the ALD windows.

Identification of the Ilex macrocarpa anthracnose pathogen and the antifungal potential of the cell-free supernatant of Bacillus velezensis against Colletotrichum fioriniae.

Introduction: Anthracnose is a significant fungal disease that affects tree growth and development, with Colletotrichum spp. exhibiting host non-specificity and targeting various organs, making disease control challenging. Methods: This study aimed to identify the pathogenic species causing anthracnose in Ilex macrocarpa in Nanchong, Sichuan Province, and screen effective fungicides, particularly biological ones. The pathogen was identified as Colletotrichum fioriniae through morphological observation, pathogenicity assays, and molecular biological methods. Three biological and five chemical fungicides were evaluated for their effects on the mycelial growth and spore germination rate of the pathogen. Results: The results indicated that prochloraz was the most effective chemical fungicide, while the cell-free supernatant (CFS) of Bacillus velezensis had the most significant inhibitory effect among the biological fungicides. Transcriptome analysis revealed that the CFS of B. velezensis significantly reduced the expression of genes associated with ribosomes, genetic information processing, membrane lipid metabolism, and sphingolipid biosynthesis in C. fioriniae. Additionally, the glutathione pathway's expression of various genes, including key genes such as GST, GFA, Grx, TRR, and POD, was induced. Furthermore, the expression of 17 MFS transporters and 9 ABC transporters was increased. Autophagy-related ATGs were also affected by the B. velezensis CFS. Discussion: These findings suggest that the B. velezensis CFS may inhibit C. fioriniae through interference with ribosomes, genetic information processing, cell membrane metabolism, and energy metabolism. These results provide potential target genes for the B. velezensis CFS and insights into the antifungal mechanism by which B. velezensis inhibits C. fioriniae.

Comprehensive Analysis of BR Receptor Expression under Hormone Treatment in the Rubber Tree (Hevea brasiliensis Muell. Arg.).

Brassinosteroids (BRs) are important for plant growth and development, with BRI1 and BAK1 kinases playing an important role in BR signal transduction. Latex from rubber trees is crucial for industry, medicine and defense use. Therefore, it is beneficial to characterize and analyze HbBRI1 and HbBAK1 genes to improve the quality of the resources obtained from Hevea brasiliensis (rubber tree). Based on bioinformatics predictions and rubber tree database, five HbBRI1s with four HbBAK1s were identified and named HbBRI1~HbBRL3 and HbBAK1a~HbBAK1d, respectively, which were clustered in two groups. HbBRI1 genes, except for HbBRL3, exclusively contain introns, which is convenient for responding to external factors, whereas HbBAK1b/c/d contain 10 introns and 11 exons, and HbBAK1a contains eight introns. Multiple sequence analysis showed that HbBRI1s include typical domains of the BRI1 kinase, indicating that HbBRI1s belong to BRI1. HbBAK1s that possess LRR and STK_BAK1_like domains illustrate that HbBAK1s belong to the BAK1 kinase. BRI1 and BAK1 play an important role in regulating plant hormone signal transduction. Analysis of the cis-element of all HbBRI1 and HbBAK1 genes identified hormone response, light regulation and abiotic stress elements in the promoters of HbBRI1s and HbBAK1s. The results of tissue expression patterns indicate that HbBRL1/2/3/4 and HbBAK1a/b/c are highly expressed in the flower, especially HbBRL2-1. The expression of HbBRL3 is extremely high in the stem, and the expression of HbBAK1d is extremely high in the root. Expression profiles with different hormones show that HbBRI1 and HbBAK1 genes are extremely induced by different hormone stimulates. These results provide theoretical foundations for further research on the functions of BR receptors, especially in response to hormone signals in the rubber tree.

Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution.

Growing RNAs fold differently as they are transcribed, which modulates their finally adopted structures. Riboswitches regulate gene expression by structural change, which are sensitive to co-transcriptionally structural biology. Here we develop a strategy to track the structural change of RNAs during transcription at single-nucleotide and single-molecule resolution and use it to monitor individual transcripts of the SAM-VI riboswitch (riboSAM) as transcription proceeds, observing co-existence of five states in riboSAM. We report a bifurcated helix in one newly identified state from NMR and single-molecule FRET (smFRET) results, and its presence directs the translation inhibition in our cellular translation experiments. A model is proposed to illustrate the distinct switch patterns and gene-regulatory outcome of riboSAM when SAM is present or absent. Our strategy enables the precise mapping of RNAs' conformational landscape during transcription, and may combine with detection methods other than smFRET for structural studies of RNAs in general.

Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.).

Brassinolide (BR) plays an important role in plant growth, development, and the adaptation adversity process. Moreover, BRI1-EMS-SUPPRESSOR 1 (BES1) genes are crucial transcription factors (TFs) in the BR signaling pathway. To realize the function of HbBES1 family is helpful to improve genetic resources for rubber tree breeding. Based on the rubber tree database, we used bioinformatics to characterize physicochemical properties, gene structure, cis-elements, and expression patterns. These results indicated that there were nine BES1 members in rubber tree, which we named HbBES1-1 to HbBES1-9 and divided into two groups (I and II) based on their genetic relationships. HbBES1 genes in the same group shared similar gene structures and motifs. Cis-acting element analysis showed that the promoter sequences of HbBES1 genes contained many regulator elements that were related to hormone and stress, indicating that HbBES1 genes might be involved in the regulation of hormone and stress signal pathways. Our analysis of tissue specificity revealed that all of the nine HbBES1 members expressed highly in branches. Gene expression profiles under different hormone treatments showed that the HbBES1 gene family was induced to varying degrees under different hormones, HbBES1-3 and HbBES1-9 were extremely induced by ethylene (ETH). These results lay the foundation for further exploration of the molecular mechanism of the BES1 gene family, especially HbBES1-3 and HbBES1-9, regulating plant stress tolerance in rubber tree.

Identification of cis conformation natural rubber and proteins in Ficus altissima Blume latex.

Ficus altissima Blume, a horticultural plant in tropical and warm subtropical regions, can produce natural rubber with comparable molecular weight to the Hevea brasiliensis rubber. The F. altissima latex has an acidic pH (about 4.89). The rubber particle size distribution is a unimodal profile, and the peak frequency is at a size of 4.5 µm. The natural rubber of F. altissima was determined to be a cis conformation via 13C NMR. The Mp (molecular weight of the peak maxima) of the deproteinized F. altissima rubber was 9.34 × 105 Da. LC-MS was used to identify the proteins of rubber particles and serum. The most abundant protein of the creamy rubber particle layer is an acid phosphatase, while the most abundant proteins of serum were an (R)-mandelonitrilelyase and a polygalacturonase inhibitor. Pharmaceutical proteins (ficins) or enzymes related to the biosynthesis of natural medicines (a cannabidiolic acid synthase and two lupeol synthase) were identified in F. altissima latex. The data of this study may be helpful for research on the functions of latex in latex-borne plants and the biosynthesis mechanism of natural rubber.

Atomic Layer Deposition of Tin Monosulfide Using Vapor from Liquid Bis(N,N'-diisopropylformamidinato)tin(II) and H2S.

The oxide and sulfide of divalent tin show considerable promise for sustainable thin-film optoelectronics, as transparent conducting and light absorbing p-type layers, respectively. Chemical vapor deposition (CVD) and atomic layer deposition (ALD) provide attractive routes to these layers. The literature on volatile tin(II) compounds used as CVD or ALD precursors shows that new compounds can provide different growth rates, film morphologies, preferred crystallographic orientations, and other material properties. We report here the synthesis and characterization of a new liquid tin(II) precursor, bis(N,N'-diisopropylformamidinato)tin(II) (1), which is effective in ALD of SnS in combination with H2S between 65 and 180 °C. Like other highly reactive tin(II) precursors, the growth per cycle linearly decreases from 0.82 Å/cycle at 65 °C to 0.4 Å/cycle at 180 °C. This is obviously different from the case of previously reported SnS ALD using bis(2,4-pentanedionato)tin(II), Sn(acac)2, and H2S; films grow at 0.22-0.24 Å/cycle almost independent of the substrate temperature (125-225 °C, J. Phys. Chem. C 2010, 114, 17597). Quartz crystal microbalance (QCM) experiments for SnS ALD using 1 at 80, 120, and 160 °C were carried out to study the linear decrease of the growth per cycle with increasing substrate temperature. On the basis of these QCM studies, although the mechanism of chemisorption-loss of one ligand or two-can be manipulated by changing the exposure of 1, the purging time, or the temperature, only the temperature changes the growth per cycle. We therefore attribute the decreasing growth per cycle with increasing temperature to a decreasing surface thiol density. Photovoltaic devices prepared from 1-derived SnS have a performance similar to those of the best devices prepared from other precursors, and the device yield and replicability of J-V properties are substantially increased by using 1.