Genome-wide characterization of the GRF transcription factors in potato (Solanum tuberosum L.) and expression analysis of StGRF genes during potato tuber dormancy and sprouting.

Growth-regulating factors (GRFs) are transcription factors that play a pivotal role in plant growth and development. This study identifies 12 Solanum tuberosum GRF transcription factors (StGRFs) and analyzes their physicochemical properties, phylogenetic relationships, gene structures and gene expression patterns using bioinformatics. The StGRFs exhibit a length range of 266 to 599 amino acids, with a molecular weight of 26.02 to 64.52 kDa. The majority of StGRFs possess three introns. The promoter regions contain a plethora of cis-acting elements related to plant growth and development, as well as environmental stress and hormone response. All the members of the StGRF family contain conserved WRC and QLQ domains, with the sequences of these two conserved domain modules exhibiting high levels of conservation. Transcriptomic data indicates that StGRFs play a significant role in the growth and development of stamens, roots, young tubers, and other tissues or organs in potatoes. Furthermore, a few StGRFs exhibit differential expression patterns in response to Phytophthora infestans, chemical elicitors, heat, salt, and drought stresses, as well as multiple hormone treatments. The results of the expression analysis indicate that StGRF1, StGRF2, StGRF5, StGRF7, StGRF10 and StGRF12 are involved in the process of tuber sprouting, while StGRF4 and StGRF9 may play a role in tuber dormancy. These findings offer valuable insights that can be used to investigate the roles of StGRFs during potato tuber dormancy and sprouting.

Penicianstinoids F-K, six undescribed meroterpenoids from the marine algicolous fungus Penicillium sp. RR-DL-1-7.

Six previously undescribed meroterpenoids, penicianstinoids F-K (1-6), together with four known analogues, dehydroaustinol (7), dehydroaustin (8), penicianstinoid A (9), and furanoaustinol (10), were isolated from the cultures of the algicolous fungus Penicillium sp. RR-DL-1-7, derived from the red alga Rhodomela confervoides. Their structures and relative configuration were established by detailed spectroscopic analysis of NMR and HR-MS experiments, and the absolute configurations were assigned by X-ray diffraction and ECD spectral analysis. None of the isolates showed obvious growth inhibitory effects against five plankton and four bacteria species tested.

Excited-State Dynamics of a CRABPII-Based Microbial Rhodopsin Mimic.

Microbial rhodopsin, a pivotal photoreceptor protein, has garnered widespread application in diverse fields such as optogenetics, biotechnology, biodevices, etc. However, current microbial rhodopsins are all transmembrane proteins, which both complicates the investigation on the photoreaction mechanism and limits their further applications. Therefore, a specific mimic for microbial rhodopsin can not only provide a better model for understanding the mechanism but also can extend the applications. The human protein CRABPII turns out to be a good template for design mimics on rhodopsin due to the convenience in synthesis and the stability after mutations. Recently, Geiger et al. designed a new CRABPII-based mimic M1-L121E on microbial rhodopsin with the 13-cis, syn (13C) isomerization after irradiation. However, it still remains a question as to how similar it is compared with the natural microbial rhodopsin, in particular, in the aspect of the photoreaction dynamics. In this article, we investigate the excited-state dynamics of this mimic by measuring its transient absorption spectra. Our results reveal that there are two components in the solution of mimic M1-L121E at pH 8, known as protonated Schiff base (PSB) and unprotonated Schiff base (USB) states. In both states, the photoreaction process from 13-cis, syn(13C) to all-trans,anti (AT) is faster than that from the inverse direction. In addition, the photoreaction process in the PSB state is faster than that in the USB state. We compared the isomerization time of the PSB state to that of microbial rhodopsin. Our findings indicate that M1-L121E exhibits behaviors similar to those of microbial rhodopsins in the general pattern of PSB isomerization, where the isomerization from 13C to AT is much faster than its inverse direction. However, our results also reveal significant differences in the excited-state dynamics of the mimic relative to the native microbial rhodopsin, including the slower PSB isomerization rates as well as the unusual USB photoreaction dynamics at pH = 8. By elucidating the distinctive characteristics of mimics M1-L121E, this study enhances our understanding of microbial rhodopsin mimics and their potential applications.

Cost effectiveness of implantable cardioverter defibrillators for 1.5 primary prevention of sudden cardiac arrest in China: an analysis from the Improve SCA study.

OBJECTIVES: Implantable cardioverter defibrillator (ICDs) for primary prevention (PP) of sudden cardiac arrest (SCA) is underutilized in developing countries. The Improve SCA study has identified a subset of 1.5 primary prevention (1.5PP) patients with a higher risk of SCA and a significant mortality benefit from ICD therapy. From the perspective of China's healthcare system, we evaluated the cost-effectiveness of ICD therapy vs. no ICD therapy among 1.5PP patients with a view to informing clinical and policy decisions. METHODS: A published Markov model was adjusted and verified to simulate the course of the disease and describe different health states of 1.5PP patients. The patient characteristics, mortality, utility and complication estimates were obtained from the Improve SCA study and other literature. Cost inputs were sourced from government tender prices, medical service prices and clinical experts' surveys in 9 Chinese public hospitals. For both ICD and no ICD therapy, the total medical costs and quality-adjusted life-years (QALYs) were modelled over a lifetime horizon and the incremental cost-effectiveness ratio (ICER) was calculated. Deterministic and probabilistic sensitivity analyses were performed to assess the uncertainty of the model parameters. We used the willingness-to-pay (WTP) threshold recommended by China Guidelines for Pharmacoeconomic Evaluations, one to three times China's GDP per capita (CNY85,698-CNY257,094) in 2022 Chinese Yuan. RESULTS: The incremental cost effectiveness ratio (ICER) of ICD therapy compared to no ICD therapy is 139,652 CNY/QALY, which is about 1-2 times China's GDP per capita. The probability that ICD therapy is cost effective was 92.1%. Results from sensitivity analysis supported the findings of the base case. CONCLUSIONS: ICD therapy compared to no ICD therapy is cost-effective for the 1.5PP patients in China.

[Prediction Spatial Distribution of Soil Organic Matter Based on Improved BP Neural Network with Optimized Sparrow Search Algorithm].

Soil organic matter is an important indicator of soil fertility, and it is necessary to improve the accuracy of regional organic matter spatial distribution prediction. In this study, we analyzed the organic matter content of 1 690 soil surface layers (0-20 cm) and collected data on the natural environment and human activities in the Weining Plain of the Yellow River Basin. The SOM spatial distribution prediction model was established with 1 348 points using classical statistics, deterministic interpolation, geostatistical interpolation, and machine learning, respectively, and 342 sample points data were used as the test set to test and analyze the prediction accuracy of different models. The results showed that the average SOM content of the surface soil of the Weining Plain was 14.34 g·kg-1, and the average soil organic matter variation across 1 690 sampling points was 34.81%, indicating a medium degree of variability. The results also revealed a spatial distribution trend, with low soil organic matter content in the northeast and southwest, high soil organic matter on the left and right banks of the Yellow River in the middle, and relatively high soil organic matter in the sloping terrain of the Weining Plain. The four types of methods in order of high to low prediction accuracy were the machine learning method, geostatistical interpolation method, deterministic interpolation method, and classical statistical method. Through comparison, the BP neural network that was improved based on the optimized sparrow search algorithm had the best prediction accuracy, and the optimized sparrow search algorithm had better convergence accuracy, avoided falling into local optimization, prevented data overfitting, and had better prediction ability. This optimization algorithm can improve the accuracy of SOM prediction and has good application prospects in soil attribute prediction.

Chemistry and biology of marine-derived Trichoderma metabolites.

Marine-derived fungi of the genus Trichoderma have been surveyed for pharmaceuticals and agrochemicals since 1993, with various new secondary metabolites being characterized from the strains of marine animal, plant, sediment, and water origin. Chemical structures and biological activities of these metabolites are comprehensively reviewed herein up to the end of 2022 (covering 30 years). More than 70 strains that belong to at least 18 known Trichoderma species have been chemically investigated during this period. As a result, 445 new metabolites, including terpenes, steroids, polyketides, peptides, alkaloids, and others, have been identified, with over a half possessing antimicroalgal, zooplankton-toxic, antibacterial, antifungal, cytotoxic, anti-inflammatory, and other activities. The research is highlighted by the molecular diversity and antimicroalgal potency of terpenes and steroids. In addition, metabolic relevance along with co-culture induction in the production of new compounds is also concluded. Trichoderma strains of marine origin can transform and degrade heterogeneous molecules, but these functions need further exploration.

DDX5 inhibits inflammation by modulating m6A levels of TLR2/4 transcripts during bacterial infection.

DExD/H-box helicases are crucial regulators of RNA metabolism and antiviral innate immune responses; however, their role in bacteria-induced inflammation remains unclear. Here, we report that DDX5 interacts with METTL3 and METTL14 to form an m6A writing complex, which adds N6-methyladenosine to transcripts of toll-like receptor (TLR) 2 and TLR4, promoting their decay via YTHDF2-mediated RNA degradation, resulting in reduced expression of TLR2/4. Upon bacterial infection, DDX5 is recruited to Hrd1 at the endoplasmic reticulum in an MyD88-dependent manner and is degraded by the ubiquitin-proteasome pathway. This process disrupts the DDX5 m6A writing complex and halts m6A modification as well as degradation of TLR2/4 mRNAs, thereby promoting the expression of TLR2 and TLR4 and downstream NF-κB activation. The role of DDX5 in regulating inflammation is also validated in vivo, as DDX5- and METTL3-KO mice exhibit enhanced expression of inflammatory cytokines. Our findings show that DDX5 acts as a molecular switch to regulate inflammation during bacterial infection and shed light on mechanisms of quiescent inflammation during homeostasis.

Research on prevention and control technology of classified rockburst in TBM construction of deeply buried tunnels.

Rock blasting and other geological disasters occur frequently in the TBM construction of deeply buried tunnels and seriously threaten construction safety and progress. Therefore, it is extremely important to conduct scientific research for effective prevention and control of rockbursts in construction. Based on a large number of field rockburst data, this study analyses the influence of rockburst on construction safety and efficiency by using statistical theory and summarizes the temporal and spatial characteristics of rockburst time, location and influence range. Using these results, combined with the characteristics of the TBM structure and construction method, classification prevention and control objectives, theoretical criteria and prevention and control technology of rock bursts are proposed. A theoretical system of classified prevention and control of rockburst is constructed, which is cooperatively controlled by microseismic monitoring, TBM equipment, TBM excavation and support measures. The system is verified to provide practical protection, demonstrating that this report provides an important reference for the prevention and control of rock bursts in ultradeep tunnels.

Two-Dimensional Electronic Spectroscopy of the Far-Red-Light Photosystem II Reaction Center.

Understanding the role of specific pigments in primary energy conversion in the photosystem II (PSII) reaction center has been impeded by the spectral overlap of its constituent pigments. When grown in far-red light, some cyanobacteria incorporate chlorophyll-f and chlorophyll-d into PSII, relieving the spectral congestion. We employ two-dimensional electronic spectroscopy to study PSII at 77 K from Synechococcus sp. PCC 7335 cells that were grown in far-red light (FRL-PSII). We observe the formation of a radical pair within ∼3 ps that we assign to ChlD1•-PD1•+. While PheoD1 is thought to act as the primary electron acceptor in PSII from cells grown in visible light, we see no evidence of its involvement, which we attribute to its reduction by dithionite treatment in our samples. Our work demonstrates that primary charge separation occurs between ChlD1 and PD1 in FRL-PSII, suggesting that PD1/PD2 may play an underappreciated role in PSII's charge separation mechanism.

A New Harziane Diterpene, Harziaketal A, and a New Sterol, Trichosterol A, from the Marine-Alga-Epiphytic Trichoderma sp. Z43.

One new diterpene, harziaketal A (1), and one new highly degraded sterol, trichosterol A (2), along with three known compounds, including one diterpene, harzianone (3), and two steroids, (22E,24R)-5α,6α-epoxy-ergosta-8(14),22-dien-3ß,7α-diol (4) and isoergokonin B (5), were isolated from the culture of the marine-alga-epiphytic fungus Trichoderma sp. Z43 by silica gel column chromatography (CC), Sephadex LH-20 CC, and preparative thin-layer chromatography (TLC). Their structures and relative configurations were assigned by nuclear magnetic resonance (NMR) and high resolution electrospray ionisation mass spectrometry (HR-ESI-MS) data, and the absolute configuration of 1 was established by X-ray diffraction. Compound 1 features a hemiketal unit situated at the four-membered ring of harziane-type diterpenes for the first time, while 2 represents the rare occurrence of sterols with rings A and B being degraded. Compounds 1 and 2 displayed weak inhibition against the tested phytoplankton (Amphidinium carterae, Heterocapsa circularisquama, Heterosigma akashiwo, and Prorocentrum donghaiense) with half maximal inhibitory concentration (IC50 ) ranging from 14 to 53 µg/mL.

Lipids and Terpenoids from the Deep-Sea Fungus Trichoderma lixii R22 and Their Antagonism against Two Wheat Pathogens.

Five new lipids, tricholixins A-E (1-5), and two known terpenoids, brasilane A (6) and harzianone A (7), were discovered from a deep-sea strain (R22) of the fungus Trichoderma lixii isolated from the cold seep sediments of the South China Sea. Their structures and relative configurations were identified by meticulous analysis of MS and IR as well as NMR data. The absolute configuration of 5 was ascertained by dimolybdenum-induced ECD data in particular. Compounds 1 and 2 represent the only two new butenolides from marine-derived Trichoderma, and they further add to the structural diversity of these molecules. Although 6 has been reported from a basidiomycete previously, it is the first brasilane aminoglycoside of Trichoderma origin. During the assay against wheat-pathogenic fungi, both 1 and 2 inhibited Fusarium graminearum with an MIC value of 25.0 µg/mL, and 6 suppressed Gaeumannomyces graminis with an MIC value of 12.5 µg/mL. Moreover, the three isolates also showed low toxicity to the brine shrimp Artemia salina.

New ophiobolin sesterterpenoid and drimane sesquiterpenoids from a marine-alga-derived fungus Aspergillus sp.

Further investigation of secondary metabolites of a marine-alga-derived fungus Aspergillus sp. RR-YLW-12 led to isolate one new ophiobolin-type sesterterpenoid (1), four new drimane-type sesquiterpenoids (2-5) and one natural occurring compound (6), together with seven known compounds (7-13). Their structures and stereochemistry were elucidated by extensive spectroscopic analysis of NMR and HRMS experiments, and by comparison with the literature data. All isolates were evaluated for growth inhibition of five marine harmful microalgae. The new compounds exhibited significant to moderate inhibitory effects towards all tested microalgae species with IC50 values ranging from 5.8 to 54.5 µg/mL.

Charge separation in the photosystem II reaction center resolved by multispectral two-dimensional electronic spectroscopy.

The photosystem II reaction center (PSII RC) performs the primary energy conversion steps of oxygenic photosynthesis. While the PSII RC has been studied extensively, the similar time scales of energy transfer and charge separation and the severely overlapping pigment transitions in the Qy region have led to multiple models of its charge separation mechanism and excitonic structure. Here, we combine two-dimensional electronic spectroscopy (2DES) with a continuum probe and two-dimensional electronic vibrational spectroscopy (2DEV) to study the cyt b559-D1D2 PSII RC at 77 K. This multispectral combination correlates the overlapping Qy excitons with distinct anion and pigment-specific Qx and mid-infrared transitions to resolve the charge separation mechanism and excitonic structure. Through extensive simultaneous analysis of the multispectral 2D data, we find that charge separation proceeds on multiple time scales from a delocalized excited state via a single pathway in which PheoD1 is the primary electron acceptor, while ChlD1 and PD1 act in concert as the primary electron donor.

Four dodecanoic acid derivatives from the cold-seep-derived fungus Cladosporium cladosporioides 8-1.

Two new compounds, cladospolides I (1) and J (2), together with two new naturally occurring ones, methyl 11-hydroxy-4-oxododecanoate (3) and 11-hydroxy-4-oxododecanoic acid (4), were isolated from the culture extract of the cold-seep sediment-derived fungus Cladosporium cladosporioides 8-1. Their structures and configurations were established by analysis of 1D/2D NMR, MS, ECD, and specific optical rotation data. Compound 3 was possibly formed by methyl esterification of 4 during the purification process due to the utilization of methanol. All compounds were evaluated for inhibition of four marine phytoplankton species and five marine-derived bacteria.

The use of a candidate gene approach to study Botrytis cinerea resistance in Gerbera hybrida.

Candidate genes (CG) for Botrytis cinerea resistance described in literature were mapped on gerbera linkage maps for which several QTL for Botrytis resistance had been found previously using a rapid, low-cost platform for SNP genotyping. In total, 29 CGs were mapped in either of two mapping populations. Four CGs were mapped within the previous identified QTL intervals and three co-localized with QTL. Two of these CGs for resistance against B. cinerea, PG1 (polygalacturonase gene) and sit (sitiens, ABA-aldehyde oxidase gene) that mapped in QTL regions for the ray floret disease resistance test were studied in detail. Virus-induced gene silencing (VIGS) was used for gene function analysis to determine the CGs' role in gerbera resistance to Botrytis. Ray florets, of which the CGs were silenced, showed a significantly delayed growth of lesions upon Botrytis infection compared to controls. Combining QTL analysis, candidate gene mapping and VIGS showed to be an useful combination to identify possible causal genes and for understanding the molecular mechanisms of Botrytis resistance in gerbera. The two genes seem to act as partial S-genes and are likely among the determining genes leading to the variation observed for B. cinerea resistance in gerbera.

Myrochromanol analogues and trichothecene derivatives from the shellfish-derived fungus Albifimbriaverrucaria.

Eight myrochromanol analogues, including three pairs of epimers at C-2 with the myrochromanol scaffold and two examples of myrochromanol with sugar moiety linked at C-4, together with twelve trichothecene derivatives were isolated from the cultures of a shellfish-derived fungus Albifimbria verrucaria CD1-4. Among them, eight compounds named 2-epi-myrochromanol, ent-myrochromanol B, 4-epi-myrochromanol B, 2-epi-myrochromanol A, myrochromanosides A and B, 6',7'-erythro-(2'E,4'Z)-trichoverrol B, 3R,8S-dihyroxyroridin H were previously undescribed fungal metabolites. Their planar structures and relative configurations were established by 1D and 2D NMR, and HR-MS data analysis, and their absolute configurations were determined using the modified Mosher's method and electronic circular dichrosim calculations. Almost all isolates were evaluated for growth rate inhibition of three marine harmful microalgae Chattonella marina, Heterosigma akashiwo, and Prorocentrum donghaiense, and lethal activity to one marine zooplankton, Artemia salina. Myrochromanosides A and B exhibited obvious inhibitory against three tested microalgae with IC50 values in the range of 9.2-108.9 µM. 8α-Hydroxyroridin H, roridin A and verrucarin A exhibited significant inhibition against P. donghaiense with IC50 values of 6.1, 5.8, and 6.0 µM and toxicity against brine shrimp larvae with LC50 values of 1.4, 2.8, and 0.26 µM, respectively.

Enhancement Mechanism of Minerals on Lignite-Water Molecule Interactions.

Five coal samples were prepared by deashing Shengli lignite in distinct phases, which consisted of residual ash from spontaneous combustion. The effects of removal and introduction of inherent minerals on the water reabsorption performance of coal samples were systematically investigated in three aspects: pore structure, oxygen-containing functional groups, and lignite materials. Low-field nuclear magnetic resonance spectroscopy was employed to investigate the changes in the water molecular adsorption tendency of coal samples with the variation in the mineral content. The study elucidates that the hygroscopic performance of the coal samples is significantly reduced due to the massive removal of inherent minerals. However, the pore structure of the coal samples after HCl/HF washing becomes more developed, and the oxygen-containing functional groups on the surface are more exposed, leading to an increase in the equilibrium adsorbed moisture content (EMC) of the coal samples. The binding force between coal samples and water molecules is reduced by the removal of the inherent minerals, which weakens the interaction forces between lignite and water molecules. The oxygen-containing functional groups on the surface of lignite interact with the residual ash from spontaneous combustion to enhance the binding force between lignite and surface water molecules, thus leading to the improved tendency of lignite to adsorb water molecules. The formation of intermediate complexes between minerals and oxygen-containing functional groups, in particular, carboxyl functional groups, on the surface of lignite enhances the acting force of polar sites, which improves the interaction of lignite-water molecules.

Reply to "Comment on: 'Isolating Vibrational Polariton 2D-IR Transmission Spectra'".

In a Comment on our recent Letter, the authors take issue with our method of refining 2D-IR transmission spectra to remove a background contribution that arises from nonpolaritonic molecules in the cavity. In our response to their Comment, we describe how our approach was motivated by the previous work of the authors, and we present a spatially dependent molecule-cavity Tavis-Cummings model that can account for the significant response from localized molecules with nonzero oscillator strengths. The telltale signature of the localized molecule response is the spectral diffusion dynamics of the bare W(CO)6 molecules in the polar butyl acetate solvent. Inhomogeneous broadening is absent from polaritonic states due to the extreme degree of exchange narrowing in coupling very large numbers of molecules to a cavity mode.

Cyclopentenone and wickerol derivatives from the marine algicolous fungus Trichoderma atroviride A-YMD-9-4.

A new cyclopentenone derivative, 4-hydroxyhypocrenone A, and a new naturally-occurring wickerol derivative, 8-acetoxywickerol A, as well as two known compounds, hypocrenone A and wickerol B, were purified from Trichoderma atroviride A-YMD-9-4, an endophytic fungus isolated from the marine red alga Gracilaria verrucosa. The structures and relative configurations of two new isolates were established by a combination of 1 D/2D NMR, IR, and mass spectroscopic methods, and the absolute configuration of 1 was assigned on the basis of ECD data analyzed by quantum chemical calculations. Compounds 1 and 2 exhibited weak inhibition of one or two marine phytoplankton species.

A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria.

Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in the absence of the corresponding immune receptor Ve1. We identify a multiallelic V. dahliae gene displaying c. 65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L), which shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve locus, does not recognize VdAve1L. Additionally, we demonstrate that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum, that is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens.