Decoding the microbiome for sustainable agriculture.

Root-associated microbiota profoundly affect crop health and productivity. Plants can selectively recruit beneficial microbes from the soil and actively balance microbe-triggered plant-growth promotion and stress tolerance enhancement. The cost associated with this is the root-mediated support of a certain number of specific microbes under nutrient limitation. Thus, it is important to consider the dynamic changes in microbial quantity when it comes to nutrient condition-induced root microbiome reassembly. Quantitative microbiome profiling (QMP) has recently emerged as a means to estimate the specific microbial load variation of a root microbiome (instead of the traditional approach quantifying relative microbial abundances) and data from the QMP approach can be more closely correlated with plant development and/or function. However, due to a lack of detailed-QMP data, how soil nutrient conditions affect quantitative changes in microbial assembly of the root-associated microbiome remains poorly understood. A recent study quantified the dynamics of the soybean root microbiome, under unbalanced fertilization, using QMP and provided data on the use of specific synthetic communities (SynComs) for sustaining crop productivity. In this editorial, we explore potential opportunities for utilizing QMP to decode the microbiome for sustainable agriculture.

Analysis of the Dynamic Expression of the SMAD Family in the Periosteum During Guided Bone Regeneration.

OBJECTIVE: The aim of this study was to investigate the dynamic expression of the SMAD family during guided bone regeneration for the reconstruction of cranio-maxillofacial bone defects. METHODS: A swine model of guided bone regeneration was established with one side of the rib as the trauma group and the contralateral as control group. Periosteal and regenerative tissue specimens were harvested at 9 time points in the early, middle, and late phases, and were subjected to gene sequencing and tissue staining. Expression data of each SMAD family were extracted for further analysis, in which the correlation of the expression of the respective members within and between groups and at different time points was analyzed. RESULTS: The expression of individual members of the SMAD family fluctuates greatly, especially during the first month. The SMAD3 and SMAD4 genes were the most highly expressed. The foldchange value of SMAD6 was the largest and remained above 1.5 throughout the process. The dynamic expression levels of SMAD2, SMAD4, SMAD5, SMAD6, and SMAD9 showed a significant positive correlation in both groups. The expression levels of each gene showed a positive correlation with other SMAD genes. Tissue staining showed that the overall contour of the regenerated bone tissue was basically formed within the first 1 month. CONCLUSION: The first month of guided bone regeneration is a critical period for bone regeneration and is an important period for the SMAD family to play a role. The SMAD6 may play an important role in the whole process of guided bone regeneration.

Intramolecular CH⋯π attraction mediated conformational polymorphism of constrained helical peptides.

In nature, biochemical processes depend on polymorphism, a phenomenon by which discrete biomolecules can adopt specific conformations based on their environment. However, it is often difficult to explore the generation mechanism and achieve polymorphic control in artificial supramolecular assembly systems. In this work, we propose a feasible thought for exploring the transformation mechanism of polymorphism in peptide assembly from the perspective of thermodynamic regulation, which enables polymorphic composition to be limited by switchable intramolecular CH⋯π attraction within a certain temperature range. Combined with the density functional theory calculations, we obtained thermodynamic theoretical data supporting the conformation transition and the underlying polymorphism formation principle. Afterward, we properly designed the peptide to alter the probability of CH⋯π attraction occurring. Then, we selectively obtained a homogeneous morphological form with corresponding molecular conformation, which further demonstrated the important role of molecular conformational manipulation in polymorphism selection. This unique template-based strategy developed in this study may provide scientists with an additional line of thought to guide assembly paths in other polymorphic systems.

SoMarker: a genetic marker searching tool for C. elegans.

Caenorhabditis elegans (C. elegans) is one of the most popular model organisms used to genetically dissect complex biological phenomena. One common technique used routinely in the C. elegans laboratory is the generation of strains carrying combinations of genetic mutations via classical genetic crosses. Here, we have developed a simple and convenient application to quickly identify useful genetic markers (phenotypical and fluorescent) and their chromosomal positions to aid in the development of genetic cross strategies. The user-friendly software identifies and prioritises markers with the least genetic distance to a gene of interest, as well as displays the strain name, ease of scoring, nature of the marker (fluorescent transgene or phenotypic information), mating efficiency, and number of available alleles. In addition, recombination frequencies between the gene of interest and each genetic marker are calculated automatically. The application, called "SoMarker", is designed for both MacOS and Windows environments and is available to freely download and modify through open-source software.

Misregulation of mitochondrial 6mA promotes the propagation of mutant mtDNA and causes aging in C. elegans.

In virtually all eukaryotes, the mitochondrial DNA (mtDNA) encodes proteins necessary for oxidative phosphorylation (OXPHOS) and RNAs required for their synthesis. The mechanisms of regulation of mtDNA copy number and expression are not completely understood but crucially ensure the correct stoichiometric assembly of OXPHOS complexes from nuclear- and mtDNA-encoded subunits. Here, we detect adenosine N6-methylation (6mA) on the mtDNA of diverse animal and plant species. This modification is regulated in C. elegans by the DNA methyltransferase DAMT-1 and demethylase ALKB-1. Misregulation of mtDNA 6mA through targeted modulation of these activities inappropriately alters mtDNA copy number and transcript levels, impairing OXPHOS function, elevating oxidative stress, and shortening lifespan. Compounding these defects, mtDNA 6mA hypomethylation promotes the cross-generational propagation of a deleterious mtDNA. Together, these results reveal that mtDNA 6mA is highly conserved among eukaryotes and regulates lifespan by influencing mtDNA copy number, expression, and heritable mutation levels in vivo.

Root Endophyte-Manipulated Alteration in Rhizodeposits Stimulates Claroideoglomus in the Rhizosphere to Enhance Drought Resistance in Peanut.

Drought dramatically affects plant growth and yield. A previous study indicated that endophytic fungus Phomopsis liquidambaris can improve the drought resistance of peanuts, which is related with the root arbuscular mycorrhizal fungi (AMF) community; however, how root endophytes mediate AMF assembly to affect plant drought resistance remains unclear. Here, we explored the mechanism by which endophytic fungus recruits AMF symbiotic partners via rhizodeposits to improve host drought resistance. The results showed that Ph. liquidambaris enhanced peanut drought resistance by enriching the AMF genus Claroideoglomus of the rhizosphere. Furthermore, metabolomic analysis indicated that Ph. liquidambaris significantly promoted isoformononetin and salicylic acid (SA) synthesis in rhizodeposits, which were correlated with the increase in Claroideoglomus abundance following Ph. liquidambaris inoculation. Coinoculation experiments confirmed that isoformononetin and SA could enrich Claroideoglomus etunicatum in the rhizosphere, thereby improving the drought resistance. This study highlights the crucial role of fungal consortia in plant stress resistance.

Spectroscopic Characterization of the 1-Boratricyclo-[4.1.0.02,7]-heptane Radical with a Delocalized Four-Center-One-Electron Bond.

The boron atom is a highly electrophilic reagent due to the presence of its empty p orbital, making it prone to undergo electrophilic addition reactions with the carbon-carbon double bonds of olefins. In this study, the classical C=C reaction pathway occurs when a boron atom attacks the C=C bond of cyclohexene, resulting in the formation of the η2 (1,2)-BC6H10 complex (A) that contains a borirane radical subunit. This complex can further undergo photoisomerization, leading to the formation of a 3,4,5,6-tetrahydroborepine radical (C) through the cleavage of C-C bonds. In addition, two 1-boratricyclo[4.1.0.02,7]heptane radicals with chair (B) and boat (B') conformations were observed through α C-H cleavage reactions. Bonding analysis indicates that these radicals involve a four-center-one-electron (4c-1e) bond. Under UV light irradiation, these two radicals undergo ring-opening and rearrangement reactions, resulting in the formation of a 1-cyclohexen-1-yl-borane radical (D), which is a sp2 C-H activation product. These findings delineate a potential pathway for the synthesis of organoboron radicals through boron-mediated C-H and C-C bond cleavage reactions in cycloolefins.

Scalp Composite Tissue Transplantation for Repairing Upper Lip Defect: A Feasible Clinical Study.

BACKGROUND: The repair of upper lip defects is difficult and can result in asymmetry. The authors have developed a postauricular scalp composite tissue for the repair of upper lip defects. Herein, the authors, present the feasibility of scalp composite tissue grafts for repairing of upper lip defects. METHODS: The authors conducted a retrospective study of 10 patients who underwent scalp composite tissue transplantation for upper lip repair. The surgical procedure consisted of the excision of skin lesions or scar tissue from the upper lip to prepare the recipient area, and then the scalp composite tissue was excised behind the ear and transplanted to the upper lip defect. The authors reviewed the photographs and clinical notes of these patients. The patients' self-reported satisfaction with the repair effect was assessed. Tissue sections and hematoxylin and eosin staining of the scalp composite tissues were performed. RESULTS: All patients successfully underwent lesion resection and scalp composite tissue transplantation to repair the wound. There was no necrosis of the scalp composite tissue in the early postoperative period. The lip wound healed completely within 2 weeks. The mean follow-up time was 16 months, ranging from 12 to 20 months. Histologic sections and hematoxylin and eosin staining showed that the scalp composite tissue had abundant capillaries and dense fibrous connective tissue. All 10 patients were satisfied with the clinical effect of the procedure. CONCLUSION: Scalp composite tissue transplantation is a viable method for repairing upper lip defects. The special histomorphological characteristics of the scalp provide the basis for clinical application. LEVEL OF EVIDENCE: IV.

Depletion of protective microbiota promotes the incidence of fruit disease.

Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.

Expression of endogenous UDP-glucosyltransferase in endophyte Phomopsis liquidambaris reduces deoxynivalenol contamination in wheat.

Fusarium head blight is a devastating disease that causes severe yield loses and mycotoxin contamination in wheat grain. Additionally, balancing the trade-off between wheat production and disease resistance has proved challenging. This study aimed to expand the genetic tools of the endophyte Phomopsis liquidambaris against Fusarium graminearum. Specifically, we engineered a UDP-glucosyltransferase-expressing P. liquidambaris strain (PL-UGT) using ADE1 as a selection marker and obtained a deletion mutant using an inducible promoter that drives Cas9 expression. Our PL-UGT strain converted deoxynivalenol (DON) into DON-3-G in vitro at a rate of 71.4 % after 36 h. DON inactivation can be used to confer tolerance in planta. Wheat seedlings inoculated with endophytic strain PL-UGT showed improved growth compared with those inoculated with wildtype P. liquidambaris. Strain PL-UGT inhibited the growth of Fusarium graminearum and reduced infection rate to 15.7 %. Consistent with this finding, DON levels in wheat grains decreased from 14.25 to 0.56 µg/g when the flowers were pre-inoculated with PL-UGT and then infected with F. graminearum. The expression of UGT in P. liquidambaris was nontoxic and did not inhibit plant growth. Endophytes do not enter the seeds nor induce plant disease, thereby representing a novel approach to fungal disease control.

A pyridinium-based strategy for lysine-selective protein modification and chemoproteomic profiling in live cells.

Protein active states are dynamically regulated by various modifications; thus, endogenous protein modification is an important tool for understanding protein functions and networks in complicated biological systems. Here we developed a new pyridinium-based approach to label lysine residues under physiological conditions that is low-toxicity, efficient, and lysine-selective. Furthermore, we performed a large-scale analysis of the ∼70% lysine-selective proteome in MCF-7 cells using activity-based protein profiling (ABPP). We quantifically assessed 1216 lysine-labeled peptides in cell lysates and identified 386 modified lysine sites including 43 mitochondrial-localized proteins in live MCF-7 cells. Labeled proteins significantly preferred the mitochondria. This pyridinium-based methodology demonstrates the importance of analyzing endogenous proteins under native conditions and provides a robust chemical strategy utilizing either lysine-selective protein labeling or spatiotemporal profiling in a living system.

ß-Carbonyl sulfonium enables cysteine-specific bioconjugation for activity-based protein profiling in live cells.

Chemical labeling methods for proteins are highly researched. Herein, we introduced ß-carbonyl sulfonium compounds for selective cysteine modification in proteins within biological systems. Structural tuning led to sulfonium-based probes with high reactivity and selectivity. These probes show excellent biocompatibility, cell uptake, and specificity towards cysteine profiling in live cells.

Synthesis and characterization of azaborepin radicals in solid neon through boron-mediated C-N bond cleavage of pyridine.

The reactivity of pyridine is a complex topic due to its unique electronic structure. The reactions of atomic boron with pyridine molecules in solid neon have been investigated using matrix isolation infrared absorption spectroscopy. Three products (marked as A, B, and C) were observed and characterized through 10B, D and 15N isotopic substitution pyridine regents as well as quantum chemical calculations. In the reaction, the ground-state boron atom can attack the lone pair electrons of the nitrogen atom in the pyridine molecule, resulting in the formation of a 1-boropyridinyl radical (A). Alternatively, addition to the aromatic π-system of pyridine can occur in a [1,4] type, leading to the formation of a B[η2(1,4)-C5H5N] complex (B). Under UV-visible light (280 < λ < 580 nm) irradiation, these two compounds can further undergo photo-isomerization to form BN-embedded seven-membered azaborepin compounds (C). The observation of species A, B, and the subsequent photo-isomerization to species C is consistent with theoretical predictions, indicating that these reactions are kinetically favorable. This research provides valuable insights into the future design and synthesis of corresponding BN heterocyclic derivatives.

Seed-borne bacterial synthetic community resists seed pathogenic fungi and promotes plant growth.

AIMS: In this study, the control effects of synthetic microbial communities composed of peanut seed bacteria against seed aflatoxin contamination caused by Aspergillus flavus and root rot by Fusarium oxysporum were evaluated. METHODS AND RESULTS: Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain isolation, and measurement of plant growth promotion indicators. Three synthetic communities showed resistance to root rot and CS had the best effect after inoculating into peanut seedlings. This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts. In addition, CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin. These effects are related to bacterial degradation of toxins and destruction of mycelia. CONCLUSIONS: Inoculation with a synthetic community composed of seed bacteria can help host peanuts resist the invasion of seeds by A. flavus and seedlings by F. oxysporum and promote the growth of peanut seedlings.

Nasofacial Groove Pedicled Flap for the Reconstruction of Lateral Alar Defect.

BACKGROUND: The repair of nasal alar defects is challenging for plastic surgeons, and there is currently no standard operation. Herein, the authors reported the clinical outcomes of a nasofacial groove pedicled flap for the reconstruction of alar defect. METHODS: This retrospective study included patients who underwent the nasofacial groove pedicled flap for the reconstruction of alar defect between January 2018 and June 2020. Photographs of standard facial postures were taken before and after surgery to record the surgical results of the patients. The patient's medical history was reviewed retrospectively. Self-reported satisfaction of patients on scar morphology and reconstructive effect were evaluated with a questionnaire survey. RESULTS: There were 26 eligible patients enrolled, and all patients were followed up for more than 1 year after surgery. All flaps were free of ischemia and necrosis and healed well. No patient experienced restricted nostril ventilation. Eight patients underwent reoperation to trim the flap pedicle and the scar. Eight patients (8/26) reported "very satisfied," and 17 patients (17/26) reported "satisfied" with the repair effect and scar morphology. One patient went through multiple laser treatments to improve her scars but still remained visible hyperpigmentation. She was dissatisfied with postoperative flap pigmentation but was satisfied with the correction effect. CONCLUSIONS: The clinical results indicated that the nasal groove flap was safe for the treatment of the lateral alar defect, and the patients were satisfied with the clinical results. The authors believe that this flap can be used as an alternative method for repairing the lateral alar defect. LEVEL OF EVIDENCE: Level -IV, therapeutic study.

Root endophyte-mediated alteration in plant H2O2 homeostasis regulates symbiosis outcome and reshapes the rhizosphere microbiota.

Endophytic symbioses between plants and fungi are a dominant feature of many terrestrial ecosystems, yet little is known about the signaling that defines these symbiotic associations. Hydrogen peroxide (H2O2) is recognized as a key signal mediating the plant adaptive response to both biotic and abiotic stresses. However, the role of H2O2 in plant-fungal symbiosis remains elusive. Using a combination of physiological analysis, plant and fungal deletion mutants, and comparative transcriptomics, we reported that various environmental conditions differentially affect the interaction between Arabidopsis and the root endophyte Phomopsis liquidambaris, and link this process to alterations in H2O2 levels and H2O2 fluxes across root tips. We found that enhanced H2O2 efflux leading to a moderate increase in H2O2 levels at the plant-fungal interface is required for maintaining plant-fungal symbiosis. Disturbance of plant H2O2 homeostasis compromises the symbiotic ability of plant roots. Moreover, the fungus-regulated H2O2 dynamics modulate the rhizosphere microbiome by selectively enriching for the phylum Cyanobacteria, with strong antioxidant defenses. Our results demonstrated that the regulation of H2O2 dynamics at the plant-fungal interface affects the symbiotic outcome in response to external conditions and highlight the importance of the root endophyte in reshaping the rhizosphere microbiota.

KDF1 Promoted Proliferation, Migration and Invasion of Lung Adenocarcinoma Cells through Activating STAT3 and AKT Pathway.

KDF1 has been reported to be correlated with carcinogenesis. However, its role and mechanism are far from clear. To explore the possible role and underlying mechanism of KDF1 in lung adenocarcinoma (LUAD), we investigated KDF1 expression in LUAD tissues and the influence of KDF1 in the phenotype of LUAD cells (A549 and PC-9) as well as the underlying mechanism. Compared to non-tumor lung epithelial cells, KDF1 was upregulated in the cancer cells of the majority of LUAD patients, and its expression was correlated with tumor size. Patients with enhanced KDF1 in cancer cells (compared with paired adjacent non-neoplastic lung epithelial cells) had shorter overall survival than patients with no increased KDF1 in cancer cells. Knockdown of KDF1 inhibited the migration, proliferation and invasion of LUAD cells in vitro. And overexpression of KDF1 increased the growth of the subcutaneous tumors in mice. In terms of molecular mechanisms, overexpression of KDF1 induced the expression of AKT, p-AKT and p-STAT3. In KDF1-overexpressing A549 cells, inhibition of the STAT3 pathway decreased the level of AKT and p-AKT, whereas inhibition of the AKT pathway had no effect on the activation of STAT3. Inhibition of STAT3 or AKT pathways reversed the promoting effects of KDF1 overexpression on the LUAD cell phenotype and STAT3 inhibition appeared to have a better effect. Finally, in the cancer cells of LUAD tumor samples, the KDF1 level was observed to correlate positively with the level of p-STAT3. All these findings suggest that KDF1, which activates STAT3 and the downstream AKT pathway in LUAD, acts as a tumor-promoting factor and may represent a therapeutic target.

Pyridinium-Based Strategy for a Bioorthogonal Conjugation-Assisted Purification Method for Profiling Cell Surface Proteome.

Cell surface proteins (CSPs) are valuable targets for therapeutic agents, but achieving highly selective CSP enrichment in cellular physiology remains a technical challenge. To address this challenge, we propose a newly developed sulfo-pyridinium ester (SPE) cross-linking probe, followed by two-step imaging and enrichment. The SPE probe showed higher efficiency in labeling proteins than similar NHS esters at the level of cell lysates and demonstrated specificity for Lys in competitive experiments. More importantly, this probe could selectively label the cell membranes in cell imaging with only negligible labeling of the intracellular compartment. Moreover, we successfully performed this strategy on MCF-7 live cells to label 425 unique CSPs from 1162 labeled proteins. Finally, we employed our probe to label the CSPs of insulin-cultured MCF-7, revealing several cell surface targets of key functional biomarkers and insulin-associated pathogenesis. The above results demonstrate that the SPE method provides a promising tool for the selective labeling of cell surface proteins and monitoring transient cell surface events.

4-Iodine N-Methylpyridinium-Mediated Peptide Synthesis.

Through systematic optimization of halopyridinium compounds, we established a peptide coupling protocol utilizing 4-iodine N-methylpyridinium (4IMP) for solid-phase peptide synthesis (SPPS). The 4IMP coupling reagent is easily prepared, bench stable, and cost-effective. Employing 4IMP in the SPPS process has showcased remarkable chemoselectivity and efficiency, effectively eliminating racemization and epimerization. This achievement has been substantiated through the successful synthesis of a range of peptides via the direct utilization of commercially available amino acid substrates for SPPS.

Covalent Peptide LSD1 Inhibitor Specifically Recognizes Cys360 in the Enzyme-Active Region.

Lysine-specific demethylase 1 (LSD1) is a promising therapeutic target, especially in cancer treatment. Despite several LSD1 inhibitors being discovered for the cofactor pocket, none are FDA-approved. We aimed to develop stabilized peptides for irreversible LSD1 binding, focusing on unique cysteine residue Cys360 in LSD1 and SNAIL1. We created LSD1 C360-targeting peptides, like cyclic peptide S9-CMC1, using our Cysteine-Methionine cyclization strategy. S9-CMC1 effectively inhibited LSD1 at the protein level, as confirmed by MS analysis showing covalent bonding to Cys360. In cells, S9-CMC1 inhibited LSD1 activity, increasing H3K4me1 and H3K4me2 levels, leading to G1 cell cycle arrest and apoptosis and inhibiting cell proliferation. Remarkably, S9-CMC1 showed therapeutic potential in A549 xenograft animal models, regulating LSD1 activity and significantly inhibiting tumor growth with minimal organ damage. These findings suggest LSD1 C360 as a promising site for covalent LSD1 inhibitors' development.