Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects.

BACKGROUND: Plant microbiota contributes to plant growth and health, including enhancing plant resistance to various diseases. Despite remarkable progress in understanding diseases resistance in plants, the precise role of rhizosphere microbiota in enhancing watermelon resistance against soil-borne diseases remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants. We further simplified SynCom and investigated the role of bacteria with synergistic interactions in promoting plant growth through a simple synthetic community. RESULTS: Our results demonstrated that the SynCom significantly enhanced the growth and disease resistance of ungrafted watermelon grown in non-sterile soil. Furthermore, analysis of the amplicon and metagenome data revealed the pivotal role of Pseudomonas in enhancing plant health, as evidenced by a significant increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial metabolomic analysis, we selected Pseudomonas along with seven other members of the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to further refine the initially constructed SynCom into a simplified SynCom comprising the eight selected bacterial species. Notably, the plant-promoting effects of simplified SynCom were similar to those of the initial SynCom. Furthermore, the simplified SynCom protected plants through synergistic effects of bacteria. CONCLUSIONS: Our findings suggest that the SynCom proliferate in the rhizosphere and mitigate soil-borne diseases through microbial synergistic interactions, highlighting the potential of synergistic effects between microorganisms in enhancing plant health. This study provides a novel insight into using the functional SynCom as a promising solution for sustainable agriculture. Video Abstract.

Minor Spliceosomal 65K/RNPC3 Interacts with ANKRD11 and Mediates HDAC3-Regulated Histone Deacetylation and Transcription.

RNA splicing is crucial in the multilayer regulatory networks for gene expression, making functional interactions with DNA- and other RNA-processing machineries in the nucleus. However, these established couplings are all major spliceosome-related; whether the minor spliceosome is involved remains unclear. Here, through affinity purification using Drosophila lysates, an interaction is identified between the minor spliceosomal 65K/RNPC3 and ANKRD11, a cofactor of histone deacetylase 3 (HDAC3). Using a CRISPR/Cas9 system, Deletion strains are constructed and found that both Dm65KΔ/Δ and Dmankrd11Δ/Δ mutants have reduced histone deacetylation at Lys9 of histone H3 (H3K9) and Lys5 of histone H4 (H4K5) in their heads, exhibiting various neural-related defects. The 65K-ANKRD11 interaction is also conserved in human cells, and the HsANKRD11 middle-uncharacterized domain mediates Hs65K association with HDAC3. Cleavage under targets and tagmentation (CUT&Tag) assays revealed that HsANKRD11 is a bridging factor, which facilitates the synergistic common chromatin-binding of HDAC3 and Hs65K. Knockdown (KD) of HsANKRD11 simultaneously decreased their common binding, resulting in reduced deacetylation of nearby H3K9. Ultimately, this study demonstrates that expression changes of many genes caused by HsANKRD11-KD are due to the decreased common chromatin-binding of HDAC3 and Hs65K and subsequently reduced deacetylation of H3K9, illustrating a novel and conserved coupling mechanism that links the histone deacetylation with minor spliceosome for the regulation of gene expression.

Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening.

UBE2T is an attractive target for drug development due to its linkage with several types of cancers. However, the druggability of ubiquitin-conjugating E2 (UBE2T) is low because of the lack of a deep and hydrophobic pocket capable of forming strong binding interactions with drug-like small molecules. Here, we performed fragment screening using 19 F-nuclear magnetic resonance (NMR) and validated the hits with 1 H-15 N-heteronuclear single quantum coherence (HSQC) experiment and X-ray crystallographic studies. The cocrystal structures obtained revealed the binding modes of the hit fragments and allowed for the characterization of the fragment-binding sites. Further screening of structural analogues resulted in the identification of a compound series with inhibitory effect on UBE2T activity. Our current study has identified two new binding pockets in UBE2T, which will be useful for the development of small molecules to regulate the function of this protein. In addition, the compounds identified in this study can serve as chemical starting points for the development of UBE2T modulators.

Nutrient status changes bacterial interactions in a synthetic community.

Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability.IMPORTANCEUnderstanding the intricate dynamics of microbial interactions is crucial for unraveling the stability and ecological roles of diverse ecosystems. However, the factors driving these interactions, leading to shifts in species fitness and ecological niches, remain inadequately explored. We demonstrate that metabolic similarity serves as a key driver of niche deformation between bacterial species. Resource availability emerges as a pivotal parameter, affecting interactions within the community. Our findings reveal heightened microbial inhibition and more negative interactions under resource-limited conditions. The prevalent facilitation is observed under conditions of high resource availability, underscoring the potential for niche expansion in such contexts. These findings emphasize that metabolic similarity induces varying degrees of resource competition, thereby altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. Our workflow has broad implications for understanding the roles of metabolic similarity and resource availability in microbial interactions and for designing synthetic microbial communities.

Metabolic interactions affect the biomass of synthetic bacterial biofilm communities.

IMPORTANCE: Co-occurrence network analysis is an effective tool for predicting complex networks of microbial interactions in the natural environment. Using isolates from a rhizosphere, we constructed multi-species biofilm communities and investigated co-occurrence patterns between microbial species in genome-scale metabolic models and in vitro experiments. According to our results, metabolic exchanges and resource competition may partially explain the co-occurrence network analysis results found in synthetic bacterial biofilm communities.

Osa-miR11117 Targets OsPAO4 to Regulate Rice Immunity against the Blast Fungus Magnaporthe oryzae.

The intricate regulatory process governing rice immunity against the blast fungus Magnaporthe oryzae remains a central focus in plant-pathogen interactions. In this study, we investigated the important role of Osa-miR11117, an intergenic microRNA, in regulating rice defense mechanisms. Stem-loop qRT-PCR analysis showed that Osa-miR11117 is responsive to M. oryzae infection, and overexpression of Osa-miR11117 compromises blast resistance. Green fluorescent protein (GFP)-based reporter assay indicated OsPAO4 is one direct target of Osa-miR11117. Furthermore, qRT-PCR analysis showed that OsPAO4 reacts to M. oryzae infection and polyamine (PA) treatment. In addition, OsPAO4 regulates rice resistance to M. oryzae through the regulation of PA accumulation and the expression of the ethylene (ETH) signaling genes. Taken together, these results suggest that Osa-miR11117 is targeting OsPAO4 to regulate blast resistance by adjusting PA metabolism and ETH signaling pathways.

Identification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer.

UBE2T is an E2 ubiquitin ligase critical for ubiquitination of substrate and plays important roles in many diseases. Despite the important function, UBE2T is considered as an undruggable target due to lack of a pocket for binding to small molecules with satisfied properties for clinical applications. To develop potent and specific UBE2T inhibitors, we adopted a high-throughput screening assay and two compounds-ETC-6152 and ETC-9004 containing a sulfone tetrazole scaffold were identified. Solution NMR study demonstrated the direct interactions between UBE2T and compounds in solution. Further co-crystal structures reveal the binding modes of these compounds. Both compound hydrolysation and formation of a hydrogen bond with the thiol group of the catalytic cysteine were observed. The formation of covalent complex was confirmed with mass spectrometry. As these two compounds inhibit ubiquitin transfer, our study provides a strategy to develop potent inhibitors of UBE2T.

Backbone 1H, 15N and 13C resonance assignments for an E2 ubiquitin conjugating enzyme-UBE2T.

Ubiquitin-conjugating enzyme E2 T (UBE2T) plays important roles in ubiquitination of proteins through participation in transferring ubiquitin to its substrate. Due to its importance in protein modifications, UBE2T associates with diverse diseases and serves as an important target for drug discovery and development. The crystal structure of UBE2T has been determined and the structure reveals the lack of a druggable pocket for binding to small molecules for clinical applications. Despite the challenge, effort has been made to develop UBE2T inhibitors. We obtained UBE2T constructs with and without the C-terminal region which is flexible in solution. Herein, we report the backbone resonance assignments for human UBE2T without the C-terminal region. The backbone dynamics of UBE2T was also explored. The available assignments will be helpful for hit identification, determining ligand binding site and understanding the mechanism of action of UBE2T inhibitors.

Polylactic Acid/Calcium Stearate Hydrocharging Melt-Blown Nonwoven Fabrics for Respirator Applications.

Non-biodegradable polypropylene, which poses a serious threat to the environment, is the most utilized material in air filtration systems. Moreover, under conditions of high temperature and high humidity, the electrostatic charge in melt-blown nonwoven fabrics treated with traditional corona electrets will quickly dissipate. Here, biodegradable polylactic acid, calcium stearate, and an innovative hydrocharging technique are reported to develop environmentally friendly polylactic acid/calcium stearate hydrocharging melt-blown nonwoven fabrics with high charge stability. Compared with polylactic acid melt-blown nonwoven fabrics, the crystallization structure and charge storage of polylactic acid/calcium stearate melt-blown nonwoven fabrics have been greatly improved due to the presence of calcium stearate. In PM0.3, it exhibited a high filtration efficiency (96.78%), a low pressure drop (65.20 Pa), and a good quality factor (0.053 Pa-1), which can meet the N95 respirator standard. Furthermore, it is worth mentioning that the filtration performance remained at a high level (>95.00%) after 2 months. Importantly, based on the test and analysis of surface electrostatic potential, crystallization, and charge storage and distribution, we proposed plausible charge generation and stable storage mechanisms. It demonstrated more potential for electret air filtration and smart respirators as the further possible step of research in the field.

Soil water stress alters differentially relative metabolic pathways affecting growth performance and metal uptake efficiency in a cadmium hyperaccumulator ecotype of Sedum alfredii.

Modeling plants for biomass production and metal uptake from surrounding environment is strongly dependent on the moisture content of soil. Therefore, experiments were conducted to find out how soil moisture affects the phenotypic traits, photosynthetic efficiency, metabolic profile, and metal accumulation in the hyperaccumulating ecotype of Sedum alfredii (S. alfredii). A total of six water potential gradients were set: 0 ~ -15 kPa (T1), -15 ~ -30 kPa (T2), -30 ~ -45 kPa (T3), -45 ~ -60 kPa (T4), -60 ~ -75 kPa (T5), and -75 ~ -90 kPa (T6). Different water potential treatments had a significant effect on plant growth and metal uptake efficiency. Compared to T3, T2 was more effective in promoting plant growth and development, with an increase in biomass of 23% and 17% in both fresh weight (FW) and dry weight (DW), respectively. T2 and T3 had the highest cadmium (Cd) content in the shoot (280.2 mg/kg) and (283.3 mg/kg), respectively, whereas T1 had the lowest values (204.7 mg/kg). Cd availability for plants in the soil was affected by moving soil moisture cycles. Changes in soil moisture that were either too high or too low compared to the ideal soil water content for S. alfredii growth resulted in a significant reduction in Cd accumulation in shoots. Tryptophan, phenylalanine, and other amino acids were accumulated in T5, whereas only tryptophan and phenylalanine slightly increased in T1. Sugars and alcohols such as sucrose, trehalose, mannitol, galactinol, and mannobiose increased in T5, while they decreased significantly in T1. Interestingly, in contrast to T1, the two impaired metabolic pathways in T5 (galactose and starch metabolism) were identified to be glucose metabolic pathways. These findings provide scientific information (based on experiments) to improve biomass production and metal uptake efficiency in hyperaccumulating ecotype of S. alfredii for phytoremediation-contaminated agricultural fields.

Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs.

Conversely to canonical splicing, back-splicing connects the upstream 3' splice site (SS) with a downstream 5'SS and generates exonic circular RNAs (circRNAs) that are widely identified and have regulatory functions in eukaryotic gene expression. However, sex-specific back-splicing in Drosophila has not been investigated and its regulation remains unclear. Here, we performed multiple RNA analyses of a variety sex-specific Drosophila samples and identified over ten thousand circular RNAs, in which hundreds are sex-differentially and -specifically back-spliced. Intriguingly, we found that expression of SXL, an RNA-binding protein encoded by Sex-lethal (Sxl), the master Drosophila sex-determination gene that is only spliced into functional proteins in females, promoted back-splicing of many female-differential circRNAs in the male S2 cells, whereas expression of a SXL mutant (SXLRRM) did not promote those events. Using a monoclonal antibody, we further obtained the transcriptome-wide RNA-binding sites of SXL through PAR-CLIP. After splicing assay of mini-genes with mutations in the SXL-binding sites, we revealed that SXL-binding on flanking exons and introns of pre-mRNAs facilitates back-splicing, whereas SXL-binding on the circRNA exons inhibits back-splicing. This study provides strong evidence that SXL has a regulatory role in back-splicing to generate sex-specific and -differential circRNAs, as well as in the initiation of sex-determination cascade through canonical forward-splicing.

SRSF3-Mediated Ki67 Exon 7-Inclusion Promotes Head and Neck Squamous Cell Carcinoma Progression via Repressing AKR1C2.

Ki67 is a well-known proliferation marker with a large size of around 350 kDa, but its biological function remains largely unknown. The roles of Ki67 in tumor prognosis are still controversial. Ki67 has two isoforms generated by alternative splicing of exon 7. The roles and regulatory mechanisms of Ki67 isoforms in tumor progression are not clear. In the present study, we surprisingly find that the increased inclusion of Ki67 exon 7, not total Ki67 expression level, was significantly associated with poor prognosis in multiple cancer types, including head and neck squamous cell carcinoma (HNSCC). Importantly, the Ki67 exon 7-included isoform is required for HNSCC cell proliferation, cell cycle progression, cell migration, and tumorigenesis. Unexpectedly, Ki67 exon 7-included isoform is positively associated with intracellular reactive oxygen species (ROS) level. Mechanically, splicing factor SRSF3 could promote exon 7 inclusion via its two exonic splicing enhancers. RNA-seq revealed that aldo-keto reductase AKR1C2 is a novel tumor-suppressive gene targeted by Ki67 exon 7-included isoform in HNSCC cells. Our study illuminates that the inclusion of Ki67 exon 7 has important prognostic value in cancers and is essential for tumorigenesis. Our study also suggested a new SRSF3/Ki67/AKR1C2 regulatory axis during HNSCC tumor progression.

Platelet-rich plasma-loaded bioactive chitosan@sodium alginate@gelatin shell-core fibrous hydrogels with enhanced sustained release of growth factors for diabetic foot ulcer healing.

The ability of autologous platelet-rich plasma (PRP) gel to promote rapid wound healing without immunological rejection has opened new avenues for the treatment of diabetic foot wounds. However, PRP gel still suffers from the quick release of growth factors (GFs) and requires frequent administration, thus resulting in decreased wound healing efficiency, higher cost as well as greater pain and suffering for the patients. In this study, the flow-assisted dynamic physical cross-linked coaxial microfluidic three-dimensional (3D) bio-printing technology, combined with the calcium ion chemical dual cross-linking method was developed to design PRP-loaded bioactive multi-layer shell-core fibrous hydrogels. The prepared hydrogels exhibited outstanding water absorption-retention capacity, good biocompatibility as well as a broad-spectrum antibacterial effect. Compared with clinical PRP gel, these bioactive fibrous hydrogels displayed a sustained release of GFs, reducing the administration frequency by 33 % availably during the wound treatment, but more prominent therapeutic effects such as effective reduced inflammation, in addition to promoting the growth of granulation tissue and angiogenesis, the formation of high-density hair follicles, and the generation of regular ordered and high-density collagen fiber network, which suggested great promise as exceptional candidates for treatment of diabetic foot ulcer in clinical settings.

Characterizing cortical responses to short-term multidisciplinary intensive rehabilitation treatment in patients with Parkinson's disease: A transcranial magnetic stimulation and electroencephalography study.

Combined transcranial magnetic stimulation and electroencephalography (TMS-EEG) is a powerful non-invasive tool for qualifying the neurophysiological effects of interventions by recording TMS-induced cortical activation with high temporal resolution and generates reproducible and reliable waves of activity without participant cooperation. Cortical dysfunction contributes to the pathogenesis of the clinical symptoms of Parkinson's disease (PD). Here, we examined changes in cortical activity in patients with PD following multidisciplinary intensive rehabilitation treatment (MIRT). Forty-eight patients with PD received 2 weeks of MIRT. The cortical response was examined following single-pulse TMS over the primary motor cortex by 64-channel EEG, and clinical symptoms were assessed before and after MIRT. TMS-evoked potentials were quantified by the global mean field power, as well as oscillatory power in theta, alpha, beta, and gamma bands, and their clinical correlations were calculated. After MIRT, motor and non-motor symptoms improved in 22 responders, and only non-motor function was enhanced in 26 non-responders. Primary motor cortex stimulation reduced global mean field power amplitudes in responders but not significantly in non-responders. Oscillations exhibited attenuated power in the theta, beta, and gamma bands in responders but only reduced gamma power in non-responders. Associations were observed between beta oscillations and motor function and between gamma oscillations and non-motor symptoms. Our results suggest that motor function enhancement by MIRT may be due to beta oscillatory power modulation and that alterations in cortical plasticity in the primary motor cortex contribute to PD recovery.

A database of water chemistry in eastern Siberian rivers.

Permafrost degradation leads to considerable changes in river ecosystems. The Eastern Siberian River Chemistry (ESRC) database was constructed to create a spatially extensive river chemistry database to assess climate warming-induced changes in freshwater systems in permafrost-dominated eastern Siberia. The database includes 9487 major ion (Na+, K+, Ca2+, Mg2+, Cl-, SO42- and HCO3-) data of chemical results from 1434 water samples collected mainly in six large river basins in eastern Siberia spanning 1940-2019. Data were obtained from public databases, scientific literature in English and Russian, and researchers and were formatted with a consistent table structure. The database is transparent and reproducible. Climate variable (air temperature and precipitation) data, discharge data, trace element concentration data, and isotope data at the basin and subbasin scales are also provided. This database enhances knowledge about the water chemistry of the permafrost region, especially in eastern Siberia, where data are scarce. The database will be useful to those assessing spatiotemporal changes in river water chemistry associated with permafrost degradation or other environmental stressors in a warmer climate.

Long-Term Organic-Inorganic Fertilization Regimes Alter Bacterial and Fungal Communities and Rice Yields in Paddy Soil.

Microorganisms are the most abundant and diverse organisms in soils and have important effects on soil fertility. In this study, effects of the long-term fertilization treatments no fertilizer (CK), chemical fertilizer (nitrogen-phosphorus-potassium (NPK)), and organic-inorganic fertilizer (NPK and organic fertilizer (NPKM)) on rice yield and soil bacterial and fungal community diversity, structure, composition, and interaction networks were evaluated. Of the three treatments, the highest rice yield was in NPKM. Bacterial richness was significantly higher in NPKM than in NPK. Fertilization treatment significantly altered ß diversity of communities, species composition of bacterial and fungal communities, and structure of soil microbial networks. The most complex bacterial and fungal interaction co-occurrence network with the highest average degree and numbers of edges and nodes was in NPKM. Relative abundance of the plant growth-promoting fungus Trichoderma increased significantly in NPKM compared with CK and NPK. The results of the study indicate that bacterial richness and microbial community member interactions (network complexity) might be suitable indicators of soil biological fertility. This research provides new insights on the effects of different fertilization regimes on responses of soil bacterial and fungal communities and their contributions to crop yield. New indicators such as bacterial richness and complexity of microbial interaction networks are also identified that can be used to evaluate soil biological fertility.

An Adaptive Information Security System for 5G-Enabled Smart Grid Based on Artificial Neural Network and Case-Based Learning Algorithms.

With the deployment of 5G Internet of Things (IoT) in the power system, the efficiency of smart grid is improved by increasing two-way interactions in different layers in smart grid. However, it introduces more attack interfaces that the traditional information security system in smart grid cannot response in time. The neuroscience-inspired models have shown their effectiveness in solving security and optimization problems in smart grid. How to improve the security mechanism in smart grid while taking into account the optimization of data transmission efficiency using neuroscience-inspired algorithms is the problem to be solved in this study. Therefore, an information security system based on artificial neural network (ANN) and improved multiple protection model is proposed. Based on the ANN algorithm, the link state sample space is used to train the model to obtain the optimal transmission path in 5G power communication network. Integrating the intelligent link state module, the zero-trust security protection platform using case-based learning algorithm is designed and taken as the first protection, the network security logical isolation facility is taken as the second protection, and the forward and backward isolation facilities are set as the third protection to achieve the strengthened security of 5G IoT in smart grid. The experimental results show the efficiency and effectiveness of the proposed algorithms. In addition, the experimental results also show that the proposed system can resist malicious terminal access, terminal hijacking, data tampering and eavesdropping, protocol fuzzy, and denial-of-service attacks, so as to reduce the security risks of 5G IoT in smart grid. Since the proposed system can be easily integrated into the existing smart grid structure in China, the proposed system can provide a reference for the design and implementation of 5G IoT in smart grid.

A multifunctional 3D dressing unit based on the core-shell hydrogel microfiber for diabetic foot wound healing.

The healing mechanism of diabetic foot wounds is very complicated, and it is difficult for a single-function medical dressing to achieve good therapeutic effects. We propose a simple coaxial biological 3D printing technology, which uses one-step 3D deposition to continuously produce multifunctional medical dressings on the basis of core-shell hydrogel fibers. These dressings have good biocompatibility, controlled drug-release performance, excellent water absorption and retention, and antibacterial and anti-inflammatory functions. In vivo experiments with type 2 diabetic rats were performed over a 14-day period to compare the performance of the multifunctional 3D dressing with a gauze control; the multifunctional 3D dressing reduced inflammation, effectively increased the post-healing thickness of granulation tissue, and promoted the formation of blood vessels, hair follicles, and highly oriented collagen fiber networks. Therefore, the proposed multifunctional dressing is expected to be suitable for clinical applications for healing diabetic foot wounds.

Secondary Structures of the Transmembrane Domain of SARS-CoV-2 Spike Protein in Detergent Micelles.

Spike protein of SARS-CoV-2 contains a single-span transmembrane (TM) domain and plays roles in receptor binding, viral attachment and viral entry to the host cells. The TM domain of spike protein is critical for viral infectivity. Herein, the TM domain of spike protein of SARS-CoV-2 was reconstituted in detergent micelles and subjected to structural analysis using solution NMR spectroscopy. The results demonstrate that the TM domain of the protein forms a helical structure in detergent micelles. An unstructured linker is identified between the TM helix and heptapeptide repeat 2 region. The linker is due to the proline residue at position 1213. Side chains of the three tryptophan residues preceding to and within the TM helix important for the function of S-protein might adopt multiple conformations which may be critical for their function. The side chain of W1212 was shown to be exposed to solvent and the side chains of residues W1214 and W1217 are buried in micelles. Relaxation study shows that the TM helix is rigid in solution while several residues have exchanges. The secondary structure and dynamics of the TM domain in this study provide insights into the function of the TM domain of spike protein.