Ionic Effect on the Microenvironment of Biomolecular Condensates.

Biomolecules such as proteins and RNA could organize to form condensates with distinct microenvironments through liquid-liquid phase separation (LLPS). Recent works have demonstrated that the microenvironment of biomolecular condensates plays a crucial role in mediating biological activities, such as the partition of biomolecules, and the subphase organization of the multiphasic condensates. Ions could influence the phase transition point of LLPS, following the Hofmeister series. However, the ion-specific effect on the microenvironment of biomolecular condensates remains unknown. In this study, we utilized fluorescence lifetime imaging microscopy (FLIM), fluorescence recovery after photobleaching (FRAP), and microrheology techniques to investigate the ion effect on the microenvironment of condensates. We found that ions significantly affect the microenvironment of biomolecular condensates: salting-in ions increase micropolarity and reduce the microviscosity of the condensate, while salting-out ions induce opposing effects. Furthermore, we manipulate the miscibility and multilayering behavior of condensates through ion-specific effects. In summary, our work provides the first quantitative survey of the microenvironment of protein condensates in the presence of ions from the Hofmeister series, demonstrating how ions impact micropolarity, microviscosity, and viscoelasticity of condensates. Our results bear implications on how membrane-less organelles would exhibit varying microenvironments in the presence of continuously changing cellular conditions.

Interaction of titanium dioxide nanoparticles with PVC-microplastics and chromium counteracts oxidative injuries in Trachyspermum ammi L. by modulating antioxidants and gene expression.

The emergence of polyvinyl chloride (PVC) microplastics (MPs) as pollutants in agricultural soils is increasingly alarming, presenting significant toxic threats to soil ecosystems. Ajwain (Trachyspermum ammi L.), a plant of significant medicinal and culinary value, is increasingly subjected to environmental stressors that threaten its growth and productivity. This situation is particularly acute given the well-documented toxicity of chromium (Cr), which has been shown to adversely affect plant biomass and escalate risks to the productivity of such economically and therapeutically important species. The present study was conducted to investigate the individual effects of different levels of PVC-MPs (0, 2, and 4 mg L-1) and Cr (0, 150, and 300 mg kg-1) on various aspects of plant growth. Specifically, we examined growth and biomass, photosynthetic pigments, gas exchange attributes, oxidative stress responses, antioxidant compound activity (both enzymatic and nonenzymatic), gene expression, sugar content, nutritional status, organic acid exudation, and Cr accumulation in different parts of Ajwain (Trachyspermum ammi L.) seedlings, which were also exposed to varying levels of titanium dioxide (TiO2) nanoparticles (NPs) (0, 25, and 50 µg mL-1). Results from the present study showed that the increasing levels of Cr and PVC-MPs in soils significantly decreased plant growth and biomass, photosynthetic pigments, gas exchange attributes, sugars, and nutritional contents from the roots and shoots of the plants. Conversely, increasing levels of Cr and PVC-MPs in the soil increased oxidative stress indicators in term of malondialdehyde, hydrogen peroxide, and electrolyte leakage, and also increased organic acid exudation pattern in the roots of T. ammi seedlings. Interestingly, the application of TiO2-NPs counteracted the toxicity of Cr and PVC-MPs in T. ammi seedlings, leading to greater growth and biomass. This protective effect is facilitated by the NPs' ability to sequester reactive oxygen species, thereby reducing oxidative stress and lowering Cr concentrations in both the roots and shoots of the plants. Our research findings indicated that the application of TiO2-NPs has been shown to enhance the resilience of T. ammi seedlings to Cr and PVC-MPs toxicity, leading to not only improved biomass but also a healthier physiological state of the plants. This was demonstrated by a more balanced exudation of organic acids, which is a critical response mechanism to metal stress.

Assessment of carbon sequestration potential of mining areas under ecological restoration in China.

Mining activities aggravate the ecological degradation and emission of greenhouse gases throughout the world, thereby affecting the global climate and posing a serious threat to the ecological safety. Vegetation restoration is considered to be an effective and sustainable strategy to improve the post-mining soil quality and functions. However, we still have a limited knowledge of the impact of vegetation restoration on carbon sequestration potential in mining areas. In this pursuit, the present study was envisaged to integrate the findings from studies on soil organic carbon (SOC) sequestration in mining areas under vegetation restoration with field monitoring data. The carbon sequestration potential under vegetation restoration in China's mining areas was estimated by using a machine learning model. The results showed that (1) Vegetation restoration exhibited a consistently positive impact on the changes in the SOC reserves. The carbon sequestration potential was the highest in mixed forests, followed by broad-leaved forests, coniferous forests, grassland, shrubland, and farmland; (2) The number of years of vegetation restoration and mean annual precipitation were found to be the important moderating variables affecting the SOC reserves in reclaimed soils in mining areas; (3) There were significant differences in the SOC sequestration potential under different vegetation restoration scenarios in mining areas in China. The SOC sequestration potential reached up to 9.86 million t C a-1, when the soil was restored to the initial state. Based on the meta-analysis, the maximal attainable SOC sequestration potential was found to be 4.26 million t C a-1. The SOC sequestration potential reached the highest level of 12.86 million t C a-1, when the optimal vegetation type in a given climate was restored. The results indicated the importance of vegetation restoration for improving the soil sequestration potential in mining areas. The time lag in carbon sequestration potential for different vegetation types in mining areas was also revealed. Our findings can assist the development of ecological restoration regimens in mining areas to mitigate the global climate change.

Unlocking the phytoremediation potential of organic acids: A study on alleviating lead toxicity in canola (Brassica napus L.).

Soil contamination with toxic heavy metals [such as lead (Pb)] is becoming a serious global problem due to the rapid development of the social economy. Organic chelating agents such as maleic acid (MA) and tartaric acid (TA) are more efficient, environmentally friendly, and biodegradable compared to inorganic chelating agents and they enhance the solubility, absorption, and stability of metals. To investigate this, we conducted a hydroponic experiment to assess the impact of MA (0.25 mM) and TA (1 mM) on enhancing the phytoremediation of Pb under its toxic concentration of 100 µM, using the oil seed crop canola (Brassica napus L.). Results from the present study showed that the Pb toxicity significantly (P < 0.05) decreased plant growth and biomass, photosynthetic pigments, gas exchange attributes and nutritional contents from the roots and shoots of the plants. In contrast, toxic concentration of Pb significantly (P < 0.05) increased oxidative stress indicators in term of malondialdehyde, hydrogen peroxide, and electrolyte leakage, increased enzymatic and non-enzymatic antixoidants and their specific gene expression and also increased organic acid exudation patter in the roots of B. napus. In addition, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed that Pb toxicity significantly affected double membranous organelles while Fourier-transform infrared (FTIR) spectroscopy showed an nveiled distinct peak variations in Pb-treated plants, when compared to control. Additionally, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed that Pb toxicity significantly affected double-membrane organelles, while Fourier-transform infrared (FTIR) spectroscopy unveiled distinct peak variations in Pb-treated plants compared to the control. The negative impact of Pb toxicity can overcome the application of MA and TA, which ultimately increased plant growth and biomass by capturing the reactive oxygen species, and decreased oxidative stress in B. napus. With the application of MA and TA, the values of the bioaccumulation factor (BAF) and translocation factor (TF) exceeded 1, indicating that the use of MA and TA enhances the phytoremediation potential of B. napus under Pb stress conditions. This finding could be beneficial for field environment studies, especially when explored through in-depth genetic and molecular analysis.

Chemical and mechanical coating of sulfur on baby corn biochar and their role in soil Pb availability, uptake, and growth of tomato under Pb contamination.

In recent ages, industrial revolution and natural weathering processes have been increasing lead (Pb) contamination in agricultural soils, therefore, green remediation technologies are becoming attractive and cost-effective. In the current pot study, 1% and 2% (w/w) application rates of sulfur (S) alone and novel chemo-mechanically S-modified baby corn biochars (CSB and MSB) were applied in a Pb-contaminated (500 mg/kg) soil to evaluate tomato (Lycopersicon esculentum L.) growth, Pb uptake and its soil availability. The results from SEM-EDS and XRD patterns confirmed the S enrichment on the surface of baby-corn biochar. Further, Pb treatment alone imposed a significant reduction in biomass accumulation, photosynthetic pigments, antioxidative mechanism, root traits, and Pb-tolerance index because of increased soil Pb availability and its uptake, translocation and biological accumulation in various tissues of tomato. However, incorporation of lower rate of elemental S (1%) and higher rates of biochars, especially chemically S-modified biochar, CSB (2%) significantly improved dry biomass production, Pb-tolerance index, physiological attributes and antioxidative defense system of tomato plants. These results might be due to a prominent decrease in soil Pb availability by 37.5%, Pb concentration in shoot by 66.7% and root by 58.3%, soil to root transfer by 33.8%, and root to shoot transfer by 20.2% in tomato plants under 2% application rate of CSB, as compared with the Pb treatment without any amendment. Moreover, sulfur treatment induced a significant impact in reduction of soil pH (from 8.97-7.47) as compared to the biochar treatments under Pb-toxicity. The current findings provided an insight that 2% chemically S-modified biochar (CSB) has significant potential to improve the tomato growth by reducing Pb bioavailability in the Pb-contaminated soil, compared to the S alone and MSB amendments.

Graphene protection improves the stability of two-dimensional halide perovskites under the electron irradiation.

The crystal structure of two-dimensional (2D) organic-inorganic halide perovskites undergoes fast structural collapse under the electron beam irradiation, hindering high-resolution transmission electron microscopy imaging. Graphene protection is an effective solution to mitigate the damage of electron-beam irradiation and has been applied in 2D materials such as MoS2 . However, the effectivity of graphene protection has not been demonstrated in 2D halide perovskites yet, as traditional wet-transfer of graphene with aqueous solution would cause serious degradation for moisture-sensitive halide perovskites. Here, we verified that graphene protection plays a protection role and developed a method using nonpolar solvent to transfer the graphene layer atop the perovskite nanosheets. With this method, the perovskite nanosheets might be well protected by graphene encapsulation. HIGHLIGHTS: Transfer method of graphene on moisture-sensitive 2D halide perovskites using nonpolar solvents was developed. Graphene substrate is proven to be able to mitigate electron-beam damage to 2D halide perovskites. Encapsulation structure of graphene/halide perovskite/graphene was demonstrated.

Low-Intensity Pulsed Ultrasound Promotes Osteogenic Potential of iPSC-Derived MSCs but Fails to Simplify the iPSC-EB-MSC Differentiation Process.

Induced pluripotent stem cell (iPSC)-derived mesenchymal stem cells (iMSCs) are a promising cell source for bone tissue engineering. However, iMSCs have less osteogenic potential than BMSCs, and the classical iPSC-EB-iMSC process to derive iMSCs from iPSCs is too laborious as it involves multiple in vitro steps. Low-intensity pulsed ultrasound (LIPUS) is a safe therapeutic modality used to promote osteogenic differentiation of stem cells. Whether LIPUS can facilitate osteogenic differentiation of iMSCs and simplify the iPSC-EB-iMSC process is unknown. We stimulated iMSCs with LIPUS at different output intensities (20, 40, and 60 mW/cm2) and duty cycles (20, 50, and 80%). Results of ALP activity assay, osteogenic gene expression, and mineralization quantification demonstrated that LIPUS was able to promote osteogenic differentiation of iMSCs, and it worked best at the intensity of 40 mW/cm2 and the duty cycle of 50% (LIPUS40/50). The Wnt/ß-catenin signaling pathway was involved in LIPUS40/50-mediated osteogenesis. When cranial bone defects were implanted with iMSCs, LIPUS40/50 stimulation resulted in a significant higher new bone filling rate (72.63 ± 17.04)% than the non-stimulated ones (34.85 ± 4.53)%. Daily exposure to LIPUS40/50 may accelerate embryoid body (EB)-MSC transition, but it failed to drive iPSCs or EB cells to an osteogenic lineage directly. This study is the first to demonstrate the pro-osteogenic effect of LIPUS on iMSCs. Although LIPUS40/50 failed to simplify the classical iPSC-EB-MSC differentiation process, our preliminary results suggest that LIPUS with a more suitable parameter set may achieve the goal. LIPUS is a promising method to establish an efficient model for iPSC application.

Downregulated miR-18a and miR-92a synergistically suppress non-small cell lung cancer via targeting Sprouty 4.

As a novel noncoding RNA cluster, miR-17-92 cluster include six members: miR-17, miR-18a, miR-19a, miR-19b-1, miR-20a, and miR-92a. Dysregulation of miR-17-92 has been proved to be connected with the advancement of a series of human diseases, but the roles of miR-17-92 cluster in non-small cell lung cancer (NSCLC) have not been absolutely elaborated. Herein, we determined that miR-17-92 cluster were upregulated significantly in NSCLC tissues, and the cell proliferation, migration and cycle progression of NSCLC were also facilitated under the function of miR-17-92 cluster. Sprouty 4 (SPRY4) was a direct target of miR-92a, and its overexpression restrained the exacerbation of NSCLC induced by miR-92a. Furthermore, the tumor xenograft assay showed that miR-92a facilitated tumor growth by inhibiting the expression of SPRY4 and mediating Epithelial-Mesenchymal Transition (EMT) in vivo. Finally, we looked into the synergistic effects of miR-92a and miR-18a on NSCLC, and found that antagomiR-18a treatment arrested the tumor growth rate of xenografted mice markedly.

BMP2 immune complexes promote new bone formation by facilitating the direct contact between osteoclasts and osteoblasts.

BMP2 antibody is proposed as a promising replacement for rhBMP2 in bone tissue engineering. Although studies have demonstrated its osteoinductive efficacy, the underlying osteogenic mechanism and adverse reactions of specific BMP2 antibody are not clarified yet, making it difficult to optimize the antibody for future application. By establishing BMP2 immune complexes (BMP2-ICs) ex vivo, we were able to introduce BMP2-ICs directly in vivo and found that BMP2-ICs promoted bone formation while suppressing osteoclastogenesis. However, ex vivo osteoclastogenic assays showed that BMP2-ICs promoted osteoclastogenesis by binding FcγR and activating PLCγ2 phosphorylation. Given that BMP2-ICs react with osteoblast and osteoclast lineage cells by the conjugated BMP2 domain and the Fc domain respectively, we introduced BMP2-ICs into coculture system of the two lineage cells and found that BMP2-ICs promoted osteogenesis while suppressing osteoclastogenesis by facilitating osteoblast-osteoclast contact and activating the EphrinB2-EphB4 signaling. This bidirectional function of BMP2-ICs was reproduced in the cranial bone resorption model, where osteoblast and osteoclast lineage cells co-localized. This study excluded the hidden problem of osteoclast overactivation that usually comes with rhBMP2 and clarified the first evidence of the mechanism of antibody-mediated bone regeneration, suggesting BMP2-ICs may present a promising therapy for bone diseases related with disrupted osteoclast-osteoblast interaction.

DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks.

BACKGROUND: Knowledge on the molecular targets of diseases and drugs is crucial for elucidating disease pathogenesis and mechanism of action of drugs, and for driving drug discovery and treatment formulation. In this regard, high-throughput gene transcriptional profiling has become a leading technology, generating whole-genome data on the transcriptional alterations caused by diseases or drug compounds. However, identifying direct gene targets, especially in the background of indirect (downstream) effects, based on differential gene expressions is difficult due to the complexity of gene regulatory network governing the gene transcriptional processes. RESULTS: In this work, we developed a network analysis method, called DeltaNeTS+, for inferring direct gene targets of drugs and diseases from gene transcriptional profiles. DeltaNeTS+ uses a gene regulatory network model to identify direct perturbations to the transcription of genes using gene expression data. Importantly, DeltaNeTS+ is able to combine both steady-state and time-course expression profiles, as well as leverage information on the gene network structure. We demonstrated the power of DeltaNeTS+ in predicting gene targets using gene expression data in complex organisms, including Caenorhabditis elegans and human cell lines (T-cell and Calu-3). More specifically, in an application to time-course gene expression profiles of influenza A H1N1 (swine flu) and H5N1 (avian flu) infection, DeltaNeTS+ shed light on the key differences of dynamic cellular perturbations caused by the two influenza strains. CONCLUSION: DeltaNeTS+ is a powerful network analysis tool for inferring gene targets from gene expression profiles. As demonstrated in the case studies, by incorporating available information on gene network structure, DeltaNeTS+ produces accurate predictions of direct gene targets from a small sample size (~ 10 s). Integrating static and dynamic expression data with transcriptional network structure extracted from genomic information, as enabled by DeltaNeTS+, is crucial toward personalized medicine, where treatments can be tailored to individual patients. DeltaNeTS+ can be freely downloaded from http://www.github.com/cabsel/deltanetsplus .

Sensory denervation increases potential of bisphosphonates to induce osteonecrosis via disproportionate expression of calcitonin gene-related peptide and substance P.

Bisphosphonate-related osteonecrosis of the jaw (BRONJ) is a serious side effect of systematic administration of bisphosphonates (BPs). Sensory innervation is crucial for bone healing. We established inferior alveolar nerve injury (IANI) and inferior alveolar nerve transection (IANT) models characterized by disorganized periosteum, increased osteoclasts, and unbalanced neuropeptide expression. Zoledronate injection disrupted neuropeptide expression in the IANI and IANT models by decreasing calcitonin gene-related peptide (CGRP) and increasing substance P (SP); associated with this, BRONJ prevalence was significantly higher in the IANT model, followed by the IANI model and the sham control. CGRP treatment significantly reduced BRONJ occurrence, whereas SP administration had the opposite effect. In vitro, RAW 264.7 cells were treated with BPs and then CGRP and/or SP to study changes in zoledronate toxicity; combined application of CGRP and SP decreased zoledronate toxicity, whereas CGRP or SP applied alone showed no effects. These results demonstrate that sensory denervation facilitates the occurrence of BRONJ and that CGRP used therapeutically may prevent BRONJ progression, provided that SP is also present. Further studies are necessary to determine the optimal ratio of CGRP to SP for promoting bone healing and to uncover the mechanism by which CGRP and SP cooperate.

Pueribacillus theae gen. nov., sp. nov., isolated from Pu'er tea.

A novel bacterial strain, designated T8T, isolated from ripened Pu'er tea, was investigated by using a polyphasic taxonomic approach. Cells stained Gram-positive and were aerobic, sporogenous and rod-shaped with flagella. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Bacillaceae in the class Bacilli and represented an independent taxon separated from other genera. Strain T8T shared low levels of 16S rRNA gene sequence similarity (<94 %) to members of other genera in the family Bacillaceae and was most closely related to Bacillus composti SgZ-9T (93.3 % sequence similarity). The DNA G+C content of strain T8T was 40 mol%. The major fatty acids (>10 %) of strain T8T were iso-C15 : 0 and iso-C16 : 0. The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. MK-7 (62 %), MK-6 (31 %) and MK-8 (7 %) were detected as the isoprenoid quinones. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine and six unidentified phospholipids. On the basis of the polyphasic evidence presented, strain T8T is considered to represent a novel genus and species in the family Bacillaceae, for which we propose the name Pueribacillus theae gen. nov., sp. nov. The type strain is T8T (=CGMCC 1.15924T=KCTC 333888T).

Coordination supramolecular assemblies of a monohydroxycucurbit[7]uril and their potential applications in gas sorption.

Coordination supramolecular assemblies of monohydroxycucurbit[7]uril ((HO)Q[7]) with alkaline earth metal ions (AE2+) have been formed in aqueous HCl solution in the presence of tetrachloride cadmium anions ([CdCl4]2-) as a structure directing agent. The driving force for the assembly could be attributed to the interaction of the positive electro-potential outer-surface of (HO)Q[7] molecules with [CdCl4]2- anions and ionic dipole interaction of the hydroxyl of (HO)Q[7] molecules with [CdCl4]2- anions. Moreover, the porous structure of the (HO)Q[7]/AE2+-based coordination supramolecular assemblies could result in potential applications in the selective sorption of polar volatile organic molecules, which may be useful in molecular sieves, sensors, absorption and separation.

Bacillus camelliae sp. nov., isolated from Pu'er tea.

A novel aerobic, Gram-stain-positive, sporogenous, rod-shaped bacterial strain, 7578-1T, was isolated from ripened Pu'er tea. Based on 16S rRNA gene sequence similarity comparisons, strain 7578-1T was grouped into the genus Bacillus and appeared to be closely related to the type strains Bacillus shackletoniiLMG 18435T (98.4 %), Bacillus acidicolaDSM 14745T (97.6 %), Bacillus paralicheniformis KACC 18426T (97.2 %) and Bacillus ginsengihumi KCTC 13944T (96.7 %). The fatty acid profile containing the major fatty acids, iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0 supported the allocation of strain 7578-1T to the genus Bacillus. The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was MK-7 (95 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified phospholipid and one unidentified lipid. The average nucleotide identity values between strain 7578-1T and its most closely related species were 67.8-82.4 % by OrthoANIu analysis. The DNA-DNA relatedness value between strain 7578-1T and the type strains of closely related species were 17-39 %, again indicating that strain 7578-1T represented a novel species in the genus Bacillus. The DNA G+C content of strain 7578-1T was 36.0 mol%. On the basis of the presented polyphasic evidence, strain 7578-1T is considered to represent a novel species of the genus Bacillus, for which we propose the name Bacillus camelliae sp. nov. The type strain is 7578-1T (=CGMCC 1.15374T=KCTC 33845T).

A New Member of the Inverted Cucurbit[n]uril Family.

A new inverted cucurbituril, namely inverted hexamethylcucurbit[3,3]uril (iMe6 Q[3,3]), has been isolated and characterized. It incorporates a single inverted un-substituted glycoluril unit oriented towards the interior of the cavity, shows good solubility in water and organic solvents (DMSO), and exhibits different selectivity for guests to those of iQ[6] and other known Q[6]s.

Paenibacillus yunnanensis sp. nov., isolated from Pu'er tea.

A novel Gram-staining-positive, aerobic, endospore-forming, rod-shaped bacterial strain, YN2T, was isolated from ripened Pu'er tea. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain represented a novel species of the genus Paenibacillus. The strains most closely related to strain YN2T were Paenibacillus vulneris JCM 18268T and Paenibacillus rigui JCM 16352T, with 16S rRNA similarities of 98.6 and 95.5 %, respectively. Chemotaxonomic data supported the affiliation of the new isolate to the genus Paenibacillus, including MK-7 as the major menaquinone, DNA G+C content of 51 mol%, cell-wall type A1γ (meso-diaminopimelic acid as the diagnostic diamino acid) and anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and phospholipid. Strain YN2T could be differentiated from recognized species of the genus Paenibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of evidence from this polyphasic study, Paenibacillus yunnanensis sp. nov., is proposed, with strain YN2T ( = CGMCC 1.12968T = JCM 30953T) as the type strain.