Noviherbaspirillum album sp. nov., an airborne bacteria isolated from an urban area of Beijing, China.

A Gram-negative, ellipsoidal to short-rod-shaped, motile bacterium was isolated from Beijing's urban air. The isolate exhibited the closest kinship with Noviherbaspirillum aerium 122213-3T, exhibiting 98.4 % 16S rRNA gene sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that it clustered closely with N. aerium 122213-3T, thus forming a distinct phylogenetic lineage within the genus Noviherbaspirillum. The average nucleotide identity and digital DNA-DNA hybridization values between strain I16B-00201T and N. aerium 122213-3T were 84.6 and 29.4 %, respectively. The respiratory ubiquinone was ubiquinone 8. The major fatty acids (>10 %) were summed feature 3 (C16:1ω6c/C16:1ω7c, 43.3 %), summed feature 8 (C18:1ω7c/C18:1ω6c, 15.9 %) and C12:0 (11.0 %). The polyamine profile showed putrescine as the predominant compound. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unknown lipids and unknown phosphatidylaminolipids. The phenotypic, phylogenetic and chemotaxonomic results consistently supported that strain I16B-00201T represented a novel species of the genus Noviherbaspirillum, for which the name Noviherbaspirillum album sp. nov. is proposed, with I16B-00201T (=CPCC 100848T=KCTC 52095T) designated as the type strain. Its DNA G+C content is 59.4 mol%. Pan-genome analysis indicated that some Noviherbaspirillum species possess diverse nitrogen and aromatic compound metabolism pathways, suggesting their potential value in pollutant treatment.

Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates.

The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.

The cardiovascular toxicity of clozapine in embryonic zebrafish and RNA sequencing-based transcriptome analysis.

Clozapine (CLZ) is the most prescribed medication for treating refractory schizophrenia but is associated with significant cardiovascular toxicity. This study aimed to investigate the cardiovascular toxicity induced by CLZ using zebrafish as a model animal. For this purpose, zebrafish developed to 80-h post-fertilization were exposed to different CLZ concentration solutions for 24 h followed by cardiac morphological observations in yolk sac edema, pericardial edema, and blood coagulation, in addition to increased SV-BA distance, functionally manifested as bradycardia, and decreased cardiac ejection fraction using the untreated embryos as control. At the same time, RNA sequencing was used to study the possible molecular mechanism of CLZ-induced cardiovascular toxicity. The results indicated that compared to the control group, the experimental groups possessed a total of 5888 differentially expressed genes (DEGs), where gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment of analysis indicated that DEGs were mainly enriched in the pathways related to ion channels. These findings may provide new insights and directions for the subsequent in-depth study of the molecular mechanism of CLZ-induced cardiovascular toxicity.

Deciphering the Role of Fatty Acid-Metabolizing CYP4F11 in Lung Cancer and Its Potential As a Drug Target.

Lung cancer is the leading cause of cancer deaths worldwide. We found that the cytochrome P450 isoform CYP4F11 is significantly overexpressed in patients with lung squamous cell carcinoma. CYP4F11 is a fatty acid ω-hydroxylase and catalyzes the production of the lipid mediator 20-hydroxyeicosatetraenoic acid (20-HETE) from arachidonic acid. 20-HETE promotes cell proliferation and migration in cancer. Inhibition of 20-HETE-generating cytochrome P450 enzymes has been implicated as novel cancer therapy for more than a decade. However, the exact role of CYP4F11 and its potential as drug target for lung cancer therapy has not been established yet. Thus, we performed a transient knockdown of CYP4F11 in the lung cancer cell line NCI-H460. Knockdown of CYP4F11 significantly inhibits lung cancer cell proliferation and migration while the 20-HETE production is significantly reduced. For biochemical characterization of CYP4F11-inhibitor interactions, we generated recombinant human CYP4F11. Spectroscopic ligand binding assays were conducted to evaluate CYP4F11 binding to the unselective CYP4A/F inhibitor HET0016. HET0016 shows high affinity to recombinant CYP4F11 and inhibits CYP4F11-mediated 20-HETE production in vitro with a nanomolar IC 50 Cross evaluation of HET0016 in NCI-H460 cells shows that lung cancer cell proliferation is significantly reduced together with 20-HETE production. However, HET0016 also displays antiproliferative effects that are not 20-HETE mediated. Future studies aim to establish the role of CYP4F11 in lung cancer and the underlying mechanism and investigate the potential of CYP4F11 as a therapeutic target for lung cancer. SIGNIFICANCE STATEMENT: Lung cancer is a deadly cancer with limited treatment options. Cytochrome P450 4F11 (CYP4F11) is significantly upregulated in lung squamous cell carcinoma. Knockdown of CYP4F11 in a lung cancer cell line significantly attenuates cell proliferation and migration with reduced production of the lipid mediator 20-hydroxyeicosatetraenoic acid (20-HETE). Studies with the unselective inhibitor HET0016 show a high inhibitory potency of CYP4F11-mediated 20-HETE production using recombinant enzyme. Overall, our studies demonstrate the potential of targeting CYP4F11 for new transformative lung cancer treatment.

Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters.

At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.

Genetic Ablation of GIGYF1, Associated With Autism, Causes Behavioral and Neurodevelopmental Defects in Zebrafish and Mice.

BACKGROUND: Autism spectrum disorder is characterized by deficits in social communication and restricted or repetitive behaviors. Due to the extremely high genetic and phenotypic heterogeneity, it is critical to pinpoint the genetic factors for understanding the pathology of these disorders. METHODS: We analyzed the exomes generated by the SPARK (Simons Powering Autism Research) project and performed a meta-analysis with previous data. We then generated 1 zebrafish knockout model and 3 mouse knockout models to examine the function of GIGYF1 in neurodevelopment and behavior. Finally, we performed whole tissue and single-nucleus transcriptome analysis to explore the molecular and cellular function of GIGYF1. RESULTS: GIGYF1 variants are significantly associated with various neurodevelopmental disorder phenotypes, including autism, global developmental delay, intellectual disability, and sleep disturbance. Loss of GIGYF1 causes similar behavioral effects in zebrafish and mice, including elevated levels of anxiety and reduced social engagement, which is reminiscent of the behavioral deficits in human patients carrying GIGYF1 variants. Moreover, excitatory neuron-specific Gigyf1 knockout mice recapitulate the increased repetitive behaviors and impaired social memory, suggesting a crucial role of Gigyf1 in excitatory neurons, which correlates with the observations in single-nucleus RNA sequencing. We also identified a series of downstream target genes of GIGYF1 that affect many aspects of the nervous system, especially synaptic transmission. CONCLUSIONS: De novo variants of GIGYF1 are associated with neurodevelopmental disorders, including autism spectrum disorder. GIGYF1 is involved in neurodevelopment and animal behavior, potentially through regulating hippocampal CA2 neuronal numbers and disturbing synaptic transmission.

Response of earthworms to microplastics in soil under biogas slurry irrigation: Toxicity comparison of conventional and biodegradable microplastics.

As a reliable environment-friendly alternative, biodegradable plastic mulching films have been introduced into agricultural practice to reduce the adverse threats posed by conventional plastic products. Information regarding whether potential untoward effects of biodegradable plastics exist in soil and how strong are such effects on terrestrial organisms, however, still remains unknown. This study examined differences in the responses of earthworm, represented by Eisenia fetida, to exposure to biodegradable (PLA: polylactic acid) and conventional microplastics (PVC: polyvinylchloride, LDPE: low-density polyethylene) in soil with biogas slurry irrigation. Mortality, growth, histopathology and biochemical enzymes of the earthworms exposed to different concentrations of microplastics (5, 20 and 50 g/kg wet weight of soil, respectively) were investigated after 28 days of incubation in the experiment. The obtained results showed that the ecotoxicity of microplastics (MPs) to earthworms was time-dependent. Regardless of MPs type, continuous exposure to MPs at the concentration of 50 g/kg induced mucous vacuolization, longitude muscle disorder, and granular lipofuscin-like deposits generation in the epithelium. Moreover, tissue fibrosis and cavity formation were also observed in intestinal tissue. The presence of MPs stimulated the oxidative stress system of the earthworms, as indicated by the enhancement of malonaldehyde (MDA) content in vivo. The antioxidative defense system in earthworms was supposed to collapse at the MPs concentration of 50 g/kg after 28 days of exposure. Interestingly, PLA exhibited similar ecotoxicity effects with LDPE, which might violate the original intention of biodegradable plastics with less harmful or nontoxic influence on the terrestrial biotas. Thus, knowledge regarding the molecular and genetic mechanisms of the earthworms in soil containing biodegradable plastics should be further explored to better understand the risk posed by biodegradable plastics in the agroecosystem.

Structure-based discovery of receptor tyrosine kinase AXL degraders with excellent anti-tumor activity by selectively degrading AXL and inducing methuosis.

The receptor tyrosine kinase (RTK) anexelekto (AXL) is mutated and/or overexpressed in various malignancies, and plays a central role in tumor development and acquired drug resistance. Although highly selective inhibitors have been developed in recent years, direct inhibition of AXL may block its ubiquitination, eventually leading to surface accumulation of the protein. Herein, we designed and synthesized a series of AXL degraders with high selectivity and without compensatory increase of AXL. In particular, compounds 20 and 22 showed significant AXL degradation capacity, which inhibited the proliferation and migration of cancer cells in vitro. In addition, these compounds induced the formation of cytoplasmic vacuoles and triggered methuosis, a new type of non-apoptotic cell death, by stimulating excessive production of macropinosomes. Vacuole formation was mediated via H-Ras activation, and was attenuated upon inhibition of its downstream regulatory factor Rac1. Furthermore, compound 20 inhibited the growth of tumor cell xenografts in vivo, and prolonged the survival of the tumor-bearing mice.

Ag(I) Pyridine-Amidoxime Complex as the Catalysis Activity Domain for the Rapid Hydrolysis of Organothiophosphate-Based Nerve Agents: Mechanistic Evaluation and Application.

Two novel Ag(I) complexes containing synergistic pyridine and amidoxime ligands (Ag-DPAAO and Ag-PAAO) were first designed as complex monomers. Taking advantage of the molecular imprinting technique and solvothermal method, molecular imprinted porous cross-linked polymers (MIPCPs) were developed as a robust platform for the first time to incorporate Ag-PAAO into a polymer material as a recyclable catalyst. Advantageously, the observed pseudo first-order rate constant (kobs) of MIPCP-Ag-PAAO-20% for ethyl-parathion (EP) hydrolysis is about 1.2 × 104-fold higher than that of self-hydrolysis (30 °C, pH = 9). Furthermore, the reaction mechanism of the MIPCP-containing Ag-PAAO-catalyzed organothiophosphate was analyzed in detail using density functional theory and experimental spectra, indicating that the amidoxime can display dual roles for both the key coordination with the silver ion and nucleophilic attack to weaken the P-OAr bond in the catalytic active site.

Zinc(II)-Dipicolylamine Analogs Mediated PEI1.8k/pDNA Vector: Effect of Ligand Structure on the Gene Transport Process.

Zinc ion complexes of dipicolylamine analogs, due to the strong synergistic effect between the Zn2+ complex of containing polypyridine derivatives and polycations in each key step of pDNA transport, have been used as the third component to mediate polyethyleneimine with molecular weight 1.8 kDa (PEI1.8k)/DNA gene delivery system. And the effects of different structural characteristics, such as the number of pyridinamine ligands, the hydrophilic-hydrophobicity of the adjacent groups, on the in vitro transfection performance of the ternary complex are systematically investigated. This ternary hybrid system provides an effective strategy to improve the gene delivery of cationic polymers.

Multifunctional oligomer immobilized on quartz crystal microbalance: a facile and stabilized molecular imprinting strategy for glycoprotein detection.

Glycoprotein detection holds great potential for early diagnosis of diverse diseases. For this purpose, the combination of quartz crystal microbalance (QCM) sensor and molecular imprinting has attracted increasing attention. Nonetheless, the recently common imprinted films fabricated on QCM electrode are thick and rigid, lacking flexibility in aqueous phase. Alternatively, small molecules immobilized on the electrode to construct molecular scale film could address this problem, while stabilization of the imprinted sites remains challenging. Herein, a co-assembly complex was obtained by the mixture of template and multifunctional oligomer, which was then immobilized on the amino-modified transducer surface through epoxy-amino reaction to form a protein-imprinted film. Afterward, the remaining epoxy groups in oligomer chains were cross-linked to conserve and stabilize the orientation of imprinted sites after template elution. Template rebinding tests show that cross-linked film has much higher imprinting factors than that of the non-cross-linked counterpart. Furthermore, control proteins that are distinct in properties and structures were employed to demonstrate the selectivity of this approach, and the imprinted assay reveals high affinity and specificity towards template protein. Graphical Abstract.

Zinc Coordinated Cationic Polymers Break Up the Paradox between Low Molecular Weight and High Transfection Efficacy.

Cationic polymers have emerged as appealing nonviral gene vectors for decades, which, however, suffer from the paradox between low molecular weight and high transfection efficacy. Low molecular weight cationic polymers (LCPs) are well cell tolerated but are perplexed by orders-of-magnitude less efficacy compared to their macromolecular counterparts. The deficiency mainly lies in weak DNA binding of polymers and difficulty in endosomal escape of formulated polyplexes. Herein, we demonstrate that, through zinc (Zn) coordinated modification of LCPs, the high transfection efficiency and low molecular weight (thus low cytotoxicity) can be achieved simultaneously. The Zn coordinated ligand shows a high affinity to phosphate components and therefore will largely benefit the DNA packaging and endosomal membrane destabilization, addressing the defects of LCPs in gene delivery. Zn coordinative functionalization of LCPs breaks up the "efficacy-toxicity" paradox and provides great promise for the development of clinically efficient and safe nonviral gene vectors.

Virus Spike and Membrane-Lytic Mimicking Nanoparticles for High Cell Binding and Superior Endosomal Escape.

Virus-inspired mimics for gene therapy have attracted increasing attention because viral vectors show robust efficacy owing to the highly infectious nature and efficient endosomal escape. Nonetheless, until now, synthetic materials have failed to achieve high "infectivity," and especially, the mimicking of virus spikes for "infection" is underappreciated. Herein, a virus spike mimic by a zinc (Zn) coordinative ligand that shows high affinity toward phosphate-rich cell membranes is reported. Surprisingly, this ligand also demonstrates superior functionality of destabilizing endosomes. Therefore, the Zn coordination is more likely to imitate the virus nature with high cell binding and endosomal membrane disruption. Following this, the Zn coordinative ligand is functionalized on a bioreducible cross-linked peptide with alkylation that imitates the viral lipoprotein shell. The ultimate virus-mimicking nanoparticle closely imitates the structures and functions of viruses, leading to robust transfection efficiency both in vitro and in vivo. More importantly, apart from targeting ligand- and cell-penetrating peptide, the metal coordinative ligand may provide another option to functionalize diverse biomaterials for enhanced efficacy, demonstrating its broad referential significance to pursue nonviral vectors with high performance.

Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA, nirS, and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity (P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile (P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria, Planctomycetes, and Cyanobacteria, the first cropping of JA with Actinobacteria, the second cropping of JA with Acidobacteria, Armatimonadetes, Gemmatimonadetes, and Proteobacteria. At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms nitrate reductase and nitrite reductase. The abundances of amoA genes decreased while nirK increased in the third cropping of JA, nirS continuously increased in the second and third cropping of JA (P < 0.05). Redundancy analysis and Mantel test found that soil organic carbon and Olsen phosphorus contents played important roles in shaping soil bacterial communities. Overall, our results revealed that continuous monocropping of JA changed soil bacterial community composition and its functional potentials.

Zinc Coordination Substitute Amine: A Noncationic Platform for Efficient and Safe Gene Delivery.

Amines have been extensively involved in vector design thus far, however, their clinical translation has been impeded by several obstacles: cytotoxicity, polyplex serum instability and low efficacy in vivo. In pursuit of functional groups to substitute amines in vector design to address these disadvantages is of great significance. Herein, we report well-tailored noncationic copolymers that contain hydrophilic, hydrophobic, and zinc coordinative moieties through reversible addition-fragmentation chain transfer (RAFT) polymerization for efficient and safe gene delivery. These polymers are capable of condensing DNA, enabling the formation of uncharged polyplexes. Especially, the zinc coordinative ligand can simultaneously benefit strong DNA binding, robust cellular uptake, efficacious endosomal destabilization, low cytotoxicity, and avoidance of serum protein adsorption. The coordinative module holds great promise to substitute amines and inspires the development of next-generation gene vectors. More importantly, the coordinative copolymers illuminate the possibility and potential of noncationic gene delivery systems for clinical applications.

Evaluation of cell death pathways initiated by antitumor drugs melatonin and valproic acid in bladder cancer cells.

Effective drug combinations have the potential to strengthen therapeutic efficacy and combat drug resistance. Both melatonin and valproic acid (VPA) exhibit antitumor activities in various cancer cells. The aim of this study was to evaluate the cell death pathways initiated by anticancer combinatorial effects of melatonin and VPA in bladder cancer cells. The results demonstrated that the combination of melatonin and VPA leads to significant synergistic growth inhibition of UC3 bladder cancer cells. Gene expression studies revealed that cotreatment with melatonin and VPA triggered the up-regulation of certain genes related to apoptosis (TNFRSF10A and TNFRSF10B), autophagy (BECN, ATG3 and ATG5) and necrosis (MLKL, PARP-1 and RIPK1). The combinatorial treatment increased the expression of endoplasmic reticulum (ER)-stress-related genes ATF6, IRE1, EDEM1 and ERdj4. Cotreatment with melatonin and VPA enhanced the expression of E-cadherin, and decreased the expression of N-cadherin, Fibronectin, Snail and Slug. Furthermore, the Wnt pathway and Raf/MEK/ERK pathway were activated by combinatorial treatment. However, the effects on the expression of certain genes were not further enhanced in cells following combinatorial treatment in comparison to individual treatment of melatonin or VPA. In summary, these findings provided evidence that cotreatment with melatonin and VPA exerted increased cytotoxicity by regulating cell death pathways in UC3 bladder cancer cells, but the clinical significance of combinatorial treatment still needs to be further exploited.