OsNPR1 Enhances Rice Resistance to Xanthomonas oryzae pv. oryzae by Upregulating Rice Defense Genes and Repressing Bacteria Virulence Genes.

The bacteria pathogen Xanthomonas oryzae pv. oryzae (Xoo) infects rice and causes the severe disease of rice bacteria blight. As the central regulator of the salic acid (SA) signaling pathway, NPR1 is responsible for sensing SA and inducing the expression of pathogen-related (PR) genes in plants. Overexpression of OsNPR1 significantly increases rice resistance to Xoo. Although some downstream rice genes were found to be regulated by OsNPR1, how OsNPR1 affects the interaction of rice-Xoo and alters Xoo gene expression remains unknown. In this study, we challenged the wild-type and OsNPR1-OE rice materials with Xoo and performed dual RNA-seq analyses for the rice and Xoo genomes simultaneously. In Xoo-infected OsNPR1-OE plants, rice genes involved in cell wall biosynthesis and SA signaling pathways, as well as PR genes and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, were significantly upregulated compared to rice variety TP309. On the other hand, Xoo genes involved in energy metabolism, oxidative phosphorylation, biosynthesis of primary and secondary metabolism, and transportation were repressed. Many virulence genes of Xoo, including genes encoding components of type III and other secretion systems, were downregulated by OsNPR1 overexpression. Our results suggest that OsNPR1 enhances rice resistance to Xoo by bidirectionally regulating gene expression in rice and Xoo.

BAFinder: A Software for Unknown Bile Acid Identification Using Accurate Mass LC-MS/MS in Positive and Negative Modes.

Most LC-MS based bile acid analyses target common bile acids. The identification of unknown bile acids remains challenging in untargeted experiments. Here, a software named BAFinder was developed to improve the identification of unknown bile acids from accurate mass LC-MS/MS data in both the positive and negative ESI modes. A wide variety of bile acid structures were covered in BAFinder, including oxidized bile acids and sugar conjugates that were often ignored. The annotation of unknown bile acids was based on a thorough investigation of MS/MS fragmentation patterns of 84 bile acid reference standards in both modes. Specifically, BAFinder took the peak alignment result and MS/MS spectra, grouped candidate features in positive and negative modes, searched their representative MS/MS spectra against a MS/MS library, and used characteristic product ions and neutral losses to annotate bile acids not covered in the library. Finally, the number of hydroxyl groups and double bonds, conjugation, and isomer information of bile acids were reported with four different levels of annotation confidence. The use of BAFinder was demonstrated through successful application to the analysis of human plasma and urine samples, in which a total of 112 and 244 bile acids were annotated and 75 and 111 of them were confirmed with standards or synthesized compounds, respectively. The software is freely available at https://bafinder.github.io/.

A second FADD mediates coelomocyte apoptosis response to Vibrio splendidus infection in sea cucumber Apostichopus japonicus.

Fas-associated protein with death domain (FADD) is a pivotal adaptor protein that functions in mediating cell death, cell cycle regulation, and particular in innate immunity by the main death receptors. In this study, a second FADD gene in sea cucumber Apostichopus japonicus (termed AjFADD-2) was cloned and its potential function in the innate responses was analyzed. The full-length cDNA of AjFADD-2 consists of 2405 bp and contains a 47 bp 5'-untranslated region (UTR), a 1629 bp 3'-UTR, and a 729 bp ORF encoding 242 amino acids. AjFADD-2 possesses two conserved domains of intracellular N-terminal death effector domain and an extracellular C-terminal death domain, which is different from the first cloned FADD gene in A. japonicus that only possesses the death domain. AjFADD-2 was examined in all sampled six tissues and was significantly induced in V. splendidus-challenged sea cucumbers and LPS-exposed coelomocytes. Subcellular localization detection showed that AjFADD-2 was primarily observed in the coelomocyte cytoplasm, and transferred to the nucleus post V. splendidus challenge. Consistently, AjFADD-2 knockdown significantly inhibited apoptosis in V. splendidus-challenged sea cucumbers and LPS-exposed coelomocytes. Taken together, our results provided evidence that AjFADD functioned as a positive regulator of coelomocytes apoptosis in response to pathogen V. splendidus challenge.

EN1 Regulates Cell Growth and Proliferation in Human Glioma Cells via Hedgehog Signaling.

Glioblastoma is an aggressive cancer of the nervous system that accounts for the majority of brain cancer-related deaths. Through cross-species transcriptome studies, we found that Engrailed 1 (EN1) is highly expressed in serum-free cultured glioma cells as well as glioma tissues, and increased expression level predicts a worse prognosis. EN1 controls glioma cell proliferation, colony formation, migration, and tumorigenic capacity in vivo. It also influences sensitivity of glioma cells to γ-ray irradiation by regulating intracellular ROS levels. Mechanistically, EN1 influences Hedgehog signaling by regulating the level of Gli1 as well as primary cilia length and the primary cilia transport-related protein TULP3. In conclusion, we demonstrate that EN1 acts as an oncogenic regulator that contributes to glioblastoma pathogenesis and could serve as a diagnostic/prognostic marker and therapeutic target for glioblastoma.

Medicinal Chemistry of Anti-HIV-1 Latency Chemotherapeutics: Biotargets, Binding Modes and Structure-Activity Relationship Investigation.

The existence of latent viral reservoirs (LVRs), also called latent cells, has long been an acknowledged stubborn hurdle for effective treatment of HIV-1/AIDS. This stable and heterogeneous reservoir, which mainly exists in resting memory CD4+ T cells, is not only resistant to highly active antiretroviral therapy (HAART) but cannot be detected by the immune system, leading to rapid drug resistance and viral rebound once antiviral treatment is interrupted. Accordingly, various functional cure strategies have been proposed to combat this barrier, among which one of the widely accepted and utilized protocols is the so-called 'shock-and-kill' regimen. The protocol begins with latency-reversing agents (LRAs), either alone or in combination, to reactivate the latent HIV-1 proviruses, then eliminates them by viral cytopathic mechanisms (e.g., currently available antiviral drugs) or by the immune killing function of the immune system (e.g., NK and CD8+ T cells). In this review, we focuse on the currently explored small molecular LRAs, with emphasis on their mechanism-directed drug targets, binding modes and structure-relationship activity (SAR) profiles, aiming to provide safer and more effective remedies for treating HIV-1 infection.

Data Driven Model-Free Adaptive Control Method for Quadrotor Formation Trajectory Tracking Based on RISE and ISMC Algorithm.

In order to solve the problems of complex dynamic modeling and parameters identification of quadrotor formation cooperative trajectory tracking control, this paper proposes a data-driven model-free adaptive control method for quadrotor formation based on robust integral of the signum of the error (RISE) and improved sliding mode control (ISMC). The leader-follower strategy is adopted, and the leader realizes trajectory tracking control. A novel asymptotic tracking data-driven controller of quadrotor is used to control the system using the RISE method. It is divided into two parts: The inner loop is for attitude control and the outer loop for position control. Both use the RISE method in the loop to eliminate interference and this method only uses the input and output data of the unmanned aerial vehicle(UAV) system and does not rely on any dynamics and kinematics model of the UAV. The followers realize formation cooperative control, introducing adaptive update law and saturation function to improve sliding mode control (SMC), and it eliminates the general SMC algorithm controller design dependence on the mathematical model of the UAV and has the chattering problem. Then, the stability of the system is proved by the Lyapunov method, and the effectiveness of the algorithm and the feasibility of the scheme are verified by numerical simulation. The experimental results show that the designed data-driven model-free adaptive control method for the quadrotor formation is effective and can effectively realize the coordinated formation trajectory tracking control of the quadrotor. At the same time, the design of the controller does not depend on the UAV kinematics and dynamics model, and it has high control accuracy, stability, and robustness.

The calcium-dependent protein kinase ZmCDPK7 functions in heat-stress tolerance in maize.

Global warming poses a serious threat to crops. Calcium-dependent protein kinases (CDPKs)/CPKs play vital roles in plant stress responses, but their exact roles in plant thermotolerance remains elusive. Here, we explored the roles of heat-induced ZmCDPK7 in thermotolerance in maize. ZmCDPK7-overexpressing maize plants displayed higher thermotolerance, photosynthetic rates, and antioxidant enzyme activity but lower H2 O2 and malondialdehyde (MDA) contents than wild-type plants under heat stress. ZmCDPK7-knockdown plants displayed the opposite patterns. ZmCDPK7 is attached to the plasma membrane but can translocate to the cytosol under heat stress. ZmCDPK7 interacts with the small heat shock protein sHSP17.4, phosphorylates sHSP17.4 at Ser-44 and the respiratory burst oxidase homolog RBOHB at Ser-99, and upregulates their expression. Site-directed mutagenesis of sHSP17.4 to generate a Ser-44-Ala substitution reduced ZmCDPK7's enhancement of catalase activity but enhanced ZmCDPK7's suppression of MDA accumulation in heat-stressed maize protoplasts. sHSP17.4, ZmCDPK7, and RBOHB were less strongly upregulated in response to heat stress in the abscisic acid-deficient mutant vp5 versus the wild type. Pretreatment with an RBOH inhibitor suppressed sHSP17.4 and ZmCDPK7 expression. Therefore, abscisic acid-induced ZmCDPK7 functions both upstream and downstream of RBOH and participates in thermotolerance in maize by mediating the phosphorylation of sHSP17.4, which might be essential for its chaperone function.

Synthesis of Active Hexafluoroisopropyl Benzoates via a Multicomponent Reaction.

Herein, we describe an efficient, practical free-metal rapid access to active hexafluoroisopropyl benzoates from anthranils, hexafluoroisopropanol, and N-alkoxy α-halogenoacetamides. Notably, this process includes anthranils that underwent a distinct pattern reaction. The protocol has good functional group tolerance and a broad substrate scope. Using a simple and general method, we accomplished potential synthetic application of active ester.

An efficient synthesis of oxazolines via a cascade reaction between azaoxyallyl cations and 1,2-benzisoxazoles.

A formal [3 + 2] cycloaddition reaction between the C and O terminals of azaoxyallyl cations formed in situ and 1,2-benzisoxazoles has been realized. This one-pot cycloaddition method provided an effective and practical pathway to synthesize oxazoline in good yields under mild conditions. The title products exhibited unique fluorescence properties.

Novel Triazolopyridine-Based BRD4 Inhibitors as Potent HIV-1 Latency Reversing Agents.

Bromodomain-containing protein 4 (BRD4) inhibitors have been proven to be a promising option for anti-HIV-1 latency therapeutics. We herein describe the design, synthesis, and anti-HIV-1 latency bioevaluation of triazolopyridine derivatives as BRD4 inhibitors. Among them, compound 13d displayed favorable HIV-1 reactivation and prominent safety profile without triggering abnormal immune activation. It exerted strong synergism when combined with the PKC activator prostratin and has the same BRD4-targeting latency mechanism as observed with JQ1, by stimulating Tat-dependent HIV-1 elongation. Besides, it neither affected the antiviral efficacies of antiviral drugs nor caused secondary infections to uninfected cells and the latency reversing potency of 13d, in turn, was not affected by different classes of antiviral drugs.

Assessing the Foodshed and Food Self-Sufficiency of the Pearl River Delta Megacity Region in China.

Food self-sufficiency has long been regarded as essential for understanding and managing urban and regional food systems; however, few studies have examined the food self-sufficiency of megacity regions within a comprehensive framework that distinguishes different types of agricultural land (i.e., arable land, horticultural landscapes, and waters). To fill these gaps, we took the Pearl River Delta as a case study and quantified the foodsheds of different types of agricultural land by calculating the land footprint of food consumption. On this basis, food self-sufficiency is defined as the ratio of available and required agricultural area for regional food demand. The results indicated that the self-sufficiency level provided by the arable land in the Pearl River Delta is low and cannot realize self-sufficiency at the regional and urban levels. The horticultural landscapes can provide self-sufficiency at the regional level, whereas the regions with water cannot, as their foodsheds extend over the boundary of the Pearl River Delta. For arable land, establishing a localized regional food system requires expanding the foodshed size. These findings provide evidence that megacity regions may face increasing difficulties in achieving self-sufficiency in the near future. This research can improve policymakers' understanding of the sustainability and resilience of regional food systems in megacity regions.

A hyaluronic acid/silk fibroin/poly-dopamine-coated biomimetic hydrogel scaffold with incorporated neurotrophin-3 for spinal cord injury repair.

Bio-factor stimulation is essential for axonal regeneration in the central nervous system. Thus, persistent and efficient factor delivery in the local microenvironment is an ideal strategy for spinal cord injury repair. We developed a biomimetic hydrogel scaffold to load biofactors in situ and release them in a controlled way as a promising therapeutic modality. Hyaluronic acid and silk fibroin were cross-linked as the basement of the scaffolds, and poly-dopamine coating was used to further increase the loading of factors and endow the hydrogel scaffolds with ideal physical and chemical properties and proper biocompatibility. Notably, neurotrophin-3 release from the hydrogel scaffolds was prolonged to 28 days. A spinal cord injury model was constructed for hydrogel scaffold transplantation. After eight weeks, significant NF200-positive nerve fibers were observed extending across the glial scar to the center of the injured area. Due to the release of neurotrophin-3, spinal cord regeneration was enhanced, and the cavity area of the injury graft site and inflammation associated with CD68 positive cells were reduced, which led to a significant improvement in hind limb motor function. The results show that the hyaluronic acid/silk fibroin/poly-dopamine-coated biomimetic hydrogel scaffold achieved locally slow release of neurotrophin-3, thus facilitating the regeneration of injured spinal cord. STATEMENT OF SIGNIFICANCE: Hydrogels have received great attention in spinal cord regeneration. Current research has focused on more efficient and controlled release of bio-factors. Here, we adopted a mussel-inspired strategy to functionalize the hyaluronic acid/silk fibroin hydrogel scaffold to increase the load of neurotrophin-3 and extend the release time. The hydrogel scaffolds have ideal physiochemical properties, proper release rate, and biocompatibility. Owing to the continuous neurotrophin-3 release from implanted scaffolds, cavity formation is reduced, inflammation alleviated, and spinal cord regeneration enhanced, indicating great potential for bio-factor delivery in soft tissue regeneration applications.

A homogeneous dopamine-silver nanocomposite coating: striking a balance between the antibacterial ability and cytocompatibility of dental implants.

Silver has been widely used for surface modification to prevent implant-associated infections. However, the inherent cytotoxicity of silver greatly limited the scope of its clinical applications. The construction of surfaces with both good antibacterial properties and favorable cytocompatibility still remains a challenge. In this study, a structurally homogeneous dopamine-silver (DA/Ag) nanocomposite was fabricated on the implant surface to balance the antibacterial activity and cytocompatibility of the implant. The results show that the DA/Ag nanocomposites prepared under the acidic conditions (pH = 4) on the titanium surface are homogeneous with higher Ag+ content, while an obvious core (AgNPs)-shell (PDA) structure is formed under neutral (pH = 7) and alkaline conditions (pH = 10), and the subsequent heat treatment enhanced the stability of PDA-AgNPs nanocomposite coatings on porous titanium. The antibacterial test, cytotoxicity test, hypodermic implantation and osteogenesis test revealed that the homogeneous PDA-AgNPs nanocomposite coating achieved the balance between the antibacterial ability and cytocompatibility, and had the best outcomes for soft tissue healing and bone formation around the implants. This study provides a facile strategy for preparing silver-loaded surfaces with both good antibacterial effect and favorable cytocompatibility, which is expected to further improve the therapeutic efficacy of silver composite-coated dental implants.

Knockdown of polypyrimidine tract binding protein facilitates motor function recovery after spinal cord injury.

After spinal cord injury (SCI), a fibroblast- and microglia-mediated fibrotic scar is formed in the lesion core, and a glial scar is formed around the fibrotic scar as a result of the activation and proliferation of astrocytes. Simultaneously, a large number of neurons are lost in the injured area. Regulating the dense glial scar and replenishing neurons in the injured area are essential for SCI repair. Polypyrimidine tract binding protein (PTB), known as an RNA-binding protein, plays a key role in neurogenesis. Here, we utilized short hairpin RNAs (shRNAs) and antisense oligonucleotides (ASOs) to knock down PTB expression. We found that reactive spinal astrocytes from mice were directly reprogrammed into motoneuron-like cells by PTB downregulation in vitro. In a mouse model of compression-induced SCI, adeno-associated viral shRNA-mediated PTB knockdown replenished motoneuron-like cells around the injured area. Basso Mouse Scale scores and forced swim, inclined plate, cold allodynia, and hot plate tests showed that PTB knockdown promoted motor function recovery in mice but did not improve sensory perception after SCI. Furthermore, ASO-mediated PTB knockdown improved motor function restoration by not only replenishing motoneuron-like cells around the injured area but also by modestly reducing the density of the glial scar without disrupting its overall structure. Together, these findings suggest that PTB knockdown may be a promising therapeutic strategy to promote motor function recovery during spinal cord repair.

A programmed surface on dental implants sequentially initiates bacteriostasis and osseointegration.

Osteogenesis surrounding dental implants is initiated by a series of early physiological events, including the inflammatory response. However, the persistence of an anti-infection surface often results in compromised histocompatibility and osseointegration. Here, we presented a programmed surface containing both silver nanoparticles (AgNPs) and silver ions (Ag+) with a heterogeneous structure and time-dependent functionalities. The AgNPs were located at the surface of the heparin-chitosan polyelectrolyte coating (PEM), whereas Ag+ was distributed at both the surface and inside of the coating under optimized conditions (pH=4). The optimized coating (Ag-4) exhibited potent bactericidal activity at the early stage (12 and 24 h after inoculation) and a sustained antibacterial efficacy in the subsequent stage (one or two weeks), as it gradually depleted. Furthermore, compared to coatings with sustained high silver concentrations in bacteria-cell coculture experiments, the degradable Ag-4 coating demonstrated improved cytocompatibility, better cell viability, and morphology over time. At a later stage (within one month), the in vivo test revealed that Ag-4-coated titanium had superior histocompatibility and osteogenesis outcomes compared to bare titanium in a bacteria-exposed environment. The programmed surface of dental implants presented in this study offers innovative ideas for sequential antibacterial effects and osseointegration.

Application and prospects of somatic cell reprogramming technology for spinal cord injury treatment.

Spinal cord injury (SCI) is a serious neurological trauma that is challenging to treat. After SCI, many neurons in the injured area die due to necrosis or apoptosis, and astrocytes, oligodendrocytes, microglia and other non-neuronal cells become dysfunctional, hindering the repair of the injured spinal cord. Corrective surgery and biological, physical and pharmacological therapies are commonly used treatment modalities for SCI; however, no current therapeutic strategies can achieve complete recovery. Somatic cell reprogramming is a promising technology that has gradually become a feasible therapeutic approach for repairing the injured spinal cord. This revolutionary technology can reprogram fibroblasts, astrocytes, NG2 cells and neural progenitor cells into neurons or oligodendrocytes for spinal cord repair. In this review, we provide an overview of the transcription factors, genes, microRNAs (miRNAs), small molecules and combinations of these factors that can mediate somatic cell reprogramming to repair the injured spinal cord. Although many challenges and questions related to this technique remain, we believe that the beneficial effect of somatic cell reprogramming provides new ideas for achieving functional recovery after SCI and a direction for the development of treatments for SCI.

Controllable AgNPs encapsulation to construct biocompatible and antibacterial titanium implant.

Silver nanoparticles (AgNPs) are progressively becoming an in-demand material for both medical and life use due to their effective antimicrobial properties. The high surface area-to-volume ratio endows AgNPs with enhanced antibacterial capacity accompanied by inevitable cytotoxicity. Surface coating technique could precisely regulate the particle shape, aggregation, and Ag+ release pattern of AgNPs, by which the cytotoxicity could be significantly reduced. Various coating methods have been explored to shell AgNPs, but it remains a great challenge to precisely control the aggregation state of AgNPs and their shell thickness. Herein, we proposed a simple method to prepare a tunable polydopamine (pDA) coating shell on AgNPs just by tuning the reaction pH and temperature, yet we obtained high antibacterial property and excellent biocompatibility. SEM and TEM revealed that pDA coated AgNPs can form core-shell structures with different aggregation states and shell thickness. Both in vitro and in vivo antibacterial tests show that acid condition and heat-treatment lead to appropriate AgNPs cores and pDA shell structures, which endow Ti with sustained antibacterial properties and preferable cell compatibility. One month of implantation in an infected animal model demonstrated that the obtained surface could promote osteogenesis and inhibit inflammation due to its strong antibacterial properties. Therefore, this study provides a promising approach to fabricate biocompatible antibacterial surface.

Intraspecific Diversity of Fission Yeast Mitochondrial Genomes.

The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.

Identification of entacapone as a chemical inhibitor of FTO mediating metabolic regulation through FOXO1.

Recent studies have established the involvement of the fat mass and obesity-associated gene (FTO) in metabolic disorders such as obesity and diabetes. However, the precise molecular mechanism by which FTO regulates metabolism remains unknown. Here, we used a structure-based virtual screening of U.S. Food and Drug Administration-approved drugs to identify entacapone as a potential FTO inhibitor. Using structural and biochemical studies, we showed that entacapone directly bound to FTO and inhibited FTO activity in vitro. Furthermore, entacapone administration reduced body weight and lowered fasting blood glucose concentrations in diet-induced obese mice. We identified the transcription factor forkhead box protein O1 (FOXO1) mRNA as a direct substrate of FTO, and demonstrated that entacapone elicited its effects on gluconeogenesis in the liver and thermogenesis in adipose tissues in mice by acting on an FTO-FOXO1 regulatory axis.

Quantitative Proteomic Analyses Identify ABA-Related Proteins and Signal Pathways in Maize Leaves under Drought Conditions.

Drought stress is one of major factors resulting in maize yield loss. The roles of abscisic acid (ABA) have been widely studied in crops in response to drought stress. However, more attention is needed to identify key ABA-related proteins and also gain deeper molecular insights about drought stress in maize. Based on this need, the physiology and proteomics of the ABA-deficient maize mutant vp5 and its wild-type Vp5 under drought stress were examined and analyzed. Malondialdehyde content increased and quantum efficiency of photosystem II decreased under drought stress in both genotypes. However, the magnitude of the increase or decrease was significantly higher in vp5 than in Vp5. A total of 7051 proteins with overlapping expression patterns among three replicates in the two genotypes were identified by Multiplex run iTRAQ-based quantitative proteomic and liquid chromatography-tandem mass spectrometry methods, of which the expression of only 150 proteins (130 in Vp5, 27 in vp5) showed changes of at least 1.5-fold under drought stress. Among the 150 proteins, 67 and 60 proteins were up-regulated and down-regulated by drought stress in an ABA-dependent way, respectively. ABA was found to play active roles in regulating signaling pathways related to photosynthesis, oxidative phosphorylation (mainly related to ATP synthesis), and glutathione metabolism (involved in antioxidative reaction) in the maize response to drought stress. Our results provide an extensive dataset of ABA-dependent, drought-regulated proteins in maize plants, which may help to elucidate the underlying mechanisms of ABA-enhanced tolerance to drought stress in maize.