Phytochrome-interacting factor 4 (PIF4) inhibits expression of SHORT HYPOCOTYL 2 (SHY2) to promote hypocotyl growth during shade avoidance in Arabidopsis.

Plants sense the presence of competing neighboring vegetation as a change in light quality. These changes initiate shade avoidance syndrome (SAS) responses. PHYTOCHROME INTERACTING FACTORS (PIFs) are crucial factors in the SAS response. In particular, they mediate the expression of multiple phytohormones and cell expansion genes. Many positive regulatory factors in the SAS response have been identified, but the negative regulation of SAS transcription factors remains poorly understood. The functions of the short hypocotyl 2 (SHY2) transcription factor during the SAS response have not been established, although its roles in the participating hormone and stress responses are well documented. Here, the SHY2 loss-of-function (shy2-31) mutant had a longer hypocotyl, but the gain-of-function (shy2-2) hypocotyl was shorter than that of the wild type under white and shade conditions. We showed that the SHY2 expression level and its associated protein significantly accumulated under shade conditions. Furthermore, SHY2 transcript levels significantly increased in mutant pifQ, but decreased in PIF4OX compared to the wild type, which indicated that PIF4 is a transcriptional repressor of SHY2. ChIP assays have consistently shown that PIF4 directly binds to the promoters of SHY2. We further show that PIF4OX partially rescued the short hypocotyl characteristic of shy2-2 under white and shade conditions. Our results provide new insights into the regulatory mechanisms controlling SAS mediated elongation of the hypocotyl by PIF4-SHY2 modules in Arabidopsis.

An identified PfHMGB1 promotes microcystin-LR-induced liver injury of yellow catfish (Pelteobagrus fulvidraco).

Microcystin-LR (MC-LR) is a potent hepatotoxin that can cause liver inflammation and injury. However, the mode of action of related inflammatory factors is not fully understood. PfHMGB1 is an inflammatory factor induced at the mRNA level in the liver of juvenile yellow catfish (Pelteobagrus fulvidraco) that were intraperitoneally injected with 50 µg/kg MC-LR. The PfHMGB1 mRNA level was highest in the liver and muscle among 11 tissues examined. The full-length cDNA sequence of PfHMGB1 was cloned and overexpressed in E. coli, and the purified protein rPfHMGB1 demonstrated DNA binding affinity. Endotoxin-free rPfHMGB1 (6-150 µg/mL) also showed dose-dependent hepatotoxicity and induced inflammatory gene expression of primary hepatocytes. PfHMGB1 antibody (anti-PfHMGB1) in vitro reduced MC-LR (30 and 50 µmol/L)-induced hepatotoxicity, suggesting PfHMGB1 is important in the toxic effects of MC-LR. In vivo study showed that MC-LR upregulated PfHMGB1 protein in the liver. The anti-PfHMGB1 blocked its counterpart and reduced ALT/AST activities after MC-LR exposure. Anti-PfHMGB1 partly neutralized MC-LR-induced hepatocyte disorganization, nucleus shrinkage, mitochondria, and rough endoplasmic reticula destruction. These findings suggest that PfHMGB1 promotes MC-LR-induced liver damage in the yellow catfish. HMGB1 may help protect catfish against widespread microcystin pollution.

PfHMGB2 protects yellow catfish (Pelteobagrus fulvidraco) from bacterial infection by promoting phagocytosis and proliferation of PBL.

HMGB2, a member of the high mobility group box family, plays an important role in host immune responses. However, the mechanism of action of HMGB2 is not well understood. Herein, a homologue from yellow catfish (Pelteobagrus fulvidraco) was cloned and named PfHMGB2. The deduced amino acid sequence of PfHMGB2 possessed a typical tripartite structure (two DNA binding boxes and an acid tail) and shared 90% identity with the predicted HMGB2 from I. punctatus. The mRNA of PfHMGB2 was widely distributed in all 11 tested tissues in healthy fish bodies and was significantly induced in the liver and head kidney when yellow catfish were injected with inactivated Aeromonas hydrophila. Consistently, PfHMGB2 mRNA could also be induced in yellow catfish peripheral blood leucocytes (PBL) by lipopolysaccharide. The recombinant PfHMGB2 protein was purified from E. coli BL21 (DE3):pET-28a/PfHMGB2 and showed DNA-binding affinity. Moreover, rPfHMGB2 improved the phagocytosis and proliferation activity and upregulated the mRNA expression of the pro-inflammatory cytokine TNFα in yellow catfish PBL. These results indicated that PfHMGB2 could protect yellow catfish from pathogen infection by activating PBL.

Differential proteome analysis of the cell differentiation regulated by BCC, CRH, CXCR4, GnRH, GPCR, IL1 signaling pathways in Chinese fire-bellied newt limb regeneration.

Following amputation, the newt has the remarkable ability to regenerate its limb, and this process involves dedifferentiation, proliferation and differentiation. To investigate the potential proteome during a dynamic network of Chinese fire-bellied newt limb regeneration (CNLR), two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrum (MS) were applied to examine changes in the proteome that occurred at 11 time points after amputation. Meanwhile, several proteins were selected to validate their expression levels by Western blot. The results revealed that 1476 proteins had significantly changed as compared to the control group. Gene Ontology annotation and protein network analysis by Ingenuity Pathway Analysis 9.0 (IPA) software suggested that the differentially expressed proteins were involved in 33 kinds of physiological activities including signal transduction, cell proliferation, cell differentiation, etc. Among these proteins, 407 proteins participated in cell differentiation with 212 proteins in the differentiation of skin cell, myocyte, neurocyte, chondrocyte and osteocyte, and 37 proteins participated in signaling pathways of BCC, CRH, CXCR4, GnRH, GPCR and IL1 which regulated cell differentiation and redifferentiation. On the other hand, the signal transduction activity and cell differentiation activity were analyzed by IPA based on the changes in the expression of these proteins. The results showed that BCC, CRH, CXCR4, GnRH, GPCR and IL1 signaling pathways played an important role in regulating the differentiation of skin cell, myocyte, neurocyte, chondrocyte and osteocyte during CNLR.

[Mechanism of 5'-to-3' degradation of eukaryotic and prokaryotic mRNA].

RNA degradation plays an important role in modulating gene expression and it affects multiple biological processes. There are three common degradation mechanisms of eukaryotic and prokaryotic mRNA: endonucleolytic, 5'-to-3' and 3'-to-5' exonucleolytic degradation. Differences do exist between the two kingdoms. For example, although the 5'-to-3' exoribonucleolytic degradation is the primary degradation mechanism of eukaryotic mRNA, it plays a minimal role in bacteria, and only in Gram-positive bacteria. Recently, novel RNA degradation mechanisms have been revealed, such as a new eukaryotic mRNA decapping mode mediated by 3'-uridylation and a new 3'-to-5' degradation pathway independent of exosome. These accumulating discoveries not only deepen the insight of mRNA degradation mechanisms, but also may contribute to the development of novel therapeutic drugs targeting parasites, viruses or cancer. In this review, we summarize the current knowledge of 5'-to-3' exonucleolytic degradation pathway of eukaryotic and prokaryotic mRNA, and its future therapeutic perspectives.

A wireless fatigue monitoring system utilizing a bio-inspired tree ring data tracking technique.

Fatigue, a hot scientific research topic for centuries, can trigger sudden failure of critical structures such as aircraft and railway systems, resulting in enormous casualties as well as economic losses. The fatigue life of certain structures is intrinsically random and few monitoring techniques are capable of tracking the full life-cycle fatigue damage. In this paper, a novel in-situ wireless real-time fatigue monitoring system using a bio-inspired tree ring data tracking technique is proposed. The general framework, methodology, and verification of this intelligent system are discussed in details. The rain-flow counting (RFC) method is adopted as the core algorithm which quantifies fatigue damages, and Digital Signal Processing (DSP) is introduced as the core module for data collection and analysis. Laboratory test results based on strain gauges and polyvinylidene fluoride (PVDF) sensors have shown that the developed intelligent system can provide a reliable quick feedback and early warning of fatigue failure. With the merits of low cost, high accuracy and great reliability, the developed wireless fatigue sensing system can be further applied to mechanical engineering, civil infrastructures, transportation systems, aerospace engineering, etc.

The complete mitochondrial genome of Phymateus saxosus (Coquerel, 1861) (Orthoptera: Pyrgomorphidae) and phylogenetic analysis.

Phymateus saxosus is a member of the family Pyrgomorphidae, Orthoptera. In this study, the complete mitochondrial genome (mitogenome) of P. saxosus was determined and analyzed. Assembled mitogenome sequence of P. saxosus is 15,672 bp in size, containing 37 genes and a control region. The gene orientation and arrangement of P. saxosus are identical to other species in the Pyrgomorphoidea family. The overall nucleotide composition is as follows: A (43.6%) > T (30.2%) > C (16.1%) > G (10.1%). Phylogenetic analysis suggested that P. saxosus forms sister groups with P. morbillosus, and the monophyly of Pyrgomorphidae is supported. In general, this study provided valuable genetic information for P. saxosus and explored the phylogenetic relationships in the family Pyrgomorphidae.

[A new target of antibacterial drugs: bacterial mRNA degradation pathways].

In bacteria, mRNA degradation plays an essential role, not only in recycling nucleotides but also in controlling gene expression in response to rapid changing growth conditions. In addition, many ribonucleases in this process can control pathogenesis by regulation of virulent factors' expression and secretion, bacterial motility and invasion, or host cell apoptosis induction. Because a great difference in mRNA degradation machinery and ribonucleases exists between bacteria and eukaryotes, it makes mRNA degradation pathways possible to serve as a potential target for exploiting antimicrobial drugs, or new platform to reduce their virulence for vaccine preparation, for combating rapid emergence of bacteria drug-resistance. In this review, the general bacterial mRNA degradation pathways and the role of RNase R, PNPase, RNase Y, RNase III, and RNase E in pathogenesis were discussed. Furthermore, the perspective of application of mRNA decay machinery for exploiting novel antibacterial targets was also speculated.

[The fidelity mechanism of DNA synthesis].

Accurate DNA synthesis is vital to maintain genome stability and ensure propagation of species. Synthetic errors have far reaching consequences. Therefore, DNA synthesis is remarkably accurate. The high fidelity is mainly achieved through three steps: ① nucleotide selection, which is based on hydrogen, base pair shape, or some other elements; ② 3'→5' exonuclease proofreading, which removes mis-incorporated nucleotides in cis or trans; ③ repair process, which could correct mismatched nucleotides escaping from proofreading, such as mismatch repair, excission repair, homologous recombination repair, and translesion DNA synthesis. Because all polymerases are suitable targets for anticancer or antiviral drugs, their fidelity is involved in drug resistance and side effects. Understanding the molecular basis of synthesis fidelity is of vital importance. In this review, the fidelity mechanisms of DNA synthesis will be discussed in detail. Furthermore, their application perspective was discussed.

[Relevance of the expression of CTNNAL1 and the resistance of respiratory tract in rat with airway hyperresponsiveness].

OBJECTIVE: To observe the relation between the expression of CTNNAL1 and the airway resistance in rats with airway hyperresponsiveness. METHODS: Thirty Wister rats were randomly divided into 5 groups: a normal control group, a 2 d ozone attack group, a 4 d ozone attack group, a 6 d ozone attack group, and a 6 d ozone attack+2 d dexamethasone treatment group (6 rats in each group). The distribution of CTNNAL1 was observed by in situ hybridization; the expression of CTNNAL1 was detected by fluorescence quantitative RT-PCR; the airway resistance was detected in by Buxco pulmonary function analysis system; and the relevance of the expression of CTNNAL1 and the resistance of respiratory tract in rat with airway hyperresponsiveness were analyzed. RESULTS: CTNNAL1 was distributed in bronchial epithelial cells, goblet cells, endothelial cells, and the alveolar wall. With the increase of the ozone attack, the expression of CTNNAL1 mRNA gradually reduced, the airway hyperresponsiveness was aggravated, and the airway resistance was increased. CONCLUSION: During airway hyperresponse, the reduction of CTNNAL1 mRNA can increase the airway resistance. There is a negative correlation between the reduction of CTNNAL1 mRNA and the airway hyperresponsiveness. CTNNAL1 is an adhesion molecule related to airway hyperresponsiveness susceptibility.

TNFAIP3 alleviates pain in lumbar disc herniation rats by inhibiting the NF-κB pathway.

Background: It's been reported that the tumor necrosis factor alpha inducible protein 3 (TNFAIP3) gene played an important role in the pathogenesis of autoimmune and chronic inflammation diseases. Moreover, in degenerative diseases of the lumbar spine the nuclear factor-κB (NF-κB) pathway is significantly activated. This study aimed to explore the role of the tumor necrosis protein-induced zinc finger protein A20 (A20) protein in degenerative diseases of the lumbar spine on the NF-κBp65 pathway. Methods: A total of 96 rats were randomly divided into 4 groups. Lumbar disc herniation (DH) was set as a sham operation group (Sham group), DH + A20 group and DH + control group (Control group); measured changes in rat paw withdrawal threshold (PWT) and paw withdrawal latency (PWL); detected the proportion of apoptotic cells in a single nucleus pulposus cell suspension, analyzed the correlation between tumor necrosis factor-α (TNF-α) content and pain in DH rats, and the expression changes of NF-κB pathway in nucleus pulposus tissue. Results: compared with the DH + Control group, the PWT and PWL of the DH + A20 group increased significantly (P<0.05); apoptosis in the DH + A20 group was significantly reduced (P<0.01); the nucleus pulposus tissue and serum levels of TNF-α and interleukin-6 (IL-6) in the DH + A20 rat group were significantly lower than those in the DH + Control group (P<0.05); the protein expression of rats in the DH + A20 group (p-p65) was significantly lower than that in the DH + Control group (P<0.05). Conclusions: The pain of lumbar disc herniation rats is related to TNF-α, and overexpression of A20 protein can reduce the pain of lumbar disc herniation by inhibiting the NF-κB pathway. Keywords: Lumbar disc herniation (lumbar DH); tumor necrosis factor-α (TNF-α); interleukin-6 (IL-6); tumor necrosis factor alpha inducible protein 3 (TNFAIP3).

5-allyl-7-gen-difluoromethoxychrysin enhances TRAIL-induced apoptosis in human lung carcinoma A549 cells.

BACKGROUND: 5-allyl-7-gen-difluoromethoxychrysin (AFMC) is a novel synthetic analogue of chrysin that has been reported to inhibit proliferation in various cancer cell lines. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a promising anti-cancer agent. METHODS: The cytotoxicity of A549 and WI-38 cells were determined using colorimetry. Apoptosis was detected by flow cytometry (FCM) after propidium iodide (PI) fluorescence staining and agarose gel electrophoresis. Caspase activities were evaluated using enzyme-linked immunosorbent assay (ELISA).The expressions of DR4 and DR5 were analyzed using FCM and western blot. RESULTS: Subtoxic concentrations of AFMC sensitize human non-small cell lung cancer (NSCLC) A549 cells to TRAIL-mediated apoptosis. Combined treatment of A549 cells with AFMC and TRAIL significantly activated caspase-3, -8 and -9. The caspase-3 inhibitor zDEVD-fmk and the caspase-8 inhibitor zIETD-fmk blocked the apoptosis of A549 cells induced by co-treatment with AFMC and TRAIL. In addition, we found that treatment of A549 cells with AFMC significantly induced the expression of death receptor 5 (DR5). AFMC-mediated sensitization of A549 cells to TRAIL was efficiently reduced by administration of a blocking antibody or small interfering RNAs against DR5. AFMC also caused increase of the Sub-G1 cells by TRAIL treatment and increased the expression levels of DR5 in other NSCLC H460 and H157 cell lines. In contrast, AFMC-mediated induction of DR5 expression was not observed in human embryo lung WI-38 cells, and AFMC did not sensitize WI-38 cells to TRAIL-induced apoptosis. CONCLUSIONS: AFMC synergistically enhances TRAIL-mediated apoptosis in NSCLC cells through up-regulating DR5 expression.

Self-assembled zinc/copper hydroxide carbonates with tunable hierarchical nanostructure.

Here, we report a synthetic, polymer-mediated method for the self-assembly of zinc/copper hydroxide carbonate superstructures including 3D hierarchical sunflower-like, urchin-like, alga-like, and rotiform-like zinc hydroxide carbonate (ZHC) microstructures, and hierarchical copper hydroxide carbonate (CHC) microspheres with radiating nanoplates and nanorods. As a capping agent, poly(vinylpyrrolidone) (PVP) was found to play an important role in directing the growth and self-assembly of such unique structures. The crystal structure of the products and the resulting hierarchical superstructure morphology, as controlled by the molecular weight and concentration of PVP, were systematically investigated. A possible growth mechanism for the formation of hierarchical superstructures with different morphologies is also proposed.

[The development of gene concepts].

One hundred years has passed since the term of "gene" was coined in 1909, the gene definition has been revised many times in the past 100 years. Gene has changed from an abstract symbol to a specific segment, which can produce protein or functional RNA, and finally became one of the most important biological words. With the accomplishment of the genome project, particularly the project of Encyclopedia of DNA Elements (ENCODE), our knowledge about the the complexity and diversity of genomic organization and dynamics of genomes posed important challenges to the classical molecular gene concept. As is becoming more evident that the relations between information stored at DNA level and functional products are very intricate, some people consider that it was time to make a redefinition of gene. In this review, we briefly outline gene definition of this history and the development of gene concept these days.

[Natural antisense transcript and its mechanism of gene regulation].

Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level through a variety of biological mechanisms, such as transcription interference, RNA masking, dsRNA-dependent mechanisms, and chromatin remodelling (modification). We speculated that both of sense and antisense transcripts may be sliced to form small RNAs, which is also an important mechanism for NATs to regulate gene expression, such as rasiRNAs in "ping-pong". Experimental and computational analyses have demonstrated the wide-spread occurrence of NATs in a wide range of species. Here, we reviewed the current understanding of NATs function and its mechanistic basis. We hypothesized that the regulation of antisense transcription and small RNAs were derived from NATs.

[The roles of RNA silencing in plant biotic stress].

RNA silencing is a common strategy shared by eukaryotic organisms to regulate gene expression, and also can operate as a defense mechanism against biotic stress. In plants, small RNAs play an important role in defensing against viruses, bacteria or herbivore attack, such as miRNAs and siRNAs. As a response to this defense system, both viruses and bacteria have evolved viral suppressors of RNA silencing (VSRs) or bacterial suppressors of RNA silencing (BSRs) to overcome the host silencing response, which can act at various steps of the different silencing pathways. This review highlights the current understanding and the new insights concerning of the roles of small RNAs in defensing against biotic stress and the mechanism of VSRs and BSRs in suppressing host RNA silencing in plants.

Targeting NLRP3 inflammasome improved the neurogenesis and post-stroke cognition in a mouse model of photothrombotic stroke.

Post-stroke cognitive impairment (PSCI) severely affects the quality of a survivor's life, but its neurophysiological basis remains unknown. Neuroinflammation has been considered as an important contributor to PSCI, which could be induced or exacerbated by system inflammation. NACHT-LRR- and pyrin-domain-containing protein 3 (NLRP3) inflammasome is the most widely studied in the initiation of inflammation. Here, using a mouse model of photothrombotic stroke, we demonstrated that NLRP3 activation plays a critical role in PSCI. Intraperitoneal injection of the lipopolysaccharide-activated NLRP3 inflammasome, exacerbated the microglial activation and decreased the number of neurons, impaired the hippocampal neurogenesis, eventually aggravated PSCI. Intraperitoneal injection of MCC950 inhibited the NLRP3 activation, decreased the number of microglia, increased the number of neurons and promoted the hippocampal neurogenesis, eventually improved PSCI. Our results identified NLRP3 inflammasome as an important modifier of neuropathology in PSCI, which could be a could be a potential therapeutic target for PSCI treatment.

Minute synthesis of extremely stable gold nanoparticles.

We describe a rapid environmentally friendly wet-chemical approach to synthesize extremely stable non-toxic, biocompatible, water-soluble monodispersed gold nanoparticles (AuNPs) in one step at room temperature. The particles have been successfully achieved in just a few minutes by merely adding sodium hydroxide (NaOH) acting as an initiator for the reduction of HAuCl(4) in aqueous solution in the presence of polyvinylpyrrolidone (PVP) without the use of any reducing agent. It is also proved to be highly efficient for the preparation of AuNPs with controllable sizes. The AuNPs show remarkable stability in water media with high concentrations of salt, various buffer solutions and physiological conditions in biotechnology and biomedicine. Moreover, the AuNPs are also non-toxic at high concentration (100 microM). Therefore, it provides great opportunities to use these AuNPs for biotechnology and biomedicine. This new approach also involved several green chemistry concepts, such as the selection of environmentally benign reagents and solvents, without energy consumption, and less reaction time.

[Advances in mechanism of small RNAs].

The discovery of RNA interference (RNAi) heralded a revolution in RNA biology. Researchers uncovered 'hidden' layers of regulation of gene expression, in which many previously unidentified families of small RNAs (consisting of approximately 20-30 nucleotides) mediate gene silencing in transcriptional and post-transcriptional levels. In eukaryotes, these small RNAs, including siRNAs, miRNAs, piRNAs, scnRNAs, 21U-RNAs, and some others, regulate gene expression, helping to control cellular metabolism, growth, and differentiation, to maintain genome integrity, to regulate stem cell renewal, and to combat viruses and mobile genetic elements. This review summarizes the current advancement in the identification and biosynthesis of small RNAs and their roles in gene regulation.

[The role of endogenous small RNAs in plant stress responses].

Crop yields are significantly reduced by biotic and abiotic stresses throughout the world. A better understanding of adaptive responses will lead to new strategies for improving plant stress tolerance. The molecular response of plants to stresses has been often considered as a complex process mainly based on the modulation of transcriptional activity of stress-related genes. Nevertheless, recently discovered endogenous small RNAs, such as miRNAs, nat-siRNAs and lisiRNAs, not only have a vital role in regulating plant development, but also have emerged as important players in plant stress responses. This review discusses recent advances in the field of small RNAs guided adaption to various stress responses, including oxidative stress, mineral nutrient deficiency, drought stress, salinity stress, ABA stress, mechanical stress, heavy metals stresses, biotic stresses, and other environmental stresses.