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RGLG1 is an E3 ubiquitin ligase in Arabidopsis thaliana that participates in ABA signaling and regulates apical dominance. Here, we present crystal structures of RGLG1 VWA domain, revealing two novel calcium ions binding sites (NCBS1 and NCBS2). Furthermore, the structures with guided mutagenesis in NCBS1 prove that Ca 2+ ions play important roles in controlling conformational change of VWA, which is stabilized in open state with Ca 2+ bound and converted to closed state after Ca 2+ removal. This allosteric regulation mechanism is distinct from the ever reported one involving the C-terminal helix in integrin α and β I domains. The mutation of a key residue in NCBS2 do not abolish its Ca 2+ -binding potential, with no conformational change. MD simulations reveals that open state of RGLG1 VWA has higher ligand affinity than its closed state, consisting with integrin. Structural comparison of ion-free-MIDAS with Mg 2+ -MIDAS reveals that Mg 2+ binding to MIDAS does not induce conformational change. With acquisition of first structure of plant VWA domain in both open state and closed state, we carefully analyze the conformational change and propose a totally new paradigm for its transition of open-closed states, which will be of great value for guiding future researches on VWA proteins and their important biological significance., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Authors.)

To examine the expression of P53-induced protein with a death domain (PIDD) at retina in animal model of optic nerve crush (ONC) and to investigate the role of PIDD in retinal glial activation and NF-κB activation induced by optic nerve damage, ONC animal model was established in Sprague-Dawley rats. PIDD has three isoforms (Isof); Western blot was performed to examine the expression of PIDD (Isof-1, Isof-2, and Isof-3, respectively) in retina at different time points after ONC. Retinal glial activation is closely associated with retinal neuronal death and is monitored by the expression of GFAP+ glial cells and IBA1+ microglia, then activated microglia leads to inflammatory cytokine production. NF-kB activation in glial cells also can promote neuronal death. In our study, the role of PIDD in retinal glial activation and NF-kB activation was investigated with PIDD inhibition selectively. PIDD expression (Isof-1 and Isof-3) was dramatically increased, and peaked at 3 days after ONC, while Isof-2 did not show any difference. In the ONC animal model, the number of GFAP+ glial cells and IBA1+ microglia in retinal layers was increased significantly, inflammatory cytokine production was upregulated, and NF-κB in glial cell was also activated. Moreover, those responses induced by optic nerve damage were attenuated with PIDD inhibition, which indicated that PIDD could regulate retinal glial activation, neuro-inflammation, and NF-κB activation. These results provided the direct demonstration that the PIDD (Isof-1and Isof-3) was overexpressed in retina after ONC, and PIDD may be involved in retinal neurodegenerative diseases by regulating retinal glial activation and NF-κB activation.

The nanosilver-based antibacterial composite film used as food packaging has a potential hazard of silver leakage into the human body. In this study, hyperbranched polyamide-amine (HPAMAM) was used as a template, reducing agent, and stabilizer to synthesize Ag nanoparticles (Ag NPs) in situ, and then HPAMAM anchored Ag NPs onto oxidized cellulose to construct a regenerated cellulose film with a low silver leakage for antibacterial food packaging. Alkali hydroxide/urea solution was used to dissolve cotton fibers, and the hydroxyl groups at C-2 and C-3 of the glucose residues were oxidized to two aldehyde groups by NaIO 4 . Then, HPAMAM/Ag NPs composites (Ag@HPAMAM NPs) were grafted on the oxidized cellulose by the reaction between aldehyde groups and amino groups. The Ag@HPAMAM NPs-embedded cellulose films were achieved by regenerating the dissolved cellulose with ethanol and drying naturally. With a low silver leakage (<10%), Ag@HPAMAM NPs-embedded cellulose films exhibited a strong antibacterial effect on Escherichia coli and Staphylococcus aureus and effectively extended the storage life of cherry tomatoes as food packaging. In addition, the physical properties of Ag@HPAMAM NPs-embedded cellulose films were improved due to the anchor of Ag NPs onto oxidized cellulose by HPAMAM. This study provides a strategy for synthesizing Ag@HPAMAM NPs-embedded cellulose film, which has the potential to be used as a biodegradable, renewable, and safe antibacterial food package material.

To explore the hypothesis that CD200Fc, a CD200R1 agonist with anti-inflammatory properties, will inhibit retinal glial cells hyperactivation and retinal ganglion cells (RGCs) apoptosis after optic nerve injury. CD200Fc was immediately administered after optic nerve crush (ONC) once by intravitreal injection. Rats were euthanized at 5 days after ONC. The density of RGCs was counted by immunostaining of retina flat mounts for Brn3a. TUNEL assay, immunoblotting analysis of ionized calcium-binding adapter molecule 1(iba1) (microglia marker) and glial fibrillary acidic protein (GFAP) (astrocytes and Müller cells marker), RT-PCR analysis of cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), monocyte chemotactic protein 1 (MCP-1), tumor necrosis factor-α (TNF-α), interleukin (IL)-8 and IL-10, ELISA measure protein levels of inflammatory cytokines and western blot analysis of CD200 and CD200R1 were evaluated. CD200Fc treatment suppressed ONC-induced RGCs loss through inhibition of RGCs apoptosis. Additionally, expression of glial cells activation markers GFAP and iba1 and production of pro-inflammatory cytokines (COX-2, iNOS, MCP-1, TNF-α, IL-8) were decreased in CD200Fc treated animals after ONC. Meanwhile, anti-inflammatory cytokine IL-10 was increased by CD200Fc treatment in ONC-induced rat retina. Finally, we found that CD200Fc significantly inhibited ONC-induced increased in expression of CD200 and raised the already high basal CD200R1 expression in the rat retina after ONC. Our results demonstrated that the anti-inflammatory effects of CD200Fc in ONC rats model through inhibited the activation of retinal glial cells via the interaction between CD200 and CD200R1, and the neuroprotective effects of CD200Fc on RGCs thought inhibited its apoptosis.

This corrects the article DOI: 10.1038/srep24765.

Cluster validation, which is the process of evaluating the quality of clustering results, plays an important role for practical machine learning systems. Categorical sequences, such as biological sequences in computational biology, have become common in real-world applications. Different from previous studies, which mainly focused on attribute-value data, in this paper, we work on the cluster validation problem for categorical sequences. The evaluation of sequences clustering is currently difficult due to the lack of an internal validation criterion defined with regard to the structural features hidden in sequences. To solve this problem, in this paper, a novel cluster validity index (CVI) is proposed as a function of clustering, with the intracluster structural compactness and intercluster structural separation linearly combined to measure the quality of sequence clusters. A partition-based algorithm for robust clustering of categorical sequences is also proposed, which provides the new measure with high-quality clustering results by the deterministic initialization and the elimination of noise clusters using an information theoretic method. The new clustering algorithm and the CVI are then assembled within the common model selection procedure to determine the number of clusters in categorical sequence sets. A case study on commonly used protein sequences and the experimental results on some real-world sequence sets from different domains are given to demonstrate the performance of the proposed method.

Background: Autogamy in cultivated tomato varieties is a derived trait from wild type tomato plants, which are mostly allogamous. However, environmental stresses can cause morphological defects in tomato flowers and hinder autogamy. Under elevated temperatures, tomato plants usually exhibit the phenotype of stigma exsertion, with severely hindered self-pollination and fruit setting, whereas the inherent mechanism of stigma exsertion have been hitherto unknown. Numerous small RNAs (sRNAs) have been shown to play significant roles in plant development and stress responses, however, none of them have been studied with respect to stamen and pistil development under high-temperature conditions. We investigated the associations between stigma exsertion and small RNAs using high-throughput sequencing technology and molecular biology approaches., Results: Sixteen sRNA libraries of Micro-Tom were constructed from plants stamen and pistil samples and sequenced after 2 d and 12 d of exposure to heat stress, respectively, from which a total of 110 known and 84 novel miRNAs were identified. Under heat stress conditions, 34 known and 35 novel miRNAs were differentially expressed in stamens, and 20 known and 10 novel miRNAs were differentially expressed in pistils. GO and KEGG pathway analysis showed that the predicted target genes of differentially expressed miRNAs were significantly enriched in metabolic pathways in both stamen and pistil libraries. Potential miRNA-target cleavage cascades that correlated with the regulation of stigma exsertion under heat stress conditions were found and validated through qRT-PCR and RLM-5' RACE., Conclusion: Overall, a global spectrum of known and novel miRNAs involved in tomato stigma exsertion and induced by high temperatures were identified using high-throughput sequencing and molecular biology approaches, laying a foundation for revealing the miRNA-mediated regulatory network involved in the development of tomato stamens and pistils under high-temperature conditions.

Objective: The aims of the present study were to detect the interaction of Wip1 and NF-κB P65 in retina of an LPS-induced astrocytes activation model., Methods: The interaction between Wip1 and nuclear factor kappa B (NF-κB) P65 was observed in lipopolysaccharide (LPS)-stimulated primary rat astrocytes derived from retina. The expressions of Wip1 and NF-κB P65 were evaluated using Western blot and RT-PCR. Small interfering RNA (siRNA) against Wip1 was transfected into astrocytes to clarify the phosphorylation status and nuclear translocation of NF-κB P65 and expressions of these proinflammatory factors. Meanwhile, expression of Wip1 was assessed following treatment with NF-κB inhibitor., Results: Wip1 and phospho-NF-κB P65 (p-P65) expressions were significantly increased and colocalization in astrocytes after LPS treatment. The expression of p-P65 was augmented by transfected with Wip1 siRNA followed by LPS. Furthermore, pre-treatment with Wip1 siRNA further enhanced LPS-induced NF-κB P65 translocation into the nuclei and proinflammatory cytokine release. Finally, inhibition of NF-κB decreases Wip1 expression and transcription in primary astrocytes., Conclusion: These data provide a mechanism for the role for a negative feedback loop of Wip1 and NF-κB in LPS-induced astrocytic activation.

Objective: The aims of the present study were to investigate the expression and distribution of Wild-type p53-induced phosphatase 1 (Wip1) in diabetic patients with proliferative diabetic retinopathy (PDR) with epiretinal membranes (ERMs) meanwhile analyze the colocalization of Wip1 and nuclear factor kappa-B (NF-κB) p65 in ERMs., Methods: ERMs samples were collected from patients with PDR (PDR group) or non-diabetic patients with idiopathic epiretinal membranes (iERMs) (control group) during pars plana vitrectomy. Real-Time PCR analysis was carried out to examine the mRNA expression of Wip1 in ERMs. Immunohistochemical analysis and Immunofluorescent analysis were performed to detect the protein expression of Wip1 in ERMs. Double immunofluorescent staining was performed to detect the colocalization of Wip1 and glial fibrillary acidic protein (GFAP) (retinal glial cells marker), also Wip1 and NF-κB., Results: ERMs were obtained from 17 eyes of 17 patients with PDR (the PDR group) and 9 eyes of 9 nondiabetic patients (the control group) with iERMs. Our results showed high expression levels of Wip1 mRNAs in ERMs after PDR, but low in iERMs. In addition, both immunohistochemistry and immunofluorescence assay showed strong immunoreactivity for Wip1 in PDR ERMs. Furthermore, Wip1 and GFAP were coexpressed in PDR membranes. Finally, the expression of Wip1 was paralleled with NF-κB., Conclusion: These data support the notion that Wip1 contributes to the formation of the ERMs in PDR membranes via NF-κB signaling.

Dimension reduction is a crucial technique in machine learning and data mining, which is widely used in areas of medicine, bioinformatics and genetics. In this paper, we propose a two-stage local dimension reduction approach for classification on microarray data. In first stage, a new L1-regularized feature selection method is defined to remove irrelevant and redundant features and to select the important features (biomarkers). In the next stage, PLS-based feature extraction is implemented on the selected features to extract synthesis features that best reflect discriminating characteristics for classification. The suitability of the proposal is demonstrated in an empirical study done with ten widely used microarray datasets, and the results show its effectiveness and competitiveness compared with four state-of-the-art methods. The experimental results on St Jude dataset shows that our method can be effectively applied to microarray data analysis for subtype prediction and the discovery of gene coexpression., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Tumor necrosis factor receptor 1 is the main receptor mediating many tumor necrosis factor-alpha-induced cellular events. Some studies have shown that tumor necrosis factor receptor 1 promotes tumorigenesis by activating nuclear factor-kappa B signaling pathway, while other studies have confirmed that tumor necrosis factor receptor 1 plays an inhibitory role in tumors growth by inducing apoptosis in breast cancer. Therefore, the function of tumor necrosis factor receptor 1 in breast cancer requires clarification. In this study, we first found that tumor necrosis factor receptor 1 was significantly increased in human breast cancer tissues and cell lines, and knockdown of tumor necrosis factor receptor 1 by small interfering RNA inhibited cell proliferation by arresting the cell cycle and inducing apoptosis. In addition, miR-29a was predicted as a regulator of tumor necrosis factor receptor 1 by TargetScan and was shown to be inversely correlated with tumor necrosis factor receptor 1 expression in human breast cancer tissues and cell lines. Luciferase reporter assay further confirmed that miR-29a negatively regulated tumor necrosis factor receptor 1 expression by binding to the 3' untranslated region. In our functional study, miR-29a overexpression remarkably suppressed cell proliferation and colony formation, arrested the cell cycle, and induced apoptosis in MCF-7 cell. Furthermore, in combination with tumor necrosis factor receptor 1 transfection, miR-29a significantly reversed the oncogenic role caused by tumor necrosis factor receptor 1 in MCF-7 cell. In addition, we demonstrated that miR-29a suppressed MCF-7 cell growth by inactivating the nuclear factor-kappa B signaling pathway and by decreasing cyclinD1 and Bcl-2/Bax protein levels. Taken together, our results suggest that miR-29a is an important regulator of tumor necrosis factor receptor 1 expression in breast cancer and functions as a tumor suppressor by targeting tumor necrosis factor receptor 1 to influence the growth of MCF-7 cell.

Background: Inferring the topology of gene regulatory networks (GRNs) from microarray gene expression data has many potential applications, such as identifying candidate drug targets and providing valuable insights into the biological processes. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of potential interactions., Results: We introduce an ensemble gene regulatory network inference method PLSNET, which decomposes the GRN inference problem with p genes into p subproblems and solves each of the subproblems by using Partial least squares (PLS) based feature selection algorithm. Then, a statistical technique is used to refine the predictions in our method. The proposed method was evaluated on the DREAM4 and DREAM5 benchmark datasets and achieved higher accuracy than the winners of those competitions and other state-of-the-art GRN inference methods., Conclusions: Superior accuracy achieved on different benchmark datasets, including both in silico and in vivo networks, shows that PLSNET reaches state-of-the-art performance.

Objectives: To improve 1,3-propanediol (1,3-PD) production and reduce byproduct concentration during the fermentation of Klebsiella pneumonia., Results: Klebsiella. pneumonia 2-1ΔldhA, K. pneumonia 2-1ΔaldH and K. pneumonia 2-1ΔldhAΔaldH mutant strains were obtained through deletion of the ldhA gene encoding lactate dehydrogenase required for lactate synthesis and the aldH gene encoding acetaldehyde dehydrogenase involved in the synthesis of ethanol. After fed-batch fermentation, the production of 1,3-PD from glycerol was enhanced and the concentrations of byproducts were reduced compared with the original strain K. pneumonia 2-1. The maximum yields of 1,3-PD were 85.7, 82.5 and 87.5 g/l in the respective mutant strains., Conclusion: Deletion of either aldH or ldhA promoted 1,3-PD production in K. pneumonia.

Objective: To evaluate the expression and possible roles of Wip1 in retinal astrocytes after optic nerve crush (ONC)., Methods: Expressions of Wip1, GFAP, and p-p65 in ONC model were analyzed by Western blot and immunofluorescence. The mRNA expressions of the pro-inflammatory cytokines (IL-8, TNF-α, IL-6 and IL-1β) were analyzed by RT-PCR., Results: Wip1 was up-regulated at 14 days after ONC by Western blot and immunofluorescence. The changes of Wip1 were striking in astrocytes. Furthermore, the protein expression level of p-p65 was paralleled with Wip1 in a time-dependent manner by ONC. In addition, co-localization of Wip1 with Phospho-NF-κB-p65 (p-p65) was detected. Finally, the mRNA expressions of the pro-inflammatory cytokines (IL-8, TNF-α, IL-6 and IL-1β) were significantly increased in retina after ONC., Conclusions: These data were consistent with the hypothesis that Wip1 was implicated in neuroinflammation of retinal astrocytes after ONC via NF-κB signaling pathway.

The two-component system (TCS), which comprises histidine kinases (HKs), phosphotransfers (HPs), and response regulator proteins (RRs), plays pivotal roles in regulating plant growth, development, and responses to biotic and abiotic stresses. TCS genes have been comprehensively identified and investigated in various crops but poorly characterized in tomato. In this work, a total of 65 TCS genes consisting of 20 HK(L)s, six HPs, and 39 RRs were identified from tomato genome. The classification, gene structures, conserved domains, chromosome distribution, phylogenetic relationship, gene duplication events, and subcellular localization of the TCS gene family were predicted and analyzed in detail. The amino acid sequences of tomato TCS family members, except those of type-B RRs, are highly conserved. The gene duplication events of the TCS family mainly occurred in the RR family. Furthermore, the expansion of RRs was attributed to both segment and tandem duplication. The subcellular localizations of the selected green fluorescent protein (GFP) fusion proteins exhibited a diverse subcellular targeting, thereby confirming their predicted divergent functionality. The majority of TCS family members showed distinct organ- or development-specific expression patterns. In addition, most of TCS genes were induced by abiotic stresses and exogenous phytohormones. The full elucidation of TCS elements will be helpful for comprehensive analysis of the molecular biology and physiological role of the TCS superfamily.

For classification problems based on microarray data, the data typically contains a large number of irrelevant and redundant features. In this paper, a new gene selection method is proposed to choose the best subset of features for microarray data with the irrelevant and redundant features removed. We formulate the selection problem as a L1-regularized optimization problem, based on a newly defined linear discriminant analysis criterion. Instead of calculating the mean of the samples, a kernel-based approach is used to estimate the class centroid to define both the between-class separability and the within-class compactness for the criterion. Theoretical analysis indicates that the global optimal solution of the L1-regularized criterion can be reached with a general condition, on which an efficient algorithm is derived to the feature selection problem in a linear time complexity with respect to the number of features and the number of samples. The experimental results on ten publicly available microarray datasets demonstrate that the proposed method performs effectively and competitively compared with state-of-the-art methods., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Objective: Based on recent information, CD200Fc, a CD200R1 agonist, could attenuate the inflammatory response of microglial cells in autoimmune diseases and neuro-degeneration. However, the exact molecular mechanisms responsible for the anti-inflammatory activity of CD200Fc in microglial cells have not been elucidated. In the present study, we investigated the anti-inflammatory effects and the molecular mechanisms of CD200Fc in lipopolysaccharide (LPS)-stimulated rat primary microglial cells., Methods: The cell viability was measured by MTT assay. The LPS-induced cytokines release (IL-1β, IL-6, TNF-α, iNOS, MCP-1, and COX-2) was monitored by ELISA or real-time PCR, while NF-κB-related signals (MyD88, p-TAK1, TRIF, p-TBK1, p-IRF3, p-IκB, and NF-κB-P65) were assessed by real-time PCR, western blot and/or Immunofluorescent staining., Results: CD200Fc and/or LPS exerted no significant cytotoxicity on microglial cells. LPS reduced the CD200R1 expression in microglial cells, and this effect was attenuated by CD200Fc. In addition, CD200Fc inhibited LPS-induced expression of TLR4 and its adapter molecules (MyD88 and p-TAK1, TRIF, p-TBK1, and p-IRF3), and abolished its interactions with MyD88, TAK1, and TRIF in microglial cells. CD200Fc also attenuated LPS-induced protein expression of p-IκB and NF-κB-P65 translocation to nucleus in microglial cells. Moreover, CD200Fc suppressed the LPS-induced release of inflammatory mediators in microglial cells, including IL-1β, IL-6, TNF-α, iNOS, MCP-1, and COX-2., Conclusion: These results indicated that CD200Fc displayed an anti-inflammatory effect in LPS-induced microglial cells by blocking TLR4-mediated NF-κB activation.

Cucumber and watermelon, which belong to Cucurbitaceae family, are economically important cultivated crops worldwide. However, these crops are vulnerable to various adverse environments. Two-component system (TCS), consisting of histidine kinases (HKs), phosphotransfers (HPs), and response regulator proteins (RRs), plays important roles in various plant developmental processes and signaling transduction in responses to a wide range of biotic and abiotic stresses. No systematic investigation has been conducted on TCS genes in Cucurbitaceae species. Based on the completion of the cucumber and watermelon genome draft, we identified 46 and 49 TCS genes in cucumber and watermelon, respectively. The cucumber TCS members included 18 HK(L)s, 7 HPs, and 21 RRs, whereas the watermelon TCS system consisted of 19 HK(L)s, 6 HPs, and 24 RRs. The sequences and domains of TCS members from these two species were highly conserved. Gene duplication events occurred rarely, which might have resulted from the absence of recent whole-genome duplication event in these two Cucurbitaceae crops. Numerous stress- and hormone-responsive cis-elements were detected in the putative promoter regions of the cucumber TCS genes. Meanwhile, quantitative real-time PCR indicated that most of the TCS genes in cucumber were specifically or preferentially expressed in certain tissues or organs, especially in the early developing fruit. Some TCS genes exhibited diverse patterns of gene expression in response to abiotic stresses as well as exogenous trans-zeatin (ZT) and abscisic acid (ABA) treatment, suggesting that TCS genes might play significant roles in responses to various abiotic stresses and hormones in Cucurbitaceae crops.

The CRISPR/Cas9 system has successfully been used in various organisms for precise targeted gene editing. Although it has been demonstrated that CRISPR/Cas9 system can induce mutation in tomato plants, the stability of heredity in later generations and mutant specificity induced by the CRISPR/Cas9 system in tomato plants have not yet been elucidated in detail. In this study, two genes, SlPDS and SlPIF4, were used for testing targeted mutagenesis in tomato plants through an Agrobacterium tumefaciens-mediated transformation method. A high mutation frequency was observed in all tested targets in the T0 transgenic tomato plants, with an average frequency of 83.56%. Clear albino phenotypes were observed for the psd mutants. High frequencies of homozygous and biallelic mutants were detected even in T0 plants. The majority of the detected mutations were 1- to 3-nucleotide deletions, followed by 1-bp insertions. The target mutations in the T0 lines were stably transmitted to the T1 and T2 generations, without new modifications or revision. Off-target activities associated with SlPDS and SlPIF4 were also evaluated by sequencing the putative off-target sites, and no clear off-target events were detected. Our results demonstrate that the CRISPR/Cas9 system is an efficient tool for generating stable and heritable modifications in tomato plants.

Background: MicroRNAs (miRNAs), a class of non-coding small RNAs (sRNAs), regulate various biological processes. Although miRNAs have been identified and characterized in several plant species, miRNAs in Asparagus officinalis have not been reported. As a dioecious plant with homomorphic sex chromosomes, asparagus is regarded as an important model system for studying mechanisms of plant sex determination., Results: Two independent sRNA libraries from male and female asparagus plants were sequenced with Illumina sequencing, thereby generating 4.13 and 5.88 million final clean reads, respectively. Both libraries predominantly contained 24-nt sRNAs, followed by 21-nt sRNAs. Further analysis identified 154 conserved miRNAs, which belong to 26 families, and 39 novel miRNA candidates seemed to be specific to asparagus. Comparative profiling revealed that 63 miRNAs exhibited significant differential expression between male and female plants, which was confirmed by real-time quantitative PCR analysis. Among them, 37 miRNAs were significantly up-regulated in the female library, whereas the others were preferentially expressed in the male library. Furthermore, 40 target mRNAs representing 44 conserved and seven novel miRNAs were identified in asparagus through high-throughput degradome sequencing. Functional annotation showed that these target mRNAs were involved in a wide range of developmental and metabolic processes., Conclusions: We identified a large set of conserved and specific miRNAs and compared their expression levels between male and female asparagus plants. Several asparagus miRNAs, which belong to the miR159, miR167, and miR172 families involved in reproductive organ development, were differentially expressed between male and female plants, as well as during flower development. Consistently, several predicted targets of asparagus miRNAs were associated with floral organ development. These findings suggest the potential roles of miRNAs in sex determination and reproductive developmental processes in asparagus.

Background: The mitogen-activated protein kinase (MAPK) cascade consists of three types of reversibly phosphorylated kinases, namely, MAPK, MAPK kinase (MAPKK/MEK), and MAPK kinase kinase (MAPKKK/MEKK), playing important roles in plant growth, development, and defense response. The MAPK cascade genes have been investigated in detail in model plants, including Arabidopsis, rice, and tomato, but poorly characterized in cucumber (Cucumis sativus L.), a major popular vegetable in Cucurbitaceae crops, which is highly susceptible to environmental stress and pathogen attack., Results: A genome-wide analysis revealed the presence of at least 14 MAPKs, 6 MAPKKs, and 59 MAPKKKs in the cucumber genome. Phylogenetic analyses classified all the CsMAPK and CsMAPKK genes into four groups, whereas the CsMAPKKK genes were grouped into the MEKK, RAF, and ZIK subfamilies. The expansion of these three gene families was mainly contributed by segmental duplication events. Furthermore, the ratios of non-synonymous substitution rates (Ka) and synonymous substitution rates (Ks) implied that the duplicated gene pairs had experienced strong purifying selection. Real-time PCR analysis demonstrated that some MAPK, MAPKK and MAPKKK genes are preferentially expressed in specific organs or tissues. Moreover, the expression levels of most of these genes significantly changed under heat, cold, drought, and Pseudoperonospora cubensis treatments. Exposure to abscisic acid and jasmonic acid markedly affected the expression levels of these genes, thereby implying that they may play important roles in the plant hormone network., Conclusion: A comprehensive genome-wide analysis of gene structure, chromosomal distribution, and evolutionary relationship of MAPK cascade genes in cucumber are present here. Further expression analysis revealed that these genes were involved in important signaling pathways for biotic and abiotic stress responses in cucumber, as well as the response to plant hormones. Our first systematic description of the MAPK, MAPKK, and MAPKKK families in cucumber will help to elucidate their biological roles in plant.

Different cupric oxide (CuO) structures have attracted intensive interest because of their promising applications in various fields. In this study, three kinds of CuO structures, namely, CuO microdisks, CuO nanoblocks, and CuO microspheres, are synthesized by solution-based synthetic methods. The morphologies and crystal structures of these CuO structures are characterized by field-emission scanning electron microscope and X-ray diffractometer, respectively. They are used as thermal conductive fillers to prepare silicone-based thermal greases, giving rise to great enhancement in thermal conductivity. Compared with pure silicone base, the thermal conductivities of thermal greases with CuO microdisks, CuO nanoblocks, and CuO microspheres are 0.283, 0256, and 0.239 W/mK, respectively, at filler loading of 9 vol.%, which increases 139%, 116%, and 99%, respectively. These thermal greases present a slight descendent tendency in thermal conductivity at elevated temperatures. These experimental data are compared with Nan's model prediction, indicating that the shape factor has a great influence on thermal conductivity improvement of thermal greases with different CuO structures. Meanwhile, due to large aspect ratio of CuO microdisks, they can form thermal networks more effectively than the other two structures, resulting in higher thermal conductivity enhancement.

Cell cycle re-entry is one of the key processes in neuronal apoptosis. Previous studies have shown that Ski-interacting protein (SKIP) played an important role in cell cycle re-entry. However, its expression and function in optic nerve injury are still with limited acquaintance. To investigate whether SKIP is involved in retinal ganglion cells (RGCs) death, we performed an optic nerve crush (ONC) model in adult rats. Western blot analysis revealed that up-regulation of SKIP was present in retina at 5 days after ONC. Immunofluorescent labeling indicated that up-regulated SKIP was found mainly in RGCs. We also investigated co-localization of SKIP with active-caspase-3 and TUNEL (apoptotic markers) -positive cells in the retina after ONC. In addition, the expression of SKIP was increased in parallel with P53 and P21 in retina after ONC. All these results suggested that up-regulation of SKIP in the retina was associated with RGCs death after ONC.

GTP-binding protein Gem, a member protein of the Ras superfamily, can regulate actin cytoskeleton reorganization mediated by Rho-associated coiled-coil-containing protein kinase (ROCK). One attractive activity of the ROCK is playing a potential role in physiological and pathological process in retinal ganglion cells (RGCs) apoptosis. However, the function of Gem in retina is still with limited understanding. To investigate whether Gem is involved in optic nerve injury, we performed an optic nerve crush (ONC) model in adult rats. Western blot analysis indicated that Gem was significantly increased in the retina at the 3rd day after ONC. Meanwhile, double-immunofluorescent staining showed that Gem expression was mainly up-regulated in ganglion cell layer and co-localized with NeuN (a marker of RGCs). Additionally, the co-localizations of Gem/active-caspase-3 and Gem/TUNEL-positive cells were detected in RGCs. Furthermore, the expression of active-caspase-3 and TUNEL-positive cells was parallel with that of Gem. Finally, expression pattern of ROCK family (only ROCK2 but not ROCK1) was increased in the differentiated process, which was collected with the expression of GEM and active-caspase-3. Based on the present results, it is suggested that Gem might play a crucial role in RGCs apoptosis after ONC, which might be involved in ROCK pathway.

Mitogen-activated protein kinase (MAPK) cascades have important functions in plant growth, development, and response to various stresses. The MAPKK and MAPKKK gene families in tomato have never been systematically analyzed. In this study, we performed a genome-wide analysis of the MAPKK and MAPKKK gene families in tomato and identified 5 MAPKK genes and 89 MAPKKK genes. Phylogenetic analyses of the MAPKK and MAPKKK gene families showed that all the MAPKK genes formed four groups (groups A, B, C, and D), whereas all the MAPKKK genes were classified into three subfamilies, namely, MEKK, RAF, and ZIK. Evolutionary analysis showed that whole genome or chromosomal segment duplications were the main factors responsible for the expansion of the MAPKK and MAPKKK gene families in tomato. Quantitative real-time RT-PCR analysis showed that the majority of MAPKK and MAPKKK genes were expressed in all tested organs with considerable differences in transcript levels indicating that they might be constitutively expressed. However, the expression level of most of these genes changed significantly under heat, cold, drought, salt, and Pseudomonas syringae treatment. Furthermore, their expression levels exhibited significant changes in response to salicylic acid and indole-3-acetic acid treatment, implying that these genes might have important roles in the plant hormone network. Our comparative analysis of the MAPKK and MAPKKK families would improve our understanding of the evolution and functional characterization of MAPK cascades in tomato.

Background: Auxin signaling has a vital function in the regulation of plant growth and development, both which are known to be mediated by auxin-responsive genes. So far, significant progress has been made toward the identification and characterization of auxin-response genes in several model plants, while no systematic analysis for these families was reported in cucumber (Cucumis sativus L.), a reference species for Cucurbitaceae crops. The comprehensive analyses will help design experiments for functional validation of their precise roles in plant development and stress responses., Results: A genome-wide search for auxin-response gene homologues identified 16 auxin-response factors (ARFs), 27 auxin/indole acetic acids (Aux/IAAs), 10 Gretchen Hagen 3 (GH3s), 61 small auxin-up mRNAs (SAURs), and 39 lateral organ boundaries (LBDs) in cucumber. Sequence analysis together with the organization of putative motifs indicated the potential diverse functions of these five auxin-related family members. The distribution and density of auxin response-related genes on chromosomes were not uniform. Evolutionary analysis showed that the chromosomal segment duplications mainly contributed to the expansion of the CsARF, CsIAA, CsGH3, and CsLBD gene families. Quantitative real-time RT-PCR analysis demonstrated that many ARFs, AUX/IAAs, GH3s, SAURs, and LBD genes were expressed in diverse patterns within different organs/tissues and during different development stages. They were also implicated in IAA, methyl jasmonic acid, or salicylic acid response, which is consistent with the finding that a great number of diverse cis-elements are present in their promoter regions involving a variety of signaling transduction pathways., Conclusion: Genome-wide comparative analysis of auxin response-related family genes and their expression analysis provide new evidence for the potential role of auxin in development and hormone response of plants. Our data imply that the auxin response genes may be involved in various vegetative and reproductive developmental processes. Furthermore, they will be involved in different signal pathways and may mediate the crosstalk between various hormone responses.

Increasing interests have been paid to nanofluids because of the intriguing heat transfer enhancement performances presented by this kind of promising heat transfer media. We produced a series of nanofluids and measured their thermal conductivities. In this article, we discussed the measurements and the enhancements of the thermal conductivity of a variety of nanofluids. The base fluids used included those that are most employed heat transfer fluids, such as deionized water (DW), ethylene glycol (EG), glycerol, silicone oil, and the binary mixture of DW and EG. Various nanoparticles (NPs) involving Al2O3 NPs with different sizes, SiC NPs with different shapes, MgO NPs, ZnO NPs, SiO2 NPs, Fe3O4 NPs, TiO2 NPs, diamond NPs, and carbon nanotubes with different pretreatments were used as additives. Our findings demonstrated that the thermal conductivity enhancements of nanofluids could be influenced by multi-faceted factors including the volume fraction of the dispersed NPs, the tested temperature, the thermal conductivity of the base fluid, the size of the dispersed NPs, the pretreatment process, and the additives of the fluids. The thermal transport mechanisms in nanofluids were further discussed, and the promising approaches for optimizing the thermal conductivity of nanofluids have been proposed.

A chemical reduction method for preparing monodispersed pure-phase copper colloids in water and ethylene glycol has been reported. Owing to the reduction property of ethylene glycol, the reaction rate in ethylene glycol is higher than that in water. In addition, the amount of reducing agent can be reduced largely. Ascorbic acid plays roles as reducing agent and antioxidant of colloidal copper, due to its ability to scavenge free radicals and reactive oxygen molecules. Thermogravimetric results reveal that the as-prepared copper nanoparticles have good stability, and they begin to be oxidized at above 210 degrees C. Polyvinyl pyrrolidone works both as size controller and polymeric capping agents, because it hinders the nuclei from aggregation through the polar groups, which strongly absorb the copper particles on the surface with coordination bonds.

The phase behavior of a system of n-butanol/n-octane/water/cationic gemini surfactant, alkanediyl-alpha,omega-(dimethydodecyl-ammonium bromide)(12-n-12, n=3,4,6), has been investigated by determination the pseudo-ternary phase diagrams. The results have shown that the spacer group of gemini surfactant has a great effect on the phase behavior. The longer the spacer group for the geminis, the more similar the geminis properties to the traditional ones. The mixing content of surfactant and cosurfactant needed for forming microemulsions increases with the geminis' spacer group. The study has also shown that the shorter spacer group of geminis is favorable for the formation of higher ordered surfactant aggregates such as liquid crystals. Furthermore, the microstructures of each region for the studied systems have been investigated by electrical conductivity measurements, UV-visible absorbance spectra of pyrene probe, and dynamic light scattering (DLS). All the results are in accord with each other. DLS makes use of the sensitivity of DLS to structural changes and as expected the hydrodynamic diameter of the microemulsion droplet changes as the transformation of microemulsion microstructures take place. Moreover, the spherical and network structures of microemulsion were further verified by freezing-etching TEM.