Fabrication of flexible transparent Ag square-shaped mesh electrode by top-flat nanosecond laser ablation.

We report a facile top-flat square nanosecond (ns) laser direct writing ablation technique in a thin silver film substrate to fabricate the silver square-shaped cell structure of flexible transparent electrodes. Square silver cell structures feature smooth surface morphology, excellent edge definition, mechanical stability, strong adhesion to the substrate, and favorable resistance and transparency. In particular, this strategy enables fabrication of a high square-shaped cell areal density (ablated square cell to the total area) Ag mesh, substantially improving transparency ($ {\gt} {85}\% $>85%) without considerably sacrificing conductivity ($ {\lt} {5}\;\Omega \;{{\rm sq}^{ - 1}}$<5Ωsq-1 unit of resistance). Consequently, the proposed metallic square-shaped structure shows compatibility with a polyethylene naphthalate flexible substrate for silver-based wearable electronic devices without any protective layer over the electrodes.

Heterogeneous selenite reduction by zero valent iron steel wool.

Mine drainage from the low-sulfur surface coal mines in southern West Virginia, USA, is circumneutral (pH > 6) but contains elevated selenium (Se) concentrations. Removal of selenite ions from aqueous solutions under anoxic condition at pH 6-8.5 by zero valent iron steel wool (ZVI-SW) was investigated in bench-scale kinetic experiments using wet chemical, microscopic and spectroscopic techniques (X-ray photoelectron spectroscopy). ZVI-SW could effectively and efficiently remove SeIV from solution with pH 6-8.5. A two-step removal mechanism was identified for SeIV reduction by ZVI-SW. The proposed mechanism was electrochemical reduction of SeIV by Fe0 in an initial lag stage, followed by a faster heterogeneous reduction, mediated by an FeII-bearing phase (hydroxide or green rust). Solution pH was a critical factor for the kinetic rate in the lag stage (0.33 h-1 for pH > 8 and 0.10 h-1 for pH 6-8). The length of lag stage was 20-30 min as determined by the time for dissolved FeII concentration to reach 0.30 ± 0.04 mg L-1 which was critical for induction of the faster stage. About 65% of the initial SeIV was reduced to Se0, the primary reductive product in both stages.

Plant siRNAs from introns mediate DNA methylation of host genes.

Small RNAs (sRNAs), largely known as microRNAs (miRNAs) and short interfering RNAs (siRNAs), emerged as the critical components of genetic and epigenetic regulation in eukaryotic genomes. In animals, a sizable portion of miRNAs reside within the introns of protein-coding genes, designated as mirtron genes. Recently, high-throughput sequencing (HTS) revealed a huge amount of sRNAs that derived from introns in plants, such as the monocot rice (Oryza sativa). However, the biogenesis and the biological functions of this kind of sRNAs remain elusive. Here, we performed a genome-scale survey of intron-derived sRNAs in rice based on HTS data. Several introns were found to have great potential to form internal hairpin structures, and the short hairpins could generate miRNAs while the larger ones could produce siRNAs. Furthermore, 22 introns, termed "sirtrons," were identified from the rice protein-coding genes. The single-stranded sirtrons produced a diverse set of siRNAs from long hairpin structures. These sirtron-derived siRNAs are dominantly 21 nt, 22 nt, and 24 nt in length, whose production relied on DCL4, DCL2, and DCL3, respectively. We also observed a strong tendency for the sirtron-derived siRNAs to be coexpressed with their host genes. Finally, the 24-nt siRNAs incorporated with Argonaute 4 (AGO4) could direct DNA methylation on their host genes. In this regard, homeostatic self-regulation between intron-derived siRNAs and their host genes was proposed.

Emerging market for pork with animal welfare attribute in China: An ethical perspective.

There is growing public concern about the welfare of farm animals, and farm animal welfare can be considered an ethical attribute of product quality. This paper elicits consumers' willingness to pay (WTP) for animal welfare attributes in pork products using a choice experiment (CE) in China. Consumers are willing to pay a premium of 13.923 to 18.493 CNY/500 g for more desirable product attributes in terms of animal welfare, branding, humane slaughter, and environmental friendliness. There is a complementary relationship between ethical morality in public policy and animal welfare farming. The findings of the study contribute to an increasing understanding of consumer preferences for animal-friendly products in emerging countries. A wide range of relevant, practical initiatives to help promote animal welfare development are needed in China, by strengthening the education of ecological ethics and animal welfare ideology, establishing an animal welfare security system by global standards, and optimising contractual arrangements for the value chain of animal-friendly products.

Advanced Platelet-Rich Fibrin Extract Treatment Promotes the Proliferation and Differentiation of Human Adipose-Derived Mesenchymal Stem Cells through Activation of Tryptophan Metabolism.

BACKGROUND: Advanced platelet-rich fibrin extract (APRFE) contains a high concentration of various cytokines that are helpful for improving stem cells repair function. OBJECTIVE: However, the underlying mechanism of APRFE improving stem cell repairing is not clear. METHODS: We produced APRFE by centrifuging fresh peripheral blood samples and isolated and identified human adipose-derived mesenchymal stem cells (ADMSCs). The abundance of cytokines contained in APRFE was detected by the Enzyme-linked immunosorbent assay (ELISA). The ADMSCs treated with or without APRFE were collected for transcriptome sequencing. RESULTS: Based on the sequencing data, the expression profiles were contracted. The differentially expressed genes and lncRNA (DEGs and DElncRNAs) were obtained using for the differential expression analysis. The lncRNA-miRNA-mRNA network was constructed based on the miRNet database. The further enrichment analysis results showed that the biological functions were mainly related to proliferation, differentiation, and cell-cell function. To explore the role of APRFE, the protein-protein interaction network was constructed among the cytokines included in APRFE and DEGs. Furthermore, we constructed the global regulatory network based on the RNAInter and TRRUST database. The pathways in the global regulatory network were considered as the core pathways. We found that the DEGs in the core pathways were associated with stemness scores. CONCLUSION: In summary, we predicted that APRFE activated three pathways (tryptophan metabolism, mTOR signaling pathway, and adipocytokine signaling) to promote the proliferation and differentiation of ADMSCs. The finding may be helpful for guiding the application of ADMSCs in the clinic.

MyBioNet: interactively visualize, edit and merge biological networks on the web.

SUMMARY: MyBioNet is a web-based application for biological network analysis, which provides user-friendly web interfaces to visualize, edit and merge biological networks. In addition, MyBioNet integrated KEGG metabolic network data from 1366 organisms and allows users to search and navigate interesting networks. AVAILABILITY AND IMPLEMENTATION: All KEGG metabolic network data are organized and stored in the MySQL database. MyBioNet is implemented in Flex/Actionscript and PHP languages and deployed on an Apache web server. MyBioNet is accessible through all the Flash-embedded browsers at http://bis.zju.edu.cn/mybionet/. CONTACT: mchen@zju.edu.cn.

Origin and evolutionary analysis of the plant-specific TIFY transcription factor family.

A substantial number of transcription factor families have been investigated from all kingdoms of life, but a particular class of plant-specific TIFY transcription factors, characterized by a highly conserved TIFY domain, lacks a systemic analysis of its origin and evolutionary relationships among different plant species. After exhaustive genome-wide searches against 14 genomes, TIFY transcription factors were identified and classified into four subfamilies TIFY, PPD, JAZ and ZML according to their different domain architectures. Results show that the TIFY domain of the ZML subfamily possesses a core "TLS[F/Y]XG" motif rather than the "TIFYXG" motif that is dominant in the other three subfamilies. A comprehensive survey of the TIFY family allowed us to discover a new group within the JAZ subfamily and to identify several novel conserved motifs via phylogenetic analysis. Evolutional analysis indicates that whole genome duplication and tandem duplication contributed to the expansion of the TIFY family in plants.

Effects of the heavy metal Cu2+ on growth, development, and population dynamics of Spodoptera litura (Lepidoptera: Noctuidae).

Spodoptera litura (F.) larvae were fed with artificial food containing four different concentrations of copper (25, 50, 100, and 200 mg/kg). Copper affected growth, development, and population dynamics of late instar larvae. Our results indicate that the fourth and fifth instar survival rates were significantly reduced at 50-200 mg/kg copper (Cu2+). Moreover, all the Cu2+ treatments significantly reduced pupation and moth emergence rates in a dose-dependent manner. Larvae fed 25 or 50 mg/kg Cu2+ showed significant reductions in development period compared with non-Cu controls, and the pupation duration of animals fed 200 mg/kg was significantly longer than in non-Cu controls. All Cu2+ concentrations significantly reduced individual pupal weights compared with controls. In addition, Cu2+ at some concentrations significantly affected fertility parameters, such as doubling population time (DT), the net reproduction rate (R(o)), the mean generation time (T), the intrinsic rate of increase (r(m)), and the finite increase rate (A). Our study demonstrates that low concentrations of Cu2+ in the diet (25 and 50 mg/kg) shorten the generation time by 4-5 d, whereas higher Cu2+ concentrations (100 and 200 mg/kg) increase DT for 1-2 d.

Advanced platelet-rich fibrin promotes the paracrine function and proliferation of adipose-derived stem cells and contributes to micro-autologous fat transplantation by modulating HIF-1α and VEGF.

Background: The micro-autologous fat transplantation (MAFT) technique has demonstrated its feasibility in multiple medical fields, such as facial rejuvenation. Advanced platelet-rich fibrin (APRF), an autologous platelet concentrated on a fibrin membrane without added external factors, has shown significant potential for tissue restoration. However, the role of APRF in the modulation of MAFT remains unclear. Here, we aimed to explore the effect of APRF on MAFT. Methods: Adipose-derived stem cells (ASCs) were isolated from human gastric subcutaneous fat and treated with APRF. ELISA assays measured cytokines. The proliferation of ASCs was analyzed by CCK-8 assays. The levels of hypoxia-inducible factor-1α (HIF-1α), heat shock protein 70 (HSP70), insulin like growth factor 2 (IGF-2), interleukin-6 (IL-6), interleukin-8 (IL-8), and vascular endothelial growth factor (VEGF) were measured by ELISA assays, quantitative reverse transcription-PCR (qRT-PCR), and Western blot analysis. The effect of APRF/HIF-1α/VEGF on MAFT in vivo was analyzed in Balb/c nude mice. The BALB/c mice were subcutaneously co-transplanted with fat, APRF, and control shRNA, HIF-1α shRNA, or VEGF shRNA into the dorsal area. The serum and protein levels of the above cytokines were analyzed by ELISA assays and Western blot analysis. Lipid accumulation was measured by Oil Red O staining. The expression of CD34 was assessed by immunohistochemical staining. Results: APRF continuously secreted multiple cytokines, including epidermal growth factor (EGF), FGF-2, insulin like growth factor 1 (IGF-1), interleukin-1beta (IL-1ß), interleukin-4 (IL-4), platelet-derived growth factor alpha polypeptide b (PDGF-AB), platelet-derived growth factor beta polypeptide b (PDGF-BB), transforming growth factor-beta (TGF-ß), and VEGF. APRF was able to promote the proliferation of ASCs. APRF dose-dependently activated the expression of HIF-1α, HSP70, IGF-2, IL-6, IL-8, and VEGF in ASCs. APRF regulated the paracrine function of ASCs by modulating HIF-1α and VEGF. APRF increased the survival of MAFT by modulating HIF-1α and VEGF in vivo. Conclusions: APRF promotes the paracrine function and proliferation of ASCs and contributes to MAFT by modulating HIF-1α and VEGF. Our findings provide new insights into the mechanism by which APRF regulates MAFT.

Rg1 Promotes the Proliferation and Adipogenic Differentiation of Human Adipose-Derived Stem Cells via FXR1/Lnc-GAS5-AS1 Pathway.

BACKGROUND: Human adipose-derived stem cells (hASCs) play an important role in regenerative medicine. OBJECTIVE: Exploring the mechanism of Rg1 in the promotion of the proliferation and adipogenic differentiation of hASCs is important in regenerative medicine research. METHODS: To observe ginsenoside Rg1 in promoting the proliferation and adipogenic differentiation of hASCs, Rg1 medium at different concentrations was established and tested using the cell counting kit-8 (CCK-8) assay, oil red O staining, alizarin red, and alcian blue. Compared to the control, differentially expressed genes (DEGs) were screened via DEG analysis, which was carried out in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. To explore the relationship among mRNA, long non-coding RNA (lncRNA) and microRNA (miRNA), we constructed a competing endogenous RNA (ceRNA) network. RESULTS: In this study, Rg1 was observed to promote the proliferation and adipogenic differentiation of hASCs. Additionally, enriched BPs and KEGG pathways may be involved in the promotion process, where FXR1 and Lnc-GAS5-AS1 were found to be regulatory factors. The regulatory network suggested that Rg1 could regulate the adipocytokine signaling pathway and IL-17 signaling pathway via FXR1 and Lnc-GAS5-AS1, which served as the mechanism encompassing the promotion of Rg1 on the proliferation and adipogenic differentiation of hASCs. CONCLUSION: A comprehensive transcriptional regulatory network related to the promotion ability of Rg1 was constructed, revealing mechanisms regarding Rg1's promotion of the proliferation and adipogenic differentiation of hASCs. The present study provides a theoretical basis for optimizing the function of hASCs.

Corrigendum to "Altered Genes and Biological Functions in Response to Severe Burns".

[This corrects the article DOI: 10.1155/2021/8836243.].

Altered Genes and Biological Functions in Response to Severe Burns.

Severe burns are acute wounds caused by local heat exposure, resulting in life-threatening systemic effects and poor survival. However, the specific molecular mechanisms remain unclear. First, we downloaded gene expression data related to severe burns from the GEO database (GSE19743, GSE37069, and GSE77791). Then, a gene expression analysis was performed to identify differentially expressed genes (DEGs) and construct protein-protein interaction (PPI) network. The molecular mechanism was identified by enrichment analysis and Gene Set Enrichment Analysis. In addition, STEM software was used to screen for genes persistently expressed during response to severe burns, and receiver operating characteristic (ROC) curve was used to identify key DEGs. A total of 2631 upregulated and 3451 downregulated DEGs were identified. PPI network analysis clustered these DEGs into 13 modules. Importantly, module genes mostly related with immune responses and metabolism. In addition, we identified genes persistently altered during the response to severe burns corresponding to survival and death status. Among the genes with high area under the ROC curve in the PPI network gene, CCL5 and LCK were identified as key DEGs, which may affect the prognosis of burn patients. Gene set variation analysis showed that the immune response was inhibited and several types of immune cells were decreased, while the metabolic response was enhanced. The results showed that persistent gene expression changes occur in response to severe burns, which may underlie chronic alterations in physiological pathways. Identifying the key altered genes may reveal potential therapeutic targets for mitigating the effects of severe burns.

Advanced-platelet-rich fibrin extract promotes adipogenic and osteogenic differentiation of human adipose-derived stem cells in a dose-dependent manner in vitro.

Advanced platelet-rich fibrin (A-PRF) is an autogenous biological material obtained from peripheral blood. A-PRF extract (A-PRFe) contains a high concentration of various cytokines that are increasingly appreciated for their roles in improving stem cell repairing function during tissue regeneration. However, the optimal A-PRFe concentration to stimulate stem cells is unknown. This study aimed to identify the optimal concentrations of A-PRFe to promote adipogenic and osteogenic differentiation of human adipose-derived stem cells (ASCs). We produced A-PRFe from A-PRF clots by centrifuging fresh peripheral blood samples and isolated and identified ASCs using surface CD markers and multilineage differentiation potential. Enzyme-linked immunosorbent assay (ELISA) showed the concentrations of several cytokines, including b-FGF, PDGF-BB, and others, increased gradually, peaked on day 7 and then decreased. Cell proliferation assays showed A-PRFe significantly stimulated ASC proliferation, and proliferation significantly increased at higher A-PRFe doses. The degree of adipogenic and osteogenic differentiation increased at higher A-PRFe concentrations in the culture medium, as determined by oil red O and alizarin red staining. Reverse transcription polymerase chain reaction (RT-PCR) showed that expression levels of genes related to adipogenic/osteogenic differentiation (PPARγ2, C/EBPα, FABP4, Adiponectin, and ALP, OPN, OCN, RUNX2), paracrine (HIF-1α, VEGF, IGF-2) and immunoregulation (HSP70, IL-8) function were higher in groups with a higher concentration of A-PRFe than in lower concentration groups. This study demonstrates that A-PRFe is ideal for use in ASC applications in regenerative medicine because it improves biological functions, including proliferation, adipogenic/osteogenic differentiation, and paracrine function in a dose-dependent manner.

Resveratrol Mediates the Apoptosis of Triple Negative Breast Cancer Cells by Reducing POLD1 Expression.

Resveratrol (RSV) is known to possess anticancer properties in many types of cancers like breast cancer, in which POLD1 may serve as a potential target. However, the anticancer mechanism of RSV on triple negative breast cancer (TNBC) remains unclear. In the present study, the antitumor effects and mechanism of RSV on TNBC cells were analyzed by RNA sequencing (RNA-seq), which was then verified via cell counting kit-8 (CCK8), immunofluorescence, immunohistochemistry, Western Blot (WB), flow cytometry, and hematoxylin-eosin (HE) staining. According to the corresponding findings, the survival rate of MDA-MB-231 cells gradually decreased as RSV treatment concentration increased. The RNA-seq analysis results demonstrated that genes affected by RSV treatment were mainly involved in apoptosis and the p53 signaling pathway. Moreover, apoptosis of MDA-MB-231 cells induced by RSV was observed to be mainly mediated by POLD1. When treated with RSV, the expression levels of full length PARP1, PCNA, and BCL-2 were found to be significantly reduced, and the expression level of Cleaved-PARP1 as well as Cleaved-Caspase3 increased significantly. Additionally, the mRNA expression of POLD1 was significantly reduced after treatment with RSV, and the protein expression level was also inhibited by RSV in a concentration-dependent manner. The prediction of domain interaction suggested that RSV may bind to at least five functional domains of the POLD1 protein (6s1m, 6s1n, 6s1o, 6tny and 6tnz). Furthermore, after RSV treatment, the anti-apoptotic index (PCNA, BCL-2) of MDA-MB-231 cells was found to decrease while the apoptosis index (caspase3) increased. Moreover, the overexpression of POLD1 reduced the extent of apoptosis observed in MDA-MB-231 cells following RSV treatment. Moreover, animal experimental results showed that RSV had a significant inhibitory effect on the growth of live tumors, while POLD1 overexpression was shown to antagonize this inhibitory effect. Accordingly, this study's findings reveal that RSV may promote the apoptosis of TNBC cells by reducing the expression of POLD1 to activate the apoptotic pathway, which may serve as a potential therapy for the treatment of TNBC.

[In vitro study on promoting migration ability of rat adipose derived stem cells modified by stromal cell-derived factor 1α].

OBJECTIVE: To explored the effect of stromal cell-derived factor 1α (SDF-1α) on promoting the migration ability of rat adipose derived stem cells (rADSCs) by constructed the rADSCs overexpression SDF-1α via adenovirus transfection. METHODS: rADSCs were isolated from adipose tissue of 6-week-old SPF Sprague Dawley rats. Morphological observation, multi-directional differentiations (osteogenic, adipogenic, and chondrogenic inductions), and flow cytometry identification were performed. Transwell cell migration experiment was used to observe and screen the optimal concentration of exogenous SDF-1α to optimize the migration ability of rADSCs; the optimal multiplicity of infection (MOI) of rADSCs was screened by observing the cell status and fluorescence expression after transfection. Then the third generation of rADSCs were divided into 4 groups: group A was pure rADSCs; group B was rADSCs co-cultured with SDF-1α at the best concentration; group C was rADSCs infected with recombinant adenovirus-mediated green fluorescent protein (Adv-GFP) with the best MOI; group D was rADSCs infected with Adv-GFP-SDF-1α overexpression adenovirus with the best MOI. Cell counting kit 8 (CCK-8) and Transwell cell migration experiment were preformed to detect and compare the effect of exogenous SDF-1α and SDF-1α overexpression on the proliferation and migration ability of rADSCs. RESULTS: The cell morphology, multi-directional differentiations, and flow cytometry identification showed that the cultured cells were rADSCs. After screening, the optimal stimulating concentration of exogenous SDF-1α was 12.5 nmol/L; the optimal MOI of Adv-GFP adenovirus was 200; the optimal MOI of Adv-GFP-SDF-1α overexpression adenovirus was 400. CCK-8 method and Transwell cell migration experiment showed that compared with groups A and C, groups B and D could significantly improve the proliferation and migration of rADSCs ( P<0.05); the effect of group D on enhancing the migration of rADSCs was weaker than that of group B, but the effect of promoting the proliferation of rADSCs was stronger than that of group D ( P<0.05). CONCLUSION: SDF-1α overexpression modification on rADSCs can significantly promote the proliferation and migration ability, which may be a potential method to optimize the application of ADSCs in tissue regeneration and wound repair.

Optimizing the synthetic nitrogen rate to balance residual nitrate and crop yield in a leguminous green-manured wheat cropping system.

Nitrate that originates from agriculture is linked to a series of deleterious environmental consequences that are closely related to human health. Therefore, it is vital to design cropping systems that can produce acceptable crop yields while minimizing the impact of surplus soil nitrate. To develop quantitative estimations, data from 2008 to 2016 were evaluated using multiple regression models. A split-plot field experiment was conducted, with the main treatments of growing Huai bean, soybean and mung bean in summer as leguminous green manure (LGM) while fallow as the control. Four synthetic N rates (0, 108, 135 and 162kgha-1) were applied as sub-treatments at wheat seeding. The N accumulation for LGMs ranged from 61 to 90kgha-1, and that of Huai bean was 46% higher than the average value of soybean and mung bean (P<0.05). The threshold of total N for wheat to produce the highest yields was 141kgha-1. For the LGM treatments, residual nitrate accumulated below the root-zone soil was not significantly increased even when their total N inputs were higher than that of fallow with 162kgha-1 of synthetic N. The estimated nitrate-holding capacity of the root-zone soil for the LGM treatments ranged from 104 to 117kgha-1, and the corresponding synthetic N limits were 97-130kgha-1. Considering the target of producing high wheat yields while keeping the residual nitrate in the root-zone soil, the optimal synthetic N rates for LGM treatments were 52-80kgha-1. In conclusion, growing LGMs can maintain high crop yield and mitigate the environmental impact of residual nitrate by substantially replacing the synthetic N to avoid nitrate leaching to deeper soils.

Coupling life-cycle assessment and the RothC model to estimate the carbon footprint of green manure-based wheat production in China.

Reducing the carbon footprint (CF) of crop production is an efficient way to mitigate climate change. Growing legume green manure (LGM) instead of summer fallow may achieve this goal by lowering synthetic nitrogen (N) fertilizer needs and replenishing the depleted soil carbon (C) pool. The Rothamsted Carbon (RothC) model was incorporated into the Life-Cycle Assessment (LCA) to evaluate the present and projected CFs of green manure-based wheat production systems in dryland agriculture on the Loess Plateau of China. The field study included four main treatments (Huai bean, soybean and mung bean grown as green manure in summer and fallow as control) and four synthetic N rates (0, 108, 135 and 162kgNha-1) applied at wheat sowing. Soybean as LGM increased averaged wheat yield over 4 synthetic N rates by 8% compared with fallow (P<0.05), and synthetic N requirement was reduced by 33% without compromising the wheat yield for all the main treatments. Although LGM treatments had higher greenhouse gas (GHG) emissions from agricultural inputs, the greater amount of C inputs elevated the corresponding SOC stocks (SOCS) by 14-24% after 8years, thus significantly reducing the CF by 25-51% compared with fallow. The modelled SOCS equilibrium indicates that the CF for cropping systems with LGM will be 53-62% lower than fallow and 23-37% lower compared with their current level. In conclusion, introducing legume green manure instead of summer fallow is a highly efficient measure for persistent CF reduction, and coupling the RothC model and LCA is an alternative method to predict the long-term impact of different cropping systems on GHG emissions.

Systematic annotation and bioinformatics analyses of large-scale Oryza sativa proteome.

Much has been now recognized on the rice (Oryza sativa L.) proteomics by using the powerful experimental tool two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). 2D-PAGE can be utilized for monitoring global changes of quantitative protein expression in specific tissues under various conditions. However, systematic annotations of the protein spots generated by 2D-PAGE are still limited for rice. In this study, a new approach for Oryza sativa proteome annotation based on the 2D-gel maps was developed. Based on the publicly available 2D-PAGE data of rice, 11,201 gel spots were annotated accounting for 87.2% of the total spots on the gel maps. Gel spot alignments were performed for the annotated gel maps belonging to 23 rice tissues or organelles. In summary, 253 alignments between 23 tissues or organelles were performed, and 26,207 co-expressed proteins were identified using our analytical strategy. Large-scale bi-cluster analysis of 23 tissues/organelles proteomes of rice was carried out to detect novel functional proteins. Function and pathway analysis identified a number of common gene products with great potential in regulating specific physiological and biochemical events within various rice tissues/organelles. It also suggested that the tissue- or organelle-specific proteins might be responsible for the functional divergence of these tissues or organelles. Taken together, this study provides us new strategies and informative resources for rice proteome research based on 2D-PAGE data.

Computational identification of protein-protein interactions in rice based on the predicted rice interactome network.

Plant protein-protein interaction networks have not been identified by large-scale experiments. In order to better understand the protein interactions in rice, the Predicted Rice Interactome Network (PRIN; http://bis.zju.edu.cn/prin/) presented 76,585 predicted interactions involving 5,049 rice proteins. After mapping genomic features of rice (GO annotation, subcellular localization prediction, and gene expression), we found that a well-annotated and biologically significant network is rich enough to capture many significant functional linkages within higher-order biological systems, such as pathways and biological processes. Furthermore, we took MADS-box domain-containing proteins and circadian rhythm signaling pathways as examples to demonstrate that functional protein complexes and biological pathways could be effectively expanded in our predicted network. The expanded molecular network in PRIN has considerably improved the capability of these analyses to integrate existing knowledge and provide novel insights into the function and coordination of genes and gene networks.