A dual-branch selective attention capsule network for classifying kiwifruit soft rot with hyperspectral images.

Kiwifruit soft rot is highly contagious and causes serious economic loss. Therefore, early detection and elimination of soft rot are important for postharvest treatment and storage of kiwifruit. This study aims to accurately detect kiwifruit soft rot based on hyperspectral images by using a deep learning approach for image classification. A dual-branch selective attention capsule network (DBSACaps) was proposed to improve the classification accuracy. The network uses two branches to separately extract the spectral and spatial features so as to reduce their mutual interference, followed by fusion of the two features through the attention mechanism. Capsule network was used instead of convolutional neural networks to extract the features and complete the classification. Compared with existing methods, the proposed method exhibited the best classification performance on the kiwifruit soft rot dataset, with an overall accuracy of 97.08% and a 97.83% accuracy for soft rot. Our results confirm that potential soft rot of kiwifruit can be detected using hyperspectral images, which may contribute to the construction of smart agriculture.

Effects of Supplemental Lighting on Flavonoid and Anthocyanin Biosynthesis in Strawberry Flesh Revealed via Metabolome and Transcriptome Co-Analysis.

The spectral composition of light influences the biosynthesis of flavonoids in many plants. However, the detailed composition of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under two light-quality treatments, red light supplemented with blue light (RB) and ultraviolet B (UVB) irradiation, remain unclear. In this study, the content of flavonoids and anthocyanins was significantly increased in strawberry fruits under RB light and UVB, respectively. The content of flavonoids and anthocyanins in strawberry fruits under UVB light was dramatically higher than that in strawberry fruits irradiated with RB light, and a total of 518 metabolites were detected by means of LC-MS/MS analysis. Among them, 18 phenolic acids, 23 flavonoids, and 8 anthocyanins were differentially accumulated in the strawberry fruits irradiated with red/blue (RB) light compared to 30 phenolic acids, 46 flavonoids, and 9 anthocyanins in fruits irradiated with UVB. The major genes associated with the biosynthesis of flavonoids and anthocyanins, including structural genes and transcription factors (TFs), were differentially expressed in the strawberry fruits under RB and UVB irradiation, as determined through RNA-seq data analysis. A correlation test of transcriptome and metabolite profiling showed that the expression patterns of most genes in the biosynthesis pathway of flavonoids and anthocyanins were closely correlated with the differential accumulation of flavonoids and anthocyanins. Two TFs, bZIP (FvH4_2g36400) and AP2 (FvH4_1g21210), induced by RB and UVB irradiation, respectively, exhibited similar expression patterns to most structural genes, which were closely correlated with six and eight flavonoids, respectively. These results indicated that these two TFs regulated the biosynthesis of flavonoids and anthocyanins in strawberry fruit under RB light and UVB, respectively. These results provide a systematic and comprehensive understanding of the accumulation of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under RB light and UVB.

Analysis of Ethylene Signal Regulating Sucrose Metabolism in Strawberry Fruits Based on RNA-seq.

Ethylene is a key hormone that regulates the maturation and quality formation of horticultural crops, but its effects on non-respiratory climacteric fruits such as strawberries are not yet clear. In this study, strawberry fruits were treated with exogenous ethephon (ETH) and 1-methylcyclopropene (1-MCP). It was found that ETH treatment increased the soluble solids and anthocyanin content of the fruits, reduced hardness, and decreased organic acid content, while 1-MCP treatment inhibited these processes. Transcriptome analysis revealed that differentially expressed genes (DEGs) were enriched in the starch-sucrose metabolism pathway. qRT-PCR results further showed significant changes in the expression levels of sucrose metabolism genes, confirming the influence of ethylene signals on soluble sugar accumulation during strawberry fruit development. This study elucidates the quality changes and molecular mechanisms of ethylene signal in the development of strawberry fruits, providing some key targets and theoretical support for guiding strawberry cultivation and variety improvement.

Ectopic Expression of MADS-Box Transcription Factor VvAGL12 from Grape Promotes Early Flowering, Plant Growth, and Production by Regulating Cell-Wall Architecture in Arabidopsis.

The MADS-box family, a substantial group of plant transcription factors, crucially regulates plant growth and development. Although the functions of AGL12-like subgroups have been elucidated in Arabidopsis, rice, and walnut, their roles in grapes remain unexplored. In this study, we isolated VvAGL12, a member of the grape MADS-box group, and investigated its impact on plant growth and biomass production. VvAGL12 was found to localize in the nucleus and exhibit expression in both vegetative and reproductive organs. We introduced VvAGL12 into Arabidopsis thaliana ecotype Columbia-0 and an agl12 mutant. The resulting phenotypes in the agl12 mutant, complementary line, and overexpressed line underscored VvAGL12's ability to promote early flowering, augment plant growth, and enhance production. This was evident from the improved fresh weight, root length, plant height, and seed production, as well as the reduced flowering time. Subsequent transcriptome analysis revealed significant alterations in the expression of genes associated with cell-wall modification and flowering in the transgenic plants. In summary, the findings highlight VvAGL12's pivotal role in the regulation of flowering timing, overall plant growth, and development. This study offers valuable insights, serving as a reference for understanding the influence of the VvAGL12 gene in other plant species and addressing yield-related challenges.

A Review of Classification, Biosynthesis, Biological Activities and Potential Applications of Flavonoids.

Flavonoids represent the main class of plant secondary metabolites and occur in the tissues and organs of various plant species. In plants, flavonoids are involved in many biological processes and in response to various environmental stresses. The consumption of flavonoids has been known to reduce the risk of many chronic diseases due to their antioxidant and free radical scavenging properties. In the present review, we summarize the classification, distribution, biosynthesis pathways, and regulatory mechanisms of flavonoids. Moreover, we investigated their biological activities and discuss their applications in food processing and cosmetics, as well as their pharmaceutical and medical uses. Current trends in flavonoid research are also briefly described, including the mining of new functional genes and metabolites through omics research and the engineering of flavonoids using nanotechnology. This review provides a reference for basic and applied research on flavonoid compounds.

Arbuscular mycorrhizal fungi influence the uptake of cadmium in industrial hemp (Cannabis sativa L.).

Phytoremediation is currently a more environmentally friendly and economical measure for the remediation of cadmium (Cd) contaminated soil. Heavy metal-resistant plant species, Cannabis sativa L. was inoculated with Rhizophagus irregularis to investigate the mechanisms of mycorrhizal in improving the Cd remediation ability of C. sativa. The results showed that after inoculation with R. irregularis, C. sativa root Cd contents increased significantly, and leaf Cd enrichment decreased significantly. At the transcriptional level, R. irregularis down-regulated the expression of the ABC transporter family but up-regulated differentially expressed genes regulating low molecular weight organic acids. The levels of malic acid, citric acid, and lactic acid were significantly increased in the rhizosphere soil, and they were significantly and strongly related to oxidizable Cd concentrations. Then citric acid levels were considerably and positively connected to exchangeable Cd concentrations. Our findings revealed that through regulating the movement of root molecules, arbuscular mycorrhizal fungus enhanced the heavy metal tolerance of C. sativa even more, meanwhile, they changed the Cd chemical forms by altering the composition of low molecular weight organic acids, which in turn affected soil Cd bioavailability.

The Glutathione S-Transferase PtGSTF1 Improves Biomass Production and Salt Tolerance through Regulating Xylem Cell Proliferation, Ion Homeostasis and Reactive Oxygen Species Scavenging in Poplar.

Glutathione S-transferases (GSTs) play an essential role in plant cell detoxification and secondary metabolism. However, their accurate functions in the growth and response to abiotic stress in woody plants are still largely unknown. In this work, a Phi class Glutathione S-transferase encoding gene PtGSTF1 was isolated from poplar (P. trichocarpa), and its biological functions in the regulation of biomass production and salt tolerance were investigated in transgenic poplar. PtGSTF1 was ubiquitously expressed in various tissues and organs, with a predominant expression in leaves and inducible expression by salt stress. Transgenic poplar overexpressing PtGSTF1 showed improved shoot growth, wood formation and improved salt tolerance, consistent with the increased xylem cell number and size under normal condition, and the optimized Na+ and K+ homeostasis and strengthened reactive oxygen species scavenging during salt stress. Further transcriptome analyses demonstrated that the expressions of genes related to hydrolase, cell wall modification, ion homeostasis and ROS scavenging were up- or down-regulated in transgenic plants. Our findings imply that PtGSTF1 improves both biomass production and salt tolerance through regulating hydrolase activity, cell wall modification, ion homeostasis and ROS scavenging in transgenic poplar, and that it can be considered as a useful gene candidate for the genetic breeding of new tree varieties with improved growth under salt stress conditions.

A super pan-genomic landscape of rice.

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

Identification of MYB Transcription Factors Involving in Fruit Quality Regulation of Fragaria × ananassa Duch.

The cultivated strawberry (Fragaria × ananassa Duch.) is an important horticultural crop. The economic values of strawberry cultivars are decided by their fruit qualities including taste, color and aroma. The important role of MYB transcription factors in fruit quality regulation is recognized increasingly with the identification of MYB genes involved in metabolism. A total of 407 MYB genes of F. × ananassa (FaMYBs) were identified in the genome-wide scale and named according to subgenome locations. The 407 FaMYBs were clustered into 36 groups based on phylogenetic analysis. According to synteny analysis, whole genome duplication and segmental duplication contributed over 90% of the expansion of the FaMYBs family. A total of 101 FaMYB loci with 1-6 alleles were identified by the homologous gene groups on homologous chromosomes. The differentially expressed FaMYB profiles of three cultivars with different fruit quality and fruit ripe processes provided the 8 candidate loci involved in fruit quality regulation. In this experiment, 7, 5, and 4 FaMYBs were screeded as candidate genes involved in the regulation of metabolism/transportation of anthocyanins, sugars or organic acids and 4-hydroxy-2, 5-dimethyl-3(2H)-furanone, respectively. These results pointed out the key FaMYBs for further functional analysis of gene regulation of strawberry fruit quality and would be helpful in the clarification on ofe roles of MYBs in the metabolism of fruit crops.

Characteristic-Aroma-Component-Based Evaluation and Classification of Strawberry Varieties by Aroma Type.

The unique fruity aroma of strawberries, a popular fruit of high economic value, is closely related to all the volatile organic compounds (VOCs) contained within them. Despite extensive studies on the identification of VOCs in strawberries, systematic studies on fruit-aroma-related VOCs are few, resulting in a lack of effective standards for accurately distinguishing aroma types. In the present study, solid-phase micro extraction and gas chromatography-mass spectrometry were used to analyze and identify VOCs in the ripe fruit of each of the 16 strawberry varieties at home and abroad and to explore their characteristic aroma components and the classification of such varieties by aroma type. The results suggested remarkable variations in the types and contents of VOCs in different strawberry varieties, of which esters were dominant. The principal volatile components, consisting of four esters, three alcohols, one aldehyde, and one ketone, in 16 strawberry varieties were detected based on the absolute and relative contents of VOCs in the fruit. The characteristic aroma components in strawberries, containing nine esters, six aldehydes, and one alcohol, were determined based on the aroma values of different VOCs, and the characteristic aroma components were divided into five types further based on aroma descriptions. Sixteen strawberry varieties were finally divided into four aroma types, namely, peachy, pineapple, fruity, and floral, based on the contributions of different types. The results provided a basis and standard for classifying strawberries by aroma type, studying the hereditary regularity of the fruity aroma of strawberries, and improving aroma quality.

OsCYP714D1 improves plant growth and salt tolerance through regulating gibberellin and ion homeostasis in transgenic poplar.

Cytochrome P450 monooxygenases (CYP450s) play crucial roles in the regulation of plant growth and response to abiotic stress. However, their functions in woody trees are still largely unknown. Previously, we reported that expression of the rice cytochrome P450 monooxygenase gene OsCYP714D1 increased gibberellic acid (GA) accumulation and shoot growth in transgenic poplar. In this work, we demonstrate that expression of OsCYP714D1 improved the salt tolerance of transgenic poplar plants. Compared to wild type, plant height and K+ content were significantly higher, whereas plant growth inhibition and Na+ content were significantly lower, in transgenic plants grown under high salt stress condition. Transcriptomic analyses revealed that OsCYP714D1 expression up-regulated the expressions of GA biosynthesis, signaling and stress responsive genes in transgenic plants under both normal and high salt stress conditions. Further gene ontology (GO) analyses indicated that genes involved in plant hormone and ion metabolic activities were significantly enriched in transgenic plants. Our findings imply that OsCYP714D1 participated in the regulation of both shoot growth and salt resistance through regulating gibberellin and ion homeostasis in transgenic poplar, and it can be used as a candidate gene for the engineering of new tree varieties with improved biomass production and salt stress resistance.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice.

BACKGROUND: Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. RESULTS: In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. CONCLUSION: The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Genome-Wide Screening of AP2 Transcription Factors Involving in Fruit Color and Aroma Regulation of Cultivated Strawberry.

Fragaria × ananassa Duch, which among the youngest fruit crops, comprises many popular cultivars that are famous for their favored color and aroma. The regulation roles of AP2/ERF (APETALA2/ethylene-responsive element-binding factor) transcription factors in fruit flavor and color regulation have been studied in several fruit crops. The AP2 family of strawberry, which was ignored in recent AP2/ERF identification studies, was explored in this study. A total of 64 FaAP2 (Fragaria × ananassa AP2) transcription factors belonging to the euAP2, euANT (AINTEGUMENTA), and baselANT groups were identified with canonical insertion motifs in two AP2 domains. The motif identification illustrated that motifs 1, 5, and 2 indicated a corresponding AP2 domain repeat 1 with a linker region, and motifs 6, 4, 3 indicated a corresponding AP2 domain repeat 2, all of which were highly conserved. By synteny analysis, FaAP2 paralogs were identified in each sub-genome, and FaAP2 gene duplication and loss explained the unequal AP2 loci of sub-genomes. The expression profile in three cultivars indicated that six FaAP2 paralogs-four WRI (WRINKLED) gene homologs and two AP2 gene homologs-were candidate regulators of red fruit color and/or special fruit aroma. All these finds provide a basis for further investigations into role of AP2 in fruit color and aroma and would be helpful in the targeted selection of strawberry fruit quality to improve breeding.

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress.

BACKGROUND: Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem. RESULT: Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research. CONCLUSIONS: The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.

PolyG mitigates silica-induced pulmonary fibrosis by inhibiting nucleolin and regulating DNA damage repair pathway.

Polyguanylic acid potassium salt (PolyG) has an anti-fibrotic G-quadruplex (G4) structure. It could inhibit the expression of nucleolin, a protein involved in cell proliferation and apoptosis. However, its role in regulating nucleolin in silicosis is still unknown. After instillation of 50 µl of crystalline silica suspension (50 mg/ml) into the trachea of C57BL/6 mice, we show that nucleolin expression is upregulated in mouse pulmonary tissue following the treatment with silica and that PolyG, which were injected 2.5 mg/kg body weight into mice by abdomen, could alleviate pulmonary fibrosis through inhibiting the expression of nucleolin. Further, we demonstrated that the expression of the DNA double-strand break (DSB) marker, γ-H2AX, increased in response to silica treatment. PolyG could efficiently reduce the protein expression of γ-H2AX and decreased the level of fibrosis-related genes, such as Col1a1 and Col3a1, as well as the levels of fibrosis-associated proteins α-SMA and vimentin in the lungs of silica-treated mice. These findings show that PolyG could regulate nucleolin and DNA damage repair to control fibrotic response in experimental silicosis and provide a new target for preventive intervention.

Proteomic analysis of the earthworm Eisenia fetida exposed to oxytetracycline in soil.

Increasing attention has been paid to the toxicity and hazards of antibiotics on non-target organisms in soil ecosystems because redundant antibiotics in the excretion of treated animals are being brought into the soil by way of manure and sewage irrigation. In order to understand the toxic mechanisms of antibiotics in soil ecosystems, the earthworm Eisenia fetida was exposed to 500 mg kg-1 of oxytetracycline (OTC) as a typical antibiotic for 7, 14 and 21 days. The total proteins of E. fetida in each treatment were separated by two-dimensional gel electrophoresis and differential expressed proteins were identified by MALDI-TOF/TOF-MS. A total of 30 proteins were successfully identified and divided into four categories based on the function. It was surprisingly found that more than 50% of identified proteins belong to the actin family, and all of them were down-regulated more than 2.0-fold. In the meantime, the fibrinolytic enzymes, an important protease with plasminogen activator activity, were suppressed in the last two weeks. The validations in the mRNA level were performed using RT-PCR. However, due to the incomplete genome sequence of E. fetida, we failed to identify more proteins response to OTC stress. This study may provide a new insight into the discovery of novel biomarkers for continuous-poured and low-toxicity pollutants.

iTRAQ-based secretome reveals that SiO2 induces the polarization of RAW264.7 macrophages by activation of the NOD-RIP2-NF-κB signaling pathway.

Silicosis is characterized by inflammation and pulmonary fibrosis due to long-term inhalation of crystalline silica (SiO2). To clarify the role of macrophage polarization in the inflammatory response of silicosis, we used iTRAQ-coupled 2D LC-MS/MS to study the change in the secretome in RAW264.7 macrophages. We successfully screened 330 differentially expressed proteins, including 120 proteins with upregulated expression and 210 proteins with down-regulated expression (p < 0.05). Bioinformatics analysis showed that the differentially expressed proteins were mainly involved in biological processes, such as oxidative stress, mitochondrial damage, apoptosis and acute inflammatory response. In particular, the expression levels of mitochondrial apoptosis-related proteins, such as AKT1, BAX, HSPD1, TNF, CASP8 and DAP, were increased after SiO2 exposure. Taken together, our study indicated that SiO2 could induce macrophage polarization by activation of the NOD-RIP2-NF-κB signaling pathway in RAW264.7 macrophages. This may represent a potential mechanism in the development of silicosis.

Intervention treatment on massive hemoptysis of pulmonary aspergilloma.

Retrospective analysis was carried out on intervention treatment and the effects of massive hemoptysis of pulmonary aspergilloma. Twenty-five cases diagnosed as massive hemoptysis of pulmonary aspergilloma were performed with imaging of bronchial arteries and other related blood vessels in order to assess blood vessel type and the number involved in the disease and perform embolotherapy on the offending artery. There were 68 bleeding arteries in 25 cases, of which there were 36 bronchial arteries (52.94%), 15 intercostal arteries (22.06%), 9 internal thoracic arteries (16.17%), 5 inferior phrenic arteries (7.35%), and 3 pulmonary arterial branches (4.41%) and all of them were in embolism condition. For 25 cases, 21 bleeding cases were stopped immediately (84.00%), 3 bleeding cases were stopped after the 2nd embolism, and 1 case had a small amount of hemoptysis after surgery discontinuously, which was stopped after corresponding treatment with no severe complications. Ten cases used polyvinyl alcohol (PVA) particulate embolization solely, 12 cases used PVA with spring coil and 3 cases used PVA, spring coil and N-butyl cyanoacrylate (NBCA) glue. In conclusion, patients who suffer from massive hemoptysis of pulmonary aspergilloma and whose medical treatments are not effective and who are not willing to receive surgical removal, intervention treatment is an effective method. PVA, spring coil and NBCA glue can be effectively used in hemoptysis embolism and pulmonary artery embolism can be considered when systemic embolism is not effective.

Down-Regulation of miR-19a as a Biomarker for Early Detection of Silicosis.

The accumulated data indicate that there is significant genetic heterogeneity underlying the etiology of silicosis. Recent reports have revealed that microRNAs (miRNAs) play an important role in regulating pulmonary fibrosis. This study, therefore, aimed to identify some miRNAs as biomarkers for silicosis, and to explore the early diagnostic value of biomarkers for silicosis. Total RNAs were collected from the peripheral blood leukocytes of 23 silicosis patients and 23 healthy controls, the different miRNAs were screened using microarrays. The potential biomarker miRNAs were identified by quantitative real-time polymerase chain reaction (qPCR) and receiver operating characteristic (ROC) curves. Eighteen differential miRNAs in leukocytes were up-regulated and twenty differential miRNAs were down-regulated in the silicosis group, compared with the control group. The expression levels of miR-181a and miR-19a were 0.8854 ± 0.1037 and 0.2929 ± 0.0342 by the relative quantitation method 2(-△△CT) of qPCR, respectively. The sensitivity and specificity for miR-181a at a cut-off value of 1.8917 were 70% and 75%, respectively, whereas, those for miR-19a at a cut-off value of 3.6828 were 95% and 95%, respectively. Thus, miR-19a in peripheral blood leukocyte could be used as an effective biomarker for silicosis. Anat Rec, 299:1300-1307, 2016. © 2016 Wiley Periodicals, Inc.

[Screening and identification of key signal transduction pathways in pulmonary silicotic fibrosis].

OBJECTIVE: To investigate the differential gene expression profile of the lung tissues in experimental silicosis rats and to screen for and identify the key signal transduction pathways in pulmonary silicotic fibrosis. METHODS: A total of 80 rats were randomly divided into control group (n = 40) and silica-instilled group (n = 40). Each group was equally divided into five subgroups, and each subgroup was treated at 1, 7, 14, 21, or 28 d. Intratracheal instillation was used to give 1 ml of silica suspension (50 mg/ml) in the silica-instilled group and normal saline in the control group. Silicotic nodules and type I and III collagen were observed through hematoxylin and eosin staining and Sirius red staining, respectively. Differentially expressed genes in pulmonary silicotic fibrosis were selected by the rat whole-genome gene expression RatRef-12 BeadChip (Illumina, USA), and a fold change cutoff was applied. Quantitative real-time polymerase chain reaction (qRT-PCR) was also used to verify differentially expressed genes. Through bioinformatics databases such as Visualization and Integrated Discovery (DAVID) and Kyoto Encyclopedia of Genes and Genomes (KEGG), preliminary research was performed on the biological pathways of differential genes, key biological signal transduction pathways were identified, and key differentially expressed genes in each pathway at different time points were searched for. RESULTS: A total of 2694 genes were differentially expressed and changed dynamically. The KEGG pathway analysis showed that 141 signal transduction pathways were involved in the development and progression of pulmonary silicotic fibrosis, among which 48 pathways were more significant than others (P < 0.01), with the mitogen-activated protein kinase (MAPK) pathway exceptionally significant. The differentially expressed genes interleukin-1 receptor (IL-1R), tumor necrosis factor receptor (TNFR), and transforming growth factor beta (TGF-ß) in the MAPK pathway were up-regulated at different time points after silica instillation. The results of real-time PCR showed that granulocyte-macrophage colony-stimulating factor (GM-CSF) was over-expressed at 4 time points and under-expressed at 1 time point compared with the control group. CONCLUSION: The MAPK signal transduction pathway plays a very important role in the development of pulmonary silicotic fibrosis. Both IL-1R and TNFR may play major roles during inflammation phase through the P38/Jun N-terminal kinase (JNK) pathway, and TGF-ß may have important function through the extracellular-signal-regulated kinase (ERK) pathway in the formation of fibrosis.