MicroRNA Omics Analysis of Camellia sinesis Pollen Tubes in Response to Low-Temperature and Nitric Oxide.

Nitric oxide (NO) as a momentous signal molecule participates in plant reproductive development and responds to various abiotic stresses. Here, the inhibitory effects of the NO-dominated signal network on the pollen tube growth of Camellia sinensis under low temperature (LT) were studied by microRNA (miRNA) omics analysis. The results showed that 77 and 71 differentially expressed miRNAs (DEMs) were induced by LT and NO treatment, respectively. Gene ontology (GO) analysis showed that DEM target genes related to microtubules and actin were enriched uniquely under LT treatment, while DEM target genes related to redox process were enriched uniquely under NO treatment. In addition, the target genes of miRNA co-regulated by LT and NO are only located on the cell membrane and cell wall, and most of them are enriched in metal ion binding and/or transport and cell wall organization. Furthermore, DEM and its target genes related to metal ion binding/transport, redox process, actin, cell wall organization and carbohydrate metabolism were identified and quantified by functional analysis and qRT-PCR. In conclusion, miRNA omics analysis provides a complex signal network regulated by NO-mediated miRNA, which changes cell structure and component distribution by adjusting Ca2+ gradient, thus affecting the polar growth of the C. sinensis pollen tube tip under LT.

Complexity of gene paralogues resolved in biosynthetic pathway of hepatoprotective iridoid glycosides in a medicinal herb, Picrorhiza kurroa through differential NGS transcriptomes.

Picrorhiza kurroa is a medicinal herb with diverse pharmacological applications due to the presence of iridoid glycosides, picroside-I (P-I), and picroside-II (P-II), among others. Any genetic improvement in this medicinal herb can only be undertaken if the biosynthetic pathway genes are correctly identified. Our previous studies have deciphered biosynthetic pathways for P-I and P-II, however, the occurrence of multiple copies of genes has been a stumbling block in their usage. Therefore, a methodological strategy was designed to identify and prioritize paralogues of pathway genes associated with contents of P-I and P-II. We used differential transcriptomes varying for P-I and P-II contents in different tissues of P. kurroa. All transcripts for a particular pathway gene were identified, clustered based on multiple sequence alignment to notify as a representative of the same gene (≥ 99% sequence identity) or a paralogue of the same gene. Further, individual paralogues were tested for their expression level via qRT-PCR in tissue-specific manner. In total 44 paralogues in 14 key genes have been identified out of which 19 gene paralogues showed the highest expression pattern via qRT-PCR. Overall analysis shortlisted 6 gene paralogues, PKHMGR3, PKPAL2, PKDXPS1, PK4CL2, PKG10H2 and PKIS2 that might be playing role in the biosynthesis of P-I and P-II, however, their functional analysis need to be further validated either through gene silencing or over-expression. The usefulness of this approach can be expanded to other non-model plant species for which transcriptome resources have been generated.

Protective role of vitamin B6 against mitochondria damage in Drosophila models of SCA3.

Polyglutamine (polyQ)-mediated mitochondria damage is one of the prime causes of polyQ toxicity, which leads to the loss of neurons and the injury of non-neuronal cells. With the discovery of the crucial role of the gut-brain axis and gut microbes in neurological diseases, the relationship between visceral damage and neurological disorders has also received extensive attention. This study successfully simulated the polyQ mitochondrial damage model by expressing 78 or 84 polyglutamine-containing Ataxin3 proteins in Drosophila intestinal enterocytes. In vivo, polyQ expression can reduce mitochondrial membrane potential, mitochondrial DNA damage, abnormal mitochondrial morphology, and loose mitochondrial cristae. Expression profiles evaluated by RNA-seq showed that mitochondrial structural genes and functional genes (oxidative phosphorylation and tricarboxylic acid cycle-related) were significantly down-regulated. More importantly, Bioinformatic analyses demonstrated that pathological polyQ expression induced vitamin B6 metabolic pathways abnormality. Active vitamin B6 participates in hundreds of enzymatic reactions and is very important for maintaining mitochondria's activities. In the SCA3 Drosophila model, Vitamin B6 supplementation significantly suppressed ECs mitochondria damage in guts and inhibited cellular polyQ aggregates in fat bodies, indicating a promising therapeutic strategy for the treatment of polyQ. Taken together, our results reveal a crucial role for the Vitamin B6-mediated mitochondrial protection in polyQ-induced cellular toxicity, which provides strong evidence for this process as a drug target in polyQ diseases treatment.

Systems pharmacology reveals the multi-level synergetic mechanism of action of Ginkgo biloba L. leaves for cardiomyopathy treatment.

ETHNOPHARMACOLOGICAL RELEVANCE: Cardiomyopathy is a common cause of heart failure and may lead to increased risk of sudden cardiac death, lacking simple, safe and effective treatment strategies due to unclear pathogenesis. Ginkgo biloba L. leaves (GBLs), a traditional Chinese medicine (TCM), has been widely used in clinical medicine for improving blood circulation, and was demonstrated to be effective on cardiomyopathy in preclinical studies. However, because of the widely known holistic therapeutic philosophy via multi-target and multi-pathway effect for most TCMs, to explore its underlying molecular mechanisms of action (MoA) remains a great challenge. AIM OF STUDY: Decipher the underlying MoA of GBLs for cardiomyopathy treatment: Study design and methods: An integrated systems pharmacology framework was employed to screen potential active compounds, identify therapeutic targets, explore the action pathways and verify mechanisms of GBLs with in vitro experiments. RESULTS: We firstly confirmed the therapeutic effect of GBLs on cardiomyopathy and subsequently screened 27 active compounds from GBLs according to their pharmacokinetic properties. Then Probability Ensemble Approach was applied to identify the compound combinations that exert synergetic effect from GBLs. Network analysis and functional enrichment analysis demonstrated that these compounds exhibit synergistic therapeutic effect by acting on multiple targets and thereby regulating multiple pathways mainly involved in pro-survival, anti-apoptotic and anti-inflammatory processes. Finally, using a doxorubicin-induced myocardial injury model, therapeutic effect of ginkgolide A, ginkgolide B, isorhamnetin, as well as their synergistic effect on PI3K-AKT and NF-κB signaling pathways were validated in vitro. Importantly, we demonstrated that Ginkgo diterpene lactone meglumine injection (GDJ), an approved injection derived from GBLs, could be a promising agent for cardiomyopathy treatment. CONCLUSION: Collectively, the multi-level synergetic mechanism of GBLs on cardiomyopathy treatment was demonstrated with systems pharmacology approach, providing a paradigm for deciphering the complicated MoA of TCMs.

Clinical trait-connected network analysis reveals transcriptional markers of active psoriasis treatment with Liangxue-Jiedu decoction.

ETHNOPHARMACOLOGICAL RELEVANCE: Psoriasis is a complex recurrent inflammatory skin disease with different pathological changes in different stages. Psoriasis in its active stage, which is comparable to the blood-heat type in traditional Chinese medicine (TCM), has been treated by Liangxue Jiedu Decoction (LJD) in TCM for decades, with proven efficacy. According to TCM theories, LJD has the function of removing heat and pathogenic factors from the blood. AIM OF THE STUDY: We aimed to investigate the molecular features associated with the active stage psoriasis and identify genes responding to LJD treatment accompanied by lesion remission. MATERIALS AND METHODS: Healthy volunteers and psoriasis patients who met specific diagnostic criteria were recruited. Twenty-six transcriptomes were profiled from the peripheral blood mononuclear cells (PBMCs) of 10 psoriasis patients (pre- and post-treatment) and 6 healthy volunteers. RNA sequencing data were analyzed using an integrated approach combining differential gene expression analysis (DGEA) and weighted gene co-expression network analysis (WGCNA), by which gene expression was linked to multiple clinical traits, including psoriasis area and severity index (PASI), as well as the improvement rate of skin lesions (ΔPASI). The actions of LJD were then verified using an in vitro cell assay coupled to flow cytometric analysis and RT-PCR. RESULTS: We identified four network modules with statistical significance (P < 0.05), two of which connected to the PASI score, while the other two connected to 8-week treatment and ΔPASI, respectively. In psoriasis patients, activated inflammatory pathways and inhibited G-protein signaling genes (GTPase IMAP family member and G protein-coupled receptor) co-occurred, with high expression of CD83 and CD69, and low expression of CD160 and CD180, compared with the health. Accompanying LJD treatment and lesion remission, the expression of CD69 and cell cycle-related genes, including CCNA2, CCNB2, CDK1, and TOP2A, was down-regulated. The inhibitory role of LJD on CD69 expression was confirmed by the decline of activating naïve CD4+ T lymphocytes. CONCLUSION: Our study suggests that active psoriasis is characterized by unbalanced immune status with dendrite cell and lymphocyte-associated inflammatory activation as well as NK cell- and B cell-associated defense response aberrance. LJD played an inhibitory role in T cell activation, a process located downstream pathological cascade of psoriasis.

Effect of Hordei Fructus Germinatus on differential gene expression in the prolactin signaling pathway in the mammary gland of lactating rats.

ETHNOPHARMACOLOGICAL RELEVANCE: In China, Hordei Fructus Germinatus (HFG) is the germinated and dried fruit of Hordeum vulgare L, which is commonly used in clinical Chinese medicine. Traditional Chinese Medicine (TCM) theory holds that HFG can be both medicinal and edible, which means that it is derived from food medicine. Raw HFG and roasted HFG are used to treat hypogalactia, hyperprolactinemia and indigestion. In recent years, the lactogenic and galactophygous effects of HFG have attracted increasing attention. Nevertheless, there is much confusion over the use of raw and processed HFG, and the mechanism of its lactogenic effect seems remains poorly understood. AIM OF THE STUDY: This study aimed to explore the lactogenic effect of raw HFG and roasted HFG on rats with overloaded lactation and to reveal the underlying molecular mechanism. MATERIALS AND METHODS: Raw and processed HFG water decoctions were given to overloaded lactation model rats at a dose of 1.7800 g kg-1·d-1, and the control group was given the same volume of water. The lactogenic effect of raw and processed HFG was evaluated by measuring daily lactation, body weight and pup body weight, serum PRL, E2, and GH contents after parturition, and the pathological characteristics of mammary tissue sections. cDNA microarrays can be used to screen diverse gene expression patterns and signaling pathways related to prolactin. The expression of relevant differentially expressed genes was verified by real-time PCR and western blotting. RESULTS: In vivo experiments demonstrated that the raw HFG water decoction stimulated mammogenesis, accelerated the transformation of the lobular acinar system, resulted in denser mammary epithelial cells and thicker glandular ducts that were full of milk and facilitated the secretion of milk. Moreover, HFG increased PRL, E2, and GH levels, pup body weight, daily lactation and the body weight of lactating rats. Following gene chip identification, KEGG pathway enrichment analysis revealed genes that were highly related to prolactin in the prolactin signaling pathway and JAK-STAT signaling pathway, and the main differentially expressed genes were Jak2 (down), Stat5α (up), cyclin D1 (up), SOCS1 (up), CISH (down) and PRLR (up). Compared with the control group, RT-PCR results indicated that Jak2 and CISH were downregulated and that Stat5α, cyclin D1, SOCS1 and PRLR were upregulated. Western blot assays showed that PRLR, STAT5α and cyclin D1 levels in the mammary glands of the raw HFG water decoction group were significantly increased, which was consistent with the results of cDNA microarray screening. CONCLUSION: The present study reveals that raw HFG effectively enhances lactation in rats, possibly by influencing the prolactin/JAK-STAT signaling pathway.

Systematic biological and proteomics strategies to explore the regulation mechanism of Shoutai Wan on recurrent spontaneous Abortion's biological network.

ETHNOPHARMACOLOGICAL RELEVANCE: Shoutai Wan (STW) is a classic herbal formula for the treatment of recurrent spontaneous abortion (RSA), and clinical studies have shown the effectiveness of STW on RSA. However, the molecular mechanism of STW treatment of RSA is still unclear. METHODS: (1) Animal experiments: The normal pregnancy model was established with CBA/J*BALB/C, and the RSA model was established by CBA/J*DBA/2. The RSA model CBA/J*DBA/2 pregnant mice were randomly divided into four groups (RSA model group, STW low, medium and high dose groups) according to the order of pregnancy, respectively. The drug administration starts from the first day of pregnancy to the 14th day of pregnancy. The embryo loss rate (ELR) of each group was calculated. (2) Proteomic analysis of decidual tissue: The total protein of decidual tissue of each group was isolated by solid phase pH gradient 2-DE technique. The differentially expressed protein spots were analyzed and identified by PDQuest images; the peptide quality fingerprinting (PMF) was obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Then, the proteins were identified by Mascot software searching, their functions were identified by bioinformatics strategy. (3) The expression of HSP27, α-enolase and Transferrin was detected by Western blotting and the expression of Annexin A2 and Transferrin was detected by immunohistochemistry. (4) The differential proteins and potential targets were analyzed by systematic biological strategy. RESULTS: (1) Compared with the normal group, the ELR in the RSA model group was significantly higher (P < 0.01). Compared with the model group, the ELR in the STW high, medium dose groups was lower (P < 0.01). (2) A 2-DE map of the decidual tissue of the RSA model group, normal pregnancy group, STW low, medium and high dose groups was established. Thirty proteins were identified. (3) The results of western blot showed that the expression of HSP27 and a-enolase in the RSA model group was higher than that in the normal group, and the expression of transferrin was lower (P < 0.01). Compared with the model group, the expression of HSP27 and a-enolase in STW high, medium dose groups was decreased (P < 0.01); Compared with the model group, the expression of Transferrin in the STW high dose group was increased (P < 0.01). (5) A lot of RSA treatment-related targets, biological processes and pathways were found after the systematic biological analysis. CONCLUSION: (1) STW may reduce the ELR of the RSA mice. (2) The results of proteomics suggest that RSA is a complex process involving multiple proteins. STW can regulate the expression of various proteins in the decidual tissue of RSA mice, suggesting that it can act on multiple targets. (3) The results of western blotting of HSP27, a-enolase, transferrin were consistent with the results of proteomic analysis. (4) STW may achieve therapeutic effects by interfering with the targets, biological processes and signaling pathways discovered in this study.

Study on the regulatory mechanism and experimental verification of icariin for the treatment of ovarian cancer based on network pharmacology.

ETHNOPHARMACOLOGICAL RELEVANCE: Herba Epimedii (Berberidaceae) has the advantages of "nourishing the kidney and reinforcing the Yang". Many species in this genus have long been used in traditional Chinese medicine (TCM) and have been used as anticancer drugs in traditional Chinese herbal medicine formulations. Icariin, a major flavonoid glycoside extracted from Epimedium brevicornum Maxim, has been widely proven to exert an inhibitory effect on ovarian cancer (OC), and icariin can induce apoptosis and inhibit invasion and migration. However, the underlying mechanism remains unclear, so further research is necessary to verify its traditional use. AIM OF THE STUDY: This study aimed to explore the regulatory mechanism of icariin in the biological network and signalling pathway of OC through network pharmacology and cytological experiments. METHODS: Public databases and R × 3.6.2 software were adopted to predict the potential targets, construct the protein-protein interaction (PPI) network, and perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. After the network pharmacological analysis, cytological experiments, real-time quantitative PCR (qPCR) and Western blot (WB) analyses were used to verify the key signalling pathway. RESULTS: The targets related to treatment were TNF, MMP9, STAT3, PIK3CA, ERBB2, MTOR, IL2, PTGS2, KDR, and F2. GO and KEGG enrichment analyses indicated that various kinases and the PI3K/AKT signalling pathway were the most enriched molecules and pathways. Icariin inhibited OC SKOV3 cell proliferation, migration and invasion in vitro and promoted apoptosis by inhibiting the PI3K/AKT signalling pathway. CONCLUSION: Icariin promotes apoptosis and suppresses SKOV3 cell activities through the PI3K-Akt signalling pathway. This research not only provides a theoretical and experimental basis for more in-depth studies but also offers an efficient method for the rational utilization of a series of icariin flavonoids as anti-tumour drugs.

Shikonin induces tumor apoptosis in glioma cells via endoplasmic reticulum stress, and Bax/Bak mediated mitochondrial outer membrane permeability.

ETHNOPHARMACOLOGICAL RELEVANCE: Shikonin, one of the main active ingredients of Chinese herbal medicine Lithospermum erythrorhizon, has been widely used to treat various disease including virus infection and inflammation in clinical. Its anti-tumor activity has been recorded in "Chinese herbal medicine". Recently, some studies about its anti-glioma effects have been reported. However, little is known about the molecular pharmacological activity of Shikonin in glioma. AIM: This study aimed to systematically uncover and validate the pharmacological mechanism of Shikonin against glioma. MATERIAL AND METHODS: Network pharmacology approach, survival analysis, and Pearson co-expression analysis were performed to uncover and test the pharmacological mechanisms of Shikonin in glioma. Apoptosis assay, Caspase-3 activity assay and immunoblot analysis were practiced to validate the mechanisms. RESULTS: Network pharmacology results suggested, anti-glioma effect of Shikonin by interfering endoplasmic reticulum (ER) stress-mediated tumor apoptosis targeting Caspase-3, and Bax/Bak-induced mitochondrial outer membrane permeabilization (MOMP) triggering cancer cell apoptosis. Survival analysis suggested the association of CASP3 with glioma (P < 0.05). Pearson correlation analysis indicated possible interaction of CASP3 with PERK through positive feedback regulation. Shikonin or in combination with 14G2a induced cell apoptosis in oligodendroglioma Hs683 cells in a dose-dependent manner with at a maximum apoptosis rate of 33%-37.5%, and 73%-77% respectively. Immunoblot analysis showed that Shikonin increased Caspase-3 activity to about 4.29 times, and increased 9 times when it combined with 14G2a. Shikonin increased also the expression levels of the proteins PERK and CHOP by about 4.4 and 5.6 folds, respectively, when it combined with 14G2a. CONCLUSIONS: This study highlights the pharmacological mechanisms of Shikonin in the induction of tumor apoptosis in glioma cells.

Gene regulatory network analysis with drug sensitivity reveals synergistic effects of combinatory chemotherapy in gastric cancer.

The combination of docetaxel, cisplatin, and fluorouracil (DCF) is highly synergistic in advanced gastric cancer. We aimed to explain these synergistic effects at the molecular level. Thus, we constructed a weighted correlation network using the differentially expressed genes between Stage I and IV gastric cancer based on The Cancer Genome Atlas (TCGA), and three modules were derived. Next, we investigated the correlation between the eigengene of the expression of the gene network modules and the chemotherapeutic drug response to DCF from the Genomics of Drug Sensitivity in Cancer (GDSC) database. The three modules were associated with functions related to cell migration, angiogenesis, and the immune response. The eigengenes of the three modules had a high correlation with DCF (-0.41, -0.40, and -0.15). The eigengenes of the three modules tended to increase as the stage increased. Advanced gastric cancer was affected by the interaction the among modules with three functions, namely cell migration, angiogenesis, and the immune response, all of which are related to metastasis. The weighted correlation network analysis model proved the complementary effects of DCF at the molecular level and thus, could be used as a unique methodology to determine the optimal combination of chemotherapy drugs for patients with gastric cancer.

Multiple protein and mRNA expression correlations in the rat cerebral cortex after ischemic injury and repair due to buchang naoxintong jiaonang (BNJ) intervention.

Stroke is the one of the most common causes of death worldwide. Systematic description and characterization of the types of stroke and the effects induced in the cerebral cortex have not been performed so far. Here, we analyzed the protein and mRNA expression in the cerebral cortex12 h after ischemic injury and repair. Drug intervention using Buchang Naoxintong Jiaonang (BNJ), which has been reported to have good clinical therapeutic effects, was selected for our study of cerebral ischemic repair in rat models. Two powerful techniques can be merged in a single study to examine and yield new perspectives in physiology and pathophysiology. Combining LC-MS/MS and DNA microarray analyses of the rat cerebral cortex confidently identified two large datasets in more than three biological replicates. Quantitative approaches were then used to quantify the differences among the four experimental groups the naive, sham, middle cerebral artery occlusion MCAO and MCAO + BNJ groups by a label-free proteomics approach and a Cy5-labeled microarray approach. In brief, 3217 unique proteins and 24,300 unique gene symbols were confidently identified. Bioinformatics analysis revealed that of these unique proteins and gene symbols, 269 proteins and 632 gene symbols were identified to be differentially expressed. The results of subcellular localization, hierarchical clustering, and pathway enrichment analyses were combined with the results of the injury and repair phase analyses, and twelve proteins and twenty-seven gene symbols were significantly differentially expressed and were identified as potential candidates for cerebral ischemic injury involvement; all the candidates were verified by western blot and quantitative real-time PCR analysis. The primary enriched MAPK signaling pathway may play a key role in the molecular mechanisms related to cerebral ischemic injury. The observations of the present study help to illuminate the regulatory mechanism of cerebral ischemic injury and repair due to BNJ intervention.

Genetic variability of morpho-physiological response to phosphorus deficiency in Tunisian populations of Brachypodium hybridum.

Brachypodium hybridum (Poaceae) is widely distributed in the dry environments in Mediterranean basin, due to its high tolerance to drought. Investigating the natural variation of B. hybridum in response to environmental stresses is crucial for unraveling the genetic network of its stress tolerance. 79 B. hybridum lines from eight Tunisian populations were screened for their performance to low P availability using morpho-physiological parameters. ANOVA showed that treatment and population*treatment factors were the most contributors in the explained variance for the majority of parameters. A considerable population differentiation was detected in control and under P level (Qst = 0.77 vs Qst = 0.62). This suggests that B. hybridum exhibit an adaptive differential response to P deficiency related environmental conditions. Results revealed that Raouad and Sejnen lines were the most tolerant to P deficiency followed by Haouaria and Enfidha lines. The remaining populations were classified as sensitive. This pattern suggests that coastal populations were more tolerant to P deficiency than the inland ones. A slightly higher heritability was evidenced under low P level for most of traits, indicating that the direct selection under P deficiency is more reliable than an indirect one under optimal P supply.

Deep Sequencing Identification of Differentially Expressed miRNAs in the Spinal Cord of Resiniferatoxin-Treated Rats in Response to Electroacupuncture.

Electroacupuncture (EA) is an effective treatment to relieve pain in patients with postherpetic neuralgia. However, the mechanisms of EA involved therein are still unknown. We first injected resiniferatoxin (RTX) into Sprague Dawley rats to construct the neuralgia model. One week after injection, the rats were treated with EA at the "Huantiao" (GB30) and "Yanglingquan" (GB34) acupoints for 5 weeks. Nociceptive behavioral tests were performed to analyze the changes in thermal sensitivity and mechanical allodynia after RTX induction and EA treatment. Deep sequencing was performed to identify differentially expressed miRNAs in the spinal cord of RTX-induced rats in response to EA treatment. The nociceptive behavioral tests showed that EA at the left GB30 and GB34 acupoints significantly reduced RTX-induced tactile sensitivity and increased RTX-inhibited thermal sensitivity. The sequencing data indicated that RTX resulted in one upregulated and five downregulated miRNAs, and EA treatment resulted in two upregulated miRNAs. Furthermore, seven upregulated and two downregulated miRNAs were found between rats subjected to EA and sham operation. Functional analysis suggested that the targets of differentially expressed miRNAs were enriched in many nervous system-related pathways. The pathway-gene-miRNA net analysis showed that miR-7a-5p had the most target genes. Moreover, miR-233-3p was downregulated after RTX injection and upregulated by EA treatment. We speculated that the upregulation of miR-7a-5p and miR-233-3p is involved in the analgesic effects of EA. Our analysis on the EA-induced differential expression of miRNAs provides novel insights into the mechanisms of EA analgesia in postherpetic neuralgia.

Perception, transduction, and integration of nitrogen and phosphorus nutritional signals in the transcriptional regulatory network in plants.

Nitrate and phosphate ions are major sources of nitrogen and phosphorus for plants. In addition to their vital roles as indispensable macronutrients, these ions function as signalling molecules and induce a variety of responses. Plants adapt to different levels of nutrients by altering their gene expression profile and subsequent physiological and morphological responses. Advances made in recent years have provided novel insights into plant nutrient sensing and modulation of gene expression. Key breakthroughs include elucidation of the mechanisms underlying post-translational regulation of NIN-LIKE PROTEIN (NLP) and PHOSPHATE STARVATION RESPONSE (PHR) family transcription factors, which function as master regulators of responses to nitrate and phosphate starvation, respectively. Determination of the mechanisms whereby these nutrient signals are integrated through NIGT1/HHO family proteins has likewise represented important progress. Further studies have revealed novel roles in nutrient signalling of transcription factors that have previously been shown to be associated with other signals, such as light and phytohormones. Nitrate and phosphate signals are thus transmitted through an intricate gene regulatory network with the help of various positive and negative transcriptional regulators. These complex regulatory patterns enable plants to integrate input signals from various environmental factors and trigger appropriate responses, as exemplified by the regulatory module involving NIGT1/HHO family proteins. These mechanisms collectively support nutrient homeostasis in plants.

Transcriptomic characterization of signaling pathways associated with osteoblastic differentiation of MC-3T3E1 cells.

Bone remodeling involves the coordinated actions of osteoclasts, which resorb the calcified bony matrix, and osteoblasts, which refill erosion pits created by osteoclasts to restore skeletal integrity and adapt to changes in mechanical load. Osteoblasts are derived from pluripotent mesenchymal stem cell precursors, which undergo differentiation under the influence of a host of local and environmental cues. To characterize the autocrine/paracrine signaling networks associated with osteoblast maturation and function, we performed gene network analysis using complementary "agnostic" DNA microarray and "targeted" NanoString nCounter datasets derived from murine MC3T3-E1 cells induced to undergo synchronized osteoblastic differentiation in vitro. Pairwise datasets representing changes in gene expression associated with growth arrest (day 2 to 5 in culture), differentiation (day 5 to 10 in culture), and osteoblast maturation (day 10 to 28 in culture) were analyzed using Ingenuity Systems Pathways Analysis to generate predictions about signaling pathway activity based on the temporal sequence of changes in target gene expression. Our data indicate that some pathways involved in osteoblast differentiation, e.g. Wnt/ß-catenin signaling, are most active early in the process, while others, e.g. TGFß/BMP, cytokine/JAK-STAT and TNFα/RANKL signaling, increase in activity as differentiation progresses. Collectively, these pathways contribute to the sequential expression of genes involved in the synthesis and mineralization of extracellular matrix. These results provide insight into the temporal coordination and complex interplay between signaling networks controlling gene expression during osteoblast differentiation. A more complete understanding of these processes may aid the discovery of novel methods to promote osteoblast development for the treatment of conditions characterized by low bone mineral density.

Paeoniflorin improves pressure overload-induced cardiac remodeling by modulating the MAPK signaling pathway in spontaneously hypertensive rats.

Paeoniflorin (PF) is a main bioactive component of the root of Paeonia lactiflora Pal, and previous investigations suggest that it may impact cardiac remodeling in spontaneous hypertensive rats (SHR) via the MAPK signaling pathway. Thus, the purpose of this investigation was to examine the impacts of paeoniflorin cardiac function in SHR rats. Cardiac function and blood pressure were observed using echocardiography and non-invasive tail pressure gauge. Heart histopathology was assessed by histological staining and transmission electron microscopy. Genomic sequencing was performed and signaling pathway enrichment analyzed the function of differentially expressed genes(DEGs). Biochemical kits were used to analyze the serum level of proinflammatory cytokines including TNF-α, IL-6 and MCP-1. qRT-PCR proved the mRNA expression of Ngfr, Grin2b, and Ntf4. MAPK pathways were determined via western blot. Paeoniflorin decreased blood pressure and increased hemodynamic indexes. 131 DEGs were identified (SHR vs. PF), and mainly enriched on the MAPK signaling pathway. Paeoniflorin reduced IL-6, MCP-1, Ngfr, Grin2b, and Ntf4, and also decreased p-JNK, p-Erk1/2, and p-p38 proteins compared with the SHR group. Paeoniflorin attenuated cardiac hypertrophy, cardiac fibrosis, and inflammation, and subsequently improved LV function. In conclusion, the cardioprotective role of paeoniflorin was associated with the inhibition of MAPK signaling pathway.

Gene network of oil accumulation reveals expression profiles in developing embryos and fatty acid composition in Upland cotton.

Cottonseed oil accumulated dramatically from 20 days post-anthesis (DPA) to 30 DPA in Upland cotton (Gossypium hirsutum L.). To reveal the gene network of oil accumulation and fatty acid composition in developing embryos, embryos at 10, 20 and 30 DPA in cottonseed were sampled and used for transcriptome sequencing (RNA-Seq). In total, 8629, 7891, and 12,555 differentially expressed genes (DEGs) were identified in the comparison sets of '20 DPA vs 10 DPA', '30 DPA vs 20 DPA', and '30 DPA vs 10 DPA', respectively. The gene network highlighted the dynamic expression profiles of oil accumulation in fatty acid (FA) synthesis, FA desaturation, and triacylglycerol (TAG) biosynthesis. WRI1 and NF-YB6 were suggested elite transcription factors in regulating lipid metabolism. Compared with the gene expression levels in developing seeds, GhPDAT was highly expressed and might play a more important role than GhDGAT in transforming diacylglycerol to TAG in cotton. Expression patterns of 12 FA-biosynthesis-related genes were validated by quantitative real-time PCR (qRT-PCR) method. To reveal the reason for the high content of linoleic acid (C18:2) in cottonseed oil, we carried out a comparative analysis of gene expression levels in Upland cotton, rapeseed (Brassica napus), and oleaster (Olea europaea). Compared with in rapeseed and oleaster, GhFAD2 genes were up-regulated and GhFAD3 genes down-regulated in cottonseed, taking into account the relative high amount of C18:2 but low content of linolenic acid (C18:3) in Upland cotton. The present study offers new information to interpret the mechanism of the FA biosynthesis network and to alter FA composition in cotton breeding projects.

Proteomics of hot-wet and cold-dry temperaments proposed in Iranian traditional medicine: a Network-based Study.

Lack of molecular biology evidence has led clinical success of alternative and complementary medicine (CAM) to be marginalized. In turn, a large portion of life Science researchers could not communicate and help to develop therapeutic potential laid in these therapeutic approaches. In this study, we began to quantify descriptive classification theory in one of the CAM branches i.e. Iranian traditional medicine (ITM). Using proteomic tools and network analysis, the expressed proteins and their relationships were studied in mitochondrial lysate isolated from PBMCs from two different temperaments i.e. Hot-wet (HW) and Cold-dry (CD). The 82% of the identified proteins are over- or under-represented in distinct temperaments. Also, our result showed the different protein-protein interaction networks (PPIN) represented in these two temperaments using centrality and module finding analysis. Following the gene ontology and pathway enrichment analysis, we have found enriched biological terms in each group which are in conformity with the physiologically known evidence in ITM. In conclusion, we argued that the network biology which naturally consider life at the system level along with the different omics data will pave the way toward explicit delineation of the CAM activities.

Correlations of inflammatory gene pathways, corticolimbic functional activities, and aggression in pediatric bipolar disorder: a preliminary study.

The mechanisms underlying aggression in adolescents with bipolar disorder have been poorly understood. The present study has investigated the associations among TNF gene expressions, functional brain activations under the frustrative non-reward task, and aggression in adolescents with bipolar disorder. Baseline gene expressions and aggressive tendencies were measured with the RNA-sequencing and Brief Rating of Aggression by Children and Adolescents (BRACHA), respectively. Our results show that activity levels of left subgenual anterior cingulate gyrus (ACG), right amygdala, left Brodmann area 10 (orbitofrontal cortex), and right thalamus were inversely correlated with BRACHA scores and were activated with frustrative non-reward during the affective Posner Task. In addition, 11 TNF related gene expressions were significantly correlated with activation of amygdala or ACG during the affective Posner Task. Three TNF gene expressions were inversely correlated with BRACHA score while one TNF gene (TNFAIP3) expression was positively correlated with BRACHA score. Therefore, TNF-related inflammatory cytokine genes may play a role in neural activity associated with frustrative non-reward and aggressive behaviors in pediatric bipolar disorder.

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape.

Despite a long-standing interest in the genetic basis of morphological diversity, the molecular mechanisms that give rise to developmental variation are incompletely understood. Here, we use comparative transcriptomics coupled with the construction of gene coexpression networks to predict a gene regulatory network (GRN) for leaf development in tomato and two related wild species with strikingly different leaf morphologies. The core network in the leaf developmental GRN contains regulators of leaf morphology that function in global cell proliferation with peripheral gene network modules (GNMs). The BLADE-ON-PETIOLE (BOP) transcription factor in one GNM controls the core network by altering effective concentration of the KNOTTED-like HOMEOBOX gene product. Comparative network analysis and experimental perturbations of BOP levels suggest that variation in BOP expression could explain the diversity in leaf complexity among these species through dynamic rewiring of interactions in the GRN. The peripheral location of the BOP-containing GNM in the leaf developmental GRN and the phenotypic mimics of evolutionary diversity caused by alteration in BOP levels identify a key role for this GNM in canalizing the leaf morphospace by modifying the maturation schedule of leaves to create morphological diversity.