Prognostic model of kidney renal clear cell carcinoma using aging-related long noncoding RNA signatures identifies THBS1-IT1 as a potential prognostic biomarker for multiple cancers.

Aging is responsible for the main intrinsic triggers of cancers; however, the studies of aging risk factors in cancer animal models and cancer patients are rare and insufficient to be represented in cancer clinical trials. For a better understanding of the complex regulatory networks of aging and cancers, 8 candidate aging related long noncoding RNAs (CarLncs) identified from the healthy aging models, centenarians and their offsprings, were selected and their association with kidney renal clear cell carcinoma (KIRC) was explored by series of cutting edge analyses such as support vector machine (SVM) and random forest (RF) algorithms. Using data downloaded from TCGA and GTEx databases, a regulatory network of CarLncs-miRNA-mRNA was constructed and five genes within the network were screened out as aging related feature genes for developing KIRC prognostic models. After a strict filtering pipeline for modeling, a formula using the transcript per million (TPM) values of feature genes "LncAging_score = 0.008* MMP11 + 0.066* THBS1-IT1 + (-0.014)* DYNLL2 + (-0.030)* RMND5A+ 0.008* PEG10" was developed. ROC analysis and nomogram suggest our model achieves a great performance in KIRC prognosis. Among the 8 CarLncs, we found that THBS1-IT1 was significantly dysregulated in 12 cancer types. A comprehensive pan-cancer analysis demonstrated that THBS1-IT1 is a potential prognostic biomarker in not only KIRC but also multiple cancers, such as LUSC, BLCA, GBM, LGG, MESO, PAAD, STAD and THCA, it was correlated with tumor microenvironment (TME) and tumor immune cell infiltration (TICI) and its high expression was related with poor survival.

Evolution of phosphorus with the promotion of KOH in supercritical water gasification of dewatered cyanobacteria from ion perspective.

Phosphorus is a very important resource, and dewatered cyanobacteria contains a large amount of it. Basic additives, such as KOH, are often used to promote hydrogen production during supercritical water gasification (SCWG) of biomass, but their effects phosphorus transformation have rarely been investigated. In this study, SCWG of dewatered cyanobacteria with potassium salt and KOH was conducted in autoclave at 400 °C for 10 min, to investigate the effect of K+ on the transformation of phosphorus under neutral and alkaline conditions. Results showed that K+ increased the proportion of phosphorus in the solid phase from 88.4% to 90.8-98.3%. Furthermore, K+ could promote the transformation of iron-combined phosphorus to calcium-combined phosphorus and occluded phosphate. Only when the reaction environment was alkaline, the proportion of phosphorus in the solid phase was significantly reduced to a minimum of 26.1%. When the amount of OH- was sufficient, can this part of phosphorus and organic phosphorus, which was decomposed and transformed by the promotion of OH-, be transferred to the liquid products. Results from this study laid a foundation simultaneously for hydrogen production and phosphorus recovery more environmentally and high-effectively.

Hydrothermal carbonization coupling with liquid dimethyl ether extraction pretreatment of sewage sludge: Hydrochar performance improvement and low-nitrogen biocrude production.

Hydrothermal carbonization of sewage sludge converts waste into hydrochar; however, the complex organic composition of feedstock limits the product value. A novel process that combines liquid dimethyl ether extraction and hydrothermal carbonization (DE-HTC) was proposed for improving the product value by simultaneously producing biocrude/hydrochar and improving feedstock suitability for thermochemical conversion. Biocrude and hydrochar with a product yield of 2.62% and 55.83% were produced via DE-HTC, respectively. The hydrochar yield increased by 12.65%-29.90% compared to traditional single-step hydrothermal carbonization. The hydrochar energy densification was decreased by 1.16%-10.28%, while hydrochar's energy yield increased by 47%-66%, and it had a more prominent porous structure. By avoiding the decomposition of proteins during thermochemical conversion, the nitrogen content of the biocrude obtained via DE-HTC was only 0.38%. The biocrude was also further qualitatively analyzed. This study provides insights into the efficacy of a novel hydrothermal method with distinct product value advantages over direct hydrothermal carbonization.

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer.

Huangqi decoction alleviates dimethylnitrosamine-induced liver fibrosis: An analysis of bile acids metabolic mechanism.

ETHNOPHARMACOLOGICAL RELEVANCE: Huangqi Decoction (HQD), a classical traditional Chinese medicine (TCM) formula, is used to treating liver injury in China. The aim of the study is to investigate mechanisms of HQD against dimethylnitrosamine (DMN)-induced liver fibrosis underlying metabolic profiles of bile acids. MATERIALS AND METHODS: DMN-induced liver fibrosis rats were administrated HQD and its compounds, astragalosides (AS), glycyrrhizic acid (GA) and their combination. The anti-fibrosis effects were evaluated and targeted metabolomics by UPLC-MS was used to examine whether HQD had an influence on bile acid metabolism. The levels of mRNAs associated with bile acid metabolism were expressed by RT-PCR. Chenodeoxycholic acid (CDCA)-induced hepatic stellate cells (HSCs) proliferation and activation were examined using MTS assay and Western blot. RESULTS: Histopathological changes and serum liver function in HQD group had significant improvements (P<0.01). Concentrations of free bile acids and taurine conjugates were significantly increased in DMN group (P<0.05). HQD and its compounds restored the increased bile acids to normal levels, and HQD was more effected on parts of bile acids. Furthermore, the levels of mRNAs related bile acid synthesis and reabsorption such as CYP7A1, CYP8B1, CYP27A1, OATP2, OATP3, OATP4 and NTCP were significantly down-regulated in DMN group (P<0.05), mRNAs related excretion such as MRP3 and BESP were up-regulated (P<0.01), and CYP7A1, CYP8B1, OATP3, OATP4, NTCP and MRP3 restored to normal levels by HQD treatment. Moreover, CDCA-induced HSCs proliferation and activation were weaken by HQD (P<0.05) with down-regulated α-SMA, TGF-ß1, p-Smad2 and p-Smad3 expressions. CONCLUSIONS: HQD alleviated DMN-induced liver fibrosis with a better effect than its compounds, which may be involved in the regulation of bile acid metabolism enzyme. Moreover, HQD may inhibit CDCA-induced HSCs proliferation and activation.

Actions of Huangqi decoction against rat liver fibrosis: a gene expression profiling analysis.

BACKGROUND: Huangqi decoction (HQD) is used for liver fibrosis and cirrhosis treatment in Chinese medicine. This study aims to investigate the pharmacological actions of HQD against liver fibrosis in rats by high-throughput gene expression profiling, network analysis and real-time qRT-PCR. METHODS: We analyzed the profiles of differentially expressed genes (DEGs) in dimethylnitrosamine (DMN)-induced liver fibrosis in rat. The liver tissue samples of control group (n = 3), model group (n = 3) and HQD group (n = 3) were examined by microarrays. Pathways were analyzed by KEGG. Pathway-gene and protein-protein interaction (PPI) networks were constructed with Cytoscape software. The expression of candidate genes was verified by qRT-PCR. P values less than 0.05 indicated statistical significance. RESULTS: Collagen deposition and hydroxyproline (Hyp) content were decreased in the HQD group compared with the model group (P < 0.001), while that of Hyp in the model group were increased compared with the control group (P < 0.001). In comparison with the model group, 1085 DEGs (all P < 0.05, |fold change| >1.5) and 52 pathways in the HQD group were identified. TGF-beta, ECM-receptor interaction, and the cell adhesion molecules pathways were significantly recovered by HQD (P < 0.001). A pathway-gene network was constructed, including 303 DEGs and 52 pathways, and 514 nodes and 2602 edges, among 142 genes with node degrees greater than 10. The expressions of PDGFra, PDGFrb, PDGFb, PDGFd, COL1A1, COL1A2, COL5A2, and THBS1 were significantly down-regulated by HQD (P < 0.001). CONCLUSION: HQD down-regulated the expressions of PDGFra, PDGFrb, PDGFb, PDGFd, COL1A1, COL1A2, COL5A2 and THBS1, and TGF-ß and PDGF signaling pathways in the DMN-induced liver fibrosis in rats.

Complement C4a inhibits the secretion of hepatitis B virus screened by surface-enhanced laser desorption ionization time-flight mass spectrometry-based ProteinChip analysis.

PURPOSE: Chronic hepatitis B (CHB) is a kind of chronic liver disease caused by persistent hepatitis B virus (HBV) infection. The study aims to seek the factors of host resistance to HBV and investigate their roles. EXPERIMENTAL DESIGN: Protein profiles of 58 healthy controls and 121 CHB patients were obtained by SELDI-TOF/MS. Predicted protein was validated by ELISA. Protein expression was evaluated by Western blot in the persistently HBV expressing cell line HepG2.2.15 and non-HBV expressing cell line HepG2. The level of HBV DNA was subsequently detected by quantitative real-time PCR in HepG2.2.15 cells with complement C4a treatment. RESULTS: Significantly altered protein peaks were found through statistical analysis, and m/z 4300 was predicted by databases and successfully matched with the fragment of complement C4a. According to ELISA, serum complement C4a was found to be significantly lower in CHB patients compared with healthy controls (p < 0.001) and the area under receiver operating characteristics curve is 0.78. Furthermore, complement C4a showed lower expression in HepG2.2.5 cells and the secretion of HBV DNA was inhibited by complement C4a. CONCLUSIONS AND CLINICAL RELEVANCE: The present study implied the important role of complement C4a in inhibiting the HBV DNA secretion in CHB.

Clinical Applications of Omics Technologies on ZHENG Differentiation Research in Traditional Chinese Medicine.

Traditional Chinese medicine (TCM) ZHENG is the basic concept of TCM theory. The effectiveness of TCM treatment depends on the accuracy of ZHENG differentiation. ZHENG differentiation, using the "four diagnostic methods," has the drawbacks of subjectivity and variability. Following development of omics technologies, which study the functional activities of human body from a system-wide perspective, it has been more and more applied in study of objectivity differentiating TCM ZHENG and understanding its biological mechanisms. This paper reviewed the literatures of clinical TCM ZHENG differentiation researches, underlying omics technologies, and indicated the increased trends of related articles with four kinds of omics technologies, including genomics, transcriptomics, proteomics and metabolomics, and the correlations between ZHENG differentiation and findings in omics studies. Moreover, the paper summarized the typical omics application in common studied diseases and TCM ZHENGs and discussed the main problems and countermeasure of ZHENG differentiation researches. The work here may provide a reference for further research of TCM ZHENG differentiation using omics technologies.

Network pharmacology: a new approach for chinese herbal medicine research.

The dominant paradigm of "one gene, one target, one disease" has influenced many aspects of drug discovery strategy. However, in recent years, it has been appreciated that many effective drugs act on multiple targets rather than a single one. As an integrated multidisciplinary concept, network pharmacology, which is based on system biology and polypharmacology, affords a novel network mode of "multiple targets, multiple effects, complex diseases" and replaces the "magic bullets" by "magic shotguns." Chinese herbal medicine (CHM) has been recognized as one of the most important strategies in complementary and alternative medicine. Though CHM has been practiced for a very long time, its effectiveness and beneficial contribution to public health has not been fully recognized. Also, the knowledge on the mechanisms of CHM formulas is scarce. In the present review, the concept and significance of network pharmacology is briefly introduced. The application and potential role of network pharmacology in the CHM fields is also discussed, such as data collection, target prediction, network visualization, multicomponent interaction, and network toxicology. Furthermore, the developing tendency of network pharmacology is also summarized, and its role in CHM research is discussed.

Progression from Excessive to Deficient Syndromes in Chronic Hepatitis B: A Dynamical Network Analysis of miRNA Array Data.

Traditional Chinese medicine (TCM) treatment is regarded as a safe and effective method for chronic hepatitis B (CHB), which requires a traditional diagnosis method to distinguish the TCM syndrome. In this study, we study the differences and similarities among excessive, excessive-deficient, and deficient syndromes, by an integrative and comparative analysis of weighted miRNA expression or miRNA-target network in CHB patients. We first calculated the differential expressed miRNAs based on random module t-test and classified three CHB TCM syndromes using SVM method. Then, miRNA target genes were obtained by validated database and predicted programs subsequently, the weighted miRNA-target networks were constructed for different TCM syndromes. Furthermore, prioritize target genes of networks of CHB TCM syndromes progression analyzed using DAVID online analysis. The results have shown that the difference between TCM syndromes is distinctly based on hierarchical cluster and network structure. GO and pathway analysis implicated that three CHB syndromes more likely have different molecular mechanisms, while the excessive-deficient and deficient syndromes are more dangerous than excessive syndrome in the process of tumorigenesis. This study suggested that miRNAs are important mediators for TCM syndromes classification as well as CHB development progression and therefore could be potential diagnosis and therapeutic molecular markers.

Characteristic Analysis from Excessive to Deficient Syndromes in Hepatocarcinoma Underlying miRNA Array Data.

Traditional Chinese medicine (TCM) treatment is regarded as a safe and effective method for many diseases. In this study, the characteristics among excessive, excessive-deficient, and deficient syndromes of Hepatocellular carcinoma (HCC) were studied using miRNA array data. We first calculated the differentially expressed miRNAs based on random module t-test and classified three TCM syndromes of HCC using SVM method. Then, the weighted miRNA-target networks were constructed for different TCM syndromes using predicted miRNA targets. Subsequently, the prioritized target genes of upexpression network of TCM syndromes were analyzed using DAVID online analysis. The results showed that there are distinctly different hierarchical cluster and network structure of TCM syndromes in HCC, but the excessive-deficient combination syndrome is extrinsically close to deficient syndrome. GO and pathway analysis revealed that the molecular mechanisms of excessive-deficient and deficient syndromes of HCC are more complex than excessive syndrome. Furthermore, although excessive-deficient and deficient syndromes have similar complex mechanisms, excessive-deficient syndrome is more involved than deficient syndrome in development of cancer process. This study suggested that miRNAs might be important mediators involved in the changing process from excessive to deficient syndromes and could be potential molecular markers for the diagnosis of TCM syndromes in HCC.

Is the sex communication of two pyralid moths, Plodia interpunctella and Ephestia kuehniella, under circadian clock regulation?

Females of the Indian meal moth, Plodia interpunctella, and females of the Mediterranean flour month, Ephestia kuehniella (both Lepidoptera: Pyralidae), exhibit daily rhythms in calling behavior. The peak in P. interpunctella calling occurs at dusk, whereas E. kuehniella calls preferentially at dawn. This behavior turned arrhythmic in P. interpunctella females in constant darkness (DD) and remained arrhythmic in constant light (LL), whereas E. kuehniella females showed a persistent rhythm in DD and suppression of the behavior in LL, indicating regulation by a circadian clock mechanism. The rhythm of male locomotor activity corresponded well with the sexual activity of females, reaching the peak at dusk in P. interpunctella and at dawn in E. kuehniella. An immunohistochemical study of the pheromone biosynthesis activating neuropeptide, corazonin, and pigment dispersing factor revealed distinct sets of neurons in the brain-subesophageal complex and in the neurohemal organs of the 2 species.

[Study on the safety and immunogenicity of MF59-adjuvanted influenza subunit vaccine in Chinese elderly].

OBJECTIVE: To compare the safety and immunogenicity between a MF59-adjuvanted influenza subunit vaccine and a conventional non-adjuvanted influenza subunit vaccine. METHODS: A randomized, blind-designed controlled study was carried out, with 600 subjects (> or = 60 years of age) received MF59-adjuvanted influenza subunit vaccine (FLUAD, n = 400) or conventional non-adjuvanted influenza subunit vaccine (Agrippal, n = 200) respectively. The local and systemic reactions were observed on 0-7 days after vaccination. Haemagglutination inhibition (HI) titers of pre-and post-vaccination were detected by the HI assay. Seroconversion (4-fold increase) rate of subjects was calculated using baseline data when it was under naive level, and the protection rate when HI titer achieving the level of protection (> or = 1:40) after vaccination. Geometric mean titer (GMT) and its increasing folds were calculated. Differences between safety and immunogenicity were also calculated. RESULTS: The local and systemic reaction rates were similar between both groups, but the duration in injection site was frequent for Agrippal (P < 0.05), while mild pain and fever in injection site were frequent for FLUAD. On immunogenicity test, for those subjects whose baseline was under naive level while the seroconversion rate against A/H3N2 viral strain after vaccination--FLUAD was significantly higher than Agrippal (P < 0.001). Aside from A/H1N1 viral strain, the rate of protection on both groups were significantly higher than those from baseline data, but for A/H3N2 viral strain, FLUAD was significantly higher than Agrippal (P < 0.001). GMT was higher than baseline (P < 0.001) after both groups being vaccinated but FLUAD group was significantly higher than Agrippal group. CONCLUSION: FLUAD was well tolerated by Chinese elderly and its immunogenicity level induced by FLUAD was higher than that of Agrippal, showing that it would benefit the elderly with hypoimmunity.

Study on the safety and immunogenicity of MF59-adjuvanted influenza subunit vaccine in Chinese elderly / 中华流行病学杂志

Objective To compare the safety and immunogenicity between a MF59-adjuvanted influenza subunit vaccine and a conventional non-adjuvanted influenza subunit vaccine.Methods A randomized, blind-designed controlled study was carried out, with 600 subjects (≥60 years of age)received MF59-adjuvanted influenza subunit vaccine (FLUAD(R), n=400) or conventional non-adjuvanted influenza subunit vaccine (Agrippal(R), n = 200) respectively. The local and systemic reactions were observed on 0-7 days after vaccination. Haemagglutination inhibition (HI) titers of pre-and post-vaccination were detected by the HI assay. Seroconversion (4-fold increase) rate of subjects was calculated using baseline data when it was under naive level, and the protection rate when HI titer achieving the level of protection(≥1:40) after vaccination.Geometric mean titer(GMT) and its increasing folds were calculated.Differences between safety and immunogenicity were also calculated. Results The local and systemic reaction rates were similar between both groups, but the duration in injection site was frequent for Agrippal(R)(P＜0.05), while mild pain and fever in injection site were frequent for FLUAD(R). On immunogenicity test, for those subjects whose baseline was under naive level while the seroconversion rate against A/H3N2 viral strain after vaccination - FLUAD(R) was significantly higher than Agrippal(R) (P＜0. 001). Aside from A/H1N1 viral strain, the rate of protection on both groups were significantly higher than those from baseline data, but for A/H3N2 viral strain, FLUAD(R) was significantly higher than Agrippal(R) (P＜0. 001 ). GMT was higher than baseline (P＜0. 001 ) after both groups being vaccinated but FLUAD(R) group was significantly higher than Agrippal(R) group. Conclusion FLUAD(R) was well tolerated by Chinese elderly and its immunogenicity level induced by FLUAD(R) was higher than that of Agrippal(R), showing that it would benefit the elderly with hypoimmunity.

The circadian rhythm of the sex-pheromone-mediated behavioral response in the turnip moth, Agrotis segetum, is not controlled at the peripheral level.

The pheromone-mediated upwind flight of male turnip moths was observed in a flight tunnel at different times of day under conditions of a light-dark (LD) cycle, constant darkness (DD), and a shifted photoperiod. Under both LD and DD conditions, a significantly larger number of males flew to the pheromone during both the scotophase and the subjective scotophase than during the photophase and the subjective photophase for 2 consecutive days. When 1-day-old moths were transferred to a shifted LD cycle with lights turned off 4 h earlier, male behavioral responses to the pheromone advanced in time accordingly by 4 h. This showed that male behavioral responses to the pheromone are under the control of an endogenous oscillator. To further examine the level at which the circadian rhythm of the male behavioral response is regulated, the authors tested the olfactory responses of male antennal receptors to pheromone stimuli by means of electroantennograms (EAG) at different times of day. No significant variation in the sensitivity of the male antennal response to the pheromone was observed in terms of time of day. The results suggest that circadian regulation of the rhythmic behavioral response to pheromones in the male Agrotis occurs at the central nervous system level.