Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression.

Background: Coronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and increased mortality when affected by COVID-19. Despite this connection, the molecular intricacies linking COVID-19, influenza, and HIV remain unclear. Our research endeavors to elucidate the shared pathways and molecular markers in individuals with HIV concurrently infected with COVID-19 and influenza. Furthermore, we aim to identify potential medications that may prove beneficial in managing these three interconnected illnesses. Methods: Sequencing data for COVID-19 (GSE157103), influenza (GSE185576), and HIV (GSE195434) were retrieved from the GEO database. Commonly expressed differentially expressed genes (DEGs) were identified across the three datasets, followed by immune infiltration analysis and diagnostic ROC analysis on the DEGs. Functional enrichment analysis was performed using GO/KEGG and Gene Set Enrichment Analysis (GSEA). Hub genes were screened through a Protein-Protein Interaction networks (PPIs) analysis among DEGs. Analysis of miRNAs, transcription factors, drug chemicals, diseases, and RNA-binding proteins was conducted based on the identified hub genes. Finally, quantitative PCR (qPCR) expression verification was undertaken for selected hub genes. Results: The analysis of the three datasets revealed a total of 22 shared DEGs, with the majority exhibiting an area under the curve value exceeding 0.7. Functional enrichment analysis with GO/KEGG and GSEA primarily highlighted signaling pathways associated with ribosomes and tumors. The ten identified hub genes included IFI44L, IFI44, RSAD2, ISG15, IFIT3, OAS1, EIF2AK2, IFI27, OASL, and EPSTI1. Additionally, five crucial miRNAs (hsa-miR-8060, hsa-miR-6890-5p, hsa-miR-5003-3p, hsa-miR-6893-3p, and hsa-miR-6069), five essential transcription factors (CREB1, CEBPB, EGR1, EP300, and IRF1), and the top ten significant drug chemicals (estradiol, progesterone, tretinoin, calcitriol, fluorouracil, methotrexate, lipopolysaccharide, valproic acid, silicon dioxide, cyclosporine) were identified. Conclusion: This research provides valuable insights into shared molecular targets, signaling pathways, drug chemicals, and potential biomarkers for individuals facing the complex intersection of COVID-19, influenza, and HIV. These findings hold promise for enhancing the precision of diagnosis and treatment for individuals with HIV co-infected with COVID-19 and influenza.

NH3 and greenhouse gas emissions during co-composting of lignite and poultry wastes and the following amendment of co-composted products in soil.

Ammonia (NH3) and greenhouse gas (GHG) emissions are substantial contributors to C and N loss in composting. Lignite can increase N retention by absorbing NH4+ and NH3. However, the effects of co-composting on NH3 and GHG emissions in view of closing nutrient cycle are still poorly investigated. In the study, poultry litter was composted without (CK) or with lignite (T1) or dewatered lignite (T2), and their respective composts NH4+Com_CK, Com_T1, and Com_T2) were tested in a soil incubation to assess NH3 and GHG emission during composting and following soil utilization. The cumulative NH3 flux in T1 and T2 were reduced by 39.3% and 50.2%, while N2O emissions were increased by 7.5 and 15.6 times, relative to CK. The total GHG emission in T2 was reduced by 16.8% compared to CK. Lignite addition significantly increased nitrification and denitrification as evidenced by the increased abundances of amoA, amoB, nirK, and nirS. The increased reduction on NH3 emission by dewatered lignite could be attributed to reduced pH and enhanced cation exchangeable capacity than lignite. The increased N2O was related to enhanced nitrification and denitrification. In the soil incubation experiment, compost addition reduced NH3 emission by 72%∼83% while increased emissions of CO2 and N2O by 306%∼740% and 208%∼454%, compared with urea. Com_T2 strongly reduced NH3 and GHG emissions after soil amendment compared to Com_CK. Overall, dewatered lignite, as an effective additive, exhibits great potential to simultaneously mitigate NH3 and GHG secondary pollution during composting and subsequent utilization of manure composts.

Fabrication of Citrus bergamia essential oil-loaded sodium caseinate/peach gum nanocomplexes: Physicochemical, spectral, and structural characterization.

`The objective of current research was to encapsulate citrus bergamia essential oil (CBEO) in nanocomplexes composed of sodium caseinate (SC) and peach gum polysaccharide (PG) in various ratios (SC/PG-1:0, 0:1, 1:1, 1:3, and 3:1). The nanocomplexes formed by the combination of SC and PG in a ratio of 1:3 exhibited a zeta potential of -21.36 mV and a PDI of 0.25. The CBEO-loaded SC/PG (1:3) nanocomplexes revealed the maximum encapsulation efficiency (82.47 %) and loading capacity (1.85 %). FTIR also confirmed the secondary structure variations in response to different ratios of CBEO-loaded SC/PG nanocomplexes. In addition, the XRD and fluorescence spectroscopy analysis also revealed structural changes among CBEO nanocomplexes. The thermal capability of CBEO-loaded SC/PG (1:3) nanocomplexes via TGA showed the minimum weight loss among other complexes. SEM and CLSM analysis demonstrated the uniform distribution and spherical morphology of CBEO-loaded SC/PG (1:3) nanocomplexes. The antioxidant activity of free CBEO was significantly improved in CBEO-loaded nanocomplexes. Likewise, the inhibitory activity of CBEO-loaded nanocomplexes exhibited significantly higher antibacterial action against S. aureus and E. coli. The aforementioned perspective suggests that SC/PG nanocomplexes have potent potential to serve as highly effective nanocarriers with a broad spectrum of uses in the pharmaceutical and food sectors.

Correlation between Polyphenol Contents and Antioxidant Activities in Different Echinacea Purpurea Varieties.

OBJECTIVE: Polyphenols are complex compounds containing multiple phenolic hydroxyl groups. They are widely distributed in plants and have antioxidant activities. Whether the antioxidant activities of the cultivated varieties of Echinacea are similar to or better than those of the wild ones and the relationship between the accumulation of polyphenols and their antioxidant activities are still not clear. METHODS: Folin-Ciocalteu method, high performance liquid chromatography (HPLC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay, ferric ion reducing antioxidant power (FRAP) assay, 2,2'-azino-bis(3-ethylbenzothiazoline-6)-sulfonic acid (ABTS) radical scavenging assay, and Fe2+ chelating ability assay were used, respectively, to detect the total polyphenols and 5 kinds of caffeic acid derivatives (chicoric acid, caffeic acid, caftaric acid, chlorogenic acid, and 1,5-dicaffeoylquinic acid) in the roots, stems, leaves, and flowers, and the antioxidant activities of 3 varieties of Echinacea: E. purpurea L., cultivar E. purpurea 'Aloha', and E. purpurea 'White Swan'. RESULTS: E. purpurea L. had the highest contents of total polyphenols, 5 caffeic acid derivatives and antioxidant activities, followed by E. purpurea 'White Swan' and E. purpurea 'Aloha', respectively. E. purpurea 'White Swan' had the strongest ability to remove the DPPH, ABTS•+ and free radicals, and to chelate Fe2+; E. purpurea L. had the strongest ability to reduce FRAP. The correlation analyses revealed that the contents of total polyphenols and caffeic acid derivatives of E. purpurea L. and E. purpurea 'White Swan' were correlated with their antioxidant activities. CONCLUSION: E. purpurea L. was the most appropriate material for the development of medicinal plants. E. purpurea 'White Swan' could be used as a substitute for E. purpurea L. in terms of its antioxidant activity.

Application of a JEG-3 organoid model to study HLA-G function in the trophoblast.

The human placenta is a unique temporary organ with a mysterious immune tolerance. The formation of trophoblast organoids has advanced the study of placental development. HLA-G is uniquely expressed in the extravillous trophoblast (EVT) and has been linked to placental disorders. With older experimental methodologies, the role of HLA-G in trophoblast function beyond immunomodulation is still contested, as is its role during trophoblast differentiation. Organoid models incorporating CRISPR/Cas9 technology were used to examine the role of HLA-G in trophoblast function and differentiation. JEG-3 trophoblast organoids (JEG-3-ORGs) were established that highly expressed trophoblast representative markers and had the capacity to differentiate into EVT. CRISPR/Cas9 based on HLA-G knockout (KO) significantly altered the trophoblast immunomodulatory effect on the cytotoxicity of natural killer cells, as well as the trophoblast regulatory effect on HUVEC angiogenesis, but had no effect on the proliferation and invasion of JEG-3 cells and the formation of TB-ORGs. RNA-sequencing analysis further demonstrated that JEG-3 KO cells followed similar biological pathways as their wild-type counterparts during the formation of TB-ORGs. In addition, neither HLA-G KO nor the exogenous addition of HLA-G protein during EVT differentiation from JEG-3-ORGs altered the temporal expression of the known EVT marker genes. Based on the JEG-3 KO (disruption of exons 2 and 3) cell line and the TB-ORGs model, it was determined that HLA-G has a negligible effect on trophoblast invasion and differentiation. Despite this, JEG-3-ORG remains a valuable model for studying trophoblast differentiation.

Di-(2-ethylhexyl) phthalate impairs angiogenesis and hematopoiesis via suppressing VEGF signaling in zebrafish.

Di-(2-ethylhexyl) phthalate (DEHP) is among the most widely used plasticizers in plastic production, which has been detected in various environments. However, DEHP safety remains poorly known. Using zebrafish models, the effects of DEHP on the angiogenesis and hematopoiesis, and the underlying mechanism, were studied. Transgenic zebrafish embryos with specific fluorescence of vascular endothelial cells, myeloid cells, or hematopoietic stem cells were exposed to 0, 100, 150, 200, or 250 nM of DEHP for 22, 46 or 70 h, followed by fluorescence observation, endogenous alkaline phosphatase activity measurement, erythrocyte staining, and gene expression analysis by quantitative PCR and whole mount in situ hybridization. High DEHP concentrations decreased the sprouting rate, average diameter, and length, and the expansion area of the vessels lowered the EAP activity and suppressed the vascular endothelial growth factor (vegf) and hematopoietic marker genes, including c-myb, hbae1, hbbe1, and lyz expressions. DEHP treatment also decreased the number of hematopoietic stem cells, erythrocytes, and myeloid cells at 24 and 72 hpf. These DEHP-induced angiogenetic and hematopoietic defects might be alleviated by vegf overexpression. Our results reveal a plausible mechanistic link between DEHP exposure-induced embryonic angiogenetic defect and hematopoietic impairment.

A diagnostic model of autoimmune hepatitis in unknown liver injury based on noninvasive clinical data.

All the diagnostic criteria of autoimmune hepatitis (AIH) include histopathology. However, some patients may delay getting this examination due to concerns about the risks of liver biopsy. Therefore, we aimed to develop a predictive model of AIH diagnostic that does not require a liver biopsy. We collected demographic, blood, and liver histological data of unknown liver injury patients. First, we conducted a retrospective cohort study in two independent adult cohorts. In the training cohort (n = 127), we used logistic regression to develop a nomogram according to the Akaike information criterion. Second, we validated the model in a separate cohort (n = 125) using the receiver operating characteristic curve, decision curve analysis, and calibration plot to externally evaluate the performance of this model. We calculated the optimal cutoff value of diagnosis using Youden's index and presented the sensitivity, specificity, and accuracy to evaluate the model in the validation cohort compared with the 2008 International Autoimmune Hepatitis Group simplified scoring system. In the training cohort, we developed a model to predict the risk of AIH using four risk factors-The percentage of gamma globulin, fibrinogen, age, and AIH-related autoantibodies. In the validation cohort, the areas under the curve for the validation cohort were 0.796. The calibration plot suggested that the model had an acceptable accuracy (p > 0.05). The decision curve analysis suggested that the model had great clinical utility if the value of probability was 0.45. Based on the cutoff value, the model had a sensitivity of 68.75%, a specificity of 76.62%, and an accuracy of 73.60% in the validation cohort. While we diagnosed the validated population by using the 2008 diagnostic criteria, the sensitivity of prediction results was 77.77%, the specificity was 89.61% and the accuracy was 83.20%. Our new model can predict AIH without a liver biopsy. It is an objective, simple and reliable method that can effectively be applied in the clinic.

Effects of Glycolysis-Related Genes on Prognosis and the Tumor Microenvironment of Hepatocellular Carcinoma.

Background: Hepatocellular carcinoma (HCC) is a common and deadly malignancy worldwide. Current treatment methods for hepatocellular carcinoma have many disadvantages; thus, it is urgent to improve the efficacy of these therapies. Glycolysis is critical in the occurrence and development of tumors. However, survival and prognosis biomarkers related to glycolysis in HCC patients remain to be fully identified. Methods: Glycolysis-related genes (GRGs) were downloaded from "The Molecular Signatures Database" (MSigDB), and the mRNA expression profiles and clinical information of HCC patients were obtained from TCGA. Consensus clustering was performed to classify the HCC patients into two subgroups. We used the least absolute shrinkage and selection operator (LASSO) regression analysis to construct the risk signature model. Kaplan-Meier (K-M) survival analysis was performed to evaluate the prognostic significance of the risk model, and the receiver operating characteristic (ROC) curve analysis was used to evaluate the prediction accuracy. The independent prediction ability of the risk model was validated by univariate and multivariate Cox regression analyses. The differences of immune infiltrates and relevant oncogenic signaling between different risk groups were compared. Finally, biological experiments were performed to explore the functions of screened genes. Results: HCC patients were classified into two subgroups, according to the expression of prognostic-related GRGs. Almost all GRGs categorized in cluster 2 showed upregulated expressions, whereas GRGs in cluster 1 conferred survival advantages. GSEA identified a positive correlation between cluster 2 and the glycolysis process. Ten genes were selected for risk signature construction. Patients were assigned to high-risk and low-risk groups based on the median risk score, and K-M survival analysis indicated that the high-risk group had a shorter survival time. Additionally, the risk gene signature can partially affect immune infiltrates within the HCC microenvironment, and many oncogenic pathways were enriched in the high-risk group, including glycolysis, hypoxia, and DNA repair. Finally, in vitro knockdown of ME1 suppressed proliferation, migration, and invasion of hepatocellular carcinoma cells. Conclusion: In our study, we successfully constructed and verified a novel glycolysis-related risk signature for HCC prognosis prediction, which is meaningful for classifying HCC patients and offers potential targets for the treatment of hepatocellular carcinoma.

Antioxidant and antibacterial properties of essential oils-loaded ß-cyclodextrin-epichlorohydrin oligomer and chitosan composite films.

Chitosan (CS) is becoming increasingly popular in food packaging due to its natural degradability and great film-forming properties. Nevertheless, its poor antibacterial properties and inadequate antioxidant properties prevent it from being used effectively. In this study, ß-cyclodextrin-epichlorohydrin (ß-CD-EP) oligomers were prepared and encapsulated with natural essential oils cinnamaldehyde and thymol, and then the inclusion complexes (IC) were incorporated into chitosan in various contents to afford a series of CS-IC composite films. The impacts of IC on the morphological, mechanical, thermal, and water resistance properties, antioxidant and antibacterial activities of chitosan films, as well as the loading and sustained release behavior of IC, were thoroughly examined. The results turned out that the essential oils were well-loaded with high encapsulation efficiency and showed a significant slow-release effect. It was also found that the tensile strength and the elongation at break decreased with increasing IC contents, while the thermal stability was enhanced. The incorporation of IC dramatically promoted the antioxidant and antibacterial properties of the chitosan films towards Gram-positive bacteria. Based on our findings, chitosan films containing essential oils-loaded ß-CD-EP oligomers may serve as an effective food packaging material.

Direct Inhibition of GSDMD by PEITC Reduces Hepatocyte Pyroptosis and Alleviates Acute Liver Injury in Mice.

Acute liver injury (ALI), often caused by viruses, alcohol, drugs, etc., is one of the most common clinical liver diseases. Although pyroptosis plays an important role in ALI, there is still a lack of effective clinical drugs related to this mechanism. Here, we show that phenethyl isothiocyanate (PEITC), a natural compound present in cruciferous vegetables, can significantly alleviate concanavalin A (ConA)-induced inflammatory liver damage and carbon tetrachloride (CCl4)-induced chemical liver damage in a dose-dependent manner. PEITC dose-dependently reversed the ALI-induced increase in plasma levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), tumor necrosis factor (TNF)-α, and interferon (IFN)-γ and reduced the protein levels of hepatocyte pyroptosis markers such as Nod-like receptor family pyrin domain containing 3 (NLRP3), cleaved caspase-1, and cleaved gasdermin D (GSDMD). In vitro experiments have also verified the inhibitory effect of PEITC on hepatocyte pyroptosis. Furthermore, PEITC inhibits pyroptosis by interacting with cysteine 191 of GSDMD. In summary, our findings establish a role for PEITC in rescuing hepatocyte pyroptosis via direct inhibition of GSDMD, which may provide a new potential therapeutic strategy for ALI.

Role of Hub Genes in the Occurrence and Development of Testicular Cancer Based on Bioinformatics.

BACKGROUND: Testicular cancer severely affects male health, so finding effective diagnosis and prognostic indicators and exploring its pathogenesis are very important. PURPOSE: This study aims to explore the hub genes that play important roles in the occurrence and development of testicular germ cell tumor (TGCT). METHODS: Data were obtained from Gene Expression Omnibus datasets (GSE3218 and GSE1818) and verified in The Cancer Genome Atlas database and the Genotype-Tissue Expression database and the Human Protein Atlas database. A protein-protein interaction network was constructed to obtain hub genes. GEO2R, R software and packages were used to analyze differentially expressed genes (DEGs), receiver operating characteristic curve assessment, Cox regression analysis, Kaplan-Meier survival curve assessment, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis, the relationship with clinicopathological information, gene set enrichment analysis, the correlation with immune cells' infiltration, and the expression in pan-cancers of the hub genes. RESULTS: PLK4, TRIP13, TPR, KIF18A, CDKN3, HMMR, PBK, PTTG1, CKS2, SYCP1, HSPA2, and MKI67 were selected as the hub genes. mRNA of PLK4, TRIP13, CDKN3, SYCP1, HSPA2, and MKI67 had high diagnostic values, and higher expression of CDKN3 and HSPA2 mRNA were poor prognostic factors for progression-free interval of TGCT. The hub genes involved organelle division and cell cycle, chromosome and centromeric region, heat shock protein binding, and more. Downregulated TPR and PLK4 were selected as research targets for continued study, and they may participate in multiple signaling pathways. The expression of TPR and PLK4 correlated with the infiltration of a variety of immune cells and differed in pan-cancers. CONCLUSION: The mRNA levels of multiple hub genes have high diagnostic and prognostic values for TGCT. TPR and PLK4 may play a role in the occurrence and development of TGCT through cancer-related signaling pathways.

Effect of cellulose nanocrystal-stabilized cinnamon essential oil Pickering emulsions on structure and properties of chitosan composite films.

The low water-resistance and limited antibacterial activity of chitosan (CS) film hinder its practical applications in food preservation field. To solve these issues, we have facilely and effectively fabricated cinnamon essential oil (CEO)-loaded composite films via incorporating cellulose nanocrystal (CNC)-stabilized CEO Pickering emulsions into CS-based film-forming matrix. Research results show the well distribution of emulsion droplets in film matrix. The insertion of CEO emulsions can improve film water-resistance and antibacterial activity, but reduces its mechanical strength. Concretely, the water contact angle and inhibition zone of composite films can increase by about 12.3° and 2 times compared with CS control film. Compared with tween-80, CNCs can increase film tensile strength by about 3.52 MPa and observably offset the decline of film mechanical property by CEO. Moreover, the film prepared with 3 w/v% CNC stabilized 30 v/v% CEO Pickering emulsion not only enhances pork preservation, but also maintain its structural stability. The fabricated antimicrobial films have considerable potential for packaging application.

Psychological Response to the Diagnosis of Advanced Cancer: A Systematic Review.

BACKGROUND: Despite major efforts to address psychological distress and quality of life (QOL) in people with cancer, only none to small intervention effect has been observed. There is reason to question whether psychosocial needs of patients have already been met under the usual oncology care. PURPOSE: The purpose of this systematic review was to examine changes in depression, anxiety and QOL during the existential plight in advanced cancer. METHODS: A literature search was performed in the PubMed and APA PsycINFO databases from year 1976 up to May 31, 2021. Longitudinal observational or experimental research targeting depression, anxiety or QOL in advanced cancer (stage III or IV), with baseline time since cancer diagnosis within 100 days, follow-up within 16 weeks post-baseline were eligible. Quality rating was based on the GRADE guidelines. RESULTS: Overall QOL did not reveal clinically relevant changes for the majority of studies as evaluated by effect size and raw score changes (median effect size 0.01, interquartile range -0.10-0.15). Nonetheless, modest to moderate improvement was found for depression (median effect size 0.28, interquartile range 0.03-0.38) and anxiety (median effect size 0.57, interquartile range 0.32-0.79). CONCLUSION: Transient distress symptoms and temporarily reduced functioning in the oncology setting may be considered normal, whereas impaired overall QOL needs to be addressed. Developing innovative interventions that enhance QOL for patients newly diagnosed with advanced cancer without interfering with patients' natural adaptation process is imperative.

A one-pot protocol for iron-catalyzed decarbonylative borylation of aryl and alkyl carboxylic acids.

We present a protocol for the eco-friendly synthesis of aryl and alkyl boronic esters from aryl and alkyl carboxylic acids. We describe steps for aryl and alkyl carboxylates preparation. We further detail procedures for the synthesis of borylated products using aryl and alkyl carboxylates through iron-catalyzed decarbonylation at 100°C-130°C, followed by purification of the crude products by flash column chromatography. For complete details on the use and execution of this protocol, please refer to Wen et al. (2022).1.

eIF3a R803K mutation mediates chemotherapy resistance by inducing cellular senescence in small cell lung cancer.

Drug resistance in small cell lung cancer (SCLC) significantly affects the efficacy of chemotherapy treatment. However, due to the lack of tumor tissue samples, especially serial tumor samples during chemotherapy, the mechanism of chemotherapy resistance has not been fully studied. Circulating tumor DNA, which can be obtained in a noninvasive manner, can complement tumor sampling approaches for research in this field. We identified an SCLC patient with acquired drug resistance from 52 SCLC patients for whom follow-up data were available. By comparing somatic mutations in circulating tumor DNA before and after chemotherapy, for the first time, we found that the somatic mutation eIF3A R803K may be related to acquired chemotherapy resistance. Then, the association between the eIF3A R803K mutation and chemotherapy resistance was confirmed by samples from 254 lung cancer patients receiving chemotherapy. We found that the eIF3a R803K mutation weakened the proliferation ability of tumor cells but increased their resistance to chemotherapy. Further studies revealed that the eIF3A R803K mutation promotes cellular senescence. In addition, fisetin showed a synergistic effect with chemotherapy in eIF3A R803K mutant cells. These results suggest that the eIF3A R803K somatic mutation has the potential to predict chemotherapy resistance in SCLC. Moreover, the eIF3A R803K mutation promotes chemotherapy resistance by inducing senescence. Furthermore, a senolytic drug, fisetin, can reverse chemotherapy resistance mediated by the eIF3A R803K mutation.

Non-Coding RNA Polymorphisms (rs2910164 and rs1333049) Associated With Prognosis of Lung Cancer Under Platinum-Based Chemotherapy.

Purpose: Lung cancer is the largest cause of cancer deaths in the world. Platinum-based chemotherapy is a foundation of first-line chemotherapy. However, the prognosis of lung cancer treated with platinum-based chemotherapy is still a challenge. Single nucleotide polymorphism of non-coding RNA has the potential to be a biomarker, but its effectiveness has yet to be comprehensively assessed. In this study, we explored the association between polymorphisms of non-coding RNA and prognosis of lung cancer patients receiving platinum-based chemotherapy. Materials and Methods: For 446 lung cancer patients receiving platinum-based chemotherapy, 22 single nucleotide polymorphisms of microRNA and long noncoding RNA were genotyped by MALDI-TOF mass spectrometry. Cox regression analysis, Kaplan-Meier method, and long-rank test have been performed to assess the association of overall and progression-free survival with polymorphisms. Results: In the additive and dominant models, genetic polymorphism of ANRIL rs1333049 (G > C) was significantly associated with progression-free survival. Additive model: CC vs GC vs GG [HR = 0.84, p = 0.021, 95% CI (0.73-0.97)]; Recessive model: CC vs GG + GC [HR = 0.77, p = 0.026, 95% CI (0.61-0.97)]. In the dominant model, compared with the CC genotype patients, lower risk of death [HR = 0.81, p = 0.036, 95% CI (0.66-0.99)] and lower risk of progression [HR = 0.81, p = 0.040, 95% CI (0.67-0.99)] have been observed on the patients with CG or GG genotype in miR-146A rs2910164. Conclusion: Our research demonstrated the potential of using ANRIL rs1333049 (G > C) and miR-146A rs2910164 (C > G) as biomarkers to support the prediction of a better prognosis for lung cancer patients receiving platinum-based chemotherapy.

STAT3 activates the transcription of lncRNA NR2F1-AS1 to promote the progression of melanoma via regulating the miR-493-5p/GOLM1 axis.

BACKGROUND: Long non-coding RNAs (lncRNAs) are vital regulators during the biological processes of melanoma. The present study aimed to uncover biological functions of lncRNA termed NR2F1 antisense RNA 1 (NR2F1-AS1) in melanoma and the potential mechanisms. METHODS: Relative levels of NR2F1-AS1 and miR-493-5p in a total of 137 paired primary melanoma tissues and corresponding non-tumor tissues, as well as three melanoma cell lines, were examined by a real-time polymerase chain reaction. The clinical significance of NR2F1-AS1 expression was analyzed statistically. The STAT3 binding motif in the promoter region of NR2F1-AS1 was identified by JASPAR (http://jaspar.genereg.net). The association between STAT3 and NR2F1-AS1 was determined by dual-luciferase reporter and chromatin immunoprecipitation assays. The effects of NR2F1-AS1 on cell proliferation, migration and were measured by cell counting kit-8 (CCK-8), Edu, transwell and wound healing assays. Dual-luciferase reporter and RNA pull-down assays were applied to validate the interaction among NR2F1-AS1, miR-493-5p and GOLM1. Furthermore, in vivo experiments were conducted to demonstrate the oncogenic role of NR2F1-AS1 in melanoma. RESULTS: Up-regulated NR2F1-AS1 and down-regulated miR-493-5p were detected in melanoma tumors and cells. The overexpression of NR2F1-AS1 was induced by STAT3. High NR2F1-AS1 expression was correlated to advanced tumor stage and poor prognosis of melanoma. Functional studies using CCK-8, Edu, transwell and wound healing assays revealed that the proliferative, migratory and invasive capacities of melanoma cells were attenuated by the by inhibition of NR2F1-AS1. Moreover, NR2F1-AS1 was able to up-regulate GOLM1 through recognizing and binding miR-493-5p. Furthermore, knockdown of miR-493-5p distinctly reversed these inhibitory effects of NR2F1-AS1 down-regulation on the tumorigenesis and progression of melanoma. CONCLUSIONS: Our findings demonstrate a key role for NR2F1-AS1 in melanoma progression via targeting miR-493-5p/GOLM1 axis.

The expansion of mesophyll cells is coordinated with the division of chloroplasts in diploid and tetraploid Arabidopsis thaliana.

MAIN CONCLUSION: Cell expression is coordinated with chloroplast division in diploid and tetraploid Arabidopsis thaliana, polyploidy promoted the expansion of mesophyll cells and chloroplast division in A. thaliana. Cell development and differentiation are always accompanied by cell expansion and chloroplast division in plants, but the relationship between them is still relatively unknown. To confirm the relationship between cell expansion and chloroplast division during the leaf development process of diploid and tetraploid Arabidopsis thaliana, we systematically analyzed the expansion of mesophyll cells and the division of chloroplasts through cytological observation and gene-expression characteristics. As a result, in diploid and tetraploid A. thaliana, there were two peaks in both mesophyll cell expansion and chloroplast division during the leaf development process. Tetraploid A. thaliana mesophyll cells were larger and contained more chloroplasts than diploid A. thaliana mesophyll cells, which indicated that cell division and cell expansion were coordinated with chloroplast division in A. thaliana and that polyploidy further promoted mesophyll cell expansion and chloroplast division.

Common variation of the NSD1 gene is associated with susceptibility to Hirschsprung's disease in Chinese Han population.

BACKGROUND: Hirschsprung's disease (HSCR) is the most common congenital cause of intestinal obstruction in children. Sotos syndrome (SoS) is an overgrowth disorder with constipation and sometimes accompanied by HSCR. NSD1 gene mutation is the main cause of SoS. We aimed to investigate association of NSD1 common single nucleotide polymorphisms (SNPs) with HSCR susceptibility in Chinese Han population. METHOD: We genotyped 15 SNPs encompassing NSD1 gene region in 420 HSCR patients and 1665 controls on Fludigm EP1 platform. Association analysis was performed between cases and controls. RESULT: Rs244709 was the most associated SNP with HSCR susceptibility of the sample set (PAllelic = 9.69 × 10-5, OR = 1.37, 95% CI: 1.17-1.61). Gender stratification analysis revealed that NSD1 SNPs were associated with HSCR in males, but not in females. The nonsynonymous coding SNP rs28932178 in NSD1 exon 5 represented the most significant signal in males (PAllelic = 6.43 × 10-5, OR = 1.42, 95% CI: 1.20-1.69). The associated SNPs were expression quantitative trait loci (eQTLs) of nearby genes in multiple tissues. NSD1 expression levels were higher in aganglionic colon tissues than ganglionic tissues (P = 3.00 × 10-6). CONCLUSION: NSD1 variation conferred risk to HSCR in males, indicating SoS and HSCR may share common genetic factors. IMPACT: This is the first study to reveal that NSD1 variation conferred risk to Hirschsprung's disease susceptibility in males of Chinese Han population, indicating Sotos syndrome and Hirschsprung's disease may share some common genetic background. This study indicates more attention should be paid to the symptom of constipation in patients with Sotos syndrome. Our results raise questions about the role of NSD1 in the development of enteric nervous system and the pathogenesis of Hirschsprung's disease.

Gas emissions during cattle manure composting and stockpiling.

Manure composting is a common management practice for cattle feedlots, but gaseous emissions from composting are poorly understood. The objective of this study was to quantify ammonia (NH3 ), nitrous oxide (N2 O), carbon dioxide (CO2 ), and methane (CH4 ) emissions from windrow composting (turning) and static stockpiling (nonturning) of manure at a commercial feedlot in Australia. An inverse-dispersion technique using an open-path Fourier transform infrared (OP-FTIR) spectrometer gas sensor was deployed to measure emissions of NH3 , N2 O, CO2 , and CH4 over a 165-d study period, and 29 and 15% of the total data intervals were actually used to calculate the fluxes for the windrow and stockpile, respectively. The nitrogen (N) lost as NH3 and N2 O emissions represented 26.4 and 3.8% of the initial N in windrow, and 5.3 and 0.8% of that in the stockpile, respectively. The carbon (C) lost as CO2 and CH4 emissions represented 44 and 0.3% of the initial C in windrow, and 54.8 and 0.7% of that in the stockpile, respectively. Total greenhouse gas (GHG) emissions from the manure windrow were 2.7 times higher than those of the stockpiled manure. This work highlights the value that could be accrued if one could reduce emissions of NH3 -N and N2 O-N from composting, which would retain manure N content while reducing GHG emissions.