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Motivation: The PAM50 signature/method is widely used for intrinsic subtyping of breast cancer samples. However, depending on the number and composition of the samples included in a cohort, the method may assign different subtypes to the same sample. This lack of robustness is mainly due to the fact that PAM50 subtracts a reference profile, which is computed using all samples in the cohort, from each sample before classification. In this paper we propose modifications to PAM50 to develop a simple and robust single-sample classifier, called MPAM50, for intrinsic subtyping of breast cancer. Like PAM50, the modified method uses a nearest centroid approach for classification, but the centroids are computed differently, and the distances to the centroids are determined using an alternative method. Additionally, MPAM50 uses unnormalized expression values for classification and does not subtract a reference profile from the samples. In other words, MPAM50 classifies each sample independently, and so avoids the previously mentioned robustness issue. Results: A training set was employed to find the new MPAM50 centroids. MPAM50 was then tested on 19 independent datasets (obtained using various expression profiling technologies) containing 9637 samples. Overall good agreement was observed between the PAM50- and MPAM50-assigned subtypes with a median accuracy of 0.792, which (we show) is comparable with the median concordance between various implementations of PAM50. Additionally, MPAM50- and PAM50-assigned intrinsic subtypes were found to agree comparably with the reported clinical subtypes. Also, survival analyses indicated that MPAM50 preserves the prognostic value of the intrinsic subtypes. These observations demonstrate that MPAM50 can replace PAM50 without loss of performance. On the other hand, MPAM50 was compared with 2 previously published single-sample classifiers, and with 3 alternative modified PAM50 approaches. The results indicated a superior performance by MPAM50. Conclusions: MPAM50 is a robust, simple, and accurate single-sample classifier of intrinsic subtypes of breast cancer. [ABSTRACT FROM AUTHOR]

Objectives: To evaluate the effect of zoledronic acid (ZA) on human umbilical vein endothelial cells (HUVECs) attached to different surfaces. Materials and Methods: A total of three groups were evaluated in this study: sandblasting and acid etching (SLA) + HUVECs; mechanically polished (MP) + HUVECs; and plastic cell culture plates + HUVECs. Scanning electron microscopy, energy‐dispersive X‐ray spectroscopy, surface roughness and water contact angle were tested for titanium surface characterisation. ZA was added at different concentrations (0, 1, 10, 50 and 100 μM). Cell adhesion, proliferation, viability, apoptosis and gene expression were evaluated. Results: Mechanically polished and SLA surfaces showed negative effects on cell adhesion and proliferation and promoted cell apoptosis with 100 μM ZA (p <.05). The highest expression of intercellular adhesion molecule‐1 (ICAM‐1) and angiopoietin‐1 was found on SLA surfaces (p <.01). The lowest expression of platelet‐endothelial cell adhesion molecule‐1 and ICAM‐1 was found on MP surfaces (p <.05). A significant decrease in von Willebrand factor was detected on MP and SLA surfaces (p <.001). Conclusions: Zoledronic acid has an anti‐angiogenic effect on HUVECs attached to titanium implants, while the SLA surface might stimulate HUVECs to express angiogenic and adhesive factor genes despite ZA treatment. [ABSTRACT FROM AUTHOR]

DNA 4 mC plays a crucial role in the genetic expression process of organisms. However, existing deep learning algorithms have shortcomings in the ability to represent DNA sequence features. In this paper, we propose a 4 mC site identification algorithm, DNABert-4mC, based on a fusion of the pruned pre-training DNABert-Pruning model and artificial feature encoding to identify 4 mC sites. The algorithm prunes and compresses the DNABert model, resulting in the pruned pre-training model DNABert-Pruning. This model reduces the number of parameters and removes redundancy from output features, yielding more precise feature representations while upholding accuracy.Simultaneously, the algorithm constructs an artificial feature encoding module to assist the DNABert-Pruning model in feature representation, effectively supplementing the information that is missing from the pre-trained features. The algorithm also introduces the AFF-4mC fusion strategy, which combines artificial feature encoding with the DNABert-Pruning model, to improve the feature representation capability of DNA sequences in multi-semantic spaces and better extract 4 mC sites and the distribution of nucleotide importance within the sequence. In experiments on six independent test sets, the DNABert-4mC algorithm achieved an average AUC value of 93.81%, outperforming seven other advanced algorithms with improvements of 2.05%, 5.02%, 11.32%, 5.90%, 12.02%, 2.42% and 2.34%, respectively. [Display omitted] • Train a new pruning pretraining model on DNA sequences to extract feature information. • The introduction of manually assisted features has expanded the search space for sequence feature. • Attention fusion strategy better promotes the fusion output of features from different dimensions. • The complementary nature of machine features and manual features better fits the target features. [ABSTRACT FROM AUTHOR]

Motivation: The precise diagnosis of the major subtypes, lung adenocarcinoma and lung squamous cell carcinoma, of non-small-cell lung cancer is of practical importance as some treatments are subtype-specific. However, in some cases diagnosis via the commonly-used method, that is staining the specimen using immunohistochemical markers, may be challenging. Hence, having a computational method that complements the diagnosis is desirable. In this paper, we propose a gene signature for this purpose. Results: We developed an expression-based method that systematically suggests a huge set of candidate gene signatures and finds the best candidate. By applying this method to a training set, the optimal gene signature was found by considering close to 765 billion candidate signatures. The 8-gene signature found for classifying the 2 aforementioned subtypes comprises TP63, CALML3, KRT5, PKP1, TESC, SPINK1, C9orf152, and KRT7. The signature achieved a high overall prediction accuracy of 0.936 when tested using 34 independent gene expression datasets obtained using different technologies and comprising 2556 adenocarcinoma and 1630 squamous cell carcinoma samples. Additionally, the signature performed well in clinically challenging cases, that is poorly differentiated tumors and specimens obtained from biopsies. In comparison with 2 previously reported signatures, our signature performed better in terms of overall accuracy and especially accuracy of classifying lung squamous cell carcinoma. Conclusions: Our signature is easy to use and accurate regardless of the technology used to obtain the gene expression profiles. It performs well even in clinically challenging cases and thus can assist pathologists in diagnosis of the ambiguous cases. [ABSTRACT FROM AUTHOR]

More couples worldwide, delay their childbearing years. The increase in age causes a gradual decrease in female ovarian function and fertility, leading to an exponential decrease in women over 35 years of age having children. Although promising for some, assisted reproductive technology (ART) is not promising for older women. Decreased fertility in advanced age has become a growing concern in the field of reproduction. In this study, high-throughput transcriptome sequencing was used to identify the differentially expressed genes (DEGs) in the ovarian granulosa cells (GCs) of older women (aged 35–44) with infertility and younger women (aged 25–34). The enriched functions and signaling pathways of DEGs were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The function of DEGs were analyzed and predicted combined with clinical ART data. Sequencing results were verified by quantitative reverse transcription-polymerase chain reaction. Retrospective clinical data and bioinformatics analyses revealed marked reductions in the retrieved oocyte, metaphase II oocyte, 2PN fertilization, and effective embryo numbers in older women. Although the clinical pregnancy and live birth rates did not differ notably between the groups, the miscarriage rate increased significantly in older women. In total, 620 DEGs were identified, of which 246 were upregulated, and 374 were downregulated in the older group. GO, and KEGG analyses indicated that the mechanism of fertility decline in older women was probably related to chronic inflammation, cytokine receptor interaction, and oxidative stress. In conclusion, combined with basic clinical ART data and pregnancy outcomes, we tried to provide a more intuitive and in-depth understanding of age-related reduction in ovarian function and pathogenesis of infertility with regard to chronic inflammation and oxidative stress. [ABSTRACT FROM AUTHOR]

Objective. We aimed to observe the impact of ginkgolic acid (GA) on the proliferation and metastasis ability of ovarian cancer (OCa) cells and to further explore whether GA affects the malignant progress of OCa via regulating the lncRNA MALAT1/JAK2 axis. Methods. OCa cells SKOV3 and CAOV3 were administered with 1 ng/ml GA, 5 ng/ml GA, 10 ng/ml GA, 20 ng/ml GA, and DSMO as control, respectively. The cell proliferation and migration ability of the abovementioned cells in each group were measured by CCK-8 test and Transwell experiments. The expression levels of lncRNA MALAT1 and JAK2 protein were examined by qRT-PCR and western blot, respectively. Subsequently, in OCa cells treated with GA, lncRNA MALAT1 overexpression vector was transfected to continue to detect the proliferation activity and migration ability of each treatment group. Finally, the regulation of GA on activity of lncRNA MALAT1/JAK2 axis in OCa cells was further explored in nude mice. Results. Our data showed that the proliferation inhibition rate of cells at each ginkgolic acid concentration was higher than that of the control group (P < 0.05), suggesting that GA has an inhibitory influence on the proliferation of OCa cells, in a dose-dependent way. GA was able to inhibit the proliferation rate and migration ability of OCa cells. Administration of ginkgolic acid downregulated the levels of lncRNA MALAT1 and JAK2 protein. Overexpression of lncRNA MALAT1 partially reversed the inhibited OCa proliferative capacity caused by GA treatment. Consistent with the results observed in vitro, we also found that the OCa tumor weight and volume of nude mice injected with lncRNA MALAT1 overexpression vector were enhanced and JAK2 protein level increased remarkably in comparison to the ginkgolic acid group. Conclusions. In summary, GA may exert its inhibitory effect on the proliferative and migratory capacities of OCa cells through suppressing the activity of lncRNA MALAT1/JAK2 axis. [ABSTRACT FROM AUTHOR]

Reprogramming of somatic cells to induced pluripotent stem cells, by overexpressing certain factors referred to as the reprogramming factors, can revolutionize regenerative medicine. To provide a coherent description of induced pluripotency from the gene regulation perspective, we use 35 microarray datasets to construct a reprogramming gene regulatory network. Comprising 276 nodes and 4471 links, the resulting network is, to the best of our knowledge, the largest gene regulatory network constructed for human fibroblast reprogramming and it is the only one built using a large number of experimental datasets. To build the network, a model that relates the expression profiles of the initial (fibroblast) and final (induced pluripotent stem cell) states is proposed and the model parameters (link strengths) are fitted using the experimental data. Twenty nine additional experimental datasets are collectively used to test the model/network, and good agreement between experimental and predicted gene expression profiles is found. We show that the model in conjunction with the constructed network can make useful predictions. For example, we demonstrate that our approach can incorporate the effect of reprogramming factor stoichiometry and that its predictions are consistent with the experimentally observed trends in reprogramming efficiency when the stoichiometric ratios vary. Using our model/network, we also suggest new (not used in training of the model) candidate sets of reprogramming factors, many of which have already been experimentally verified. These results suggest our model/network can potentially be used in devising new recipes for induced pluripotency with higher efficiencies. Additionally, we classify the links of the network into three classes of different importance, prioritizing them for experimental verification. We show that many of the links in the top ranked class are experimentally known to be important in reprogramming. Finally, comparing with other methods, we show that using our model is advantageous. [ABSTRACT FROM AUTHOR]

• CUM reduced the initial biofilm production capacity and disrupt the three-dimensional architecture of S. aureus biofilm. • CUM inhibited cell motility, cell surface hydrophobicity and extracellular polymers production of S. aureus. • CUM interfered with the expression of adhesion genes associated with biofilm formation such as agrA, icaA, sigB, ebpS, fnbA, fib and clfA. • CUM bound to SarA by H-bonds to inhibit S. aureus biofilm. In Iranian, ethnopharmacological studies show that Cuminum cyminum is commonly used in pain relief. The most abundant component in C. cyminum seeds is cuminaldehyde (CUM). However, there are few articles that have evaluated the anti-biofilm activity against Staphylococcus aureus (S. aureus). The nobility of this study was to evaluate the anti-biofilm effect of CUM and to investigate its possible mechanism of action. Crystal violet staining assay showed that CUM decreased biofilm biomass. The morphological observation indicated that CUM restrained the adhesion of biofilm, and destroyed the integrated and cohesive structure of biofilm. MTT assay proved that the metabolic activity of adherent cells treated with CUM was reduced. In vitro assays exhibited that cell motility, cell surface hydrophobicity, and extracellular polymers production of S. aureus were also inhibited in the presence of CUM. Furthermore, quantitative real-time PCR analysis confirmed the ability of CUM to interfere with the expression of adhesion genes associated with biofilm formation such as agrA, icaA, sigB, ebpS, fnbA, fib and clfA. Molecular docking speculated that the interaction of CUM with SarA could inhibit SarA-DNA binding, and ultimately inhibit the formation of biofilm. The results of this trial provided scientific experimental data for the use of CUM as an anti-biofilm agent. [ABSTRACT FROM AUTHOR]

Background: Gastric cancer (GC) is known for its lymph node metastasis and outstanding morbidity and mortality. Thus, improvement in the current knowledge regarding the molecular mechanism of GC is urgently needed to discover novel biomarkers involved in its progression and prognosis. Several long, non-coding RNAs (lncRNAs) play important roles in gastric tumorigenesis and metastasis. However, the signature of lncRNA-associated metastasis in GC is not fully clarified.Methods: We determined the lncRNA and mRNA expression profiles correlating to GC with or without lymph node-metastasis based on microarray analysis. Twelve differentially expressed lncRNAs and six differentially expressed mRNAs were validated by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay.Results: The relationships between the aberrantly expressed lncRNAs XLOC_010235 or RP11-789C1.1 and lymph node metastasis, pathologic metastasis status, distal metastasis and TNM (tumour, node, and metastasis) stage were found to be significantly different. Via survival analysis, patients who had high-expressed XLOC_010235 or low-expressed RP11-789C1.1 showed significantly worse survival than patients with inverse-expressed XLOC_010235 or RP11-789C1.1.Conclusion: In summary, this current study highlights some evidence regarding the potential role of lncRNAs in GC and posits that specific lncRNAs can be identified as novel, poor prognostic biomarkers in GC. [ABSTRACT FROM AUTHOR]

Major depressive disorder (MDD) is a prevalent, chronic, and relapse-prone psychiatric disease. However, the intermediate molecules resulting from stress and neurological impairment in different brain regions are still unclear. To clarify the pathological changes in the dentate gyrus (DG) and anterior cingulate cortex (ACC) regions of the MDD brain, which are the most closely related to the disease, we investigated the published microarray profile dataset GSE84183 to identify unpredictable chronic mild stress- (UCMS-) induced differentially expressed genes (DEGs) in the DG and ACC regions. Based on the DEG data, functional annotation, protein-protein interaction, and transcription factor (TF) analyses were performed. In this study, 1071 DEGs (679 upregulated and 392 downregulated) and 410 DEGs (222 upregulated and 188 downregulated) were identified in DG and ACC, respectively. The pathways and GO terms enriched by the DEGs in the DG, such as cell adhesion, proteolysis, ion transport, transmembrane transport, chemical synaptic transmission, immune system processes, response to lipopolysaccharide, and nervous system development, may reveal the molecular mechanism of MDD. However, the DEGs in the ACC involved metabolic processes, proteolysis, visual learning, DNA methylation, innate immune responses, cell migration, and circadian rhythm. Sixteen hub genes in the DG (Fn1, Col1a1, Anxa1, Penk, Ptgs2, Cdh1, Timp1, Vim, Rpl30, Rps21, Dntt, Ptk2b, Jun, Avp, Slit1, and Sema5a) were identified. Eight hub genes in the ACC (Prkcg, Grin1, Syngap1, Rrp9, Grwd1, Pik3r1, Hnrnpc, and Prpf40a) were identified. In addition, eleven TFs (Chd2, Zmiz1, Myb, Etv4, Rela, Tcf4, Tcf12, Chd1, Mef2a, Ubtf, and Mxi1) were predicted to regulate more than two of these hub genes. The expression levels of ten randomly selected hub genes that were specifically differentially expressed in the MDD-like animal model were verified in the corresponding regions in the human brain. These hub genes and TFs may be regarded as potential targets for future MDD treatment strategies, thus aiding in the development of new therapeutic approaches to MDD. [ABSTRACT FROM AUTHOR]

Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant–pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18–30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence‐related sRNAs in the response to pathogens and our current understanding of their effects on plant–pathogen interactions. The main content of this review article includes the roles of sRNAs in plant–pathogen interactions, cross‐kingdom sRNA trafficking between host and pathogen, and the application of RNA‐based fungicides for plant disease control. [ABSTRACT FROM AUTHOR]

Grape is an economically important crop but recalcitrant to Agrobacterium-mediated genetic transformation and in vitro regeneration. Here, we have developed a protocol for transient transformation of grapes by investigating the effects of explant pre-culture and duration of vacuum infiltration on transformation efficiency. Using sliced grape berries of "Shine-Muscat" (Vitis labrusca × Vitis vinifera) between the end of fruit expansion phase and the mature stage as explants, we firstly compared the effect of pre-culture explants into a susceptible state (incubation on Murashige and Skoog (MS) agar plate in the dark at 25 ± 1 °C for 48 h) with no pre-culture and then tested different vacuum infiltration times on transformation efficiency using β-glucuronidase (GUS) reporter system. Pre-culture increased the susceptibility of explants to the agrobacteria infection and increased transient transformation efficiency as assessed by histochemical GUS activity, with intense blue coloration compared with the faint staining observed in the non-susceptible explants. Using a Circulating Water Vacuum Pump system to facilitate agrobacteria entry into berry cells, we tested vacuum durations of 5, 10, and 15 min and observed that transformation efficiency increased with vacuum duration of infiltration. These results were confirmed by relative gene expression of GUS transgene as assessed by RT-qPCR and GUS activity assay. To further confirm the usefulness of our protocol, we transiently transformed grape berries with the hydrogen peroxide sensor gene VvHPCA3, and this was confirmed by gene expression analysis as well as increased sensitivity of the explants to hydrogen peroxide treatment. Overall, this study has resulted in a simple but efficient transient transformation protocol for grape berries and would be a valuable tool for the rapid testing of gene function and the study of key regulatory networks in this important crop. [ABSTRACT FROM AUTHOR]

Grape (Vitis vinifera L.) berries are susceptible to quality deterioration after harvest. This study aimed to investigate the effect of folic acid (FA) treatment on the postharvest quality of table grape berries. Harvested 'Kyoho' (V. vinifera × V. labrusca L.) bunches were immersed in 1 mg L−1 FA solution for 15 min, then stored for sample collection and phenotype observation. Treatment with FA decreased the rates of berry abscission, water loss, and berry softening, reduced the accumulation of reactive oxygen species (ROS), and altered ROS metabolism-associated enzyme activities and gene expression levels. Transcriptome analysis revealed 507, 684, and 250 differentially expressed genes (DEGs) between FA-treated and non-treated berries at 3, 6, and 9 d after treatment, respectively. The DEGs were grouped into six modules according to a weighted correlation network analysis. A hub transcription factor, annotated as a WRKY transcription factor, was screened from the module associated with cell wall metabolism and identified as VvWRKY31. Transient transformation of grape berry slices revealed that overexpression of VvWRKY31 enhanced the relative expression level of VvRboh. The dual-luciferase assay showed that VvWRKY31 was capable of binding to VvRboh promoter. The present results provide insights into the potential molecular mechanism underlying FA-induced delay postharvest quality deterioration of grape berries. Specifically, FA inhibits expression of genes associated with ROS generation by reducing VvWRKY31 expression, thereby delaying quality deterioration induced by excessive accumulation of ROS. These results will be helpful in table grape breeding programs focused on delaying deterioration in postharvest quality. • Folic acid affects ROS metabolism in postharvest grape. • VvWRKY31 is a hub transcription factor in cell wall metabolism. • VvWRKY31 promotes VvRboh expression by binding its promoter. [ABSTRACT FROM AUTHOR]

Simple Summary: Melanoma is a malignant and invasive cancer with high mortality and poor prognosis, and the incidence is increasing yearly. However, the current therapy options for melanoma are still insufficient and challenging. Recently, exosomes as essential intercellular messengers are receiving great interest for their important roles in melanoma progression, diagnosis, and treatment. Especially, the miRNAs derived from the exosomes are crucial during this process. Here, we summarized the miRNAs derived from melanoma exosomes, and analyzed their function in the progression of melanoma, including invasion and metastasis, microenvironment establishment, angiogenesis, and immune escape. In addition, we also listed the potential miRNAs including exosomal miRNAs as diagnostic markers for melanoma and introduced new therapeutic strategies for melanoma based on miRNAs and exosomes. Melanoma is a malignant and aggressive cancer, and its progression is greatly affected by interactions between melanoma cells and their surroundings. Exploration on mechanism of melanoma and improved diagnostic and therapeutic strategies are becoming increasingly important. Unlike extracellular messengers that mainly work on targeted cells through corresponding receptors, exosomes are essential intercellular messengers that deliver biologically active substances such as nucleic acids and proteins to target cells for cell–cell communication. Of them, microRNAs (miRNAs) are common and important exosomal components that can regulate the expression of a wide range of target genes. Accordingly, exosome-derived miRNAs play a significant role in melanoma progression, including invasion and metastasis, microenvironment establishment, angiogenesis, and immune escape. MiRNA signatures of exosomes are specific in melanoma patients compared to healthy controls, thus circulating miRNAs, especially exosomal miRNAs, become potential diagnostic markers and therapeutic targets for melanoma. This review aims to summarize recent studies on the role of exosomal miRNAs in melanoma as well as ongoing efforts in melanoma treatment. [ABSTRACT FROM AUTHOR]

Background. Tao-He-Cheng-Qi Formula (THCQF) is a traditional Chinese medicine that has been proven to have antitumor effects. The aim of this study was to elucidate the molecular targets and mechanisms of THCQF against colon cancer and construct a prognostic model based on network pharmacology, bioinformatics analysis, and in vitro experiments. Methods. Potential THCQF compounds and targets were retrieved from the Traditional Chinese Medicine Systems Pharmacology and Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine databases. Differentially expressed genes for colon cancer were screened in The Cancer Genome Atlas and Gene Expression Omnibus databases. The anticolon cancer mechanisms of THCQF were explored using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Molecular docking simulations and molecular dynamics analysis were used to evaluate the binding between target proteins and active compounds. Finally, the identified compounds were used to treat colon cancer cells from the HCT116 cell line, and expression of mRNA and protein after relevant posttreatment were tested using real-time polymerase chain reaction and western blotting. Results. A total of 27 anticolon cancer targets of THCQF were selected, among which four genes (CCNB1, CCNA2, IL1A, and MMP3) were shown to effectively predict patient outcomes in a prognostic colon cancer model. GO and KEGG enrichment analyses indicated that the activity against colon cancer of THCQF was associated with the interleukin (IL)-4 and IL-3 signaling pathways. Two compounds in THCQF, aloe emodin (AE) and quercetin (QR), were shown to efficiently bind to cyclin B1, the protein encoded by CCNB1. Finally, incubation of HCT116 cells with AE and QR significantly decreased CCNB1 mRNA expression and cyclin B1 levels. Conclusions. Taken together, the results indicate that AE and QR are the pivotal active compounds of THCQF, and CCNB1 is the main molecular target through which THCQF exerts its anticolon cancer effects. The study findings provide insight for studies investigating the anticancer effects of other traditional Chinese medicines. [ABSTRACT FROM AUTHOR]

Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 mounts specific acid-resistance systems against acid stress, making it more difficult to eradicate in food industry. To date, RNAseq-based analysis focusing on the virulence factors within an acidic environment is restricted to asmall part of virulence gene clusters. In this study E.coli O157:H7 survived HCl stress at pH 3.0 for up to 1 h preceded by acid adaptation at pH 5.5 for 1 h. At the same time, bacteria without stimulus were cultured in neutral TSB broth for 2 h.Then, transcriptome analysis was performed to compare virulence-related genes at neutral and acidic pH. Though transcripts indicated adownshift of the flagellar, fimbriae and LEE-associated genes, the increased expression of adhesin-related genes, iron uptake genes and some potential virulence factors were identified. Comparison of the gene expression with respect to virulence factors revealed strongest cell response to the relevant stress and increased protective response for survival in the acidic pH. This suggests that E.coli O157:H7 might be still virulent following HCl stress. [ABSTRACT FROM AUTHOR]

Cardiac hypertrophy and ventricular remodeling following heart failure are important causes of high mortality in heart disease patients. The cardiac lymphatic system has been associated with limited research, but it plays an important role in the improvement of myocardial edema and the promotion of fluid balance. LCZ696 is a novel combination of angiotensin and neprilysin inhibitors. Here, we studied the role played by LCZ696 during transverse aortic constriction (TAC) induced cardiac hypertrophy and changes in the lymphatic system. Mice undergoing aortic coarctation were constructed to represent a cardiac hypertrophy model and then divided into random groups that either received treatment with LCZ696 (60 mg/kg/d) or no treatment. Cardiac ultrasonography was used to detect cardiac function, and hematoxylin and eosin (H&E) and Masson staining were used to detect myocardial hypertrophy and fibrosis. The proinflammatory factors interleukin-6 (IL-6), IL-1β, and tumor necrosis factor-α (TNF-α) were detected in the blood and heart tissues of mice. The protein expression levels of lymphatic-specific markers, such as vascular endothelial growth factor C (VEGF-C), VEGF receptor 3 (VEGFR3), and lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1) were detected in mouse heart tissues. We also examined the colocalization of lymphatic vessels and macrophages by immunofluorescence. The results showed that LCZ696 significantly improved heart dysfunction, cardiac hypertrophy, and fibrosis and inhibited the expression of proinflammatory factors IL-6, IL-1β, and TNF-α in the circulating blood and heart tissues of mice. LCZ696 also decreased the protein expression levels of VEGF-C, VEGFR3, and LYVE-1 in mouse heart tissues, ameliorated the transport load of lymphatic vessels to macrophages, and improved the remodeling of the lymphatic system in the hypertrophic cardiomyopathy model induced by TAC. [ABSTRACT FROM AUTHOR]

Background: 5-Azacytidine (5-azaC) promotes the development of 'Kyoho' grape berry but the associated changes in gene expression have not been reported. In this study, we performed transcriptome analysis of grape berry at five developmental stages after 5-azaC treatment to elucidate the gene expression networks controlling berry ripening. Results: The expression patterns of most genes across the time series were similar between the 5-azaC treatment and control groups. The number of differentially expressed genes (DEGs) at a given developmental stage ranged from 9 (A3_C3) to 690 (A5_C5). The results indicated that 5-azaC treatment had not very great influences on the expressions of most genes. Functional annotation of the DEGs revealed that they were mainly related to fruit softening, photosynthesis, protein phosphorylation, and heat stress. Eight modules showed high correlation with specific developmental stages and hub genes such as PEROXIDASE 4, CAFFEIC ACID 3-O-METHYLTRANSFERASE 1, and HISTONE-LYSINE N-METHYLTRANSFERASE EZA1 were identified by weighted gene correlation network analysis. Conclusions: 5-AzaC treatment alters the transcriptional profile of grape berry at different stages of development, which may involve changes in DNA methylation. [ABSTRACT FROM AUTHOR]

Background: The development of nanoparticle drug delivery systems with targeted ligands has the potential to increase treatment efficiency in ovarian cancer. Methods: We developed a 21-amino acid peptide, YTRDLVYGDPARPGIQGTGTF (L-FP21) conjugated to polyethylenimine (PEI) and methoxy polyethylene glycol (mPEG) to prepare a nanoparticle drug vehicle to target follicle-stimulating hormone receptor (FSHR) in ovarian cancer. At the same time, we optimized the ligand of the nanoparticle vehicle using D-peptides, which consist of D-amino acids (D-FP21). Nanoparticle vehicles carrying the therapeutic gene plasmid growth-regulated oncogene alpha (pGRO-α) short hairpin RNA (shRNA) (FP21-PEG-PEI/pGRO-α) were prepared for further investigation. Results: Compared with L-FP21, D-FP21 exhibited improved biological stability and higher uptake rate for FSHR-expressing ovarian cancer cells. The cytotoxicity of the L, D-FP21-PEG-PEI/pGRO-α complexes were significantly lower than that of the PEI/pGRO-α complex. The nanoparticle drug with the targeted ligand showed higher transfection efficiencies and improved anti-proliferation effects for ovarian cancer cells than that without the targeted ligand (mPEG-PEI/pGRO-α). Furthermore, an in vivo evaluation of an antitumor assay indicated that D-FP21-PEG-PEI/pGRO-α inhibited the growth of tumor spheroids considerably more than L-FP21-PEG-PEI/pGRO-α; their tumor inhibition rates were 58.5% and 33.3%, respectively. Conclusions: D-FP21-PEG-PEI/plasmid DNA is a safe and efficient gene delivery vehicle for ovarian cancer targeted therapy. [ABSTRACT FROM AUTHOR]

Our appreciation for the extent of Epstein Barr virus (EBV) transcriptome complexity continues to grow through findings of EBV encoded microRNAs, new long non-coding RNAs as well as the more recent discovery of over a hundred new polyadenylated lytic transcripts. Here we report an additional layer to the EBV transcriptome through the identification of a repertoire of latent and lytic viral circular RNAs. Utilizing RNase R-sequencing with cell models representing latency types I, II, and III, we identified EBV encoded circular RNAs expressed from the latency Cp promoter involving backsplicing from the W1 and W2 exons to the C1 exon, from the EBNA BamHI U fragment exon, and from the latency long non-coding RPMS1 locus. In addition, we identified circular RNAs expressed during reactivation including backsplicing from exon 8 to exon 2 of the LMP2 gene and a highly expressed circular RNA derived from intra-exonic backsplicing within the BHLF1 gene. While expression of most of these circular RNAs was found to depend on the EBV transcriptional program utilized and the transcription levels of the associated loci, expression of LMP2 exon 8 to exon 2 circular RNA was found to be cell model specific. Altogether we identified over 30 unique EBV circRNAs candidates and we validated and determined the structural features, expression profiles and nuclear/cytoplasmic distributions of several predominant and notable viral circRNAs. Further, we show that two of the EBV circular RNAs derived from the RPMS1 locus are detected in EBV positive clinical stomach cancer specimens. This study increases the known EBV latency and lytic transcriptome repertoires to include viral circular RNAs and it provides an essential foundation and resource for investigations into the functions and roles of this new class of EBV transcripts in EBV biology and diseases. [ABSTRACT FROM AUTHOR]

• Grapevine plants were dwarfed by Chlormequat chloride (CCC). • Transcriptome data analysis showed that VviEXPA7 plays an important role. • The high expression of VviRAP2.12 transcription factor suppressed the expression of VviEXPA7 after CCC treatment, which led to the inhibition of cell elongation and plant dwarfing. Treatment with chlormequat chloride (CCC) can lead to dwarfism, which has been studied in many plants. However, the underlying molecular mechanisms have been less studied. Herein, the phenotypic changes and gene expression levels of grapevine in response to CCC were investigated. Results showed that the height of grape plants became significantly shorter after CCC treatment, especially between the first two stems above the roots. Transcriptome sequencing was then performed and analyzed, 120 differentially expressed genes (DEGs) were detected in the stems after CCC treatment compared to the control. The gene ontology (GO) enrichment results showed that processes such as cellulose synthase (UDP-forming) activity, regulation of the auxin-mediated signaling pathway, and the cellulose biosynthetic process were common. In addition, weighted gene co-expression network analysis (WGCNA) identified the strong correlation between the MEbrown module and stem development. VviEXAP7 was selected from the genes belonging to key GO pathways and WGCNA modules. The quantitative real-time PCR (qRT-PCR) results showed that VviEXPA7 was significantly downregulated because of the CCC treatment. Additionally, analysis of VviEXPA7 promoter activity showed that VviEXPA7 activated GUS gene expression, and was induced by CCC, abscisic acid (ABA), and other hormones. VviEXPA7 was used as a target gene for transcription factor prediction, and after employing the PlantTFDB and JASPAR databases, VviRAP2.12 was identified as a transcription factor that might regulate VviEXPA7. qRT-PCR revealed that VviRAP2.12 was significantly upregulated after CCC treatment. Finally, the interaction between VviEXPA7 and VviRAP2.12 was verified by the dual-luciferase assay. Thus, the current study shows that CCC decreased the expression of the cell growth-related gene VviEXPA7 by promoting the expression of VviRAP2.12, which resulted in dwarfed plants. This study generated new information that will increase our understanding of the mechanism of action of CCC and provides a scientific basis for simplified cultivation of grapes. [ABSTRACT FROM AUTHOR]

• Six genes are determined as proline biosynthesis- or proline catabolism-related genes in grapevines. • P5CS1, OAT, PDH and P5CDH can be significantly induced by osmotic and oxidative stresses. • Proline is greatly accumulated under abiotic stresses, especially osmotic and oxidative stresses. • Proline biosynthesis and proline catabolism-related genes synergistically regulate proline accumulation in response to abiotic stresses. Proline is an important osmotic regulator for plants under abiotic stresses. Proline accumulation is regulated by various enzymes, while genes encoding these enzymes have not been fully investigated in grapevines. In this study, we identified four proline biosynthesis-related genes (P5CS1, P5CS2, P5CR and OAT) and two proline catabolism-related genes (PDH and P5CDH) from grapevines, and conducted bioinformatics analysis including protein characteristic, gene structure, phylogenetic relationship and cis-acting element of promoters. Promoter analysis found that cis-acting elements related to stress and phytohormone responsiveness were present in the promoters of these genes. Tissue-specific expression analysis of these genes indicated that P5CS2, OAT and PDH expressed highly in flower, and P5CS1, P5CR and P5CDH had highest expression levels in tendril, berry and leaf respectively. Expression patterns of these genes under abiotic stresses revealed that P5CS1, OAT and PDH could be significantly induced by salt, dehydration, PEG and H 2 O 2 treatments, and P5CDH was significantly suppressed under these stress treatments. By measuring proline accumulation in grapevines, we found that proline content dramatically increased after treatments of salt, dehydration, PEG and H 2 O 2. Our results revealed the molecular responses (especially P5CS1, OAT, PDH and P5CDH) in the proline metabolism pathway to osmotic and oxidative stresses in grapevines, demonstrating that proline synthesis and proline catabolism synergistically regulate proline accumulation in response to abiotic stresses. [ABSTRACT FROM AUTHOR]

Bradysia odoriphaga (Diptera: Sciaridae) is the most important pest of Chinese chive (Allium tuberosum) in Asia; however, the molecular genetics are poorly understood. To explore the molecular biological mechanism of development, Illumina sequencing and de novo assembly were performed in the third-instar, fourth-instar, and pupal B. odoriphaga. The study resulted in 16.2 Gb of clean data and 47,578 unigenes (≥125bp) contained in 7,632,430contigs, 46.21% of which were annotated from non-redundant protein (NR), Gene Ontology (GO), Clusters of Orthologous Groups (COG), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. It was found that 19.67% of unigenes matched the homologous species mainly, including Aedes aegypti, Culex quinquefasciatus, Ceratitis capitata, and Anopheles gambiae. According to differentially expressed gene (DEG) analysis, 143, 490, and 309 DEGs were annotated as involved in the developmental process in the GO database respectively, in the comparisons of third-instar and fourth-instar larvae, third-instar larvae and pupae, and fourth-instar larvae and pupae. Twenty-five genes were closely related to these processes, including developmental process, reproduction process, and reproductive organs development and programmed cell death (PCD). The information of unigenes assembled in B. odoriphaga through transcriptome and DEG analyses could provide a detailed genetic basis and regulated information for elaborating the developmental mechanism from the larval, pre-pupal to pupal stages of B. odoriphaga. [ABSTRACT FROM AUTHOR]

Background: OCT4, SOX2, and NANOG are major transcription factors related to stem cell self-renewal and differentiation. The aim of this study was to examine the association of OCT4, SOX2, and NANOG expression levels with the development and prognosis of patients with oral squamous cell carcinoma (OSCC). Materials and Methods: Expression levels of OCT4, SOX2, and NANOG were evaluated by immunohistochemistry with tissue microarray slides of 436 OSCC, 362 corresponding tumor-adjacent normal (CTAN) tissues, and 71 normal uvula epithelium tissues. The clinicopathologic and follow-up data of the OSCC patients were recorded. Results: OCT4 expression was significantly higher in normal and CTAN tissues than in tumor tissue (both P < 0.001). SOX2 expression in CTAN tissue was significantly higher than that in normal (P = 0.021) and tumor tissues (P < 0.001). However, NANOG expression was significantly higher in CTAN (P = 0.014) and tumor tissues (P = 0.009) than in normal tissue. Higher OCT4 and SOX2 expressions were associated with earlier AJCC stage (P = 0.002 and P < 0.001), small tumor size (P = 0.017 and P = 0.001), and the absence of lymph node metastasis (P = 0.015 and P = 0.025). Higher levels of SOX2 expression were associated with better disease-specific survival (P = 0.002) even after adjustment for clinicopathologic factors. Discussion: OCT4 and SOX2 are biomarkers of tumorigenesis and early stage OSCC. SOX2 is an independent prognostic factor for OSCC. [ABSTRACT FROM AUTHOR]

To accurately evaluate gene expression levels and obtain more accurate quantitative real-time RT-PCR (qRT-PCR) data, normalization relative to reliable reference gene(s) is required. Drosophila suzukii, is an invasive fruit pest native to East Asia, and recently invaded Europe and North America, the stability of its reference genes have not been previously investigated. In this study, ten candidate reference genes (RPL18, RPS3, AK, EF-1β, TBP, NADH, HSP22, GAPDH, Actin, α-Tubulin), were evaluated for their suitability as normalization genes under different biotic (developmental stage, tissue and population), and abiotic (photoperiod, temperature) conditions. The three statistical approaches (geNorm, NormFinder and BestKeeper) and one web-based comprehensive tool (RefFinder) were used to normalize analysis of the ten candidate reference genes identified α-Tubulin, TBP and AK as the most stable candidates, while HSP22 and Actin showed the lowest expression stability. We used three most stable genes (α-Tubulin, TBP and AK) and one unstably expressed gene to analyze the expression of P-glycoprotein in abamectin-resistant and sensitive strains, and the results were similar to reference genes α-Tubulin, TBP and AK, which show good stability, while the result of HSP22 has a certain bias. The three validated reference genes can be widely used for quantification of target gene expression with qRT-PCR technology in D.suzukii. [ABSTRACT FROM AUTHOR]

All-trans retinoic acid (ATRA) is a revolutionary agent for acute promyelocytic leukemia (APL) treatment via differentiation induction. However, ATRA treatment also increases cytokine, chemokine, and adhesive molecule (mainly ICAM-1) expression, which can cause clinical complications, including a severe situation known as differentiation syndrome (DS) which can cause death. Therefore, it is of clinical significance to find a strategy to specifically blunt inflammatory effects while preserving differentiation. Here we report that the natural compound, celastrol, could effectively block lung infiltrations in DS animal models created by loading ATRA-induced APL cell line NB4. In ATRA-treated NB4 cells, celastrol could potently inhibit ICAM-1 elevation and partially reduce TNF-α and IL-1β secretion, though treatment showed no effects on IL-8 and MCP-1 levels. Celastrol’s effect on ICAM-1 in ATRA-treated NB4 was related to reducing MEK1/ERK1 activation. Strikingly and encouragingly, celastrol showed no obvious effects on ATRA-induced NB4 differentiation, as determined by morphology, enzymes, and surface markers. Our results show that celastrol is a promising and unique agent for managing the side effects of ATRA application on APL, and suggest that hyper-inflammatory ability is accompanied by, but not necessary for, APL differentiation. Thus we offered an encouraging novel strategy to further improve differentiation therapy. [ABSTRACT FROM AUTHOR]

Phenazinomycin is a hybrid natural product consisting of two chemical entities, a phenazine and a cyclic terpenoid. Phenazinomycin exhibits potent activity against murine tumors and adriamycin-resistant P388 leukemia cells. Streptomyces iakyrus DSM 41873 is known to produce five actinomycin G2- G6. In the previous study, we identified the gene cluster directing the biosynthesis of actinomycin G2-G4. Inactivation of acm G5′ gene in the actinomycin G gene cluster in S. iakyrus completely abolished the production of actinomycin G. Metabolic profiling, chemical isolation, and structural elucidation of the resulting mutant SIAΔ acm G5′ showed a previously unnoticed metabolite phenazinomycin in S. iakyrus. In silico analysis identified a hybrid biosynthetic gene cluster in the genome of S. iakyrus that could be responsible for the biosynthesis of phenazinomycin. It is proposed that the perturbation of actinomycin G to enhance the phenazinomycin production in the mutant may result from the lifted competition of chorismate, the common precursor of the biosynthetic pathways of these two structurally unrelated natural products. [ABSTRACT FROM AUTHOR]

CD103 is a marker for identification of effector/memory regulatory Τ cells (Tregs). CD103+ Tregs are potent suppressors of tissue inflammation in several infectious diseases, autoimmune diseases, and cancers. However, the underlying mechanisms for this potent suppression ability remain unclear. The current study was designed to clarify this issue. Unexpectedly, we found both CD103+ and CD103- Tregs had similar suppression capacity in vitro. We then chose a murine tumor model for investigation of the in vivo behavior of these Tregs. The suppression ability in vivo against the anti-tumor ability of CD8+ Τ cells was restricted to CD103+ Tregs although both Tregs had equal in vitro suppression ability. In addition, CD103+ Tregs expressed significantly higher levels of CCR5 than those of CD103- Tregs and accumulated more in tumors than did CD103- Tregs. Furthermore, blockade of CCR5 signaling, either by CCR5-/-CD103+ Tregs or by CCL5 knockdown tumor, could reduce the migration of CD103+ Tregs into tumors and impair their in vivo suppression ability. In conclusion, these results indicate that the potent in vivo suppression ability of CD103+ Tregs is due to the tissue-migration ability through CCR5 expression. [ABSTRACT FROM AUTHOR]

Abstract: Holomycin is a dithiolopyrrolone antibiotic natural product produced by Streptomyces clavuligerus, ATCC 27064. This paper reports on the identification of a gene cluster from S. clavuligerus that directs holomycin biosynthesis. Heterologous expression of the cluster in S. albus then induced the production of holomycin. Bioinformatics analysis of the gene cluster revealed that holomycin was assembled by a single multidomain non-ribosomal peptide synthetase (NRPS) consisting of heterocyclization, adenylation, and thiolation domains (Cy-A-T), a free-standing condensation domain, two thioesterases, five tailoring enzymes involved in oxidative reactions and two regulatory and transcriptional genes. Knock out of the gene, HomI, completely abolished the production of holomycin, which is consistent with its role as a key biosynthetic gene and is likely involved in the formation of the disulfide bond generating the final precursor, holothin. [Copyright &y& Elsevier]

The article presents a study which describes the OstrinlysC, a c-type lysozomes from the Asian corn borer, and demonstrates its activity against Gram-positive and Gram-negative bacteria. It states that the OstrinlysC gene profile was studied by quantitative real-time polymerase chain reaction (PCR). It says that OstrinlysC gene was up-regulated in immune tissues after injection of the larvae with bacteria. It suggests that OstrinlysC gene plays a role in immune responses.

Abstract: Schistosomiasis japonica is currently one of the most serious parasitic diseases and over 670000 people are infected in China by the end of 2006. In order to establish an effective diagnostic method, the gene coding for Sj14-3-3 and Sj26kDa GST were cloned and expressed separately in Escherichia coli as fusion protein with His-tag. The rSj14-3-3 and 26kDa rSjGST were combinedly used as antigens for enzyme-linked immunosorbent assays (ELISA) to diagnose acute and chronic S. japonica. Our results showed that the sensitivity in diagnoses of both acute and chronic schistosomiasis was 94.4% (67/71) and 80.7% (96/119), respectively. The specificity was 94.7% applying 132 sera from people living in S. japonicum-free areas. The data also showed that the recombinant proteins cross-react with Clonorchis sinensis and hookworms at a rate of 11.8% and 5.3% respectively. Parallel tests were conducted among ELISA, indirect hemagglutination assay (IHA) and circular ovum precipitin test (COPT) to determine anti-S. japonicum antibodies in sera of patients with schistosomiasis, healthy control, and those infected with other parasites and the results showed no significant difference in sensitivity for acute schistosomiasis between ELISA and IHA assays (χ 2 =1.33, P >0.05), but significant between ELISA and COPT assays (χ 2 =6.72, P <0.01). Our results also revealed significant difference in positive rate between ELISA and IHA (χ 2 =24.74, P <0.005), as well as between ELISA and COPT (χ 2 =58.14, P <0.005). These results suggest that the rSj14-3-3 and r26kDa SjGST would be effective diagnostic antigens for detection of antibodies to S. japonicum in human. Due to the easy production, high sensitivity and specificity, the recombinant proteins tested in this study can be considered as candidate reagent for immunological diagnosis of human schistosomiasis. [Copyright &y& Elsevier]

Despite increasing interest in the molecular mechanisms of floral diversity, few studies have investigated the developmental and genetic bases of petaloid bracts. This study examined morphological patterns of bract initiation and expression patterns of B-class MADS-box genes in bracts of several Cornus species. We suggest that petaloid bracts in this genus may not share a single evolutionary origin., Developmental pathways of bracts and spatiotemporal expression of B-class genes in bracts and flowers were examined for four closely related dogwood species., Divergent morphological progressions and gene expression patterns were found in the two sister lineages with petaloid bracts, represented by Cornus florida and Cornus canadensis. Phylogeny-based analysis identified developmental and gene expression changes that are correlated with the evolution of petaloid bracts in C. florida and C. canadensis., Our data support the existence of independent evolutionary origins of petaloid bracts in C. canadensis and C. florida. Additionally, we suggest that functional transference within B-class gene families may have contributed to the origin of bract petaloidy in C. florida. However, the underlying mechanisms of petaloid bract development likely differ between C. florida and C. canadensis. In the future this hypothesis can be tested by functional analyses of Cornus B-class genes. [ABSTRACT FROM AUTHOR]

Background: In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To reveal the molecular mechanism, RNA-sequencing analysis was conducted on the different developmental stages of Kyoho berry treated with H2O2. Results: In the comparison of treatment and control groups, 406 genes were up-regulated and 683 were down-regulated. Time course sequencing (TCseq) analysis showed that the expression patterns of most of the genes were similar between the treatment and control, except for some genes related to chlorophyll binding and photosynthesis. Differential expression analysis and the weighted gene co-expression network were used to screen significantly differentially expressed genes and hub genes associated with oxidative stress (heat shock protein, HSP), cell wall deacetylation (GDSL esterase/lipase, GDSL), cell wall degradation (xyloglucan endotransglucosylase/ hydrolase, XTH), and photosynthesis (chlorophyll a-b binding protein, CAB1). Gene expression was verified with RT-qPCR, and the results were largely consistent with those of RNA sequencing. Conclusions: The RNA-sequencing analysis indicated that H2O2 treatment promoted the early ripening of Kyoho berry by affecting the expression levels of HSP, GDSL, XTH, and CAB1 and- photosynthesis- pathways. [ABSTRACT FROM AUTHOR]

The development of multidrug resistance (MDR) in cancer patients, which is often associated with the overexpression of ABCB1 (MDR1, P-glycoprotein) in cancer cells, remains a significant problem in cancer chemotherapy. ABCB1 is one of the major adenosine triphosphate (ATP)-binding cassette (ABC) transporters that can actively efflux a range of anticancer drugs out of cancer cells, causing MDR. Given the lack of Food and Drug Administration (FDA)-approved treatment for multidrug-resistant cancers, we explored the prospect of repurposing erdafitinib, the first fibroblast growth factor receptor (FGFR) kinase inhibitor approved by the FDA, to reverse MDR mediated by ABCB1. We discovered that by reducing the function of ABCB1, erdafitinib significantly resensitized ABCB1-overexpressing multidrug-resistant cancer cells to therapeutic drugs at sub-toxic concentrations. Results of erdafitinib-stimulated ABCB1 ATPase activity and in silico docking analysis of erdafitinib binding to the substrate-binding pocket of ABCB1 further support the interaction between erdafitinib and ABCB1. Moreover, our data suggest that ABCB1 is not a major mechanism of resistance to erdafitinib in cancer cells. In conclusion, we revealed an additional action of erdafitinib as a potential treatment option for multidrug-resistant cancers, which should be evaluated in future drug combination trials. [ABSTRACT FROM AUTHOR]

Previous study has demonstrated that the riboflavin treatment promoted the early ripening of the 'Kyoho' grape berry. However, the molecular mechanism causing this was unclear. In order to reveal the regulation mechanism of riboflavin treatment on grape berry development and ripening, the different berry developmental stages of the 'Kyoho' berry treated with 0.5 mmol/L of riboflavin was sampled for transcriptome profiling. RNA-seq revealed that 1526 and 430 genes were up-regulated and down-regulated, respectively, for the comparisons of the treatment to the control. TCseq analysis showed that the expression patterns of most of the genes were similar between the treatment and the control, except for some genes that were related to the chlorophyll metabolism, photosynthesis–antenna proteins, and photosynthesis, which were revealed by the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differentially expressed genes and weighted gene co-expression network analysis (WGCNA) analysis identified some significantly differentially expressed genes and some hub genes, including up-regulation of the photosynthesis-related ELIP1 and growth and development-related GDSL; and down-regulation of the oxidative stress-related ATHSP22 and berry softening-related XTH32 and GH9B15. The results suggested that the riboflavin treatment resulted in the variations of the expression levels of these genes, and then led to the early ripening of the 'Kyoho' berry. [ABSTRACT FROM AUTHOR]

Previous investigations proposed a link between the Epstein-Barr virus (EBV) and lung cancer (LC), but the results are highly controversial largely due to the insufficient sample size and the inherent limitation of the traditional viral screening methods such as PCR. Unlike PCR, current next-generation sequencing (NGS) utilizes an unbiased method for the global assessment of all exogenous agents within a cancer sample with high sensitivity and specificity. In our current study, we aim to resolve this long-standing controversy by utilizing our unbiased NGS-based informatics approaches in conjunction with traditional molecular methods to investigate the role of EBV in a total of 1127 LC. In situ hybridization analysis of 110 LC and 10 normal lung samples detected EBV transcripts in 3 LC samples. Comprehensive virome analyses of RNA sequencing (RNA-seq) data sets from 1017 LC and 110 paired adjacent normal lung specimens revealed EBV transcripts in three lung squamous cell carcinoma and one lung adenocarcinoma samples. In the sample with the highest EBV coverage, transcripts from the BamHI A region accounted for the majority of EBV reads. Expression of EBNA-1, LMP-1 and LMP-2 was observed. A number of viral circular RNA candidates were also detected. Thus, we for the first time revealed a type II latency-like viral transcriptome in the setting of LC in vivo. The high-level expression of viral BamHI A transcripts in LC suggests a functional role of these transcripts, likely as long non-coding RNA. Analyses of cellular gene expression and stained tissue sections indicated an increased immune cell infiltration in the sample expressing high levels of EBV transcripts compared to samples expressing low EBV transcripts. Increased level of immune checkpoint blockade factors was also detected in the sample with higher levels of EBV transcripts, indicating an induced immune tolerance. Lastly, inhibition of immune pathways and activation of oncogenic pathways were detected in the sample with high EBV transcripts compared to the EBV-low LC indicating the direct regulation of cancer pathways by EBV. Taken together, our data support the notion that EBV likely plays a pathological role in a subset of LC. [ABSTRACT FROM AUTHOR]