Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster ( Crassostrea ariakensis).

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters. The Jinjiang oyster ( Crassostrea ariakensis) is an economically and ecologically important species in China. In the present study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents. Analysis identified 9 483 differentially expressed genes (DEGs) and 7 215 genes with significantly differential chromatin accessibility (DCAGs) were obtained, with an overlap of 2 600 genes between them. Notably, a significant proportion of these genes were enriched in pathways related to glycogen metabolism, including "Glycogen metabolic process" and "Starch and sucrose metabolism". In addition, genome-wide association study (GWAS) identified 526 single nucleotide polymorphism (SNP) loci associated with glycogen content. These loci corresponded to 241 genes, 63 of which were categorized as both DEGs and DCAGs. This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C. ariakensis.

Novel Plasma Proteomic Biomarkers for Early Identification of Induction Chemotherapy Beneficiaries in Locoregionally Advanced Nasopharyngeal Carcinoma.

Background: Induction chemotherapy (IC) can alleviate locoregionally advanced nasopharyngeal carcinoma (LA-NPC), but effectiveness differs between patients, toxicity is problematic, and effective blood-based IC efficacy predictors are lacking. Here, we aimed to identify biomarkers for early identification of IC beneficiaries. Methods: Sixty-four pairs of matched plasma samples collected before and after IC from LA-NPC patients including 34 responders and 30 non-responders, as well as 50 plasma samples of healthy individuals, were tested using data-independent acquisition mass spectrometry. The proteins associated with clinical traits or IC benefits were investigated by weighted gene co-expression network analysis (WGCNA) and soft cluster analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional annotations were performed to determine the potential function of the identified proteins. The area under the receiver operating characteristic curve (AUC) was used to evaluate the performance of candidate biomarkers in predicting IC beneficiaries. Results: Compared with healthy individuals, 1027 differentially expressed proteins (DEPs) were found in the plasma of LA-NPC patients. Based on feedback from IC outcomes, 463 DEPs were identified in the pre-IC plasma between responders and non-responders. A total of 1212 DEPs represented the proteomic changes before and after IC in responders, while 276 DEPs were identified in post-IC plasma between responders and non-responders. WGCNA identified nine protein co-expression modules correlated with clinical traits. Soft cluster analysis identified four IC benefits-related protein clusters. Functional enrichment analysis showed that these proteins may play a role in IC via immunity, complement, coagulation, glycosaminoglycan and serine. Four proteins differentially expressed in all group comparisons, paraoxonase/arylesterase 1 (PON1), insulin-like growth factor-binding protein 3 (IGFBP-3), rheumatoid factor D5 light chain (v-kappa-3) and RNA helicase (DDX55), were associated with clinical traits or IC benefits. A four-protein model accurately identified potential IC beneficiaries (AUC=0.95) while diagnosing LA-NPC (AUC=0.92), and the prediction performance was verified using the models to confirm the effective IC (AUC=0.97) and evaluate IC outcome (AUC=0.94). Conclusion: The plasma protein profiles among IC responders and non-responders were different. PON1, IGFBP3, v-kappa-3 and DDX55 could serve as potential biomarkers for early identification of IC beneficiaries for individualised treatment of LA-NPC.

A novel three-microRNA signature for predicting survival in patients with nasopharyngeal carcinoma.

BACKGROUND/PURPOSE: Nasopharyngeal carcinoma (NPC) is a malignant neoplasm of the head and neck. This study aims to use integrated bioinformatics technologies to develop a predictive miRNA-signature correlated with the prognosis of NPC. MATERIALS AND METHODS: Initially, the differentially expressed miRNAs (DEMs) in NPC were identified, and then DEMs related to the prognosis of NPC were further screened. Subsequently, the relatively important DEMs identified by random forest algorithm were used to construct a predictive signature by multivariate COX regression analysis. Moreover, PCA, Kaplan-Meier analysis, time-dependent ROC analysis, and univariate and multivariate COX regression analysis were performed to evaluate the ability of the signature in risk identification and prognosis prediction in NPC. RESULTS: Hsa-miR-29c, hsa-miR-30e and hsa-miR-93 were selected from DEMs to construct a signature, and their abnormal expression was significantly associated with poor prognosis of NPC. The average AUC values of 1- to 5-year OS, DFS and DMFS predicted by the signature were all above 0.7, and showed better clinical independence than other indexes. In addition, 295 differentially expressed mRNAs could be used as potential target genes of the 3 DEMs. Among them, 56 differentially expressed mRNAs were related to PFS. GO and KEGG enrichment analysis indicated that the poor prognosis of NPC was related to the abnormality of chromosomes, cytokines, and chemokines. CONCLUSION: We constructed a three-miRNA signature with good independent performance in predicting the prognosis for NPC. This study may lay the foundation for exploring new therapeutic targets and improving survival outcomes in NPC patients.

[Effects of water quality on the reproductive behavior and capacity of Andrias davidianus under tourism disturbance.] / æ— æ¸¸å¹²æ‰°ä¸‹æ°´è´¨å¯¹å¤§é²µç¹æ®–è¡Œä¸ºä¸Žç¹æ®–åŠ›çš„å½±å“.

Water quality under tourism disturbance was simulated through controlling the water intake of the ecological breeding ponds of Chinese giant salamander (Andrias davidianus, CGS). Both the reproductive behavior (oviposition and parental care) and capacity (relative egg production, fertilizing rate of eggs, and hatching rate of fertilized eggs) of CGS were examined using a real-time infrared digital monitoring system. The relationships among reproductive behavior, capacity, and the corresponding parameters of water quality were analyzed, to understand how water quality under tourism disturbance would affect the reproductive behavior and capacity of CGS. The examined oviposition behavior and capacity of CGS showed no variation in general, but the parental care behavior such as tail fanning and agitation time of the male CGS were prolonged significantly in the groups under tourism disturbance. Such prolonged behaviors would help increase the content of dissolved oxygen (DO) to meet the high demands of DO during embryonic development of CGS. In addition, the overall hatching time of fertilized eggs was increased significantly under disturbance conditions when it compared with the control, which would ensure the overall hatching rate among these comparative groups unaffected. In summary, the prolongations of some reproductive behavior (tail fanning and agitation of the male CGS and the development time of fertilized egg) would be a kind of positive actions of CGS in response to the changes of water quality resulted from tourism disturbance.

The dynamic expression of aquaporins 1 and 4 in rats with hydrocephalus induced by subarachnoid haemorrhage.

INTRODUCTION: Hydrocephalus is a common complication of subarachnoid haemorrhage (SAH). As transmembrane water channels, aquaporins 1 and 4 (AQP1 and AQP4) are involved in the pathogenesis of hydrocephalus. We aimed to assess the association between the expressions of AQP1 and AQP4 and the severity and duration of hydrocephalus after SAH. MATERIAL AND METHODS: A double haemorrhage model by injection of autologous blood into the cisterna magna was used to induce SAH in rats. Sham rats received the same procedures, but with the injection of normal saline. The SAH group was divided into the SAH with hydrocephalus group and SAH without hydrocephalus group after identifying hydrocephalus histologically. AQP1 and AQP4 in ventricle regions were detected by immunofluorescence, quantitative polymerase chain reaction (qPCR) and western blot. RESULTS: Hydrocephalus was the most severe at day 3 after SAH. AQP1 and AQP4 mRNA and protein levels increased at day 1 and peaked at day 3. The SAH with hydrocephalus group had a higher expression of AQP1 and AQP4 than the SAH without hydrocephalus group. Higher AQP1 levels were found at the apical and basolateral membrane of the choroid plexus epithelium, while higher AQP4 levels were found in the ependymal cells. A positive correlation between the relative lateral ventricle area and the ratio of AQP1/AQP4 proteins was identified. CONCLUSIONS: AQP1 and AQP4 are remarkably correlated with the severity of hydrocephalus induced by SAH. AQP1 and AQP4 are potential drug targets for developing therapeutic strategies against hydrocephalus.

Complete mitochondrial genome of Ark shell Scapharca subcrenata.

Complete mitochondrial genome of Scapharca subcrenata was determined in this report. It is 48,161 bp in length, being the largest mitochondrial genome among reported shellfish at present. The entire mitochondrial genome consists of 57 genes including 12 protein-coding genes, 2 ribosomal RNAs and 41 transfer RNAs.

Molecular cloning, expression analysis and cellular localization of an LFRFamide gene in the cuttlefish Sepiella japonica.

Neuropeptides are important regulators of physiological processes in metazoans, such as feeding, reproduction, and heart activities. In this study, an LFRFamide gene was identified from the cuttlefish Sepiella japonica (designated as SjLFRFamide). The full-length sequence of SjLFRFamide cDNA has 841bp, and the open reading frame contains 567bp encoding 188 amino acids, which shared high similarity with precursor SOFaRP2 from Sepia officinalis. The deduced SjLFRFamdie precursor protein contains a signal peptide and four different FLPs (FMRFamide-like peptides): one pentapeptide (TIFRFamide), two hexapeptides (NSLFRFamide and GNLFRFamide) and one heptapeptide (PHTPFRFamide). Multiple sequence alignment showed that SjLFRFamide contains rather conserved mature peptides, which all ended in FRF. The phylogenetic analysis suggests that SjLFRFamide belongs to the LFRFamide subfamily. The tissue distribution analysis through quantitative real-time PCR method showed that SjLFRFamide mRNA is significantly expressed in the brain, and slight trace are detected in female nidamental gland and accessory nidamental gland. In situ hybridization assay of the brain indicated that SjLFRFamide is transcribed in several different functional lobes, suggesting SjLFRFamide might associate with multiple physiological regulations, such as feeding, chromatophore regulation and reproduction. This is the first study describing LFRFamide in S. japonica, which might have great importance for cuttlefish artificial breeding.

Downregulation of rho-associated protein kinase 1 by miR-124 in colorectal cancer.

AIM: To investigate the roles and interactions of rho-associated protein kinase (ROCK)1 and miR-124 in human colorectal cancer (CRC). METHODS: Expression of ROCK1 protein was examined by Western blotting, and quantitative reverse transcriptase PCR was performed to measure expression of ROCK1 mRNA and miR-124. Two cancer cell lines were transfected with pre-miR-124 (mimic) and anti-miR-124 (inhibitor) and the effects on ROCK1 protein and mRNA expression were observed. In addition, cell proliferation was assessed via a 5-ethynyl-2' deoxyuridine assay. Soft agar formation assay, and cell migration and invasion assays were used to determine the effect of survivin on the transformation and invasion activity of CRC cells. RESULTS: miR-124 was significantly downregulated in CRC compared to normal specimens (0.603 ± 0.092 vs 1.147 ± 0.286, P = 0.016) and in metastatic compared to nonmetastatic CRC specimens (0.416 ± 0.047 vs 0.696 ± 0.089, P = 0.020). Expression of miR-124 was significantly associated with CRC metastasis, tumor T and N stages, and tumor grade (all P < 0.05). ROCK1 protein was significantly increased in CRC compared to normal tissues (1.896 ± 0.258 vs 0.866 ± 0.136, P = 0.026), whereas ROCK1 mRNA expression was unaltered (2.613 ± 0.251 vs 2.325 ± 0.246). miR-124 and ROCK1 were inversely expressed in CRC tissues and cell lines. ROCK1 mRNA was unaltered in cells transfected with miR-124 mimic and miR-124 inhibitor, compared to normal controls. There was a significant reduction in ROCK1 protein in cells transfected with miR-124 mimic and a significant increase in cells transfected with miR-124 inhibitor (Ps < 0.05). Transformation and invasion of cells transfected with miR-124 inhibitor were significantly increased compared to those in normal controls (P < 0.05). Cells transfected with miR-124 inhibitor showed increased cell proliferation. CONCLUSION: miR-124 promotes hyperplasia and contributes to invasion of CRC cells, but downregulates ROCK1. ROCK1 and miR-124 may play important roles in CRC.

Reduced expression of circulating microRNA-218 in gastric cancer and correlation with tumor invasion and prognosis.

AIM: To investigate the expression of microRNA-218 (miR-218) in serum from gastric cancer patients and its relationship with clinicopathological characteristics. METHODS: A total of 68 patients with pathologically diagnosed gastric cancer and 56 healthy individuals were recruited to this study. The expression of miR-218 was detected in the serum of gastric cancer patients and healthy individuals by quantitative real-time polymerase chain reaction. The clinical data were collected and analyzed by statistical software. RESULTS: miR-218 was reduced significantly in the serum of gastric cancer patients compared to healthy individuals (1.15 ± 0.08 vs 0.37 ± 0.023; P = 0.026). In the gastric cancer group, serum expression of miR-218 was lower in patients with metastasis and poorly differentiated cancer compared with non-metastatic and well-differentiated cancer (0.19 ± 0.011 vs 0.45 ± 0.021, P = 0.031 and 0.21 ± 0.019 vs 0.49 ± 0.021, P = 0.025). Serum miR-218 was found to be significantly associated with gastric cancer metastasis (P = 0.003), tumor T stage (P = 0.018) and tumor grade (P = 0.012). Low serum expression of miR-218 was related to an increase in the stage of gastric cancer. The expression level of miR-218 in the serum was correlated with the 3-year survival. Ninety-seven percent of patients with a high level of miR-218 expression survived for 3 years, while only 54% of those with low miR-218 expression survived. CONCLUSION: miR-218 is deregulated in gastric cancer patients and is strongly correlated with tumor stage, grade and metastasis. Serum expression of miR-218 may be a prognostic marker.

The complete mitochondrial genome of the pen shell Atrina pectinata (Mollusca: Bivalvia: Pinnidae): the first representative from the family Pinnidae.

In this study, we described the complete mitochondrial genome of the pen shell Atrina pectinata. It was 16,811 bp in length and consisted of 35 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 21 transfer RNAs (trnS2 and atp8 lacked). All genes were encoded on the same strand. In gene order, there was no completely identical block compared to those of Mytilus edulis, Crassostrea gigas, Chlamys farreri and Venerupis philippinarum. It may be a ground pattern of Pinnidae mitochondrial genomes.

[Effect of slice thickness on drying process of Polygonum multiflorum root tuber].

OBJECTIVE: To study the effect of slice thickness on drying process of Polygonum multiflorum root tuber. METHODS: The root tuber of Polygonum multiflorum was sliced with thickness of 2, 5 and 8 mm. Drying experiments were conducted at temperatures of 45, 55, 65 and 75 degrees C. The experimental data were fitted to ten thin-layer drying models to select a suitable model for describing the drying characteristic of Polygonum multiflorum root tuber. Based on thin-layer drying theory, the kinetics parameters of drying process were calculated. RESULTS: The drying processes of Polygonum multiflorum root tuber were consisted of two regions, 1st and 2nd falling rate periods when the slice thickness was thick or the drying temperature was high. Aghbashlo model was the best one to describe its drying behavior. The variation of thickness had significant effect on effective moisture diffusivity (D), but had little effect on activation energy E(a). CONCLUSION: Thin-layer drying theory can be an effective tool for the study of drying behavior of Polygonum multiflorum root tuber. The result provides experimental basis for the quality control of Polygonum multiflorum root tuber drying process.

[Seasonal influence on the diagnosis of food allergy in children less than 3 years of age].

OBJECTIVE: To investigate the seasonal influence on the diagnosis of food allergy in children under 3 years of age. METHOD: The data of epidemiological studies about food allergy of children under 3 years of age attending routine well-baby checks at the Department of Primary Child Care, Children's Hospital of Chongqing Medical University in the winter and summer, 2009, including questionnaires, results of skin prick test (SPT), food elimination and oral food challenge (OFC) were analyzed. All the data were analyzed by SPSS 17.0. RESULT: The age and sex distribution, and both the rates of the drop-out in two studies were similar. Ninety infants were positive for SPT, 40 infants were positive for OFC, and 31 infants dropped out in winter; while 65 infants were positive for SPT, 25 positive for OFC, and 31 dropped out in summer. The percentage of positive SPT in the children performed in winter was higher than that in summer (14.9%, 90/603 vs 10.7%, 65/607) (P = 0.028). Skin prick test accuracy was similar when the studies were performed in winter and in summer [sensitivity 0.85 and 0.84, positive predictive value (PPV) 0.54 and 0.47, negative predictive value (NPV) 0.99 and 0.99]. The prevalence of food allergy in the children studied in winter was higher than that in summer (7.0% vs 4.3%), but the difference was not significant. After correcting the prevalence for dropout children, the prevalence of food allergy (FA) investigated in winter was significantly higher than that in summer (9.3% vs 5.9%). The results of circular distribution analysis showed the date of birth corresponding to estimated value of peak point of SPT in winter were not consistent with it in summer, so was OFC. Either the results of skin prick test or oral food challenge in two studies were not correlated with the seasons of birth. CONCLUSION: Our data showed that the rates of positive SPT and the prevalence of food allergy were correlated with the seasons, but the seasons of birth did not influence the results of skin prick test or oral food challenge in children, while the real age of children were related to them.