RNA-seq analysis provides insight into molecular adaptations of Andrias davidianus.

The Chinese giant salamander Andrias davidianus is regarded as an ideal model for studying local adaptations, such as longevity, tolerance to starvation, and cutaneous respiration. Transcriptome analysis is useful for studying the large and complex genomes of amphibians. Based on the coding gene set of adult A. davidianus, dozens of A. davidianus-specific genes were identified and three signaling pathway (JAK-STAT, HIF-1, and FoxO) genes were expanded as compared with other amphibians. The results of the pathway analysis of A. davidianus-specific genes indicated that the molecular adaptation of A. davidianus may have required a more rapid evolution of the immune system. Additionally, for the first time, the gene expressions in different parts of the skin tissue were compared. The results of the comparison analysis demonstrated that lateral skin could be more focused on mucus secretion, dorsal skin on immunity and melanogenesis, and abdominal skin on water and salt metabolism. This study provides the first insight into studying longevity and starvation tolerance in A. davidianus, and offers a basis for further investigation of the molecular mechanisms of adaptations in amphibians.

Differential proteome analysis of the cell differentiation regulated by BCC, CRH, CXCR4, GnRH, GPCR, IL1 signaling pathways in Chinese fire-bellied newt limb regeneration.

Following amputation, the newt has the remarkable ability to regenerate its limb, and this process involves dedifferentiation, proliferation and differentiation. To investigate the potential proteome during a dynamic network of Chinese fire-bellied newt limb regeneration (CNLR), two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrum (MS) were applied to examine changes in the proteome that occurred at 11 time points after amputation. Meanwhile, several proteins were selected to validate their expression levels by Western blot. The results revealed that 1476 proteins had significantly changed as compared to the control group. Gene Ontology annotation and protein network analysis by Ingenuity Pathway Analysis 9.0 (IPA) software suggested that the differentially expressed proteins were involved in 33 kinds of physiological activities including signal transduction, cell proliferation, cell differentiation, etc. Among these proteins, 407 proteins participated in cell differentiation with 212 proteins in the differentiation of skin cell, myocyte, neurocyte, chondrocyte and osteocyte, and 37 proteins participated in signaling pathways of BCC, CRH, CXCR4, GnRH, GPCR and IL1 which regulated cell differentiation and redifferentiation. On the other hand, the signal transduction activity and cell differentiation activity were analyzed by IPA based on the changes in the expression of these proteins. The results showed that BCC, CRH, CXCR4, GnRH, GPCR and IL1 signaling pathways played an important role in regulating the differentiation of skin cell, myocyte, neurocyte, chondrocyte and osteocyte during CNLR.

Study on the activity of the signaling pathways regulating hepatocytes from G0 phase into G1 phase during rat liver regeneration.

Under normal physiological conditions, the majority of hepatocytes are in the functional state (G0 phase). After injury or liver partial hepatectomy (PH), hepatocytes are rapidly activated to divide. To understand the mechanism underlying hepatocyte G0/G1 transition during rat liver regeneration, we used the Rat Genome 230 2.0 Array to determine the expression changes of genes, then searched the GO and NCBI databases for genes associated with the G0/G1 transition, and QIAGEN and KEGG databases for the G0/G1 transition signaling pathways. We used expression profile function (E t ) to calculate the activity level of the known G0/G1 transition signal pathways, and Ingenuity Pathway Analysis 9.0 (IPA) to determine the interactions among these signaling pathways. The results of our study show that the activity of the signaling pathways of HGF, IL-10 mediated by p38MAPK, IL-6 mediated by STAT3, and JAK/STAT mediated by Ras/ERK and STAT3 are significantly increased during the priming phase (2-6 h after PH) of rat liver regeneration. This leads us to conclude that during rat liver regeneration, the HGF, IL-10, IL-6 and JAK/STAT signaling pathways play a major role in promoting hepatocyte G0/G1 transition in the regenerating liver.

Robust Immune Responses Elicited by a Hybrid Adjuvant Based on ß-Glucan Particles from Yeast for the Hepatitis B Vaccine.

The use of particulate adjuvants offers an interesting method for enhancing and modulating the immune responses elicited by vaccines. Aluminum salt (Alum) is one of the most important immune adjuvants approved by the Food and Drug Administration for use in humans because of its safety and efficacy, but it lacks the capacity to induce strong cellular and mucosal immune responses. In this study, we designed an antigen delivery system that combines aluminum salts with ß-glucan particles. The ß-glucan-aluminum particles (GP-Al) exhibited a highly uniform size of 2-4 µm and could highly specifically target antigen-presenting cells (APCs) and strongly induce dendritic cell (DC) maturation and cytokine secretion. In vivo studies showed that both WT mice and HBV-Tg mice immunized with hepatitis B surface antigen (HBsAg)-containing GP-Al displayed high anti-HBsAg IgG titers in the serum. Furthermore, in contrast to mice receiving the antigen alone, mice immunized with the particulate adjuvant exhibited IgG2a antibody titers and higher antigen-specific IFN-γ levels in splenocytes. In conclusion, we developed GP-Al microspheres to serve as a hepatitis B vaccine to enhance both humoral and cellular immune responses, representing a safe and promising system for antigen delivery.

Effects of different CT angiography technology-based nursing methods on patients with coronary artery heart diseases.

To study the nursing effects of different CT angiography (CTA) technology-based nursing methods on patients with coronary artery heart diseases (CHD), CHD patients treated in Dongying People's Hospital were selected as the research objects and were divided into the control group and the observation group. Different coronary CTA nursing methods, i.e. the routine nursing and the psychological nursing, were performed to the control group and the observation group respectively. During the experiment, patients performed self-evaluations, which included the Self-rating Anxiety Scale (SAS) and the Self-rating Depression Scale (SDS). Biological indicators of patients, including heart rate (HR), diastolic blood pressure (DBP), and systolic blood pressure (SBP), were measured before and after patients accepted different nursing methods. In addition, the quality of coronary CTA images was evaluated. The results showed that HR, DBP, SBP, SAS scores, and SDS scores of patients in the observation group were obviously lower than those in the control group, and the differences were statistically significant, besides, the image quality of the observation group was significantly greater than that of the control group, which was helpful for diagnosis and had statistical significances. Therefore, it is proved that the psychological nursing of CHD patients can effectively reduce the negative emotions of patients, such as anxiety and depression, which is conducive to CTA and can assist clinical diagnosis. The results provide a basis and ideas for more accurate research in the future.

Long non-coding RNA FAM99A modulated YAP1 to affect trophoblast cell behaviors in preeclampsia by sponging miR-134-5p.

Preeclampsia (PE) is a complex pregnancy syndrome. Convincing evidence indicates that long non-coding RNAs (lncRNAs) are involved in the pathogenesis of PE. This research mainly investigated the mechanism of family with sequence similarity 99 member A (FAM99A) in PE. The expressions of FAM99A, miR-134-5p, and YAP1 were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell apoptosis, migration, and invasion were detected by flow cytometry or transwell assay. The interaction between miR-134-5p and FAM99A or YAP1 was confirmed by dual-luciferase reporter assay. The protein expression of YAP1 was determined by western blot assay. FAM99A and YAP1 were significantly up-regulated, and miR-134-5p was significantly down-regulated in PE tissues (n=30). miR-134-5p was verified as a candidate of FAM99A and YAP1. FAM99A promoted cell metastasis, but reduced apoptosis in HTR8/SVneo cells by regulating miR-134-5p. miR-134-5p down-regulated YAP1 expression to suppress cell metastasis, while it induced apoptosis in HTR8/SVneo cells. FAM99A positively modulated YAP1 expression by sponging miR-134-5p. FAM99A modulated YAP1 to accelerate cell migration and invasion, and inhibited cell apoptosis in PE cells by sponging miR-134-5p. The novel regulatory network may shed light on the pathogenesis of PE.

Differential Proteomic Analysis of Chinese Giant Salamander Liver in Response to Fasting.

Chinese giant salamander Andrias davidianus has strong tolerance to starvation. Fasting triggers a complex array of adaptive metabolic responses, a process in which the liver plays a central role. Here, a high-throughput proteomic analysis was carried out on liver samples obtained from adult A. davidianus after 3, 7, and 11 months of fasting. As a result, the expression levels of 364 proteins were significantly changed in the fasted liver. Functional analysis demonstrated that the expression levels of key proteins involved in fatty acid oxidation, tricarboxylic acid cycle, gluconeogenesis, ketogenesis, amino acid oxidation, urea cycle, and antioxidant systems were increased in the fasted liver, especially at 7 and 11 months after fasting. In contrast, the expression levels of vital proteins involved in pentose phosphate pathway and protein synthesis were decreased after fasting. We also found that fasting not only activated fatty acid oxidation and ketogenesis-related transcription factors PPARA and PPARGC1A, but also activated gluconeogenesis-related transcription factors FOXO1, HNF4A, and KLF15. This study confirms the central role of lipid and acetyl-CoA metabolism in A. davidianus liver in response to fasting at the protein level and provides insights into the molecular mechanisms underlying the metabolic response of A. davidianus liver to fasting.

Selective and sensitive detection of chronic myeloid leukemia using fluorogenic DNAzyme probes.

One of the major challenges facing the early diagnosis of chronic myelogenous leukemia (CML) patients today is enhancing the simplicity, rapidness, sensitivity and specificity of detection assay for easy clinical implementation. RNA-cleaving fluorogenic DNAzymes (RFDs) are single-stranded DNA molecules with catalytic activity and can produce fluorescent signals when combined with specific targets. As K562 cells were the first established human immortalized myelogenous leukemia line, we try to screen several RFDs using the crude extracellular mixture of K562 cells through the SELEX process. We obtained an RFD probe A1-3 that is able to distinguish K562 cells from other tumor cell lines. 10 nM of A1-3 can induce an increase of detectable fluorescence signal. Moreover, the RFD assay system can work well for target detection in complex serum matrix. The optimized RFD assay system with low cost also has a desirable ability to exactly distinguish K562 cells after truncation of 20 bases in the 5'end of A1-3. This study is the first report to investigate the RFD system for detection of K562 cells using cell culture supernatants as the complex target. This RFD assay system could potentially be applied for the diagnosis of CML.

Proteomic analysis of eleven tissues in the Chinese giant salamander (Andrias davidianus).

The Chinese giant salamander (Andrias davidianus, CGS) is the largest extant amphibian species in the world. Global quantitative proteome analysis of multiple tissues would indicate tissue-specific physiological processes and clarify the function of each protein from a whole-organism perspective. This study performed proteome analysis of eleven tissues collected from adult CGSs using iTRAQ coupled with LC-MS/MS technology. Based on the predicted protein database from previously obtained CGS transcriptome data, 2153 proteins were identified for subsequent analysis. A weighted gene co-expression network analysis (WGCNA) clustered 2153 proteins into 17 co-expressed modules, which will be useful for predicting the functions of unannotated proteins. The protein levels of molecular complexes with housekeeping functions, such as ribosomes, spliceosomes and mitochondrial respiratory chain complexes, were tightly regulated in different tissues of the CGS, as they are in mammalian tissues. Transcription regulator, pathway and bio-functional analysis of tissue-specific proteins showed that highly expressed proteins largely reflected the physiological functions of specific tissues. Our data, as an initial atlas of protein expression of an amphibian species, will be useful for further molecular biology research on CGS.

A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus.

BACKGROUND: Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ∼50 GB making it extremely difficult to be assembled. RESULTS: We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog. CONCLUSIONS: These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.

Proteomic analysis of the skin from Chinese fire-bellied newt and comparison to Chinese giant salamander.

Animal skin that directly interfaces with the external environment has developed diverse adaptive functions to a variety of ecological conditions laden with pathogenic infection and physical harm. Amphibians exhibit various adaptations related to their "incomplete" shift from the aquatic to the terrestrial habitat. Therefore, it is very necessary to explore the molecular basis of skin function and adaptation in amphibians. Currently, the studies on the molecular mechanisms of skin functions in anuran amphibians have been reported, but in urodele amphibians are rare. This study identified the skin proteomes of Chinese fire-bellied newt Cynops orientalis by a proteomic method, and compared the results to the skin proteomes of Chinese giant salamander Andrias davidianus obtained previously. A total of 452 proteins were identified in the newt skin by MALDI-TOF/MS, and functional annotation results by DAVID analysis showed that special functions such as wound healing, immune response, defense and respiration, were significantly enriched. Comparison results showed that the two species had a great difference in the aspects of protein kinds and abundance, and the highly expressed proteins may tightly correlate with living conditions. Moreover, the newt skin might have stronger immunity, but weaker respiration than the giant salamander skin to adapt to various living environments. This research provides a molecular basis for further studies on amphibian skin function and adaptation.

Overexpression of transcription factor Foxa2 and Hnf1α induced rat bone mesenchymal stem cells into hepatocytes.

Hepatocytes differentiated from induced pluripotent stem cells and adult stem cells could be utilized as a tool for the study of liver diseases, screening for drug metabolism and hepatotoxicity. Thus further investigation of the method to efficiently generate hepatocytes is in great need. Bone Mesenchymal Stem Cells (BMSCs) were collected from rat femurs and tibias. FOXA2 and HNF1α genes were constructed into a lentiviral vector and introduced into BMSCs by a lentivirus-mediated overexpression system. Three weeks after the induction, the expressions of FOXA2 and HNF1α, and liver specific genes were analyzed, and hepatocyte-function related assays were performed. Overexpression of both FOXA2 and HNF1α induced the BMSCs to differentiate into hepatocyte-like cells (HLCs). Hepatocyte-specific gene and protein were detected by RT-PCR, Western Blot and Immunofluorescence. These HLCs also exerted some typical hepatocyte functions such as glycogen storage, indocyanine green absorption and lipid accumulation. The combination of FOXA2 and HNF1α can effectively induce BMSCs to differentiate into HLCs. This is a novel and efficient method to prepare HLCs within a short timeline.

Integrative proteomic and microRNA analysis of the priming phase during rat liver regeneration.

The partial hepatectomy (PH) model provides an effective medium for study of liver regeneration (LR). Considering that LR is regulated by microRNAs (miRNAs), investigation of the regulatory role of miRNAs is critical for revealing how regenerative processes are initiated and controlled. Using high-throughput sequencing technology, we examined miRNA expression profiles of the regenerating rat liver after PH, and found that 23 miRNAs were related to rat LR. Among them, several miRNAs were significantly altered at 2h and 6h after PH, corresponding to the priming phase of LR. Furthermore, we examined the protein profiles in the regenerating rat liver at 2h and 6h after PH by iTRAQ coupled with LC-MS/MS, and found that 278 proteins were significantly changed. Subsequently, an integrative proteomic and microRNA analysis by Ingenuity Pathway Analysis 9.0 (IPA) software showed that miR-125a, miR-143, miR-150, miR-181c, miR-182, miR-183, miR-199a, miR-429 regulated the priming phase of rat LR by modulating the expression of proteins involved in networks critical for cell apoptosis, cell survival, cell cycle, inflammatory response, metabolism, etc. Thus, our studies provide novel evidence for a functional molecular network populated by the down-regulated targets of the up-regulated miRNAs in the priming phase of rat LR.

High-Level Secretory Expression and Purification of Recombinant Human Interleukin 1 Beta in Pichia pastoris.

As an important pro-inflammatory cytokine, interleukin-1beta (IL-1ß) participates in a variety of physiological and pathological responses. In order to obtain higher yielded recombinant human interleukin-1 beta (rhIL-1ß), we cloned hIL-1ß cDNA sequences based on the coding sequence of human mature IL-1ß. After recombinant pPICZαA/hIL-1ß was separated and sequenced, we transformed recombinant pPICZαA/hIL-1ß into Pichia pastoris GS115, SMD1168 and X-33 strain via electroporation. The results showed that recombinant pPICZαA/ hIL-1ß had the highest expression level in X-33 Pichia pastoris. Subsequently, rhIL-1ß was purified by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and identified by Western blot. Then the fermentation process was optimized to increase product yield. Under the fermentation conditions of the absorption value of fermentation liquor before induction of 600, oxygen concentration of 20%, methanol concentration of 0.25% with pH 5.0, the yield of rhIL-1ß reached to 250 mg/L after 72 h induction at 26°C. After aqueous two-phase extraction combined with chromatography, the purity of rhIL-1ß was 95% and the yield was up to 85%. The biological activity of rhIL-1ß was detected by MTT assay, and the result showed that rhIL-1ß significantly inhibited the growth and proliferation of B16 melanoma cells.

Long non-coding RNA FAM99A modulated YAP1 to affect trophoblast cell behaviors in preeclampsia by sponging miR-134-5p

Preeclampsia (PE) is a complex pregnancy syndrome. Convincing evidence indicates that long non-coding RNAs (lncRNAs) are involved in the pathogenesis of PE. This research mainly investigated the mechanism of family with sequence similarity 99 member A (FAM99A) in PE. The expressions of FAM99A, miR-134-5p, and YAP1 were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell apoptosis, migration, and invasion were detected by flow cytometry or transwell assay. The interaction between miR-134-5p and FAM99A or YAP1 was confirmed by dual-luciferase reporter assay. The protein expression of YAP1 was determined by western blot assay. FAM99A and YAP1 were significantly up-regulated, and miR-134-5p was significantly down-regulated in PE tissues (n=30). miR-134-5p was verified as a candidate of FAM99A and YAP1. FAM99A promoted cell metastasis, but reduced apoptosis in HTR8/SVneo cells by regulating miR-134-5p. miR-134-5p down-regulated YAP1 expression to suppress cell metastasis, while it induced apoptosis in HTR8/SVneo cells. FAM99A positively modulated YAP1 expression by sponging miR-134-5p. FAM99A modulated YAP1 to accelerate cell migration and invasion, and inhibited cell apoptosis in PE cells by sponging miR-134-5p. The novel regulatory network may shed light on the pathogenesis of PE.

iTRAQ-based proteomic analysis of adaptive response in the regenerating limb of the Cynops orientalis newt.

The newt has the powerful capacity to regenerate lost limbs following amputation, and represents an excellent model organism to study regenerative processes. However, the molecular basis of the adaptive response in the regenerating limb of the Chinese fire-bellied newt Cynops orientalis immediately after amputation remains unclear. To better understand the adaptive response immediately after limb amputation at the protein level, we used isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS methods to analyze changes in the proteome of the regenerating newt limb that occurred 2 h and 8 h after amputation. We identified 152 proteins with more than 1.5-fold change in expression compared to control. GO annotation analysis classified these proteins into several categories such as signaling, Ca(2+) binding and translocation, transcription and translation, immune response, cell death, cytoskeleton, metabolism, etc. Further ingenuity pathway analysis (IPA) showed that several signaling pathways were significantly changed at 2 h and 8 h after amputation, including EIF2 signaling, acute phase response signaling, tight junction signaling and calcium signaling, suggesting these pathways may be closely related to the adaptive response immediately after limb amputation. This work provides novel insights into understanding the molecular processes related to newt limb regeneration immediately after amputation, and a basis for further study of regenerative medicine.

Proteomic analysis of the skin of Chinese giant salamander (Andrias davidianus).

The Chinese giant salamander (Andrias davidianus), renowned as a living fossil, is the largest and longest-lived amphibian species in the world. Its skin has developed mucous gland which could secrete a large amount of mucus under the scraping and electric stimulation, and the molting is the degraded skin stratum corneum. Although several proteomic studies have focused on functional proteomes of mammalian and frog skin, the skin proteome of Chinese giant salamander has not yet been carefully studied. To establish the functional skin proteome of Chinese giant salamander, two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) were applied to detect the composition and relative abundance of the proteins in the skin, mucus and molting. Our findings indicated that 249 proteins were identified in the skin, 155 proteins in the mucus, and 97 proteins in the molting. Furthermore, Gene Ontology (GO) analysis showed that these proteins participated in various physiological activities, including extracellular matrix organization, defense, immune response, wound healing, respiration, etc. In conclusion, the proteomic results provide new insight in the aspects of the proteomes in the skin, mucus and the molting of Chinese giant salamander. BIOLOGICAL SIGNIFICANCE: This was the first study to examine the protein expression abundance in the skin, mucus and molting of Chinese giant salamander by a proteomics approach. Meantime, the identification of a more global proteome in normal skin may provide a basis for characterizing and comparing the skin proteomes from other amphibian species.

Data from proteomic analysis of the skin of Chinese giant salamander (Andrias davidianus).

The Chinese giant salamander (Andrias davidianus), renowned as a living fossil, is the largest and longest-lived amphibian species in the world. Its skin is rich in collagens, and has developed mucous gland which could secrete a large amount of mucus under the scraping and electric stimulation. The molting is the degraded skin stratum corneum. To establish the functional skin proteome of Chinese giant salamander, two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) were applied to detect the composition and relative abundance of the proteins in the skin, mucus and molting. The determination of the general proteome in the skin can potentially serve as a foundation for future studies characterizing the skin proteomes from diseased salamander to provide molecular and mechanistic insights into various disease states and potential therapeutic interventions. Data presented here are also related to the research article "Proteomic analysis of the skin of Chinese giant salamander (Andrias davidianus)" in the Journal of Proteomics [1].

iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians.

The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians.

Glyoxalase I in tumor cell proliferation and survival and as a potential target for anticancer therapy.

Glyoxalase I (GLO1) belongs to the glyoxalase system, which catalyzes the conversion of deleterious methylglyoxal, mainly produced by glycolysis, to non-toxic D-lactate. The expression of GLO1 was up-regulated in tumor tissues with high metabolic rate, whereas inhibition of GLO1 expression led to the accumulation of glyoxal and methylglyoxal, significantly inducing cell damage or apoptosis. This suggests that GLO1 may play an important role in tumor cell proliferation and survival, and may represent a potential therapeutic target for tumors. Moreover, overexpression of GLO1 was associated with multidrug resistance in cancer chemotherapy. This review describes the role of GLO1 in tumor cell proliferation and survival, and the potential of GLO1 as a biomarker for tumor diagnosis and as a target for anticancer drug development.