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1.  Instability of Succinate Dehydrogenase in SDHD Polymorphism Connects Reactive Oxygen Species Production to Nuclear and Mitochondrial Genomic Mutations in Yeast 
Antioxidants & Redox Signaling  2015;22(7):587-602.
Abstract
Aims: Mitochondrial succinate dehydrogenase (SDH) is an essential complex of the electron transport chain and tricarboxylic acid cycle. Mutations in the human SDH subunit D frequently lead to paraganglioma (PGL), but the mechanistic consequences of the majority of SDHD polymorphisms have yet to be unraveled. In addition to the originally discovered yeast SDHD subunit Sdh4, a conserved homolog, Shh4, has recently been identified in budding yeast. To assess the pathogenic significance of SDHD mutations in PGL patients, we performed functional studies in yeast. Results: SDHD protein expression was reduced in SDHD-related carotid body tumor tissues. A BLAST search of SDHD to the yeast protein database revealed a novel protein, Shh4, that may have a function similar to human SDHD and yeast Sdh4. The missense SDHD mutations identified in PGL patients were created in Sdh4 and Shh4, and, surprisingly, a severe respiratory incompetence and reduced expression of the mutant protein was observed in the sdh4Δ strain expressing shh4. Although shh4Δ cells showed no respiratory-deficient phenotypes, deletion of SHH4 in sdh4Δ cells further abolished mitochondrial function. Remarkably, sdh4Δ shh4Δ strains exhibited increased reactive oxygen species (ROS) production, nuclear DNA instability, mtDNA mutability, and decreased chronological lifespan. Innovation and Conclusion: SDHD mutations are associated with protein and nuclear and mitochondrial genomic instability and increase ROS production in our yeast model. These findings reinforce our understanding of the mechanisms underlying PGL tumorigenesis and point to the yeast Shh4 as a good model to investigate the possible pathogenic relevance of SDHD in PGL polymorphisms. Antioxid. Redox Signal. 22, 587–602.
doi:10.1089/ars.2014.5966
PMCID: PMC4334101  PMID: 25328978
2.  Imbalance of Th17/Tregs in rats with smoke inhalation-induced acute lung injury 
Scientific Reports  2016;6:21348.
T helper (Th) 17 cells and CD4+ CD25+ regulatory T (Treg) cells are supposed to be critically involved in regulating autoimmune and inflammatory diseases. The aim of this study was to investigate the Th17/Treg pattern in rats with gunpowder smog-induced acute lung injury. Wistar rats were equally randomized to three groups: normal control group, ALI 6 h group (smoke inhalation for 6 h) and ALI 24 h group (smoke inhalation for 24 h). We observed changes in cell counting in bronchoalveolar lavage fluid (BALF), alveolar-capillary membrane permeability and lung tissue pathology. Moreover, rats in ALI 6 h and ALI 24 h group showed increased expression of Th17 cell and related cytokines (IL-17 A, IL-6, TGF-β and IL-23). Meanwhile, Treg prevalence and related cytokines (IL-10, IL-2 and IL-35) were decreased. Consequently, the ratio of Th17/Treg was higher after smoke inhalation. Additionally, Th1 cell decreased while Th2 cell increased at 6 h and 24 h after smoke inhalation. In conclusion, Th17/Treg imbalance exists in rats with smoke inhalation-induced acute lung injury, suggesting its potential role in the pathogenesis of this disease.
doi:10.1038/srep21348
PMCID: PMC4756332  PMID: 26884314
3.  Systematic manipulation of glutathione metabolism in Escherichia coli for improved glutathione production 
Background
l-glutathione (GSH) is a non-protein thiol compound with important biological properties and is widely used in pharmaceutical, food, cosmetic and health products. The cellular GSH is determined by the activity and characteristic of GSH-synthesizing enzymes, energy and precursor supply, and degradation of formed GSH.
Results
In this study, genes encoding enzymes related to the precursor amino acid degradation and glycogen formation as well as GSH degradation were systematically manipulated in Escherichia coli strains over-expressing gshF from Actinobacillus succinogenes. The manipulation included disrupting the precursor degradation pathways (tnaA and sdaA), eliminating l-glutathione degradation (ggt and pepT), and manipulating the intracellular ATP level (disruption of glgB). However the constructed mutants showed lower levels of GshF expression. 2-D electrophoresis was performed to elucidate the reasons for this discrepancy, and the results indicated obvious changes in central metabolism and amino acid metabolism in the penta-mutant. Fed-batch culture of the penta-mutant ZJ12345 was performed where the GshF expression level was enhanced, and both the GSH production (19.10 mM) and the yield based on added l-cysteine (0.76 mmol/mmol) were significantly increased.
Conclusion
By interrupting the degradation pathways of l-cysteine, serine and GSH and blocking glycogen formation, the GSH production efficiency was significantly improved.
doi:10.1186/s12934-016-0439-1
PMCID: PMC4754818  PMID: 26883423
Escherichia coli; Glutathione; Systematic manipulation; Bifunctional glutathione synthetase; Fed-batch fermentation
4.  ROCK1 Induces Endothelial-to-Mesenchymal Transition in Glomeruli to Aggravate Albuminuria in Diabetic Nephropathy 
Scientific Reports  2016;6:20304.
Endothelial-to-mesenchymal transition (EndMT) can cause loss of tight junctions, which in glomeruli are associated with albuminuria. Here we evaluated the role of EndMT in the development of albuminuria in diabetic nephropathy (DN). We demonstrated that EndMT occurs in the glomerular endothelium of patients with DN, showing by a decrease in CD31 but an increase in α-SMA expression. In glomeruli of db/db mice, there was an increased ROCK1 expression in the endothelium plus a decreased CD31-positive cells. Cultured glomerular endothelial cells (GEnCs) underwent EndMT when stimulated by 30 mM glucose, and exhibited increased permeability. Meanwhile, they showed a higher ROCK1 expression and activation. Notably, inhibition of ROCK1 largely blocked EndMT and the increase in endothelial permeability under this high-glucose condition. In contrast, overexpression of ROCK1 induced these changes. Consistent alterations were observed in vivo that treating db/db mice with the ROCK1 inhibitor, fasudil, substantially suppressed the expression of α-SMA in the glomerular endothelium, and reduced albuminuria. Thus we conclude that ROCK1 is induced by high glucose and it stimulates EndMT, resulting in increased endothelial permeability. Inhibition of ROCK1 could be a therapeutic strategy for preventing glomerular endothelial dysfunction and albuminuria in developing DN.
doi:10.1038/srep20304
PMCID: PMC4740844  PMID: 26842599
5.  Increased serum microRNAs are closely associated with the presence of microvascular complications in type 2 diabetes mellitus 
Scientific Reports  2016;6:20032.
Circulating microRNAs (miRNAs) are emerging biomarkers for type 2 diabetes mellitus (T2DM). However, a comprehensive characterization of the serum miRNA profile in patients with T2DM-associated microvascular disease (T2DMC) has rarely been reported. In this study, we obtained serum samples from 184 T2DM patients (92 with microvascular complications and 92 free of complications) and 92 age/gender-matched controls. The levels of 754 miRNAs were initially analyzed using a TaqMan Low Density Array (TLDA) in three pooled samples from 24 T2DM patients, 24 T2DMC patients and 24 controls. Markedly upregulated miRNAs in the patients’ groups were subsequently validated individually by quantitative reverse-transcription PCR (RT-qPCR) in the same samples used for TLDA and further confirmed in another larger cohort consisting of 68 patients with T2DM, 68 patients with T2DMC and 68 controls. Five miRNAs were significantly upregulated in T2DM patients (p < 0.05) including miR-661, miR-571, miR-770-5p, miR-892b and miR-1303. Moreover, the levels of the five miRNAs were higher in patients with complications than in those without complications. Regression analyses revealed the five miRNAs were significantly correlated with microvascular complications (p < 0.05). The five serum miRNAs identified in our study hold potential as auxiliary biomarkers and novel risk factors for T2DM-associated microvascular complications.
doi:10.1038/srep20032
PMCID: PMC4735518  PMID: 26831044
6.  Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition 
Background
Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome.
Results
Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed.
Conclusion
These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.
Electronic supplementary material
The online version of this article (doi:10.1186/s13068-016-0440-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s13068-016-0440-2
PMCID: PMC4731972  PMID: 26834834
Lignocellulose degradation; Metagenomics; Compost ecosystem; Actinobacteria
7.  Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types 
Nature Communications  2016;7:10499.
Cancer-testis (CT) genes represent the similarity between the processes of spermatogenesis and tumorigenesis. It is possible that their selective expression pattern can help identify driver genes in cancer. In this study, we integrate transcriptomics data from multiple databases and systematically identify 876 new CT genes in 19 cancer types. We explore their relationship with testis-specific regulatory elements. We propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms. We find mutually exclusive associations between EECTGs and somatic mutations in mutated genes, such as PIK3CA in breast cancer. We also provide evidence that promoter demethylation and close non-coding RNAs (namely, CT-ncRNAs) may be two mechanisms to reactivate EECTG gene expression. We show that the meiosis-related EECTG (MEIOB) and its nearby CT-ncRNA have a role in tumorigenesis in lung adenocarcinoma. Our findings provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.
Genes normally expressed in the testis but aberrantly expressed in cancer are termed cancer testis antigens. In this study, the authors catalogue the expression of these genes in 19 different cancer types and correlate expression with some somatically mutated oncogenes.
doi:10.1038/ncomms10499
PMCID: PMC4737856  PMID: 26813108
8.  Differentiation of Bone Marrow Mesenchymal Stem Cells in Osteoblasts and Adipocytes and its Role in Treatment of Osteoporosis 
Osteoporosis is a systemic metabolic bone disorder characterized by a decrease in bone mass and degradation of the bone microstructure, leaving bones that are fragile and prone to fracture. Most osteoporosis treatments improve symptoms, but to date there is no quick and effective therapy. Bone marrow mesenchymal stem cells (BMMSCs) have pluripotent potential. In adults, BMMSCs differentiate mainly into osteoblasts and adipocytes in the skeleton. However, if this differentiation is unbalanced, it may lead to a decrease in bone mass. If the number of adipocyte cells increases and that of osteoblast cells decreases, osteoporosis can result. A variety of hormones and cytokines play an important role in the regulation of BMMSCs bidirectional differentiation. Therefore, a greater understanding of the regulation mechanism of BMMSC differentiation may provide new methods to prevent and treat osteoporosis. In addition, autologous, allogeneic BMMSCs or genetically modified BMMSC transplantation can effectively increase bone mass and density, increase bone mechanical strength, correct the imbalance in bone metabolism, and increase bone formation, and is expected to provide a new strategy and method for the treatment of osteoporosis.
doi:10.12659/MSM.897044
PMCID: PMC4727494  PMID: 26795027
Adipocytes; Cell Transplantation; Osteoblasts; Osteoporosis; Stem Cell Research
9.  Pulmonary interstitial cholesterol crystals associated with diffuse lung cysts in adult: a case report and literature review 
Background
Cholesterol pneumonitis or endogenous lipoid pneumonia (ELP) result from the accumulation of endogenous cholesterol esters in the lungs, leading to a fibroblastic interstitial inflammatory process, and may be complicated by a secondary bacterial or fungal infection. Striking features were cholesterol clefts in the alveolar and interstitial spaces and alveolar wall-thickening with lymphocytic infiltrations, which was called pulmonary interstitial and intra-alveolar cholesterol granulomas (PICG).
Case Presentation
We report a case of pneumothorax with diffuse lung cysts and pulmonary interstitial cholesterol in a 26-year-old woman. Our case is unique because development of PICG or ELP has been observed in children, but rarely in adult. Most cases could be linked to exogenous sources like inhalation of lipid material or gastroesophageal reflex (GER). In our case, no signs of GER could be discovered. Diffuse lung cysts coexisting with pulmonary interstitial cholesterol crystals are never reported. Additionally, no multinucleated giant cells or granuloma are found pathologically, which make the diagnosis of PICG or lipoid pneumonia difficult.
Conclusions
Pulmonary interstitial cholesterol crystals may develop gradually and evenly distributed throughout the entire lung and resulted in severe distortion of the native structure of the lung.
doi:10.1186/s13019-016-0397-z
PMCID: PMC4717644  PMID: 26781770
Cholesterol crystals; Endogenous lipoid pneumonia; Lung cysts
10.  Associations of gut-flora-dependent metabolite trimethylamine-N-oxide, betaine and choline with non-alcoholic fatty liver disease in adults 
Scientific Reports  2016;6:19076.
Many studies suggest that trimethylamine-N-oxide (TMAO), a gut-flora-dependent metabolite of choline, contributes to the risk of cardiovascular diseases, but little is known for non-alcoholic fatty liver disease (NAFLD). We examined the association of circulating TMAO, choline and betaine with the presence and severity of NAFLD in Chinese adults. We performed a hospital-based case-control study (CCS) and a cross-sectional study (CSS). In the CCS, we recruited 60 biopsy-proven NAFLD cases and 35 controls (18–60 years) and determined serum concentrations of TMAO, choline and betaine by HPLC-MS/MS. For the CSS, 1,628 community-based adults (40-75 years) completed the blood tests and ultrasonographic NAFLD evaluation. In the CCS, analyses of covariance showed adverse associations of ln-transformed serum levels of TMAO, choline and betaine/choline ratio with the scores of steatosis and total NAFLD activity (NAS) (all P-trend <0.05). The CSS revealed that a greater severity of NAFLD was independently correlated with higher TMAO but lower betaine and betaine/choline ratio (all P-trend <0.05). No significant choline-NAFLD association was observed. Our findings showed adverse associations between the circulating TMAO level and the presence and severity of NAFLD in hospital- and community-based Chinese adults, and a favorable betaine-NAFLD relationship in the community-based participants.
doi:10.1038/srep19076
PMCID: PMC4705470  PMID: 26743949
11.  MicroRNA-26a suppresses epithelial-mesenchymal transition in human hepatocellular carcinoma by repressing enhancer of zeste homolog 2 
Background
Our previous study reported that microRNA-26a (miR-26a) inhibited tumor progression by inhibiting tumor angiogenesis and intratumoral macrophage infiltration in hepatocellular carcinoma (HCC). The direct roles of miR-26a on tumor cell invasion remain poorly understood. In this study, we aim to explore the mechanism of miR-26a in modulating epithelial-mesenchymal transition (EMT) in HCC.
Methods
In vitro cell morphology and cell migration were compared between the hepatoma cell lines HCCLM3 and HepG2, which were established in the previous study. Overexpression and down-regulation of miR-26a were induced in these cell lines, and Western blot and immunofluorescence assays were used to detect the expression of EMT markers. Xenograft nude mouse models were used to observe tumor growth and pulmonary metastasis. Immunohistochemical assays were conducted to study the relationships between miR-26a expression and enhancer of zeste homolog 2 (EZH2) and E-cadherin expression in human HCC samples.
Results
Down-regulation of miR-26a in HCCLM3 and HepG2 cells resulted in an EMT-like cell morphology and high motility in vitro and increased in tumor growth and pulmonary metastasis in vivo. Through down-regulation of EZH2 expression and up-regulation of E-cadherin expression, miR-26a inhibited the EMT process in vitro and in vivo. Luciferase reporter assay showed that miR-26a directly interacted with EZH2 messenger RNA (mRNA). Furthermore, the expression of miR-26a was positively correlated with E-cadherin expression and inversely correlated with EZH2 expression in human HCC tissue.
Conclusions
miR-26a inhibited the EMT process in HCC by down-regulating EZH2 expression.
doi:10.1186/s13045-015-0229-y
PMCID: PMC4702409  PMID: 26733151
microRNA-26a (miR-26a); Hepatocellular carcinoma (HCC); Enhancer of zeste homolog 2 (EZH2); Epithelial-mesenchymal transition (EMT)
12.  Renal and perinephric abscesses in West China Hospital: 10-year retrospective-descriptive study 
World Journal of Nephrology  2016;5(1):108-114.
AIM: To elucidate the clinical, radiological and laboratory profiles of renal abscess (RA) and perinephric abscess (PNA), along with related treatment and outcome.
METHODS: Ninety-eight patients diagnosed with RA or PNA using the primary discharge diagnoses identified from the International Statistical Classification of Diseases and Related Health Problems Tenth Edition (ICD-10) codes (RA: N15.101, PNA: N15.102) between September 2004 and December 2014 in West China Hospital were selected. Medical records including patients’ characteristics, symptoms and signs, high-risk factors, radiological features, causative microorganisms and antibiotic-resistance profiles, treatment approaches, and clinical outcomes were collected and analyzed.
RESULTS: The mean age of the patients was 46.49 years with a male to female ratio of 41:57. Lumbar pain (76.5%) and fever (53.1%) were the most common symptoms. Other symptoms and signs included chills (28.6%), anorexia and vomiting (25.5%), lethargy (10.2%), abdominal pain (11.2%), flank mass (12.2%), flank fistula (2.0%), gross hematuria (7.1%), frequency (14.3%), dysuria (9.2%), pyuria (5.1%) and weight loss (1.0%). Painful percussion of the costovertebral angle (87.8%) was the most common physical finding. The main predisposing factors were lithiasis (48.0%), diabetes mellitus (33.7%) followed by history of urological surgery (16.3%), urinary tract infections (14.3%), renal function impairment (13.3%), liver cirrhosis (2.0%), neurogenic bladder (1.0%), renal cyst (1.0%), hydronephrosis (1.0%), chronic hepatitis B (1.0%), post-discectomy (1.0%) and post-colectomy (1.0%). Ultrasound (US) and computed tomography were the most valuable diagnostic tools and US was recommended as the initial diagnostic imaging choice. Escherichia coli (51.4%), Staphylococcus aureus (10.0%) and Klebsiella pneumoniae (8.6%) were the main causative microorganisms. Intravenous antibiotic therapy was necessary while intervention including surgical and nonsurgical approaches were reserved for larger abscesses, multiple abscesses, PNAs and non-responders.
CONCLUSION: Heightened alertness, prompt diagnosis, and especially proper antibiotics in conjunction with interventional approaches allow a promising clinical outcome of renal and perinephric abscesses.
doi:10.5527/wjn.v5.i1.108
PMCID: PMC4707163  PMID: 26788470
Renal abscess; Causative pathogens; Perinephric abscess; Diagnosis; Antibiotic resistance; Interventional treatment; Conservative treatment
13.  To Operate or Not: Prediction of 3-Month Postoperative Mortality in Geriatric Cancer Patients 
Journal of Cancer  2016;7(1):14-21.
Context: Appropriate selection of aging patient who fit for cancer surgery is an art-of-state.
Objectives: This study aimed to identify predictive factors pertinent to 3-month postoperative mortality in geriatric cancer patients.
Methods: A total of 8,425 patients over 70 years old with solid cancer received radical surgery between 2007 and 2012 at four affiliated hospitals of the Chang Gung Memorial Hospital were included. The clinical variables of patients who died within 3 months post-surgery were analyzed retrospectively. Recursive partitioning analysis (RPA) was performed by randomly selecting 50% of the patients (testing set) to identify specific groups of patients with the lowest and highest probability of 3-month postoperative mortality. The remaining 50% were used as validation set of the model.
Results: Patients' gender, Eastern Cooperative Oncology Group performance (ECOG scale), Charlson comorbidity index (CCI), American Society of Anesthesiologist physical status, age, tumor staging, and mode of admission were independent variables that predicted 3-month postoperative mortality. The RPA model identified patients with an ECOG scale of 0-2, localized tumor stage, and a CCI of 0-2 as having the lowest probability of 3-month postoperative mortality (1.1% and 1.3% in the testing set and validation set, respectively). Conversely, an ECOG scale of 3-4 and a CCI >2 were associated with the highest probability of 3-month postoperative mortality (55.2% and 47.8% in the testing set and validation set, respectively).
Conclusion: We identified ECOG scale and CCI score were the two most influencing factors that determined 3-month postoperative mortality in geriatric cancer patients.
doi:10.7150/jca.13126
PMCID: PMC4679376  PMID: 26722355
postoperative mortality; solid cancer; geriatric patients; predictive factors
14.  Comparison of bone regeneration in alveolar bone of dogs on mineralized collagen grafts with two composition ratios of nano-hydroxyapatite and collagen 
Regenerative Biomaterials  2015;3(1):33-40.
To study the effect of two composition ratios of nano-hydroxyapatite and collagen (NHAC) composites on repairing alveolar bone defect of dogs. Eighteen healthy adult dogs were randomly divided into three groups. Two kinds of the NHAC composites were prepared according to the constituent ratios of 3:7 and 5:5; immediately after extraction of the mandibular second premolars, each kind of the NHAC composite was implanted into extraction socket, respectively: Group I, nHA/Col = 3:7; Group II, nHA/Col = 5:5 and Group III, blank control group. The bone-repairing ability of the two grafts was separately analyzed by morphometric measurement, X-ray tomography examination and biomechanical analysis at 1st, 3rd and 6th month post-surgical, respectively.
The NHAC composites were absorbed gradually after implanting into alveolar bone defect and were replaced by new bone. The ratios of new bone formation of Group I was significantly higher than that of Group II after 3 months (P < 0.05). The structure and bioactive performance can be improved when the ratio between the collagen and the hydroxyapatite was reasonable, and the repairing ability and effect in extraction sockets are obviously better.
doi:10.1093/rb/rbv025
PMCID: PMC4723277  PMID: 26816654
nano-hydroxyapatite; collagen; dental extraction socket; alveolar ridge preservation; ratios
15.  Application of Different Imaging Methods in the Early Diagnosis of Primary Hepatic Carcinoma 
Primary hepatic carcinoma (PHC) is the one of the most common tumors and the common cause of cancer death in the world. Detecting PHC in its early stage by imaging methods may greatly increase survival rates of patients. Ultrasound, computed tomography, magnetic resonance imaging, and positron emission tomography/computed tomography are common imaging methods in the diagnosis of PHC. In this paper, the application of different imaging methods in diagnosing the primary hepatic carcinoma will be discussed.
doi:10.1155/2016/8763205
PMCID: PMC4706941  PMID: 26819614
16.  Direct observation of laser guided corona discharges 
Scientific Reports  2015;5:18681.
Laser based lightning control holds a promising way to solve the problem of the long standing disaster of lightning strikes. But it is a challenging project due to insufficient understanding of the interaction between laser plasma channel and high voltage electric filed. In this work, a direct observation of laser guided corona discharge is reported. Laser filament guided streamer and leader types of corona discharges were observed. An enhanced ionization took place in the leader (filament) through the interaction with the high voltage discharging field. The fluorescence lifetime of laser filament guided corona discharge was measured to be several microseconds, which is 3 orders of magnitude longer than the fluorescence lifetime of laser filaments. This work could be advantageous towards a better understanding of laser assisted leader development in the atmosphere.
doi:10.1038/srep18681
PMCID: PMC4683528  PMID: 26679271
18.  Bioinformatics identification of potentially involved microRNAs in Tibetan with gastric cancer based on microRNA profiling 
Objective
The incidence of gastric cancer is high in Chinese Tibetan. This study aimed to identify the differentially expressed microRNAs (miRNAs) and further explore their potential roles in Tibetan with gastric cancer so as to predict potential therapeutic targets.
Methods
A total of 10 Tibetan patients (male:female = 6:4) with gastric cancer were enrolled for isolation of matched gastric cancer and adjacent non-cancerous tissue samples. Affymetrix GeneChip microRNA 3.0 Array was employed for detection of miRNA expression in samples. Differential expression analysis between two sample groups was analyzed using Limma package. Then, MultiMiR package was used to predict targets for miRNAs. Following, the target genes were put into DAVID (Database for Annotation, Visualization and Integrated Discovery) to identify the significant pathways of miRNAs.
Results
Using Limma package in R, a total of 27 differentially expressed miRNAs were screened out in gastric cancer, including 25 down-regulated (e.g. hsa-miR-148a-3p, hsa-miR-148b-3p and hsa-miR-363-3p) and 2 up-regulated miRNAs. According to multiMiR package, a number of 1445 target genes (e.g. Wnt1, KLF4 and S1PR1) of 13 differentially expressed miRNAs were screened out. Among those miRNAs, hsa-miR-148a-3p, hsa-miR-148b-3p and hsa-miR-363-3p were identified with the most target genes. Furthermore, three miRNAs were significantly enriched in numerous common cancer-related pathways, including “Wnt signaling pathway”, “MAPK signaling pathway” and “Jak-STAT signaling pathway”.
Conclusions
The present study identified a downregulation and enrichment in cancer-related pathways of hsa-miR-148a-3p, hsa-miR-148b-3p and hsa-miR-363-3p in Tibetan with gastric cancer, which can be suggested as therapeutic targets.
Electronic supplementary material
The online version of this article (doi:10.1186/s12935-015-0266-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s12935-015-0266-1
PMCID: PMC4676900  PMID: 26692821
Gastric cancer; miRNA microarray; Differentially expressed miRNAs; Enrichment analysis; Network of miRNAs-targets
19.  Effect of α-Amylase Degradation on Physicochemical Properties of Pre-High Hydrostatic Pressure-Treated Potato Starch 
PLoS ONE  2015;10(12):e0143620.
The effect of high hydrostatic pressure (HHP) on the susceptibility of potato starch (25%, w/v) suspended in water to degradation by exposure to bacterial α-amylase (0.02%, 0.04% and 0.06%, w/v) for 40 min at 25°C was investigated. Significant differences (p < 0.05) in the structure, morphology and physicochemical properties were observed. HHP-treated potato starch (PS) exposed to α-amylase (0.06%, w/v) showed a significantly greater degree of hydrolysis and amount of reducing sugar released compared to α-amylase at a concentration of 0.04% (w/v) or 0.02% (w/v). Native PS (NPS) granules have a spherical and elliptical form with a smooth surface, whereas the hydrolyzed NPS (hNPS) and hydrolyzed HHP-treated PS granules showed irregular and ruptured forms with several cracks and holes on the surface. Hydrolysis of HHP-treated PS by α-amylase could decrease the average granule size significantly (p <0.05) from 29.43 to 20.03 μm. Swelling power decreased and solubility increased with increasing enzyme concentration and increasing pressure from 200–600 MPa, with the exception of the solubility of HHP-treated PS at 600 MPa (HHP600 PS). Fourier transform infrared spectroscopy (FTIR) showed extensive degradation of the starch in both the ordered and the amorphous structure, especially in hydrolyzed HHP600 PS. The B-type of hydrolyzed HHP600 PS with α-amylase at a concentration 0.06% (w/v) changed to a B+V type with an additional peak at 2θ = 19.36°. The HHP600 starch with 0.06% (w/v) α-amylase displayed the lowest value of To (onset temperature), Tc (conclusion temperature) and ΔHgel (enthalpies of gelatinization). These results indicate the pre-HHP treatment of NPS leads to increased susceptibility of the granules to enzymatic degradation and eventually changes of both the amorphous and the crystalline structures.
doi:10.1371/journal.pone.0143620
PMCID: PMC4671678  PMID: 26642044
20.  NLRP9B protein is dispensable for oocyte maturation and early embryonic development in the mouse 
Nlrp9a, Nlrp9b and Nlrp9c are preferentially expressed in oocytes and early embryos in the mouse. Simultaneous genetic ablation of Nlrp9a and Nlrp9c does not affect early embryonic development, but the function of Nlrp9b in the process of oocyte maturation and embryonic development has not been elucidated. Here we show that both Nlrp9b mRNA and its protein are expressed in ovaries and the small intestine. Moreover, the NLRP9B protein was restricted to oocytes in the ovary and declined with oocyte aging. After ovulation and fertilization, NLRP9B protein was found in preimplantation embryos. Confocal microscopy demonstrated that it was mainly localized in the cytoplasm in the oocytes and blastomeres. Thus, this protein might play a role in oocyte maturation and early embryonic development. However, knockdown of Nlrp9b expression in GV-stage oocytes using RNA interference did not affect oocyte maturation or subsequent parthenogenetic development after Nlrp9b-deficient oocytes were activated. Furthermore, Nlrp9b knockdown zygotes could reach the blastocyst stage after being cultured for 3.5 days in vitro. These results provide the first evidence that the NLRP9B protein is dispensable for oocyte maturation and early embryonic development in the mouse.
doi:10.1262/jrd.2015-050
PMCID: PMC4685222  PMID: 26411641
Early development; Mouse; NLRP9B protein; Oocyte maturation
21.  Transcriptomic Analysis of the Porcine Endometrium during Embryo Implantation 
Genes  2015;6(4):1330-1346.
In pigs, successful embryo implantation is an important guarantee for producing litter size, and early embryonic loss occurring on day 12–30 of gestation critically affects the potential litter size. The implantation process is regulated by the expression of numerous genes, so comprehensive analysis of the endometrium is necessary. In this study, RNA sequencing (RNA-Seq) technology is used to analyze endometrial tissues during early pregnancy. We investigated the changes of gene expression between three stages (day 12, 18, and 25) by multiple comparisons. There were 1557, 8951, and 2345 differentially expressed genes (DEGs) revealed between the different periods of implantation. We selected several genes for validation by the use of quantitative real-time RT-PCR. Bioinformatic analysis of differentially expressed genes in the endometrium revealed a number of biological processes and pathways potentially involved in embryo implantation in the pig, most noticeably cell proliferation, regulation of immune response, interaction of cytokine-cytokine receptors, and cell adhesion. These results showed that specific gene expression patterns reflect the different functions of the endometrium in three stages (maternal recognition, conceptus attachment, and embryo implantation). This study identified comprehensive transcriptomic profile in the porcine endometrium and thus could be a foundation for targeted studies of genes and pathways potentially involved in abnormal endometrial receptivity and embryo loss in early pregnancy.
doi:10.3390/genes6041330
PMCID: PMC4690044  PMID: 26703736
embryo implantation; endometrium; pigs; pregnancy; sows; transcriptome
22.  Investigation of the Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonate (PFOS) on Apoptosis and Cell Cycle in a Zebrafish (Danio rerio) Liver Cell Line 
This study aimed to explore the effects of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) on apoptosis and cell cycle in a zebrafish (Danio rerio) liver cell line (ZFL). Treatment groups included a control group, PFOA-IC50, PFOA-IC80, PFOS-IC50 and PFOS-IC80 groups. IC50 and IC80 concentrations were identified by cellular modeling and MTT assays. mRNA levels of p53, Bcl-2, Bax, Caspase-3 and NF-κB p65 were detected by qPCR. Cell apoptosis and cell cycle were detected by flow cytometry and the protein levels of p53, Bcl-2, Bax, Caspase-3 and NF-κB p65 were determined by western blotting. Both PFOA and PFOS inhibited the growth of zebrafish liver cells, and the inhibition rate of PFOS was higher than that of PFOA. Bcl-2 expression levels in the four groups were significantly higher than the control group and Bcl-2 increased significantly in the PFOA-IC80 group. However, the expression levels of Bax in the four treatment groups were higher than the control group. The percentage of cell apoptosis increased significantly with the treatment of PFOA and PFOS (p < 0.05). Cell cycle and cell proliferation were blocked in both the PFOA-IC80 and PFOS-IC80 groups, indicating that PFOA-IC80 and PFOS-IC50 enhanced apoptosis in ZFL cells.
doi:10.3390/ijerph121215012
PMCID: PMC4690948  PMID: 26690195
perfluorooctanoic acid (PFOA); perfluorooctane sulfonate (PFOS); zebrafish liver cells (ZFL); apoptosis
23.  Achieving high strength and high ductility in magnesium alloy using hard-plate rolling (HPR) process 
Scientific Reports  2015;5:17100.
Magnesium alloys are highly desirable for a wide range of lightweight structural components. However, rolling Mg alloys can be difficult due to their poor plasticity, and the strong texture yielded from rolling often results in poor plate forming ability, which limits their further engineering applications. Here we report a new hard-plate rolling (HPR) route which achieves a large reduction during a single rolling pass. The Mg-9Al-1Zn (AZ91) plates processed by HPR consist of coarse grains of 30–60 μm, exhibiting a typical basal texture, fine grains of 1–5 μm and ultrafine (sub) grains of 200–500 nm, both of the latter two having a weakened texture. More importantly, the HPR was efficient in gaining a simultaneous high strength and uniform ductility, i.e., ~371 MPa and ~23%, respectively. The superior properties should be mainly attributed to the cooperation effect of the multimodal grain structure and weakened texture, where the former facilitates a strong work hardening while the latter promotes the basal slip. The HPR methodology is facile and effective, and can avoid plate cracking that is prone to occur during conventional rolling processes. This strategy is applicable to hard-to-deform materials like Mg alloys, and thus has a promising prospect for industrial application.
doi:10.1038/srep17100
PMCID: PMC4658522  PMID: 26603776
24.  Flexible, highly efficient all-polymer solar cells 
Nature Communications  2015;6:8547.
All-polymer solar cells have shown great potential as flexible and portable power generators. These devices should offer good mechanical endurance with high power-conversion efficiency for viability in commercial applications. In this work, we develop highly efficient and mechanically robust all-polymer solar cells that are based on the PBDTTTPD polymer donor and the P(NDI2HD-T) polymer acceptor. These systems exhibit high power-conversion efficiency of 6.64%. Also, the proposed all-polymer solar cells have even better performance than the control polymer-fullerene devices with phenyl-C61-butyric acid methyl ester (PCBM) as the electron acceptor (6.12%). More importantly, our all-polymer solar cells exhibit dramatically enhanced strength and flexibility compared with polymer/PCBM devices, with 60- and 470-fold improvements in elongation at break and toughness, respectively. The superior mechanical properties of all-polymer solar cells afford greater tolerance to severe deformations than conventional polymer-fullerene solar cells, making them much better candidates for applications in flexible and portable devices.
All-polymer solar cells have advantages over fullerene-based solar cells due to improved stability and tunable chemical and electronic properties. Here, Kim et al. develop highly efficient and robust solar cells based on PBDTTTPD and P(NDI2HD-T), highlighting their potential in flexible and portable electronics.
doi:10.1038/ncomms9547
PMCID: PMC4633811  PMID: 26449658
25.  Ebola Virus Outbreak Investigation, Sierra Leone, September 28–November 11, 2014  
Emerging Infectious Diseases  2015;21(11):1921-1927.
Knowledge of epidemiologic, clinical, and viral features of the outbreak is critical for optimizing control and treatment measures.
During 2014–2015, an outbreak of Ebola virus disease (EVD) swept across parts of West Africa. The China Mobile Laboratory Testing Team was dispatched to support response efforts; during September 28–November 11, 2014, they conducted PCR testing on samples from 1,635 suspected EVD patients. Of those patients, 50.4% were positive, of whom 84.6% lived within a 3-km zone along main roads connecting rural towns and densely populated cities. The median time from symptom onset to testing was 5 days. At testing, 75.7% of the confirmed patients had fever, and 94.1% reported at least 1 gastrointestinal symptom; all symptoms, except rash and hemorrhage, were more frequent in confirmed than nonconfirmed patients. Virus loads were significantly higher in EVD patients with fever, diarrhea, fatigue, or headache. The case-fatality rate was lower among patients 15–44 years of age and with virus loads of <100,000 RNA copies/mL. These findings are key for optimizing EVD control and treatment measures.
doi:10.3201/eid2111.150582
PMCID: PMC4622249  PMID: 26485317
Ebola virus disease; Ebola virus; Sierra Leone; western Africa; epidemiologic characteristics; clinical features; virus load; transmission; viruses; laboratory testing; investigation; epidemiology; epidemic; outbreak; control measures; treatment

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