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1.  Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation 
BMC Bioinformatics  2011;12:409.
Background
With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched.
Results
In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in Escherichia coli and Saccharomyces cerevisiae respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology.
Conclusions
By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.
doi:10.1186/1471-2105-12-409
PMCID: PMC3215753  PMID: 22024143
2.  Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context 
BMC Systems Biology  2011;5(Suppl 1):S6.
Background
Enzymes are known as the largest class of proteins and their functions are usually annotated by the Enzyme Commission (EC), which uses a hierarchy structure, i.e., four numbers separated by periods, to classify the function of enzymes. Automatically categorizing enzyme into the EC hierarchy is crucial to understand its specific molecular mechanism.
Results
In this paper, we introduce two key improvements in predicting enzyme function within the machine learning framework. One is to introduce the efficient sequence encoding methods for representing given proteins. The second one is to develop a structure-based prediction method with low computational complexity. In particular, we propose to use the conjoint triad feature (CTF) to represent the given protein sequences by considering not only the composition of amino acids but also the neighbor relationships in the sequence. Then we develop a support vector machine (SVM)-based method, named as SVMHL (SVM for hierarchy labels), to output enzyme function by fully considering the hierarchical structure of EC. The experimental results show that our SVMHL with the CTF outperforms SVMHL with the amino acid composition (AAC) feature both in predictive accuracy and Matthew’s correlation coefficient (MCC). In addition, SVMHL with the CTF obtains the accuracy and MCC ranging from 81% to 98% and 0.82 to 0.98 when predicting the first three EC digits on a low-homologous enzyme dataset. We further demonstrate that our method outperforms the methods which do not take account of hierarchical relationship among enzyme categories and alternative methods which incorporate prior knowledge about inter-class relationships.
Conclusions
Our structure-based prediction model, SVMHL with the CTF, reduces the computational complexity and outperforms the alternative approaches in enzyme function prediction. Therefore our new method will be a useful tool for enzyme function prediction community.
doi:10.1186/1752-0509-5-S1-S6
PMCID: PMC3121122  PMID: 21689481
3.  MicroRNA-378 controls classical brown fat expansion to counteract obesity 
Nature communications  2014;5:4725.
Both classical brown adipocytes and brown-like beige adipocytes are considered as promising therapeutic targets for obesity; however, their development, relative importance, and functional coordination are not well understood. Here we show that a modest expression of miR-378/378* in adipose tissue specifically increases classical brown fat (BAT) mass, but not white fat (WAT) mass. Remarkably, BAT expansion, rather than miR-378 per se, suppresses formation of beige adipocytes in subcutaneous WAT. Despite this negative feedback, the expanded BAT depot is sufficient to prevent both genetic and high fat diet-induced obesity. At the molecular level, we find that miR-378 targets phosphodiesterase Pde1b in BAT, but not in WAT. Indeed, miR-378 and Pde1b inversely regulate brown adipogenesis in vitro in the absence of phosphodiesterase inhibitor IBMX. Our work identifies miR-378 as a key regulatory component underlying classical BAT-specific expansion and obesity resistance, and adds novel insights into the physiological cross-talk between BAT and WAT.
doi:10.1038/ncomms5725
PMCID: PMC4167820  PMID: 25145289
4.  Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing 
Nature  2014;512(7513):155-160.
SUMMARY
Sequencing studies of breast tumor cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumors. Here, we developed a whole-genome and exome single cell sequencing approach called Nuc-Seq that utilizes G2/M nuclei to achieve 91% mean coverage breadth. We applied this method to sequence single normal and tumor nuclei from an estrogen-receptor positive breast cancer and a triple-negative ductal carcinoma. In parallel, we performed single nuclei copy number profiling. Our data show that aneuploid rearrangements occurred early in tumor evolution and remained highly stable as the tumor masses clonally expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumor mass by targeted single-molecule sequencing. Using mathematical modeling we found that the triple-negative tumor cells had an increased mutation rate (13.3X) while the ER+ tumor cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.
doi:10.1038/nature13600
PMCID: PMC4158312  PMID: 25079324
5.  Learning curve for hand-assisted laparoscopic D2 radical gastrectomy 
AIM: To describe the learning curves of hand-assisted laparoscopic D2 radical gastrectomy (HALG) for the treatment of gastric cancer.
METHODS: The HALG surgical procedure consists of three stages: surgery under direct vision via the port for hand assistance, hand-assisted laparoscopic surgery, and gastrointestinal tract reconstruction. According to the order of the date of surgery, patients were divided into 6 groups (A-F) with 20 cases in each group. All surgeries were performed by the same group of surgeons. We performed a comprehensive and in-depth retrospective comparative analysis of the clinical data of all patients, with the clinical data including general patient information and intraoperative and postoperative observation indicators.
RESULTS: There were no differences in the basic information among the patient groups (P > 0.05). The operative time of the hand-assisted surgery stage in group A was 8-10 min longer than the other groups, with the difference being statistically significant (P = 0.01). There were no differences in total operative time between the groups (P = 0.30). Postoperative intestinal function recovery time in group A was longer than that of other groups (P = 0.02). Lengths of hospital stay and surgical quality indicators (such as intraoperative blood loss, numbers of detected lymph nodes, intraoperative side injury, postoperative complications, reoperation rate, and readmission rate 30 d after surgery) were not significantly different among the groups.
CONCLUSION: HALG is a surgical procedure that can be easily mastered, with a learning curve closely related to the operative time of the hand-assisted laparoscopic surgery stage.
doi:10.3748/wjg.v21.i5.1606
PMCID: PMC4316103  PMID: 25663780
Learning curve; Gastric cancer; Hand-assisted laparoscopic D2 radical gastrectomy; Operative time; Surgical quality indicators
6.  Evaluation of the Quantitative Accuracy of 3D Reconstruction of Edentulous Jaw Models with Jaw Relation Based on Reference Point System Alignment 
PLoS ONE  2015;10(2):e0117320.
Objectives
To apply contact measurement and reference point system (RPS) alignment techniques to establish a method for 3D reconstruction of the edentulous jaw models with centric relation and to quantitatively evaluate its accuracy.
Methods
Upper and lower edentulous jaw models were clinically prepared, 10 pairs of resin cylinders with same size were adhered to axial surfaces of upper and lower models. The occlusal bases and the upper and lower jaw models were installed in the centric relation position. Faro Edge 1.8m was used to directly obtain center points of the base surface of the cylinders (contact method). Activity 880 dental scanner was used to obtain 3D data of the cylinders and the center points were fitted (fitting method). 3 pairs of center points were used to align the virtual model to centric relation. An observation coordinate system was interactively established. The straight-line distances in the X (horizontal left/right), Y (horizontal anterior/posterior), and Z (vertical) between the remaining 7 pairs of center points derived from contact method and fitting method were measured respectively and analyzed using a paired t-test.
Results
The differences of the straight-line distances of the remaining 7 pairs of center points between the two methods were X: 0.074 ± 0.107 mm, Y: 0.168 ± 0.176 mm, and Z: −0.003± 0.155 mm. The results of paired t-test were X and Z: p >0.05, Y: p <0.05.
Conclusion
By using contact measurement and the reference point system alignment technique, highly accurate reconstruction of the vertical distance and centric relation of a digital edentulous jaw model can be achieved, which meets the design and manufacturing requirements of the complete dentures. The error of horizontal anterior/posterior jaw relation was relatively large.
doi:10.1371/journal.pone.0117320
PMCID: PMC4319956  PMID: 25659133
7.  Efficient generation of gene-modified pigs via injection of zygote with Cas9/sgRNA 
Scientific Reports  2015;5:8256.
Co-injection of zygotes with Cas9 mRNA and sgRNA has been proven to be an efficient gene-editing strategy for genome modification of different species. Genetic engineering in pigs holds a great promise in biomedical research. By co-injection of one-cell stage embryos with Cas9 mRNA and Npc1l1 sgRNA, we achieved precise Npc1l1 targeting in Chinese Bama miniature pigs at the efficiency as high as 100%. Meanwhile, we carefully analyzed the Npc1l1 sgRNA:Cas9-mediated on- and off-target mutations in various somatic tissues and ovaries, and demonstrated that injection of zygotes with Cas9 mRNA and sgRNA is an efficient and reliable approach for generation of gene-modified pigs.
doi:10.1038/srep08256
PMCID: PMC4317696  PMID: 25653176
8.  Effects of Ferulic Acid and γ-Oryzanol on High-Fat and High-Fructose Diet-Induced Metabolic Syndrome in Rats 
PLoS ONE  2015;10(2):e0118135.
Background
The high morbidity of metabolic dysfunction diseases has heightened interest in seeking natural and safe compounds to maintain optimal health. γ-Oryzanol (OZ), the ferulic acid (FA) ester with phytosterols, mainly present in rice bran has been shown to improve markers of metabolic syndrome. This study investigates the effects of FA and OZ on alleviating high-fat and high-fructose diet (HFFD)-induced metabolic syndrome parameters.
Methods
Male SD rats were fed with a regular rodent diet, HFFD, or HFFD supplemented with 0.05% FA or 0.16% OZ (equimolar concentrations) for 13 weeks. Food intake, organ indices, serum lipid profiles, glucose metabolism, insulin resistance (IR) index and cytokine levels were analyzed. The mechanisms were further investigated in oleic acid-stimulated HepG2 cells by analyzing triglyceride (TG) content and lipogenesis-related gene expressions.
Results
In the in vivo study, FA and OZ exhibited similar effects in alleviating HFFD-induced obesity, hyperlipidemia, hyperglycemia, and IR. However, only OZ treatment significantly decreased liver index and hepatic TG content, lowered serum levels of C-reactive protein and IL-6, and increased serum concentration of adiponectin. In the in vitro assay, only OZ administration significantly inhibited intracellular TG accumulation and down-regulated expression of stearoyl coenzyme-A desaturase-1, which might facilitate OZ to enhance its hepatoprotective effect.
Conclusion
OZ is more effective than FA in inhibiting hepatic fat accumulation and inflammation. Thus, FA and OZ could be used as dietary supplements to alleviate the deleterious effects of HFFD.
doi:10.1371/journal.pone.0118135
PMCID: PMC4315454  PMID: 25646799
9.  New Clustered Regularly Interspaced Short Palindromic Repeat Locus Spacer Pair Typing Method Based on the Newly Incorporated Spacer for Salmonella enterica 
Journal of Clinical Microbiology  2014;52(8):2955-2962.
A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections.
doi:10.1128/JCM.00696-14
PMCID: PMC4136180  PMID: 24899040
10.  Epidural Sustained Release Ropivacaine Prolongs Anti-Allodynia and Anti-Hyperalgesia in Developing and Established Neuropathic Pain 
PLoS ONE  2015;10(1):e0117321.
Ropivacaine is a local anesthetic widely used for regional anesthesia and epidural analgesia, but its relatively short duration limits its clinical use. A novel sustained release lipid formulation of ropivacaine has been recently developed to prolong its duration. We examined the epidural anti-hypersensitivity and preemptive effects of ropivacaine in mesylate injection and sustained release suspension forms in a rat model of neuropathy produced by peripheral nerve injury. Epidural administration of ropivacaine mesylate injection specifically blocked mechanical allodynia and thermal hyperalgesia by approximately 50% with a biological half-effective duration of approximately 3 hrs. The equivalent dose of ropivacaine free-base in sustained release suspension significantly prolonged the duration of anti-allodynia and anti-hyperalgesia by approximately 2 times. Multiple daily epidural injections of ropivacaine in both the mesylate injection and sustained-release suspension forms did not induce tolerance or potentiation to anti-allodynia or anti-hyperalgesia. Moreover, the single or multiple daily administration of ropivacaine mesylate injection before surgery in particular, markedly blocked the initiation and development of neuropathic pain, increasing the biological half-effective duration from less than 4 hrs up to 1 or 2 days. The single and multiple daily epidural injection of ropivacaine sustained release suspension further delayed the biological half-lives to 2 and 3 days, respectively. Our results indicate that the epidural administration of ropivacaine effectively blocks neuropathic pain without the induction of analgesic tolerance, and significantly delays the development of neuropathy produced by peripheral nerve injury. Epidural ropivacaine sustained release suspension produces much longer blockade effects of mechanical allodynia and heat hyperalgesia, and more significantly delays the development of neuropathic pain.
doi:10.1371/journal.pone.0117321
PMCID: PMC4305322  PMID: 25617901
11.  Roles of 3,3′,4′,5-tetrachlorosalicylanilide in regulating extracellular electron transfer of Shewanella oneidensis MR-1 
Scientific Reports  2015;5:7991.
Microbial extracellular electron transfer (EET) is critically involved in many pollutant conversion processes in both natural environment and engineered bioelectrochemical systems (BES), but typically with limited efficiency and poor controllability. In this study, we discover an important role of uncouplers in affecting the microbial energy metabolism and EET. Dose of lower-concentration 3,3′,4′,5-tetrachlorosalicylanilide (TCS) in the anolyte promoted the current generation and substrate degradation of an MFC inoculated with Shewanella oneidensis MR-1. However, higher TCS dosage caused obvious microbial inhibition. Our results suggest a previously unknown role of uncouplers in regulating the microbial EET. In addition, the underlying mechanisms of such processes are investigated. This work broadens our view about the EET behaviors of microorganisms in real water environment where uncouplers are usually present, and suggests a possible new approach to regulate microbial EET in BES.
doi:10.1038/srep07991
PMCID: PMC4303895  PMID: 25612888
12.  BET Bromodomain Inhibition Triggers Apoptosis of NF1-associated Malignant Peripheral Nerve Sheath Tumors through Bim Induction 
Cell reports  2013;6(1):81-92.
Summary
Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are highly aggressive sarcomas that develop sporadically or in Neurofibromatosis type 1 (NF1) patients. There is no effective treatment for MPNSTs and they are typically fatal. To gain insights into MPNST pathogenesis, we utilized a novel MPNST mouse model that allowed us to study the evolution of these tumors at the transcriptome level. Strikingly, in MPNSTs we found upregulation of chromatin regulator Brd4, and show that BRD4 inhibition profoundly suppresses both growth and tumorigenesis. Our findings reveal new roles for BET bromodomains in MPNST development, and report a novel mechanism by which bromodomain inhibition induces apoptosis through induction of pro-apoptotic Bim, which may represent a paradigm shift in therapy for MPNST patients. Moreover, these findings indicate novel epigenetic mechanisms underlying the balance of anti-/pro-apoptotic molecules, and that bromodomain inhibition can shift this balance in favor of cancer cell apoptosis.
doi:10.1016/j.celrep.2013.12.001
PMCID: PMC3904298  PMID: 24373973
Neurofibromatosis Type1; NF1; Malignant Peripheral Nerve Sheath Tumor; MPNST; Neurofibrosarcomas; apoptosis; BRD4; BET Bromodomain; BIM; BCL-2; CyclinD1
13.  Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis 
Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2′,4,4′-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge.
doi:10.3389/fmicb.2014.00799
PMCID: PMC4294214  PMID: 25642227
PBDEs; sponge-associated bacterial community; 16S rRNA gene pyrosequencing; metagenomics; symbionts
14.  Real-Time Web-Based Assessment of Total Population Risk of Future Emergency Department Utilization: Statewide Prospective Active Case Finding Study 
Background
An easily accessible real-time Web-based utility to assess patient risks of future emergency department (ED) visits can help the health care provider guide the allocation of resources to better manage higher-risk patient populations and thereby reduce unnecessary use of EDs.
Objective
Our main objective was to develop a Health Information Exchange-based, next 6-month ED risk surveillance system in the state of Maine.
Methods
Data on electronic medical record (EMR) encounters integrated by HealthInfoNet (HIN), Maine’s Health Information Exchange, were used to develop the Web-based surveillance system for a population ED future 6-month risk prediction. To model, a retrospective cohort of 829,641 patients with comprehensive clinical histories from January 1 to December 31, 2012 was used for training and then tested with a prospective cohort of 875,979 patients from July 1, 2012, to June 30, 2013.
Results
The multivariate statistical analysis identified 101 variables predictive of future defined 6-month risk of ED visit: 4 age groups, history of 8 different encounter types, history of 17 primary and 8 secondary diagnoses, 8 specific chronic diseases, 28 laboratory test results, history of 3 radiographic tests, and history of 25 outpatient prescription medications. The c-statistics for the retrospective and prospective cohorts were 0.739 and 0.732 respectively. Integration of our method into the HIN secure statewide data system in real time prospectively validated its performance. Cluster analysis in both the retrospective and prospective analyses revealed discrete subpopulations of high-risk patients, grouped around multiple “anchoring” demographics and chronic conditions. With the Web-based population risk-monitoring enterprise dashboards, the effectiveness of the active case finding algorithm has been validated by clinicians and caregivers in Maine.
Conclusions
The active case finding model and associated real-time Web-based app were designed to track the evolving nature of total population risk, in a longitudinal manner, for ED visits across all payers, all diseases, and all age groups. Therefore, providers can implement targeted care management strategies to the patient subgroups with similar patterns of clinical histories, driving the delivery of more efficient and effective health care interventions. To the best of our knowledge, this prospectively validated EMR-based, Web-based tool is the first one to allow real-time total population risk assessment for statewide ED visits.
doi:10.2196/ijmr.4022
PMCID: PMC4319080  PMID: 25586600
ED; machine learning; HIE; EMR; modeling
15.  Genome Sequence of an Extensively Drug-Resistant Strain of Klebsiella pneumoniae, Strain YN-1, with Carbapenem Resistance 
Genome Announcements  2015;3(1):e01279-14.
The emergence and spread of multidrug-resistant (MDR) Klebsiella pneumoniae has been regarded as one of the major challenges among health care-associated infections worldwide. Here, we report the draft genome sequence of an extensively drug-resistant (XDR) K. pneumoniae strain isolated in 2013 from Yunnan Province, China.
doi:10.1128/genomeA.01279-14
PMCID: PMC4290976  PMID: 25573939
16.  Emergence and Prevalence of Non-H2S-Producing Salmonella enterica Serovar Senftenberg Isolates Belonging to Novel Sequence Type 1751 in China 
Journal of Clinical Microbiology  2014;52(7):2557-2565.
Salmonella enterica serovar Senftenberg is a common nontyphoidal Salmonella serotype which causes human Salmonella infections worldwide. In this study, 182 S. Senftenberg isolates, including 17 atypical non-hydrogen sulfide (H2S)-producing isolates, were detected in China from 2005 to 2011. The microbiological and genetic characteristics of the non-H2S-producing and selected H2S-producing isolates were determined by using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and clustered regularly interspaced short palindromic repeat (CRISPR) analysis. The phs operons were amplified and sequenced. The 17 non-H2S-producing and 36 H2S-producing isolates belonged to 7 sequence types (STs), including 3 new STs, ST1751, ST1757, and ST1758. Fourteen of the 17 non-H2S-producing isolates belonged to ST1751 and had very similar PFGE patterns. All 17 non-H2S-producing isolates had a nonsense mutation at position 1621 of phsA. H2S-producing and non-H2S-producing S. Senftenberg isolates were isolated from the same stool sample from three patients; isolates from the same patients displayed the same antimicrobial susceptibility, ST, and PFGE pattern but could be discriminated based on CRISPR spacers. Non-H2S-producing S. Senftenberg isolates belonging to ST1751 have been prevalent in Shanghai, China. It is possible that these emerging organisms will disseminate further, because they are difficult to detect. Thus, we should strengthen the surveillance for the spread of this atypical S. Senftenberg variant.
doi:10.1128/JCM.00377-14
PMCID: PMC4097678  PMID: 24829240
17.  MIR106B and MIR93 Prevent Removal of Bacteria from Epithelial Cells by Disrupting ATG16L1-Mediated Autophagy 
Gastroenterology  2013;146(1):10.1053/j.gastro.2013.09.006.
BACKGROUND & AIMS
Variants in genes that regulate autophagy have been associated with Crohn’s disease (CD). Defects in autophagy-mediated removal of pathogenic microbes could contribute to pathogenesis of CD. We investigated the role of the micro-RNAs (miRs) MIR106B and MIR93 in induction of autophagy and bacterial clearance in human cell lines, and the correlation between MIR106B and autophagy-related gene 16L1 (ATG16L1) expression in tissues from patients with CD.
METHODS
We studied the ability of MIR106B and MIR93 to regulate ATG transcripts in human cancer cell lines (HCT116, SW480, HeLa, and U2OS) using luciferase report assays and bioinformatics analyses; MIR106B and MIR93 mimics and antagonists were transfected into cells to modify levels of miRs. Cells were infected with LF82, a CD-associated adherent-invasive strain of Escherichia coli, and monitored by confocal microscopy and for colony-forming units. Colon tissues from 41 healthy individuals (controls), 22 with active CD, 16 with inactive CD, and 7 with chronic inflammation were assessed for levels of MIR106B and ATG16L1 by in situ hybridization and immunohistochemistry.
RESULTS
Silencing Dicer 1, an essential processor of miRs, increased levels of ATG protein and formation of autophagosomes in cells, indicating that miRs regulate autophagy. Luciferase reporter assays indicated that MIR106B and MIR93 targeted ATG16L1 mRNA. MIR106B and MIR93 reduced levels of ATG16L1 and autophagy; these increased following expression of ectopic ATG16L1. In contrast, MIR106B and MIR93 antagonists increased formation of autophagosomes. Levels of MIR106B were increased in intestinal epithelia from patients with active CD, whereas levels of ATG16L1 were reduced, compared with controls. Levels of CMYC were also increased in intestinal epithelia of patients with active CD, compared with controls. These alterations could impair removal of CD-associated bacteria by autophagy.
CONCLUSIONS
In human cell lines, MIR106B and MIR93 reduce levels of ATG16L1 and autophagy, and prevent autophagy-dependent eradication of intracellular bacteria. This process also appears to be altered in colon tissues from patients with active CD.
doi:10.1053/j.gastro.2013.09.006
PMCID: PMC3870037  PMID: 24036151
inflammatory bowel disease; microRNA; cell biology; infection
18.  Peripheral Blood Mononuclear Cell Traffic Plays a Crucial Role in Mother-to-Infant Transmission of Hepatitis B Virus 
The role of peripheral blood mononuclear cells (PBMCs) in HBV intrauterine infection is not fully defined. Particularly the origin of PBMCs in HBV-infected neonates remains to be addressed. We carried out a population-based nested case-control study by enrolling 312 HBsAg-positive mothers and their babies. PBMC HBV DNA as well as serum HBsAg and HBV DNA was tested in cohort entry samples. Totally, 45.5% (142/312) of the newborns were found to be infected with HBV in perinatal transmission. 119 mother-infant pairs were identified to be different in the genetic profile of maternal and fetal PBMCs by AS-PCR and hemi-nested PCR. Among them, 57.1% (68/119) of the maternal PBMCs in index cases were positive for HBV DNA while 83.8% (57/68) of the HBV DNA positive maternal PBMCs passed the placental barrier and entered the fetus. Furthermore, maternal PBMC HBV infection was significantly associated with newborn infants HBV infection. PBMC traffic from mother to fetus resulted in a 9.5-fold increased risk of HBV infection in PBMC HBV DNA positive newborn infants. These data indicate that maternal PBMCs infected with HBV contribute to HBV intrauterine infection of newborn infants via PBMC traffic from mother to fetus.
doi:10.7150/ijbs.10813
PMCID: PMC4323366
Hepatitis B virus; mother-to-infant transmission; peripheral blood mononuclear cell; fetomaternal cellular traffic.
19.  Genome Sequence of a Pandrug-Resistant Pseudomonas aeruginosa Strain, YN-1 
Genome Announcements  2014;2(6):e01280-14.
A highly rampant multidrug-resistant strain of Pseudomonas aeruginosa appeared in a hospital in Yunnan Province, China. Here, we report the genome sequence of the pandrug-resistant (PDR) P. aeruginosa strain recovered from a patient in 2013.
doi:10.1128/genomeA.01280-14
PMCID: PMC4276817  PMID: 25540339
20.  Prognostic significance of osteopontin in patients with lung cancer: a meta-analysis 
Both plasma/serum/pleural effusion osteopontin concentration (PSPO) and tumor tissue osteopontin expression (TTO) have recently been reported to be involved in the prognosis of lung cancer. In this study, we performed a meta-analysis to demonstrate the association between PSPO/TTO and survival in patients with lung cancer. We searched in PubMed, EMBASE, Cochrane library, Web of Science and Chinese Biomedical database (CBM) for relevant literatures. Stata 12.0 was applied to pool the eligible studies and synthesize hazard ratios (HRs) and its corresponding 95% confidence interval (CI). For PSPO, a total of 8 studies with 1000 patients were included in final analysis. Combined HR suggested high PSPO predicted an unfavorable overall survival (OS) (HR=1.52, 95% CI: 1.13-2.05) and progress-free survival (PFS) (HR=1.73, 95% CI: 1.35-2.21). For TTO, 5 studies with a total of 747 patients were employed in final analysis. Pooled HR indicated that elevated TTO was associated with poor OS (HR=2.16, 95% CI: 1.65-2.83) and disease/relapse-free survival (D/RFS) (HR=2.36, 95% CI: 1.79-3.12). Subgroup analysis was performed to explore the causes of heterogeneity. Publication bias by begg’s test was not statistically significant. Sensitivity analysis showed that the pooled results were robust. This study revealed that both high TTO and PSPO are associated with poor prognosis in patients with lung cancer.
PMCID: PMC4307405  PMID: 25663958
Osteopontin; lung cancer; prognosis; meta-analysis
21.  Health Services Utilisation in Breast Cancer Survivors in Taiwan 
Scientific Reports  2014;4:7466.
Surveillance guidelines for breast cancer survivors recommend regular history and physical and mammography, and against routine imaging for detecting distant metastasis. Stage 0, I, II breast cancer cases treated at a major cancer center were identified from the Taiwan Cancer Registry. We used multivariable negative binomial and logistic regression analyses on institutional claims data to examine factors contributing to utilisation patterns of surveillance visits and tests in disease-free survivors. The mean number of surveillance visits during months 13 to 60 after cancer treatment initiation was 18.5 (SD 8.2) among the 2,090 breast cancer survivors followed for at least five years. After adjusting for patient and disease factors, the number of visits was the highest among patients mainly followed by medical oncologists compared to surgeons and radiation oncologists. Patient cohorts treated in more recent years had lower number of visits associated with care coordination effort, the adjusted mean being 19.2 visits for the 2002 cohort, and 16.3 visits for the 2008 cohort (p < 0.0001). Although imaging tests were highly utilised, there was a significant decrease in tumor marker testing from the 2002 to the 2008 treatment cohort (adjusted rate 99.4% to 35.1% respectively, p < 0.0001) in association with an institutional guideline change.
doi:10.1038/srep07466
PMCID: PMC4264011  PMID: 25502076
22.  Phosphoproteomic Profiling of Selenate-Treated Alzheimer's Disease Model Cells 
PLoS ONE  2014;9(12):e113307.
The reversible phosphorylation of proteins regulates most biological processes, while abnormal phosphorylation is a cause or consequence of many diseases including Alzheimer's disease (AD). One of the hallmarks of AD is the formation of neurofibrillary tangles (NFTs), which is composed of hyperphosphorylated tau proteins. Sodium selenate has been recently found to reduce tau hyperphosphorylation and NFTs formation, and to improve spatial learning and motor performance in AD mice. In the current study, the phosphoproteomics of N2aSW cells treated with selenate were investigated. To avoid missing low-abundance phosphoproteins, both the total proteins of cells and the phosphor-enriched proteins were extracted and subjected to the two-dimensional gel electrophoresis with Pro-Q diamond staining and then LC-MS/MS analysis. A total of 65 proteins were altered in phosphorylation level, of which 39 were up-regulated and 26 were down-regulated. All identified phosphoproteins were bioinformatically annotated according to their physiochemical features, subcellular location, and biological function. Most of these significantly changed phosphoproteins are involved in crucial neural processes such as protesome activity, oxidative stress, cysteine and methionine metabolism, and energy metabolism. Furthermore, decreases were found in homocysteine, phosphor-tau and amyloid β upon selenate treatment. Our results suggest that selenate may intervene in the pathological process of AD by altering the phosphorylation of some key proteins involved in oxidative stress, energy metabolism and protein degradation, thus play important roles in maintaining redox homeostasis, generating ATP, and clearing misfolded proteins and aggregates. The present paper provides some new clues to the mechanism of selenate in AD prevention.
doi:10.1371/journal.pone.0113307
PMCID: PMC4259334  PMID: 25485856
23.  Microfluidic Array with Integrated Oxygenation Control for Real-Time Live-Cell Imaging: Effect of Hypoxia on Physiology of Microencapsulated Pancreatic Islets 
Analytical chemistry  2013;85(23):11240-11249.
In this report, we present a novel microfluidic islet array based on a hydrodynamic trapping principle. The lab-on-a-chip studies with live-cell multiparametric imaging allow understanding of physiological and pathophysiological changes of microencapsulated islets under hypoxic conditions. Using this microfluidic array and imaging analysis techniques, we demonstrate that hypoxia impairs the function of microencapsulated islets at single islet level, showing a heterogeneous pattern reflected in intracellular calcium signaling, mitochondrial energetic, and redox activity. Our approach demonstrates an improvement over conventional hypoxia chambers that is able to rapidly equilibrate to true hypoxia levels through the integration of dynamic oxygenation. This work demonstrates the feasibility of array-based cellular analysis and opens up new modality to conduct informative analysis and cell-based screening for microencapsulated pancreatic islets.
doi:10.1021/ac401297v
PMCID: PMC3921903  PMID: 24083835
Microfluidic; Hydrodynamic trap; Islet trapping array; Microencapsulation; Pancreatic islets of Langerhans; Hypoxia; Calcium; Mitochondrial potential; Insulin secretion
24.  Effect of Soluble Inducible Costimulator Level and Its Polymorphisms on Age-Related Macular Degeneration 
DNA and Cell Biology  2013;32(12):717-721.
Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly population. Evidence has shown that the human immune system may play critical roles in this disease. Inducible costimulator (ICOS) promotes T-cell activation, differentiation, and T:B-cell interactions. The aim of the study was to understand the effect of ICOS on the development of AMD from genetic polymorphism perspective and serum level perspective. Two ICOS polymorphisms, rs10183087A/C and rs10932037C/T, were tested in 223 AMD cases and 262 healthy controls. The serum level of soluble ICOS (sICOS) was compared among subjects with different genotypes, as well as between AMD patients and controls. Data showed that prevalence of rs10183087CC genotype was significantly increased in AMD than in controls (p=0.001). Function analysis revealed that subjects carrying rs10183087CC genotype had higher serum levels of sICOS than those with AA or AC genotypes (p<0.05). When we compared serum levels of sICOS between cases and controls, results showed that AMD patients had significantly increased sICOS levels than healthy donors (p<0.05). Also, wet type cases were observed to have higher sICOS levels than cases with dry type (p<0.05). These data suggested ICOS polymorphism could affect the susceptibility to AMD by elevating protein expression, and serum levels of sICOS may be closed correlated with the development and progression of this disease.
doi:10.1089/dna.2013.2127
PMCID: PMC3864366  PMID: 24083358
25.  Oligodendrocyte Lineage and Subventricular Zone Response to Traumatic Axonal Injury in the Corpus Callosum 
Traumatic brain injury frequently causes traumatic axonal injury (TAI) in white matter tracts. Experimental TAI in the corpus callosum of adult mice was used to examine the effects on oligodendrocyte lineage cells and myelin in conjunction with neuroimaging. The injury targeted the corpus callosum over the subventricular zone, a source of neural stem/progenitor cells. TAI was produced in the rostral body of the corpus callosum by impact onto the skull at bregma. During the first week post-injury, magnetic resonance diffusion tensor imaging showed that axial diffusivity decreased in the corpus callosum and that corresponding regions exhibited significant axon damage accompanied by hypertrophic microglia and reactive astrocytes. Oligodendrocyte progenitor proliferation increased in the subventricular zone and corpus callosum. Oligodendrocytes in the corpus callosum shifted toward upregulation of myelin gene transcription. Plp/CreERT:R26IAP reporter mice showed normal reporter labeling of myelin sheaths 0 to 2 days post-injury but labeling was increased between 2 to 7 days post-injury. Electron microscopy revealed axon degeneration, demyelination and redundant myelin figures. These findings expand the cell types and responses to white matter injuries that inform diffusion tensor imaging evaluation and identify pivotal white matter changes following TAI that may affect axon vulnerability vs. recovery following brain injury.
doi:10.1097/NEN.0000000000000009
PMCID: PMC4130339  PMID: 24226267
Traumatic brain injury; Axonal damage; Corpus callosum; Diffusion tensor imaging; Oligodendrocyte progenitor; Redundant myelin; Regeneration

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