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1.  Nutrition and physical activity randomized control trial in child care centers improves knowledge, policies, and children’s body mass index 
BMC Public Health  2014;14:215.
Background
To address the public health crisis of overweight and obese preschool-age children, the Nutrition And Physical Activity Self Assessment for Child Care (NAP SACC) intervention was delivered by nurse child care health consultants with the objective of improving child care provider and parent nutrition and physical activity knowledge, center-level nutrition and physical activity policies and practices, and children’s body mass index (BMI).
Methods
A seven-month randomized control trial was conducted in 17 licensed child care centers serving predominantly low income families in California, Connecticut, and North Carolina, including 137 child care providers and 552 families with racially and ethnically diverse children three to five years old. The NAP SACC intervention included educational workshops for child care providers and parents on nutrition and physical activity and consultation visits provided by trained nurse child care health consultants. Demographic characteristics and pre - and post-workshop knowledge surveys were completed by providers and parents. Blinded research assistants reviewed each center’s written health and safety policies, observed nutrition and physical activity practices, and measured randomly selected children’s nutritional intake, physical activity, and height and weight pre- and post-intervention.
Results
Hierarchical linear models and multiple regression models assessed individual- and center-level changes in knowledge, policies, practices and age- and sex-specific standardized body mass index (zBMI), controlling for state, parent education, and poverty level. Results showed significant increases in providers’ and parents’ knowledge of nutrition and physical activity, center-level improvements in policies, and child-level changes in children’s zBMI based on 209 children in the intervention and control centers at both pre- and post-intervention time points.
Conclusions
The NAP SACC intervention, as delivered by trained child health professionals such as child care health consultants, increases provider knowledge, improves center policies, and lowers BMI for children in child care centers. More health professionals specifically trained in a nutrition and physical activity intervention in child care are needed to help reverse the obesity epidemic.
Trial registration
National Clinical Trials Number NCT01921842
doi:10.1186/1471-2458-14-215
PMCID: PMC3945995  PMID: 24580983
Child care; Nutrition; Physical activity; Body mass index; Child care health consultants; Obesity; Overweight
2.  PAQR3 Modulates Insulin Signaling by Shunting Phosphoinositide 3-Kinase p110α to the Golgi Apparatus 
Diabetes  2013;62(2):444-456.
Phosphoinositide 3-kinase (PI3K) mediates insulin actions by relaying signals from insulin receptors (IRs) to downstream targets. The p110α catalytic subunit of class IA PI3K is the primary insulin-responsive PI3K implicated in insulin signaling. We demonstrate here a new mode of spatial regulation for the p110α subunit of PI3K by PAQR3 that is exclusively localized in the Golgi apparatus. PAQR3 interacts with p110α, and the intracellular targeting of p110α to the Golgi apparatus is reduced by PAQR3 downregulation and increased by PAQR3 overexpression. Insulin-stimulated PI3K activity and phosphoinositide (3,4,5)-triphosphate production are enhanced by Paqr3 deletion and reduced by PAQR3 overexpression in hepatocytes. Deletion of Paqr3 enhances insulin-stimulated phosphorylation of AKT and glycogen synthase kinase 3β, but not phosphorylation of IR and IR substrate-1 (IRS-1), in hepatocytes, mouse liver, and skeletal muscle. Insulin-stimulated GLUT4 translocation to the plasma membrane and glucose uptake are enhanced by Paqr3 ablation. Furthermore, PAQR3 interacts with the domain of p110α involved in its binding with p85, the regulatory subunit of PI3K. Overexpression of PAQR3 dose-dependently reduces the interaction of p85α with p110α. Thus, PAQR3 negatively regulates insulin signaling by shunting cytosolic p110α to the Golgi apparatus while competing with p85 subunit in forming a PI3K complex with p110α.
doi:10.2337/db12-0244
PMCID: PMC3554364  PMID: 23086038
3.  An Approach to Vicinal t-Boc-Amino Dibromides via Catalytic Aminobromination of Nitrostyrenes without using Chromatography and Recrystallization 
The Journal of organic chemistry  2013;78(3):1171-1175.
1.0 % Mol of K3PO4·3H2O was found to catalyze aminohalogenation reaction of nitrostyrenes with N,N-dibromo-tert-butylcarbamate (t-Boc-NBr2) in dichloroethane system. Good to excellent yields and complete regioselectivity have been achieved by taking advantage of the GAP work-up without using traditional purification techniques such as column chromatography and recrystallization. New mechanism was proposed involving radical and ionic catalytic cycles and an intramolecular migration.
doi:10.1021/jo302727v
PMCID: PMC3568972  PMID: 23311641
Aminohalogenation; bromoamine; Group-Assistant-Purification (GAP) chemistry; N,N-dibromo-tert-butylcarbamate; nitrostyrenes
4.  A Randomized, Double-Blind, Controlled Trial of the 17D Yellow Fever Virus Vaccine Given in Combination with Immune Globulin or Placebo: Comparative Viremia and Immunogenicity 
We evaluated whether coadministration of the yellow fever (YF) virus vaccine with human immunoglobulin (Ig) that contained YF virus-neutralizing antibodies would reduce post-vaccination viremia without compromising immunogenicity and thus, potentially mitigate YF vaccine-associated adverse events. We randomized 80 participants to receive either YF vaccine and Ig or YF vaccine and saline placebo. Participants were followed for 91 days for safety and assessments of viremia and immunogenicity. There were no differences found between the two groups in the proportion of vaccinated participants who developed viremia, seroconversion, cluster of differentiation (CD)-8+ and CD4+ T-cell responses, and cytokine responses. These results argue against one putative explanation for the increased reporting of YF vaccine side effects in recent years (i.e., a change in travel clinic practice after 1996 when hepatitis A prophylaxis with vaccine replaced routine use of pre-travel Ig, thus potentially removing an incidental YF vaccine-attenuating effect of anti-YF virus antibodies present in Ig) (ClinicalTrials.gov identifier: NCT00254826).
doi:10.4269/ajtmh.2012.12-0179
PMCID: PMC3541731  PMID: 23208880
5.  Asymmetric synthesis of α-alkenyl homoallylic primary amines via 1,2-addition of Grignard reagent to α,β-unsaturated phosphonyl imines 
RSC advances  2013;3(36):15820-15826.
A series of chiral N-phosphonyl protected α-alkenyl homoallylic primary amines were synthesized by asymmetric addition of allylmagnesium bromide Grignard reagent towards chiral α,β-unsaturated imines. Only 1,2-adduct was obtained for all the imines with good yields and excellent diastereoselectivities. The chiral auxiliary could be easily removed under simple conditions, giving free multiple functionalized primary amines.
doi:10.1039/C3RA42927J
PMCID: PMC3804338  PMID: 24159373
6.  Homocysteine Homeostasis and Betaine-Homocysteine S-Methyltransferase Expression in the Brain of Hibernating Bats 
PLoS ONE  2013;8(12):e85632.
Elevated homocysteine is an important risk factor that increases cerebrovascular and neurodegenerative disease morbidity. In mammals, B vitamin supplementation can reduce homocysteine levels. Whether, and how, hibernating mammals, that essentially stop ingesting B vitamins, maintain homocysteine metabolism and avoid cerebrovascular impacts and neurodegeneration remain unclear. Here, we compare homocysteine levels in the brains of torpid bats, active bats and rats to identify the molecules involved in homocysteine homeostasis. We found that homocysteine does not elevate in torpid brains, despite declining vitamin B levels. At low levels of vitamin B6 and B12, we found no change in total expression level of the two main enzymes involved in homocysteine metabolism (methionine synthase and cystathionine β-synthase), but a 1.85-fold increase in the expression of the coenzyme-independent betaine-homocysteine S-methyltransferase (BHMT). BHMT expression was observed in the amygdala of basal ganglia and the cerebral cortex where BHMT levels were clearly elevated during torpor. This is the first report of BHMT protein expression in the brain and suggests that BHMT modulates homocysteine in the brains of hibernating bats. BHMT may have a neuroprotective role in the brains of hibernating mammals and further research on this system could expand our biomedical understanding of certain cerebrovascular and neurodegenerative disease processes.
doi:10.1371/journal.pone.0085632
PMCID: PMC3871600  PMID: 24376891
7.  Capsular Types of Klebsiella pneumoniae Revisited by wzc Sequencing 
PLoS ONE  2013;8(12):e80670.
Capsule is an important virulence factor in bacteria. A total of 78 capsular types have been identified in Klebsiella pneumoniae. However, there are limitations in current typing methods. We report here the development of a new genotyping method based on amplification of the variable regions of the wzc gene. Fragments corresponding to the variable region of wzc were amplified and sequenced from 76 documented capsular types of reference or clinical strains. The remaining two capsular types (reference strains K15 and K50) lacked amplifiable wzc genes and were proven to be acapsular. Strains with the same capsular type exhibited ≧94% DNA sequence identity across the variable region (CD1-VR2-CD2) of wzc. Strains with distinct K types exhibited <80% DNA sequence identity across this region, with the exception of three pairs of strains: K22/K37, K9/K45, and K52/K79. Strains K22 and K37 shared identical capsular polysaccharide synthesis (cps) genes except for one gene with a difference at a single base which resulted in frameshift mutation. The wzc sequences of K9 and K45 exhibited high DNA sequence similarity but possessed different genes in their cps clusters. K52 and K79 exhibited 89% wzc DNA sequence identity but were readily distinguished from each other at the DNA level; in contrast, strains with the same capsular type as K52 exhibited 100% wzc sequence identity. A total of 29 strains from patients with bacteremia were typed by the wzc system. wzc DNA sequences confirmed the documented capsular type for twenty-eight of these clinical isolates; the remaining strain likely represents a new capsular type. Thus, the wzc genotyping system is a simple and useful method for capsular typing of K. pneumoniae.
doi:10.1371/journal.pone.0080670
PMCID: PMC3857182  PMID: 24349011
8.  Prediction of essential proteins based on gene expression programming 
BMC Genomics  2013;14(Suppl 4):S7.
Background
Essential proteins are indispensable for cell survive. Identifying essential proteins is very important for improving our understanding the way of a cell working. There are various types of features related to the essentiality of proteins. Many methods have been proposed to combine some of them to predict essential proteins. However, it is still a big challenge for designing an effective method to predict them by integrating different features, and explaining how these selected features decide the essentiality of protein. Gene expression programming (GEP) is a learning algorithm and what it learns specifically is about relationships between variables in sets of data and then builds models to explain these relationships.
Results
In this work, we propose a GEP-based method to predict essential protein by combing some biological features and topological features. We carry out experiments on S. cerevisiae data. The experimental results show that the our method achieves better prediction performance than those methods using individual features. Moreover, our method outperforms some machine learning methods and performs as well as a method which is obtained by combining the outputs of eight machine learning methods.
Conclusions
The accuracy of predicting essential proteins can been improved by using GEP method to combine some topological features and biological features.
doi:10.1186/1471-2164-14-S4-S7
PMCID: PMC3856491  PMID: 24267033
9.  Critical Roles of p53 in Epithelial-Mesenchymal Transition and Metastasis of Hepatocellular Carcinoma Cells 
PLoS ONE  2013;8(9):e72846.
Hepatocellular carcinoma (HCC) is one of the most malignant tumors and the biggest obstacle in curing HCC is its high metastasis potential. Alteration of p53 is the most frequent genetic change found in HCC. Although the biological function of p53 in tumor initiation and progression has been well characterized, whether or not p53 is implicated in metastasis of HCC is largely unknown. In this study, we analyzed the potential functions of p53 in epithelial-mesenchymal transition (EMT) and metastasis of HCC cells. Both insulin- and TGF-β1-induced changes of critical EMT markers were greatly enhanced by p53 knockdown in HCC cells. The insulin- and TGF-β1-stimulated migration of HCC cells were enhanced by p53 knockdown. Furthermore, in vivo metastasis of HCC cells using different mouse models was robustly enhanced by p53 knockdown. In addition, we found that p53 regulation on EMT and metastasis involves β-catenin signaling. The nuclear accumulation and transcriptional activity of β-catenin was modulated by p53. The enhanced EMT phenotype, cell migration and tumor metastasis of HCC cells by p53 knockdown were abrogated by inhibiting β-catenin signal pathway. In conclusion, this study reveals that p53 plays a pivotal role in EMT and metastasis of HCC cells via its regulation on β-catenin signaling.
doi:10.1371/journal.pone.0072846
PMCID: PMC3759437  PMID: 24023784
10.  Iron-catalyzed decarboxylative alkenylation of cycloalkanes with arylvinyl carboxylic acids via a radical process 
Summary
A Fe(acac)3-catalyzed decarboxylative coupling of 2-(aryl)vinyl carboxylic acids with cycloalkanes was developed by using DTBP as an oxidant through a radical process. This reaction tolerates a wide range of substrates, and products are obtained in good to excellent yields (71–95%). The reaction also shows excellent stereoselectivity, and only trans-isomers are obtained.
doi:10.3762/bjoc.9.197
PMCID: PMC3778410  PMID: 24062833
alkenylation; cycloalkanes; decarboxylative; Fe(acac)3; free radical; sp3 C–H bonds
11.  Isolation of a Bacteriophage Specific for a New Capsular Type of Klebsiella pneumoniae and Characterization of Its Polysaccharide Depolymerase 
PLoS ONE  2013;8(8):e70092.
Background
Klebsiella pneumoniae is one of the major pathogens causing hospital-acquired multidrug-resistant infections. The capsular polysaccharide (CPS) is an important virulence factor of K. pneumoniae. With 78 capsular types discovered thus far, an association between capsular type and the pathogenicity of K. pneumoniae has been observed.
Methodology/Principal Findings
To investigate an initially non-typeable K. pneumoniae UTI isolate NTUH-K1790N, the cps gene region was sequenced. By NTUH-K1790N cps-PCR genotyping, serotyping and determination using a newly isolated capsular type-specific bacteriophage, we found that NTUH-K1790N and three other isolates Ca0507, Ca0421 and C1975 possessed a new capsular type, which we named KN2. Analysis of a KN2 CPS− mutant confirmed the role of capsule as the target recognized by the antiserum and the phage. A newly described lytic phage specific for KN2 K. pneumoniae, named 0507-KN2-1, was isolated and characterized using transmission electron microscopy. Whole-genome sequencing of 0507-KN2-1 revealed a 159 991 bp double-stranded DNA genome with a G+C content of 46.7% and at least 154 open reading frames. Based on its morphological and genomic characteristics, 0507-KN2-1 was classified as a member of the Myoviridae phage family. Further analysis of this phage revealed a 3738-bp gene encoding a putative polysaccharide depolymerase. A recombinant form of this protein was produced and assayed to confirm its enzymatic activity and specificity to KN2 capsular polysaccharides. KN2 K. pneumoniae strains exhibited greater sensitivity to this depolymerase than these did to the cognate phage, as determined by spot analysis.
Conclusions/Significance
Here we report that a group of clinical strains possess a novel Klebsiella capsular type. We identified a KN2-specific phage and its polysaccharide depolymerase, which could be used for efficient capsular typing. The lytic phage and depolymerase also have potential as alternative therapeutic agents to antibiotics for treating K. pneumoniae infections, especially against antibiotic-resistant strains.
doi:10.1371/journal.pone.0070092
PMCID: PMC3732264  PMID: 23936379
12.  A Study on Bone Mass in Elderly Chinese Foot-Binding Women 
The aim of this study is to understand the influences of the social custom of foot binding on female osteoporosis by means of comparing and analyzing the lumbar vertebrae and hip bone mass differences between the foot-binding aged women and unbound women of the same age at Qujing District of Yunnan Province. Of the examined people, 81.37% suffer from osteoporosis on the basis of lumbar vertebra (L1–L4) and femoral neck BMD, of which 82.14% for the foot-binding group and 80.44% for the unbound group. There is no statistical difference for the osteoporosis morbidity of the two groups. Compare the BMD value for various vertebrae, femoral neck, and rehabilitation of the two groups and find the BMD value for the other parts have no statistical difference except the BMD value of L1 centrum, which shows that foot binding does not significantly influence the overall bone mineral density of foot-binding women.
doi:10.1155/2013/351670
PMCID: PMC3707270  PMID: 23864856
13.  Prevalence of metabolic syndrome among urban community residents in China 
BMC Public Health  2013;13:599.
Background
Metabolic risk factors and abnormalities such as obesity and hypertension are rapidly rising among the Chinese population following China’s tremendous economic growth and widespread westernization of lifestyle in recent decades. Limited information is available about the current burden of metabolic syndrome (MetS) in China.
Methods
We analyzed data on metabolic risk factors among 22,457 adults aged ≥ 32 years participating in the “Zhabei Health 2020” survey (2009–2010), a cross-sectional study of a representative sample of community residents in Zhabei District. We defined MetS using Chinese-specific cut-off points for central obesity according to consensus criteria recently endorsed by several international and national organizations in defining MetS in different populations worldwide. We used a multiple logistic regression model to assess the associations of potential risk factors with MetS.
Results
The unadjusted prevalence of the MetS was 35.1% for men and 32.5% for women according to the consensus criteria for Chinese. The prevalence increased progressively from 12.1% among participants aged 32–45 years to 45.4% among those aged ≥ 75 years. Age, smoking, family history of diabetes, and education are significantly associated with risk of MetS.
Conclusions
The MetS is highly prevalent and has reached epidemic proportion in Chinese urban adult community residents.
doi:10.1186/1471-2458-13-599
PMCID: PMC3734094  PMID: 23786855
Metabolic syndrome; Prevalence; Population-based survey; China
14.  Adaptation of Phenylalanine and Tyrosine Catabolic Pathway to Hibernation in Bats 
PLoS ONE  2013;8(4):e62039.
Some mammals hibernate in response to harsh environments. Although hibernating mammals may metabolize proteins, the nitrogen metabolic pathways commonly activated during hibernation are not fully characterized. In contrast to the hypothesis of amino acid preservation, we found evidence of amino acid metabolism as three of five key enzymes, including phenylalanine hydroxylase (PAH), homogentisate 1,2-dioxygenase (HGD), fumarylacetoacetase (FAH), involved in phenylalanine and tyrosine catabolism were co-upregulated during hibernation in two distantly related species of bats, Myotis ricketti and Rhinolophus ferrumequinum. In addition, the levels of phenylalanine in the livers of these bats were significantly decreased during hibernation. Because phenylalanine and tyrosine are both glucogenic and ketogenic, these results indicate the role of this catabolic pathway in energy supply. Since any deficiency in the catabolism of these two amino acids can cause accumulations of toxic metabolites, these results also suggest the detoxification role of these enzymes during hibernation. A higher selective constraint on PAH, HPD, and HGD in hibernators than in non-hibernators was observed, and hibernators had more conserved amino acid residues in each of these enzymes than non-hibernators. These conserved amino acid residues are mostly located in positions critical for the structure and activity of the enzymes. Taken together, results of this work provide novel insights in nitrogen metabolism and removal of harmful metabolites during bat hibernation.
doi:10.1371/journal.pone.0062039
PMCID: PMC3631164  PMID: 23620802
15.  PAQR10 and PAQR11 mediate Ras signaling in the Golgi apparatus 
Cell Research  2011;22(4):661-676.
Ras plays a pivotal role in many cellular activities, and its subcellular compartmentalization provides spatial and temporal selectivity. Here we report a mode of spatial regulation of Ras signaling in the Golgi apparatus by two highly homologous proteins PAQR10 and PAQR11 of the progestin and AdipoQ receptors family. PAQR10 and PAQR11 are exclusively localized in the Golgi apparatus. Overexpression of PAQR10/PAQR11 stimulates basal and EGF-induced ERK phosphorylation and increases the expression of ERK target genes in a dose-dependent manner. Overexpression of PAQR10/PAQR11 markedly elevates Golgi localization of HRas, NRas and KRas4A, but not KRas4B. PAQR10 and PAQR11 can also interact with HRas, NRas and KRas4A, but not KRas4B. The increased Ras protein at the Golgi apparatus by overexpression of PAQR10/PAQR11 is in an active state. Consistently, knockdown of PAQR10 and PAQR11 reduces EGF-stimulated ERK phosphorylation and Ras activation at the Golgi apparatus. Intriguingly, PAQR10 and PAQR11 are able to interact with RasGRP1, a guanine nucleotide exchange protein of Ras, and increase Golgi localization of RasGRP1. The C1 domain of RasGRP1 is both necessary and sufficient for the interaction of RasGRP1 with PAQR10/PAQR11. The simulation of ERK phosphorylation by overexpressed PAQR10/PAQR11 is abrogated by downregulation of RasGRP1. Furthermore, differentiation of PC12 cells is significantly enhanced by overexpression of PAQR10/PAQR11. Collectively, this study uncovers a new paradigm of spatial regulation of Ras signaling in the Golgi apparatus by PAQR10 and PAQR11.
doi:10.1038/cr.2011.161
PMCID: PMC3317553  PMID: 21968647
Ras; Signal transduction; Golgi apparatus; compartmentalization; ERK
16.  An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation 
BMC Systems Biology  2013;7:28.
Background
Identifying protein complexes from protein-protein interaction network is fundamental for understanding the mechanism of cellular component and protein function. At present, many methods to identify protein complexes are mainly based on the topological characteristics or the functional similarity features, neglecting the fact that proteins must be in their active forms to interact with others and the formation of protein complex is following a just-in-time mechanism.
Results
This paper firstly presents a protein complex formation model based on the just-in-time mechanism. By investigating known protein complexes combined with gene expression data, we find that most protein complexes can be formed in continuous time points, and the average overlapping rate of the known complexes during the formation is large. A method is proposed to refine the protein complexes predicted by clustering algorithms based on the protein complex formation model and the properties of known protein complexes. After refinement, the number of known complexes that are matched by predicted complexes, Sensitivity, Specificity, and f-measure are significantly improved, when compared with those of the original predicted complexes.
Conclusion
The refining method can discard the spurious proteins by protein activity and generate new complexes by just-in-time assemble mechanism, which can enhance the ability to predict complex.
doi:10.1186/1752-0509-7-28
PMCID: PMC3648373  PMID: 23537347
Protein activity; Protein complex formation model; Just-in-time; Refining; Gene expression
17.  An outbreak of norovirus gastroenteritis associated with a secondary water supply system in a factory in south China 
BMC Public Health  2013;13:283.
Background
Between September 17 and October 3, 2009, hundreds of workers employed in a manufacturing factory in Shenzhen, a city in south China developed a sudden onset of acute gastroenteritis. A retrospective cohort study is designed to identify the risk factors and control this outbreak.
Methods
Information on demographic characteristics, working place, the history of contact with a person having diarrhea and/or vomiting, drink water preference and frequency, eating in the company cafeteria or outside the company, hand-washing habits and eating habits is included. Furthermore, in order to find the contamination source, we investigated the environment around the underground reservoir and collected water samples from the junction between municipal supply water system and underground reservoir to test potential bacteria and virus, examine the seepage tracks on the wall of the underground reservoir from the side of septic tank, and check the integrity and attitude of this lid. Relative risk was presented and Chi-square test was performed. All the analyses were performed with OpenEpi software version 2.3.1 online.
Results
The cohort study demonstrated that the workers who had direct drink water were 3.0 fold more likely to suffer from acute gastroenteritis than those who consumed commercial bottled water. The direct drinking water, water of the tank of buildings, and the underground reservoir were positive only for norovirus. Norovirus was also detected from stool and rectal swab samples from patients with acute gastroenteritis. The underground reservoir was found to be the primary contamination source. Further environmental investigation showed that the norovirus contaminated substance entered into the underground reservoir via access holes in lid covering this underground reservoir.
Conclusion
This acute gastroenteritis outbreak was caused by the secondary supply system contaminated by norovirus in this factory. The outbreak of gastroenteritis cases caused by norovirus frequently occurred in China due to a lack of surveillance and supervision, and due to faults in the construction of such water systems. Therefore, more attentions should pay to the secondary supply water system in China.
doi:10.1186/1471-2458-13-283
PMCID: PMC3679847  PMID: 23537289
Norovirus; Acute gastroenteritis; Outbreak; Secondary water supply system
18.  Association of CASP9, CASP10 gene polymorphisms and tea drinking with colorectal cancer risk in the Han Chinese population*  
The initiators caspase-9 (CASP9) and caspase-10 (CASP10) are two key controllers of apoptosis and play important roles in carcinogenesis. This study aims to explore the association between CASPs gene polymorphisms and colorectal cancer (CRC) susceptibility in a population-based study. A two-stage designed population-based case-control study was carried out, including a testing set with 300 cases and 296 controls and a validation set with 206 cases and 845 controls. A total of eight tag selected single nucleotide polymorphisms (SNPs) in CASP9 and CASP10 were chosen based on HapMap and the National Center of Biotechnology Information (NCBI) datasets and genotyped by restriction fragment length polymorphism (RFLP) assay. Multivariate logistic regression models were applied to evaluate the association of SNPs with CRC risk. In the first stage, from eight tag SNPs, three polymorphisms rs4646077 (odds ratio (OR)AA+AG: 0.654, 95% confidence interval (CI): 0.406–1.055; P=0.082), rs4233532 (ORCC: 1.667, 95% CI: 0.967–2.876; ORCT: 1.435, 95% CI: 0.998–2.063; P=0.077), and rs2881930 (ORCC: 0.263, 95% CI: 0.095–0.728, P=0.036) showed possible association with CRC risk. However, none of the three SNPs, rs4646077 (ORAA+AG: 1.233, 95% CI: 0.903–1.683), rs4233532 (ORCC: 0.892, 95% CI: 0.640–1.243; ORCT: 1.134, 95% CI: 0.897–1.433), and rs2881930 (ORCC: 1.096, 95% CI: 0.620–1.938; ORCT: 1.009, 95% CI: 0.801–1.271), remained significant with CRC risk in the validation set, even after stratification for different tumor locations (colon or rectum). In addition, never tea drinking was associated with a significantly increased risk of CRC in testing set together with validation set (OR: 1.755, 95% CI: 1.319–2.334). Our results found that polymorphisms of CASP9 and CASP10 genes may not contribute to CRC risk in Chinese population and thereby the large-scale case-control studies might be in consideration. In addition, tea drinking was a protective factor for CRC.
doi:10.1631/jzus.B1200218
PMCID: PMC3542958  PMID: 23303631
CASP9; CASP10; Colorectal cancer; Single nucleotide polymorphisms; Susceptibility to cancer; Tea drinking
19.  Associations of CFH Polymorphisms and CFHR1-CFHR3 Deletion with Blood Pressure and Hypertension in Chinese Population 
PLoS ONE  2012;7(7):e42010.
Dysregulation of the complement system has been linked to pathogenesis of hypertension. However, whether genetic changes of complement factor H (CFH) and its related genes are associated with hypertension is unknown. We genotyped three SNPs in the CFH gene cluster that are closely linked to age-related macular degeneration, namely rs1061170 (Y402H), rs2274700 (A473A) and rs7542235 (CFHR1–3Δ), and tested for their associations with blood pressure and hypertension risk in a population-based cohort including 3,210 unrelated Chinese Hans (50–70 years of age) from Beijing and Shanghai. We found that rs2274700 (A473A) and rs7542235 (CFHR1–3Δ) were both significantly associated with diastolic blood pressure (DBP) (β = 0.632–1.431, P≤0.038) and systolic blood pressure (SBP) (β = 1.567–4.445, P≤0.008), and rs2274700 (A473A) was associated with hypertension risk (OR [95%CI]: 1.175 [1.005–1.373], P = 0.048). Notably, the associations of rs2274700 (A473A) with DBP (P = 2.1×10−3), SBP (P = 8×10−5) and hypertension risk (P = 7.9×10−3) were significant only in the individuals with low CRP levels (<2.0 mg/l), but not in those with CRP levels ≥2.0 mg/l (P≥0.0807) (P for interaction ≤0.0467). However, no significant association between rs1061170 (Y402H) and blood pressure or hypertension risk was observed (P≥0.259). In conclusion, our results suggest that genetic variations in CFH and its related genes may contribute to hypertension risk in Chinese Hans.
doi:10.1371/journal.pone.0042010
PMCID: PMC3405009  PMID: 22848687
20.  Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks 
BMC Systems Biology  2012;6:87.
Background
Identification of essential proteins plays a significant role in understanding minimal requirements for the cellular survival and development. Many computational methods have been proposed for predicting essential proteins by using the topological features of protein-protein interaction (PPI) networks. However, most of these methods ignored intrinsic biological meaning of proteins. Moreover, PPI data contains many false positives and false negatives. To overcome these limitations, recently many research groups have started to focus on identification of essential proteins by integrating PPI networks with other biological information. However, none of their methods has widely been acknowledged.
Results
By considering the facts that essential proteins are more evolutionarily conserved than nonessential proteins and essential proteins frequently bind each other, we propose an iteration method for predicting essential proteins by integrating the orthology with PPI networks, named by ION. Differently from other methods, ION identifies essential proteins depending on not only the connections between proteins but also their orthologous properties and features of their neighbors. ION is implemented to predict essential proteins in S. cerevisiae. Experimental results show that ION can achieve higher identification accuracy than eight other existing centrality methods in terms of area under the curve (AUC). Moreover, ION identifies a large amount of essential proteins which have been ignored by eight other existing centrality methods because of their low-connectivity. Many proteins ranked in top 100 by ION are both essential and belong to the complexes with certain biological functions. Furthermore, no matter how many reference organisms were selected, ION outperforms all eight other existing centrality methods. While using as many as possible reference organisms can improve the performance of ION. Additionally, ION also shows good prediction performance in E. coli K-12.
Conclusions
The accuracy of predicting essential proteins can be improved by integrating the orthology with PPI networks.
doi:10.1186/1752-0509-6-87
PMCID: PMC3472210  PMID: 22808943
21.  Genetic epistasis between heparan sulfate and FGF-Ras signaling controls lens development 
Developmental biology  2011;355(1):12-20.
Vertebrate lens development depends on a complex network of signaling molecules to coordinate cell proliferation, migration and differentiation. In this study, we have studied the role of heparan sulfate in lens specific signaling by generating a conditional ablation of heparan sulfate modification genes, Ndst1 and Ndst2. In this mutant, N-sulfation of heparan sulfate was disrupted after the lens induction stage, resulting in reduced lens cell proliferation, increased cell death and defective lens fiber differentiation in later lens development. The loss of Ndst function also prevented the assembly of Fgf/Fgfr complexes on the lens cell surface and disrupted ERK signaling within the lens. We further demonstrated that Ndst mutation completely inhibited the FGF1 and Fgf3 overexpression phenotypes, but Kras reactivation was sufficient to reverse the Ndst deficient lens differentiation defect. The epistatic relationship between Ndst and FGF-Ras signaling demonstrates that FGF signaling is the predominant signaling pathway controlled by Ndst in lens development.
doi:10.1016/j.ydbio.2011.04.007
PMCID: PMC3104109  PMID: 21536023
Ndst; lens; heparan sulfate; FGF; Ras
22.  Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data 
BMC Bioinformatics  2012;13:109.
Background
Identification of protein complexes and functional modules from protein-protein interaction (PPI) networks is crucial to understanding the principles of cellular organization and predicting protein functions. In the past few years, many computational methods have been proposed. However, most of them considered the PPI networks as static graphs and overlooked the dynamics inherent within these networks. Moreover, few of them can distinguish between protein complexes and functional modules.
Results
In this paper, a new framework is proposed to distinguish between protein complexes and functional modules by integrating gene expression data into protein-protein interaction (PPI) data. A series of time-sequenced subnetworks (TSNs) is constructed according to the time that the interactions were activated. The algorithm TSN-PCD was then developed to identify protein complexes from these TSNs. As protein complexes are significantly related to functional modules, a new algorithm DFM-CIN is proposed to discover functional modules based on the identified complexes. The experimental results show that the combination of temporal gene expression data with PPI data contributes to identifying protein complexes more precisely. A quantitative comparison based on f-measure reveals that our algorithm TSN-PCD outperforms the other previous protein complex discovery algorithms. Furthermore, we evaluate the identified functional modules by using “Biological Process” annotated in GO (Gene Ontology). The validation shows that the identified functional modules are statistically significant in terms of “Biological Process”. More importantly, the relationship between protein complexes and functional modules are studied.
Conclusions
The proposed framework based on the integration of PPI data and gene expression data makes it possible to identify protein complexes and functional modules more effectively. Moveover, the proposed new framework and algorithms can distinguish between protein complexes and functional modules. Our findings suggest that functional modules are closely related to protein complexes and a functional module may consist of one or multiple protein complexes. The program is available at http://netlab.csu.edu.cn/bioinfomatics/limin/DFM-CIN/index.html.
doi:10.1186/1471-2105-13-109
PMCID: PMC3434013  PMID: 22621308
23.  Fasting-Induced Protein Phosphatase 1 Regulatory Subunit Contributes to Postprandial Blood Glucose Homeostasis via Regulation of Hepatic Glycogenesis 
Diabetes  2011;60(5):1435-1445.
OBJECTIVE
Most animals experience fasting–feeding cycles throughout their lives. It is well known that the liver plays a central role in regulating glycogen metabolism. However, how hepatic glycogenesis is coordinated with the fasting–feeding cycle to control postprandial glucose homeostasis remains largely unknown. This study determines the molecular mechanism underlying the coupling of hepatic glycogenesis with the fasting–feeding cycle.
RESEARCH DESIGN AND METHODS
Through a series of molecular, cellular, and animal studies, we investigated how PPP1R3G, a glycogen-targeting regulatory subunit of protein phosphatase 1 (PP1), is implicated in regulating hepatic glycogenesis and glucose homeostasis in a manner tightly orchestrated with the fasting–feeding cycle.
RESULTS
PPP1R3G in the liver is upregulated during fasting and downregulated after feeding. PPP1R3G associates with glycogen pellet, interacts with the catalytic subunit of PP1, and regulates glycogen synthase (GS) activity. Fasting glucose level is reduced when PPP1R3G is overexpressed in the liver. Hepatic knockdown of PPP1R3G reduces postprandial elevation of GS activity, decreases postprandial accumulation of liver glycogen, and decelerates postprandial clearance of blood glucose. Other glycogen-targeting regulatory subunits of PP1, such as PPP1R3B, PPP1R3C, and PPP1R3D, are downregulated by fasting and increased by feeding in the liver.
CONCLUSIONS
We propose that the opposite expression pattern of PPP1R3G versus other PP1 regulatory subunits comprise an intricate regulatory machinery to control hepatic glycogenesis during the fasting–feeding cycle. Because of its unique expression pattern, PPP1R3G plays a major role to control postprandial glucose homeostasis during the fasting–feeding transition via its regulation on liver glycogenesis.
doi:10.2337/db10-1663
PMCID: PMC3292316  PMID: 21471512
24.  FAK is required for the assembly of podosome rosettes 
The Journal of Cell Biology  2011;195(1):113-129.
FAK opposes Rho activity and vimentin intermediate filament formation to promote podosome rosette assembly.
Podosomes are dynamic actin-enriched membrane structures that play an important role in invasive cell motility and extracellular matrix degradation. They are often found to assemble into large rosettelike structures in highly invasive cells. However, the mechanism of this assembly remains obscure. In this study, we identified focal adhesion kinase (FAK) as a key molecule necessary for assembly. Moreover, phosphorylation of p130Cas and suppression of Rho signaling by FAK were found to be important for FAK to induce the assembly of podosome rosettes. Finally, we found that suppression of vimentin intermediate filaments by FAK facilitates the assembly of podosome rosettes. Collectively, our results strongly suggest a link between FAK, podosome rosettes, and tumor invasion and unveil a negative role for Rho signaling and vimentin filaments in podosome rosette assembly.
doi:10.1083/jcb.201103016
PMCID: PMC3187704  PMID: 21969470
25.  Nonclassical Protein Secretion by Bacillus subtilis in the Stationary Phase Is Not Due to Cell Lysis ▿ 
Journal of Bacteriology  2011;193(20):5607-5615.
The carboxylesterase Est55 has been cloned and expressed in Bacillus subtilis strains. Est55, which lacks a classical, cleavable N-terminal signal sequence, was found to be secreted during the stationary phase of growth such that there is more Est55 in the medium than inside the cells. Several cytoplasmic proteins were also secreted in large amounts during late stationary phase, indicating that secretion in B. subtilis is not unique to Est55. These proteins, which all have defined cytoplasmic functions, include GroEL, DnaK, enolase, pyruvate dehydrogenase subunits PdhB and PdhD, and SodA. The release of Est55 and those proteins into the growth medium is not due to gross cell lysis, a conclusion that is supported by several lines of evidence: constant cell density and secretion in the presence of chloramphenicol, constant viability count, the absence of EF-Tu and SecA in the culture medium, and the lack of effect of autolysin-deficient mutants. The shedding of these proteins by membrane vesicles into the medium is minimal. More importantly, we have identified a hydrophobic α-helical domain within enolase that contributes to its secretion. Thus, upon the genetic deletion or replacement of a potential membrane-embedding domain, the secretion of plasmid gene-encoded mutant enolase is totally blocked, while the wild-type chromosomal enolase is secreted normally in the same cultures during the stationary phase, indicating differential specificity. We conclude that the secretion of Est55 and several cytoplasmic proteins without signal peptides in B. subtilis is a general phenomenon and is not a consequence of cell lysis or membrane shedding; instead, their secretion is through a process(es) in which protein domain structure plays a contributing factor.
doi:10.1128/JB.05897-11
PMCID: PMC3187209  PMID: 21856851

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