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author:("Zhang, haib")
1.  Circadian rhythms: From basic mechanisms to the intensive care unit 
Critical care medicine  2012;40(1):246-253.
Objective
Circadian rhythms are intrinsic timekeeping mechanisms that allow for adaptation to cyclic environmental changes. Increasing evidence suggests that circadian rhythms may influence progression of a variety of diseases as well as effectiveness and toxicity of drugs commonly used in the intensive care unit. In this perspective, we provide a brief review of the molecular mechanisms of circadian rhythms and its relevance to critical care.
Data Sources, Study Selection, Data Extraction, and Data Synthesis
Articles related to circadian rhythms and organ systems in normal and disease conditions were searched through the PubMed library with the goal of providing a concise review.
Conclusions
Critically ill patients may be highly vulnerable to disruption of circadian rhythms as a result of the severity of their underlying diseases as well as the intensive care unit environment where noise and frequent therapeutic/diagnostic interventions take place. Further basic and clinical research addressing the importance of circadian rhythms in the context of critical care is warranted to develop a better understanding of the complex pathophysiology of critically ill patients as well as to identify novel therapeutic approaches for these patients.
doi:10.1097/CCM.0b013e31822f0abe
PMCID: PMC3977926  PMID: 21926587 CAMSID: cams2913
clock gene; diurnal variation; inflammation
2.  Protective effects of adenosine A2A receptor agonist in ventilator-induced lung injury in rats 
Critical care medicine  2009;37(7):2235-2241.
Objectives
Mechanical ventilation is associated with overwhelming inflammatory responses that are associated with ventilator- induced lung injury (VILI) in patients with acute respiratory distress syndrome. The activation of adenosine A2A receptors has been reported to attenuate inflammatory cascades.
Hypothesis
The administration of A2A receptors agonist ameliorates VILI.
Methods
Rats were subjected to hemorrhagic shock and resuscitation as a first hit to induce systemic inflammation. The animals randomly received the selective A2A receptor agonist CGS-21680 or a vehicle control in a blinded fashion at the onset of resuscitation phase. They were then randomized to receive mechanical ventilation as a second hit with a high tidal volume of 20 mL/kg and zero positive end-expiratory pressure, or a low tidal volume of 6 mL/kg with positive end-expiratory pressure of 5 cm H2O.
Results
The administration of CGS-21680 attenuated lung injury as evidenced by a decrease in respiratory elastance, lung edema, lung injury scores, neutrophil recruitment in the lung, and production of inflammatory cytokines, compared with the vehicle treated animals.
Conclusions
The selective A2A receptor agonist may have a place as a novel therapeutic approach in reducing VILI.
doi:10.1097/CCM.0b013e3181a55273
PMCID: PMC3951985  PMID: 19487932 CAMSID: cams2915
acute respiratory distress syndrome; inflammation; neutrophils
3.  The Wnt Signaling Pathway Effector TCF7L2 Controls Gut and Brain Proglucagon Gene Expression and Glucose Homeostasis 
Diabetes  2013;62(3):789-800.
The type 2 diabetes risk gene TCF7L2 is the effector of the Wnt signaling pathway. We found previously that in gut endocrine L-cell lines, TCF7L2 controls transcription of the proglucagon gene (gcg), which encodes the incretin hormone glucagon-like peptide-1 (GLP-1). Whereas peripheral GLP-1 stimulates insulin secretion, brain GLP-1 controls energy homeostasis through yet-to-be defined mechanisms. We aim to determine the metabolic effect of a functional knockdown of TCF7L2 by generating transgenic mice that express dominant-negative TCF7L2 (TCF7L2DN) specifically in gcg-expressing cells. The gcg-TCF7L2DN transgenic mice showed reduced gcg expression in their gut and brain, but not in pancreas. Defects in glucose homeostasis were observed in these mice, associated with attenuated plasma insulin levels in response to glucose challenge. The defect in glucose disposal was exacerbated with high-fat diet. Brain Wnt activity and feeding-mediated hypothalamic AMP-activated protein kinase (AMPK) repression in these mice were impaired. Peripheral injection of the cAMP-promoting agent forskolin increased brain β-cat Ser675 phosphorylation and brain gcg expression and restored feeding-mediated hypothalamic AMPK repression. We conclude that TCF7L2 and Wnt signaling control gut and brain gcg expression and glucose homeostasis and speculate that positive cross-talk between Wnt and GLP-1/cAMP signaling is an underlying mechanism for brain GLP-1 in exerting its metabolic functions.
doi:10.2337/db12-0365
PMCID: PMC3581223  PMID: 22966074
4.  Microbial production of sabinene—a new terpene-based precursor of advanced biofuel 
Background
Sabinene, one kind of monoterpene, accumulated limitedly in natural organisms, is being explored as a potential component for the next generation of aircraft fuels. And demand for advanced fuels impels us to develop biosynthetic routes for the production of sabinene from renewable sugar.
Results
In this study, sabinene was significantly produced by assembling a biosynthetic pathway using the methylerythritol 4-phosphate (MEP) or heterologous mevalonate (MVA) pathway combining the GPP and sabinene synthase genes in an engineered Escherichia coli strain. Subsequently, the culture medium and process conditions were optimized to enhance sabinene production with a maximum titer of 82.18 mg/L. Finally, the fed-batch fermentation of sabinene was evaluated using the optimized culture medium and process conditions, which reached a maximum concentration of 2.65 g/L with an average productivity of 0.018 g h-1 g-1 dry cells, and the conversion efficiency of glycerol to sabinene (gram to gram) reached 3.49%.
Conclusions
This is the first report of microbial synthesis of sabinene using an engineered E. coli strain with the renewable carbon source as feedstock. Therefore, a green and sustainable production strategy has been established for sabinene.
doi:10.1186/1475-2859-13-20
PMCID: PMC3923588  PMID: 24512040
Sabinene; Geranyl diphosphate synthase; Sabinene synthase; Escherichia coli
5.  Reliability of intramyocardial electrogram for the noninvasive diagnosis of acute allograft rejection after heart transplantation in rats 
Journal of Thoracic Disease  2014;6(2):126-133.
Objectives
To examine the reliability of the QRS amplitude of the autonomous intramyocardial electrogram (IMEG) and the maximum slope of the descending T wave (Tslew) of the ventricular evoked response (VER) for surveillance of acute allograft rejection (AR) after heart transplantation in rats.
Methods
Forty rats underwent heterotopic heart transplantation, including ten isograft (isograft group) and 30 allograft (allograft group) recipients. Autonomous IMEG and VER were recorded with epicardiac pacing leads. Isograft recipients were sacrificed on postoperative day 7 and allograft recipients on postoperative days 3, 5 and 7. Graft heart histopathological examinations were performed at the corresponding time points.
Results
Postoperative QRS amplitude and Tslew gradually decreased in the allograft group, but were unaltered in the isograft group. Decreases in the allograft group QRS amplitudes and Tslew values correlated with the histopathological results. At the optimal cutoff point of 90%, Tslew had 94.74% sensitivity, 81.82% specificity, 82.61% positive and 90% negative predictive values. QRS had 68.42% sensitivity, 90.91% specificity, 92.86% positive and 62.50% negative predictive values at its optimal cutoff point of 72.3%.
Conclusions
The QRS amplitude of the autonomous IMEG and Tslew of VER are reliable markers for monitoring AR after heart transplantation in rats.
doi:10.3978/j.issn.2072-1439.2014.02.01
PMCID: PMC3944186  PMID: 24605226
Heart transplantation; acute allograft rejection; intramyocardial electrogram (IMEG)
6.  Correction: Long-Term Results of a Minimally Invasive Surgical Pulmonary Vein Isolation and Ganglionic Plexi Ablation for Atrial Fibrillation 
PLoS ONE  2014;9(1):10.1371/annotation/c46d8841-f33e-45ea-9c17-b754e1017641.
doi:10.1371/annotation/c46d8841-f33e-45ea-9c17-b754e1017641
PMCID: PMC3880343
7.  Intensive Care Unit-Acquired Bacteremia in Mechanically Ventilated Patients: Clinical Features and Outcomes 
PLoS ONE  2013;8(12):e83298.
Intensive care unit (ICU)-acquired bacteremia (IAB) is associated with high medical expenditure and mortality. Mechanically ventilated patients represent one third of all patients admitted to ICU, but the clinical features and outcomes in mechanically ventilated patients who develop IAB remain unknown. We conducted a 3-year retrospective observational cohort study, and 1,453 patients who received mechanical ventilation on ICU admission were enrolled. Among patients enrolled, 126 patients who had developed IAB ≧48 hours after ICU admission were identified. The study patients were divided into IAB and no IAB groups, and clinical characteristics of IAB based on specific bacterial species were further analyzed. The multivariate Cox regression analysis showed that ventilator support for chronic obstructive pulmonary disease and congestive heart failure, and patients admitted from nursing home were the independent risk factors for developing IAB. Patients with IAB were significantly associated with longer length of ICU stay, prolonged ventilator use, lower rate of successful weaning, and higher rate of ventilator dependence and ICU mortality as compared to those without IAB. IAB was the independent risk factor for ICU mortality (HR, 1.510, 95% CI 1.054–1.123; p = 0.010). The clinical characteristics of IAB related to specific bacterial species included IAB due to Pseudomonas aeruginosa being likely polymicrobial, lung source and prior antibiotic use; Escherichia coli developing earlier and from urinary tract source; methicillin-resistant Staphylococcus aureus related to central venous catheter and multiple sets of positive hemoculture; and Elizabethkingia meningoseptica significantly associated with delayed/inappropriate antibiotic treatment. In summary, IAB was significantly associated with poor patient outcomes in mechanically ventilated ICU patients. The clinical features related to IAB and clinical characteristics of IAB based on specific bacterial species identified in our study may be utilized to refine the management of IAB.
doi:10.1371/journal.pone.0083298
PMCID: PMC3871544  PMID: 24376683
8.  Correction: Rapamycin Inhibits IGF-1-Mediated Up-Regulation of MDM2 and Sensitizes Cancer Cells to Chemotherapy 
PLoS ONE  2013;8(12):10.1371/annotation/f1a4d192-57b9-43fb-a248-379e0f5a46ca.
doi:10.1371/annotation/f1a4d192-57b9-43fb-a248-379e0f5a46ca
PMCID: PMC3866301
9.  Year in review 2011: Critical Care - respirology 
Critical Care  2012;16(6):243.
Management of acute respiratory failure is an important component of intensive care. In this review, we analyze 21 original research articles published last year in Critical Care in the field of respiratory and critical care medicine. The articles are summarized according to the following topic categories: acute respiratory distress syndrome, mechanical ventilation, adjunctive therapies, and pneumonia.
doi:10.1186/cc11422
PMCID: PMC3672547  PMID: 23249764
11.  Long-Term Results of a Minimally Invasive Surgical Pulmonary Vein Isolation and Ganglionic Plexi Ablation for Atrial Fibrillation 
PLoS ONE  2013;8(11):e79755.
Background
Ganglionated plexi (GP) ablation has been become an adjunct to pulmonary vein isolation (PVI). This study describes the long-term results of minimally invasive surgical PVI, ablation of GPs, and exclusion of the left atrial appendage for atrial fibrillation (AF).
Methods
Long-term follow-up of 55 months was performed in 139 consecutive patients (age 58.3±20.8 years) with symptomatic, drug-refractory lone AF who underwent minimally invasive surgical PVI, GPs ablation, and exclusion of the left atrial appendage. Success was defined as freedom from AF, atrial flutter, or atrial tachycardia off antiarrhythmic drugs.
Results
AF was paroxysmal in 77.7%, persistent in 12.2% and long-standing persistent in 10.1%. Single-procedure success rate was 71.7%, 59.4% and 46.6% at 12, 24 and 60 months respectively. Single-procedure success rate was 72.9%, 62.6% and 51.8% for paroxysmal AF, 64.7%, 35.3%, and 28.2% for persistent AF, 71.4%, 64.3% and 28.6% for long-standing persistent AF at 12, 24 and 60 months respectively. Duration of AF>24 months (hazard ratio [HR]: 3.09, 95% confidence interval [CI]: 1.51 to 6.32; p = 0.002), left atrial diameter≥40 mm (HR: 4.03, 95% CI: 1.88 to 8.65; p<0.001), early recurrence of AF (HR: 4.66, 95% CI: 2.25 to 9.63; p<0.001) independently predicted long-term recurrence of AF. There was no procedure-related death. One patient converted to median sternotomy because of uncontrolled bleeding. Two patients underwent perioperative cerebrovascular events.
Conclusions
At nearly 5-year of clinical follow-up, single-procedure success rate of minimally invasive surgical PVI with GP ablation was 51.8% for paroxysmal AF, 28.2% for persistent AF, 28.6% for long-standing persistent AF after initial procedure. Patients with AF duration≤24 months, left atrial diameter<40 mm and no early recurrence of AF, had favorable outcomes.
doi:10.1371/journal.pone.0079755
PMCID: PMC3823568  PMID: 24244556
12.  Dynamics of translation by single ribosomes through mRNA secondary structures 
During protein synthesis, the ribosome translates nucleotide triplets in single-stranded mRNA into polypeptide sequences. Strong downstream mRNA secondary (2°) structures, which must be unfolded for translation, can slow or even halt protein synthesis. Here we employ single molecule fluorescence resonance energy transfer to determine reaction rates for specific steps within the elongation cycle as the Escherichia coli ribosome encounters stem loop or pseudoknot mRNA 2° structures. Downstream stem-loops containing 100% G-C base pairs decrease the rates of both tRNA translocation within the ribosome and deacylated tRNA dissociation from the ribosomal exit (E) site. Downstream stem-loops or pseudoknots containing both G-C and A-U pairs also decrease the rate of tRNA dissociation, but they have little effect on tRNA translocation rate. Thus, somewhat surprisingly, unfolding of mRNA 2° structures is more closely coupled to E-site tRNA dissociation than to tRNA translocation.
doi:10.1038/nsmb.2544
PMCID: PMC3648610  PMID: 23542154
13.  Biodegradation-inspired bioproduction of methylacetoin and 2-methyl-2,3-butanediol 
Scientific Reports  2013;3:2445.
Methylacetoin (3-hydroxy-3-methylbutan-2-one) and 2-methyl-2,3-butanediol are currently obtained exclusively via chemical synthesis. Here, we report, to the best of our knowledge, the first alternative route, using engineered Escherichia coli. The biological synthesis of methylacetoin was first accomplished by reversing its biodegradation, which involved modifying the enzyme complex involved, switching the reaction substrate, and coupling the process to an exothermic reaction. 2-Methyl-2,3-butanediol was then obtained by reducing methylacetoin by exploiting the substrate promiscuity of acetoin reductase. A complete biosynthetic pathway from renewable glucose and acetone was then established and optimized via in vivo enzyme screening and host metabolic engineering, which led to titers of 3.4 and 3.2 g l−1 for methylacetoin and 2-methyl-2,3-butanediol, respectively. This work presents a biodegradation-inspired approach to creating new biosynthetic pathways for small molecules with no available natural biosynthetic pathway.
doi:10.1038/srep02445
PMCID: PMC3744081  PMID: 23945710
14.  The Joint Effect of hOGG1, APE1, and ADPRT Polymorphisms and Cooking Oil Fumes on the Risk of Lung Adenocarcinoma in Chinese Non-Smoking Females 
PLoS ONE  2013;8(8):e71157.
Background
The human 8-oxoguanine DNA glycosylase 1 (hOGG1), apurinic/apyrimidinic endonuclease 1 (APE1), and adenosine diphosphate ribosyl transferase (ADPRT) genes play an important role in the DNA base excision repair pathway. Single nucleotide polymorphisms (SNPs) in critical genes are suspected to be associated with the risk of lung cancer. This study aimed to identify the association between the polymorphisms of hOGG1 Ser326Cys, APE1 Asp148Glu, and ADPRT Val762Ala, and the risk of lung adenocarcinoma in the non-smoking female population, and investigated the interaction between genetic polymorphisms and environmental exposure in lung adenocarcinoma.
Methods
We performed a hospital-based case-control study, including 410 lung adenocarcinoma patients and 410 cancer-free hospital control subjects who were matched for age. Each case and control was interviewed to collect information by well-trained interviewers. A total of 10 ml of venous blood was collected for genotype testing. Three polymorphisms were analyzed by the polymerase chain reaction-restriction fragment length polymorphism technique.
Results
We found that individuals who were homozygous for the variant hOGG1 326Cys/Cys showed a significantly increased risk of lung adenocarcinoma (OR = 1.54; 95% CI: 1.01–2.36; P = 0.045). When the combined effect of variant alleles was analyzed, we found an increased OR of 1.89 (95% CI: 1.24–2.88, P = 0.003) for lung adenocarcinoma individuals with more than one homozygous variant allele. In stratified analyses, we found that the OR for the gene-environment interaction between Ser/Cys and Cys/Cys genotypes of hOGG1 codon 326 and cooking oil fumes for the risk of lung adenocarcinoma was 1.37 (95% CI: 0.77–2.44; P = 0.279) and 2.79 (95% CI: 1.50–5.18; P = 0.001), respectively.
Conclusions
The hOGG1 Ser326Cys polymorphism might be associated with the risk of lung adenocarcinoma in Chinese non-smoking females. Furthermore, there is a significant gene-environment association between cooking oil fumes and hOGG1 326 Cys/Cys genotype in lung adenocarcinoma among female non-smokers.
doi:10.1371/journal.pone.0071157
PMCID: PMC3741325  PMID: 23951099
15.  Metabolic Engineering of Escherichia coli for the Production of Xylonate 
PLoS ONE  2013;8(7):e67305.
Xylonate is a valuable chemical for versatile applications. Although the chemical synthesis route and microbial conversion pathway were established decades ago, no commercial production of xylonate has been obtained so far. In this study, the industrially important microorganism Escherichia coli was engineered to produce xylonate from xylose. Through the coexpression of a xylose dehydrogenase (xdh) and a xylonolactonase (xylC) from Caulobacter crescentus, the recombinant strain could convert 1 g/L xylose to 0.84 g/L xylonate and 0.10 g/L xylonolactone after being induced for 12 h. Furthermore, the competitive pathway for xylose catabolism in E. coli was blocked by disrupting two genes (xylA and xylB) encoding xylose isomerase and xylulose kinase. Under fed-batch conditions, the finally engineered strain produced up to 27.3 g/L xylonate and 1.7 g/L xylonolactone from 30 g/L xylose, about 88% of the theoretical yield. These results suggest that the engineered E. coli strain has a promising perspective for large-scale production of xylonate.
doi:10.1371/journal.pone.0067305
PMCID: PMC3702539  PMID: 23861757
16.  Acute respiratory distress syndrome: new definition, current and future therapeutic options 
Journal of Thoracic Disease  2013;5(3):326-334.
Since acute respiratory distress syndrome (ARDS) was first described in 1967 there has been large number of studies addressing its pathogenesis and therapies. Despite this intense research activity, there are very few effective therapies for ARDS other than the use of lung protection strategies. This lack of therapeutic modalities is not only related to the complex pathogenesis of this syndrome but also the insensitive and nonspecific diagnostic criteria to diagnose ARDS. This review article will summarize the key features of the new definition of ARDS, and provide a brief overview of innovative therapeutic options that are being assessed in the management of ARDS.
doi:10.3978/j.issn.2072-1439.2013.04.05
PMCID: PMC3698298  PMID: 23825769
Acute respiratory distress syndrome (ARDS); pathogenesis; therapeutic options
17.  Antibacterial and Cytotoxic New Napyradiomycins from the Marine-Derived Streptomyces sp. SCSIO 10428 
Marine Drugs  2013;11(6):2113-2125.
Three new napyradiomycins (1–3) were isolated from the culture broth of a marine-derived actinomycete strain SCSIO 10428, together with six known related analogues napyradiomycin A1 (4), 18-oxonapyradiomycin A1 (5), napyradiomycin B1 (6), napyradiomycin B3 (7), naphthomevalin (8), and napyradiomycin SR (9). The strain SCSIO 10428 was identified as a Streptomyces species by the sequence analysis of its 16S rRNA gene. The structures of new compounds 1–3, designated 4-dehydro-4a-dechloronapyradiomycin A1 (1), 3-dechloro-3-bromonapyradiomycin A1 (2), and 3-chloro-6,8-dihydroxy-8-α-lapachone (3), respectively, were elucidated by comparing their 1D and 2D NMR spectroscopic data with known congeners. None of the napyradiomycins 1–9 showed antioxidative activities. Napyradiomycins 1–8 displayed antibacterial activities against three Gram-positive bacteria Staphylococcus and Bacillus strains with MIC values ranging from 0.25 to 32 μg mL−1, with the exception that compound 3 had a MIC value of above 128 μg mL−1 against Staphylococcus aureus ATCC 29213. Napyradiomycins 2, 4, 6, and 7 exhibited moderate cytotoxicities against four human cancer cell lines SF-268, MCF-7, NCI-H460, and HepG-2 with IC50 values below 20 μM, while the IC50 values for other five napyradiomycins 1, 3, 5, 8 and 9 were above 20 μM.
doi:10.3390/md11062113
PMCID: PMC3721223  PMID: 23771045
napyradiomycins; marine actinomycetes; natural products; antibacterial; cytotoxicity
18.  Metabolic engineering of Escherichia coli for the biosynthesis of alpha-pinene 
Background
α-Pinene is an important natural product that is widely used in flavorings, fragrances, medicines, fine chemicals and high-density renewable fuels. Currently, α-Pinene used in industry is mainly produced either by tapping trees (gum turpentine) or as a byproduct of paper pulping (crude sulfate turpentine, CST). However, the extraction of it from trees is tedious and inefficient and requires substantial expenditure of natural resources. Therefore, it is necessary to seek sustainable technologies for α-pinene production.
Results
To construct the microbial synthetic pathway of α-pinene in E. coli, we co-expressed native geranyl diphosphate synthase (IspA) from E. coli and α-pinene synthase (Pt30) from Pinus taeda, and then to increase the geranyl diphosphate (GPP) content in the cells, a suitable geranyl diphosphate synthase (GPPS2) was selected from two different origins. Furthermore, to enhance α-pinene production, a novel biosynthetic pathway of α-pinene was assembled in E. coli BL21(DE3) with the heterologous hybrid mevalonate (MVA) pathway, GPPS2 and α-pinene synthase (Pt30). The final genetic strain, YJM28, harboring the above novel biosynthetic pathway of α-pinene, accumulated α-pinene up to 5.44 mg/L and 0.97 g/L under flask and fed-batch fermentation conditions, respectively. The conversion efficiency of glucose to α-pinene (gram to gram) in the metabolically engineered strain reached 2.61%.
Conclusions
In this paper, by using metabolic engineering techniques, the more efficient biosynthetic pathway of α-pinene was successfully assembled in E. coli BL21(DE3) with the heterologous hybrid MVA pathway, GPPS2 and α-pinene synthase (Pt30). In addition, this is the first report on α-pinene fed-batch fermentation, and our results represent improvements over previous reports.
doi:10.1186/1754-6834-6-60
PMCID: PMC3667116  PMID: 23631625
α-Pinene; Geranyl diphosphate synthase; α-Pinene Synthase; E. coli
19.  Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels 
Background
The isopentenols, including isoprenol and prenol, are excellent alternative fuels. However, they are not compounds largely accumulated in natural organism. The need for the next generation of biofuels with better physical and chemical properties impels us to develop biosynthetic routes for the production of isoprenol and prenol from renewable sugar. In this study, we use the heterogenous mevalonate-dependent (MVA) isoprenoid pathway for the synthesis of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) intermediates, and then convert IPP and DMAPP to isoprenol and prenol, respectively.
Results
A mevalonate titer of 1.7 g/L was obtained by constructing an efficient MVA upper pathway in engineered E. coli. Different phosphatases and pyrophosphatases were investigated for their abilities in hydrolyzing the IPP and DMAPP. Consequently, ADP-ribose pyrophosphatase was found to be an efficient IPP and DMAPP hydrolase. Moreover, ADP-ribose pyrophosphatase from Bacillus subtilis (BsNudF) exhibited a equivalent substrate specificity towards IPP and DMAPP, while ADP-ribose pyrophosphatase from E. coli (EcNudF) presented a high substrate preference for DMAPP. Without the expression of any phosphatases or pyrophosphatases, a background level of isopentenols was synthesized. When the endogenous pyrophosphatase genes (EcNudF and yggV) that were capable of enhancing the hydrolyzation of the IPP and DMAPP were knocked out, the background level of isopentenols was still obtained. Maybe the synthesized IPP and DMAPP were hydrolyzed by some unknown hydrolases of E. coli. Finally, 1.3 g/L single isoprenol was obtained by blocking the conversion of IPP to DMAPP and employing the BsNudF, and 0.2 g/L ~80% prenol was produced by employing the EcNudF. A maximal yield of 12% was achieved in both isoprenol and prenol producing strains.
Conclusions
To the best of our knowledge, this is the first successful report on high-specificity production of isoprenol and prenol by microbial fermentation. Over 1.3 g/L isoprenol achieved in shake-flask experiments represents a quite encouraging titer of higher alcohols. In addition, the substrate specificities of ADP-ribose pyrophosphatases were determined and successfully applied for the high-specificity synthesis of isoprenol and prenol. Altogether, this work presents a promising strategy for high-specificity production of two excellent biofuels, isoprenol and prenol.
doi:10.1186/1754-6834-6-57
PMCID: PMC3654967  PMID: 23618128
Isoprenol; Prenol; Metabolic engineering; Escherichia coli; Biofuel
20.  A Novel Statistical Prognostic Score Model That Includes Serum CXCL5 Levels and Clinical Classification Predicts Risk of Disease Progression and Survival of Nasopharyngeal Carcinoma Patients 
PLoS ONE  2013;8(2):e57830.
Background
Aberrant expression of C-X-C motif chemokine 5 (CXCL5) contributes to the progression of various cancers. This study analyzed the clinical significance of serum CXCL5 (sCXCL5) levels of nasopharyngeal carcinoma (NPC) patients, with the goal of building a novel prognostic score model.
Experimental Design
Serum samples were collected prior to treatment from 290 NPC patients for the detection of sCXCL5 with ELISA. Half of the patients (n = 145) were randomly assigned to the training set to generate the sCXCL5 cutoff point using receiver operator characteristic (ROC) analysis, while the other half (n = 145) were assigned to the testing set for validation. Associations between sCXCL5 levels and clinical characteristics were analyzed. A prognostic score model was built using independent predictors derived from multivariate analysis. A concordance index (C-Index) was used to evaluate prognostic ability.
Results
The sCXCL5 cutoff point was 0.805 ng/ml. Sex, age, histology, T classification, clinical classification and local recurrence were not associated with sCXCL5 levels. However, sCXCL5 levels were positively associated with N classification, distant metastasis and disease progression (P<0.05). A high sCXCL5 level predicted poor 6-year overall survival (OS), poor 6-year distant metastasis-free survival (DMFS), and poor 6-year progression-free survival (PFS). A prognostic score model was subsequently constructed based on sCXCL5 levels and clinical classification (C-C model), which are independent predictors of OS, DMFS, and PFS, as confirmed by the multivariate analysis. Furthermore, this novel model successfully divided the patients into four risk subgroups in the training set, the testing set and the entire set of patients. The C-Indices were 0.751 and 0.762 for the training set and the testing set, respectively.
Conclusions
sCXCL5 level was determined to be an independent prognostic factor for NPC patients. The novel statistical C-C model, which includes sCXCL5 levels and clinical classification, could be helpful in predicting the prognosis of NPC patients.
doi:10.1371/journal.pone.0057830
PMCID: PMC3585222  PMID: 23469080
21.  Exposing the Complex III Qo semiquinone radical 
Biochimica et biophysica acta  2007;1767(7):883-887.
Complex III Qo site semiquinone has been assigned pivotal roles in productive energy-conversion and destructive superoxide generation. After a 30 year search, a genetic heme bH knockout arrests this transient semiquinone EPR radical, revealing the natural engineering balance pitting energy-conserving, short-circuit minimizing, split electron transfer and catalytic speed against damaging oxygen reduction.
doi:10.1016/j.bbabio.2007.04.004
PMCID: PMC3554237  PMID: 17560537
Complex III; Cytochrome bc1; Semiquinone; Qo; Superoxide; Electron transfer
23.  Genome-Wide Association Study Identifies a Novel Susceptibility Locus at 12q23.1 for Lung Squamous Cell Carcinoma in Han Chinese 
PLoS Genetics  2013;9(1):e1003190.
Adenocarcinoma (AC) and squamous cell carcinoma (SqCC) are two major histological subtypes of lung cancer. Genome-wide association studies (GWAS) have made considerable advances in the understanding of lung cancer susceptibility. Obvious heterogeneity has been observed between different histological subtypes of lung cancer, but genetic determinants in specific to lung SqCC have not been systematically investigated. Here, we performed the GWAS analysis specifically for lung SqCC in 833 SqCC cases and 3,094 controls followed by a two-stage replication in additional 2,223 lung SqCC cases and 6,409 controls from Chinese populations. We found that rs12296850 in SLC17A8-NR1H4 gene region at12q23.1 was significantly associated with risk of lung SqCC at genome-wide significance level [additive model: odds ratio (OR) = 0.78, 95% confidence interval (CI) = 0.72–0.84, P = 1.19×10−10]. Subjects carrying AG or GG genotype had a 26% (OR = 0.74, 95% CI = 0.67–0.81) or 32% (OR = 0.68, 95% CI = 0.56–0.83) decreased risk of lung SqCC, respectively, as compared with AA genotype. However, we did not observe significant association between rs12296850 and risk of lung AC in a total of 4,368 cases with lung AC and 9,486 controls (OR = 0.96, 95% CI = 0.90–1.02, P = 0.173). These results indicate that genetic variations on chromosome 12q23.1 may specifically contribute to lung SqCC susceptibility in Chinese population.
Author Summary
Previous genome-wide association studies (GWAS) strongly suggested the importance of genetic susceptibility for lung cancer. However, the studies specific to different histological subtypes of lung cancer were limited. We performed the GWAS analysis specifically for lung squamous cell carcinoma (SqCC) with 570,009 autosomal SNPs in 833 SqCC cases and 3,094 controls and replicated in additional 2,223 lung SqCC cases and 6,409 controls from Chinese populations (822 SqCC cases and 2,243 controls for the first replication stage and 1,401 SqCC cases and 4,166 controls for the second replication stage). We found a novel association at rs12296850 (SLC17A8-NR1H4) on12q23.1. However, rs12296850 didn't show significant association with risk of lung adenocacinoma (AC) in 4,368 lung AC cases and 9,486 controls. These results indicate that genetic variations on chromosome 12q23.1 may specifically contribute to lung SqCC susceptibility in Chinese population.
doi:10.1371/journal.pgen.1003190
PMCID: PMC3547794  PMID: 23341777

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