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1.  An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform 
Microbiome  2014;2:6.
Background
To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical limitations inherent to the sequencing platforms. Sequencing low sequence diversity libraries such as 16S rRNA amplicons has been problematic on the Illumina MiSeq platform and often generates sequences of suboptimal quality.
Results
Here we present an improved dual-indexing amplification and sequencing approach to assess the composition of microbial communities from clinical samples using the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform. We introduced a 0 to 7 bp “heterogeneity spacer” to the index sequence that allows an equal proportion of samples to be sequenced out of phase.
Conclusions
Our approach yields high quality sequence data from 16S rRNA gene amplicons using both 250 bp and 300 bp paired-end MiSeq protocols and provides a flexible and cost-effective sequencing option.
doi:10.1186/2049-2618-2-6
PMCID: PMC3940169  PMID: 24558975
2.  Efficacy and Safety of Therapies for Acute Ischemic Stroke in China: A Network Meta-Analysis of 13289 Patients from 145 Randomized Controlled Trials 
PLoS ONE  2014;9(2):e88440.
Background
Many of these therapies have been compared against placebos, but have not been directly compared against each other. To evaluate the efficacy and safety of several commonly used drugs for AIS directly or indirectly.
Methods
A systematic literature review was performed to identify randomized controlled trials (RCTs) published prior to April 2013 for AIS therapies. The primary outcome measures were the National Institutes of Health Stroke Scale (NIHSS) scores and the clinical effective rate. A fixed-effects meta-analysis and meta-regression are performed; lastly, performed a mixed treatment comparison was performed through the Bayesian methods.
Results
Outcome of Efficacy of therapies for acute ischemic stroke are as followed: All of the therapies mentioned above yielded results a more effective result than placebo, Sodium ozagrel (RR 3.86, 95%CI 3.18–4.61); Sodium ozagrel + edaravone (RR 9.60, 95%CI 7.04–13.06); Edaravone (RR 4.07, 95%CI 3.30–5.01); Edaravone + Kininogenase (RR 15.33, 95%CI 10.03–23.05). The significant difference in efficacy between edaravone monotherapy and Sodium ozagrel + edaravone was evident (RR 0.43, 95%CI 0.08–0.61) and was also significant between efficacy of edaravone + Kininogenase and Sodium ozagrel (RR 4.00, 95%CI 2.47–6.24). The differences between the risk and benefit were not significant when comparing Sodium ozagrel and edaravone or edaravone + Kininogenase and Sodium ozagrel + Edaravone for AIS. Outcome of the defect of neurological function: Placebo served a significant difference in treating the defects of neurological function compared with Sodium ozagrel (WMD = −3.11, 95%CI −4.43 to −1.79), Sodium ozagrel + edaravone (WMD = −6.25, 95%CI −7.96 to −4.54) and Edaravone + Kininogenase (WMD =  −3.47, 95%CI −5.73 to −1.21).
Conclusions
It provides that the efficacy of edaravone monotherapy in treatment was not more effective than Sodium ozagrel + edaravone.The efficacy of edaravone + Kininogenase monotherapy in treatment was more effective than Sodium ozagrel. Edaravone + Kininogenase and Sodium ozagrel + Edaravone appeared the most effective treatments. And Sodium ozagrel, Sodium ozagrel + edaravone, Edaravone + Kininogenase can improve the nerve dysfunction.
doi:10.1371/journal.pone.0088440
PMCID: PMC3923787  PMID: 24551100
3.  Role of Chitin and Chitinase/Chitinase-Like Proteins in Inflammation, Tissue Remodeling, and Injury 
Annual review of physiology  2011;73:10.1146/annurev-physiol-012110-142250.
The 18 glycosyl hydrolase family of chitinases is an ancient gene family that is widely expressed from prokaryotes to eukaryotes. In mammals, despite the absence of endogenous chitin, a number of chitinases and chitinase-like proteins (C/CLPs) have been identified. However, their roles have only recently begun to be elucidated. Acidic mammalian chitinase (AMCase) inhibits chitin-induced innate inflammation; augments chitin-free, allergen-induced Th2 inflammation; and mediates effector functions of IL-13. The CLPs BRP-39/YKL-40 (also termed chitinase 3-like 1) inhibit oxidant-induced lung injury, augments adaptive Th2 immunity, regulates apoptosis, stimulates alternative macrophage activation, and contributes to fibrosis and wound healing. In accord with these findings, levels of YKL-40 in the lung and serum are increased in asthma and other inflammatory and remodeling disorders and often correlate with disease severity. Our understanding of the roles of C/CLPs in inflammation, tissue remodeling, and tissue injury in health and disease is reviewed below.
doi:10.1146/annurev-physiol-012110-142250
PMCID: PMC3864643  PMID: 21054166
asthma; fibrosis; BRP-39/YKL-40; AMCase; chitotriosidase
4.  Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis 
Microbiome  2013;1:29.
Background
Bacterial vaginosis (BV) is a common gynecologic diagnosis characterized by dysbiosis of the vaginal microbiota. It is often accompanied by vaginal symptoms such as odor and discharge, but can be asymptomatic. Despite over 50 years of research, the etiology of BV is not well understood, which is a major impediment to treatment and prevention of BV.
Results
Here we report on the temporal dynamics of 25 vaginal communities over a 10 week period using samples collected daily from women who were diagnosed with symptomatic BV (15 women), asymptomatic BV (6 women), and women who did not have BV (4 women).
Conclusion
This unique resource of samples and data will contribute to a better understanding of the role that the vaginal microbes have in the natural history of BV and lead to improved diagnosis and treatment.
doi:10.1186/2049-2618-1-29
PMCID: PMC3968321  PMID: 24451163
5.  The Risk of Metabolic Syndrome in Patients with Rheumatoid Arthritis: A Meta-Analysis of Observational Studies 
PLoS ONE  2013;8(10):e78151.
Background
Observational studies suggest an association between the incidence of rheumatoid arthritis (RA) and the prevalence of metabolic syndrome (MetS). However, the relationship between RA and MetS is controversial and research in this area is currently lacking.
Objective
The aim of this study was to assess whether the prevalence of MetS was higher in a group of RA patients compared to subjects without RA.
Design
A PubMed database search was conducted during April 2013 to identify observational studies of RA and risk of MetS. Reference lists of retrieved articles were also reviewed. Two authors independently extracted information on the study design, the characteristics of the study participants, exposure and outcome assessments, and the method used to control for potential confounding factors. A random-effects model was used for the risk estimates.
Results
Our meta-analysis of four cross-sectional controlled studies plus eight case-control studies involving a total of 2283 cases and 4403 controls identified a significant association between RA and risk of MetS, with an overall OR of 1.24 (95% CI, 1.03-1.50).
Conclusion
This meta-analysis provides further evidence supporting patients with RA have a higher prevalence of MetS than subjects without RA. In addition, the geographic region of the population and the criteria used for MetS diagnosis could influence the association. However, these observations would need to be evaluated using prospective, randomized studies.
doi:10.1371/journal.pone.0078151
PMCID: PMC3808281  PMID: 24205134
6.  Complete Genome Sequence of a Nephropathogenic Infectious Bronchitis Virus Strain Isolated in China 
Genome Announcements  2013;1(5):e00815-13.
Infectious bronchitis virus (IBV) causes tremendous economic losses to the poultry industry. Here, we report the complete genome analysis results for a new natural recombination nephropathogenic IBV strain named SAIBK, which was isolated in the Sichuan province of China in 2005.
doi:10.1128/genomeA.00815-13
PMCID: PMC3795213  PMID: 24115543
7.  Fabrication of Nanofiber Scaffolds with Gradations in Fiber Organization and Their Potential Applications 
Macromolecular bioscience  2012;12(10):1336-1341.
A new and simple method for fabrication of nanofiber scaffolds with gradations in fiber organization is reported. The nanofiber organization, achieved by deposition of random fibers on the uniaxially-aligned nanofiber mat in a gradient manner, directed morphological changes of applied adipose-derived stem cells. These morphological changes and resultant biochemical changes can help mimic the structural orientation of complex biomechanical structures like the collagen fiber structure at the tendon-to-bone insertion site. In addition, chemical gradients can be established through nanoencapsulation in this novel scaffold allowing for enhanced biomedical applications.
doi:10.1002/mabi.201200115
PMCID: PMC3544006  PMID: 22847852
Electrospinning; Gradient; Nanofibers; Organization; Tendon-to-Bone
8.  The vaginal microbiome: rethinking health and diseases 
Annual review of microbiology  2012;66:371-389.
Vaginal microbiota form a mutually beneficial relationship with their host and have major impact on health and disease. In recent years our understanding of vaginal bacterial community composition and structure has significantly broadened as a result of investigators using cultivation-independent methods based on the analysis of 16S ribosomal RNA (rRNA) gene sequences. In asymptomatic, otherwise healthy women, several kinds of vaginal microbiota exist, the majority often dominated by species of Lactobacillus, while others comprise a diverse array of anaerobic microorganisms. Bacterial vaginosis is the most common vaginal conditions and is vaguely characterized as the disruption of the equilibrium of the ‘normal’ vaginal microbiots. A better understanding of ‘normal’ and ‘healthy’ vaginal ecosystems that is based on its ‘true’ function and not simply on its composition would help better define health and further improve disease diagnostics as well as the development of more personalized regimens to promote health and treat diseases.
doi:10.1146/annurev-micro-092611-150157
PMCID: PMC3780402  PMID: 22746335
vaginal microbiota; vaginal ecosystem; bacterial vaginosis; health and disease
9.  Chitinase 3-like-1 Promotes Streptococcus pneumoniae Killing and Augments Host Tolerance to Lung Antibacterial Responses 
Cell host & microbe  2012;12(1):34-46.
SUMMARY
Host antibacterial responses include mechanisms that kill bacteria, but also those that protect or tolerize the host to potentially damaging antibacterial effects. We determined that Chitinase 3-like-1 (Chi3l1), a conserved prototypic chitinase-like protein, is induced by Streptococcus pneumoniae and plays central roles in promoting bacterial clearance and mediating host tolerance. S. pneumoniae-infected Chi3l1 null mice exhibit exaggerated lung injury, inflammation and hemorrhage, more frequent bacterial dissemination, decreased bacterial clearance, and enhanced mortality compared to controls. Chi3l1 augments macrophage bacterial killing by inhibiting caspase-1-dependent macrophage pyroptosis and augments host tolerance by controlling inflammasome activation, ATP accumulation, expression of ATP receptor P2×7R, and production of thymic stromal lymphopoietin and type 1, type 2, and type 17 cytokines. These data demonstrate that Chi3l1 is induced during infection, where it promotes bacterial clearance while simultaneously augmenting host tolerance, and that these roles likely contributed to the retention of Chi3l1 over species and evolutionary time.
doi:10.1016/j.chom.2012.05.017
PMCID: PMC3613130  PMID: 22817986
10.  Renal Protective Role of Xiexin Decoction with Multiple Active Ingredients Involves Inhibition of Inflammation through Downregulation of the Nuclear Factor-κB Pathway in Diabetic Rats 
In Chinese medicine, Xiexin decoction (XXD) has been used for the clinical treatment of diabetes for at least 1700 years. The present study was conducted to investigate the effective ingredients of XXD and their molecular mechanisms of antidiabetic nephropathy in rats. Rats with diabetes induced by high-fat diet and streptozotocin were treated with XXD extract for 12 weeks. XXD significantly improved the glucolipid metabolism disorder, attenuated albuminuria and renal pathological changes, reduced renal advanced glycation end-products, inhibited receptor for advanced glycation end-product and inflammation factors expression, suppressed renal nuclear factor-κB pathway activity, and downregulated renal transforming growth factor-β1. The concentrations of multiple components in plasma from XXD were determined by liquid chromatography and tandem mass spectrometry. Pharmacokinetic/pharmacodynamic analysis using partial least square regression revealed that 8 ingredients of XXD were responsible for renal protective effects via actions on multiple molecular targets. Our study suggests that the renal protective role of XXD with multiple effective ingredients involves inhibition of inflammation through downregulation of the nuclear factor-κB pathway, reducing renal advanced glycation end-products and receptor for advanced glycation end-product in diabetic rats.
doi:10.1155/2013/715671
PMCID: PMC3713598  PMID: 23935673
11.  Evaluation of an Automatic Registration-Based Algorithm for Direct Measurement of Volume Change in Tumors 
Purpose
Assuming that early tumor volume change is a biomarker for response to therapy, accurate quantification of early volume changes could aid in adapting an individual patient’s therapy and lead to shorter clinical trials. We investigated an image registration–based approach for tumor volume change quantification that may more reliably detect smaller changes that occur in shorter intervals than can be detected by existing algorithms.
Methods and Materials
Variance and bias of the registration-based approach were evaluated using retrospective, in vivo, very-short-interval diffusion magnetic resonance imaging scans where true zero tumor volume change is unequivocally known and synthetic data, respectively. The interval scans were nonlinearly registered using two similarity measures: mutual information (MI) and normalized cross-correlation (NCC).
Results
The 95% confidence interval of the percentage volume change error was (−8.93% to 10.49%) for MI-based and (−7.69%, 8.83%) for NCC-based registrations. Linear mixed-effects models demonstrated that error in measuring volume change increased with increase in tumor volume and decreased with the increase in the tumor’s normalized mutual information, even when NCC was the similarity measure being optimized during registration. The 95% confidence interval of the relative volume change error for the synthetic examinations with known changes over ±80% of reference tumor volume was (−3.02% to 3.86%). Statistically significant bias was not demonstrated.
Conclusion
A low-noise, low-bias tumor volume change measurement algorithm using nonlinear registration is described. Errors in change measurement were a function of tumor volume and the normalized mutual information content of the tumor.
doi:10.1016/j.ijrobp.2011.07.040
PMCID: PMC3401904  PMID: 22172911
Tumor volume change; Image registration; Dual baseline examination; Coffee-break examination; Linear mixed-effects model
12.  Inferring ancient metabolism using ancestral core metabolic models of enterobacteria 
BMC Systems Biology  2013;7:46.
Background
Enterobacteriaceae diversified from an ancestral lineage ~300-500 million years ago (mya) into a wide variety of free-living and host-associated lifestyles. Nutrient availability varies across niches, and evolution of metabolic networks likely played a key role in adaptation.
Results
Here we use a paleo systems biology approach to reconstruct and model metabolic networks of ancestral nodes of the enterobacteria phylogeny to investigate metabolism of ancient microorganisms and evolution of the networks. Specifically, we identified orthologous genes across genomes of 72 free-living enterobacteria (16 genera), and constructed core metabolic networks capturing conserved components for ancestral lineages leading to E. coli/Shigella (~10 mya), E. coli/Shigella/Salmonella (~100 mya), and all enterobacteria (~300-500 mya). Using these models we analyzed the capacity for carbon, nitrogen, phosphorous, sulfur, and iron utilization in aerobic and anaerobic conditions, identified conserved and differentiating catabolic phenotypes, and validated predictions by comparison to experimental data from extant organisms.
Conclusions
This is a novel approach using quantitative ancestral models to study metabolic network evolution and may be useful for identification of new targets to control infectious diseases caused by enterobacteria.
doi:10.1186/1752-0509-7-46
PMCID: PMC3694032  PMID: 23758866
Constraint-based modeling; Enterobacteria; Metabolic network reconstruction; Ancient metabolism; Paleo systems biology; Ancestral core
13.  Chitinase-like Proteins in Lung Injury, Repair, and Metastasis 
This report explains how our studies of asthma and Th2 inflammation led us to investigate the roles of chitinase-like proteins (CLPs) in lung injury and repair and puts forth an overall hypothesis that can explain the roles that these moieties play in biology and a hypothesis regarding the ways that dysregulated CLP expression may contribute to the pathogenesis of a variety of diseases. We test this hypothesis by assessing the contributions of the CLP breast regression protein (BRP)-39 in the pathogenesis of malignant melanoma metastasis to the lung.
doi:10.1513/pats.201112-056MS
PMCID: PMC3359113  PMID: 22550243
BRP-39/YKL-40; inflammation; injury; repair; metastasis
14.  Studies of Vascular Endothelial Growth Factor in Asthma and Chronic Obstructive Pulmonary Disease 
Vascular endothelial growth factor (VEGF) is a potent stimulator of vascular angiogenesis, permeability, and remodeling that also plays important roles in wound healing and tissue cytoprotection. To begin to define the roles of VEGF in diseases like asthma and COPD, we characterized the effects of lung-targeted transgenic VEGF165 and defined the innate immune pathways that regulate VEGF tissue responses. The former studies demonstrated that VEGF plays an important role in Th2 inflammation because, in addition to stimulating angiogenesis and edema, VEGF induced eosinophilic inflammation, mucus metaplasia, subepithelial fibrosis, myocyte hyperplasia, dendritic cell activation, and airways hyperresponsiveness via IL-13–dependent and -independent mechanisms. VEGF was also produced at sites of aeroallergen-induced Th2 inflammation, and VEGF receptor blockade ameliorated adaptive Th2 inflammation and Th2 cytokine elaboration. The latter studies demonstrated that activation of the RIG-like helicase (RLH) innate immune pathway using viral pathogen–associated molecular patterns such as Poly(I:C) or viruses ameliorated VEGF-induced tissue responses. In accord with these findings, Poly(I:C)-induced RLH activation also abrogated aeroallergen-induced Th2 inflammation. When viewed in combination, these studies suggest that VEGF excess can contribute to the pathogenesis of Th2 inflammatory disorders such as asthma and that abrogation of VEGF signaling via RLH activation can contribute to the pathogenesis of viral disorders such as virus-induced COPD exacerbations. They also suggest that RLH activation may be a useful therapeutic strategy in asthma and related disorders.
doi:10.1513/pats.201102-018MW
PMCID: PMC3359071  PMID: 22052929
asthma; chronic obstructive pulmonary disease; virus; RIG-like helicase; mitochondrial antiviral signaling molecule
15.  Mechanisms Decreasing In Vitro Susceptibility to the LpxC Inhibitor CHIR-090 in the Gram-Negative Pathogen Pseudomonas aeruginosa 
Testing P. aeruginosa efflux pump mutants showed that the LpxC inhibitor CHIR-090 is a substrate for MexAB-OprM, MexCD-OprJ, and MexEF-OprN. Utilizing P. aeruginosa PAO1 with a chromosomal mexC::luxCDABE fusion, luminescent mutants arose on medium containing 4 μg/ml CHIR-090, indicating upregulation of MexCD-OprJ. These mutants were less susceptible to CHIR-090 (MIC, 4 μg/ml) and had mutations in the mexCD-oprJ repressor gene nfxB. Nonluminescent mutants (MIC, 4 μg/ml) that had mutations in the mexAB-oprM regulator gene mexR were also observed. Plating the clinical isolate K2153 on 4 μg/ml CHIR-090 selected mutants with alterations in mexS (immediately upstream of mexT), which upregulates MexEF-OprN. A mutant altered in the putative1ribosomal binding site (RBS) upstream of lpxC and overexpressing LpxC was selected on a related LpxC inhibitor and exhibited reduced susceptibility to CHIR-090. Overexpression of LpxC from a plasmid reduced susceptibility to CHIR-090, and introduction of the altered RBS in this construct further increased expression of LpxC and decreased susceptibility to CHIR-090. Using a mutS (hypermutator) strain, a mutant with an altered lpxC target gene (LpxC L18V) was also selected. Purified LpxC L18V had activity similar to that of wild-type LpxC in an in vitro assay but had reduced inhibition by CHIR-090. Finally, an additional class of mutant, typified by an extreme growth defect, was identified. These mutants had mutations in fabG, indicating that alteration in fatty acid synthesis conferred resistance to LpxC inhibitors. Passaging experiments showed progressive decreases in susceptibility to CHIR-090. Therefore, P. aeruginosa can employ several strategies to reduce susceptibility to CHIR-090 in vitro.
doi:10.1128/AAC.05417-11
PMCID: PMC3256010  PMID: 22024823
16.  Comparison of Storage Conditions for Human Vaginal Microbiome Studies 
PLoS ONE  2012;7(5):e36934.
Background
The effect of storage conditions on the microbiome and metabolite composition of human biological samples has not been thoroughly investigated as a potential source of bias. We evaluated the effect of two common storage conditions used in clinical trials on the bacterial and metabolite composition of the vaginal microbiota using pyrosequencing of barcoded 16S rRNA gene sequencing and 1H-NMR analyses.
Methodology/Principal Findings
Eight women were enrolled and four mid-vaginal swabs were collected by a physician from each woman. The samples were either processed immediately, stored at −80°C for 4 weeks or at −20°C for 1 week followed by transfer to −80°C for another 4 weeks prior to analysis. Statistical methods, including Kolmogorovo-Smirnov and Wilcoxon tests, were performed to evaluate the differences in vaginal bacterial community composition and metabolites between samples stored under different conditions. The results showed that there were no significant differences between samples processed immediately after collection or stored for varying durations. 1H-NMR analysis of the small molecule metabolites in vaginal secretions indicated that high levels of lactic acid were associated with Lactobacillus-dominated communities. Relative abundance of lactic acid did not appear to correlate with relative abundance of individual Lactobacillus sp. in this limited sample, although lower levels of lactic acid were observed when L. gasseri was dominant, indicating differences in metabolic output of seemingly similar communities.
Conclusions/Significance
These findings benefit large-scale, field-based microbiome and metabolomic studies of the vaginal microbiota.
doi:10.1371/journal.pone.0036934
PMCID: PMC3360033  PMID: 22655031
17.  RIG-like Helicase Innate Immunity Inhibits Vascular Endothelial Growth Factor Tissue Responses via a Type I IFN–dependent Mechanism 
Rationale: Vascular endothelial growth factor (VEGF) regulates vascular, inflammatory, remodeling, and cell death responses. It plays a critical role in normal pulmonary physiology, and VEGF excess and deficiency have been implicated in the pathogenesis of asthma and chronic obstructive pulmonary disease, respectively. Although viruses are an important cause of chronic obstructive pulmonary disease exacerbations and innate responses play an important role in these exacerbations, the effects of antiviral responses on VEGF homeostasis have not been evaluated.
Objectives: We hypothesized that antiviral innate immunity regulates VEGF tissue responses.
Methods: We compared the effects of transgenic VEGF165 in mice treated with viral pathogen–associated molecular pattern polyinosinic:polycytidylic acid [poly(I:C)], mice treated with live virus, and control mice.
Measurements and Main Results: Transgenic VEGF stimulated angiogenesis, edema, inflammation, and mucin accumulation. Each of these was abrogated by poly(I:C). These inhibitory effects were dose dependent, noted when poly(I:C) was administered before and after transgene activation, and mediated by a Toll-like receptor-3–independent and RIG-like helicase (RLH)– and type I IFN receptor–dependent pathway. VEGF stimulated the expression of VEGF receptor-1 and poly(I:C) inhibited this stimulation. Poly(I:C) also inhibited the ability of VEGF to activate extracellular signal–regulated kinase-1, Akt, focal adhesion kinase, and endothelial nitric oxide synthase, and aeroallergen-induced adaptive helper T-cell type 2 inflammation. Influenza and respiratory syncytial virus also inhibited VEGF-induced angiogenesis.
Conclusions: These studies demonstrate that poly(I:C) and respiratory viruses inhibit VEGF-induced tissue responses and adaptive helper T-cell type 2 inflammation and highlight the importance of a RLH- and type I IFN receptor–dependent pathway(s) in these regulatory events. They define a novel link between VEGF and antiviral and RLH innate immune responses and a novel pathway that regulates pulmonary VEGF activity.
doi:10.1164/rccm.201008-1276OC
PMCID: PMC3114061  PMID: 21278304
RIG-like helicase; mitochondrial antiviral signaling molecule; influenza virus; chronic obstructive pulmonary disease
18.  Total Synthesis of the Antimitotic Bicyclic Peptide Celogentin C 
An account of the total synthesis of celogentin C is presented. A right-to-left synthetic approach to this bicyclic octapeptide was unsuccessful due to an inability to elaborate derivatives of the right-hand ring. In the course of these efforts, it was discovered that the mild Braslau modification of the McFadyen–Stevens reaction offers a useful method of reducing recalcitrant esters to aldehydes. A left-to-right synthetic strategy was then examined. The unusual Leu–Trp side-chain cross-link present in the left-hand macrocycle was fashioned via a three-step sequence comprised of an intermolecular Knoevenagel condensation, a radical conjugate addition, and a SmI2-mediated nitro reduction. A subsequent macrolactamization provided the desired ring system. The high yield and concise nature of the left-hand ring synthesis offset the modest diastereoselectivity of the radical conjugate addition. Formation of the Trp–His side chain linkage characteristic of the right-hand ring was then accomplished by means of an indole–imidazole oxidative coupling. Notably, Pro-OBn was required as an additive in this reaction. Detailed mechanistic investigations indicated that Pro-OBn moderates the concentration of NCS in the reaction mixture, thereby minimizing the production of an undesired dichlorinated byproduct. The natural product was obtained after macrolactamization and deprotection. The chemical shifts of the imidazole hydrogen atoms exhibited significant dependence on temperature, concentration, and pH. Antitumor screening indicated that celogentin C inhibits the growth of some cancer cell lines.
doi:10.1021/ja909870g
PMCID: PMC2810426  PMID: 20038144
19.  Investigating the Role of P311 in the Hypertrophic Scar 
PLoS ONE  2010;5(4):e9995.
The mechanisms of hypertrophic scar formation are not fully understood. We previously screened the differentially expressed genes of human hypertrophic scar tissue and identified P311 gene as upregulated. As the activities of P311 in human fibroblast function are unknown, we examined the distribution of it and the effects of forced expression or silencing of expression of P311. P311 expression was detected in fibroblast-like cells from the hypertrophic scar of burn injury patients but not in peripheral blood mononuclear cells, bone marrow mesenchymal stem cells, epidermal cells or normal skin dermal cells. Transfection of fibroblasts with P311 gene stimulated the expression of alpha-smooth muscle actin (α-SMA), TGF-β1 and α1(I) collagen (COL1A1), and enhanced the contraction of fibroblast populated collagen lattices (FPCL). In contrast, interference of fibroblast P311 gene expression decreased the TGF-β1 mRNA expression and reduced the contraction of fibroblasts in FPCL. These results suggest that P311 may be involved in the pathogenesis of hypertrophic scar via induction of a myofibroblastic phenotype and of functions such as TGF-β1 expression. P311 could be a novel target for the control of hypertrophic scar development.
doi:10.1371/journal.pone.0009995
PMCID: PMC2852399  PMID: 20404911
20.  Voxel-by-Voxel Functional Diffusion Mapping for Early Evaluation of Breast Cancer Treatment 
Quantitative isotropic diffusion MRI and voxel-based analysis of the apparent diffusion coefficient (ADC) changes have been demonstrated to be able to accurately predict early response of brain tumors to therapy. The ADC value changes measured during pre- and post-therapy interval are closely correlated to treatment response. This work was demonstrated using a voxel-based analysis of ADC change during therapy in the brains of both rats and humans, following rigidly registering pre- and post-therapeutic ADC MRI exams. The primary goal of this paper is to extend this voxel-by-voxel analysis to assess therapeutic response in breast cancer. Nonlinear registration (with higher degrees of freedom) between the pre- and post-treatment exams is needed to ensure that the corresponding voxels actually contain similar cellular partial contributions due to soft tissue deformations in the breast and compartmental tumor changes during treatment as well. With limited data sets, we have observed the correlation between changes of ADC values and treatment response also exists in breast cancers. With diffusion scans acquired at three different timepoints (pre-treatment, early post-treatment and late post-treatment), we have also shown that ADC changes across responders within 5 weeks are a function of time interval after the initiation of treatment. Comparison of the experimental results with pathology shows that ADC changes can be used to evaluate early response of breast cancer treatment.
PMCID: PMC2804941  PMID: 19694270
21.  Phylogeny and Virulence of Naturally Occurring Type III Secretion System-Deficient Pectobacterium Strains▿  
Applied and Environmental Microbiology  2009;75(13):4539-4549.
Pectobacterium species are enterobacterial plant-pathogenic bacteria that cause soft rot disease in diverse plant species. Previous epidemiological studies of Pectobacterium species have suffered from an inability to identify most isolates to the species or subspecies level. We used three previously described DNA-based methods, 16S-23S intergenic transcribed spacer PCR-restriction fragment length polymorphism analysis, multilocus sequence analysis (MLSA), and pulsed-field gel electrophoresis, to examine isolates from diseased stems and tubers and found that MLSA provided the most reliable classification of isolates. We found that strains belonging to at least two Pectobacterium clades were present in each field examined, although representatives of only three of five Pectobacterium clades were isolated. Hypersensitive response and DNA hybridization assays revealed that strains of both Pectobacterium carotovorum and Pectobacterium wasabiae lack a type III secretion system (T3SS). Two of the T3SS-deficient strains assayed lack genes adjacent to the T3SS gene cluster, suggesting that multiple deletions occurred in Pectobacterium strains in this locus, and all strains appear to have only six rRNA operons instead of the seven operons typically found in Pectobacterium strains. The virulence of most of the T3SS-deficient strains was similar to that of T3SS-encoding strains in stems and tubers.
doi:10.1128/AEM.01336-08
PMCID: PMC2704834  PMID: 19411432
22.  Breast Ultrasound Image Improvement By Pixel Compounding of Compression Sequence 
Pixel compounding is a technique that synthesizes the information of an image sequence involving slow decorrelation of the speckle to form a detail-recovered and speckle reduced image. To avoid extra data acquisition time and patient exposure, reuse of the existing data is desirable. In the procedure of elasticity imaging, a set of B-mode images with slight changes due to deformation is produced, which provides an ideal input for the pixel compounding. The improvement in image quality is evaluated quantitatively using a figure-of-merit (FOM) that indicates the goodness of boundary information recovery and the contrast-to-noise ratio (CNR) over the phantom images. The increase in average CNR is from 0.4 in the original images to 0.8 in the pixel compounded images. The improvement in average FOM is from 0.15 to over 0.5 on a scale of 0 to 1. In vivo results with a breast cyst, a fibroadenoma, and a breast cancer1 are also presented and the image quality improvement is subjectively evaluated. The results suggest that B-mode breast images from compression procedures are suitable data for pixel compounding, and that a speckle reduced and detail-recovered or detail-maintained image can be produced. The improved imaging may provide alternative or better information for detection and diagnosis. A similar approach could be extended to elasticity imaging with other modalities.
doi:10.1109/TUFFC.2009.1065
PMCID: PMC2778488  PMID: 19411207
medical imaging; B-mode ultrasound; super resolution; detail recovery; speckle reduction
23.  Image Registration for Detection and Quantification of Change on Digital Tomosynthesis Mammographic Volumes 
Objective
The purpose of this study was to achieve 3D registration of digital tomosynthesis mammographic volumes using mutual information.
Conclusion
Registration of digital breast digital tomosynthesis mammographic volumes was achieved with an average error of 1.8 +/- 1.4 mm.
doi:10.2214/AJR.08.1388
PMCID: PMC2735867  PMID: 19155398
24.  Novel Cinchona alkaloid derived ammonium salts as catalysts for the asymmetric synthesis of β-hydroxy α-amino acids via aldol reactions 
Tetrahedron letters  2007;48(12):2083-2086.
Using the cinchonidine-derived phase-transfer catalyst de veloped by Park and Jew as a lead structure, we have prepared novel chiral ammonium salts and investigated their efficacy for the preparation of β-hydroxy α-amino acids via asymmetric aldol reactions. The modifications were performed at C3 of the cinchonidine nucleus and include dimers as well as catalysts possessing electron-deficient alkyne and alkene moieties. Some of the new catalysts yielded improvements relative to the Park–Jew catalyst in the aldol reaction.
doi:10.1016/j.tetlet.2007.01.132
PMCID: PMC1855095  PMID: 18350108
Cinchona alkaloids; β-hydroxy α-amino acids; Sonogashira coupling; Heck reaction; asymmetric aldol reaction
25.  Effects of Acetazolamide Combined with or without NaHCO3 on Suppressing Neoplasm Growth, Metastasis and Aquaporin-1 (AQP1) Protein Expression 
This study was made to explore the effects of acetazolamide on tumor growth, metastasis and the possible mechanisms. The mice bearing with Lewis lung carcinomas were taken as the animal model. The effects of acetazolamide were compared with the combination treatment of NaHCO3 on tumor growth, metastasis and carbonic anhydrase activity in lung and tumor tissues using imidazole-Tris technique. And also the possible role of AQP1 in tumor tissues was investigated by Western blot and immuno-histochemical analysis. Results showed that acetazolamide alone could sharply reduce the number of lung metastasis and primary tumor growth, and appeared in a dose-dependent manner. Acetazolamide significantly inhibited carbonic anhydrase activity in tumor tissue. After the addition of NaHCO3, the suppression of acetazolamide on tumor growth, number of metastasis and carbonic anhydrase activity in primary tumor tissue could not be altered significantly, but the inhibitory rate of metastasis in lung and carbonic anhydrase activity in lung tissue appeared to show a reversal trend in the dose dependency from the acetazolamide treatment alone. The exactly mechanisms need to be clarified in future. Western blot and immunohistochemical analysis demonstrated that AQP1 expression in the tumor tissue was higher than both tissue of normal and treated with acetazolamide treatment alone. Combination with NaHCO3 could not synergistically inhibit the expression of AQP1 with acetazolamide. The results suggested that the mechanism of acetazolamide on anti-tumor especially on its anti-metastasis actions might partly involve either inhibiting the carbonic anhydrase activity or reducing AQP1 water channel protein expression, whatever if treated with or without NaHCO3.
PMCID: PMC3685237
acetazolamide; aquaporin; carbonic anhydrase; tumor; metastasis

Results 1-25 (33)