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Design of Pd/PANI/Pd Sandwich-Structured Nanotube Array Catalysts with Special Shape Effects and Synergistic Effects for Ethanol Electrooxidation

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2013年第29期135卷 10703-10709页

作者： Wang, An-Liang Xu, Han Feng, Jin-Xian Ding, Liang-Xin Tong, Ye-Xiang Li, Gao-Ren Sun Yat Sen Univ Sch Chem & Chem Engn KLGHEI Environm & Energy Chem MOE Lab Bioinorgan & Synthet Chem Guangzhou 510275 Guangdong Peoples R China

Low cost, high activity, and long-term durability are the main requirements for commercializing fuel cell electrocatalysts. Despite tremendous efforts, developing non-Pt anode electrocatalysts with high activity and long-term durability at low cost remains a significant technical challenge. Here we report a new type of hybrid Pd/PANI/Pd sandwich-structured nanotube array (SNTA) to exploit shape effects and synergistic effects of Pd-PANI composites for the oxidation of small organic molecules for direct alcohol fuel cells. These synthesized Pd/PANI/Pd SNTAs exhibit significantly improved electrocatalytic activity and durability compared with Pd NTAs and commercial Pd/C catalysts. The unique SNTAs provide fast transport and short diffusion paths for electroactive species and high utilization rate of catalysts. Besides the merits of nanotube arrays, the improved electrocatalytic activity and durability are especially attributed to the special Pd/PANI/Pd sandwich-like nanostructures, which results in electron delocalization between Pd d orbitals and PANI pi-conjugated ligands and in electron transfer from Pd to PANI.

关键词： CATALYSTS -- Synthesis ELECTROCATALYSTS NANOTUBES -- Synthesis POLYANILINES PALLADIUM catalysts microarray technology ETHANOL

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High-Throughput Screening of Small Molecule Ligands Targeted to Live Bacteria Surface

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ANALYTICAL CHEMISTRY 2013年第7期85卷 3508-3514页

作者： Lee, Jeong Heon Park, Sunny Hyun, Hoon Bordo, Mark W. Oketokoun, Rafiou Nasr, Khaled A. Frangioni, John V. Choi, Hak Soo Beth Israel Deaconess Med Ctr Robot Chem Grp Ctr Mol Imaging Boston MA 02215 USA Beth Israel Deaconess Med Ctr Dept Med Div Hematol Oncol Boston MA 02215 USA Beth Israel Deaconess Med Ctr Dept Radiol Boston MA 02215 USA US FDA Ctr Devices & Radiol Hlth Silver Spring MD 20993 USA Univ Texas SW Med Ctr Dallas Adv Imaging Res Ctr Dallas TX 75390 USA

The discovery of small molecule ligands targeted to the surface of live pathogenic bacteria would enable an entirely new class of antibiotics. We report the development and validation of a microarray-based high-throughput screening platform for bacteria that exploits 300 mu m diameter chemical spots in a 1 in. x 3 in. nanolayered glass slide format. Using 24 model compounds and 4 different bacterial strains, we optimized the screening technology, including fluorophore-based optical deconvolution for automated scoring of affinity and cyan-magenta-yellow-key (CMYK) color-coding for scoring of both affinity and specificity. The latter provides a lossless, one-dimensional view of multidimensional data. By linking in silico analysis with cell binding affinity and specificity, we could also begin to identify the physicochemical factors that affect ligand performance. The technology we describe could form the foundation for developing new classes of antibiotics.

关键词： LIGANDS (Biochemistry) PATHOGENIC bacteria ANTIBIOTICS microarray technology FLUOROPHORES CHEMICAL affinity DATA analysis CHEMICAL models

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A meta-analysis study of gene expression datasets in mouse liver under PPARα knockout

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GENETICS RESEARCH 2013年第2-3期95卷 78-88页

作者： He, Kan Wang, Zhen Wang, Qishan Pan, Yuchun Shanghai Jiao Tong Univ Sch Agr & Biol Dept Anim Sci Shanghai 200240 Peoples R China Shanghai Key Lab Vet Biotechnol Shanghai 200240 Peoples R China

Gene expression profiling of peroxisome-proliferator-activated receptor alpha (PPAR alpha) has been used in several studies, but there were no consistent results on gene expression patterns involved in PPAR alpha activation in genome-wide due to different sample sizes or platforms. Here, we employed two published microarray datasets both PPAR alpha dependent in mouse liver and applied meta-analysis on them to increase the power of the identification of differentially expressed genes and significantly enriched pathways. As a result, we have improved the concordance in identifying many biological mechanisms involved in PPAR alpha activation. We suggest that our analysis not only leads to more identified genes by combining datasets from different resources together, but also provides some novel hepatic tissue-specific marker genes related to PPAR alpha according to our re-analysis.

关键词： META-analysis GENE expression PEROXISOME proliferator-activated receptors LIVER -- Physiology KNOCKOUT mice CELL proliferation microarray technology

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Thymic Stromal Lymphopoietin Is Up-Regulated in the Skin of Patients With Systemic Sclerosis and Induces Profibrotic Genes and Intracellular Signaling That Overlap With Those Induced by Interleukin-13 and Transforming Growth Factor β

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ARTHRITIS AND RHEUMATISM 2013年第5期65卷 1335-1346页

作者： Christmann, Romy B. Mathes, Allison Affandi, Alsya J. Padilla, Cristina Nazari, Banafsheh Bujor, Andreea M. Stifano, Giuseppina Lafyatis, Robert Boston Univ Sch Med Boston MA 02118 USA Univ Med Ctr Utrecht Utrecht Netherlands

Objective To explore the expression of thymic stromal lymphopoietin (TSLP) in patients with diffuse cutaneous systemic sclerosis (dcSSc) and compare its effects in vivo and in vitro with those of interleukin-13 (IL-13) and transforming growth factor (TGF). Methods Skin biopsy specimens from patients with dcSSc (n = 14) and healthy controls (n = 13) were analyzed by immunohistochemistry and immunofluorescence for TSLP, TSLP receptor, CD4, CD8, CD31, and CD163 markers. Wild-type, IL-4R1, and TSLP-deficient mice were treated with TGF, IL-13, poly(I-C), or TSLP by osmotic pump. Human fibroblasts and peripheral blood mononuclear cells (PBMCs) were stimulated with TGF, IL-13, poly(I-C), or TSLP. microarray analysis and quantitative polymerase chain reaction were performed to determine gene expression, and protein levels of phospho-Smad2 and macrophage marker CD163 were tested. Results TSLP was highly expressed in the skin of dcSSc patients, more strongly in perivascular areas and in immune cells, and was produced mainly by CD163+ cells. The skin of TSLP-treated mice showed up-regulated clusters of gene expression that overlapped strongly with those in IL-13 and TGF-treated mice. TSLP up-regulated specific genes, including CXCL9, proteasome, and interferon (IFN)regulated genes. TSLP treatment in IL-4R1deficient mice promoted similar cutaneous inflammation as in wild-type mice, though TSLP-induced arginase 1, CCL2, and matrix metalloproteinase 12 messenger RNA levels were blocked. In PBMCs, TSLP up-regulated tumor necrosis factor , Mx-1, IFN, CXCL9, and mannose receptor 1 gene expression. TSLP-deficient mice treated with TGF showed less fibrosis and blocked expression of plasminogen activator inhibitor 1 and osteopontin 1. Poly(I-C)treated mice showed high levels of cutaneous TSLP. Conclusion TSLP is highly expressed in the skin of dcSSc patients and interacts in a complex manner with 2 other profibrotic cytokines, TGF and IL-13, strongly suggesting that it might promote SS

关键词： ACADEMIC medical centers ANALYSIS of variance ANIMAL experimentation BIOPSY FLOW cytometry FLUORESCENT antibody technique IMMUNOHISTOCHEMISTRY MICE PATHOLOGY POLYMERASE chain reaction FINANCING of research RNA SKIN STATISTICS SYSTEMIC scleroderma T-test (Statistics) THYMUS WESTERN immunoblotting GENOMICS DATA analysis EQUIPMENT & supplies REVERSE transcriptase polymerase chain reaction microarray technology

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An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition

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ENVIRONMENTAL MICROBIOLOGY 2013年第6期15卷 1870-1881页

作者： Nuccio, Erin E. Hodge, Angela Pett-Ridge, Jennifer Herman, Donald J. Weber, Peter K. Firestone, Mary K. Univ Calif Berkeley Berkeley CA 94720 USA Univ York York YO10 5DD N Yorkshire England Lawrence Livermore Natl Lab Livermore CA USA

Arbuscular mycorrhizal fungi (AMF) perform an important ecosystem service by improving plant nutrient capture from soil, yet little is known about how AMF influence soil microbial communities during nutrient uptake. We tested whether an AMF modifies the soil microbial community and nitrogen cycling during litter decomposition. A two-chamber microcosm system was employed to create a root-free soil environment to control AMF access to 13C- and 15N-labelled root litter. Using a 16S rRNA gene microarray, we documented that approximately 10% of the bacterial community responded to the AMF, Glomus hoi. Taxa from the Firmicutes responded positively to AMF, while taxa from the Actinobacteria and Comamonadaceae responded negatively to AMF. Phylogenetic analyses indicate that AMF may influence bacterial community assembly processes. Using nanometre-scale secondary ion mass spectrometry (NanoSIMS) we visualized the location of AMF-transported 13C and 15N in plant roots. Bulk isotope ratio mass spectrometry revealed that the AMF exported 4.9% of the litter 15N to the host plant (Plantago lanceolataL.), and litter-derived 15N was preferentially exported relative to litter-derived 13C. Our results suggest that the AMF primarily took up N in the inorganic form, and N export is one mechanism by which AMF could modify the soil microbial community and decomposition processes.

关键词： VESICULAR-arbuscular mycorrhizas SOIL microbiology NITROGEN cycle PLANT nutrients FOREST litter microarray technology BACTERIA -- Phylogeny ACTINOBACTERIA

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Proteome Analysis of the Two-Component SalK/SalR System in Epidemic Streptococcus suis Serotype 2

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CURRENT MICROBIOLOGY 2013年第1期67卷 118-122页

作者： Shen, Xiaodong Zhong, Qiu Zhao, Yan Yin, Supeng Chen, Tian Hu, Fuquan Li, Ming Third Mil Med Univ Dept Microbiol Chongqing 400038 Peoples R China Third Mil Med Univ Dept Biochem & Mol Biol Chongqing 400038 Peoples R China

Streptococcus suis serotype 2 (SS2) is a major swine pathogen of significant commercial importance worldwide and an emerging zoonotic agent of human streptococcal toxic shock-like syndrome. We previously reported that the Chinese highly pathogenic SS2 strains specifically harbor an 89K pathogenicity island, and the SalK/SalR two-component system encoded within this island mediates a piglet-lethal phenotype. However, its regulatory mechanism remains obscure. In the present study, we performed a proteome analysis to identify the target proteins regulated by the SalK/SalR system. This expression profiling analysis reveals 14 down-regulated proteins and 1 up-regulated protein. In partial accord with our previous microarray analysis, 9 out of the 14 down-regulated genes are also repressed at the transcriptional level. From the 9 matched genes, 5 were selected and further subjected to gene knockout and experimental infection of mice. The results show that the selected 5 genes are potential virulence factors and participate to various extents in the pathogenesis of SS2 infection, and may contribute to the attenuation of virulence mediated by the SalK/SalR system.

关键词： STREPTOCOCCUS suis SEROTYPES EPIDEMICS GENOMES PHENOTYPE microarray technology GENETIC transcription

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Anaphylaxis caused by hidden soybean allergens in pillows

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JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY 2013年第1期131卷 228-230页

作者： Armentia, Alicia Pineda, Fernando Martin, Blanca San Miguel, Angel Javier Martin Gil, Francisco Puente, Yolanda de Lecea, Carlos Palacios, Ricardo UMDAI Allergy Unit Valladolid Spain UMDAI Res Unit IEN Valladolid Spain UMDAI Rio Hortega Univ Hosp Clin Chem Serv Valladolid Spain DIATER Labs Madrid Spain Hosp Virgen de la Macarena Allergy Serv Seville Spain Grp Ferrer Barcelona Spain

Pillow stuffing can contain polyester, feathers, down, or, more recently, soy-based materials. Component-resolved diagnosis and microarray technology might be useful in patients with food-sensitized allergies or anaphylaxis caused by hidden *** report 4 patients with repeated anaphylaxis, which was defined as a decrease in blood pressure and possibly life-threatening adverse reactions1 during sleep at home but not in other places. Patient 1 was a 64-year-old woman with previous nocturnal rhinitis who began to experience anaphylaxis during sleep. Patient 2 was a 58-year-old man with progressive rhinitis, asthma, and anaphylaxis after changing his bedroom furniture and bed linen. Patient 3 was a 64-year-old woman with previous sensitization to Anisakis simplex and nocturnal pharyngeal angi-oedema unrelated to eating fish or other sources of A simplex who experienced severe anaphylaxis during sleep. Patient 4 was a 69-year-old woman with nocturnal anaphylaxis for 1 year before diagnosis.

关键词： Anaphylaxis pillow microarray technology Sleep Nocturnal Hypotension Anisakis simplex Patients

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A temporal switch model for estimating transcriptional activity in gene expression

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BIOINFORMATICS 2013年第9期29卷 1158-1165页

作者： Jenkins, Dafyd J. Finkenstaedt, Baerbel Rand, David A. Univ Warwick Warwick Syst Biol Ctr Coventry CV4 7AL W Midlands England Univ Warwick Dept Stat Coventry CV4 7AL W Midlands England

Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription-polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states. Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation.

关键词： GENETIC transcription GENE expression TIME series analysis microarray technology POLYMERASE chain reaction NUCLEOTIDE sequence MESSENGER RNA

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Correlation of interferon-inducible chemokine plasma levels with disease severity in systemic sclerosis

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ARTHRITIS AND RHEUMATISM 2013年第1期65卷 226-235页

作者： Liu, Xiaochun Mayes, Maureen D. Tan, Filemon K. Wu, Minghua Reveille, John D. Harper, Brock E. Draeger, Hilda T. Gonzalez, Emilio B. Assassi, Shervin Univ Texas Hlth Sci Ctr Houston Houston TX 77030 USA Univ Texas Med Branch Galveston TX 77555 USA Univ Texas Hlth Sci Ctr San Antonio San Antonio TX 78229 USA

Objective To measure interferon (IFN)inducible chemokines in the plasma of patients with systemic sclerosis (SSc) and investigate whether the chemokine levels are correlated with disease severity. Methods Plasma levels of the IFN-inducible chemokines IFN?-inducible protein 10 (IP-10/CXCL10), IFN-inducible T cell a chemoattractant (I-TAC/CXCL11), and monocyte chemoattractant protein 1 (CCL2) were measured in SSc patients and examined for correlation with the IFN gene expression signature. A composite IFN-inducible chemokine score was generated for chemokines showing a correlation with the IFN gene signature (IP-10 and I-TAC), and this score was compared between 266 patients with SSc enrolled in the Genetics versus Environment in Scleroderma Outcome Study (GENISOS) cohort and 97 matched control subjects. Subsequently, the correlation between the IFN-inducible chemokine score at baseline and markers of disease severity was assessed. In addition, the course of the IFN-inducible chemokine score over time was examined. Results The plasma IFN-inducible chemokine score correlated with the IFN gene expression signature, and this score was higher in SSc patients compared to controls. The IFN-inducible chemokine score was also associated with the absence of antiRNA polymerase III antibodies and presence of antiU1 RNP antibodies, but not with disease duration, disease type, or other autoantibodies. The chemokine score correlated with concomitantly obtained scores on the Medsger Severity Index for muscle, skin, and lung involvement in SSc, as well as the forced vital capacity, diffusing capacity for carbon monoxide, and creatine kinase levels. The association of the chemokine score with disease severity was independent of the presence of antiU1 RNP or other potential confounders (age, sex, ethnicity, disease duration, and treatment with immunosuppressive agents). Finally, there was not a significant change in the IFN-inducible chemokine score over time. Conclusion The IFN-induci

关键词： SYSTEMIC scleroderma PROGNOSIS PUBLIC health surveillance METHODOLOGY ACADEMIC medical centers CHEMOKINES CONFIDENCE intervals CORRELATION (Statistics) ENZYME-linked immunosorbent assay INTERFERONS POLYMERASE chain reaction REGRESSION analysis FINANCING of research STATISTICS DATA analysis EQUIPMENT & supplies SEVERITY of illness index CASE-control method DATA analysis software microarray technology DESCRIPTIVE statistics SYMPTOMS

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Proteomic Analysis of Synovial Fluid From the Osteoarthritic Knee: Comparison With Transcriptome Analyses of Joint Tissues

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ARTHRITIS AND RHEUMATISM 2013年第4期65卷 981-992页

作者： Ritter, Susan Y. Subbaiah, Roopashree Bebek, Gurkan Crish, James Scanzello, Carla R. Krastins, Bryan Sarracino, David Lopez, Mary F. Crow, Mary K. Aigner, Thomas Goldring, Mary B. Goldring, Steven R. Lee, David M. Gobezie, Reuben Aliprantis, Antonios O. Brigham & Womens Hosp Boston MA 02115 USA Harvard Univ Sch Med Boston MA USA Case Western Reserve Univ Sch Med Cleveland OH 44106 USA Case Western Reserve Univ Cleveland OH 44106 USA Cleveland Clin Cleveland OH 44106 USA Rush Univ Med Ctr Chicago IL 60612 USA Thermo Fisher Sci Cambridge MA USA Hosp Special Surg New York NY 10021 USA Weill Cornell Med Coll New York NY USA Coburg Med Ctr Coburg Germany Harvard Univ Brigham & Womens Hosp Sch Med Boston MA 02115 USA Harvard Univ Sch Publ Hlth Boston MA 02115 USA

Objective The pathophysiology of the most common joint disease, osteoarthritis (OA), remains poorly understood. Since synovial fluid (SF) bathes joint cartilage and synovium, we reasoned that a comparative analysis of its protein constituents in health and OA could identify pathways involved in joint damage. We undertook this study to perform a proteomic analysis of knee SF from OA patients and control subjects and to compare the results to microarray expression data from cartilage and synovium. Methods Age-matched knee SF samples from 10 control subjects, 10 patients with early-stage OA, and 10 patients with late-stage OA were compared using 2-dimensional difference-in-gel electrophoresis and mass spectrometry (MS). MS with a multiplexed peptide selected reaction monitoring assay was used to confirm differential expression of a subset of proteins in an independent OA patient cohort. Proteomic results were analyzed by Ingenuity Pathways Analysis and compared to published synovial tissue and cartilage messenger RNA profiles. Results Sixty-six proteins were differentially present in healthy and OA SF. Three major pathways were identified among these proteins: the acute-phase response signaling pathway, the complement pathway, and the coagulation pathway. Differential expression of 5 proteins was confirmed by selected reaction monitoring assay. A focused analysis of transcripts corresponding to the differentially present proteins indicated that both synovial and cartilage tissues may contribute to the OA SF proteome. Conclusion Proteins involved in the acute-phase response signaling pathway, the complement pathway, and the coagulation pathway are differentially regulated in SF from OA patients, suggesting that they contribute to joint damage. Validation of these pathways and their utility as biomarkers or therapeutic targets in OA is warranted.

关键词： PROTEOMICS EVALUATION ACADEMIC medical centers ANALYSIS of variance KNEE diseases MASS spectrometry OSTEOARTHRITIS FINANCING of research STATISTICS SYNOVIAL fluid T-test (Statistics) DATA analysis EQUIPMENT & supplies CASE-control method DATA analysis software microarray technology

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