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Comparison and Validation of Putative Pathogenicity-Related Genes Identified by T-DNA Insertional Mutagenesis and microarray Expression Profiling in Magnaporthe oryzae

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BIOMED RESEARCH INTERNATIONAL 2017年第20170101期2017卷 7198614-7198614页

作者： Wang, Ying Wang, Ying Tan, Qi Gao, Ying Nv Li, Yan Bao, Da Peng Shanghai Acad Agr Sci Natl Engn Res Ctr Edible Fungi Key Lab Edible Fungi Resources & Utilizat South Minist AgrInst Edible Fungi Shanghai 201403 Peoples R China

High-throughput technologies of functional genomics such as T-DNA insertional mutagenesis and microarray expression profiling have been employed to identify genes related to pathogenicity in Magnaporthe oryzae. However, validation of the functions of individual genes identified by these high-throughput approaches is laborious. In this study, we compared two published lists of genes putatively related to pathogenicity in M. oryzae identified by T-DNA insertional mutagenesis (comprising 1024 genes) and microarray expression profiling (comprising 236 genes), respectively, and then validated the functions of some overlapped genes between the two lists by knocking them out using the method of target gene replacement. Surprisingly, only 13 genes were overlapped between the two lists, and none of the four genes selected from the overlapped genes exhibited visible phenotypic changes on vegetative growth, asexual reproduction, and infection ability in their knockout mutants. Our results suggest that both of the lists might contain large proportions of unrelated genes to pathogenicity and therefore comparing the two gene lists is hardly helpful for the identification of genes that are more likely to be involved in pathogenicity as we initially expected.

关键词： ANALYSIS of DNA COMPARATIVE studies DNA FUNGI IMMUNOBLOTTING MUTATION (Biology) MYCOSES NUCLEOTIDE separation PHOTOGRAPHY PLANT diseases POLYMERASE chain reaction PROBABILITY theory FINANCING of research STATISTICS VIRULENCE (Microbiology) PHENOTYPE DATA analysis microarray technology GENE expression profiling DESCRIPTIVE statistics

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Combined Bacteria microarray and Quartz Crystal Microbalance Approach for Exploring Glycosignatures of Nontypeable Haemophilus influenzae and Recognition by Host Lectins

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ANALYTICAL CHEMISTRY 2016年第11期88卷 5950-5957页

作者： Kalograiaki, Ioanna Euba, Begona Proverbio, Davide Campanero-Rhodes, Maria A. Aastrup, Teodor Garmendia, Junkal Solis, Dolores CSIC Inst Quim Fis Rocasolano Serrano 119 E-28006 Madrid Spain CIBER Enfermedades Resp CIBERES Avda Monforte Lemos 3-5 Madrid 28029 Spain CSIC UPNa Gobierno Navarra Inst Agrobiotecnol Avda Pamplona 123 Mutilva 31192 Spain Attana Bjornnasvagen 21 S-11419 Stockholm Sweden

Recognition of bacterial surface epitopes by host receptors plays an important role in the infectious process and is intimately associated with bacterial virulence. Delineation of bacteria host interactions commonly relies on the detection of binding events between purified bacteria- and host-target molecules. In this work, we describe a combined microarray and quartz crystal microbalance (QCM) approach for the analysis of carbohydrate-mediated interactions directly on the bacterial surface, thus preserving the native environment of the bacterial targets. Nontypeable Haemophilus influenzae (NTHi) was selected as a model pathogenic species not displaying a polysaccharide capsule or O-antigen-containing lipopolysaccharide, a trait commonly found in several important respiratory pathogens. Here, we demonstrate the usefulness of NTHi microarrays for exploring the presence of carbohydrate structures on the bacterial surface. Furthermore, the microarray approach is shown to be efficient for detecting strain-selective binding of three innate immune lectins, namely, surfactant protein D, human galectin-8, and Siglec-14, to different NTHi clinical isolates. In parallel, QCM bacteria-chips were developed for the analysis of lectin-binding kinetics and affinity. This novel QCM approach involves capture of NTHi on lectin-derivatized chips followed by formaldehyde fixation, rendering the bacteria an integrated part of the sensor chip, and subsequent binding assays with label-free lectins. The binding parameters obtained for selected NTHi-lectin pairs provide further insights into the interactions occurring at the bacterial surface.

关键词： microarray technology QUARTZ crystal microbalances HAEMOPHILUS influenzae LECTINS BACTERIAL cell surfaces ANTIGENIC determinants

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Grating coupled SPR microarray analysis of proteins and cells in blood from mice with breast cancer

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ANALYST 2016年第2期141卷 704-712页

作者： Mendoza, A. Torrisi, D. M. Sell, S. Cady, N. C. Lawrence, D. A. New York State Dept Hlth Wadsworth Ctr Albany NY 12208 USA SUNY Polytech Inst Albany NY 12203 USA

Biomarker discovery for early disease diagnosis is highly important. Of late, much effort has been made to analyze complex biological fluids in an effort to develop new markers specific for different cancer types. Recent advancements in label-free technologies such as surface plasmon resonance (SPR)-based biosensors have shown promise as a diagnostic tool since there is no need for labeling or separation of cells. Furthermore, SPR can provide rapid, real-time detection of antigens from biological samples since SPR is highly sensitive to changes in surface-associated molecular and cellular interactions. Herein, we report a lab-on-a-chip microarray biosensor that utilizes grating-coupled surface plasmon resonance (GCSPR) and grating-coupled surface plasmon coupled fluorescence (GCSPCF) imaging to detect circulating tumor cells (CTCs) from a mouse model (FVB-MMTV-PyVT). GCSPR and GCSPCF analysis was accomplished by spotting antibodies to surface cell markers, cytokines and stress proteins on a nanofabricated GCSPR microchip and screening blood samples from FVB control mice or FVB-MMTV-PyVT mice with developing mammary carcinomas. A transgenic MMTV-PyVT mouse derived cancer cell line was also analyzed. The analyses indicated that CD24, CD44, CD326, CD133 and CD49b were expressed in both cell lines and in blood from MMTV-PyVT mice. Furthermore, cytokines such as IL-6, IL-10 and TNF-alpha, along with heat shock proteins HSP60, HSP27, HSc70(HSP73), HSP90 total, HSP70/HSc70, HSP90, HSP70, HSP90 alpha, phosphotyrosine and HSF-1 were overexpressed in MMTV-PyVT mice.

关键词： Surface plasmon resonance Breast cancer -- Diagnosis Phosphotyrosine microarray technology Proteins -- Analysis Gene expression in mammals

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Whole genome microarray data of chronic wound debridement prior to application of dermal skin substitutes

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WOUND REPAIR AND REGENERATION 2016年第5期24卷 870-875页

作者： Ashrafi, Mohammed Sebastian, Anil Shih, Barbara Greaves, Nicholas Alonso-Rasgado, Teresa Baguneid, Mohamed Bayat, Ardeshir Univ Manchester Inst Inflammat & Repair Ctr Dermatol Res Plast & Reconstruct Surg Res Oxford Rd Manchester M13 9PT Lancs England Univ Manchester Sch Mat Bioengn Grp Manchester Lancs England Univ Hosp South Manchester NHS Fdn Trust Wythenshawe Hosp Manchester Lancs England

Clinical consensus is that debridement is necessary for successful application of dermal skin substitutes (DSS) to chronic wounds. The aim here was to identify commonly expressed genes associated with wound healing in untreated acute wounds and chronic wounds treated with wound debridement followed by DSS. Cutaneous biopsies were taken at two time points from untreated acute and chronic wounds and from chronic wounds treated with DSS following debridement. microarray analysis identified significant differences (p<0.05) related to proliferation (HIPK2, LGR4, FGFR1, SRRT), migration (RHOC, PRPF40A, FGFR1), differentiation (TCF4, COL13A1, GNPTAB, HUWE1, FGFR1), angiogenesis (HIPK2, CASP8), extracellular matrix organization (VWA1), and apoptosis (BBC3, HIPK2, KLF11, PSME3, MSFD10, TOP2A, MLH1, CASP8, PDIA3, XAF1) when comparing untreated chronic wounds to chronic wounds treated with DSS, with similar expression levels compared to untreated acute wounds. Chronic wounds treated with debridement followed by DSS resemble untreated acute wounds at a genomic level. These novel findings, albeit with limited clinical specimen numbers, strengthen the recommendation to transform chronic into acute wounds prior to application of DSS.

关键词： CHRONIC wounds & injuries ACADEMIC medical centers DEBRIDEMENT MEDICAL cooperation PROBABILITY theory RESEARCH FINANCING of research WOUND healing DATA analysis software microarray technology ARTIFICIAL skin GENE expression profiling DESCRIPTIVE statistics TREATMENT LEG ulcers

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Tuning the emission properties of a fluorescent polymer using a polymer microarray approach - identification of an optothermo responsive polymer

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CHEMICAL COMMUNICATIONS 2016年第69期52卷 10521-10524页

作者： Wang, Guirong Duan, Zongquan Sheng, Yang Neumann, Kevin Deng, Linhong Li, Jian Bradley, Mark Zhang, Rong Changzhou Univ Sch Mat Sci & Engn Changzhou 213164 Jiangsu Peoples R China Univ Edinburgh Sch Chem EaStCHEM Joseph Black BldgWest Mains Rd Edinburgh EH9 3JJ Midlothian Scotland Changzhou Univ Inst Biomed Engn & Hlth Sci Changzhou 213164 Jiangsu Peoples R China Changzhou Univ Jiangsu Collaborat Innovat Ctr Photovolta Sci & E Changzhou 213164 Jiangsu Peoples R China

Polymer microarrays were prepared using inkjet printing mixtures of acrylate monomers each with a common fluorescent fluorene co-polymer. Fluorescence analysis of each of the features on the array allowed identification of polymers that could tune the fluorescence under a variety of insults. The "hit" polymers were made into beads via reverse suspension polymerization and their fluorescence properties were analyzed.

关键词： FLUORESCENT polymers microarray technology INK-jet printing ACRYLATES FLUORIMETRY

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A portable optical waveguide resonance light-scattering scanner for microarray detection

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ANALYST 2016年第1期141卷 199-205页

作者： Xing, Xuefeng Liu, Wanyao Li, Tao Xing, Shu Fu, Xueqi Wu, Dongyang Liu, Dianjun Wang, Zhenxin Chinese Acad Sci Changchun Inst Appl Chem State Key Lab Electroanalyt Chem Changchun 130022 Peoples R China Jilin Univ Sch Life Sci Edmond H Fischer Signal Transduct Lab Changchun 130012 Peoples R China

In the present work, a portable and low-cost planar waveguide based resonance light scattering (RLS) scanner (termed as: PW-RLS scanner) has been developed for microarray detection. The PW-RLS scanner employs a 2 x 4 white light emitting diode array (WLEDA) as the excitation light source, a folded optical path with a complementary metal oxide semiconductor (CMOS) as the signal/image acquisition device and stepper motors with gear drives as the mechanical drive system. The biological binding/recognizing events on the microarray can be detected with an evanescent waveguide-directed illumination and light-scattering label (e.g., nanoparticles) while the microarray slide acts as an evanescent waveguide substrate. The performance of the as-developed PW-RLS scanner has been evaluated by analyzing type 2 diabetes mellitus (T2DM) risk genes. Highly selective and sensitive (less than 1% allele frequency at the attomole-level) T2DM risk gene detection is achieved using single-stranded DNA functionalized gold nanoparticles (ssDNA-GNPs) as detection probes. Additionally, the successful simultaneous analysis of 15 T2DM patient genotypes suggests that the device has great potential for the realization of a personalized diagnostic test for a given disease or patient follow-up.

关键词： OPTICAL waveguides OPTICAL properties of gold nanoparticles COMPLEMENTARY metal oxide semiconductors GENE frequency microarray technology GOLD nanoparticles spectra

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microarray study reveals a transforming growth factor-β-dependent mechanism of fibrosis in discoid lupus erythematosus

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BRITISH JOURNAL OF DERMATOLOGY 2016年第2期175卷 302-313页

作者： Sole, C. Gimenez-Barcons, M. Ferrer, B. Ordi-Ros, J. Cortes-Hernandez, J. Univ Autonoma Barcelona Inst Recerca VHIR Hosp Univ Vall dHebron Dept MedSyst Autoimmune Dis Unit Barcelona Spain Univ Autonoma Barcelona Hosp Univ Vall dHebron Dept Immunol Passeig Vall dHebron 119-129 Barcelona 08035 Spain Univ Autonoma Barcelona Hosp Univ Vall dHebron Dept Pathol Passeig Vall dHebron 119-129 Barcelona 08035 Spain

Background Discoid lupus erythematosus (DLE) is characterized by scarring lesions that develop and perpetuate fibrotic lesions. These are not observed in subacute cutaneous lupus erythematosus (SCLE). The pathophysiological basis of this is currently unknown. Objectives To identify contradistinctive signalling pathways and cellular signatures between the two type of lupus, with a focus on the molecular mechanisms leading to fibrosis. Methods We conducted a gene expression microarray analysis in lesional and non-lesional skin biopsy specimens of patients with DLE (n = 10) and SCLE (n = 10). Confirmatory reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry were performed on selected transcripts in a new cohort of paraffin-embedded skin biopsies (n = 20). Changes over time of a group of selected inflammatory and fibrotic genes were also evaluated in a second biopsy taken 12 weeks later. In vitro functional studies were performed in primary isolated fibroblasts. Results Compared with nonlesional skin, DLE samples expressed a distinctive T-cell gene signature. DLE samples displayed a significant CD4 T-cell enrichment with an imbalance towards T helper 1 cytokine predominance and a relative increased forkhead box (FOX) P3 response. RT-qPCR and immunochemical analysis over time showed a progressive increment of fibrotic markers and persistent FOXP3 recruitment. Ex vivo upregulation of SERPINE1, MMP9, TGFBR1, phosphorylated SMAD3 and TGFB1 suggested a transforming growth factor (TGF)-beta-dependent mechanism of fibrosis in DLE, also confirmed by the results observed following in vitro stimulation with TGF-beta. Conclusions These results highlight major pathogenic pathways in DLE and provide novel molecular targets for the development of new therapies. The data suggest the existence of a TGF-beta-dependent pathway inducing fibrosis in DLE.

关键词： LUPUS erythematosus microarray technology COLLAGEN diseases DEVELOPMENTAL biology SKIN diseases

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Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding

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JOURNAL OF CHEMICAL PHYSICS 2017年第15期146卷 155103-155103页

作者： Bush, Derek B. Knotts, Thomas A. Brigham Young Univ Dept Chem Engn Provo UT 84602 USA

Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces. To overcome this limitation, this study uses molecular simulation and an advanced, experimentally validated, coarse-grain, protein-surface model to compare fab-lysozyme binding in bulk solution and when the fab is tethered to hydrophobic and hydrophilic surfaces. The results show that the tether site in the fab, as well as the surface hydrophobicity, significantly impacts the binding process and suggests that the optimal design involves tethering fabs upright on a hydrophilic surface. The results offer an unprecedented, molecular-level picture of the binding process and give hope that the rational design of protein-microarrays is possible. Published by AIP Publishing.

关键词： MOLECULAR probes HYDROPHOBIC surfaces MOLECULAR orientation ANTIGEN-antibody reactions BINDING sites (Biochemistry) microarray technology

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microarray Analysis of Circular RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells

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BioMed Research International 2017年第0期2017卷 8421614-8421614页

作者： Xiong, Wei Ai, Yi-Qin Li, Yun-Fen Ye, Qing Chen, Zheng-Ting Qin, Ji-Yong Liu, Qiu-Yan Wang, Hong Ju, Yun-He Li, Wen-Hui Li, Yun-Feng Department of Radiation Oncology Yunnan Cancer Hospital Third Affiliated Hospital of Kunming Medical University Kunming China Department of Radiation Oncology First Affiliated Hospital of Kunming Medical University Kunming China Department of Colorectal Surgery Yunnan Cancer Hospital Third Affiliated Hospital of Kunming Medical University Kunming China

Preoperative 5-fluorouracil- (5-FU-) based chemoradiotherapy is a standard treatment for locally advanced colorectal cancer (CRC). However, the effect of 5-FU-based chemoradiotherapy on CRC is limited due to the development of chemoradiation resistance (CRR), and the molecular mechanisms underlying this resistance are yet to be investigated. Recently, circular RNAs (circRNAs), which can function as microRNA sponges, were found to be involved in the development of several cancers. In this study, we focused on clarifying the modulation of the expression profiles of circRNAs in CRR. microarray analysis identified 71 circRNAs differentially expressed in chemoradiation-resistant CRC cells. Among them, 47 were upregulated and 24 were downregulated by more than twofold. Furthermore, expression modulation of five representative circRNAs was validated by quantitative reverse transcription PCR (qRT-PCR). Moreover, these modulated circRNAs were predicted to interact with 355 miRNAs. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the most modulated circRNAs regulate several cancers and cancer-related pathways, and the possible mechanism underlying CRR was discussed. This is the first report revealing the circRNA modulations in 5-FU chemoradiation-resistant CRC cells by microarray. The study provided a useful database for further understanding CRR and presents potential targets to overcome CRR in CRC. © 2017 Wei Xiong et al.

关键词： CIRCULAR RNA CELL physiology COLON tumors DRUG resistance in cancer cells FLUOROURACIL microarray technology GENE expression profiling CHEMORADIOTHERAPY RECTUM tumors

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Detection of 22q11.2 microduplication by cell-free DNA screening and chromosomal microarray in fetus with multiple anomalies

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ULTRASOUND IN OBSTETRICS & GYNECOLOGY 2016年第4期48卷 530-U270页

作者： Wu, W. -J. Ma, G. -C. Lin, Y. -S. Yeang, C. -H. Ni, Y. -H. Li, W. -C. Tsai, H. -D. Gau, S. Shur-Fen Chen, M. Changhua Christian Hosp Dept Genom Med Changhua Taiwan Changhua Christian Hosp Ctr Med Genet Changhua Taiwan Changhua Christian Hosp Healthcare Syst Dept Genom Sci & Technol Changhua Taiwan Changhua Christian Hosp Dept Obstet & Gynecol Changhua Taiwan Chung Shan Med Univ Inst Biochem Microbiol & Immunol Taichung Taiwan Cent Taiwan Univ Sci & Technol Dept Med Lab Sci & Biotechnol Taichung Taiwan Welgene Biotechnol Co Nangang Business Pk Taipei Taiwan Acad Sinica Inst Stat Sci Taipei Taiwan Natl Taiwan Univ Hosp & Coll Med Dept Pediat Taipei Taiwan Puli Christian Hosp Dept Obstet & Gynecol Nantou Taiwan Natl Taiwan Univ Hosp & Coll Med Dept Psychiat Taipei Taiwan Natl Taiwan Univ Hosp Dept Med Genet Taipei Taiwan Natl Taiwan Univ Hosp & Coll Med Dept Obstet & Gynecol Taipei Taiwan Tunghai Univ Dept Life Sci Taichung Taiwan

A letter to the editor is presented regarding the detection of microdeletion syndromes in fetus with multiple anomalies through non-invasive prenatal cell-free DNA (cfDNA) testing.

关键词： DIAGNOSIS of fetus abnormalities PRENATAL genetic testing ANALYSIS of DNA MULTIPLE human abnormalities DIAGNOSIS CELLS CHROMOSOMES KARYOTYPES PRENATAL diagnosis microarray technology

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