Sample records for progression tissue microarray

  1. NCI-Frederick PHL - Tissue Microarray

    Cancer.gov

    Services Price List Courier Services & Shipment Procedures Scheduling Contact Information Related Links Establishing an Account PHL Forms PHL Portal Rodent Tissue Microarray Tissue microarays allow the possibility to represent a large number of tissue

  2. High throughput screening of meningioma biomarkers using a tissue microarray

    Microsoft Academic Search

    Eriks A. Lusis; Michael R. Chicoine; Arie Perry

    2005-01-01

    Summary Meningiomas are histologically and clinically diverse CNS neoplasms with few available immunohistochemical markers of differentiation and progression. Therefore, we investigated a panel of potentially useful meningioma-associated biomarkers using high throughput tissue microarray immunohistochemistry (TMA-IHC) with a TMA that includes 9 hemangiopericytomas (HPCs) and 41 meningiomas spanning all grades, as well as two subsets of atypical meningiomas, stratified according to

  3. An alternative high output tissue microarray technique

    PubMed Central

    2013-01-01

    Background Tissue microarray (TMA) is a high throughput research tool, which has greatly facilitated and accelerated in situ tissue analyses. However, its productivity has been restricted due to the confined thickness of traditional donor block. Here, we introduce an improved high output TMA method that is applicable to a broader range of tissue samples. Methods In this method, a 3.6 cm long and 2.7 cm wide recipient block with 88 square lattices (3 mm in width) was first prepared using several commercial instruments. A 2 mm wide and 6 mm long tissue rod was then prepared using a self-made blade-shaped knife from each paraffin embedded donor block of gastrointestinal stromal tumors. These rods were manually arrayed one by one into the corresponding lattices of the 60°C pre-softened recipient block with the guide of holes drilled with a steel needle. A 70-rod TMA was made to testify this method. Results The prepared TMA had well defined array configurations, good tissue morphology and fully preserved proteins and DNA. A total of 500–1000 TMA sections could be easily obtained from a TMA block. Conclusion This low-cost and time-saving method provides an alternative sampling tool for high output TMA. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1979605867857990 PMID:23336116

  4. A colorful future of quantitative pathology: validation of Vectra technology using chromogenic multiplexed immunohistochemistry and prostate tissue microarrays.

    PubMed

    Huang, Wei; Hennrick, Kenneth; Drew, Sally

    2013-01-01

    The Vectra platform (Caliper Life Sciences, Hopkinton, MA) is an advanced multispectral imaging system for biomarker quantitation in tissue microarray or intact tissue sections. This is the first study to validate its reliability for quantitating spatially overlapping biomarkers using chromogenic multiplexed immunohistochemistry on prostate tissue microarrays. Two tissue microarray cohorts (an outcome tissue microarray and a progression tissue microarray) were used. The outcome tissue microarray cohort consists of 462 duplicate cores with more than 5-year outcome information. The progression tissue microarray cohort consists of 384 duplicate cores from different disease (stage) groups. The tissue microarray slides were stained with different combinations of antibodies (anti-androgen receptor, anti-E-cadherin, anti-erythroblastosis virus E26 oncogene-related gene product, and anti-?-methylacyl-CoA racemase). Three outcome tissue microarrays were stained with androgen receptor + erythroblastosis virus E26 oncogene-related gene + E-cadherin (outcome tissue microarray 1), androgen receptor + E-cadherin (outcome tissue microarray 2), and erythroblastosis virus E26 oncogene-related gene + E-cadherin (outcome tissue microarray 3), respectively. One progression tissue microarray section was stained with E-cadherin and ?-methylacyl-CoA racemase; tissue microarray slides were then scanned with the Vectra platform. Biomarker expression analysis was performed with Vectra software-Nuance 3.0.0, and inForm 1.2. IBM SPSS Statistics 19 was used for statistical and correlation analysis (SPSS, Chicago, IL). Close concordance was found between the triple- and double-immunostaining assays used for quantitating spatially overlapping biomarkers androgen receptor and erythroblastosis virus E26 oncogene-related gene using outcome tissue microarrays (r = 0.897 for androgen receptor and 0.613 for erythroblastosis virus E26 oncogene-related gene, respectively). ?-Methylacyl-CoA racemase and E-cadherin expression levels measured in progression tissue microarray were consistent with previously published data by other groups. In conclusion, Vectra technology is reliable for objective and high-throughput biomarker quantitation and colocalization study using chromogenic multiplexed immunohistochemistry. PMID:22944297

  5. Digitized tissue microarray classification using sparse reconstruction

    NASA Astrophysics Data System (ADS)

    Xing, Fuyong; Liu, Baiyang; Qi, Xin; Foran, David J.; Yang, Lin

    2012-02-01

    In this paper, we propose a novel image classification method based on sparse reconstruction errors to discriminate cancerous breast tissue microarray (TMA) discs from benign ones. Sparse representation is employed to reconstruct the samples and separate the benign and cancer discs. The method consists of several steps including mask generation, dictionary learning, and data classification. Mask generation is performed using multiple scale texton histogram, integral histogram and AdaBoost. Two separate cancer and benign TMA dictionaries are learned using K-SVD. Sparse coefficients are calculated using orthogonal matching pursuit (OMP), and the reconstructive error of each testing sample is recorded. The testing image will be divided into many small patches. Each small patch will be assigned to the category which produced the smallest reconstruction error. The final classification of each testing sample is achieved by calculating the total reconstruction errors. Using standard RGB images, and tested on a dataset with 547 images, we achieved much better results than previous literature. The binary classification accuracy, sensitivity, and specificity are 88.0%, 90.6%, and 70.5%, respectively.

  6. Microarray data integration for genome-wide analysis of human tissue-selective gene expression

    Microsoft Academic Search

    Liangjiang Wang; Anand K Srivastava; Charles E Schwartz

    2010-01-01

    BACKGROUND: Microarray gene expression data are accumulating in public databases. The expression profiles contain valuable information for understanding human gene expression patterns. However, the effective use of public microarray data requires integrating the expression profiles from heterogeneous sources. RESULTS: In this study, we have compiled a compendium of microarray expression profiles of various human tissue samples. The microarray raw data

  7. Gene expression changes in progression of cervical neoplasia revealed by microarray analysis of cervical neoplastic keratinocytes.

    PubMed

    Rotondo, John Charles; Bosi, Silvia; Bassi, Cristian; Ferracin, Manuela; Lanza, Giovanni; Gafà, Roberta; Magri, Eros; Selvatici, Rita; Torresani, Stefania; Marci, Roberto; Garutti, Paola; Negrini, Massimo; Tognon, Mauro; Martini, Fernanda

    2015-04-01

    To evaluate the gene expression changes involved in neoplastic progression of cervical intraepithelial neoplasia. Using microarray analysis, large-scale gene expression profile was carried out on HPV16-CIN2, HPV16-CIN3, and normal cervical keratinocytes derived from two HPV16-CIN2, two HPV-CIN3 lesions, and two corresponding normal cervical tissues, respectively. Differentially expressed genes were analyzed in normal cervical keratinocytes compared with HPV16-CIN2 keratinocytes and in HPV16-CIN2 keratinocytes compared with HPV16-CIN3 keratinocytes; 37 candidate genes with continuously increasing or decreasing expression during CIN progression were identified. One of these genes, phosphoglycerate dehydrogenase, was chosen for further characterization. Quantitative reverse transcription-polymerase chain reaction and immunohistochemical analysis confirmed that expression of phosphoglycerate dehydrogenase consistently increases during progression of CIN toward cancer. Gene expression changes occurring during CIN progression were investigated using microarray analysis, for the first time, in CIN2 and CIN3 keratinocytes naturally infected with HPV16. Phosphoglycerate dehydrogenase is likely to be associated with tumorigenesis and may be a potential prognostic marker for CIN progression. PMID:25205602

  8. Assessing expression of apoptotic markers using large cohort tissue microarrays.

    PubMed

    Pick, Elah; McCarthy, Mary M; Kluger, Harriet M

    2008-01-01

    Apoptotic markers include proteins from the intrinsic and extrinsic pathways. These cascades include both pro-apoptotic and anti-apoptotic elements. The expression levels of these elements can be assessed by immunohistochemistry (IHC) and can indicate general trends in prov-ersus anti-apoptotic tendencies of the cells. IHC is particularly useful when studying large cohorts of paraffin-embedded specimens. Advances in tissue microarray (TMA) technology have facilitated evaluation of large cohorts of specimens, as cores from hundreds of patients can be represented on a single glass slide and stained in a uniform fashion. In this chapter, we discuss construction and staining methods of TMAs and present examples of assessment of apoptotic marker expression in malignant and benign cells using a novel method of automated, quantitative analysis of in situ protein expression. PMID:18175814

  9. Guidelines and considerations for conducting experiments using tissue microarrays.

    PubMed

    Ilyas, Mohammad; Grabsch, Heike; Ellis, Ian O; Womack, Chris; Brown, Robert; Berney, Dan; Fennell, Dean; Salto-Tellez, Manuel; Jenkins, Martin; Landberg, Goran; Byers, Richard; Treanor, Darren; Harrison, David; Green, Andrew R; Ball, Graham; Hamilton, Peter

    2013-05-01

    Tissue microarrays (TMAs) represent a powerful method for undertaking large-scale tissue-based biomarker studies. While TMAs offer several advantages, there are a number of issues specific to their use which need to be considered when employing this method. Given the investment in TMA-based research, guidance on design and execution of experiments will be of benefit and should help researchers new to TMA-based studies to avoid known pitfalls. Furthermore, a consensus on quality standards for TMA-based experiments should improve the robustness and reproducibility of studies, thereby increasing the likelihood of identifying clinically useful biomarkers. In order to address these issues, the National Cancer Research Institute Biomarker and Imaging Clinical Studies Group organized a 1-day TMA workshop held in Nottingham in May 2012. The document herein summarizes the conclusions from the workshop. It includes guidance and considerations on all aspects of TMA-based research, including the pre-analytical stages of experimental design, the analytical stages of data acquisition, and the postanalytical stages of data analysis. A checklist is presented which can be used both for planning a TMA experiment and interpreting the results of such an experiment. For studies of cancer biomarkers, this checklist could be used as a supplement to the REMARK guidelines. PMID:23672312

  10. Agarose mold embedding of cultured cells for tissue microarrays.

    PubMed

    Moskaluk, Christopher A; Stoler, Mark H

    2002-12-01

    There are several indications for the placement of samples of cultured cells in tissue microarrays (TMAs). To optimize this technique, three embedding procedures were compared: embedding of fixed cells pelleted by centrifugation, embedding of cells dispersed in an agarose matrix, and embedding of pelleted cells packed into the center of hollow agarose molds. TMAs were made from these preparations. The number of cells per tissue spot and the number of histologic sections that could be obtained from the preparations were determined. The agarose matrix and agarose mold techniques resulted in the longest core samples, while the cell pellet and agarose mold methods resulted in the greatest cell density. Thus, the use of cylindrical agarose molds optimizes both the number of cells present on a histologic section of a TMA, and the number of histologic sections that can be obtained from a TMA. This technique results in a paraffin-embedded cell preparation that yields a cell density of approximately 1000 cells per 0.6-mm diameter circular histologic section, and that produces uniform core samples the full thickness of the donor block. Histologic sections of TMAs prepared in this manner were validated in immunohistochemical and in situ hybridization assays. PMID:12459640

  11. Microarrays

    ERIC Educational Resources Information Center

    Plomin, Robert; Schalkwyk, Leonard C.

    2007-01-01

    Microarrays are revolutionizing genetics by making it possible to genotype hundreds of thousands of DNA markers and to assess the expression (RNA transcripts) of all of the genes in the genome. Microarrays are slides the size of a postage stamp that contain millions of DNA sequences to which single-stranded DNA or RNA can hybridize. This…

  12. Identification of different subtypes of breast cancer using tissue microarray.

    PubMed

    Munirah, M A; Siti-Aishah, M A; Reena, M Z; Sharifah, N A; Rohaizak, M; Norlia, A; Rafie, M K M; Asmiati, A; Hisham, A; Fuad, I; Shahrun, N S; Das, S

    2011-01-01

    Breast cancer may be classified into luminal A, luminal B, HER2+/ER-, basal-like and normal-like subtypes based on gene expression profiling or immunohistochemical (IHC) characteristics. The main aim of the present study was to classify breast cancer into molecular subtypes based on immunohistochemistry findings and correlate the subtypes with clinicopathological factors. Two hundred and seventeen primary breast carcinomas tumor tissues were immunostained for ER, PR, HER2, CK5/6, EGFR, CK8/18, p53 and Ki67 using tissue microarray technique. All subtypes were significantly associated with Malay ethnic background (p=0.035) compared to other racial origins. The most common subtypes of breast cancers were luminal A and was significantly associated with low histological grade (p<0.000) and p53 negativity (p=0.003) compared to HER2+/ER-, basal-like and normal-like subtypes with high histological grade (p<0.000) and p53 positivity (p=0.003). Luminal B subtype had the smallest mean tumor size (p=0.009) and also the highest mean number of lymph nodes positive (p=0.032) compared to other subtypes. All markers except EGFR and Ki67 were significantly associated with the subtypes. The most common histological type was infiltrating ductal carcinoma, NOS. Majority of basal-like subtype showed comedo-type necrosis (68.8%) and infiltrative margin (81.3%). Our studies suggest that IHC can be used to identify the different subtypes of breast cancer and all subtypes were significantly associated with race, mean tumor size, mean number of lymph node positive, histological grade and all immunohistochemical markers except EGFR and Ki67. PMID:21655659

  13. Soy consumption and histopathologic markers in breast tissue using tissue microarrays.

    PubMed

    Maskarinec, Gertraud; Erber, Eva; Verheus, Martijn; Hernandez, Brenda Y; Killeen, Jeffrey; Cashin, Suzanne; Cline, J Mark

    2009-01-01

    This study examined the relation of soy intake with hormonal and proliferation markers in benign and malignant breast tissue using tissue microarrays (TMAs). TMAs with up to 4 malignant and 4 benign tissue samples for 268 breast cancer cases were constructed. Soy intake in early life and in adulthood was assessed by questionnaire. The TMAs were stained for estrogen receptor (ER) alpha, ERbeta, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2/neu), proliferating cell nuclear antigen (PCNA), and Ki-67 using standard immunohistochemical methods. Logistic regression was applied for statistical analysis. A higher percentage of women showed positive marker expression in malignant than in benign tissue. With one exception, HER2/neu, no significant associations between soy intake and pathologic markers were observed. Early life soy intake was associated with lower HER2/neu and PCNA staining of malignant tissue. In benign tissue, early life soy intake showed higher ER and PR expression, but no difference in proliferation markers. The results of this investigation provide some assurance that soy intake does not adversely affect markers of proliferation. TMAs were shown to be a useful tool for epidemiologic research. PMID:19838945

  14. Merging Discovery with Validation in Tissue Based Translation Research: Toward the Goal of Multiplex Testing of Tissue Microarrays

    Cancer.gov

    April 30, 2015 10:30 AM - 11:30 AM Shady Grove Room TE 406 + Add to Outlook Calendar Title:  Merging Discovery with Validation in Tissue Based Translation Research: Toward the Goal of Multiplex Testing of Tissue Microarrays Speaker: Lawrence R Sternberg,

  15. A DNA microarray survey of gene expression in normal human tissues

    Microsoft Academic Search

    Radha Shyamsundar; Young H Kim; John P Higgins; Kelli Montgomery; Michelle Jorden; Anand Sethuraman; Matt van de Rijn; David Botstein; Patrick O Brown; Jonathan R Pollack

    2005-01-01

    Background: Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states. Comparatively little is known about the genes expressed across the gamut of normal human tissues. Systematic studies of global gene-expression patterns, by linking variation in the expression of specific genes to phenotypic variation in the cells or tissues in which they are expressed,

  16. Support vector machine classification and validation of cancer tissue samples using microarray expression data

    Microsoft Academic Search

    Terrence S. Furey; Nello Cristianini; Nigel P. Duffy; David W. Bednarski; Michèl Schummer; David Haussler

    2000-01-01

    MOTIVATION: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data using support vector machines (SVMs). This analysis consists of both classification of the tissue samples, and

  17. Microarray Evidences the Role of Pathologic Adipose Tissue in Insulin Resistance and Their Clinical Implications

    PubMed Central

    Mathur, Sandeep Kumar; Jain, Priyanka; Mathur, Prashant

    2011-01-01

    Clustering of insulin resistance and dysmetabolism with obesity is attributed to pathologic adipose tissue. The morphologic hallmarks of this pathology are adipocye hypertrophy and heightened inflammation. However, it's underlying molecular mechanisms remains unknown. Study of gene function in metabolically active tissues like adipose tissue, skeletal muscle and liver is a promising strategy. Microarray is a powerful technique of assessment of gene function by measuring transcription of large number of genes in an array. This technique has several potential applications in understanding pathologic adipose tissue. They are: (1) transcriptomic differences between various depots of adipose tissue, adipose tissue from obese versus lean individuals, high insulin resistant versus low insulin resistance, brown versus white adipose tissue, (2) transcriptomic profiles of various stages of adipogenesis, (3) effect of diet, cytokines, adipokines, hormones, environmental toxins and drugs on transcriptomic profiles, (4) influence of adipokines on transcriptomic profiles in skeletal muscle, hepatocyte, adipose tissue etc., and (5) genetics of gene expression. The microarray evidences of molecular basis of obesity and insulin resistance are presented here. Despite the limitations, microarray has potential clinical applications in finding new molecular targets for treatment of insulin resistance and classification of adipose tissue based on future risk of insulin resistance syndrome. PMID:21603273

  18. Improved technique for manually constructing tissue microarrays for large-core arrays.

    PubMed

    Tsao, Shu-Chuan; Wu, Chun-Chieh; Wen, Chien-Hui; Chai, Chee-Yin; Chen, Yi-Ting

    2013-01-01

    Tissue microarrays were originally developed to enable alignment of multiple tissue cores in a single paraffin block and to enable high-throughput laboratory analysis. However, a major drawback is the loss of tissue cores during slide preparation, especially when sectioning the tissue block. Tissue cylinders directly aligned in the metal box without preheating tend to detach from the surrounding paraffin, which results in incomplete or folded tissue sections. The proposed solution is preheating all tissue cylinders on a hot plate to facilitate fusion between the paraffin within the core and the paraffin surrounding the core. In this study, 6 tissue microarray blocks were constructed from 528 tissue cores extracted from various formalin-fixed, paraffin-embedded human tissue samples. The tissue cores in the arrays revealed good homogenization with the surrounding paraffin wax, and the tissue sections were obtained intact. Both hematoxylin-eosin and immunohistochemical staining confirmed satisfactory results. This simple and economical method is easily performed in the laboratory without expensive instrumentation. PMID:22595943

  19. Validation of Tissue Microarrays for Immunohistochemical Profiling of Cancer Specimens Using the Example of Human Fibroblastic Tumors

    Microsoft Academic Search

    Axel Hoos; Marshall J. Urist; Alexander Stojadinovic; Stephen Mastorides; Maria E. Dudas; Denis H. Y. Leung; David Kuo; Murray F. Brennan; Jonathan J. Lewis; Carlos Cordon-Cardo

    2001-01-01

    Tissue microarrays allow high-throughput molecular profiling of cancer specimens by immunohistochemistry. Phenotype information of sections from arrayed biopsies on a multitissue block needs to be representative of full sections, as protein expression varies throughout the entire tumor specimen. To validate the use of tissue microarrays for immunophenotyping, we studied a group of 59 fibroblastic tumors with variable protein expression patterns

  20. Analysis of methylation microarray for tissue specific detection.

    PubMed

    Muangsub, Tachapol; Samsuwan, Jarunya; Tongyoo, Pumipat; Kitkumthorn, Nakarin; Mutirangura, Apiwat

    2014-12-10

    The role of human DNA methylation has been extensively studied in genomic imprinting, X-inactivation, and disease. However, studies of tissue-specific methylation remain limited. In this study, we use bioinformatics methods to analyze methylation data and reveal loci that are exclusively methylated or unmethylated in individual tissues. We collect 39 previously published DNA methylation profiles using an Illumina® HumanMethylation 27 BeadChip Kit containing 22 common tissues and involving 27,578 CpG loci across the human genome. We found 86 positions of tissue specific methylation CpG (TSM) that encompass 34 hypermethylated TSMs (31 genes) and 52 hypomethylated TSMs (47 genes). Tissues were found to contain 1 to 25 TSM loci, with the majority in the liver (25), testis (18), and brain (16). Fewer TSM loci were found in the muscle (8), ovary (7), adrenal gland (3), pancreas (2-4), kidney, spleen, and stomach (1 each). TSMs are predominantly located 0-300 base pairs in the 3' direction after the transcription start site. Similar to known promoters of methylation, hypermethylated TSM genes suppress transcription, while hypomethylated TSMs allow gene transcription. The majority of hypermethylated TSM genes encode membrane proteins and receptors, while hypomethylated TSM genes primarily encode signal peptides and tissue-specific proteins. In summary, the database of TSM loci produced herein is useful for the selection of tissue-specific DNA markers as diagnostic tools, as well as for the further study of the mechanisms and roles of TSM. PMID:25281015

  1. [Gene expression profiling of three tissues of chicken after heat stress treatment by microarray technique].

    PubMed

    Song, Xiaoyan; Zhang, Dexiang; Zhang, Wenwu; Ji, Congliang; Zhang, Xiquan; Luo, Qingbin

    2014-08-01

    In the present study, tissue samples were collected from the cerebrum, liver, and leg muscle of 8-day-old dwarf chicks that were exposed to a 3 h treatment of 28?± 1? (control group) or 40?± 1? (treatment group). Differentially expressed (DE) genes in these samples were detected using whole-genome microarray chips, and their functions were. PMID:25143278

  2. Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays

    Microsoft Academic Search

    Charles W. Sugnet; Karpagam Srinivasan; Tyson A. Clark; Georgeann O'Brien; Melissa S. Cline; Hui Wang; Alan Williams; David Kulp; John E. Blume; David Haussler; Manuel Ares

    2006-01-01

    Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for

  3. [Binding capability of lidamycin apoprotein to human breast cancer detected by tissue microarrays].

    PubMed

    Cai, Lin; Gao, Rui-Juan; Guo, Xiao-Zhong; Li, Yi; Zhen, Yong-Su

    2010-05-01

    This study is to investigate the binding capability of lidamycin apoprotein (LDP), an enediyne-associated apoprotein of the chromoprotein antitumor antibiotic family, to human breast cancer and normal tissues, the correlation of LDP binding capability to human breast cancer tissues and the expression of tumor therapeutic targets such as VEGF and HER2. In this study, the binding capability of LDP to human breast cancer tissues was detected with tissue microarray. The correlation study of LDP binding capability to human breast tumor tissues and relevant therapeutic targets was performed on breast cancer tissue microarrays. Immunocytochemical examination was used to detect the binding capability of LDP to human breast carcinoma MCF-7 cells. As a result, tissue microarray showed that LDP staining of 73.2% (30/41) of breast cancer tissues was positive, whereas that of 48.3% (15/31) of the adjacent normal breast specimens was positive. The difference between the tumor and normal samples was significant (Chi2 = 4.63, P < 0.05). LDP immunoreactivity in breast cancer correlated significantly with the overexpression of VEGF and HER2 (P < 0.001 and < 0.01, r = 0.389 and 0.287, respectively). Determined with confocal immunofluorescent analysis, LDP showed the binding capability to mammary carcinoma MCF-7 cells. It is demonstrated that LDP can bind to human breast cancer tissues and there is significant difference between the breast cancer tissues and the corresponding normal tissues. Notably, the binding reactivity shows positive correlation with the expression of VEGF and HER2 in breast carcinoma tissues. The results imply that LDP may have a potential use as targeting drug carrier in the research and development of new anticancer therapeutics. This study may provide reference for drug combination of LDM and other therapeutic agents. PMID:20931759

  4. Tissue MicroArray Analyses of Pancreatic Duodenal Homeobox-1 in Human Cancers

    Microsoft Academic Search

    Xiao-Ping Wang; Zhi-Jun Li; Jonas Magnusson; F. Charles Brunicardi

    2005-01-01

    In previous studies, we demonstrated that rat insulin promoter (RIP)-driven gene therapy successfully targeted human pancreatic tumor PANC-1 cells and mouse insulinoma NIT-1 cells, which are both pancreatic duodenal homeobox-1 (PDX-1)-positive. The purpose of this study was to perform a human tissue array analysis to determine potential targets for RIP-driven gene therapy. A custom-designed tissue MicroArray analysis of various human

  5. Candidate genes for the progression of malignant gliomas identified by microarray analysis

    Microsoft Academic Search

    Oliver Bozinov; Sylvia Köhler; Birgit Samans; Ludwig Benes; Dorothea Miller; Markus Ritter; Ulrich Sure; Helmut Bertalanffy

    2008-01-01

    Malignant astrocytomas of World Health Organization (WHO) grade III or IV have a reduced median survival time, and possible\\u000a pathways have been described for the progression of anaplastic astrocytomas and glioblastomas, but the molecular basis of\\u000a malignant astrocytoma progression is still poorly understood. Microarray analysis provides the chance to accelerate studies\\u000a by comparison of the expression of thousands of genes

  6. Tissue factor, angiogenesis and tumour progression

    PubMed Central

    Bluff, Joanne E; Brown, Nicola J; Reed, Malcolm WR; Staton, Carolyn A

    2008-01-01

    Tissue factor, the primary initiator of the coagulation cascade, maintains vascular integrity in response to injury. It is now recognised that, in addition to the role as a procoagulant activator, tissue factor participates in many tumour-related processes that contribute to malignant disease progression. The present review details the recent evidence supporting a role for tissue factor in tumour haemostasis, angiogenesis, metastasis and malignant cell survival. Furthermore, future research directions are discussed that may enhance our understanding of the role and regulation of this protein, which could ultimately lead to the innovative design and development of new anticancer therapies. PMID:18373885

  7. Tissue Microarray Immunohistochemical Detection of Brachyury Is Not a Prognostic Indicator in Chordoma

    PubMed Central

    Schwab, Joseph H.; Nielsen, G. Petur; Choy, Edwin; Ye, Shunan; Zhang, Zhan; Mankin, Henry; Hornicek, Francis J.; Duan, Zhenfeng

    2013-01-01

    Brachyury is a marker for notochord-derived tissues and neoplasms, such as chordoma. However, the prognostic relevance of brachyury expression in chordoma is still unknown. The improvement of tissue microarray technology has provided the opportunity to perform analyses of tumor tissues on a large scale in a uniform and consistent manner. This study was designed with the use of tissue microarray to determine the expression of brachyury. Brachyury expression in chordoma tissues from 78 chordoma patients was analyzed by immunohistochemical staining of tissue microarray. The clinicopathologic parameters, including gender, age, location of tumor and metastatic status were evaluated. Fifty-nine of 78 (75.64%) tumors showed nuclear staining for brachyury, and among them, 29 tumors (49.15%) showed 1+ (<30% positive cells) staining, 15 tumors (25.42%) had 2+ (31% to 60% positive cells) staining, and 15 tumors (25.42%) demonstrated 3+ (61% to 100% positive cells) staining. Brachyury nuclear staining was detected more frequently in sacral chordomas than in chordomas of the mobile spine. However, there was no significant relationship between brachyury expression and other clinical variables. By Kaplan-Meier analysis, brachyury expression failed to produce any significant relationship with the overall survival rate. In conclusion, brachyury expression is not a prognostic indicator in chordoma. PMID:24086644

  8. Cell and Tissue Microarray Technologies for Protein and Nucleic Acid Expression Profiling

    PubMed Central

    Cardano, Marina; Diaferia, Giuseppe R.; Falavigna, Maurizio; Spinelli, Chiara C.; Sessa, Fausto; DeBlasio, Pasquale

    2013-01-01

    Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform. PMID:23172795

  9. Cell and tissue microarray technologies for protein and nucleic acid expression profiling.

    PubMed

    Cardano, Marina; Diaferia, Giuseppe R; Falavigna, Maurizio; Spinelli, Chiara C; Sessa, Fausto; DeBlasio, Pasquale; Biunno, Ida

    2013-02-01

    Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform. PMID:23172795

  10. Phosphoprotein Stability in Clinical Tissue and Its Relevance for Reverse Phase Protein Microarray Technology

    PubMed Central

    Espina, Virginia; Mueller, Claudius; Liotta, Lance A.

    2013-01-01

    Phosphorylated proteins reflect the activity of specific cell signaling nodes in biological kinase protein networks. Cell signaling pathways can be either activated or deactivated depending on the phosphorylation state of the constituent proteins. The state of these kinase pathways reflects the in vivo activity of the cells and tissue at any given point in time. As such, cell signaling pathway information can be extrapolated to infer which phosphorylated proteins/pathways are driving an individual tumor’s growth. Reverse Phase Protein Microarrays (RPMA) are a sensitive and precise platform that can be applied to the quantitative measurement of hundreds of phosphorylated signal proteins from a small sample of tissue. Pre-analytical variability originating from tissue procurement and preservation may cause significant variability and bias in downstream molecular analysis. Depending on the ex vivo delay time in tissue processing, and the manner of tissue handling, protein biomarkers such as signal pathway phosphoproteins will be elevated or suppressed in a manner that does not represent the biomarker levels at the time of excision. Consequently, assessment of the state of these kinase networks requires stabilization, or preservation, of the phosphoproteins immediately post tissue procurement. We have employed reverse phase protein microarray analysis of phosphoproteins to study the factors influencing stability of phosphoproteins in tissue following procurement. Based on this analysis we have established tissue procurement guidelines for clinical research with an emphasis on quantifying phosphoproteins by RPMA. PMID:21901591

  11. Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray

    Microsoft Academic Search

    Christine P. Hans; Dennis D. Weisenburger; Timothy C. Greiner; Randy D. Gascoyne; Jan Delabie; German Ott; H. Konrad Muller-Hermelink; Elias Campo; Rita M. Braziel; Elaine S. Jaffe; Zenggang Pan; Pedro Farinha; Lynette M. Smith; Brunangelo Falini; Alison H. Banham; Andreas Rosenwald; Louis M. Staudt; Joseph M. Connors; James O. Armitage; Wing C. Chan

    2004-01-01

    Diffuse large B-cell lymphoma (DLBCL) can be divided into prognostically impor- tant subgroups with germinal center B- cell-like (GCB), activated B-cell-like (ABC), and type 3 gene expression pro- files using a cDNA microarray. Tissue microarray (TMA) blocks were created from 152 cases of DLBCL, 142 of which had been successfully evaluated by cDNA microarray (75 GCB, 41 ABC, and 26

  12. Application of a new technique, spiral tissue microarrays constructed using needle biopsy specimens, to prostate cancer research.

    PubMed

    Komiya, Akira; Kato, Tomonori; Hori, Takashi; Fukuoka, Junya; Yasuda, Kenji; Fuse, Hideki

    2014-01-01

    Tissue microarrays were constructed using prostate needle biopsy specimens obtained from 58 patients who underwent radical prostatectomy for localized or locally advanced prostate cancer (PC). We used the spiral array (SA) technique, a novel approach for tissue array construction in a spiral form, which has advantages over small needle biopsy specimens. Roll-shaped tissue pieces produced by slicing a prostate biopsy tissue block and trimming the cancer segment were used to obtain a tissue array block. Cancer segments measuring >3 mm were incorporated into the tissue arrays. Cancer fragments (n=253) were obtained from formalin-fixed, paraffin-embedded needle biopsy specimens. The median number of cancer fragments per patient was four (1-8, min-max). On SA, the median number of confirmed cancer fragments per patient was four (1-7) and 224 cancer fragments (88.5%) were confirmed histologically. Each core of reeled tissue contained at least one cancer fragment. The expressions of multiple prognostic molecular markers for PC (Ki-67, p53 and bcl-2) were immunohistochemically measured using the SA. The Ki-67 and bcl-2 expressions were significantly associated with the Gleason score (GS). A univariate analysis identified Ki-67, bcl-2 and GS as significant predictors of cancer-specific survival, p53 and bcl-2 as significant predictors of overall survival and Ki-67, adjuvant androgen deprivation and GS as significant predictors of biochemical progression. In a multivariate analysis, p53 was independently associated with overall survival, while adjuvant androgen deprivation and GS were associated with biochemical progression. These results indicate that SA has potential as a new tool for translational research on PC. PMID:24220327

  13. Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data

    PubMed Central

    2013-01-01

    Background Understanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. The accurate predictions of tissue-specific gene targets could provide useful information for biomarker development and drug target identification. Results In this study, we have developed a machine learning approach for predicting the human tissue-specific genes using microarray expression data. The lists of known tissue-specific genes for different tissues were collected from UniProt database, and the expression data retrieved from the previously compiled dataset according to the lists were used for input vector encoding. Random Forests (RFs) and Support Vector Machines (SVMs) were used to construct accurate classifiers. The RF classifiers were found to outperform SVM models for tissue-specific gene prediction. The results suggest that the candidate genes for brain or liver specific expression can provide valuable information for further experimental studies. Our approach was also applied for identifying tissue-selective gene targets for different types of tissues. Conclusions A machine learning approach has been developed for accurately identifying the candidate genes for tissue specific/selective expression. The approach provides an efficient way to select some interesting genes for developing new biomedical markers and improve our knowledge of tissue-specific expression. PMID:23369200

  14. Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis

    PubMed Central

    Chang, Cheng-Wei; Cheng, Wei-Chung; Chen, Chaang-Ray; Shu, Wun-Yi; Tsai, Min-Lung; Huang, Ching-Lung; Hsu, Ian C.

    2011-01-01

    Background Categorizing protein-encoding transcriptomes of normal tissues into housekeeping genes and tissue-selective genes is a fundamental step toward studies of genetic functions and genetic associations to tissue-specific diseases. Previous studies have been mainly based on a few data sets with limited samples in each tissue, which restrained the representativeness of their identified genes, and resulted in low consensus among them. Results This study compiled 1,431 samples in 43 normal human tissues from 104 microarray data sets. We developed a new method to improve gene expression assessment, and showed that more than ten samples are needed to robustly identify the protein-encoding transcriptome of a tissue. We identified 2,064 housekeeping genes and 2,293 tissue-selective genes, and analyzed gene lists by functional enrichment analysis. The housekeeping genes are mainly involved in fundamental cellular functions, and the tissue-selective genes are strikingly related to functions and diseases corresponding to tissue-origin. We also compared agreements and related functions among our housekeeping genes and those of previous studies, and pointed out some reasons for the low consensuses. Conclusions The results indicate that sufficient samples have improved the identification of protein-encoding transcriptome of a tissue. Comprehensive meta-analysis has proved the high quality of our identified HK and TS genes. These results could offer a useful resource for future research on functional and genomic features of HK and TS genes. PMID:21818400

  15. Decentralized Data Sharing of Tissue Microarrays for Investigative Research in Oncology

    PubMed Central

    Chen, Wenjin; Schmidt, Cristina; Parashar, Manish; Reiss, Michael; Foran, David J.

    2007-01-01

    Tissue microarray technology (TMA) is a relatively new approach for efficiently and economically assessing protein and gene expression across large ensembles of tissue specimens. Tissue microarray technology holds great potential for reducing the time and cost associated with conducting research in tissue banking, proteomics, and outcome studies. However, the sheer volume of images and other data generated from even limited studies involving tissue microarrays quickly approach the processing capacity and resources of a division or department. This challenge is compounded by the fact that large-scale projects in several areas of modern research rely upon multi-institutional efforts in which investigators and resources are spread out over multiple campuses, cities, and states. To address some of the data management issues several leading institutions have begun to develop their own “in-house” systems, independently, but such data will be only minimally useful if it isn’t accessible to others in the scientific community. Investigators at different institutions studying the same or related disorders might benefit from the synergy of sharing results. To facilitate sharing of TMA data across different database implementations, the Technical Standards Committee of the Association for Pathology Informatics organized workshops in efforts to establish a standardized TMA data exchange specification. The focus of our research does not relate to the establishment of standards for exchange, but rather builds on these efforts and concentrates on the design, development and deployment of a decentralized collaboratory for the unsupervised characterization, and seamless and secure discovery and sharing of TMA data. Specifically, we present a self-organizing, peer-to-peer indexing and discovery infrastructure for quantitatively assessing digitized TMA’s. The system utilizes a novel, optimized decentralized search engine that supports flexible querying, while guaranteeing that once information has been stored in the system, it will be found with bounded costs. PMID:19081778

  16. Datamining approach for automation of diagnosis of breast cancer in immunohistochemically stained tissue microarray images.

    PubMed

    Prasad, Keerthana; Zimmermann, Bernhard; Prabhu, Gopalakrishna; Pai, Muktha

    2010-01-01

    Cancer of the breast is the second most common human neoplasm, accounting for approximately one quarter of all cancers in females after cervical carcinoma. Estrogen receptor (ER), Progesteron receptor and human epidermal growth factor receptor (HER-2/neu) expressions play an important role in diagnosis and prognosis of breast carcinoma. Tissue microarray (TMA) technique is a high throughput technique which provides a standardized set of images which are uniformly stained, facilitating effective automation of the evaluation of the specimen images. TMA technique is widely used to evaluate hormone expression for diagnosis of breast cancer. If one considers the time taken for each of the steps in the tissue microarray process workflow, it can be observed that the maximum amount of time is taken by the analysis step. Hence, automated analysis will significantly reduce the overall time required to complete the study. Many tools are available for automated digital acquisition of images of the spots from the microarray slide. Each of these images needs to be evaluated by a pathologist to assign a score based on the staining intensity to represent the hormone expression, to classify them into negative or positive cases. Our work aims to develop a system for automated evaluation of sets of images generated through tissue microarray technique, representing the ER expression images and HER-2/neu expression images. Our study is based on the Tissue Microarray Database portal of Stanford university at http://tma.stanford.edu/cgi-bin/cx?n=her1, which has made huge number of images available to researchers. We used 171 images corresponding to ER expression and 214 images corresponding to HER-2/neu expression of breast carcinoma. Out of the 171 images corresponding to ER expression, 104 were negative and 67 were representing positive cases. Out of the 214 images corresponding to HER-2/neu expression, 112 were negative and 102 were representing positive cases. Our method has 92.31% sensitivity and 93.18% specificity for ER expression image classification and 96.67% sensitivity and 88.24% specificity for HER-2/neu expression image classification. PMID:21589855

  17. Datamining Approach for Automation of Diagnosis of Breast Cancer in Immunohistochemically Stained Tissue Microarray Images

    PubMed Central

    Prasad, Keerthana; Zimmermann, Bernhard; Prabhu, Gopalakrishna; Pai, Muktha

    2010-01-01

    Cancer of the breast is the second most common human neoplasm, accounting for approximately one quarter of all cancers in females after cervical carcinoma. Estrogen receptor (ER), Progesteron receptor and human epidermal growth factor receptor (HER-2/neu) expressions play an important role in diagnosis and prognosis of breast carcinoma. Tissue microarray (TMA) technique is a high throughput technique which provides a standardized set of images which are uniformly stained, facilitating effective automation of the evaluation of the specimen images. TMA technique is widely used to evaluate hormone expression for diagnosis of breast cancer. If one considers the time taken for each of the steps in the tissue microarray process workflow, it can be observed that the maximum amount of time is taken by the analysis step. Hence, automated analysis will significantly reduce the overall time required to complete the study. Many tools are available for automated digital acquisition of images of the spots from the microarray slide. Each of these images needs to be evaluated by a pathologist to assign a score based on the staining intensity to represent the hormone expression, to classify them into negative or positive cases. Our work aims to develop a system for automated evaluation of sets of images generated through tissue microarray technique, representing the ER expression images and HER-2/neu expression images. Our study is based on the Tissue Microarray Database portal of Stanford university at http://tma.stanford.edu/cgi-bin/cx?n=her1, which has made huge number of images available to researchers. We used 171 images corresponding to ER expression and 214 images corresponding to HER-2/neu expression of breast carcinoma. Out of the 171 images corresponding to ER expression, 104 were negative and 67 were representing positive cases. Out of the 214 images corresponding to HER-2/neu expression, 112 were negative and 102 were representing positive cases. Our method has 92.31% sensitivity and 93.18% specificity for ER expression image classification and 96.67% sensitivity and 88.24% specificity for HER-2/neu expression image classification. PMID:21589855

  18. Cancer and Leukemia Group B Pathology Committee Guidelines for Tissue Microarray Construction Representing Multicenter Prospective Clinical Trial Tissues

    PubMed Central

    Rimm, David L.; Nielsen, Torsten O.; Jewell, Scott D.; Rohrer, Daniel C.; Broadwater, Gloria; Waldman, Frederic; Mitchell, Kisha A.; Singh, Baljit; Tsongalis, Gregory J.; Frankel, Wendy L.; Magliocco, Anthony M.; Lara, Jonathan F.; Hsi, Eric D.; Bleiweiss, Ira J.; Badve, Sunil S.; Chen, Beiyun; Ravdin, Peter M.; Schilsky, Richard L.; Thor, Ann; Berry, Donald A.

    2011-01-01

    Practice-changing evidence requires confirmation, preferably in multi-institutional clinical trials. The collection of tissue within such trials has enabled biomarker studies and evaluation of companion diagnostic tests. Tissue microarrays (TMAs) have become a standard approach in many cooperative oncology groups. A principal goal is to maximize the number of assays with this precious tissue. However, production strategies for these arrays have not been standardized, possibly decreasing the value of the study. In this article, members of the Cancer and Leukemia Group B Pathology Committee relay our experiences as array facility directors and propose guidelines regarding the production of high-quality TMAs for cooperative group studies. We also discuss statistical issues arising from having a proportion of patients available for TMAs and the possibility that patients with TMAs fail to represent the greater study population. PMID:21519016

  19. Automatic handling of tissue microarray cores in high-dimensional microscopy images.

    PubMed

    Fernández-Carrobles, M del Milagro; Bueno, Gloria; Déniz, Oscar; Salido, Jesús; García-Rojo, Marcial

    2014-05-01

    This paper describes a specific tool for automatically segmenting and archiving of tissue microarray (TMA) cores in microscopy images at different magnifications. TMA enables researchers to extract the small cylinders of a single tissue (core sections) from histological sections and arrange them in an array on a paraffin block such that hundreds can be analyzed simultaneously. A crucial step to improve the speed and quality of this process is the correct localization of each tissue core in the array. However, usually the tissue cores are not aligned in the microarray, the TMA cores are incomplete and the images are noisy and with distorted colors. We develop a robust framework to handle core sections under these conditions. The algorithms are able to detect, stitch, and archive the TMA cores at different magnifications. Once the TMA cores are segmented they are stored in a relational database allowing their processing for further studies of benign-malignant classification. The method was shown to be reliable for handling the TMA cores and therefore enabling further large-scale molecular pathology research. PMID:24107985

  20. Biofunctionalization of surfaces by energetic ion implantation: Review of progress on applications in implantable biomedical devices and antibody microarrays

    NASA Astrophysics Data System (ADS)

    Bilek, Marcela M. M.

    2014-08-01

    Despite major research efforts in the field of biomaterials, rejection, severe immune responses, scar tissue and poor integration continue to seriously limit the performance of today's implantable biomedical devices. Implantable biomaterials that interact with their host via an interfacial layer of active biomolecules to direct a desired cellular response to the implant would represent a major and much sought after improvement. Another, perhaps equally revolutionary, development that is on the biomedical horizon is the introduction of cost-effective microarrays for fast, highly multiplexed screening for biomarkers on cell membranes and in a variety of analyte solutions. Both of these advances will rely on effective methods of functionalizing surfaces with bioactive molecules. After a brief introduction to other methods currently available, this review will describe recently developed approaches that use energetic ions extracted from plasma to facilitate simple, one-step covalent surface immobilization of bioactive molecules. A kinetic theory model of the immobilization process by reactions with long-lived, mobile, surface-embedded radicals will be presented. The roles of surface chemistry and microstructure of the ion treated layer will be discussed. Early progress on applications of this technology to create diagnostic microarrays and to engineer bioactive surfaces for implantable biomedical devices will be reviewed.

  1. Multiplex quantitative measurement of mRNAs from fixed tissue microarray sections.

    PubMed

    Armani, Michael; Tangrea, Michael; Yang, Brian; Rosenberg, Alex; Ylaya, Kris; Morris, Jennifer; Rodriguez-Canales, Jaime; Hanson, Jeffrey; Shapiro, Benjamin; Emmert-Buck, Michael R; Smela, Elisabeth; Hewitt, Stephen M

    2014-01-01

    The development of prognostic and diagnostic biomarkers, such as those from gene expression studies, requires independent validation in clinical specimens. Immunohistochemical analysis on tissue microarrays (TMAs) of formalin-fixed paraffin-embedded tissue is often used to increase the statistical power, and it is used more often than in situ hybridization, which can be technically limiting. Herein, we introduce a method for performing quantitative gene expression analysis across a TMA using an adaptation of 2D-RT-qPCR, a recently developed technology for measuring transcript levels in a histologic section while maintaining 2-dimensional positional information of the tissue sample. As a demonstration of utility, a TMA with tumor and normal human prostate samples was used to validate expression profiles from previous array-based gene discovery studies of prostate cancer. The results show that 2D-RT-qPCR expands the utility of TMAs to include sensitive and accurate gene expression measurements. PMID:24809843

  2. Classification of polycyclic aromatic hydrocarbons based on mutagenicity in lung tissue through DNA microarray.

    PubMed

    Hirano, Minoru; Tanaka, Shiho; Asami, Osamu

    2013-11-01

    Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental pollutants produced in the combustion of organic matter. Exposure to PAHs raises the risk of lung cancer and inflammatory and allergic disorders such as asthma. DNA microarray technologies have been applied to research on toxicogenomics in the recent years. To evaluate the mutagenicity of PAHs and constituents of environmental pollutants in lung tissue, including metabolic activation, human alveolar epithelial type II cells (A549) were treated with nonmutagenic PAH pyrene and with the mutagenic PAHs benzo-[a]-pyrene, 1-nitropyrene, or 1,8-dinitropyrene. Comparison of genome-wide microarray expression profiles between a nonmutagenic and a mutagenic PAH-treated group revealed that xenobiotic response genes such as CYP1B1 were commonly upregulated in two groups and that DNA damage induced genes, especially p53-downstream genes such as p21 (CDKN1A) were upregulated only in the mutagenic PAH-treated group. Pretreatment with cytochrome P450 inhibitor ?-naphthoflavone or p53 inhibitor pifithrin-? inhibited the benzo-[a]-pyrene-induced p21 expression. These data suggest that when PAHs enter the cells, lung epithelium induces PAH metabolic activating enzymes, and then the DNA damages-recognition signal is converged with p53 downstream genes. This metabolic activation and DNA damage is induced in lung epithelium, and the mutagenicity of PAHs can be classified by DNA microarray expression profiles. PMID:21887816

  3. MALDI Imaging Mass Spectrometry Profiling of N-Glycans in Formalin-Fixed Paraffin Embedded Clinical Tissue Blocks and Tissue Microarrays

    PubMed Central

    Powers, Thomas W.; Neely, Benjamin A.; Shao, Yuan; Tang, Huiyuan; Troyer, Dean A.; Mehta, Anand S.; Haab, Brian B.; Drake, Richard R.

    2014-01-01

    A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed tissues from normal mouse kidney, human pancreatic and prostate cancers, and a human hepatocellular carcinoma tissue microarray were processed by antigen retrieval followed by on-tissue digestion with peptide N-glycosidase F. The released N-glycans were detected by MALDI-IMS analysis, and the structural composition of a subset of glycans could be verified directly by on-tissue collision-induced fragmentation. Other structural assignments were confirmed by off-tissue permethylation analysis combined with multiple database comparisons. Imaging of mouse kidney tissue sections demonstrates specific tissue distributions of major cellular N-linked glycoforms in the cortex and medulla. Differential tissue distribution of N-linked glycoforms was also observed in the other tissue types. The efficacy of using MALDI-IMS glycan profiling to distinguish tumor from non-tumor tissues in a tumor microarray format is also demonstrated. This MALDI-IMS workflow has the potential to be applied to any FFPE tissue block or tissue microarray to enable higher throughput analysis of the global changes in N-glycosylation associated with cancers. PMID:25184632

  4. Tissue factor proangiogenic signaling in cancer progression.

    PubMed

    Schaffner, Florence; Yokota, Naho; Ruf, Wolfram

    2012-04-01

    Cancer progression from a dormant, non-vascularized benign tumor to metastatic disease is a multiple steps process that critically depends on contributions from the hemostatic system. Tissue factor (TF), protease activated receptors (PARs), factor VIIa, and the endothelial protein C receptor (EPCR) are expressed by tumor cells as well as the host compartment. These components of the hemostatic system regulate tumor growth, angiogenesis and metastasis. Here we review the evidence that TF-dependent signaling is the major driver of primary tumor growth, whereas TF-initiated coagulation and interactions of procoagulant tumor cells with the host compartments initiate multiple pathways that support and regulate the efficiency of metastatic tumor dissemination. PMID:22682123

  5. The HOPE-technique permits Northern blot and microarray analyses in paraffin-embedded tissues.

    PubMed

    Goldmann, Torsten; Flohr, Aljoscha M; Murua Escobar, Hugo; Gerstmayer, Bernhard; Janssen, Uwe; Bosio, Andreas; Loeschke, Siegfried; Vollmer, Ekkehard; Bullerdiek, Jörn

    2004-01-01

    There is an increasing demand for tissue samples that, after having been used for conventional histologic examination, are also suited for molecular analyses. As to formalin-fixed, paraffin embedded (FFPE) tissue, the latter applications are very limited. The HOPE (Hepes-Glutamic acid buffer mediated Organic solvent Protection Effect) technique comprises a new protection-solution with an organic buffer, with acetone as the only dehydrating agent, and pure paraffin of 52-54 degrees C melting temperature, allowing for all pathologic routine investigations. In contrast to FFPE tissue, the HOPE-technique allows for the application of molecular methods, such as high molecular DNA and RNA isolation, which can be used for PCR and reverse transcription PCR (RT-PCR). In this study, we investigated whether RNA from HOPE-fixed tissue samples is suitable for Northern blot and microarray analyses. RNAs of two HOPE-fixed breast cancer specimens of different histologic grade were used to carry out an array experiment. It turned out that RNA from HOPE-fixed tissue is of high quality and can be successfully used for array experiments. In addition, by detecting GAPDH and high mobility group protein gene B1 (HMGB1)-specific transcripts, we were able to demonstrate that RNA from HOPE-fixed tissue can also be used for Northern blot hybridization. PMID:15462498

  6. Upregulation of URI/RMP gene expression in cervical cancer by high-throughput tissue microarray analysis

    PubMed Central

    Gu, Junxia; Li, Xiaoyun; Liang, Yuting; Qiao, Longwei; Ran, Deyuan; Lu, Yaojuan; Li, Xingang; Wei, Wenxiang; Zheng, Qiping

    2013-01-01

    URI, or RMP, is a RNA polymerase II subunit RPB5-associated protein known to play essential roles in ubiquitination and transcription. Recently, we and others have shown that URI/RMP is also important for progression of hepatocellular carcinoma, ovarian, and prostate cancers. To identify the mechanistic basis of URI/RMP during multiple cellular processes, we investigated URI/RMP expression in a tissue microarray (TMA) containing multiple normal human tissues. The results showed that URI/RMP is ubiquitously but differentially expressed in these human tissues which partially explains its multiple cellular functions. To elucidate the role of URI/RMP during oncogenesis of multiple malignancies, especially the tumors of reproductive system, we analyzed URI/RMP expression in a TMA containing multiple reproductive system tumors. We did not observe significant difference of URI/RMP expression between cancerous and adjacent tissues of the prostate, breast, ovarian, and endometrial cancers. However, increased URI/RMP expression was observed in two of the three cases of cervical SCC (squamous cell carcinoma) cells compared to their adjacent epithelial cells. Moreover, we detected significantly upregulated URI/RMP expression not only in cervical cancers but also in pre-cancerous CINs (cervical intra-epithelial neoplasias) in a TMA that covers the whole spectrum of normal cervix, CINs, and cervical cancers. No difference of URI/RMP expression was observed between CINs and cervical cancers. Given the high risk of CINs (especially CIN3) turning into cervical cancer if left untreated, the increased URI/RMP expression in CINs as well as in cervical cancers suggest a clinical relevance of URI/RMP upon cervical cancer tumorigenesis and worth further investigation. PMID:23573313

  7. Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

    PubMed Central

    Kampf, Caroline; Olsson, IngMarie; Ryberg, Urban; Sjöstedt, Evelina; Pontén, Fredrik

    2012-01-01

    The tissue microarray (TMA) technology provides the means for high-throughput analysis of multiple tissues and cells. The technique is used within the Human Protein Atlas project for global analysis of protein expression patterns in normal human tissues, cancer and cell lines. Here we present the assembly of 1 mm cores, retrieved from microscopically selected representative tissues, into a single recipient TMA block. The number and size of cores in a TMA block can be varied from approximately forty 2 mm cores to hundreds of 0.6 mm cores. The advantage of using TMA technology is that large amount of data can rapidly be obtained using a single immunostaining protocol to avoid experimental variability. Importantly, only limited amount of scarce tissue is needed, which allows for the analysis of large patient cohorts 1 2. Approximately 250 consecutive sections (4 ?m thick) can be cut from a TMA block and used for immunohistochemical staining to determine specific protein expression patterns for 250 different antibodies. In the Human Protein Atlas project, antibodies are generated towards all human proteins and used to acquire corresponding protein profiles in both normal human tissues from 144 individuals and cancer tissues from 216 different patients, representing the 20 most common forms of human cancer. Immunohistochemically stained TMA sections on glass slides are scanned to create high-resolution images from which pathologists can interpret and annotate the outcome of immunohistochemistry. Images together with corresponding pathology-based annotation data are made publically available for the research community through the Human Protein Atlas portal (www.proteinatlas.org) (Figure 1) 3 4. The Human Protein Atlas provides a map showing the distribution and relative abundance of proteins in the human body. The current version contains over 11 million images with protein expression data for 12.238 unique proteins, corresponding to more than 61% of all proteins encoded by the human genome. PMID:22688270

  8. Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays

    PubMed Central

    Sugnet, Charles W; Srinivasan, Karpagam; Clark, Tyson A; O'Brien, Georgeann; Cline, Melissa S; Wang, Hui; Williams, Alan; Kulp, David; Blume, John E; Haussler, David; Ares, Manuel

    2006-01-01

    Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5? splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families. PMID:16424921

  9. Rapid microarray-based genotyping of Chlamydia spp. strains from clinical tissue samples.

    PubMed

    Sachse, Konrad; Ruettger, Anke

    2015-01-01

    Pathogenic Chlamydia (C.) psittaci and C. trachomatis strains can be genotyped based on variations in the ompA genomic locus. In the present chapter, we describe rapid genotyping assays for both chlamydial agents using the ArrayStrip™ (AS) microarray platform. The test is targeting multiple discriminatory sites in the variable domains of the ompA gene by using 35 (C. psittaci) and 61 (C. trachomatis) oligonucleotide probes representing genotype-specific polymorphisms. In addition to discrimination among the established genotypes, this approach allows identification of atypical strains that were not accessible to typing using previously established techniques, such as PCR-RFLP or serotyping. The present DNA microarray assay can be conducted directly on clinical tissue samples and is suitable for tracing epidemiological chains and exploring the dissemination of particular genotypes. The procedure is easy to handle and economically affordable, and it allows genotyping of up to 32 clinical samples per day, thus lending itself for routine diagnosis as well. PMID:25399111

  10. Identification of Novel Tissue-Specific Genes by Analysis of Microarray Databases: A Human and Mouse Model

    PubMed Central

    Suh, Yeunsu; Davis, Michael E.; Lee, Kichoon

    2013-01-01

    Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI?s Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved. PMID:23741331

  11. Recent progress in tissue optical clearing

    PubMed Central

    Zhu, Dan; Larin, Kirill V; Luo, Qingming; Tuchin, Valery V

    2013-01-01

    Tissue optical clearing technique provides a prospective solution for the application of advanced optical methods in life sciences. This paper gives a review of recent developments in tissue optical clearing techniques. The physical, molecular and physiological mechanisms of tissue optical clearing are overviewed and discussed. Various methods for enhancing penetration of optical-clearing agents into tissue, such as physical methods, chemical-penetration enhancers and combination of physical and chemical methods are introduced. Combining the tissue optical clearing technique with advanced microscopy image or labeling technique, applications for 3D microstructure of whole tissues such as brain and central nervous system with unprecedented resolution are demonstrated. Moreover, the difference in diffusion and/or clearing ability of selected agents in healthy versus pathological tissues can provide a highly sensitive indicator of the tissue health/pathology condition. Finally, recent advances in optical clearing of soft or hard tissue for in vivo imaging and phototherapy are introduced. PMID:24348874

  12. Role of ?-catenin expression in paediatric mesenchymal lesions: a tissue microarray-based immunohistochemical study

    PubMed Central

    Santoro, A.; Pannone, G.; Errico, M.E.; Bifano, D.; Lastilla, G.; Bufo, P.; Loreto, C.; Donofrio, V.

    2012-01-01

    Beta-catenin is a major protein in the Wnt signalling pathway. Although it has been studied in various types of carcinoma, little is known about its expression in mesenchymal tumours. In this study 41 specimens of a variety of mesenchymal childhood tumours were compared to 24 samples of the corresponding adult tumours to assess the diagnostic value of nuclear ?-catenin expression using tissue microarray-based immunohistochemistry. Similar to adult sarcoma and fibromatosis, ?-catenin was not expressed in the majority of childhood sarcomas, and its nuclear translocation was detected in paediatric fibromatosis; non-negligible levels of nuclear staining in other tumour types demonstrate Wnt pathway activation in mesenchymal neoplasms of childhood and adolescence. PMID:23027341

  13. A metadata-aware application for remote scoring and exchange of tissue microarray images

    PubMed Central

    2013-01-01

    Background The use of tissue microarrays (TMA) and advances in digital scanning microscopy has enabled the collection of thousands of tissue images. There is a need for software tools to annotate, query and share this data amongst researchers in different physical locations. Results We have developed an open source web-based application for remote scoring of TMA images, which exploits the value of Microsoft Silverlight Deep Zoom to provide a intuitive interface for zooming and panning around digital images. We use and extend existing XML-based standards to ensure that the data collected can be archived and that our system is interoperable with other standards-compliant systems. Conclusion The application has been used for multi-centre scoring of TMA slides composed of tissues from several Phase III breast cancer trials and ten different studies participating in the International Breast Cancer Association Consortium (BCAC). The system has enabled researchers to simultaneously score large collections of TMA and export the standardised data to integrate with pathological and clinical outcome data, thereby facilitating biomarker discovery. PMID:23635078

  14. TMA Navigator: Network inference, patient stratification and survival analysis with tissue microarray data.

    PubMed

    Lubbock, Alexander L R; Katz, Elad; Harrison, David J; Overton, Ian M

    2013-07-01

    Tissue microarrays (TMAs) allow multiplexed analysis of tissue samples and are frequently used to estimate biomarker protein expression in tumour biopsies. TMA Navigator (www.tmanavigator.org) is an open access web application for analysis of TMA data and related information, accommodating categorical, semi-continuous and continuous expression scores. Non-biological variation, or batch effects, can hinder data analysis and may be mitigated using the ComBat algorithm, which is incorporated with enhancements for automated application to TMA data. Unsupervised grouping of samples (patients) is provided according to Gaussian mixture modelling of marker scores, with cardinality selected by Bayesian information criterion regularization. Kaplan-Meier survival analysis is available, including comparison of groups identified by mixture modelling using the Mantel-Cox log-rank test. TMA Navigator also supports network inference approaches useful for TMA datasets, which often constitute comparatively few markers. Tissue and cell-type specific networks derived from TMA expression data offer insights into the molecular logic underlying pathophenotypes, towards more effective and personalized medicine. Output is interactive, and results may be exported for use with external programs. Private anonymous access is available, and user accounts may be generated for easier data management. PMID:23761446

  15. Expression of IRAK1 in lung cancer tissues and its clinicopathological significance: a microarray study

    PubMed Central

    Zhang, Xiuling; Dang, Yiwu; Li, Ping; Rong, Minhua; Chen, Gang

    2014-01-01

    The interleukin-1 receptor associated kinases 1 (IRAK1) is a down stream effector molecule of the toll like receptor (TLR) signaling pathway, which is involved in inflammation, autoimmunity and cancer. However, the role of IRAK1 in lung cancer remains unclarified. Herein, we investigated the protein expression and the clinicopathological significance of IRAK1 in 3 formalin-fixed paraffin-embedded lung cancer tissue microarrays by using immunohistochemistry, which included 365 tumor and 30 normal lung tissues. We found that the expression of IRAK1 in lung cancer was significantly higher compared with that in normal lung tissues (P=0.002). Receiver operating characteristic (ROC) curves were generated to evaluate the power of IRAK1 to distinguish lung cancer from non-cancerous lung tissue. The area under curve (AUC) of ROC of IRAK1 was 0.643 (95% CI 0.550~0.735, P=0.009). Additionally, IRAK1 expression was related to clinical TNM stage (r=0.241, P < 0.001), lymph node metastasis (r=0.279, P < 0.001) and tumor size (r=0.299, P < 0.001) in lung cancer. In the subgroup of non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC), the positive rates of IRAK1 were both higher than that in the normal lung tissues (P=0.003, P=0.002, respectively). Further spearman analysis showed that IRAK1 protein in NSCLC was positive correlated with clinical TNM stage (r=0.222, P < 0.001), lymph node metastasis (r=0.277, P < 0.001), tumor size (r=0.292, P < 0.001) and distal metastasis (r=0.110, P=0.043). In conclusion, the expression of IRAK1 protein might be valuable in identifying patients with increased risks of lung cancer and might act as a target for diagnosis and gene therapy for lung cancer. PMID:25550857

  16. Digital pathology for the validation of tissue microarrays in peripheral T-cell lymphomas.

    PubMed

    Pedersen, Martin B; Riber-Hansen, Rikke; Nielsen, Patricia S; Bendix, Knud; Hamilton-Dutoit, Stephen J; D'Amore, Francesco; Steiniche, Torben

    2014-09-01

    Systematic validation of construction and analysis parameters when using tissue microarray (TMA) in rare, morphologically heterogenous entities such as peripheral T-cell lymphoma (PTCL) is not reported. We describe a tissue-saving virtual TMA to predetermine the number of cores needed to represent whole tissue sections (WTS) from the same biopsies, using automated and traditional manual methods for the quantification of immunohistochemical stains. Whole paraffin hematoxylin and eosin- and immunohistochemical (CD2, CD30, and Ki-67)-stained sections from 30 PTCLs were digitalized. A virtual TMA with six 1-mm cores per slide was designed to compare agreements in the immunohistochemical scoring. Using digital image analysis and manual stereological counting, immunohistochemical positivity was quantified. Associations were analyzed using the Bland-Altman and correlation plots. In PTCL, we report that 4 cores are required to represent WTS results (ie, agreement within ±10%). High concordance was demonstrated between digital results obtained with WTS compared with 4-core virtual TMA (correlation coefficients: 0.89-0.98), and in the comparative evaluation of 4-core virtual TMA by digital image analysis versus manual stereology (correlation coefficients: 0.91 to 0.99). Virtual TMAs provide an efficient tool for optimizing and validating TMA construction parameters when planning a study. The method can be applied to the same tissues used in a subsequent formal study, without wasting scarce tissue resources. In PTCL, TMAs constructed with four 1-mm cores are representative of WTS. In parallel tests using TMAs and WTS from PTCLs, there is a high level of agreement comparing automated digital with manual stereological methods for the quantification of immunohistochemical biomarker staining. PMID:24897068

  17. Association of adipocyte genes with ASP expression: a microarray analysis of subcutaneous and omental adipose tissue in morbidly obese subjects

    Microsoft Academic Search

    Robin E MacLaren; Wei Cui; HuiLing Lu; Serge Simard; Katherine Cianflone

    2010-01-01

    BACKGROUND: Prevalence of obesity is increasing to pandemic proportions. However, obese subjects differ in insulin resistance, adipokine production and co-morbidities. Based on fasting plasma analysis, obese subjects were grouped as Low Acylation Stimulating protein (ASP) and Triglyceride (TG) (LAT) vs High ASP and TG (HAT). Subcutaneous (SC) and omental (OM) adipose tissues (n = 21) were analysed by microarray, and

  18. High-throughput immunophenotyping of 43 ferret lymphomas using tissue microarray technology.

    PubMed

    Hammer, A S; Williams, B; Dietz, H H; Hamilton-Dutoit, S J

    2007-03-01

    To validate the use of the tissue microarray (TMA) method for immunophenotyping of ferret lymphomas, a TMA was constructed containing duplicate 1-mm cores sampled from 112 paraffin-embedded lymphoma tissue specimens obtained from 43 ferret lymphoma cases. Immunohistochemical (IHC) expression of CD3, CD79alpha, and Ki-67 (MIB-1) was determined by TMA and whole mount (WM) staining of each individual case for result comparison. There was a high correlation between CD79alpha and CD3 results comparing ferret TMA and WM sections (kappa statistic 0.71-0.73 for single-core TMA and 0.79-0.95 for duplicate-core TMA) and between continuous data from Ki-67 staining of ferret TMA sections and WM sections (concordance correlation coefficients 0.77 for single cores and 0.87 for duplicate cores). Subsequently, a panel of commercially available antibodies was applied to the TMA for the analysis of expression in ferret lymphomas. The results of this study confirmed previously published results suggesting specific cross-reactivity of the applied IHC markers (CD3, CD79alpha, Ki67) with ferret lymphoma tissue. Other IHC markers (CD45Ro, bcl2, bcl10, MUM1, CD30, vimentin) were also expressed in subsets of the included ferret lymphomas. Further studies are necessary to determine the usefulness of these markers for diagnostic and prognostic evaluation of ferret lymphomas. In conclusion, the TMA technology was useful for rapid and accurate analysis of protein expression in large archival cohorts of ferret lymphoma cases. PMID:17317796

  19. Selective invocation of shape priors for deformable segmentation and morphologic classification of prostate cancer tissue microarrays.

    PubMed

    Ali, Sahirzeeshan; Veltri, Robert; Epstein, Jonathan I; Christudass, Christhunesa; Madabhushi, Anant

    2015-04-01

    Shape based active contours have emerged as a natural solution to overlap resolution. However, most of these shape-based methods are computationally expensive. There are instances in an image where no overlapping objects are present and applying these schemes results in significant computational overhead without any accompanying, additional benefit. In this paper we present a novel adaptive active contour scheme (AdACM) that combines boundary and region based energy terms with a shape prior in a multi level set formulation. To reduce the computational overhead, the shape prior term in the variational formulation is only invoked for those instances in the image where overlaps between objects are identified; these overlaps being identified via a contour concavity detection scheme. By not having to invoke all three terms (shape, boundary, region) for segmenting every object in the scene, the computational expense of the integrated active contour model is dramatically reduced, a particularly relevant consideration when multiple objects have to be segmented on very large histopathological images. The AdACM was employed for the task of segmenting nuclei on 80 prostate cancer tissue microarray images from 40 patient studies. Nuclear shape based, architectural and textural features extracted from these segmentations were extracted and found to able to discriminate different Gleason grade patterns with a classification accuracy of 86% via a quadratic discriminant analysis (QDA) classifier. On average the AdACM model provided 60% savings in computational times compared to a non-optimized hybrid active contour model involving a shape prior. PMID:25466771

  20. Immunohistochemical localization of steroid receptor coactivators in chondrosarcoma: an in vivo tissue microarray study.

    PubMed

    Li, Wei; Fu, Jingshu; Bian, Chen; Zhang, Jiqiang; Xie, Zhao

    2014-12-01

    Chondrosarcoma is the second most common type of primary bone malignancy following up osteosarcoma, characterized by resistance to conventional chemotherapeutic agents and radiation regimens. The p160 family members steroid receptor coactivator-1 and -3 (SRC-1 and SRC-3) have been implied in the regulation of cancer growth, migration, invasion, metastasis and chemotherapeutic resistance; but we still lack detailed information about the levels of SRCs in chondrosarcoma. In this study, expression of SRC-1 and SRC-3 in chondrosarcoma was examined by immunohistochemistry with tissue microarrays; the four score system (0, 1, 2 and 3) was used to evaluate the staining. The results showed that there were no gender-, site- or age-differences regarding the expression of SRC-1 or SRC-3 (p>0.05); organ (bone or cartilage) -differences were only detected for SRC-1 but not SRC-3 (p<0.05). Significant higher levels of SRC-1 and SRC-3 were detected in MDC and PDC when compared to WDC. Our study clearly demonstrated differentiation-dependant expression of SRC-1 and SRC-3 in chondrosarcoma, may be novel targets for the prognosis and/or treatment of chondrosarcoma, would have opened a new avenue and established foundation for studying chondrosarcoma. PMID:24875297

  1. Comparative microarray analyses of adult female midgut tissues from feeding Rhipicephalus species.

    PubMed

    van Zyl, Willem A; Stutzer, Christian; Olivier, Nicholas A; Maritz-Olivier, Christine

    2015-02-01

    The cattle tick, Rhipicephalus microplus, has a debilitating effect on the livestock industry worldwide, owing to its being a vector of the causative agents of bovine babesiosis and anaplasmosis. In South Africa, co-infestation with R. microplus and R. decoloratus, a common vector species on local livestock, occurs widely in the northern and eastern parts of the country. An alternative to chemical control methods is sought in the form of a tick vaccine to control these tick species. However, sequence information and transcriptional data for R. decoloratus is currently lacking. Therefore, this study aimed at identifying genes that are shared between midgut tissues of feeding adult female R. microplus and R. decoloratus ticks. In this regard, a custom oligonucleotide microarray comprising of 13,477 R. microplus sequences was used for transcriptional profiling and 2476 genes were found to be shared between these Rhipicephalus species. In addition, 136 transcripts were found to be more abundantly expressed in R. decoloratus and 1084 in R. microplus. Chi-square analysis revealed that genes involved in lipid transport and metabolism are significantly overrepresented in R. microplus and R. decoloratus. This study is the first transcriptional profiling of R. decoloratus and is an additional resource that can be evaluated further in future studies for possible tick control. PMID:25448423

  2. HER2 status in gastroesophageal cancer: a tissue microarray study of 1040 cases.

    PubMed

    Cappellesso, Rocco; Fassan, Matteo; Hanspeter, Esther; Bornschein, Jan; S G d'Amore, Emanuele; Cuorvo, Lucia V; Mazzoleni, Guido; Barbareschi, Mattia; Pizzi, Marco; Guzzardo, Vincenza; Malfertheiner, Peter; Micev, Marjan; Guido, Maria; Giacomelli, Luciano; Tsukanov, Vladislav V; Zagonel, Vittorina; Nitti, Donato; Rugge, Massimo

    2015-05-01

    Among patients with gastric cancer (GC) and gastroesophageal cancer (G-EC), HER2 amplification identifies those who may benefit from trastuzumab. HER2 status assessment, however, is influenced by preanalytic, analytic, and postanalytic variables. In a series of 5426 microarray cancer tissue cores obtained from 1040 GC/G-ECs (824 GC, 216 G-EC) and 720 synchronous nodal metastases, we evaluated both the performances of 2 different immunohistochemistry (IHC) protocols and the HER2 status intratumor variability. The prevalence of HER2 amplification and protein overexpression were assessed by chromogenic in situ hybridization and by 2 IHC protocols (CB11 and 4B5). HER2 was amplified in 114 (11%) of 1040 cases; in 6 (5.3%) of 114 cases, gene amplification only involved nodal metastasis. HER2 amplification prevailed in intestinal-type (P = .001) and low-grade (P < .001) tumors, showing no correlation with patients' age/sex, tumor location, stage, and Ming histotype. Overall, 12.5% and 13.7% of cases IHC scored 2+/3+ using the CB11-IHC and the 4B5-IHC protocol, respectively. HER2 amplification was not associated with protein overexpression (score 0/1+) in 11.4% and 6.2% of cases using the CB11-IHC and the 4B5-IHC protocol, respectively. The 4B5-IHC protocol proved more sensitive than CB11-IHC (93.9% versus 88.6%) and just as specific (96.1% versus 96.9%). Tested by chromogenic in situ hybridization, intratumor HER2 status was "substantially" consistent in different tissue cores obtained from the same case (? = 0.78). Similar results were obtained for HER2 protein expression (CB11-IHC, ? = 0.78, and 4B5-IHC, ? = 0.83). Immunohistochemistry testing, however, fails in identifying about 10% of HER2-amplified cancers, potentially excluding these patients from anti-HER2 therapy. PMID:25800719

  3. MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues

    Microsoft Academic Search

    Omer Barad; Eti Meiri; Amir Avniel; Ranit Aharonov; Adi Barzilai; Isaac Bentwich; Uri Einav; Shlomit Gilad; Patrick Hurban; Yael Karov; Edward K. Lobenhofer; Eilon Sharon; Yoel M. Shiboleth; Marat Shtutman; Zvi Bentwich; Paz Einat

    2006-01-01

    MicroRNAs (MIRs) are a novel group of conserved short ?22 nucleotide-long RNAs with important roles in regulating gene expression. We have established a MIR-specific oligonucleotide microarray system that enables efficient analysis of the expression of the human MIRs identified so far. We show that the 60-mer oligonucleotide probes on the microarrays hybridize with labeled cRNA of MIRs, but not with

  4. Current progress in 3D printing for cardiovascular tissue engineering.

    PubMed

    Mosadegh, Bobak; Xiong, Guanglei; Dunham, Simon; Min, James K

    2015-01-01

    3D printing is a technology that allows the fabrication of structures with arbitrary geometries and heterogeneous material properties. The application of this technology to biological structures that match the complexity of native tissue is of great interest to researchers. This mini-review highlights the current progress of 3D printing for fabricating artificial tissues of the cardiovascular system, specifically the myocardium, heart valves, and coronary arteries. In addition, how 3D printed sensors and actuators can play a role in tissue engineering is discussed. To date, all the work with building 3D cardiac tissues have been proof-of-principle demonstrations, and in most cases, yielded products less effective than other traditional tissue engineering strategies. However, this technology is in its infancy and therefore there is much promise that through collaboration between biologists, engineers and material scientists, 3D bioprinting can make a significant impact on the field of cardiovascular tissue engineering. PMID:25775166

  5. Tissue microarray in a subset of South African patients with DLBCL.

    PubMed

    Sissolak, Gerhard; Wood, Lucille; Smith, Lynette; Chan, John Wing C; Armitage, James; Jacobs, Peter

    2013-10-01

    Tissue samples from 93 de novo diffuse large B-cell lymphoma patients seen between 1995 and 2009 randomly receiving either standard combination chemotherapy (CHOP, n=48) or the identical program with rituximab (n=45) were subtyped using an investigational immunohistochemical (IHC) based tissue microarray (TMA) and contrasted to the approximately corresponding categories as defined either by Hans and associates using a three marker panel into germinal or non-germinal centre subtypes or by Choi and colleagues with two additional antibodies into germinal centre (GCB) or activated B-cells (ABC). Each of these primary subdivisions was further evaluated for expression of BCL2 and LMO2 both of which are recognised to predicate response. The addition of rituximab to the uniform drug regimen did not show any significant improvement in 5 years overall (63% versus 59%, p 0.68) or event-free survival (42% versus 39%, p 0.94), for CHOP versus R-CHOP comparisons. Similarly no differences were evident in subtype analysis. Interestingly however, when segregated on the Choi criteria, cytotoxic drugs alone showed a non-significant trend in improved survival (74% versus 55%, p 0.32) as well as event-free survival (44% versus 40%, p 0.42) for the germinal centre as opposed to the activated B-cell subtype. Nevertheless not even a small difference could be demonstrated in the presence of the anti CD 20 monoclonal antibody. According to Choi, both regimens (chemotherapy or immunotherapy antibody) revealed similar results to the Hans algorithm on 5 years OS as well as 3 year EFS when comparing GCB versus ABC or non-GCB subgroups. BCL2 and LMO2 marker expression of the respective immunohistochemical (IHC) subtype, despite small sample size, revealed the following. Analysis by Choi criteria on survival for BCL2, no matter for which subsets (GCB or ABC) or treatment modality (chemotherapy with or without the addition of rituximab) showed no difference in 5 years OS or EFS. In contrast, a significant difference for better EFS (p=0.0015) in the BCL2 positive group of the ABC subgroups subtypes treated with rituximab containing chemotherapy. For LMO2 similar results on survival outcome were seen thus showing no difference in 5 years OS or EFS - regardless of subtype or treatment modality. Also here, this was contrasted by better EFS (p=0.039) in the LMO2 positive group of ABC subtypes when treated with the rituximab containing regimen. The use of the IHC based TMA methodology has shown to be a simple, cost effective and a robust alternative to gene expression profiling (GEP) which is currently regarded as the gold standard for the classification in lymphomas. It provides a useful prognostic tool in stratifying DLBCL or other entities in future, even when frozen tissue samples are not available for GEP analysis. With the current budgetary limitations in South African public hospitals chemotherapy protocols for lymphoproliferative disorders exclude agents such as rituximab. Local therapeutic drug committees consider the approximately 15% overall survival benefit seen at 5 years for DLBCL when rituximab is added to combination chemotherapy as too marginal for justifying the arising additional expenses. Accordingly, demonstration that a specific molecular subtype accounts for superior outcome, when using these regimens, is needed. Such an option would provide convincing evidence for the use of immunochemotherapy in a resource constrained setting. PMID:23942329

  6. JMJD2B as a potential diagnostic immunohistochemical marker for hepatocellular carcinoma: a tissue microarray-based study.

    PubMed

    Lu, Jeng-Wei; Ho, Yi-Jung; Lin, Liang-In; Huang, Yen-Chi; Yeh, Kun-Tu; Lin, Yu-Hsiang; Lin, Yueh-Min; Tzeng, Tsai-Yu

    2015-01-01

    The purpose of this study was to examine JMJD2B expression in human hepatocellular carcinoma (HCC) and elucidate relationships between various expression patterns and clinicopathological parameters of HCC patients. Immunohistochemical techniques were performed to detect JMJD2B expression in a tissue microarray from patients with breast, cerebrum, colon, esophagus, kidney, liver, lung, prostate, stomach, and uterus cancers. We performed immunohistochemical staining of a multiple tissue array to examine the expression profile of JMJD2B. Our results demonstrate that JMJD2B protein levels were upregulated in malignant human tumors, including breast, colon, liver, and lung. Immunohistochemistry staining examination of liver tumor tissue microarray revealed that the expression of JMJD2B is significant according to the histological grade and TNM stage of liver tumor. Moreover, JMJD2B was also correlated with Ki-67 expression in HCC samples. These results reveal that JMJD2B is dramatically upregulated in HCC, making it a potential diagnostic marker for the further development of HCC treatment therapies. PMID:25533242

  7. Quantitative assessment of Tn antigen in breast tissue micro-arrays using CdSe aqueous quantum dots.

    PubMed

    Au, Giang H T; Mejias, Linette; Swami, Vanlila K; Brooks, Ari D; Shih, Wan Y; Shih, Wei-Heng

    2014-03-01

    In this study, we examined the use of CdSe aqueous quantum dots (AQDs) each conjugated to three streptavidin as a fluorescent label to image Tn antigen expression in various breast tissues via a sandwich staining procedure where the primary monoclonal anti-Tn antibody was bound to the Tn antigen on the tissue, a biotin-labeled secondary antibody was bound to the primary anti-Tn antibody, and finally the streptavidin-conjugated AQDs were bound to the biotin on the secondary antibody. We evaluated the AQD staining of Tn antigen on tissue microarrays consisting of 395 cores from 115 cases including three tumor cores and one normal-tissue core from each breast cancer case and three tumor cores from each benign case. The results indicated AQD-Tn staining was positive in more than 90% of the cells in the cancer cores but not the cells in the normal-tissue cores and the benign tumor cores. As a result, AQD-Tn staining exhibited 95% sensitivity and 90% specificity in differentiating breast cancer against normal breast tissues and benign breast conditions. These results were better than the 90% sensitivity and 80% specificity exhibited by the corresponding horse radish peroxidase (HRP) staining using the same antibodies on the same tissues and those of previous studies that used different fluorescent labels to image Tn antigen. In addition to sensitivity and specificity, the current AQD-Tn staining with a definitive threshold was quantitative. PMID:24411673

  8. A Novel Survival-Based Tissue Microarray of Pancreatic Cancer Validates MUC1 and Mesothelin as Biomarkers

    PubMed Central

    Winter, Jordan M.; Tang, Laura H.; Klimstra, David S.; Brennan, Murray F.; Brody, Jonathan R.; Rocha, Flavio G.; Jia, Xiaoyu; Qin, Li-Xuan; D’Angelica, Michael I.; DeMatteo, Ronald P.; Fong, Yuman; Jarnagin, William R.; O’Reilly, Eileen M.; Allen, Peter J.

    2012-01-01

    Background One–fifth of patients with seemingly ‘curable’ pancreatic ductal adenocarcinoma (PDA) experience an early recurrence and death, receiving no definable benefit from a major operation. Some patients with advanced stage tumors are deemed ‘unresectable’ by conventional staging criteria (e.g. liver metastasis), yet progress slowly. Effective biomarkers that stratify PDA based on biologic behavior are needed. To help researchers sort through the maze of biomarker data, a compendium of ?2500 published candidate biomarkers in PDA was compiled (PLoS Med, 2009. 6(4) p. e1000046). Methods and Findings Building on this compendium, we constructed a survival tissue microarray (termed s-TMA) comprised of short-term (cancer-specific death <12 months, n?=?58) and long-term survivors (>30 months, n?=?79) who underwent resection for PDA (total, n?=?137). The s-TMA functions as a biological filter to identify bona fide prognostic markers associated with survival group extremes (at least 18 months separate survival groups). Based on a stringent selection process, 13 putative PDA biomarkers were identified from the public biomarker repository. Candidates were tested against the s-TMA by immunohistochemistry to identify the best markers of tumor biology. In a multivariate model, MUC1 (odds ratio, OR?=?28.95, 3+ vs. negative expression, p?=?0.004) and MSLN (OR?=?12.47, 3+ vs. negative expression, p?=?0.01) were highly predictive of early cancer-specific death. By comparison, pathologic factors (size, lymph node metastases, resection margin status, and grade) had ORs below three, and none reached statistical significance. ROC curves were used to compare the four pathologic prognostic features (ROC area?=?0.70) to three univariate molecular predictors (MUC1, MSLN, MUC2) of survival group (ROC area?=?0.80, p?=?0.07). Conclusions MUC1 and MSLN were superior to pathologic features and other putative biomarkers as predicting survival group. Molecular assays comparing cancers from short and long survivors are an effective strategy to screen biomarkers and prioritize candidate cancer genes for diagnostic and therapeutic studies. PMID:22792233

  9. Construction of High-Density Tissue Microarrays at Low Cost by Using Self-Made Manual Microarray Kits and Recipient Paraffin Blocks

    PubMed Central

    Choi, Chang Hwan; Kim, Kyu Ho; Song, Ju Young; Kim, Lucia; Park, In Suh; Han, Jee Young; Kim, Joon Mee; Chu, Young Chae

    2012-01-01

    Background Advances of tissue microarray (TMA) technology have enabled simultaneous in situ analysis of biomarker expression in a large number of archived pathology specimens. However, the relatively high cost of TMA construction may hamper many researchers from using this essential tool of modern pathology research. We discuss methods for making TMA kits and recipient blocks for manual construction of high-density TMAs at low cost. Methods Ordinary cannula piercing needles, hypodermic needles, bone marrow biopsy needles, metallic ink cartridges of ballpoint pens, and disposable skin biopsy punches were used to construct self-made manual TMA kits. The recipient blocks were manufactured by boring holes in the conventional bare paraffin blocks. A mini electric hand drill and a microcompound table assembled on a drill stand were used to maximize the capacity of the recipient blocks. Results By using TMA kits made from cannula piercing needles (16- and 18-gauge), it was possible to construct TMAs with 1 mm×140 cores, 0.6 mm×320 cores, 2 mm×70 cores, 3 mm×35 cores, and 5 mm×12 cores. The capacity of the recipient blocks could be dramatically increased by drilling holes. Conclusions Construction of TMAs using self-made TMA kits is an inexpensive alternative to construction of TMAs using commercial devices. PMID:23323107

  10. Tissue oxygen saturation during hyperthermic progressive central hypovolemia.

    PubMed

    Schlader, Zachary J; Rivas, Eric; Soller, Babs R; Convertino, Victor A; Crandall, Craig G

    2014-09-15

    During normothermia, a reduction in near-infrared spectroscopy (NIRS)-derived tissue oxygen saturation (So2) is an indicator of central hypovolemia. Hyperthermia increases skin blood flow and reduces tolerance to central hypovolemia, both of which may alter the interpretation of tissue So2 during central hypovolemia. This study tested the hypothesis that maximal reductions in tissue So2 would be similar throughout normothermic and hyperthermic central hypovolemia to presyncope. Ten healthy males (means ± SD; 32 ± 5 yr) underwent central hypovolemia via progressive lower-body negative pressure (LBNP) to presyncope during normothermia (skin temperature ?34°C) and hyperthermia (+1.2 ± 0.1°C increase in internal temperature via a water-perfused suit, skin temperature ?39°C). NIRS-derived forearm (flexor digitorum profundus) tissue So2 was measured throughout and analyzed as the absolute change from pre-LBNP. Hyperthermia reduced (P < 0.001) LBNP tolerance by 49 ± 33% (from 16.7 ± 7.9 to 7.2 ± 3.9 min). Pre-LBNP, tissue So2 was similar (P = 0.654) between normothermia (74 ± 5%) and hyperthermia (73 ± 7%). Tissue So2 decreased (P < 0.001) throughout LBNP, but the reduction from pre-LBNP to presyncope was greater during normothermia (-10 ± 6%) than during hyperthermia (-6 ± 5%; P = 0.041). Contrary to our hypothesis, these findings indicate that hyperthermia is associated with a smaller maximal reduction in tissue So2 during central hypovolemia to presyncope. PMID:25031230

  11. Progress in developing a composite tissue-engineered aortic valve.

    PubMed

    Vesely, I; Shi, Y; Dobkin, D; Iyer, R; Soundararajan, A

    2005-01-01

    This paper reviews the rationale for developing a tissue-engineered aortic valve by building up the complex microstructure from its basic components, and presents recent progress towards that goal. Over the past 4 years, we have been working on engineering the functional components of the composite valve the collagen fiber bundles, the elastin sheets, and the hyaluronan matrix that keeps the tissue hydrated. Most recently, we have been working on optimizing the geometry and material properties of the collagen constructs, by varying their size and aspect ratio, and the types of loading protocols the constructs experience during the culture process. PMID:17281919

  12. Microarray analysis of CA1 pyramidal neurons in a mouse model of tauopathy reveals progressive synaptic dysfunction

    PubMed Central

    Alldred, Melissa J.; Duff, Karen E.; Ginsberg, Stephen D.

    2011-01-01

    The hTau mouse model of tauopathy was utilized to assess gene expression changes in vulnerable hippocampal CA1 neurons. CA1 pyramidal neurons were microaspirated via laser capture microdissection followed by RNA amplification in combination with custom-designed microarray analysis and qPCR validation in hTau mice and nontransgenic (ntg) littermates aged 11-14 months. Statistical analysis revealed ?8% of all the genes on the array platform were dysregulated, with notable downregulation of several synaptic-related markers including synaptophysin (Syp), synaptojanin, and synaptobrevin, among others. Downregulation was also observed for select glutamate receptors (GluRs), Psd-95, TrkB, and several protein phosphatase subunits. In contrast, upregulation of tau isoforms and a calpain subunit were found. Microarray assessment of synaptic-related markers in a separate cohort of hTau mice at 7-8 months of age indicated only a few alterations compared to the 11-14 month cohort, suggesting progressive synaptic dysfunction occurs as tau accumulates in CA1 pyramidal neurons. An assessment of SYP and PSD-95 expression was performed in the hippocampal CA1 sector of hTau and ntg mice via confocal laser scanning microscopy along with hippocampal immunoblot analysis for protein-based validation of selected microarray observations. Results indicate significant decreases in SYP-immunoreactive and PSD-95-immunoreactive puncta as well as downregulation of SYP-immunoreactive and PSD-95-immunoreactive band intensity in hTau mice compared to age-matched ntg littermates. In summary, the high prevalence of downregulation of synaptic-related genes indicates that the moderately aged hTau mouse may be a model of tau-induced synaptodegeneration, and has profound effects on how we perceive progressive tau pathology affecting synaptic transmission in AD. PMID:22079237

  13. Identification of Differentially Expressed Genes in Human Gliomas by DNA Microarray and Tissue Chip Techniques

    Microsoft Academic Search

    Satu-Leena Sallinen; Pauli K. Sallinen; Hannu K. Haapasalo; Heikki J. Helin; Pauli T. Helen; Peter Schraml; Juha Kononen

    2000-01-01

    New genomic large-scale screening techniques have made the task of establishing an accurate molecular fingerprint of cancer cells feasible. Here, we have used a two-phase strategy for identification of molecular alterations in gliomas. First, cDNA microarrays (Clontech Laboratories, Inc., Research Genetics) were used to pinpoint differentially expressed genes between normal brain and diffuse astrocytomas (grades II-IV), and between a primary

  14. A Texture Based Pattern Recognition Approach to Distinguish Melanoma from Non-Melanoma Cells in Histopathological Tissue Microarray Sections

    PubMed Central

    Rexhepaj, Elton; Agnarsdóttir, Margrét; Bergman, Julia; Edqvist, Per-Henrik; Bergqvist, Michael; Uhlén, Mathias; Gallagher, William M.; Lundberg, Emma; Ponten, Fredrik

    2013-01-01

    Aims Immunohistochemistry is a routine practice in clinical cancer diagnostics and also an established technology for tissue-based research regarding biomarker discovery efforts. Tedious manual assessment of immunohistochemically stained tissue needs to be fully automated to take full advantage of the potential for high throughput analyses enabled by tissue microarrays and digital pathology. Such automated tools also need to be reproducible for different experimental conditions and biomarker targets. In this study we present a novel supervised melanoma specific pattern recognition approach that is fully automated and quantitative. Methods and Results Melanoma samples were immunostained for the melanocyte specific target, Melan-A. Images representing immunostained melanoma tissue were then digitally processed to segment regions of interest, highlighting Melan-A positive and negative areas. Color deconvolution was applied to each region of interest to separate the channel containing the immunohistochemistry signal from the hematoxylin counterstaining channel. A support vector machine melanoma classification model was learned from a discovery melanoma patient cohort (n?=?264) and subsequently validated on an independent cohort of melanoma patient tissue sample images (n?=?157). Conclusion Here we propose a novel method that takes advantage of utilizing an immuhistochemical marker highlighting melanocytes to fully automate the learning of a general melanoma cell classification model. The presented method can be applied on any protein of interest and thus provides a tool for quantification of immunohistochemistry-based protein expression in melanoma. PMID:23690928

  15. Microarray gene expression profiling of neural tissues in bovine spastic paresis

    PubMed Central

    2013-01-01

    Background Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease. Results Microarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway’s classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated. Conclusions The cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases. PMID:23782433

  16. Microarray gene expression profiles from mature gonad tissues of Atlantic bluefin tuna, Thunnus thynnus in the Gulf of Mexico

    PubMed Central

    2012-01-01

    Background Bluefin tunas are highly prized pelagic fish species representing a significant economic resource to fisheries throughout the world. Atlantic bluefin tuna (Thunnus thynnus) populations have significantly declined due to overexploitation. As a consequence of their value and population decline, T. thynnus has been the focus of considerable research effort concerning many aspects of their life history. However, in-depth understanding of T. thynnus reproductive biology is still lacking. Knowledge of reproductive physiology is a very important tool for determining effective fisheries and aquaculture management. Transcriptome techniques are proving powerful and provide novel insights into physiological processes. Construction of a microarray from T. thynnus ESTs sourced from reproductive tissues has provided an ideal platform to study the reproductive physiology of bluefin tunas. The aim of this investigation was to compare transcription profiles from the ovaries and testes of mature T. thynnus to establish sex specific variations underlying their reproductive physiology. Results Male and females T. thynnus gonad tissues were collected from the wild and histologically staged. Sub-samples of sexually mature tissues were also measured for their mRNA differential expression among the sexes using the custom microarray design BFT 4X44K. A total of 7068 ESTs were assessed for differential expression of which 1273 ESTs were significantly different (p<0.05) with >2 fold change in expression according to sex. Differential expression for 13 of these ESTs was validated with quantitative PCR. These include genes involved in egg envelope formation, hydration, and lipid transport/accumulation more highly expressed in ovaries compared with testis, while genes involved in meiosis, sperm motility and lipid metabolism were more highly expressed in testis compared with ovaries. Conclusions This investigation has furthered our knowledge of bluefin tunas reproductive biology by using a contemporary transcriptome approach. Gene expression profiles in T. thynnus sexually mature testes and ovaries were characterized with reference to gametogenesis and potential alternative functions. This report is the first application of microarray technology for bluefin tunas and demonstrates the efficacy by which this technique may be used for further characterization of specific biological aspects for this valuable teleost fish. PMID:23036107

  17. Contribution of DNA and tissue microarray technology to the identification and validation of biomarkers and personalised medicine in breast cancer.

    PubMed

    Brennan, Donal J; Kelly, Catherine; Rexhepaj, Elton; Dervan, Peter A; Duffy, Michael J; Gallagher, William M

    2007-01-01

    Completion of the human genome project has revolutionised translational medicine. High-throughput technology now permits investigators to systematically interrogate the genome, transcriptome, proteome and metabolome. It is expected that these advances will eventually be translated into new more sensitive diagnostic tests and less toxic therapeutics. A major shift is expected in clinical oncology over the next few decades as we start to move away from currently practiced, population-based approaches to personalised medicine. In this emerging approach, the molecular and pathophysiological characteristics of an individual patient and tumour will be measured and tailored therapeutic regimens will be administered based on these profiles. One of the key steps in this process will be the identification and validation of biomarkers. Whilst great advances have been made in the discovery of putative biomarkers, disappointingly few have been translated into clinically applicable assays. It is widely believed that this is due to a lack of well-designed, thorough validation studies. Here, we review the role of DNA microarrays and tissue microarrays in the validation of biomarkers in breast cancer, with emphasis on their potential application to determine mode of personalised therapy in the future. PMID:17878516

  18. The manufacture and assessment of tissue microarrays: suggestions and criteria for analysis, with breast cancer as an example.

    PubMed

    Pinder, Sarah E; Brown, John P; Gillett, Cheryl; Purdie, Colin A; Speirs, Valerie; Thompson, Alastair M; Shaaban, Abeer M

    2013-03-01

    Tissue microarray (TMA) is an established and valuable tool, particularly in translational research and clinical trials, allowing resource-efficient use, and high-throughput profiling, of large numbers of tumours. Despite this, there is little evidence, or guidance, on the optimum manufacture, use and assessment of TMAs. Here we review some of the literature, using breast cancer as an example, to highlight good practice and pitfalls in the design and manufacture of TMAs. Issues, such as the size, number, spacing and layout of cores, as well as the assessment and reporting of studies using TMAs are addressed. We make some suggestions regarding these challenges, and propose a checklist of features that should be considered in order to stimulate debate and improve the quality of data produced by TMA analysis. PMID:23087330

  19. Characteristics of aortic wall extracellular matrix in patients with acute myocardial infarction: tissue microarray detection of collagen I, collagen III and elastin levels

    PubMed Central

    Kong, Chee Hoe; Lin, Xiao Yun; Woo, Chin Cheng; Wong, Hung Chew; Lee, Chuen Neng; Richards, A. Mark; Sorokin, Vitaly A.

    2013-01-01

    OBJECTIVES Extracellular matrix (ECM) remodelling of the vessel wall is hypothesized to be an important step in atherosclerosis. Changes of the ECM are associated with the gradual progression of an atherosclerotic lesion from a lipid streak to complicated unstable plaque, leading to a complete vessel occlusion and eventually myocardial infarction (MI). Understanding of this process is critical in the treatment and prevention of ischaemic heart disease (IHD). METHODS We investigated the histopathological characteristics of aortic wall ECM in IHD patients. Collagen I, collagen III and elastin were assessed immunohistochemically in patients with acute MI and those with stable angina, using aortic punch tissues obtained from coronary artery bypass graft surgery. Fluorescence tissue images were analysed using the tissue microarray technique. RESULTS The results showed that collagen III expression was found to be significantly lower in the acute MI group (P < 0.001). As a result of this change, the patients with MI also revealed a significant reduction in the collagen III/collagen I ratio. The elastin/collagen III ratio was significantly higher in the MI group (P < 0.001). CONCLUSIONS Our study provided evidence of a decrease in collagen III content in patients with MI, which could possibly explain the mechanism of plaque vulnerability and weakening of the plaque cap. A reduction in collagen III content, particularly away from the atherosclerotic lesions, might be explained by the systemic vascular changes in patients with MI, and inflammation and immune responses could be potential causes of these systemic transformations. The biochemical mechanisms and factors regulating collagen III production might be potential markers to predict possible cardiovascular events. PMID:23049084

  20. Clinical significance of molecular expression profiles of Hürthle cell tumors of the thyroid gland analyzed via tissue microarrays.

    PubMed

    Hoos, Axel; Stojadinovic, Alexander; Singh, Bhuvanesh; Dudas, Maria E; Leung, Denis H Y; Shaha, Ashok R; Shah, Jatin P; Brennan, Murray F; Cordon-Cardo, Carlos; Ghossein, Ronald

    2002-01-01

    Hürthle cell tumors are rare thyroid neoplasms for which disease biology is poorly understood and diagnosis of carcinoma can be challenging. The aim of the study was to characterize molecular expression profiles of Hürthle cell tumors and to determine the clinical significance of identified phenotypes. Paraffin-embedded tissue cores of normal thyroid (n = 18), and histopathologically well-defined Hürthle cell adenomas (n = 27), Hürthle cell tumors of unknown malignant behavior (n = 7), and minimally (n = 14) and widely (n = 21) invasive Hürthle cell carcinomas were arrayed in triplicate on tissue microarrays. Expression profiles of p53, mdm-2, p21, Bcl-2, cyclin D1, and Ki-67 were detected by immunohistochemistry and correlated with clinicopathological data and patient outcome using standard statistical methodology. Median follow-up time was 8 years. High Ki-67 proliferative index was evident only in the clinically aggressive widely invasive Hürthle cell carcinomas and was associated with significantly reduced relapse-free (P = 0.001) and disease-specific (P < 0.001) survival. The molecular phenotype of Hürthle cell tumors, independent of histopathological subtype diagnosis, was characterized by p53(-), mdm-2(+), p21(+/-), cyclin D1(-), and Bcl-2(+/-). Normal thyroid tissue demonstrated a p53(-), mdm-2(-), p21(-), cyclin D1(-), and Bcl-2(+) phenotype. The Bcl-2(+) phenotype was associated with improved relapse-free survival (P = 0.04) and disease-specific survival (P = 0.01) in widely invasive carcinomas and the Ki-67(+)/Bcl-2(-) phenotype was associated with the diagnosis of widely invasive Hürthle cell carcinoma (P < 0.001). This study demonstrates that tissue microarray-based profiling allows identification of molecular markers that are associated with patient prognosis. High Ki-67 proliferative index was associated with adverse outcome in Hürthle cell neoplasms. Together with down-regulation of Bcl-2, high Ki-67 proliferative index may be useful for diagnosing widely invasive Hürthle cell carcinomas. Molecular alterations in the p53 pathway play a role in Hürthle cell tumorigenesis, but other unidentified molecular changes seem to be required to induce the malignant phenotype. PMID:11786411

  1. Tissue MicroArray: A Cost and Time-Effective Method for Correlative Studies by Regional and National Cancer Study Groups

    Microsoft Academic Search

    Martha Milanes-Yearsley; M. Elizabeth H. Hammond; Thomas F. Pajak; Jay S. Cooper; Chu Chang; Thomas Griffin; Diana Nelson; George Laramore; Milijenko Pilepich

    2002-01-01

    Tissue micro-arrays have been used for molecular and immunohistochemical studies. We sought to evaluate whether such arrays could substitute for whole sections in correlative studies performed by the Radiation Therapy Oncology Group. Four multitumor 150-sample arrays were built using formalin-fixed, paraffin-embedded, archival prostate, brain, and head\\/neck tumor blocks from RTOG tissue bank. p53 immunostaining of arrays and whole sections was

  2. Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer

    PubMed Central

    2013-01-01

    Background Although omic-based discovery approaches can provide powerful tools for biomarker identification, several reservations have been raised regarding the clinical applicability of gene expression studies, such as their prohibitive cost. However, the limited availability of antibodies is a key barrier to the development of a lower cost alternative, namely a discrete collection of immunohistochemistry (IHC)-based biomarkers. The aim of this study was to use a systematic approach to generate and screen affinity-purified, mono-specific antibodies targeting progression-related biomarkers, with a view towards developing a clinically applicable IHC-based prognostic biomarker panel for breast cancer. Methods We examined both in-house and publicly available breast cancer DNA microarray datasets relating to invasion and metastasis, thus identifying a cohort of candidate progression-associated biomarkers. Of these, 18 antibodies were released for extended analysis. Validated antibodies were screened against a tissue microarray (TMA) constructed from a cohort of consecutive breast cancer cases (n?=?512) to test the immunohistochemical surrogate signature. Results Antibody screening revealed 3 candidate prognostic markers: the cell cycle regulator, Anillin (ANLN); the mitogen-activated protein kinase, PDZ-Binding Kinase (PBK); and the estrogen response gene, PDZ-Domain Containing 1 (PDZK1). Increased expression of ANLN and PBK was associated with poor prognosis, whilst increased expression of PDZK1 was associated with good prognosis. A 3-marker signature comprised of high PBK, high ANLN and low PDZK1 expression was associated with decreased recurrence-free survival (p?

  3. Tissue Damage Disrupts Developmental Progression and Ecdysteroid Biosynthesis in Drosophila

    PubMed Central

    Hackney, Jennifer F.; Zolali-Meybodi, Omid; Cherbas, Peter

    2012-01-01

    In humans, chronic inflammation, severe injury, infection and disease can result in changes in steroid hormone titers and delayed onset of puberty; however the pathway by which this occurs remains largely unknown. Similarly, in insects injury to specific tissues can result in a global developmental delay (e.g. prolonged larval/pupal stages) often associated with decreased levels of ecdysone – a steroid hormone that regulates developmental transitions in insects. We use Drosophila melanogaster as a model to examine the pathway by which tissue injury disrupts developmental progression. Imaginal disc damage inflicted early in larval development triggers developmental delays while the effects are minimized in older larvae. We find that the switch in injury response (e.g. delay/no delay) is coincident with the mid-3rd instar transition – a developmental time-point that is characterized by widespread changes in gene expression and marks the initial steps of metamorphosis. Finally, we show that developmental delays induced by tissue damage are associated with decreased expression of genes involved in ecdysteroid synthesis and signaling. PMID:23166607

  4. Prognostic Value of Ki-67 in Breast Carcinoma: Tissue Microarray Method Versus Whole Section Analysis- Potentials and Pitfalls.

    PubMed

    Dedi? Plaveti?, Natalija; Jaki?-Razumovi?, Jasminka; Kuli?, Ana; Sirotkovi?-Skerlev, Maja; Bari?, Marina; Vrbanec, Damir

    2014-08-01

    In our study we have compared the prognostic value of two distinct methods of immunohistochemical Ki-67 determination, tissue microarray (TMA) and classical whole section analysis. "Cut-off" values were used according to the 2009 St. Gallen Consensus. Tissue specimens were obtained from a consecutive retrospective series of 215 female patients with primary invasive tumours. Two hundred and thirteen patients were included in the study. Data on Ki-67 was collected by both tissue microarray (TMA) and whole section analysis. Follow up data on overall (OS) and disease-free survival (DFS) were collected. Median follow-up was 95 months (range from 7.8 through 107 months). Mutual correlation of two Ki-67 determination methods was non-significant (Person's r?=?0.13417; p?=?0.0528). There was statistically significant association of whole section Ki-67 expression with histological and nuclear grade, progesterone receptor and HER2/neu status. The expression of Ki-67 protein in TMAs correlated only with histological and nuclear grade, but not with other traditional clinicopathological factors. Statistically significant differences in DFS (p?=?0.0156) and OS (p?=?0.0028) were confirmed between subgroups with low and high whole section Ki-67 expression. When subgroups with high and intermediate expression were compared, significant difference was found in DFS (p?=?0.0272), but not in OS (p?=?0.0624). On the other hand, there was no statistically significant difference either in DFS, or in OS, according to the expression of Ki-67 in TMAs (p?=?0.6529; p?=?0.7883; p?=?0.7966 for DFS, and p?=?0.8917; p?=?0.6448; p?=?0.4323 for OS, respectively). In our study, classical whole section was superior to TMA analysis in terms of prognosis and clinicopathological correlation. Our results indicate that the method used may have impact on prognostic significance of Ki-67. Further studies are needed, covering a greater number of patients and including a precisely defined stage and treatment patient cohorts, in order to solve controversies in Ki-67 assessment methodology. PMID:25096394

  5. Microarray profiling of human white adipose tissue after exogenous leptin injection

    Microsoft Academic Search

    S. Taleb; R. Van Haaften; C. Henegar; C. Hukshorn; W. H. M. Saris; V. Pelloux; B. Hanczar; N. Viguerie; D. Langin; C. Evelo; J. Zucker; K. Clement

    2006-01-01

    Background Leptin is a secreted adipocyte hormone that plays a key role in the regulation of body weight homeostasis. The leptin effect on human white adipose tissue (WAT) is still debated. Objective The aim of this study was to assess whether the administration of polyethylene glycol-leptin (PEG-OB) in a single supraphysiological dose has transcriptional effects on genes of WAT and

  6. Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue

    SciTech Connect

    Pohjanvirta, Raimo [Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, P.O. Box 66, FI-00014, University of Helsinki (Finland); Finnish Food Safety Authority EVIRA, Research Unit of Kuopio, P.O. Box 92, FI-70701 Kuopio (Finland); National Public Health Institute, Laboratory of Toxicology, P.O. Box 95, FI-70701 Kuopio (Finland)], E-mail: raimo.pohjanvirta@helsinki.fi; Boutros, Paul C.; Moffat, Ivy D. [Department of Pharmacology, University of Toronto, MSB, Toronto, Ontario, M5S 1A8 (Canada); Linden, Jere; Wendelin, Dominique [Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, P.O. Box 66, FI-00014, University of Helsinki (Finland); Okey, Allan B. [Department of Pharmacology, University of Toronto, MSB, Toronto, Ontario, M5S 1A8 (Canada)

    2008-07-01

    Acute progressive feed restriction (APFR) represents a specific form of caloric restriction in which feed availability is increasingly curtailed over a period of a few days to a few weeks. It is often used for control animals in toxicological and pharmacological studies on compounds causing body weight loss to equalize weight changes between experimental and control groups and thereby, intuitively, to also set their metabolic states to the same phase. However, scientific justification for this procedure is lacking. In the present study, we analyzed by microarrays the impact on hepatic gene expression in rats of two APFR regimens that caused identical diminution of body weight (19%) but differed slightly in duration (4 vs. 10 days). In addition, white adipose tissue (WAT) was also subjected to the transcriptomic analysis on day-4. The data revealed that the two regimens led to distinct patterns of differentially expressed genes in liver, albeit some major pathways of energy metabolism were similarly affected (particularly fatty acid and amino acid catabolism). The reason for the divergence appeared to be entrainment by the longer APFR protocol of peripheral oscillator genes, which resulted in derailment of circadian rhythms and consequent interaction of altered diurnal fluctuations with metabolic adjustments in gene expression activities. WAT proved to be highly unresponsive to the 4-day APFR as only 17 mRNA levels were influenced by the treatment. This study demonstrates that body weight is a poor proxy of metabolic state and that the customary protocols of feed restriction can lead to rhythm entrainment.

  7. Quantitative multiplex quantum dot in-situ hybridisation based gene expression profiling in tissue microarrays identifies prognostic genes in acute myeloid leukaemia

    SciTech Connect

    Tholouli, Eleni [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom)] [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); MacDermott, Sarah [The Medical School, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom)] [The Medical School, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Hoyland, Judith [School of Biomedicine, Faculty of Medical and Human Sciences, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom)] [School of Biomedicine, Faculty of Medical and Human Sciences, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Yin, John Liu [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom)] [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); Byers, Richard, E-mail: richard.byers@cmft.nhs.uk [School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, The University of Manchester, Stopford Building, Oxford Road, M13 9PT Manchester (United Kingdom)] [School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, The University of Manchester, Stopford Building, Oxford Road, M13 9PT Manchester (United Kingdom)

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer Development of a quantitative high throughput in situ expression profiling method. Black-Right-Pointing-Pointer Application to a tissue microarray of 242 AML bone marrow samples. Black-Right-Pointing-Pointer Identification of HOXA4, HOXA9, Meis1 and DNMT3A as prognostic markers in AML. -- Abstract: Measurement and validation of microarray gene signatures in routine clinical samples is problematic and a rate limiting step in translational research. In order to facilitate measurement of microarray identified gene signatures in routine clinical tissue a novel method combining quantum dot based oligonucleotide in situ hybridisation (QD-ISH) and post-hybridisation spectral image analysis was used for multiplex in-situ transcript detection in archival bone marrow trephine samples from patients with acute myeloid leukaemia (AML). Tissue-microarrays were prepared into which white cell pellets were spiked as a standard. Tissue microarrays were made using routinely processed bone marrow trephines from 242 patients with AML. QD-ISH was performed for six candidate prognostic genes using triplex QD-ISH for DNMT1, DNMT3A, DNMT3B, and for HOXA4, HOXA9, Meis1. Scrambled oligonucleotides were used to correct for background staining followed by normalisation of expression against the expression values for the white cell pellet standard. Survival analysis demonstrated that low expression of HOXA4 was associated with poorer overall survival (p = 0.009), whilst high expression of HOXA9 (p < 0.0001), Meis1 (p = 0.005) and DNMT3A (p = 0.04) were associated with early treatment failure. These results demonstrate application of a standardised, quantitative multiplex QD-ISH method for identification of prognostic markers in formalin-fixed paraffin-embedded clinical samples, facilitating measurement of gene expression signatures in routine clinical samples.

  8. The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line

    PubMed Central

    Conway, Catherine M; O'Shea, Deirdre; O'Brien, Sallyann; Lawler, Darragh K; Dodrill, Graham D; O'Grady, Anthony; Barrett, Helen; Gulmann, Christian; O'Driscoll, Lorraine; Gallagher, William M; Kay, Elaine W; O'Shea, Daniel G

    2006-01-01

    Background The Tissue Microarray (TMA) facilitates high-throughput analysis of hundreds of tissue specimens simultaneously. However, bottlenecks in the storage and manipulation of the data generated from TMA reviews have become apparent. A number of software applications have been developed to assist in image and data management; however no solution currently facilitates the easy online review, scoring and subsequent storage of images and data associated with TMA experimentation. Results This paper describes the design, development and validation of the Virtual Tissue Matrix (VTM). Through an intuitive HTML driven user interface, the VTM provides digital/virtual slide based images of each TMA core and a means to record observations on each TMA spot. Data generated from a TMA review is stored in an associated relational database, which facilitates the use of flexible scoring forms. The system allows multiple users to record their interpretation of each TMA spot for any parameters assessed. Images generated for the VTM were captured using a standard background lighting intensity and corrective algorithms were applied to each image to eliminate any background lighting hue inconsistencies or vignetting. Validation of the VTM involved examination of inter-and intra-observer variability between microscope and digital TMA reviews. Six bladder TMAs were immunohistochemically stained for E-Cadherin, ?-Catenin and PhosphoMet and were assessed by two reviewers for the amount of core and tumour present, the amount and intensity of membrane, cytoplasmic and nuclear staining. Conclusion Results show that digital VTM images are representative of the original tissue viewed with a microscope. There were equivalent levels of inter-and intra-observer agreement for five out of the eight parameters assessed. Results also suggest that digital reviews may correct potential problems experienced when reviewing TMAs using a microscope, for example, removal of background lighting variance and tint, and potential disorientation of the reviewer, which may have resulted in the discrepancies evident in the remaining three parameters. PMID:16707006

  9. Spontaneous canine gliomas: overexpression of EGFR, PDGFR? and IGFBP2 demonstrated by tissue microarray immunophenotyping

    Microsoft Academic Search

    Robert J. HigginsPeter; Peter J. Dickinson; Richard A. LeCouteur; Andrew W. Bollen; Huamin Wang; Hua Wang; Linda J. Corely; Lynnette M. Moore; Wei Zang; Gregory N. Fuller

    2010-01-01

    Fifty-seven spontaneous canine gliomas were histologically classified and graded using the latest World Health Organization\\u000a (WHO 2007) criteria for classification of human gliomas. A total of 19 canine astrocytomas were classified as follows: grade\\u000a IV (GBM) n = 7; grade III n = 5; and grade II, n = 7. Thirty-eight oligodendrogliomas were classified as either grade III (anaplastic) n = 35 or low grade II n = 3. Tissue

  10. A metadata-aware application for remote scoring and exchange of tissue microarray images

    E-print Network

    Morris, Lorna; Tsui, Andrew; Crichton, Charles; Harris, Steve; Maccallum, Peter H; Howat, William J; Davies, Jim; Brenton, James D; Caldas, Carlos

    2013-05-01

    Shing Centre, Cambridge CB2 0RE, UK 2Cambridge Experimental Cancer Medicine Centre, Li Ka Shing Centre,by immunohistochemistry (IHC) using antibodies to de-Phase III breast cancer trials and ten different studies participating in the International Breast... include the Virtual Tissue Matrix and TMAJ [7,8]. The former focuses on facilitating on-line review of TMAs, with the facility to zoom and pan around TMA core images and associate a score, which is stored in a relational database. In TMAJ the user can...

  11. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3.

    PubMed

    Ching, Tsui-Ting; Maunakea, Alika K; Jun, Peter; Hong, Chibo; Zardo, Giuseppe; Pinkel, Daniel; Albertson, Donna G; Fridlyand, Jane; Mao, Jian-Hua; Shchors, Ksenya; Weiss, William A; Costello, Joseph F

    2005-06-01

    CpG islands are present in one-half of all human and mouse genes and typically overlap with promoters or exons. We developed a method for high-resolution analysis of the methylation status of CpG islands genome-wide, using arrays of BAC clones and the methylation-sensitive restriction enzyme NotI. Here we demonstrate the accuracy and specificity of the method. By computationally mapping all NotI sites, methylation events can be defined with single-nucleotide precision throughout the genome. We also demonstrate the unique expandability of the array method using a different methylation-sensitive restriction enzyme, BssHII. We identified and validated new CpG island loci that are methylated in a tissue-specific manner in normal human tissues. The methylation status of the CpG islands is associated with gene expression for several genes, including SHANK3, which encodes a structural protein in neuronal postsynaptic densities. Defects in SHANK3 seem to underlie human 22q13 deletion syndrome. Furthermore, these patterns for SHANK3 are conserved in mice and rats. PMID:15895082

  12. DGEM--a microarray gene expression database for primary human disease tissues.

    PubMed

    Xia, Yuni; Campen, Andrew; Rigsby, Dan; Guo, Ying; Feng, Xingdong; Su, Eric W; Palakal, Mathew; Li, Shuyu

    2007-01-01

    Gene expression patterns can reflect gene regulations in human tissues under normal or pathologic conditions. Gene expression profiling data from studies of primary human disease samples are particularly valuable since these studies often span many years in order to collect patient clinical information and achieve a large sample size. Disease-to-Gene Expression Mapper (DGEM) provides a beneficial community resource to access and analyze these data; it currently includes Affymetrix oligonucleotide array datasets for more than 40 human diseases and 1400 samples. The data are normalized to the same scale and stored in a relational database. A statistical-analysis pipeline was implemented to identify genes abnormally expressed in disease tissues or genes whose expressions are associated with clinical parameters such as cancer patient survival. Data-mining results can be queried through a web-based interface at http://dgem.dhcp.iupui.edu/. The query tool enables dynamic generation of graphs and tables that are further linked to major gene and pathway resources that connect the data to relevant biology, including Entrez Gene and Kyoto Encyclopedia of Genes and Genomes (KEGG). In summary, DGEM provides scientists and physicians a valuable tool to study disease mechanisms, to discover potential disease biomarkers for diagnosis and prognosis, and to identify novel gene targets for drug discovery. The source code is freely available for non-profit use, on request to the authors. PMID:17570735

  13. Progress on thermobrachytherapy surface applicator for superficial tissue disease

    NASA Astrophysics Data System (ADS)

    Arunachalam, Kavitha; Craciunescu, Oana I.; Maccarini, Paolo F.; Schlorff, Jaime L.; Markowitz, Edward; Stauffer, Paul R.

    2009-02-01

    This work reports the ongoing development of a combination applicator for simultaneous heating of superficial tissue disease using a 915 MHz DCC (dual concentric conductor) array and High Dose Rate (HDR) brachytherapy delivered via an integrated conformal catheter array. The progress includes engineering design changes in the waterbolus, DCC configurations and fabrication techniques of the conformal multilayer applicator. The dosimetric impact of the thin copper DCC array is also assessed. Steady state fluid dynamics of the new waterbolus bag indicates nearly uniform flow with less than 1°C variation across a large (19×32cm) bolus. Thermometry data of the torso phantom acquired with computer controlled movement of fiberoptic temperature probes inside thermal mapping catheters indicate feasibility of real time feedback control for the DCC array. MR (magnetic resonance) scans of a torso phantom indicate that the waterbolus thickness across the treatment area is controlled by the pressure applied by the surrounding inflatable airbladder and applicator securing straps. The attenuation coefficient of the DCC array was measured as 3+/- 0.001% and 2.95+/-0.03 % using an ion chamber and OneDose dosimeters respectively. The performance of the combination applicator on patient phantoms provides valuable feedback to optimize the applicator prior use in the patient clinic.

  14. Immunohistochemical expression of ARID1A in penile squamous cell carcinomas: a tissue microarray study of 112 cases.

    PubMed

    Faraj, Sheila F; Chaux, Alcides; Gonzalez-Roibon, Nilda; Munari, Enrico; Cubilla, Antonio L; Shih, Ie-Ming; Netto, George J

    2015-05-01

    ARID1A, a member of the chromatin remodeling genes family, has been suggested as a novel tumor suppressor gene in gynecologic malignancies. However, its role in penile cancer has yet to be determined. This study assesses the immunohistochemical expression of ARID1A in penile squamous cell carcinoma (SCC) and its association with pathologic features, human papillomavirus (HPV) status, and previously reported mammalian target of rapamycin pathway markers in the same cohort. Four tissue microarrays were constructed from 112 cases of formalin-fixed, paraffin-embedded penile SCC from Paraguay. Each tumor was sampled 3 to 12 times. ARID1A expression was evaluated by immunohistochemistry using a polyclonal rabbit anti-ARID1A (BAF250A) antibody. An H score was calculated in each spot as the sum of expression intensity (0-3+) by extent (0%-100%). Median H score per case was used for statistical analysis. ARID1A expression was observed in all cases, ranging from 3% to 100% of tumor cells (median, 95%). In 96 cases (86%), ARID1A expression was observed in 90% or more tumor cells. HPV DNA was detected in 20 (38%) of 52 analyzed samples. There was a significant trend of association between ARID1A and histologic grade. ARID1A expression was not associated with histologic subtype (P = .61) or HPV status (P = .18). ARID1A expression decreased with decreasing levels of PTEN expression (P = .01). ARID1A was expressed in penile SCC, in most cases at high levels. A significant trend of association was found between histologic grade and ARID1A expression, with lower ARID1A expression, lower histologic grades, and decreased PTEN expression. PMID:25776029

  15. Overview of Protein Microarrays

    PubMed Central

    Reymond Sutandy, FX; Qian, Jiang; Chen, Chien-Sheng; Zhu, Heng

    2013-01-01

    Protein microarray is an emerging technology that provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput way. Two major classes of protein microarrays are defined to describe their applications: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. While the fabrication technology is maturing, applications of protein microarrays, especially functional protein microarrays, have flourished during the past decade. Here, we will first review recent advances in the protein microarray technologies, and then present a series of examples to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. The research areas will include detection of various binding properties of proteins, study of protein posttranslational modifications, analysis of host-microbe interactions, profiling antibody specificity, and identification of biomarkers in autoimmune diseases. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade. PMID:23546620

  16. Hydrogel scaffolds for tissue engineering: Progress and challenges

    PubMed Central

    El-Sherbiny, Ibrahim M.; Yacoub, Magdi H.

    2013-01-01

    Designing of biologically active scaffolds with optimal characteristics is one of the key factors for successful tissue engineering. Recently, hydrogels have received a considerable interest as leading candidates for engineered tissue scaffolds due to their unique compositional and structural similarities to the natural extracellular matrix, in addition to their desirable framework for cellular proliferation and survival. More recently, the ability to control the shape, porosity, surface morphology, and size of hydrogel scaffolds has created new opportunities to overcome various challenges in tissue engineering such as vascularization, tissue architecture and simultaneous seeding of multiple cells. This review provides an overview of the different types of hydrogels, the approaches that can be used to fabricate hydrogel matrices with specific features and the recent applications of hydrogels in tissue engineering. Special attention was given to the various design considerations for an efficient hydrogel scaffold in tissue engineering. Also, the challenges associated with the use of hydrogel scaffolds were described. PMID:24689032

  17. Recent progress in interfacial tissue engineering approaches for osteochondral defects.

    PubMed

    Castro, Nathan J; Hacking, S Adam; Zhang, Lijie Grace

    2012-08-01

    This review provides a brief synopsis of the anatomy and physiology of the osteochondral interface, scaffold-based and non-scaffold based approaches for engineering both tissues independently as well as recent developments in the manufacture of gradient constructs. Novel manufacturing techniques and nanotechnology will be discussed with potential application in osteochondral interfacial tissue engineering. PMID:22677924

  18. Fiber-Based Tissue Engineering: Progress, Challenges, and Opportunities

    PubMed Central

    Tamayol, Ali; Akbari, Mohsen; Annabi, Nasim; Paul, Arghya; Khademhosseini, Ali; Juncker, David

    2013-01-01

    Tissue engineering aims to improve the function of diseased or damaged organs by creating biological substitutes. To fabricate a functional tissue, the engineered construct should mimic the physiological environment including its structural, topographical, and mechanical properties. Moreover, the construct should facilitate nutrients and oxygen diffusion as well as removal of metabolic waste during tissue regeneration. In the last decade, fiber-based techniques such as weaving, knitting, braiding, as well as electrospinning, and direct writing have emerged as promising platforms for making 3D tissue constructs that can address the above mentioned challenges. Here, we critically review the techniques used to form cell-free and cell-laden fibers and to assemble them into scaffolds. We compare their mechanical properties, morphological features and biological activity. We discuss current challenges and future opportunities of fiber-based tissue engineering (FBTE) for use in research and clinical practice. PMID:23195284

  19. Fiber-based tissue engineering: Progress, challenges, and opportunities.

    PubMed

    Tamayol, Ali; Akbari, Mohsen; Annabi, Nasim; Paul, Arghya; Khademhosseini, Ali; Juncker, David

    2013-01-01

    Tissue engineering aims to improve the function of diseased or damaged organs by creating biological substitutes. To fabricate a functional tissue, the engineered construct should mimic the physiological environment including its structural, topographical, and mechanical properties. Moreover, the construct should facilitate nutrients and oxygen diffusion as well as removal of metabolic waste during tissue regeneration. In the last decade, fiber-based techniques such as weaving, knitting, braiding, as well as electrospinning, and direct writing have emerged as promising platforms for making 3D tissue constructs that can address the abovementioned challenges. Here, we critically review the techniques used to form cell-free and cell-laden fibers and to assemble them into scaffolds. We compare their mechanical properties, morphological features and biological activity. We discuss current challenges and future opportunities of fiber-based tissue engineering (FBTE) for use in research and clinical practice. PMID:23195284

  20. Differential Adipose Tissue Gene Expression Profiles in Abacavir Treated Patients That May Contribute to the Understanding of Cardiovascular Risk: A Microarray Study

    PubMed Central

    Shahmanesh, Mohsen; Phillips, Kenneth; Boothby, Meg; Tomlinson, Jeremy W.

    2015-01-01

    Objective To compare changes in gene expression by microarray from subcutaneous adipose tissue from HIV treatment naïve patients treated with efavirenz based regimens containing abacavir (ABC), tenofovir (TDF) or zidovidine (AZT). Design Subcutaneous fat biopsies were obtained before, at 6- and 18–24-months after treatment, and from HIV negative controls. Groups were age, ethnicity, weight, biochemical profile, and pre-treatment CD4 count matched. Microarray data was generated using the Agilent Whole Human Genome Microarray. Identification of differentially expressed genes and genomic response pathways was performed using limma and gene set enrichment analysis. Results There were significant divergences between ABC and the other two groups 6 months after treatment in genes controlling cell adhesion and environmental information processing, with some convergence at 18–24 months. Compared to controls the ABC group, but not AZT or TDF showed enrichment of genes controlling adherence junction, at 6 months and 18–24 months (adjusted p<0.05) and focal adhesions and tight junction at 6 months (p<0.5). Genes controlling leukocyte transendothelial migration (p<0.05) and ECM-receptor interactions (p = 0.04) were over-expressed in ABC compared to TDF and AZT at 6 months but not at 18–24 months. Enrichment of pathways and individual genes controlling cell adhesion and environmental information processing were specifically dysregulated in the ABC group in comparison with other treatments. There was little difference between AZT and TDF. Conclusion After initiating treatment, there is divergence in the expression of genes controlling cell adhesion and environmental information processing between ABC and both TDF and AZT in subcutaneous adipose tissue. If similar changes are also taking place in other tissues including the coronary vasculature they may contribute to the increased risk of cardiovascular events reported in patients recently started on abacavir-containing regimens. PMID:25617630

  1. Progress and opportunities for tissue-engineered skin

    NASA Astrophysics Data System (ADS)

    MacNeil, Sheila

    2007-02-01

    Tissue-engineered skin is now a reality. For patients with extensive full-thickness burns, laboratory expansion of skin cells to achieve barrier function can make the difference between life and death, and it was this acute need that drove the initiation of tissue engineering in the 1980s. A much larger group of patients have ulcers resistant to conventional healing, and treatments using cultured skin cells have been devised to restart the wound-healing process. In the laboratory, the use of tissue-engineered skin provides insight into the behaviour of skin cells in healthy skin and in diseases such as vitiligo, melanoma, psoriasis and blistering disorders.

  2. Robotic multimodality stereotactic brain tissue identification: work in progress

    NASA Technical Reports Server (NTRS)

    Andrews, R.; Mah, R.; Galvagni, A.; Guerrero, M.; Papasin, R.; Wallace, M.; Winters, J.

    1997-01-01

    Real-time identification of tissue would improve procedures such as stereotactic brain biopsy (SBX), functional and implantation neurosurgery, and brain tumor excision. To standard SBX equipment has been added: (1) computer-controlled stepper motors to drive the biopsy needle/probe precisely; (2) multiple microprobes to track tissue density, detect blood vessels and changes in blood flow, and distinguish the various tissues being penetrated; (3) neural net learning programs to allow real-time comparisons of current data with a normative data bank; (4) three-dimensional graphic displays to follow the probe as it traverses brain tissue. The probe can differentiate substances such as pig brain, differing consistencies of the 'brain-like' foodstuff tofu, and gels made to simulate brain, as well as detect blood vessels imbedded in these substances. Multimodality probes should improve the safety, efficacy, and diagnostic accuracy of SBX and other neurosurgical procedures.

  3. Tendon Tissue Engineering: Progress, Challenges, and Translation to the Clinic

    PubMed Central

    Shearn, Jason T.; Kinneberg, Kirsten R.C.; Dyment, Nathaniel A.; Galloway, Marc T.; Kenter, Keith; Wylie, Christopher; Butler, David L.

    2013-01-01

    The tissue engineering field has made great strides in understanding how different aspects of tissue engineered constructs (TECs) and the culture process affect final tendon repair. However, there remain significant challenges in developing strategies that will lead to a clinically effective and commercially successful product. In an effort to increase repair quality, a better understanding of normal development, and how it differs from adult tendon healing, may provide strategies to improve tissue engineering. As tendon tissue engineering continues to improve, the field needs to employ more clinically relevant models of tendon injury such as degenerative tendons. We need to translate successes to larger animal models to begin exploring the clinical implications of our treatments. By advancing the models used to validate our TECs, we can help convince our toughest customer, the surgeon, that our products will be clinically efficacious. As we address these challenges in musculoskeletal tissue engineering, the field still needs to address the commercialization of products developed in the laboratory. TEC commercialization faces numerous challenges because each injury and patient is unique. This review aims to provide tissue engineers with a summary of important issues related to engineering tendon repairs and potential strategies for producing clinically successful products. PMID:21625053

  4. A PROGRESSIVE RUPTURE MODEL OF SOFT TISSUE STRESS RELAXATION

    PubMed Central

    Bates, Jason H.T.; Ma, Baoshun

    2013-01-01

    A striking feature of stress relaxation in biological soft tissue is that it frequently follows a power law in time with an exponent that is independent of strain even when the elastic properties of the tissue are highly nonlinear. This kind of behavior is an example of quasi-linear viscoelasticity, and is usually modeled in a purely empirical fashion. The goal of the present study was to account for quasi-linear viscoelasticity in mechanistic terms based on our previously developed hypothesis that it arises as a result of isolated micro-yield events occurring in sequence throughout the tissue, each event passing the stress it was sustaining on to other regions of the tissue until they themselves yield. We modeled stress relaxation computationally in a collection of stress-bearing elements. Each element experiences a stochastic sequence of either increases in elastic equilibrium length or decreases in stiffness according to the stress imposed upon it. This successfully predicts quasi-linear viscoelastic behavior, and in addition predicts power-law stress relaxation that proceeds at the same slow rate as observed in real biological soft tissue. PMID:23508634

  5. Recent progresses in gene delivery-based bone tissue engineering.

    PubMed

    Lu, Chia-Hsin; Chang, Yu-Han; Lin, Shih-Yeh; Li, Kuei-Chang; Hu, Yu-Chen

    2013-12-01

    Gene therapy has converged with bone engineering over the past decade, by which a variety of therapeutic genes have been delivered to stimulate bone repair. These genes can be administered via in vivo or ex vivo approach using either viral or nonviral vectors. This article reviews the fundamental aspects and recent progresses in the gene therapy-based bone engineering, with emphasis on the new genes, viral vectors and gene delivery approaches. PMID:23994567

  6. DNA microarray (spot) .

    E-print Network

    1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

  7. Matrix Metalloproteases and Tissue Inhibitors of Metalloproteinases in Medial Plica and Pannus-like Tissue Contribute to Knee Osteoarthritis Progression

    PubMed Central

    Yang, Chih-Chang; Lin, Cheng-Yu; Wang, Hwai-Shi; Lyu, Shaw-Ruey

    2013-01-01

    Osteoarthritis (OA) is characterized by degradation of the cartilage matrix, leading to pathologic changes in the joints. However, the pathogenic effects of synovial tissue inflammation on OA knees are not clear. To investigate whether the inflammation caused by the medial plica is involved in the pathogenesis of osteoarthritis, we examined the expression of matrix metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), interleukin (IL)-1?, and tumor necrosis factor (TNF)-? in the medial plica and pannus-like tissue in the knees of patients with medial compartment OA who underwent either arthroscopic medial release (stage II; 15 knee joints from 15 patients) or total knee replacement (stage IV; 18 knee joints from 18 patients). MMP-2, MMP-3, MMP-9, IL-1?, and TNF-? mRNA and protein levels measured, respectively, by quantitative real-time PCR and Quantibody human MMP arrays, were highly expressed in extracts of medial plica and pannus-like tissue from stage IV knee joints. Immunohistochemical staining also demonstrated high expression of MMP-2, MMP-3, and MMP-9 in plica and pannus-like tissue of stage IV OA knees and not in normal cartilage. Some TIMP/MMP ratios decreased significantly in both medial plica and pannus-like tissue as disease progressed from stage II to stage IV. Furthermore, the migration of cells from the pannus-like tissue was enhanced by IL-1?, while plica cell migration was enhanced by TNF-?. The results suggest that medial plica and pannus-like tissue may be involved in the process of cartilage degradation in medial compartment OA of the knee. PMID:24223987

  8. Microarray analysis of differentially expressed genes in vaginal tissues from women with stress urinary incontinence compared with asymptomatic women

    Microsoft Academic Search

    Bertha Chen; Yan Wen; Zhaomei Zhang; Yaqian Guo; Janet A. Warrington

    2006-01-01

    BACKGROUND: The pathophysiology of pelvic floor dysfunction resulting in stress urinary incontinence (SUI) in women is complex. Evidence suggests that there is also a genetic predisposition towards SUI. We sought to identify differentially expressed genes involved in extracellular matrix (ECM) metabolism in vaginal tissues from women with SUI in the secretory phase of menses compared with asymptomatic women. METHODS: Tissue

  9. A Graph-Theoretic Technique for Classification of Normal and Tumor Tissues Using Gene Expression Microarray Data

    E-print Network

    Kim, Saejoon

    of a biological cell or tissue of interest. For this reason, it is used for many applications including identifi], pharmacogenomics and clinical studies, and many more. The classification of normal and cancerous tissues, or cancer investigated in the literature in the past including the initial work of [1] that used a simple voting scheme

  10. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

    PubMed

    Horn, Heike; Bausinger, Julia; Staiger, Annette M; Sohn, Maximilian; Schmelter, Christopher; Gruber, Kim; Kalla, Claudia; Ott, M Michaela; Rosenwald, Andreas; Ott, German

    2014-01-01

    Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL) and six malignant mesothelioma (MM) samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches. PMID:24733537

  11. Numerical and Structural Genomic Aberrations Are Reliably Detectable in Tissue Microarrays of Formalin-Fixed Paraffin-Embedded Tumor Samples by Fluorescence In-Situ Hybridization

    PubMed Central

    Horn, Heike; Bausinger, Julia; Staiger, Annette M.; Sohn, Maximilian; Schmelter, Christopher; Gruber, Kim; Kalla, Claudia; Ott, M. Michaela; Rosenwald, Andreas; Ott, German

    2014-01-01

    Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL) and six malignant mesothelioma (MM) samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches. PMID:24733537

  12. Endothelial necrosis at 1h post-burn predicts progression of tissue injury

    PubMed Central

    Hirth, Douglas; McClain, Steve A.; Singer, Adam J.; Clark, Richard A.F.

    2013-01-01

    Burn injury progression has not been well characterized at the cellular level. To define burn injury progression in terms of cell death, histopathologic spatiotemporal relationships of cellular necrosis and apoptosis were investigated in a validated porcine model of vertical burn injury progression. Cell necrosis was identified by High Mobility Group Box 1 protein and apoptosis by Caspase 3a staining of tissue samples taken 1h, 24h and 7 days post-burn. Level of endothelial cell necrosis at 1h was predictive of level of apoptosis at 24h (Pearson's r=0.87) and of level of tissue necrosis at 7 days (Pearson's r=0.87). Furthermore, endothelial cell necrosis was deeper than interstitial cell necrosis at 1h (p<0.001). Endothelial cell necrosis at 1h divided the zone of injury progression (Jackson's zone of stasis) into an upper subzone with necrotic endothelial cells and initially viable adnexal and interstitial cells at 1h that progressed to necrosis by 24h, and a lower zone with initially viable endothelial cells at 1h, but necrosis and apoptosis of all cell types by 24h. Importantly, this spatiotemporal series of events and rapid progression resembles myocardial infarction and stroke, and implicates mechanisms of these injuries, ischemia, ischemia reperfusion, and programmed cell death, in burn progression. PMID:23627744

  13. ACE inhibition reduces glomerulosclerosis and regenerates glomerular tissue in a model of progressive renal disease

    Microsoft Academic Search

    A Remuzzi; E Gagliardini; F Sangalli; M Bonomelli; M Piccinelli; A Benigni; G Remuzzi

    2006-01-01

    Today angiotensin II inhibition is primarily used to slow the rate of progression of kidney diseases. There is evidence that these therapies can induce a partial regression of glomerular lesions. However, we do not know yet the extent of sclerotic lesion regression and whether new glomerular tissue is formed to help support the renal function. We used male Munich Wistar

  14. Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Preliminary assessment of cross-platform concordance

    PubMed Central

    Kelly, Andrew D.; Hill, Katherine E.; Correll, Mick; Hu, Lan; Wang, Yaoyu; Rubio, Renee; Duan, Shenghua; Quackenbush, John; Spentzos, Dimitrios

    2014-01-01

    Next-generation sequencing is increasingly employed in biomedical investigations. Strong concordance between microarray and mRNA-seq levels has been reported in high quality specimens but information is lacking on formalin-fixed, paraffin-embedded (FFPE) tissues, and particularly for microRNA (miRNA) analysis. We conducted a preliminary examination of the concordance between miRNA-seq and cDNA-mediated annealing, selection, extension, and ligation (DASL) miRNA assays. Quantitative agreement between platforms is moderate (Spearman correlation 0.514–0.596) and there is discordance of detection calls on a subset of miRNAs. Quantitative PCR (q-RT-PCR) performed for several discordant miRNAs confirmed the presence of most sequences detected by miRNA-seq but not by DASL but also that miRNA-seq did not detect some sequences, which DASL confidently detected. Our results suggest that miRNA-seq is specific, with few false positive calls, but it may not detect certain abundant miRNAs in FFPE tissue. Further work is necessary to fully address these issues that are pertinent for translational research. PMID:23562991

  15. Serial Analysis of 38 Proteins during the Progression of Human Breast Tumor in Mice Using an Antibody Colocalization Microarray.

    PubMed

    Li, Huiyan; Bergeron, Sébastien; Annis, Matthew G; Siegel, Peter M; Juncker, David

    2015-04-01

    Proteins in serum or plasma hold great potential for use in disease diagnosis and monitoring. However, the correlation between tumor burden and protein biomarker concentration has not been established. Here, using an antibody colocalization microarray, the protein concentration in serum was measured and compared with the size of mammary xenograft tumors in 11 individual mice from the time of injection; seven blood samples were collected from each tumor-bearing mouse as well as control mice on a weekly basis. The profiles of 38 proteins detected in sera from these animals were analyzed by clustering, and we identified 10 proteins with the greatest relative increase in serum concentration that correlated with growth of the primary mammary tumor. To evaluate the diagnosis of cancer based on these proteins using either an absolute threshold (i.e. a concentration cutoff) or self-referenced differential threshold based on the increase in concentration before cell injection, receiver operating characteristic curves were produced for 10 proteins with increased concentration, and the area under curve was calculated for each time point based on a single protein or on a panel of proteins, in each case showing a rapid increase of the area under curve. Next, the sensitivity and specificity of individual and optimal protein panels were calculated, showing high accuracy as early as week 2. These results provide a foundation for studies of tumor growth through measuring serial changes of protein concentration in animal models. PMID:25680959

  16. Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium.

    PubMed

    Schurmann, Claudia; Heim, Katharina; Schillert, Arne; Blankenberg, Stefan; Carstensen, Maren; Dörr, Marcus; Endlich, Karlhans; Felix, Stephan B; Gieger, Christian; Grallert, Harald; Herder, Christian; Hoffmann, Wolfgang; Homuth, Georg; Illig, Thomas; Kruppa, Jochen; Meitinger, Thomas; Müller, Christian; Nauck, Matthias; Peters, Annette; Rettig, Rainer; Roden, Michael; Strauch, Konstantin; Völker, Uwe; Völzke, Henry; Wahl, Simone; Wallaschofski, Henri; Wild, Philipp S; Zeller, Tanja; Teumer, Alexander; Prokisch, Holger; Ziegler, Andreas

    2012-01-01

    Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data preprocessing and the variability due to sample processing in whole blood cell and blood monocyte gene expression data, measured on the Illumina HumanHT-12 v3 BeadChip array.Gene expression signal intensities were similar after applying the log(2) or the variance-stabilizing transformation. In all cohorts, the first principal component (PC) explained more than 95% of the total variation. Technical factors substantially influenced signal intensity values, especially the Illumina chip assignment (33-48% of the variance), the RNA amplification batch (12-24%), the RNA isolation batch (16%), and the sample storage time, in particular the time between blood donation and RNA isolation for the whole blood cell samples (2-3%), and the time between RNA isolation and amplification for the monocyte samples (2%). White blood cell composition parameters were the strongest biological factors influencing the expression signal intensities in the whole blood cell samples (3%), followed by sex (1-2%) in both sample types. Known single nucleotide polymorphisms (SNPs) were located in 38% of the analyzed probe sequences and 4% of them included common SNPs (minor allele frequency >5%). Out of the tested SNPs, 1.4% significantly modified the probe-specific expression signals (Bonferroni corrected p-value<0.05), but in almost half of these events the signal intensities were even increased despite the occurrence of the mismatch. Thus, the vast majority of SNPs within probes had no significant effect on hybridization efficiency.In summary, adjustment for a few selected technical factors greatly improved reliability of gene expression analyses. Such adjustments are particularly required for meta-analyses. PMID:23236413

  17. Progressive Overgrowth of the Cerebriform Connective Tissue Nevus in Patients with Proteus Syndrome

    PubMed Central

    Beachkofsky, Thomas M.; Sapp, Julie C.; Biesecker, Leslie G.; Darling, Thomas N.

    2011-01-01

    Background Proteus syndrome is a rare overgrowth disorder that almost always affects the skin. Objective Our purpose was to evaluate progression of skin lesions in patients with Proteus syndrome. Methods Skin findings were documented in 36 patients with Proteus syndrome. Progression of skin lesions in 16 of these patients was assessed by comparing photographs obtained on repeat visits for an average total duration of 53 months. Results The skin lesion most characteristic of Proteus syndrome, the cerebriform connective tissue nevus showed progression in 13 children but not in 3 adults. The cerebriform connective tissue nevus progressed by expansion into previously uninvolved skin, increased thickness, and development of new lesions. Lipomas increased in size and/or number in 8/10 children with lipomas. In contrast, epidermal nevi and vascular malformations generally did not spread or increase in number. Limitations Only 3 adults with Proteus syndrome were evaluated longitudinally. Conclusion The cerebriform connective tissue nevus in Proteus syndrome grows throughout childhood but tends to remain stable in adulthood. PMID:20709429

  18. Beyond Microarrays

    NSDL National Science Digital Library

    Michael B. Yaffe (American Association for the Advancement of Science; Science Signaling REV)

    2008-12-23

    Microarray analysis of RNA expression has been changing the way gene expression is assayed, but challenges remain in analyzing the results and interpreting the data to gain biologically meaningful mechanistic insights.

  19. Potential Upstream Regulators of Cannabinoid Receptor 1 Signaling in Prostate Cancer: A Bayesian Network Analysis of Data From a Tissue Microarray

    PubMed Central

    Häggström, Jenny; Cipriano, Mariateresa; Forshell, Linus Plym; Persson, Emma; Hammarsten, Peter; Stella, Nephi; Fowler, Christopher J

    2014-01-01

    BACKGROUND The endocannabinoid system regulates cancer cell proliferation, and in prostate cancer a high cannabinoid CB1 receptor expression is associated with a poor prognosis. Down-stream mediators of CB1 receptor signaling in prostate cancer are known, but information on potential upstream regulators is lacking. RESULTS Data from a well-characterized tumor tissue microarray were used for a Bayesian network analysis using the max-min hill-climbing method. In non-malignant tissue samples, a directionality of pEGFR (the phosphorylated form of the epidermal growth factor receptor) ? CB1 receptors were found regardless as to whether the endocannabinoid metabolizing enzyme fatty acid amide hydrolase (FAAH) was included as a parameter. A similar result was found in the tumor tissue, but only when FAAH was included in the analysis. A second regulatory pathway, from the growth factor receptor ErbB2 ? FAAH was also identified in the tumor samples. Transfection of AT1 prostate cancer cells with CB1 receptors induced a sensitivity to the growth-inhibiting effects of the CB receptor agonist CP55,940. The sensitivity was not dependent upon the level of receptor expression. Thus a high CB1 receptor expression alone does not drive the cells towards a survival phenotype in the presence of a CB receptor agonist. CONCLUSIONS The data identify two potential regulators of the endocannabinoid system in prostate cancer and allow the construction of a model of a dysregulated endocannabinoid signaling network in this tumor. Further studies should be designed to test the veracity of the predictions of the network analysis in prostate cancer and other solid tumors. Prostate 74:1107–1117, 2014. © 2014 The Authors. The Prostate published by Wiley Periodicals, Inc. PMID:24913716

  20. Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays

    Microsoft Academic Search

    A Aleman; L Adrien; L Lopez-Serra; C Cordon-Cardo; M Esteller; T J Belbin; M Sanchez-Carbayo

    2008-01-01

    CpG island arrays represent a high-throughput epigenomic discovery platform to identify global disease-specific promoter hypermethylation candidates along bladder cancer progression. DNA obtained from 10 pairs of invasive bladder tumours were profiled vs their respective normal urothelium using differential methylation hybridisation on custom-made CpG arrays (n=12 288 clones). Promoter hypermethylation of 84 clones was simultaneously shown in at least 70% of

  1. Progress in Raman spectroscopy in the fields of tissue engineering, diagnostics and toxicological testing

    Microsoft Academic Search

    Chris A. Owen; Ioan Notingher; Robert Hill; Molly Stevens; Larry L. Hench

    2006-01-01

    This review summarises progress in Raman spectroscopy and its application in diagnostics, toxicological testing and tissue\\u000a engineering. Applications of Raman spectroscopy in cell biology are in the early stages of development, however, recent publications\\u000a have demonstrated its utilisation as a diagnostic and development tool with the key advantage that investigations of living\\u000a cells can be performed non-invasively.\\u000a \\u000a Some of the

  2. Tissue microarray analysis of ezrin, KBA.62, CD166, nestin, and p-Akt in melanoma versus banal and atypical nevi, and nonmelanocytic lesions.

    PubMed

    Shanesmith, Rebecca P; Smart, Chandra; Cassarino, David S

    2011-10-01

    Multiple melanocytic markers are useful for differentiating between melanoma and nonmelanocytic lesions but generally do not distinguish melanoma from nevi and atypical melanocytic lesions. We sought to determine if several immunohistochemical markers recently described in the literature, including ezrin, KBA.62, p-Akt, CD166, and nestin, may be helpful in distinguishing these lesions. One hundred ten tissue microarray samples were scored for nestin and CD166 and 220 samples for ezrin, KBA.62, and p-Akt. We found that putative stem cell markers nestin and CD166 were both expressed in most melanomas (86% and 65% of samples, respectively), including desmoplastic melanoma, but were also expressed at similar levels in nevi (79% and 74%, respectively). In addition, these markers were not specific for melanocytic lesions. Ezrin was also expressed in both nevi and melanoma (81% each), including desmoplastic melanoma (75%), and in neural tumors. KBA.62 stained more cases of nevi versus melanoma (93% and 65%, respectively) and was positive in 53% of desmoplastic melanoma. However, it was also positive in several nonmelanocytic tumors. P-Akt expression was generally weak but was increased in nevi (75%) versus melanoma (43%), and was lost in desmoplastic melanomas (5%). Overall, only KBA.62 and p-Akt expression differed between melanoma and nevi, and none of these markers were completely specific for melanocytic tumors versus nonmelanocytic lesions. PMID:21915031

  3. A high-density tissue microarray from patients with clinically localized prostate cancer reveals ERG and TATI exclusivity in tumor cells

    PubMed Central

    Lippolis, G; Edsjö, A; Stenman, U-H; Bjartell, A

    2013-01-01

    Background: Prostate cancer (PCa) is characterized by high tumor heterogeneity. In 2005, the fusion between the androgen-regulated gene TMPRSS2 and members of the ETS family was discovered in prostate cancer. In particular, fusion of TMPRSS2 with ERG was found in approximately 50% of prostate cancers and considered as an early event in the onset of the disease. The prognostic value of this fusion is still contradictory. Bioinformatics showed that overexpression of SPINK1 gene in a subset of fusion-gene-negative prostate cancers was associated with a poor prognosis. In theory, overexpression of the tumor-associated trypsin inhibitor (TATI) protein encoded by SPINK1 in fusion-gene-negative tumor cells opens the way to selected treatments for genotypically different cases. However, their expression has never been assessed at the cellular level in the same tissue samples. Methods: As ERG expression has been shown to be a surrogate of fusion gene occurrence in prostate cancer, we have used double immunohistochemical staining to assess expression of ERG and TATI on a large tissue microarray comprising 4177 cases of localized prostate cancer. Results: We did not detect any co-expression of ERG and TATI in the same cancer cells, which confirms previous suggestions from in silico studies. ERG was associated with Gleason score (GS), surgical margins and pathological stage, but had no prognostic value in this cohort. TATI was weakly associated with pathological stage but had no significant association with outcome. Conclusions: We here provide a morphological basis for ERG and TATI exclusivity in prostate cancer cells. Future therapies should be based on a combination of different targets in order to eradicate tumor cells with gene fusions and cells expressing other tumor-associated antigens. Further studies are needed to understand why ERG and TATI are not co-expressed in the same prostatic tumor cells. PMID:23459095

  4. RUNX2 correlates with subtype-specific breast cancer in a human tissue microarray, and ectopic expression of Runx2 perturbs differentiation in the mouse mammary gland

    PubMed Central

    McDonald, Laura; Ferrari, Nicola; Terry, Anne; Bell, Margaret; Mohammed, Zahra M.; Orange, Clare; Jenkins, Alma; Muller, William J.; Gusterson, Barry A.; Neil, James C.; Edwards, Joanne; Morris, Joanna S.; Cameron, Ewan R.; Blyth, Karen

    2014-01-01

    RUNX2, a master regulator of osteogenesis, is oncogenic in the lymphoid lineage; however, little is known about its role in epithelial cancers. Upregulation of RUNX2 in cell lines correlates with increased invasiveness and the capacity to form osteolytic disease in models of breast and prostate cancer. However, most studies have analysed the effects of this gene in a limited number of cell lines and its role in primary breast cancer has not been resolved. Using a human tumour tissue microarray, we show that high RUNX2 expression is significantly associated with oestrogen receptor (ER)/progesterone receptor (PR)/HER2-negative breast cancers and that patients with high RUNX2 expression have a poorer survival rate than those with negative or low expression. We confirm RUNX2 as a gene that has a potentially important functional role in triple-negative breast cancer. To investigate the role of this gene in breast cancer, we made a transgenic model in which Runx2 is specifically expressed in murine mammary epithelium under the control of the mouse mammary tumour virus (MMTV) promoter. We show that ectopic Runx2 perturbs normal development in pubertal and lactating animals, delaying ductal elongation and inhibiting lobular alveolar differentiation. We also show that the Runx2 transgene elicits age-related, pre-neoplastic changes in the mammary epithelium of older transgenic animals, suggesting that elevated RUNX2 expression renders such tissue more susceptible to oncogenic changes and providing further evidence that this gene might have an important, context-dependent role in breast cancer. PMID:24626992

  5. DNA Microarray

    NSDL National Science Digital Library

    This animated YouTube video, created by Southwest Center for Microsystems Education (SCME), illustrates how DNA microarrays work in the context of nanofabrication. The animation and associated narration describe "how a DNA microarray identifies complementary DNA (cDNA) strands from a sample. On the substrate of the array are synthetic ssDNA stands or oligonucleotides (oligos). Each grid in the microarray contains hundreds to thousands of oligos with a unique DNA sequence. These oligos hybridize with cDNA from one of two samples. There are thousands of grids on the array allowing for the simultaneous identification of thousands of different DNA sequences. Each sample cDNA is "tagged" with the red or green tag as shown in the animation. The "tags" enable an interpretation of the DNA hybridizations." A supporting learning module and activities can be downloaded from the SCME website.

  6. Tissue mechanics modulate microRNA-dependent PTEN expression to regulate malignant progression

    PubMed Central

    Mouw, Janna K; Yui, Yoshihiro; Damiano, Laura; Bainer, Russell O; Lakins, Johnathan N; Acerbi, Irene; Ou, Guanqing; Wijekoon, Amanda C; Levental, Kandice R; Gilbert, Penney M; Chen, Yunn-Yi; Weaver, Valerie M

    2014-01-01

    Tissue mechanics regulate development and homeostasis and are consistently modified in tumor progression. Nevertheless, the fundamental molecular mechanisms through which altered mechanics regulate tissue behavior and the clinical relevance of these changes remain unclear. We demonstrate that increased matrix stiffness modulates microRNA expression to drive tumor progression through integrin activation of ?-catenin and MYC. Specifically, in human and mouse tissue, increased matrix stiffness induced miR-18a to reduce levels of the tumor suppressor PTEN, both directly and indirectly by decreasing levels of HOXA9. Clinically, extracellular matrix stiffness correlated significantly with miR-18a in human breast tumor biopsies. miR-18a expression was highest in basal-like breast cancers in which PTEN and HOXA9 levels were lowest and predicted for poor prognosis in patients with luminal breast cancers. Our findings identify a mechanically-regulated microRNA circuit that can promote malignancy and suggest potential prognostic roles for HOXA9 and miR-18a levels in stratifying patients with luminal breast cancers. PMID:24633304

  7. A Seven-Marker Signature and Clinical Outcome in Malignant Melanoma: A Large-Scale Tissue-Microarray Study with Two Independent Patient Cohorts

    PubMed Central

    Bosserhoff, Anja K.; Hofstädter, Ferdinand; Pauer, Armin; Roth, Volker; Buhmann, Joachim M.; Moll, Ingrid; Anagnostou, Nikos; Brandner, Johanna M.; Ikenberg, Kristian; Moch, Holger; Landthaler, Michael; Vogt, Thomas; Wild, Peter J.

    2012-01-01

    Background Current staging methods such as tumor thickness, ulceration and invasion of the sentinel node are known to be prognostic parameters in patients with malignant melanoma (MM). However, predictive molecular marker profiles for risk stratification and therapy optimization are not yet available for routine clinical assessment. Methods and Findings Using tissue microarrays, we retrospectively analyzed samples from 364 patients with primary MM. We investigated a panel of 70 immunohistochemical (IHC) antibodies for cell cycle, apoptosis, DNA mismatch repair, differentiation, proliferation, cell adhesion, signaling and metabolism. A marker selection procedure based on univariate Cox regression and multiple testing correction was employed to correlate the IHC expression data with the clinical follow-up (overall and recurrence-free survival). The model was thoroughly evaluated with two different cross validation experiments, a permutation test and a multivariate Cox regression analysis. In addition, the predictive power of the identified marker signature was validated on a second independent external test cohort (n?=?225). A signature of seven biomarkers (Bax, Bcl-X, PTEN, COX-2, loss of ?-Catenin, loss of MTAP, and presence of CD20 positive B-lymphocytes) was found to be an independent negative predictor for overall and recurrence-free survival in patients with MM. The seven-marker signature could also predict a high risk of disease recurrence in patients with localized primary MM stage pT1-2 (tumor thickness ?2.00 mm). In particular, three of these markers (MTAP, COX-2, Bcl-X) were shown to offer direct therapeutic implications. Conclusions The seven-marker signature might serve as a prognostic tool enabling physicians to selectively triage, at the time of diagnosis, the subset of high recurrence risk stage I–II patients for adjuvant therapy. Selective treatment of those patients that are more likely to develop distant metastatic disease could potentially lower the burden of untreatable metastatic melanoma and revolutionize the therapeutic management of MM. PMID:22685558

  8. Role of Deregulated microRNAs in Breast Cancer Progression Using FFPE Tissue

    PubMed Central

    Chen, Liang; Li, Youhuai; Fu, Yebo; Peng, Jin; Mo, Meng-Hsuan; Stamatakos, Michael; Teal, Christine B.; Brem, Rachel F.; Stojadinovic, Alexander; Grinkemeyer, Michael; McCaffrey, Timothy A.; Man, Yan-gao; Fu, Sidney W.

    2013-01-01

    MicroRNAs (miRNAs) contribute to cancer initiation and progression by silencing the expression of their target genes, causing either mRNA molecule degradation or translational inhibition. Intraductal epithelial proliferations of the breast are histologically and clinically classified into normal, atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). To better understand the progression of ductal breast cancer development, we attempt to identify deregulated miRNAs in this process using Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from breast cancer patients. Following tissue microdissection, we obtained 8 normal, 4 ADH, 6 DCIS and 7 IDC samples, which were subject to RNA isolation and miRNA expression profiling analysis. We found that miR-21, miR-200b/c, miR-141, and miR-183 were consistently up-regulated in ADH, DCIS and IDC compared to normal, while miR-557 was uniquely down-regulated in DCIS. Interestingly, the most significant miRNA deregulations occurred during the transition from normal to ADH. However, the data did not reveal a step-wise miRNA alteration among discrete steps along tumor progression, which is in accordance with previous reports of mRNA profiling of different stages of breast cancer. Furthermore, the expression of MSH2 and SMAD7, two important molecules involving TGF-? pathway, was restored following miR-21 knockdown in both MCF-7 and Hs578T breast cancer cells. In this study, we have not only identified a number of potential candidate miRNAs for breast cancer, but also found that deregulation of miRNA expression during breast tumorigenesis might be an early event since it occurred significantly during normal to ADH transition. Consequently, we have demonstrated the feasibility of miRNA expression profiling analysis using archived FFPE tissues, typically with rich clinical information, as a means of miRNA biomarker discovery. PMID:23372687

  9. COMPARISON OF TRANSCRIPTIONAL RESONSES FROM AVIAN GUT TISSUES AFTER EIMERIA ACERVULINA AND E. MAXIMA INFECTIONS USING cDNA MICROARRAY TECHNOLOGY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the host response during pathogen infection will extend our knowledge of pathogenesis and enhance the development of novel preventive methodologies against important infectious diseases. Microarray technology is a powerful tool to analyze host transcriptional responses. Coccidiosis re...

  10. E-cadherin Suppression Accelerates Squamous Cell Carcinoma Progression in Three-Dimensional Human Tissue Constructs

    Microsoft Academic Search

    Alexander Margulis; Weitian Zhang; Addy Alt-holland; Howard C. Crawford; Norbert E. Fusenig; Jonathan A. Garlick

    Abstract We studied,the,link between,loss of E-cadherin–mediated adhesion,and,acquisition,of malignant,properties,in three- dimensional, human tissue constructs that mimicked the initial stages of squamous,cell cancer,progression. Suppres- sion of E-cadherin expression in early-stage, skin-derived tumor,cells (HaCaT-II-4) was,induced,by,cytoplasmic sequestration,of hh-catenin,upon,stable,expression,of,a dominant-negative E-cadherin fusion,protein,(H-2K,-Ecad–expressing tissue constructs,that was,blocked,by,MMP inhibition,(GM6001). Quantitative reverse,transcription–PCR showed,a,2.5-fold increase,in

  11. Direct comparison of microarray gene expression profiles between non-amplification and a modified cDNA amplification procedure applicable for needle biopsy tissues

    Microsoft Academic Search

    Yiwei Li; Shadan Ali; Philip A Philip; Fazlul H Sarkar

    2003-01-01

    Global gene expression profiling by cDNA microarray analysis has been used to discover the biomarkers for early diagnosis of various cancers, subclassing cancer type, and prediction of patient’s treatment outcome. The information provided by gene expression profiling may contribute to the design of molecular mechanism-based strategies for cancer prevention and\\/or treatment. However, the standard procedure for cDNA microarray analysis requires

  12. Hypoxia-Inducible Factors: Mediators of Cancer Progression; Prognostic and Therapeutic Targets in Soft Tissue Sarcomas

    PubMed Central

    Sadri, Navid; Zhang, Paul J.

    2013-01-01

    Soft-tissue sarcomas remain aggressive tumors that result in death in greater than a third of patients due to either loco-regional recurrence or distant metastasis. Surgical resection remains the main choice of treatment for soft tissue sarcomas with pre- and/or post-operational radiation and neoadjuvant chemotherapy employed in more advanced stage disease. However, in recent decades, there has been little progress in the average five-year survival for the majority of patients with high-grade soft tissue sarcomas, highlighting the need for improved targeted therapeutic agents. Clinical and preclinical studies demonstrate that tumor hypoxia and up-regulation of hypoxia-inducible factors (HIFs) is associated with decreased survival, increased metastasis, and resistance to therapy in soft tissue sarcomas. HIF-mediated gene expression regulates many critical aspects of tumor biology, including cell survival, metabolic programming, angiogenesis, metastasis, and therapy resistance. In this review, we discuss HIFs and HIF-mediated genes as potential prognostic markers and therapeutic targets in sarcomas. Many pharmacological agents targeting hypoxia-related pathways are in development that may hold therapeutic potential for treating both primary and metastatic sarcomas that demonstrate increased HIF expression. PMID:24216979

  13. Microarray analysis of thioacetamide-treated type 1 diabetic rats

    SciTech Connect

    Devi, Sachin S. [Department of Toxicology, College of Pharmacy, University of Louisiana at Monroe, 700 University Ave, Sugar Hall 306, Monroe, LA 71209-0470 (United States); Mehendale, Harihara M. [Department of Toxicology, College of Pharmacy, University of Louisiana at Monroe, 700 University Ave, Sugar Hall 306, Monroe, LA 71209-0470 (United States)]. E-mail: mehendale@ulm.edu

    2006-04-01

    It is well known that diabetes imparts high sensitivity to numerous hepatotoxicants. Previously, we have shown that a normally non-lethal dose of thioacetamide (TA, 300 mg/kg) causes 90% mortality in type 1 diabetic (DB) rats due to inhibited tissue repair allowing progression of liver injury. On the other hand, DB rats exposed to 30 mg TA/kg exhibit delayed tissue repair and delayed recovery from injury. The objective of this study was to investigate the mechanism of impaired tissue repair and progression of liver injury in TA-treated DB rats by using cDNA microarray. Gene expression pattern was examined at 0, 6, and 12 h after TA challenge, and selected mechanistic leads from microarray experiments were confirmed by real-time RT-PCR and further investigated at protein level over the time course of 0 to 36 h after TA treatment. Diabetic condition itself increased gene expression of proteases and decreased gene expression of protease inhibitors. Administration of 300 mg TA/kg to DB rats further elevated gene expression of proteases and suppressed gene expression of protease inhibitors, explaining progression of liver injury in DB rats after TA treatment. Inhibited expression of genes involved in cell division cycle (cyclin D1, IGFBP-1, ras, E2F) was observed after exposure of DB rats to 300 mg TA/kg, explaining inhibited tissue repair in these rats. On the other hand, DB rats receiving 30 mg TA/kg exhibit delayed expression of genes involved in cell division cycle, explaining delayed tissue repair in these rats. In conclusion, impaired cyclin D1 signaling along with increased proteases and decreased protease inhibitors may explain impaired tissue repair that leads to progression of liver injury initiated by TA in DB rats.

  14. Progress of tissue culture and genetic transformation research in pigeon pea [Cajanus cajan (L.) Millsp.].

    PubMed

    Krishna, Gaurav; Reddy, P Sairam; Ramteke, P W; Bhattacharya, P S

    2010-10-01

    Pigeon pea [Cajanus cajan (L.) Millsp.] (Family: Fabaceae) is an important legume crop cultivated across 50 countries in Asia, Africa, and the Americas; and ranks fifth in area among pulses after soybean, common bean, peanut, and chickpea. It is consumed as a major source of protein (21%) to the human population in many developing countries. In India, it is the second important food legume contributing to 80% of the global production. Several biotic and abiotic stresses are posing a big threat to its production and productivity. Attempts to address these problems through conventional breeding methods have met with partial success. This paper reviews the chronological progress made in tissue culture through organogenesis and somatic embryogenesis, including the influence of factors such as genotypes, explant sources, and culture media including the supplementation of plant growth regulators. Comprehensive lists of morphogenetic pathways involved in in vitro regeneration through organogenesis and somatic embryogenesis using different explant tissues of diverse pigeon pea genotypes are presented. Similarly, the establishment of protocols for the production of transgenics via particle bombardment and Agrobacterium-mediated transformation using different explant tissues, Agrobacterium strains, Ti plasmids, and plant selectable markers, as well as their interactions on transformation efficiency have been discussed. Future research thrusts on the use of different promoters and stacking of genes for various biotic and abiotic stresses in pigeon pea are suggested. PMID:20652570

  15. Filter versus wrapper gene selection approaches in DNA microarray domains

    Microsoft Academic Search

    Iñaki Inza; Pedro Larrañaga; Rosa Blanco; Antonio J. Cerrolaza

    2004-01-01

    DNA microarray experiments generating thousands of gene expression measurements, are used to collect information from tissue and cell samples regarding gene expression differences that could be useful for diagnosis disease, distinction of the specific tumor type, etc. One important application of gene expression microarray data is the classification of samples into known categories.As DNA microarray technology measures the gene expression

  16. Polymer microarrays for cell based applications 

    E-print Network

    Hansen, Anne Klara Brigitte

    2012-11-28

    The development and identification of new biomaterials that can replace specific tissues and organs is desirable. In the presented PhD thesis polymer microarrays were applied for the screening of polyacrylates and ...

  17. Peripheral Ovine Progressive Pneumonia Provirus Levels Correlate with and Predict Histological Tissue Lesion Severity in Naturally Infected Sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Studies were undertaken to determine whether host immune responses in the form of serum anti-ovine progressive pneumonia virus (OPPV) antibody responses or virus replication in the form of peripheral OPP provirus levels associate with the degree of histological tissue lesions in naturally OPPV infec...

  18. Progress on ThermoBrachytherapy Surface Applicator for Superficial Tissue Diseases

    PubMed Central

    Arunachalam, Kavitha; Craciunescu, Oana I.; Maccarini, Paolo F.; Schlorff, Jaime L.; Markowitz, Edward; Stauffer, Paul R.

    2013-01-01

    This work reports the ongoing development of a combination applicator for simultaneous heating of superficial tissue disease using a 915 MHz DCC (dual concentric conductor) array and High Dose Rate (HDR) brachytherapy delivered via an integrated conformal catheter array. The progress includes engineering design changes in the waterbolus, DCC configurations and fabrication techniques of the conformal multilayer applicator. The dosimetric impact of the thin copper DCC array is also assessed. Steady state fluid dynamics of the new waterbolus bag indicates nearly uniform flow with less than 1°C variation across a large (19×32cm) bolus. Thermometry data of the torso phantom acquired with computer controlled movement of fiberoptic temperature probes inside thermal mapping catheters indicate feasibility of real time feedback control for the DCC array. MR (magnetic resonance) scans of a torso phantom indicate that the waterbolus thickness across the treatment area is controlled by the pressure applied by the surrounding inflatable airbladder and applicator securing straps. The attenuation coefficient of the DCC array was measured as 3± 0.001% and 2.95±0.03 % using an ion chamber and OneDose™ dosimeters respectively. The performance of the combination applicator on patient phantoms provides valuable feedback to optimize the applicator prior use in the patient clinic. PMID:24392196

  19. IMPROVING THE RELIABILITY OF MICROARRAYS FOR TOXICOLOGY RESEARCH: A COLLABORATIVE APPROACH

    EPA Science Inventory

    Microarray-based gene expression profiling is a critical tool to identify molecular biomarkers of specific chemical stressors. Although current microarray technologies have progressed from their infancy, biological and technical repeatability and reliability are often still limit...

  20. Macro-Microarray

    NSDL National Science Digital Library

    2012-07-12

    In this activity, learners explore the "nuts and bolts" of gene chips. Learners construct a simple model of a DNA microarray (also known as gene chips) and learn how microarrays can be used to identify and treat disease--including cancer. This resource includes references and an explanation of microarrays.

  1. MicroRNA-203 inhibits the progression of esophageal squamous cell carcinoma with restored epithelial tissue architecture in vivo.

    PubMed

    Okumura, Tomoyuki; Shimada, Yutaka; Moriyama, Makoto; Takei, Yoshinori; Omura, Tetsuya; Sekine, Shinichi; Nagata, Takuya; Shimizu, Kazuharu; Tsukada, Kazuhiro

    2014-06-01

    MicroRNA (miR)-203 has been shown to induce squamous differentiation of epidermal stem cells through the suppression of p63. The aim of this study was to assess the tumor suppressor effect of miR-203 in esophageal squamous cell carcinoma (ESCC) with focus on the regulation of the cell fate decisions and organization of tumor tissue architecture in vivo. Our investigation establishing stable clones from ESCC cell lines with induced miR-203 expression resulted in significant growth inhibition in a mouse xenograft model. Small foci were observed in xenograft tumors with stratified squamous differentiation in conjunction with restored baso-apical polarity. The expression of the basement membrane protein laminine was localized at the center of the foci and the basal cell marker p75NTR was expressed in the innermost layer. The expression of ki67 and p63 was co-localized at the center layers, while involucrin was expressed in the outer layers. Flow cytometry revealed that the p75NTR-positive cells expressing p63 and Bmi1 were well maintained, while the expression of p63 was suppressed in the p75NTR-negative cells. Our cDNA microarray analysis demonstrated the upregulation of genes involved in regulating tissue architecture, such as BMP-4 and ZO-1 in the mir-203 transfectant. Investigation using surgically removed ESCC specimens revealed that the expression of miR-203 significantly correlated with a favorable prognosis. These results demonstrated that miR-203 regulated both basal and supra-basal cell components to induce differentiation with restored epithelial tissue architecture, leading to significant tumor growth inhibition in vivo. Those results suggest the use of miR-203 as a novel therapeutic and diagnostic target in patients with ESCC. PMID:24692008

  2. Manufacturing of microarrays.

    PubMed

    Petersen, David W; Kawasaki, Ernest S

    2007-01-01

    DNA microarray technology has become a powerful tool in the arsenal of the molecular biologist. Capitalizing on high precision robotics and the wealth of DNA sequences annotated from the genomes of a large number of organisms, the manufacture of microarrays is now possible for the average academic laboratory with the funds and motivation. Microarray production requires attention to both biological and physical resources, including DNA libraries, robotics, and qualified personnel. While the fabrication of microarrays is a very labor-intensive process, production of quality microarrays individually tailored on a project-by-project basis will help researchers shed light on future scientific questions. PMID:17265711

  3. Hippocampus neuronal metabolic gene expression outperforms whole tissue data in accurately predicting Alzheimer's disease progression

    E-print Network

    Ruppin, Eytan

    Hippocampus neuronal metabolic gene expression outperforms whole tissue data in accurately hippocampus tissue and hippocampal neurons of AD patients to investigate the ability of metabolic gene score. Notably, the expression of top predictive neuronal genes in AD is significantly higher than

  4. Analysis of Variance for Gene Expression Microarray Data

    Microsoft Academic Search

    M. Kathleen Kerr; Mitchell Martin; Gary A. Churchill

    2000-01-01

    Spotted cDNA microarrays are emerging as a powerful and cost-effective tool for large- scale analysis of gene expression. Microarrays can be used to measure the relative quantities of specié c mRNAs in two or more tissue samples for thousands of genes simultaneously. While the power of this technology has been recognized, many open questions remain about appropriate analysis of microarray

  5. Microarray and RNAi Analysis of P450s in Anopheles gambiae Male and Female Steroidogenic Tissues: CYP307A1 Is Required for Ecdysteroid Synthesis

    PubMed Central

    Pondeville, Emilie; David, Jean-Philippe; Guittard, Emilie; Maria, Annick; Ranson, Hilary

    2013-01-01

    In insects, the steroid hormone 20-hydroxyecdysone (20E) coordinates major developmental transitions. While the first and the final steps of 20E biosynthesis are characterized, the pathway from 7-dehydrocholesterol to 5?-ketodiol, commonly referred as the “black box”, remains hypothetical and whether there are still unidentified enzymes is unknown. The black box would include some oxidative steps, which are believed to be mediated by P450 enzymes. To identify new enzyme(s) involved in steroid synthesis, we analyzed by small-scale microarray the expression of all the genes encoding P450 enzymes of the malaria mosquito Anopheles gambiae in active steroidogenic organs of adults, ovaries from blood-fed females and male reproductive tracts, compared to inactive steroidogenic organs, ovaries from non-blood-fed females. Some genes encoding P450 enzymes were specifically overexpressed in female ovaries after a blood-meal or in male reproductive tracts but only three genes were found to be overexpressed in active steroidogenic organs of both females and males: cyp307a1, cyp4g16 and cyp6n1. Among these genes, only cyp307a1 has an expression pattern similar to other mosquito steroidogenic genes. Moreover, loss-of-function by transient RNAi targeting cyp307a1 disrupted ecdysteroid production demonstrating that this gene is required for ecdysteroid biosynthesis in Anopheles gambiae. PMID:24324583

  6. Portrait of Ependymoma Recurrence in Children: Biomarkers of Tumor Progression Identified by Dual-Color Microarray-Based Gene Expression Analysis

    PubMed Central

    Andreiuolo, Felipe; Puget, Stéphanie; Lacroix, Ludovic; Drusch, Françoise; Scott, Véronique; Varlet, Pascale; Mauguen, Audrey; Dessen, Philippe; Lazar, Vladimir; Vassal, Gilles; Grill, Jacques

    2010-01-01

    Background Children with ependymoma may experience a relapse in up to 50% of cases depending on the extent of resection. Key biological events associated with recurrence are unknown. Methodology/Principal Findings To discover the biology behind the recurrence of ependymomas, we performed CGHarray and a dual-color gene expression microarray analysis of 17 tumors at diagnosis co-hybridized with the corresponding 27 first or subsequent relapses from the same patient. As treatment and location had only limited influence on specific gene expression changes at relapse, we established a common signature for relapse. Eighty-seven genes showed an absolute fold change ?2 in at least 50% of relapses and were defined as the gene expression signature of ependymoma recurrence. The most frequently upregulated genes are involved in the kinetochore (ASPM, KIF11) or in neural development (CD133, Wnt and Notch pathways). Metallothionein (MT) genes were downregulated in up to 80% of the recurrences. Quantitative PCR for ASPM, KIF11 and MT3 plus immunohistochemistry for ASPM and MT3 confirmed the microarray results. Immunohistochemistry on an independent series of 24 tumor pairs at diagnosis and at relapse confirmed the decrease of MT3 expression at recurrence in 17/24 tumor pairs (p?=?0.002). Conversely, ASPM expression was more frequently positive at relapse (87.5% vs 37.5%, p?=?0.03). Loss or deletion of the MT genes cluster was never observed at relapse. Promoter sequencing after bisulfite treatment of DNA from primary tumors and recurrences as well as treatment of short-term ependymoma cells cultures with a demethylating agent showed that methylation was not involved in MT3 downregulation. However, in vitro treatment with a histone deacetylase inhibitor or zinc restored MT3 expression. Conclusions/Significance The most frequent molecular events associated with ependymoma recurrence were over-expression of kinetochore proteins and down-regulation of metallothioneins. Metallothionein-3 expression is epigenetically controlled and can be restored in vitro by histone deacetylase inhibitors. PMID:20885975

  7. Tissue and serum mesothelin are potential markers of neoplastic progression in Barrett’s–associated esophageal adenocarcinoma

    PubMed Central

    Rizk, Nabil P.; Servais, Elliot L.; Tang, Laura H.; Sima, Camelia S.; Gerdes, Hans; Fleisher, Martin; Rusch, Valerie W.; Adusumilli, Prasad S.

    2012-01-01

    Background Mesothelin is overexpressed in several malignancies and is purportedly a specific marker of malignant transformation. In this pilot study, we investigated whether tissue and serum mesothelin are potential markers of neoplastic progression in Barrett’s esophagus (BE) and in esophageal adenocarcinoma (EAC). Methods Mesothelin expression was retrospectively evaluated in normal, BE, and EAC tissue from surgically resected esophageal specimens (n = 125). In addition, soluble mesothelin-related peptide (SMRP) levels were measured in serum. Results Normal esophageal mucosa did not express mesothelin. BE tissue with high-grade dysplasia specifically expressed mesothelin, whereas BE tissue with low-grade or without dysplasia did not. Fifty-seven (46%) EAC tumors were positive for mesothelin. EAC tumors with BE expressed mesothelin more often than those without BE (58% vs 35%, P = 0.01). SMRP levels were elevated in 70% of EAC patients (mean, 0.89 nM; range, 0.03-3.77 nM), but not in patients with acid reflux and/or BE. Conclusions Mesothelin is commonly expressed in BE-associated esophageal adenocarcinoma. Based on this pilot study, a prospective study is under way to evaluate tissue and serum mesothelin are potential markers of neoplastic progression in BE and in EAC (NCT01393483). Impact Current surveillance methods in Barrett’s esophagus are invasive and neither cost-effective nor sensitive. This pilot study suggests that serum mesothelin is a marker of neoplastic transformation in BE and may provide a noninvasive method to improve identification of malignant transformation. PMID:22237988

  8. Peripheral Ovine Progressive Pneumonia Provirus Levels Correlate with and Predict Histological Tissue Lesion Severity in Naturally Infected Sheep?

    PubMed Central

    Herrmann-Hoesing, Lynn M.; Noh, Susan M.; White, Stephen N.; Snekvik, Kevin R.; Truscott, Thomas; Knowles, Donald P.

    2009-01-01

    Studies were undertaken to determine whether anti-ovine progressive pneumonia virus (OPPV) antibody responses in serum or OPP provirus levels in peripheral blood associate with the degree of histologically measured tissue lesions in naturally OPPV-infected sheep. Sections of formalin-fixed, paraffin-embedded, and hematoxylin- and eosin-stained lung, mammary gland, carpal synovial membrane, and brain tissues from 11 OPPV-infected ewes (mean age of 8.6 years) and 5 OPPV-uninfected ewes (mean age of 6 years) were evaluated for lesion severity. Ovine progressive pneumonia (OPP) provirus levels and anti-OPPV antibody titers in peripheral blood and serum samples, respectively, were measured upon euthanasia and 3 years prior to euthanasia. Both mean peripheral OPP provirus levels and mean serum anti-surface envelope glycoprotein (anti-SU) antibody titers at the time of euthanasia were significantly higher in ewes with moderate to severe histological lesions than in ewes with no to mild histological lesions. However, although mean peripheral blood OPP provirus levels at euthanasia and 3 years prior to euthanasia significantly correlated with the highest histological lesion score for any affected tissue (two-tailed P values, 0.03 and 0.02), mean serum anti-SU antibody titers, anti-capsid antibody titers, and anti-transmembrane 90 antibody titers at euthanasia did not show a significant correlation with the highest histological lesion score for any tissue (two-tailed P values, 0.32, 0.97, and 0.18, respectively). These data are the first to show that OPP provirus levels predict and correlate with the extent of OPPV-related histological lesions in various OPPV-affected tissues. These findings suggest that peripheral OPP provirus levels quantitatively contribute more to the development of histological lesions than the systemic anti-SU antibody host immune response. PMID:19261772

  9. 8.7: Presentation session: BRAiN measurement and imaging technologies: “Transparent microarrays of vertically aligned carbon nanofibers as a multimodal tissue interface”

    Microsoft Academic Search

    Tim McKnight

    2010-01-01

    Instability of the brain\\/implant interface, driven predominantly by reactive tissue responses, remains a critical limitation in the long term efficacy of bioelectric prostheses. Several research groups are investigating the incorporation of nanostructured materials as functional elements of neural prostheses as a means of providing either more effective stimulus and monitoring of electrophysiological signals, or as a structural element to locally

  10. The role of abscisic acid in plant tissue culture: a review of recent progress

    Microsoft Academic Search

    Manoj K. Rai; N. S. Shekhawat; Harish; Amit K. Gupta; M. Phulwaria; Kheta Ram; U. Jaiswal

    2011-01-01

    Abscisic acid (ABA) plays a significant role in the regulation of many physiological processes of plants. It is often used\\u000a in tissue culture systems to promote somatic embryogenesis and enhance somatic embryo quality by increasing desiccation tolerance\\u000a and preventing precocious germination. ABA is also employed to induce somatic embryos to enter a quiescent state in plant\\u000a tissue culture systems and

  11. Disease progression in iridocorneal angle tissues of BMP2-induced ocular hypertensive mice with optical coherence tomography

    PubMed Central

    Li, Guorong; Farsiu, Sina; Qiu, Jianming; Dixon, Angela; Song, Chunwei; McKinnon, Stuart J.; Yuan, Fan; Gonzalez, Pedro

    2014-01-01

    Purpose The goal of the present study was to test for the first time whether glaucomatous-like disease progression in a mouse can be assessed morphologically and functionally with spectral domain optical coherence tomography (SD-OCT). Methods We monitored progressive changes in conventional outflow tissues of living mice overexpressing human bone morphogenetic protein 2 (BMP2), a model for glaucoma. Intraocular pressure (IOP) and outflow tissue morphology/Young's modulus were followed in mice for 36 days with rebound tonometry and SD-OCT, respectively. Results were compared to standard histological methods. Outflow facility was calculated from flow measurements with direct cannulation of anterior chambers subjected to three sequential pressure steps. Results Overexpression of BMP2 significantly elevated IOP in a biphasic manner over time compared to mice that overexpressed green fluorescent protein in outflow cells and naïve controls. SD-OCT revealed changes in outflow tissues overexpressing BMP2 that corresponded with the timing of the IOP phases and decreased outflow facility. In the first phase, the angle was open, but the trabecular meshwork and the cornea were thickened. OCT detected increased trabecular meshwork stiffness after provocative IOP challenges of the BMP2 eyes, which corresponded to increased collagen deposition with transmission electron microscopy. In contrast, the angle was closed in the second phase. IOP elevation over 36 days due to BMP2 overexpression resulted in significant retinal ganglion cell and axon loss. Conclusions Although not a feasible open-angle glaucoma model, the BMP2 mice were useful for demonstrating the utility of SD-OCT in following disease progression and differentiating between two forms of ocular pathology over time that resulted in ocular hypertension. PMID:25558173

  12. Prevention of hyperglycemia in Zucker diabetic fatty rats by exercise training: effects on gene expression in insulin-sensitive tissues determined by high-density oligonucleotide microarray analysis.

    PubMed

    Colombo, Michele; Gregersen, Soeren; Kruhoeffer, Mogens; Agger, Andreas; Xiao, Jianzhong; Jeppesen, Per Bendix; Orntoft, Torben; Ploug, Thorkil; Galbo, Henrik; Hermansen, Kjeld

    2005-12-01

    Exercise training (ET) causes metabolic improvement in the prediabetic and diabetic states. However, only little information exists on the changes to ET at the transcriptional level in insulin-sensitive tissues. We have investigated the gene expression changes in skeletal muscle, liver, fat, and pancreatic islets after ET in male Zucker diabetic fatty (ZDF) rats. Eighteen ZDF rats (7 weeks old) were divided in a control and ET group. Exercise was performed using a motorized treadmill (20 m/min 1 hour daily for 6 days a week). Blood glucose, weight, and food intake were measured weekly. After 5 weeks, blood samples, soleus muscle, liver, visceral fat (epididymal fat pads), and islet tissue were collected. Gene expression was quantified with Affymetrix RG-U34A array (16 chips). Exercise training ameliorates the development of hyperglycemia and reduces plasma free fatty acid and the level of glucagon-insulin ratio (P < .05). In skeletal muscle, the expression of 302 genes increased, whereas that of 119 genes decreased. These changes involved genes related to skeletal muscle plasticity, Ca(2+) signals, energy metabolism (eg, glucose transporter 1, phosphorylase kinase), and other signaling pathways as well as genes with unknown functions (expressed sequence tags). In the liver, expression of 148 genes increased, whereas that of 199 genes decreased. These were primarily genes involved in lipogenesis and detoxification. Genes coding for transcription factors were changed in parallel in skeletal muscle and liver tissue. Training did not markedly influence the gene expression in islets. In conclusion, ET changes the expression of multiple genes in the soleus muscle and liver tissue and counteracts the development of diabetes, indicating that ET-induced changes in gene transcription may play an important role en the prevention of diabetes. PMID:16311088

  13. Paracrine and Endocrine Effects of Adipose Tissue on Cancer Development and Progression

    PubMed Central

    Park, Jiyoung; Euhus, David M.

    2011-01-01

    The past few years have provided substantial evidence for the vital role of the local tumor microenvironment for various aspects of tumor progression. With obesity and its pathophysiological sequelae still on the rise, the adipocyte is increasingly moving center stage in the context of tumor stroma-related studies. To date, we have limited insight into how the systemic metabolic changes associated with obesity and the concomitant modification of the paracrine and endocrine panel of stromal adipocyte-derived secretory products (“adipokines”) influence the incidence and progression of obesity-related cancers. Here, we discuss the role of adipocyte dysfunction associated with obesity and its potential impact on cancer biology. PMID:21642230

  14. A Cell-Regulatory Mechanism Involving Feedback between Contraction and Tissue Formation Guides Wound Healing Progression

    PubMed Central

    Valero, Clara; Javierre, Etelvina; García-Aznar, José Manuel; Gómez-Benito, María José

    2014-01-01

    Wound healing is a process driven by cells. The ability of cells to sense mechanical stimuli from the extracellular matrix that surrounds them is used to regulate the forces that cells exert on the tissue. Stresses exerted by cells play a central role in wound contraction and have been broadly modelled. Traditionally, these stresses are assumed to be dependent on variables such as the extracellular matrix and cell or collagen densities. However, we postulate that cells are able to regulate the healing process through a mechanosensing mechanism regulated by the contraction that they exert. We propose that cells adjust the contraction level to determine the tissue functions regulating all main activities, such as proliferation, differentiation and matrix production. Hence, a closed-regulatory feedback loop is proposed between contraction and tissue formation. The model consists of a system of partial differential equations that simulates the evolution of fibroblasts, myofibroblasts, collagen and a generic growth factor, as well as the deformation of the extracellular matrix. This model is able to predict the wound healing outcome without requiring the addition of phenomenological laws to describe the time-dependent contraction evolution. We have reproduced two in vivo experiments to evaluate the predictive capacity of the model, and we conclude that there is feedback between the level of cell contraction and the tissue regenerated in the wound. PMID:24681636

  15. Inflammation and adipose tissue: effects of progressive load training in rats

    Microsoft Academic Search

    Fábio S Lira; José C Rosa; Gustavo D Pimentel; Victor AF Tarini; Ricardo M Arida; Flávio Faloppa; Eduardo S Alves; Cláudia O do Nascimento; Lila M Oyama; Marília Seelaender; Marco T de Mello; Ronaldo VT Santos

    2010-01-01

    INTRODUCTION: Cytokines (IL-6, IL-10 and TNF-?) are increased after exhaustive exercise in the rat retroperitoneal (RPAT) and mesenteric adipose tissue (MEAT) pads. On the other hand, these cytokines show decreased expression in these depots in response to a chronic exercise protocol. However, the effect of exercise with overload combined with a short recovery period on pro- and anti-inflammatory cytokine expression

  16. Microarray annotation Benedikt Brors

    E-print Network

    Spang, Rainer

    - nes. #12;The relation of clone information to genes and proteins · Microarrays are produced using- ble) for proteins. Hence, there is a need to map a clone sequence ID to a protein ID. This is non-trivial. #12;The relation of clone information to genes and proteins · Microarrays are produced using

  17. Microarray Annotation Marc Zapatka

    E-print Network

    Spang, Rainer

    databases on human genes. #12;The relation of clone information to genes and proteins Microarrays of clone information to genes and proteins Microarrays are produced using information on expressed (and available) for proteins. Hence, there is a need to map a clone sequence ID to a protein ID

  18. Revisiting the immune microenvironment of diffuse large B-cell lymphoma using a tissue microarray and immunohistochemistry: robust semi-automated analysis reveals CD3 and FoxP3 as potential predictors of response to R-CHOP

    PubMed Central

    Coutinho, Rita; Clear, Andrew J.; Mazzola, Emanuele; Owen, Andrew; Greaves, Paul; Wilson, Andrew; Matthews, Janet; Lee, Abigail; Alvarez, Rute; da Silva, Maria Gomes; Cabeçadas, José; Neuberg, Donna; Calaminici, Maria; Gribben, John G.

    2015-01-01

    Gene expression studies have identified the microenvironment as a prognostic player in diffuse large B-cell lymphoma. However, there is a lack of simple immune biomarkers that can be applied in the clinical setting and could be helpful in stratifying patients. Immunohistochemistry has been used for this purpose but the results are inconsistent. We decided to reinvestigate the immune microenvironment and its impact using immunohistochemistry, with two systems of image analysis, in a large set of patients with diffuse large B-cell lymphoma. Diagnostic tissue from 309 patients was arrayed onto tissue microarrays. Results from 161 chemoimmunotherapy-treated patients were used for outcome prediction. Positive cells, percentage stained area and numbers of pixels/area were quantified and results were compared with the purpose of inferring consistency between the two semi-automated systems. Measurement cutpoints were assessed using a recursive partitioning algorithm classifying results according to survival. Kaplan-Meier estimators and Fisher exact tests were evaluated to check for significant differences between measurement classes, and for dependence between pairs of measurements, respectively. Results were validated by multivariate analysis incorporating the International Prognostic Index. The concordance between the two systems of image analysis was surprisingly high, supporting their applicability for immunohistochemistry studies. Patients with a high density of CD3 and FoxP3 by both methods had a better outcome. Automated analysis should be the preferred method for immunohistochemistry studies. Following the use of two methods of semi-automated analysis we suggest that CD3 and FoxP3 play a role in predicting response to chemoimmunotherapy in diffuse large B-cell lymphoma. PMID:25425693

  19. Revisiting the immune microenvironment of diffuse large B-cell lymphoma using a tissue microarray and immunohistochemistry: robust semi-automated analysis reveals CD3 and FoxP3 as potential predictors of response to R-CHOP.

    PubMed

    Coutinho, Rita; Clear, Andrew J; Mazzola, Emanuele; Owen, Andrew; Greaves, Paul; Wilson, Andrew; Matthews, Janet; Lee, Abigail; Alvarez, Rute; Silva, Maria Gomes da; Cabeçadas, José; Neuberg, Donna; Calaminici, Maria; Gribben, John G

    2015-03-01

    Gene expression studies have identified the microenvironment as a prognostic player in diffuse large B-cell lymphoma. However, there is a lack of simple immune biomarkers that can be applied in the clinical setting and could be helpful in stratifying patients. Immunohistochemistry has been used for this purpose but the results are inconsistent. We decided to reinvestigate the immune microenvironment and its impact using immunohistochemistry, with two systems of image analysis, in a large set of patients with diffuse large B-cell lymphoma. Diagnostic tissue from 309 patients was arrayed onto tissue microarrays. Results from 161 chemoimmunotherapy-treated patients were used for outcome prediction. Positive cells, percentage stained area and numbers of pixels/area were quantified and results were compared with the purpose of inferring consistency between the two semi-automated systems. Measurement cutpoints were assessed using a recursive partitioning algorithm classifying results according to survival. Kaplan-Meier estimators and Fisher exact tests were evaluated to check for significant differences between measurement classes, and for dependence between pairs of measurements, respectively. Results were validated by multivariate analysis incorporating the International Prognostic Index. The concordance between the two systems of image analysis was surprisingly high, supporting their applicability for immunohistochemistry studies. Patients with a high density of CD3 and FoxP3 by both methods had a better outcome. Automated analysis should be the preferred method for immunohistochemistry studies. Following the use of two methods of semi-automated analysis we suggest that CD3 and FoxP3 play a role in predicting response to chemoimmunotherapy in diffuse large B-cell lymphoma. PMID:25425693

  20. Estrogen Receptor (ER)?-regulated Lipocalin 2 Expression in Adipose Tissue Links Obesity with Breast Cancer Progression.

    PubMed

    Drew, Brian G; Hamidi, Habib; Zhou, Zhenqi; Villanueva, Claudio J; Krum, Susan A; Calkin, Anna C; Parks, Brian W; Ribas, Vicent; Kalajian, Nareg Y; Phun, Jennifer; Daraei, Pedram; Christofk, Heather R; Hewitt, Sylvia C; Korach, Kenneth S; Tontonoz, Peter; Lusis, Aldons J; Slamon, Dennis J; Hurvitz, Sara A; Hevener, Andrea L

    2015-02-27

    Obesity is associated with increased breast cancer (BrCA) incidence. Considering that inactivation of estrogen receptor (ER)? promotes obesity and metabolic dysfunction in women and female mice, understanding the mechanisms and tissue-specific sites of ER? action to combat metabolic-related disease, including BrCA, is of clinical importance. To study the role of ER? in adipose tissue we generated fat-specific ER? knock-out (FERKO) mice. Herein we show that ER? deletion increased adipocyte size, fat pad weight, and tissue expression and circulating levels of the secreted glycoprotein, lipocalin 2 (Lcn2), an adipokine previously associated with BrCA development. Chromatin immunoprecipitation and luciferase reporter studies showed that ER? binds the Lcn2 promoter to repress its expression. Because adipocytes constitute an important cell type of the breast microenvironment, we examined the impact of adipocyte ER? deletion on cancer cell behavior. Conditioned medium from ER?-null adipocytes and medium containing pure Lcn2 increased proliferation and migration of a subset of BrCA cells in culture. The proliferative and promigratory effects of ER?-deficient adipocyte-conditioned medium on BrCA cells was reversed by Lcn2 deletion. BrCA cell responsiveness to exogenous Lcn2 was heightened in cell types where endogenous Lcn2 expression was minimal, but components of the Lcn2 signaling pathway were enriched, i.e. SLC22A17 and 3-hydroxybutyrate dehydrogenase (BDH2). In breast tumor biopsies from women diagnosed with BrCA we found that BDH2 expression was positively associated with adiposity and circulating Lcn2 levels. Collectively these data suggest that reduction of ER? expression in adipose tissue promotes adiposity and is linked with the progression and severity of BrCA via increased adipocyte-specific Lcn2 production and enhanced tumor cell Lcn2 sensitivity. PMID:25468909

  1. Hidden Treasures in “Ancient” Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue

    PubMed Central

    Kerkentzes, Konstantinos; Lagani, Vincenzo; Tsamardinos, Ioannis; Vyberg, Mogens; Røe, Oluf Dimitri

    2014-01-01

    Objective: Novel statistical methods and increasingly more accurate gene annotations can transform “old” biological data into a renewed source of knowledge with potential clinical relevance. Here, we provide an in silico proof-of-concept by extracting novel information from a high-quality mRNA expression dataset, originally published in 2001, using state-of-the-art bioinformatics approaches. Methods: The dataset consists of histologically defined cases of lung adenocarcinoma (AD), squamous (SQ) cell carcinoma, small-cell lung cancer, carcinoid, metastasis (breast and colon AD), and normal lung specimens (203 samples in total). A battery of statistical tests was used for identifying differential gene expressions, diagnostic and prognostic genes, enriched gene ontologies, and signaling pathways. Results: Our results showed that gene expressions faithfully recapitulate immunohistochemical subtype markers, as chromogranin A in carcinoids, cytokeratin 5, p63 in SQ, and TTF1 in non-squamous types. Moreover, biological information with putative clinical relevance was revealed as potentially novel diagnostic genes for each subtype with specificity 93–100% (AUC?=?0.93–1.00). Cancer subtypes were characterized by (a) differential expression of treatment target genes as TYMS, HER2, and HER3 and (b) overrepresentation of treatment-related pathways like cell cycle, DNA repair, and ERBB pathways. The vascular smooth muscle contraction, leukocyte trans-endothelial migration, and actin cytoskeleton pathways were overexpressed in normal tissue. Conclusion: Reanalysis of this public dataset displayed the known biological features of lung cancer subtypes and revealed novel pathways of potentially clinical importance. The findings also support our hypothesis that even old omics data of high quality can be a source of significant biological information when appropriate bioinformatics methods are used. PMID:25325012

  2. Microarray data analysis and mining

    Microsoft Academic Search

    Marco Botta; Raffaele A. Calogero; Enrico Caserta; Alessandro Guffanti

    2008-01-01

    Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target identification. Large-scale microarray studies are also becoming crucial to a new way of conceiving experimental biology. A main issue in microarray transcription profiling is data analysis and mining. When microarrays became a methodology of general use, considerable effort

  3. Applications of Functional Protein Microarrays in Basic and Clinical Research

    PubMed Central

    Zhu, Heng; Qian, Jiang

    2013-01-01

    The protein microarray technology provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. It is viewed as a new tool that overcomes the limitation of DNA microarrays. On the basis of its application, protein microarrays fall into two major classes: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be directly spotted on a slide to form the so-called “reverse-phase” protein microarray. In the last decade, applications of functional protein microarrays in particular have flourished in studying protein function and construction of networks and pathways. In this chapter, we will review the recent advancements in the protein microarray technology, followed by presenting a series of examples to illustrate the power and versatility of protein microarrays in both basic and clinical research. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade. PMID:22989767

  4. Chromosomal Microarray versus Karyotyping for Prenatal Diagnosis

    PubMed Central

    Wapner, Ronald J.; Martin, Christa Lese; Levy, Brynn; Ballif, Blake C.; Eng, Christine M.; Zachary, Julia M.; Savage, Melissa; Platt, Lawrence D.; Saltzman, Daniel; Grobman, William A.; Klugman, Susan; Scholl, Thomas; Simpson, Joe Leigh; McCall, Kimberly; Aggarwal, Vimla S.; Bunke, Brian; Nahum, Odelia; Patel, Ankita; Lamb, Allen N.; Thom, Elizabeth A.; Beaudet, Arthur L.; Ledbetter, David H.; Shaffer, Lisa G.; Jackson, Laird

    2013-01-01

    Background Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. Methods Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. Results We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down’s syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. Conclusions In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.) PMID:23215555

  5. Microarray submissions to Experibase

    E-print Network

    Downes, Aidan Rawle

    2005-01-01

    Experibase is an experimental database that supports the storage of data from leading biological experiment techniques. Experibase ontology was extended to include a robust representation of microarray data, a leading ...

  6. DNA Microarray Technology

    SciTech Connect

    WERNER-WASHBURNE, MARGARET; DAVIDSON, GEORGE S.

    2002-01-01

    Collaboration between Sandia National Laboratories and the University of New Mexico Biology Department resulted in the capability to train students in microarray techniques and the interpretation of data from microarray experiments. These studies provide for a better understanding of the role of stationary phase and the gene regulation involved in exit from stationary phase, which may eventually have important clinical implications. Importantly, this research trained numerous students and is the basis for three new Ph.D. projects.

  7. Tissue transglutaminase as a central mediator in inflammation-induced progression of breast cancer

    PubMed Central

    2013-01-01

    TGM2 is a stress-responsive gene that encodes a multifunctional and structurally complex protein called tissue transglutaminase (abbreviated as TG2 or tTG). TGM2 expression is frequently upregulated during inflammation and wounding. Emerging evidence indicates that TGM2 expression is aberrantly upregulated in multiple cancer cell types, particularly those selected for resistance to chemotherapy and radiation therapy and those isolated from metastatic sites. It is becoming increasingly evident that chronic expression of TG2 in epithelial cancer cells initiates a complex series of signaling networks which contributes to the development of drug resistance and an invasive phenotype. For example, forced or basal high expression of TG2 in mammary epithelial cells is associated with activation of nuclear transcription factor-kappa B (NF-?B), Akt, focal adhesion kinase, and hypoxia-inducible factor. All of these changes are considered hallmarks of aggressive tumors. TG2 expression is able to induce the developmentally regulated program of epithelial-to-mesenchymal transition (EMT) and to confer cancer stem cell (CSC) traits in mammary epithelial cells; both EMT and CSCs have been implicated in cancer metastasis and resistance to standard therapies. Importantly, TG2 expression in tumor samples is associated with poor disease outcome, increased drug resistance, and increased incidence of metastasis. These observations imply that TG2 plays a crucial role in promoting an aggressive phenotype in mammary epithelial cells. In this review, we discuss recent evidence that TG2-regulated pathways contribute to the aggressive phenotype in breast cancer. PMID:23673317

  8. Sporophytic ovule tissues modulate the initiation and progression of apomixis in Hieracium.

    PubMed

    Tucker, Matthew R; Okada, Takashi; Johnson, Susan D; Takaiwa, Fumio; Koltunow, Anna M G

    2012-05-01

    Apomixis in Hieracium subgenus Pilosella initiates in ovules when sporophytic cells termed aposporous initial (AI) cells enlarge near sexual cells undergoing meiosis. AI cells displace the sexual structures and divide by mitosis to form unreduced embryo sac(s) without meiosis (apomeiosis) that initiate fertilization-independent embryo and endosperm development. In some Hieracium subgenus Pilosella species, these events are controlled by the dominant LOSS OF APOMEIOSIS (LOA) and LOSS OF PARTHENOGENESIS (LOP) loci. In H. praealtum and H. piloselloides, which both contain the same core LOA locus, the timing and frequency of AI cell formation is altered in derived mutants exhibiting abnormal funiculus growth and in transgenic plants expressing rolB which alters cellular sensitivity to auxin. The impact on apomictic and sexual reproduction was examined here when a chimeric RNAse gene was targeted to the funiculus and basal portions of the ovule, and also when polar auxin transport was inhibited during ovule development following N-1-naphthylphthalamic acid (NPA) application. Both treatments led to ovule deformity in the funiculus and distal parts of the ovule and LOA-dependent alterations in the timing, position, and frequency of AI cell formation. In the case of NPA treatment, this correlated with increased expression of DR5:GFP in the ovule, which marks the accumulation of the plant hormone auxin. Our results show that sporophytic information potentiated by funiculus growth and polar auxin transport influences ovule development, the initiation of apomixis, and the progression of embryo sac development in Hieracium. Signals associated with ovule pattern formation and auxin distribution or perception may influence the capacity of sporophytic ovule cells to respond to LOA. PMID:22378948

  9. Discovery and analysis of hepatocellular carcinoma genes using cDNA microarrays

    Microsoft Academic Search

    Yao Li; Yali Li; Rong Tang; Hong Xu; Minyan Qiu; Qin Chen; Juxiang Chen; Zhiren Fu; Kang Ying; Yi Xie; Yumin Mao

    2002-01-01

    Purpose. Microarray analysis on a genomic scale was used to profile changes in gene expression accompanying hepatocellular carcinoma. Methods. Gene expression profiles of liver tissues from twelve hepatocellular carcinoma samples relative to the gene expression profile of the normal liver tissue were analyzed using 4096 chips and 12800 chips. The results of microarray experiments were verified by the Northern blot

  10. Assessing difierential gene expression using two-component microarray mixture models

    Microsoft Academic Search

    Geofi Laslett; Phil Browny; Albert Trajstman

    Microarray experiments are today's challenge for statisticians. Already numerous formal and informal methods of analysis have been proposed, and it is unclear which are best suited. We are concerned with replicated microarray studies in which cDNA from a tissue of interest is labelled red, say, and from a control tissue is labelled green, and there are no external covariates or

  11. Microenvironmental Regulators of Tissue Structure and Function Also Regulate Tumor Induction and Progression: The Role of Extracellular Matrix and Its Degrading Enzymes

    PubMed Central

    Bissell, M.J.; Kenny, P.A.; Radisky, D.C.

    2010-01-01

    It is now widely accepted that elements of the cellular and tissue microenvironment are crucial regulators of cell behavior in culture and homeostasis in vivo, and that many of the same factors influence the course of tumor progression. Less well established is the extent to which extracellular factors actually cause cancer, and the circumstances under which this may occur. Using physiologically relevant three-dimensional culture assays and transgenic animals, we have explored how the environmental and architectural context of cells, tissues, and organs controls mammary-specific gene expression, growth regulation, apoptosis, and drug resistance and have found that loss of tissue structure is a prerequisite for cancer progression. Here we summarize this evidence and highlight two of our recent studies. Using mouse mammary epithelial cells, we show that exposure to matrix metalloproteinase-3 (MMP-3) stimulates production of reactive oxygen species (ROS) that destabilize the genome and induce epithelial-mesenchymal transition, causing malignant transformation. Using a human breast cancer progression series, we find that ADAM-dependent growth factor shedding plays a crucial role in acquisition of the malignant phenotype. These findings illustrate how normal tissue structure controls the response to extracellular signals so as to preserve tissue specificity and growth status. PMID:16869771

  12. Hybridization and Selective Release of DNA Microarrays

    SciTech Connect

    Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K

    2011-11-29

    DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.

  13. Microarrays and Stem Cells

    NSDL National Science Digital Library

    Mary Colvard

    2010-01-01

    In this activity, learners use microarray technology to determine which genes are turned on and off at various points in the differentiation of pluripotent stem cells on their way to becoming pancreatic ? cells. An introductory PowerPoint, reading, video clip and an animation provide learners with background information needed to interpret the results of a paper microarray simulation. Learners will position cDNA strips on mini-microarrays to discover which genes are expressing, to what degree they are expressing, and which are not. They use these findings to trace the differentiation of embryonic stem cells that give rise to pancreatic ? cells and other cell types. The role of growth factors and proximity of other cell types is central to learners understanding how researchers may direct the ultimate fate of stem cells. The value of this in treating diabetes is also discussed. This activity is recommended for learners studying Biology at the High School (honors, IB and AP) or Undergraduate level.

  14. Designing Microarray Experiments

    NASA Astrophysics Data System (ADS)

    Sebastiani, Paola; Milton, Jacqui; Wang, Ling

    Gene expression microarrays have become an important exploratory tool in many screening experiments that aim to discover the genes that change expression in two or more biological conditions and can be used to build molecular profiles for both diagnostic and prognostic use. The still very high costs of microarrays and the difficulty in generating the biological samples are critical issues of microarraybased screening experiments, and the experimental design plays a crucial role in how informative an experiment is going to be. In this chapter, we describe some of the major issues related to the design of either randomized control trials or observational studies and discuss the choice of powerful sample sizes, the selection of informative experimental conditions, and experimental strategies that can minimize confounding. We conclude with a discussion of some of the open problems in the design and analysis of microarray experiments that need further research.

  15. APPLICATIONS OF DNA MICROARRAYS IN BIOLOGY

    Microsoft Academic Search

    Roland B. Stoughton

    2005-01-01

    ? Abstract DNA microarrays,have enabled,biology researchers to conduct,large- scale quantitative experiments. This capacity has produced,qualitative changes,in the breadth of hypotheses,that can be explored. In what has become,the dominant,mode,of use, changes in the transcription rate of nearly all the genes in a genome, taking place in a particular tissue or cell type, can be measured in disease states, during development, and

  16. Paradoxical effects of human adipose tissue-derived mesenchymal stem cells on progression of experimental arthritis in SKG mice.

    PubMed

    Kim, Jin-Hee; Lee, Yong Taek; Oh, Keunhee; Cho, Jaejin; Lee, Dong-Sup; Hwang, Young-il

    2014-01-01

    We evaluated the therapeutic effect of human adipose tissue-derived mesenchymal stem cells (hAd-MSCs) in a SKG arthritis model, a relevant animal model for human rheumatoid arthritis. hAd-MSCs were administered intraperitoneally into the mice for five consecutive days from on day 12 or 34 after arthritis induction, when the average clinical score was 0.5 or 5, respectively. They remarkably suppressed arthritis when administered on day 12. Disease suppression was correlated with reduction of pro-inflammatory cytokines and with increased levels of TGF-? and IL-10 from splenocytes. However, when hAd-MSCs were administered on day 34, the clinical scores were not improved, the histopathological scores were aggravated, and cytokine profiles were differed. Thus, hAd-MSCs showed paradoxical effects, according to the disease phase when they were administered. These suggest that the same cells acted differently depending on the disease progress, and cautions should be paid for safe and effective use of MSCs. PMID:25460084

  17. DNA Microarray Learning Module

    NSDL National Science Digital Library

    The Southwest Center for Microsystems Education is a Regional Advanced Technology Education Center funded in part by the National Science Foundation. This learning module introduces users to DNA microarrays, including how they are used in biomedical applications as well as how they are fabricated and interpreted. The unit also allows students the opportunity to discuss the ethics of such devices. A comprehensive PowerPoint presentation is included along with instructor and participant guides and a Zip file with DNA microarray animations. Visitors are encouraged to create an account and log in in order to access the full set of resources.

  18. Macromodel of Microarray

    NSDL National Science Digital Library

    Molly Malone

    2004-01-01

    This is an educator-led demonstration of microarray technology using a model created from a pizza box and ping-pong balls. This “macroarray” model demonstrates how single-stranded DNA segments affixed to a solid support are used to separate and identify DNA segments in a solution.

  19. Application of microarrays for DNA methylation profiling.

    PubMed

    Schumacher, Axel; Weinhäusl, Andreas; Petronis, Arturas

    2008-01-01

    Comprehensive analyses of the human epigenome may be of critical importance in understanding the molecular mechanisms of complex diseases, development, aging, tissue specificity, parental origin effects, and sex differences, among other systemic aspects of human biology. However, traditional DNA methylation methods allowed for screening of only relatively short DNA fragments. The advent of microarrays has provided new possibilities in DNA methylation analysis, because this technology is able to interrogate a very large number of loci in a highly parallel fashion. There are several permutations of the microarray application in DNA methylation profiling, and such include microarray analysis of bisulfite modified DNA and also the enriched unmethylated or hypermethylated DNA fractions using methylation-sensitive restriction enzymes or antibodies against methylated cytosines. The method described in detail here is based on the analysis of the enriched unmethylated DNA fraction, using a series of treatments with methylation-sensitive restriction enzymes, adaptor ligation, PCR amplification, and quantitative mapping of unmethylated DNA sequences using microarrays. The key advantages of this approach are the ability to investigate DNA methylation patterns using very small DNA amounts and relatively high informativeness in comparison to the other restriction-enzyme- based strategies for DNA methylation profiling [1]. PMID:18370099

  20. Fabrication and use of microenvironment microarrays (MEArrays).

    PubMed

    Lin, Chun-Han; Lee, Jonathan K; LaBarge, Mark A

    2012-01-01

    The interactions between cells and their surrounding microenvironment have functional consequences for cellular behaviour. On the single cell level, distinct microenvironments can impose differentiation, migration, and proliferation phenotypes, and on the tissue level the microenvironment processes as complex as morphogenesis and tumorigenesis(1). Not only do the cell and molecular contents of microenvironments impact the cells within, but so do the elasticity(2) and geometry(3) of the tissue. Defined as the sum total of cell-cell, -ECM, and -soluble factor interactions, in addition to physical characteristics, the microenvironment is complex. The phenotypes of cells within a tissue are partially due to their genomic content and partially due to the combinatorial interactions with the microenviroment. A major challenge is to link specific combinations of microenvironmental components with distinctive behaviours. Here, we present the microenvironment microarray (MEArray) platform for cell-based functional screening of interactions with combinatorial microenvironments(4). The method allows for simultaneous control of the molecular composition and the elastic modulus, and combines the use of widely available microarray and micropatterning technologies. MEArray screens require as few as 10,000 cells per array, which facilitates functional studies of rare cell types such as adult progenitor cells. A limitation of the technology is that entire tissue microenvironments cannot be completely recapitulated on MEArrays. However, comparison of responses in the same cell type to numerous related microenvironments, for instance pairwise combinations of ECM proteins that characterize a given tissue, will provide insights into how microenvironmental components elicit tissue-specific functional phenotypes. MEArrays can be printed using a wide variety of recombinant growth factors, cytokines, and purified ECM proteins, and combinations thereof. The platform is limited only by the availability of specific reagents. MEArrays are amenable to time-lapsed analysis, but most often are used for end point analyses of cellular functions that are measureable with fluorescent probes. For instance, DNA synthesis, apoptosis, acquisition of differentiated states, or production of specific gene products are commonly measured. Briefly, the basic flow of an MEArray experiment is to prepare slides coated with printing substrata and to prepare the master plate of proteins that are to be printed. Then the arrays are printed with a microarray robot, cells are allowed to attach, grow in culture, and then are chemically fixed upon reaching the experimental endpoint. Fluorescent or colorimetric assays, imaged with traditional microscopes or microarray scanners, are used to reveal relevant molecular and cellular phenotypes (Figure 1). PMID:23093325

  1. Muscling in on microarrays.

    PubMed

    Virtanen, Carl; Takahashi, Mark

    2008-02-01

    Adaptations that are the result of exercise require a multitude of changes at the level of gene expression. The mechanisms involved in regulating these changes are many, and can occur at various points in the pathways that affect gene expression. The completion of the human genome sequence, along with the genomes of related species, has provided an enormous amount of information to help dissect and understand these pathways. High-throughput methods, such as DNA microarrays, were the first on the scene to take advantage of this wealth of information. A new generation of microarrays has now taken the next step in revealing the mechanisms controlling gene expression. Analysis of the regulation of gene expression can now be profiled in a high-throughput fashion. However, the application of this technology has yet to be fully realized in the exercise physiology community. This review will highlight some of the latest advances in microarrays and briefly discuss some potential applications to the field of exercise physiology. PMID:18347662

  2. Pancreatic Tissue Microarray (TMA) - SEER Residual Tissue Repository Program

    Cancer.gov

    SEER is an authoritative source of information on cancer incidence and survival in the United States. SEER currently collects and publishes cancer incidence and survival data from population-based cancer registries covering approximately 28 percent of the U.S. population.

  3. Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray

    Microsoft Academic Search

    A. Avila-Fernandez; D. Cantalapiedra; E. Aller; E. Vallespin; J. Aguirre-Lamban; F. Blanco-Kelly; M. Corton; R. Riveiro-Alvarez; R. Allikmets; M. J. Trujillo-Tiebas; J. M. Millan; F. P. M. Cremers; C. Ayuso

    2010-01-01

    PURPOSE: Retinitis pigmentosa (RP) is a genetically heterogeneous disorder characterized by progressive loss of vision. The aim of this study was to identify the causative mutations in 272 Spanish families using a genotyping microarray. METHODS: 272 unrelated Spanish families, 107 with autosomal recessive RP (arRP) and 165 with sporadic RP (sRP), were studied using the APEX genotyping microarray. The families

  4. Agilent Microarray Grant Program The Agilent Microarray Grant Program is designed to promote increased awareness of the Agilent Microarray

    E-print Network

    Richardson, David

    1 Agilent Microarray Grant Program The Agilent Microarray Grant Program is designed to promote increased awareness of the Agilent Microarray services offered through the Duke IGSP Microarray Core Facility and to help seed promising new integrated genomics projects. Use Agilent microarrays in your

  5. Application and optimization of microarray technologies for human postmortem brain studies

    Microsoft Academic Search

    Margaret M Ryan; Stephen J Huffaker; Maree J Webster; Matt Wayland; Tom Freeman; Sabine Bahn

    2004-01-01

    A number of microarray investigations using human postmortem brain tissue have been published recently, exploring a multitude of human brain disorders with the aim of unraveling the underlying pathologies. Although the technology is still developing and lacks sufficient sensitivity with regard to detecting splice variants and low abundance transcripts, microarrays are becoming the prominent method for candidate gene screening in

  6. Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology

    Microsoft Academic Search

    Johan Lindberg; Erik af Klint; Ann-Kristin Ulfgren; André Stark; Tove Andersson; Peter Nilsson; Lars Klareskog; Joakim Lundeberg

    2006-01-01

    In recent years microarray technology has been used increasingly to acquire knowledge about the pathogenic processes involved in rheumatoid arthritis. The present study investigated variations in gene expression in synovial tissues within and between patients with rheumatoid arthritis. This was done by applying microarray technology on multiple synovial biopsies obtained from the same knee joints. In this way the relative

  7. MICROARRAY ANALYSIS IDENTIFIES GENES INVOLVED IN CROWN BUD DORMANCY IN LEAFY SPURGE (EUPHORBIA ESULA L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leafy spurge is a perennial rangeland weed that has become a model for weed genomics and cross-species research. Microarray analysis allows the simultaneous characterization of the expression from thousands of different genes from any given sampled tissue. We have used microarray analysis to follow ...

  8. Surface chemistries for antibody microarrays

    SciTech Connect

    Seurynck-Servoss, Shannon L.; Baird, Cheryl L.; Rodland, Karin D.; Zangar, Richard C.

    2007-05-01

    Enzyme-linked immunosorbent assay (ELISA) microarrays promise to be a powerful tool for the detection of disease biomarkers. The original technology for printing ELISA microarray chips and capturing antibodies on slides was derived from the DNA microarray field. However, due to the need to maintain antibody structure and function when immobilized, surface chemistries used for DNA microarrays are not always appropriate for ELISA microarrays. In order to identify better surface chemistries for antibody capture, a number of commercial companies and academic research groups have developed new slide types that could improve antibody function in microarray applications. In this review we compare and contrast the commercially available slide chemistries, as well as highlight some promising recent advances in the field.

  9. Disc-based immunoassay microarrays

    Microsoft Academic Search

    Horacio Kido; Angel Maquieira; Bruce D. Hammock

    2000-01-01

    Microarray technology as applied to areas that include genomics, diagnostics, environmental, and drug discovery, is an interesting research topic for which different chip-based devices have been developed. As an alternative, we have explored the principle of compact disc-based microarrays. This new methodology successfully combined high-density microarrays applied via a piezoelectric inkjet applicator with circular indexing on a polycarbonate disc. As

  10. Magnetic Analysis of Post-mortem Hippocampal Tissue from Alzheimer's Patients: Changes with Progression of the Disease

    Microsoft Academic Search

    M. Fuller; P. Zinin; J. Favia; L. Tatsumi; G. Kletetschka; T. Adachi

    2007-01-01

    Increases of iron in the human brain with age have been observed and may be accompanied by the development of neurodegenerative diseases, such as Alzheimer's. We have measured the magnetic characteristics of several sets of slides of hippocampal tissue from deceased Alzheimer patients. The slides were made available by the Harvard Brain Bank. The pathology of the tissue was classified

  11. Differentiated miRNA expression and validation of signaling pathways in apoE gene knockout mice by cross-verification microarray platform

    PubMed Central

    Han, Hui; Wang, Yu-Hong; Qu, Guang-Jin; Sun, Ting-Ting; Li, Feng-Qing; Jiang, Wei; Luo, Shan-Shun

    2013-01-01

    The microRNA (miRNA) regulation mechanisms associated with atherosclerosis are largely undocumented. Specific selection and efficient validation of miRNA regulation pathways involved in atherosclerosis development may be better assessed by contemporary microarray platforms applying cross-verification methodology. A screening platform was established using both miRNA and genomic microarrays. Microarray analysis was then simultaneously performed on pooled atherosclerotic aortic tissues from 10 Apolipoprotein E (apoE) knockout mice (apoE?/?) and 10 healthy C57BL/6 (B6) mice. Differentiated miRNAs were screened and cross-verified against an mRNA screen database to explore integrative mRNA–miRNA regulation. Gene set enrichment analysis was conducted to describe the potential pathways regulated by these mRNA–miRNA interactions. High-throughput data analysis of miRNA and genomic microarrays of knockout and healthy control mice revealed 75 differentially expressed miRNAs in apoE?/? mice at a threshold value of 2. The six miRNAs with the greatest differentiation expression were confirmed by real-time quantitative reverse-transcription PCR (qRT–PCR) in atherosclerotic tissues. Significantly enriched pathways, such as the type 2 diabetes mellitus pathway, were observed by a gene-set enrichment analysis. The enriched molecular pathways were confirmed through qRT–PCR evaluation by observing the presence of suppressor of cytokine signaling 3 (SOCS3) and SOCS3-related miRNAs, miR-30a, miR-30e and miR-19b. Cross-verified high-throughput microarrays are optimally accurate and effective screening methods for miRNA regulation profiles associated with atherosclerosis. The identified SOCS3 pathway is a potentially valuable target for future development of targeted miRNA therapies to control atherosclerosis development and progression. PMID:23470715

  12. Microarrays in primary breast cancer - lessons from chemotherapy studies

    Microsoft Academic Search

    P E Lønning; C M Perou; P O Brown; D Botstein

    2001-01-01

    Current development in molecular techniques has extended the opportunities to explore genetic alterations in malignant tissue. There is a need to improve prognostication and, in particular, to understand the mechanisms of treatment resistance in different tumours. Gene analyses by microarrays allow concomitant analyses of several genes in concert, providing new opportunities for tumour classification and understanding of key biological disturbances.

  13. Validation of the Swine Protein-Annotated Oligonucleotide Microarray

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The specificity and utility of the Swine Protein-Annotated Oligonucleotide Microarray, or Pigoligoarray (www.pigoligoarray.org), has been evaluated by profiling the expression of transcripts from four porcine tissues. Tools for comparative analyses of expression on the Pigoligoarray were developed i...

  14. Three-dimensional lithographically-defined organotypic tissue arrays for quantitative analysis of morphogenesis and neoplastic progression

    SciTech Connect

    Nelson, Celeste M.; Inman, Jamie L.; Bissell, Mina J.

    2008-02-13

    Here we describe a simple micromolding method to construct three-dimensional arrays of organotypic epithelial tissue structures that approximate in vivo histology. An elastomeric stamp containing an array of posts of defined geometry and spacing is used to mold microscale cavities into the surface of type I collagen gels. Epithelial cells are seeded into the cavities and covered with a second layer of collagen. The cells reorganize into hollow tissues corresponding to the geometry of the cavities. Patterned tissue arrays can be produced in 3-4 h and will undergo morphogenesis over the following one to three days. The protocol can easily be adapted to study a variety of tissues and aspects of normal and neoplastic development.

  15. Full Genome Microarrays Data Analysis

    E-print Network

    Campbell, A. Malcolm

    Microarray Protocols ¸ Produce Public Domain Microarray Analysis Software ¸ Create High Success Rate RNA-Free Methods ¸ Create Virtual Community of Teachers ¸ Share Lessons, Protocols, Advice ¸ Assess Learning for undergraduates MAGIC Tool finds the spots, quantifies the signals, and allows the users to choose from many

  16. Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles

    E-print Network

    Domany, Eytan

    , growth, and metastasis. DNA microarray human cancers normal human tissues tissue-selective gene genes are overexpressed in cancer. Using DNA microarray and cluster analysis of gene-expression data, we to different types of human solid cancers, we have now analyzed DNA microarray data obtained from 566 samples

  17. Imaging the morphological change of tissue structure during the early phase of esophageal tumor progression using multiphoton microscopy

    NASA Astrophysics Data System (ADS)

    Xu, Jian; Kang, Deyong; Xu, Meifang; Zhu, Xiaoqin; Zhuo, Shuangmu; Chen, Jianxin

    2012-12-01

    Esophageal cancer is a common malignancy with a very poor prognosis. Successful strategies for primary prevention and early detection are critically needed to control this disease. Multiphoton microscopy (MPM) is becoming a novel optical tool of choice for imaging tissue architecture and cellular morphology by two-photon excited fluorescence. In this study, we used MPM to image microstructure of human normal esophagus, carcinoma in situ (CIS), and early invasive carcinoma in order to establish the morphological features to differentiate these tissues. The diagnostic features such as the appearance of cancerous cells, the significant loss of stroma, the absence of the basement membrane were extracted to distinguish between normal and cancerous esophagus tissue. These results correlated well with the paired histological findings. With the advancement of clinically miniaturized MPM and the multi-photon probe, combining MPM with standard endoscopy will therefore allow us to make a real-time in vivo diagnosis of early esophageal cancer at the cellular level.

  18. Development of a Highly Sensitive Glycan Microarray for Quantifying AFP-L3 for Early Prediction of Hepatitis B Virus–Related Hepatocellular Carcinoma

    PubMed Central

    Chou, Ruey-Hwang; Yen, Chia-Jui; Huang, Wei-Chien; Wu, Chung-Yi; Yu, Yung-Luen

    2014-01-01

    The ?-fetoprotein fraction L3 (AFP-L3), which is synthesized by malignant cells and incorporates a fucosylated oligosaccharide, has been investigated as a diagnostic and prognostic marker for hepatocellular carcinoma (HCC). Quantification of AFP-L3 by conventional enzyme-linked immunosorbent assay (ELISA) has not always produced reliable results for serum samples with low AFP, and thus we evaluated the clinical utility of quantifying AFP-L3 using a new and highly sensitive glycan microarray assay. Sera from 9 patients with chronic hepatitis B and 32 patients with hepatitis B virus (HBV)-related HCC were tested for AFP-L3 level using the glycan microarray. Additionally, we compared receiver operator characteristic curves for the ELISA and glycan microarray methods for determination of the AFP-L3: AFP-L1 ratio in patient samples. This ratio was calculated for 8 HCC patients who underwent transarterial embolization therapy pre- or post-treatment with AFP-L3. Glycan microarrays showed that the AFP-L3 ratio of HBV-related HCC patients was significantly higher than that measured for chronic hepatitis B patients. Overall parameters for estimating AFP-L3% in HCC samples were as follows: sensitivity, 53.13%; specificity, 88.89%; and area under the curve, 0.75. The elevated AFP-L3% in the 8 patients with HBV-related HCC was strongly associated with HCC progression. Following one month of transarterial embolization therapy, the relative mean AFP-L3% decreased significantly. In addition, we compared Fut8 gene expression between paired tumor and non-tumor tissues from 24 patients with HBV-related HCC. The Fut8 mRNA expression was significantly increased in tumorous tissues in these patients than that in non-tumor tissue controls. Higher expression of Fut8 mRNA in tumorous tissues in these patients was associated with poor differentiation than well and moderate differentiation. Our results describe a new glycan microarray for the sensitive and rapid quantification of fucosylated AFP; this method is potentially applicable to screening changes in AFP-L3 level for assessment of HCC progression. PMID:24927126

  19. Ultrahigh density microarrays of

    E-print Network

    Cai, Long

    pathology laboratory equipment was used to generate a CEMA array containing 11,928 individual formalin-fixed, paraf- fin-embedded liver and kidney tissue features within the unfrosted area of a standard pathology are taken from the face of the specimen blocks, trimmed into plates and bonded into tissue stacks. Second

  20. Microarray methods for protein biomarker detection

    PubMed Central

    Lee, Hye Jin; Wark, Alastair W.; Corn, Robert M.

    2009-01-01

    The application of protein biomarkers as an aid for the detection and treatment of diseases has been subject to intensified interest in recent years. The quantitative assaying of protein biomarkers in easily obtainable biological fluids such as serum and urine offers the opportunity to improve patient care via earlier and more accurate diagnoses in a convenient, non-invasive manner as well as providing a potential route towards more individually targeted treatment. Essential to achieving progress in biomarker technology is the ability to screen large numbers of proteins simultaneously in a single experiment with high sensitivity and selectivity. In this article, we highlight recent progress in the use of microarrays for high-throughput biomarker profiling and discuss some of the challenges associated with these efforts. PMID:18645635

  1. The bioinformatics of microarrays to study cancer: Advantages and disadvantages

    NASA Astrophysics Data System (ADS)

    Rodríguez-Segura, M. A.; Godina-Nava, J. J.; Villa-Treviño, S.

    2012-10-01

    Microarrays are devices designed to analyze simultaneous expression of thousands of genes. However, the process will adds noise into the information at each stage of the study. To analyze these thousands of data is necessary to use bioinformatics tools. The traditional analysis begins by normalizing data, but the obtained results are highly dependent on how it is conducted the study. It is shown the need to develop new strategies to analyze microarray. Liver tissue taken from an animal model in which is chemically induced cancer is used as an example.

  2. Discovering patterns in microarray data.

    PubMed

    Burke, H B

    2000-12-01

    The human genome is a complex system characterized by gene interactions and nonlinear behaviors. Complex systems cannot be viewed as the aggregate of their isolated pieces but must be studied as an integrated whole. Microarray technologies offer the opportunity to see the entire biological system as it existed at one moment in time. It is tempting to try to analyze the entire microarray at once to immediately discover the pattern being sought, for example, the pattern of a breast cancer. However, such an analysis would be a mistake because microarrays provide massively parallel information, the analysis of which is a nondeterministic polynomial time (NP)-hard problem. Current statistical methods are not sufficiently powerful to solve this NP-hard problem. The best approach to microarray analysis is to begin with a small number of the elements in the microarray known to be a pattern and ask questions of the other elements in the microarray; i.e., perform instantaneous scientific experiments regarding whether each of the other elements in the microarray are related to the known pattern. PMID:11172499

  3. Pro-oncogene Pokemon promotes breast cancer progression by upregulating survivin expression

    Microsoft Academic Search

    Xuyu Zu; Jun Ma; Hongxia Liu; Feng Liu; Chunyan Tan; Lingling Yu; Jue Wang; Zhenhua Xie; Deliang Cao; Yuyang Jiang

    2011-01-01

    Introduction  Pokemon is an oncogenic transcription factor involved in cell growth, differentiation and oncogenesis, but little is known\\u000a about its role in human breast cancer. In this study, we aimed to reveal the role of Pokemon in breast cancer progression\\u000a and patient survival and to understand its underlying mechanisms.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  Tissue microarray analysis of breast cancer tissues from patients with complete clinicopathological

  4. Applications of Bayesian statistical methods in microarray data analysis.

    PubMed

    Yang, Dongyan; Zakharkin, Stanislav O; Page, Grier P; Brand, Jacob P L; Edwards, Jode W; Bartolucci, Alfred A; Allison, David B

    2004-01-01

    Microarray technology allows one to measure gene expression levels simultaneously on the whole-genome scale. The rapid progress generates both a great wealth of information and challenges in making inferences from such massive data sets. Bayesian statistical modeling offers an alternative approach to frequentist methodologies, and has several features that make these methods advantageous for the analysis of microarray data. These include the incorporation of prior information, flexible exploration of arbitrarily complex hypotheses, easy inclusion of nuisance parameters, and relatively well developed methods to handle missing data. Recent developments in Bayesian methodology generated a variety of techniques for the identification of differentially expressed genes, finding genes with similar expression profiles, and uncovering underlying gene regulatory networks. Bayesian methods will undoubtedly become more common in the future because of their great utility in microarray analysis. PMID:14987122

  5. Genomic microarray analysis on formalin-fixed paraffin-embedded material for uveal melanoma prognostication.

    PubMed

    Minca, Eugen C; Tubbs, Raymond R; Portier, Bryce P; Wang, Zhen; Lanigan, Christopher; Aronow, Mary E; Triozzi, Pierre L; Singh, Arun; Cook, James R; Saunthararajah, Yogen; Plesec, Thomas P; Schoenfield, Lynn; Cawich, Victoria; Sulpizio, Scott; Schultz, Roger A

    2014-01-01

    Cytogenetic alterations are strong outcome prognosticators in uveal melanoma (UVM). Monosomy 3 (-3) and MYC amplification at 8q24 are commonly tested by fluorescence in situ hybridization (FISH). Alternatively, microarray analysis provides whole genome data, detecting partial chromosome loss, loss of heterozygosity (LOH), or abnormalities unrepresented by FISH probes. Nonfixed frozen tissue is conventionally used for microarray analysis but may not always be available. We assessed the feasibility of genomic microarray analysis for high resolution interrogation of UVM using formalin-fixed paraffin-embedded tissue (FFPET) as an alternative to frozen tissue (FZT). Enucleations from 44 patients (clinical trial NCT00952939) yielded sufficient DNA from FFPET (n = 34) and/or frozen tissue (n = 41) for comparative genomic hybridization and select single nucleotide polymorphism analysis (CGH/SNP) on Roche-NimbleGen OncoChip arrays. CEP3 FISH analysis was performed on matched cytology ThinPrep material. CGH/SNP analysis was successful in 30 of 34 FFPET and 41 of 41 FZT samples. Of 27 paired FFPET/FZT samples, 26 (96.3%) were concordant for at least four of six major recurrent abnormalities (-3, +8q, -1p, +6p, -6q, -8p), and 25 of 27 (92.6%) were concordant for -3. Results of CGH/SNP were concordant with the CEP3 FISH results in 27 of 30 (90%) FFPET and 38 of 41 (92.6%) FZT cases; partial -3q was detected in two CEP3 FISH-negative cases and whole chromosome 3, 4, and 6 SNP-LOH in one case. CGH detection of -3, +8q, -8p on FFPET and FZT showed significant correlation with the clinical outcome measures (metastasis development, time to progression, survival). Results of the UVM genotyping by CGH/SNP on FFPET are highly concordant with those of the FZT analysis and with those of the CEP3 FISH analysis, and therefore CGH/SNP is a practical method for UVM prognostication. Genome-wide coverage provides additional data with potential relevance to UVM biology, diagnosis, and prognosis. PMID:25442074

  6. Medical image computing and computer-aided medical interventions applied to soft tissues. Work in progress in urology

    E-print Network

    Troccaz, Jocelyne; Berkelman, Peter; Cinquin, Philippe; Daanen, Vincent; Leroy, Antoine; Marchal, Maud; Payan, Yohan; Promayon, Emmanuel; Voros, Sandrine; Bart, Stéphane; Bolla, Michel; Chartier-Kastler, Emmanuel; Descotes, Jean-Luc; Dusserre, Andrée; Giraud, Jean-Yves; Long, Jean-Alexandre; Moalic, Ronan; Mozer, Pierre

    2006-01-01

    Until recently, Computer-Aided Medical Interventions (CAMI) and Medical Robotics have focused on rigid and non deformable anatomical structures. Nowadays, special attention is paid to soft tissues, raising complex issues due to their mobility and deformation. Mini-invasive digestive surgery was probably one of the first fields where soft tissues were handled through the development of simulators, tracking of anatomical structures and specific assistance robots. However, other clinical domains, for instance urology, are concerned. Indeed, laparoscopic surgery, new tumour destruction techniques (e.g. HIFU, radiofrequency, or cryoablation), increasingly early detection of cancer, and use of interventional and diagnostic imaging modalities, recently opened new challenges to the urologist and scientists involved in CAMI. This resulted in the last five years in a very significant increase of research and developments of computer-aided urology systems. In this paper, we propose a description of the main problems rel...

  7. Exploration and Analysis of DNA Microarray Data

    E-print Network

    Cabrera, Javier

    1 Exploration and Analysis of DNA Microarray Data Dhammika Amaratunga Senior Research Fellow and toxicity mechanisms medical diagnostics and prognostics #12;7 DNA microarrays DNA microarray technology is one of the most promising tools for obtaining gene expression data. A DNA microarray is a tiny glass

  8. Noninvasive near-infrared fluorescent protein-based imaging of tumor progression and metastases in deep organs and intraosseous tissues

    NASA Astrophysics Data System (ADS)

    Jiguet-Jiglaire, Carine; Cayol, Mylène; Mathieu, Sylvie; Jeanneau, Charlotte; Bouvier-Labit, Corinne; Ouafik, L.'houcine; El-Battari, Assou

    2014-01-01

    Whole-body imaging of experimental tumor growth is more feasible within the near-infrared (NIR) optical window because of the highest transparency of mammalian tissues within this wavelength spectrum, mainly due to improved tissue penetration and lower autofluorescence. We took advantage from the recently cloned infrared fluorescent protein (iRFP) together with a human immunodeficiency virus (HIV)-based lentiviral vector to produce virally transduced tumor cells that permanently express this protein. We then noninvasively explored metastatic spread as well as primary tumor growth in deep organs and behind bone barriers. Intrabone tumor growth was investigated through intracranial and intratibial injections of glioblastoma and osteosarcoma cells, respectively, and metastasis was assessed by tail vein injection of melanoma cells. We found that the emitted fluorescence is captured as sharp images regardless of the organ or tissue considered. Furthermore, by overlaying fluorescence spots with the white light, it was possible to afford whole-body images yet never observed before. This approach allowed us to continuously monitor the growth and dissemination of tumor cells with a small number of animals, minimal animal handling, and without the need for any additive. This iRFP-based system provides high-resolution readouts of tumorigenesis that should greatly facilitate preclinical trials with anticancer therapeutic molecules.

  9. Extracellular Matrix, Nuclear and Chromatin Structure and GeneExpression in Normal Tissues and Malignant Tumors: A Work inProgress

    SciTech Connect

    Spencer, Virginia A.; Xu, Ren; Bissell, Mina J.

    2006-08-01

    Almost three decades ago, we presented a model where theextracellular matrix (ECM) was postulated to influence gene expressionand tissue-specificity through the action of ECM receptors and thecytoskeleton. This hypothesis implied that ECM molecules could signal tothe nucleus and that the unit of function in higher organisms was not thecell alone, but the cell plus its microenvironment. We now know that ECMinvokes changes in tissue and organ architecture and that tissue, cell,nuclear, and chromatin structure are changed profoundly as a result ofand during malignant progression. Whereas some evidence has beengenerated for a link between ECM-induced alterations in tissuearchitecture and changes in both nuclear and chromatin organization, themanner by which these changes actively induce or repress gene expressionin normal and malignant cells is a topic in need of further attention.Here, we will discuss some key findings that may provide insights intomechanisms through which ECM could influence gene transcription and howtumor cells acquire the ability to overcome these levels ofcontrol.

  10. Raman microprobe investigation of molecular structure and organization in the native state of woody tissue. Progress report, April 1, 1987--July 31, 1989

    SciTech Connect

    Atalla, R.H.

    1989-08-01

    Although the primary emphasis of our program has remained with the application of Raman spectroscopy to the study of native tissue, the scope of the work has been expanded to include a number of complementary approaches. These have included Solid State 13C NMR, autoradiography of radiolabeled woody tissue sections, and the generation of biomimetic tertiary aggregates which simulate states of aggregation characteristic of cell walls. Our Raman spectroscopic studies have resulted in progress in the areas of interpretation of the spectral features, and confirmation of the variability of the patterns of orientation of lignin reported earlier. We have assembled and made operational our new microprobe and spectrometer systems acquired under the DOE-URIP program. We have also demonstrated that, operating with gated detection and pulsed laser excitation, we can discriminate against the laser-excited fluorescence characteristic of most woody tissue. Our studies of celluloses, which combine Raman spectroscopy and 13C NMR have shown that all native celluloses are composites of two forms which have the same secondary structure but different tertiary structures.

  11. Microarray Analysis of Microbial Weathering

    NASA Astrophysics Data System (ADS)

    Olsson-Francis, K.; van Houdt, R.; Leys, N.; Mergeay, M.; Cockell, C. S.

    2010-04-01

    Microarray analysis of the heavy metal resistant bacterium, Cupriavidus metallidurans CH34 was used to investigate the genes involved in the weathering. The results demonstrated that large porin and membrane transporter genes were unregulated.

  12. Can Zipf's law be adapted to normalize microarrays?

    PubMed Central

    Lu, Tim; Costello, Christine M; Croucher, Peter JP; Häsler, Robert; Deuschl, Günther; Schreiber, Stefan

    2005-01-01

    Background Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented. Results Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques. Conclusion Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays). PMID:15727680

  13. Genomewide histone acetylation microarrays.

    PubMed

    Robyr, Daniel; Grunstein, Michael

    2003-09-01

    Histone acetylation and methylation are important regulators of gene activity. Chromatin immunoprecipitation (ChIP or ChrIP) has made it possible to examine not only the state of histone acetylation at a gene but also that of histone methylation and may soon be extended to other histone modifications such as phosphorylation and ubiquitination. In principle such studies are possible as long as an antibody is available to the particular histone modification. Once a target gene is identified it is instructive to see the effect of mutating putative enzymes responsible for the modification to determine how a particular enzyme is responsible for altering chromatin of that gene. Although specific target genes have been studied that contain such modifications recent technical advances have made it possible to study histone modifications genomewide. This not only allows for alternate views of particular paradigms to be investigated, but also uncovers chromosomal patterns of histone modification that would be missed in analyzing individual genes. We describe here an approach to rapidly study histone modifications genomewide by combining chromatin immunoprecipitation and DNA microarrays. PMID:12893177

  14. Transurethral resection of prostate: technical progress and clinical experience using the bipolar Gyrus plasmakinetic tissue management system

    Microsoft Academic Search

    Gianni Martis; Antonio Cardi; Diana Massimo; Maurizio Ombres; Bruno Mastrangeli

    2008-01-01

    Background  The efficacy and safety of a new transurethral endoscopic device using bipolar electrocautery, the Gyrus system, were evaluated.\\u000a This system permits rapid prostate tissue removal by endoscopic vaporization with little bleeding using saline irrigation,\\u000a therefore eliminating transurethral resection of the prostate (TURP) syndrome.\\u000a \\u000a \\u000a \\u000a Methods  Between January 2000 and December 2006 a total of 401 patients with benign prostatic hyperplasia underwent transurethral

  15. Tissue injury and hypoxia promote malignant progression of prostate cancer by inducing CXCL13 expression in tumor myofibroblasts

    PubMed Central

    Ammirante, Massimo; Shalapour, Shabnam; Kang, Youngjin; Jamieson, Christina A. M.; Karin, Michael

    2014-01-01

    Prostate cancer (PC) is a slowly progressing malignancy that often responds to androgen ablation or chemotherapy by becoming more aggressive, acquiring a neuroendocrine phenotype, and undergoing metastatic spread. We found that B lymphocytes recruited into regressing androgen-deprived tumors by C-X-C motif chemokine 13 (CXCL13), a chemokine whose expression correlates with clinical severity, play an important role in malignant progression and metastatic dissemination of PC. We now describe how androgen ablation induces CXCL13 expression. In both allografted and spontaneous mouse PC, CXCL13 is expressed by tumor-associated myofibroblasts that are activated on androgen ablation through a hypoxia-dependent mechanism. The same cells produce CXCL13 after chemotherapy. Myofibroblast activation and CXCL13 expression also occur in the normal prostate after androgen deprivation, and CXCL13 is expressed by myofibroblasts in human PC. Hypoxia activates hypoxia-inducible factor 1 (HIF-1) and induces autocrine TGF-? signaling that promotes myofibroblast activation and CXCL13 induction. In addition to TGF-? receptor kinase inhibitors, myofibroblast activation and CXCL13 induction are blocked by phosphodiesterase 5 (PDE5) inhibitors. Both inhibitor types and myofibroblast immunodepletion block the emergence of castration-resistant PC in the transgenic adenocarcinoma of the mouse prostate (TRAMP) model of spontaneous metastatic PC with neuroendocrine differentiation. PMID:25267627

  16. Rapid Spoligotyping of Mycobacterium tuberculosis Complex Bacteria by Use of a Microarray System with Automatic Data Processing and Assignment

    PubMed Central

    Ruettger, Anke; Nieter, Johanna; Skrypnyk, Artem; Engelmann, Ines; Ziegler, Albrecht; Moser, Irmgard; Monecke, Stefan; Ehricht, Ralf

    2012-01-01

    Membrane-based spoligotyping has been converted to DNA microarray format to qualify it for high-throughput testing. We have shown the assay's validity and suitability for direct typing from tissue and detecting new spoligotypes. Advantages of the microarray methodology include rapidity, ease of operation, automatic data processing, and affordability. PMID:22553239

  17. Comparing Bacterial DNA Microarray Fingerprints

    SciTech Connect

    Willse, Alan R.; Chandler, Darrell P.; White, Amanda M.; Protic, Miroslava; Daly, Don S.; Wunschel, Sharon C.

    2005-08-15

    Detecting subtle genetic differences between microorganisms is an important problem in molecular epidemiology and microbial forensics. In a typical investigation, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial strains, where the patterns of DNA fragment sizes are proxies for a microbe's genotype. The limited genomic sample captured on a gel is often insufficient to discriminate nearly identical strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if the number of probes on the microarray is sufficiently large, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate the statistical fingerprinting problem for 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

  18. Traumatic Brain Injury in Young Rats Leads to Progressive Behavioral Deficits Coincident with Altered Tissue Properties in Adulthood

    PubMed Central

    Ajao, David O.; Pop, Viorela; Kamper, Joel E.; Adami, Arash; Rudobeck, Emil; Huang, Lei; Vlkolinsky, Roman; Hartman, Richard E.; Ashwal, Stephen; Obenaus, André

    2012-01-01

    Abstract Traumatic brain injury (TBI) affects many infants and children, and results in enduring motor and cognitive impairments with accompanying changes in white matter tracts, yet few experimental studies in rodent juvenile models of TBI (jTBI) have examined the timeline and nature of these deficits, histologically and functionally. We used a single controlled cortical impact (CCI) injury to the parietal cortex of rats at post-natal day (P) 17 to evaluate behavioral alterations, injury volume, and morphological and molecular changes in gray and white matter, with accompanying measures of electrophysiological function. At 60 days post-injury (dpi), we found that jTBI animals displayed behavioral deficits in foot-fault and rotarod tests, along with a left turn bias throughout their early developmental stages and into adulthood. In addition, anxiety-like behaviors on the zero maze emerged in jTBI animals at 60?dpi. The final lesion constituted only ?3% of brain volume, and morphological tissue changes were evaluated using MRI, as well as immunohistochemistry for neuronal nuclei (NeuN), myelin basic protein (MBP), neurofilament-200 (NF200), and oligodendrocytes (CNPase). White matter morphological changes were associated with a global increase in MBP immunostaining and reduced compound action potential amplitudes at 60?dpi. These results suggest that brain injury early in life can induce long-term white matter dysfunction, occurring in parallel with the delayed development and persistence of behavioral deficits, thus modeling clinical and longitudinal TBI observations. PMID:22697253

  19. Development and function of membrane systems in plant tissue. Annual technical progress report, 15 September 1981-15 August 1982

    SciTech Connect

    Hanson, J B

    1982-01-01

    Over the past 11 months we have continued investigation of ion transport mechanisms in corn roots and mitochondria. In mitochondria we find that only citrate and isocitrate are transported by the H/sup +//citrate symporter. However, the in vivo function of this carrier remains in doubt because citrate does not appear to be an effective substrate for corn mitochondria. Studies with roots have been directed to why various types of injury or shock all result in temporary blockage of the H/sup +/-efflux pump in the plasmamembrane. It appears this may be due to an injury-mediated Ca/sup 2 +/ influx into the tissue, which by raising free Ca/sup 2 +/ in the cytosal activates calmodulin (CaM). In turn, the Ca.CaM complex appears to activate protein kinase, phosphorylating membrane proteins. It is possible that one of these phosphorylated proteins is responsible for inactivation of the H/sup +/-ATPase. Future work is planned around the consequences of Ca/sup 2 +/ influx into the root cell subsequent to injury, investigating the recovery of the H/sup +/-ATPase and the initiation of the biosyntheses which lead to augmented ion transport.

  20. Components of the endocannabinoid and dopamine systems are dysregulated in Huntington's disease: analysis of publicly available microarray datasets

    PubMed Central

    Laprairie, Robert B; Bagher, Amina M; Precious, Sophie V; Denovan-Wright, Eileen M

    2015-01-01

    The endocannabinoid system (ECS) and the dopaminergic system (DAS) are two major regulators of basal ganglia function. During Huntington's disease (HD) pathogenesis, the expression of genes in both the ECS and DAS is dysregulated. The purpose of this study was to determine the changes that were consistently observed in the ECS and DAS during HD progression in the central nervous system (CNS) and in the periphery in different models of HD and human HD tissue. To do this, we conducted a meta-analysis of differential gene expression in the ECS and DAS using publicly available microarray data. The consolidated data were summarized as observed changes in gene expression (OCGE) using a weighted sum for each gene. In addition, consolidated data were compared to previously published studies that were not available in the gene expression omnibus (GEO) database. The resulting data confirm gene expression changes observed using different approaches and provide novel insights into the consistency between changes observed in human tissue and various models, as well as disease stage- and tissue-specific transcriptional dysregulation in HD. The major implication of the systems-wide data presented here is that therapeutic strategies targeting the ECS or DAS must consider the dynamic changes in gene expression over time and in different body areas, which occur during HD progression and the interconnectedness of the two systems. PMID:25692022

  1. Components of the endocannabinoid and dopamine systems are dysregulated in Huntington's disease: analysis of publicly available microarray datasets.

    PubMed

    Laprairie, Robert B; Bagher, Amina M; Precious, Sophie V; Denovan-Wright, Eileen M

    2015-02-01

    The endocannabinoid system (ECS) and the dopaminergic system (DAS) are two major regulators of basal ganglia function. During Huntington's disease (HD) pathogenesis, the expression of genes in both the ECS and DAS is dysregulated. The purpose of this study was to determine the changes that were consistently observed in the ECS and DAS during HD progression in the central nervous system (CNS) and in the periphery in different models of HD and human HD tissue. To do this, we conducted a meta-analysis of differential gene expression in the ECS and DAS using publicly available microarray data. The consolidated data were summarized as observed changes in gene expression (OCGE) using a weighted sum for each gene. In addition, consolidated data were compared to previously published studies that were not available in the gene expression omnibus (GEO) database. The resulting data confirm gene expression changes observed using different approaches and provide novel insights into the consistency between changes observed in human tissue and various models, as well as disease stage- and tissue-specific transcriptional dysregulation in HD. The major implication of the systems-wide data presented here is that therapeutic strategies targeting the ECS or DAS must consider the dynamic changes in gene expression over time and in different body areas, which occur during HD progression and the interconnectedness of the two systems. PMID:25692022

  2. Immunoprofiling using NAPPA protein microarrays.

    PubMed

    Sibani, Sahar; LaBaer, Joshua

    2011-01-01

    Protein microarrays provide an efficient method to immunoprofile patients in an effort to rapidly identify disease immunosignatures. The validity of using autoantibodies in diagnosis has been demonstrated in type 1 diabetes, rheumatoid arthritis, and systemic lupus, and is now being strongly considered in cancer. Several types of protein microarrays exist including antibody and antigen arrays. In this chapter, we describe the immunoprofiling application for one type of antigen array called NAPPA (nucleic acids programmable protein array). We provide a guideline for setting up the screening study and designing protein arrays to maximize the likelihood of obtaining quality data. PMID:21370064

  3. DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

    PubMed Central

    Diaz, Elva; Barisone, Gustavo A.

    2011-01-01

    Microarray expression profiling of the nervous system provides a powerful approach to identifying gene activities in different stages of development, different physiological or pathological states, response to therapy, and, in general, any condition that is being experimentally tested1. Expression profiling of neural tissues requires isolation of high quality RNA, amplification of the isolated RNA and hybridization to DNA microarrays. In this article we describe protocols for reproducible microarray experiments from brain tumor tissue2. We will start by performing a quality control analysis of isolated RNA samples with Agilent's 2100 Bioanalyzer "lab-on-a-chip" technology. High quality RNA samples are critical for the success of any microarray experiment, and the 2100 Bioanalyzer provides a quick, quantitative measurement of the sample quality. RNA samples are then amplified and labeled by performing reverse transcription to obtain cDNA, followed by in vitro transcription in the presence of labeled nucleotides to produce labeled cRNA. By using a dual-color labeling kit, we will label our experimental sample with Cy3 and a reference sample with Cy5. Both samples will then be combined and hybridized to Agilent's 4x44 K arrays. Dual-color arrays offer the advantage of a direct comparison between two RNA samples, thereby increasing the accuracy of the measurements, in particular for small changes in expression levels, because the two RNA samples are hybridized competitively to a single microarray. The arrays will be scanned at the two corresponding wavelengths, and the ratio of Cy3 to Cy5 signal for each feature will be used as a direct measurement of the relative abundance of the corresponding mRNA. This analysis identifies genes that are differentially expressed in response to the experimental conditions being tested. PMID:21445042

  4. Collagenase and tissue plasminogen activator production in developing rat calvariae: normal progression despite fetal exposure to microgravity

    NASA Technical Reports Server (NTRS)

    Davis, B. A.; Sipe, B.; Gershan, L. A.; Fiacco, G. J.; Lorenz, T. C.; Jeffrey, J. J.; Partridge, N. C.

    1998-01-01

    Exposure to zero gravity has been shown to cause a decrease in bone formation. This implicates osteoblasts as the gravity-sensing cell in bone. Osteoblasts also are known to produce neutral proteinases, including collagenase and tissue plasminogen activator (tPA), which are thought to be important in bone development and remodeling. The present study investigated the effects of zero gravity on development of calvariae and their expression of collagenase and tPA. After in utero exposure to zero gravity for 9 days on the NASA STS-70 space shuttle mission, the calvariae of rat pups were examined by immunohistochemistry for the presence and location of these two proteinases. The ages of the pups were from gestational day 20 (G20) to postnatal (PN) day 35. Both collagenase and tPA were found to be present at all ages examined, with the greatest amount of both proteinases present in the PN14 rats. At later ages, high amounts were maintained for tPA but collagenase decreased substantially between ages PN21 to PN35. The location of collagenase was found to be associated with bone-lining cells, osteoblasts, osteocytes, and in the matrix along cement lines. In contrast, tPA was associated with endothelial cells lining the blood vessels entering bone. The presence and developmental expression of these two proteinases appeared to be unaffected by the exposure to zero gravity. The calvarial thickness of the pups was also examined; again the exposure to zero gravity showed little to no effect on the growth of the calvariae. Notably, from G20 to PN14, calvarial thickness increased dramatically, reaching a plateau after this age. It was apparent that elevated collagenase expression correlated with rapid bone growth in the period from G20 to PN14. To conclude, collagenase and tPA are present during the development of rat calvariae. Despite being produced by the same cell in vitro, i.e., the osteoblast, they are located in distinctly different places in bone in vivo. Their presence, developmental expression, and quantity do not seem to be affected by a brief exposure to zero gravity in utero.

  5. Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray

    E-print Network

    Gerstein, Mark

    Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray for analyzing traditional gene-centric DNA microarrays, so the rst challenge in analyzing the advanced- anistic aspects with the traditional DNA microarrays, but in several respects, are quite dierent

  6. Study on the Control System of Microarrayer

    Microsoft Academic Search

    Qiang Zhou; Fengxin Yu; Shouqian Yu

    2006-01-01

    The control system is the key parts of microarrayer. The working process and configuration of microarrayer are introduced briefly. Special attention is paid to the analysis and computation method of the working path in microarray fabrication. On the condition of given parameters, such as sample variety, slip quantity, spot matrix module, pin matrix module etc., the working path has been

  7. Chasing the dream: plant EST microarrays

    Microsoft Academic Search

    Todd Richmond; Shauna Somerville

    2000-01-01

    DNA microarray technology is poised to make an important contribution to the field of plant biology. Stimulated by recent funding programs, expressed sequence tag sequencing and microarray production either has begun or is being contemplated for most economically important plant species. Although the DNA microarray technology is still being refined, the basic methods are well established. The real challenges lie

  8. Agilent Technologies Microarray-Based Gene

    E-print Network

    Richardson, David

    Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol For use with Agilent Gene Expression oligo microarrays Version 6.5, May 2010 Microarrays manufactured with Agilent SurePrint Technology Research Use Only. Not for use in Diagnostic Procedures. #12

  9. Agilent Technologies Microarray-Based Gene

    E-print Network

    Richardson, David

    Agilent Technologies Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol For use with Agilent Gene Expression oligo microarrays Version 6.5, May 2010 Microarrays manufactured with Agilent SurePrint Technology Research Use Only. Not for use in Diagnostic Procedures. #12

  10. DNA Microarray Experiments: Biological and Technological Aspects

    Microsoft Academic Search

    Danh V. Nguyen; A. Bulak Arpat; Naisyin Wang; Raymond J. Carroll

    2002-01-01

    SUMMARY. DNA microarray technologies, such as cDNA and oligonucleotide microarrays, promise to rev- olutionize biological research and further our understanding of biological processes. Due to the complex nature and sheer amount of data produced from microarray experiments, biologists have sought the collab- oration of experts in the analytical sciences, including statisticians, among others. However, the biological and technical intricacies of

  11. Approximating Border Length for DNA Microarray Synthesis

    E-print Network

    Wong, Prudence W.H.

    Approximating Border Length for DNA Microarray Synthesis Cindy Y. Li1 Prudence W.H. Wong1 Qin Xin2 Introduction DNA microarrays [9] have become a very important research tool which have proved to benefit areas about the pres- ence or absence of biological target sequences in a sample. A DNA microarray ("chip

  12. The Microarray Revolution: Perspectives from Educators

    ERIC Educational Resources Information Center

    Brewster, Jay L.; Beason, K. Beth; Eckdahl, Todd T.; Evans, Irene M.

    2004-01-01

    In recent years, microarray analysis has become a key experimental tool, enabling the analysis of genome-wide patterns of gene expression. This review approaches the microarray revolution with a focus upon four topics: 1) the early development of this technology and its application to cancer diagnostics; 2) a primer of microarray research,…

  13. Human cancers overexpress genes that are specific to a variety of normal human tissues

    E-print Network

    Domany, Eytan

    of the cancers, including their metastatic potential. cancer cell lines DNA microarray gene expression patterns by using DNA microarray expres- sion data from normal human tissues (11), different human cancer cell lines in different types of cancers. Materials and Methods Data Sets. Three DNA microarray data sets were used

  14. Microarray analysis of replicative senescence

    Microsoft Academic Search

    Dawne N. Shelton; Edwin Chang; Peter S. Whittier; Donghee Choi; Walter D. Funk

    1999-01-01

    Background: Limited replicative capacity is a defining characteristic of most normal human cells and culminates in senescence, an arrested state in which cells remain viable but display an altered pattern of gene and protein expression. To survey widely the alterations in gene expression, we have developed a DNA microarray analysis system that contains genes previously reported to be involved in

  15. ANALYSIS OF DNA MICROARRAY DATA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of DNA microarrays involves the extraction of fluorescent intensity from raw image files generated by the scanner, storing the extracted data in a database, normalizing the data, conducting statistical analysis and finally querying the analyzed data to find biologically meaningful results. ...

  16. DNA Microarray Methodology - Flash Animation

    NSDL National Science Digital Library

    Campbell, A. Malcolm

    This animation demonstrates how DNA microarray experiments are performed. DNA chips are used to determine which genes are activated and which genes are repressed when two populations are compared. In this case, the comparison is between yeast cells grown under either aerobic or anaerobic conditions. This animation is very effective for many different education levels. Teachers and students love this one.

  17. (gene expression) DNA (DNA microarrays).

    E-print Network

    Athens, University of

    µ µ DNA . , µ . , µ . , . µ µµ µ µ (gene expression) . µ, µ µ DNA µ 100%. I. µ , µ [1]. µ µµ µ µ (gene expression. [2] M. K. Deyholos, and D. W. Galbraith, "High- Density Microarrays for Gene Expression Analysis

  18. Retraction. "Immunohistochemical prognostic markers in diffuse large B-cell lymphoma: validation of tissue microarray as a prerequisite for broad clinical applications (a study from the Lunenburg Lymphoma Biomarker Consortium)" (J Clin Pathol 2009;62:128–38;doi:10.1136/jcp.2008.057257).

    PubMed

    2012-09-01

    The Journal of Clinical Pathology wishes to inform its readers of the authors' retraction of the following article for redundancy. The original article by D de Jong, W Xie, Rosenwald, M Chhanabhai, P Gaulard,W Klapper, A Lee, B Sander, C Thorns,E Campo, T Molina, A Hagenbeek,S Horning, A Lister, J Raemaekers, G Salles, R D Gascoyne and E Weller entitled "Immunohistochemical prognostic markersi n diffuse large B-cell lymphoma: validation of tissue microarray as a prerequisite for broad clinical applications (a study from the Lunenburg Lymphoma Biomarker Consortium)" (J Clin Pathol 2009;62:128–38;doi:10.1136/jcp.2008.057257) published online on 15 September 2008, contained substantial overlap in text, data, and conclusions compared with a previous article with the same title published in Journal of Clinical Oncology on 1 March 2007 by Daphne de Jong, Andreas Rosenwald, Mukesh Chhanabhai, Philippe Gaulard,Wolfram Klapper, Abigail Lee, Birgitta Sander, Christoph Thorns, Elias Campo, Thierry Molina, Andrew Norton, Anton Hagenbeek, Sandra Horning, Andrew Lister, John Raemaekers, Randy D Gascoyne, Gilles Salles and Edie Weller (doi:10.1200/JCO.2006.09.4490). In addition, the authors did not cite the Journal of Clinical Oncology article in the paper published in Journal of Clinical Pathology. PMID:22930798

  19. A rapid and robust assay for detection of S-phase cell cycle progression in plant cells and tissues by using ethynyl deoxyuridine

    PubMed Central

    2010-01-01

    Background Progress in plant cell cycle research is highly dependent on reliable methods for detection of cells replicating DNA. Frequency of S-phase cells (cells in DNA synthesis phase) is a basic parameter in studies on the control of cell division cycle and the developmental events of plant cells. Here we extend the microscopy and flow cytometry applications of the recently developed EdU (5-ethynyl-2'-deoxyuridine)-based S-phase assay to various plant species and tissues. We demonstrate that the presented protocols insure the improved preservation of cell and tissue structure and allow significant reduction in assay duration. In comparison with the frequently used detection of bromodeoxyuridine (BrdU) and tritiated-thymidine incorporation, this new methodology offers several advantages as we discuss here. Results Applications of EdU-based S-phase assay in microscopy and flow cytometry are presented by using cultured cells of alfalfa, Arabidopsis, grape, maize, rice and tobacco. We present the advantages of EdU assay as compared to BrdU-based replication assay and demonstrate that EdU assay -which does not require plant cell wall digestion or DNA denaturation steps, offers reduced assay duration and better preservation of cellular, nuclear and chromosomal morphologies. We have also shown that fast and efficient EdU assay can also be an efficient tool for dual parameter flow cytometry analysis and for quantitative assessment of replication in thick root samples of rice. Conclusions In plant cell cycle studies, EdU-based S-phase detection offers a superior alternative to the existing S-phase assays. EdU method is reliable, versatile, fast, simple and non-radioactive and it can be readily applied to many different plant systems. PMID:20181034

  20. M@IA: a modular open-source application for microarray workflow and integrative datamining.

    PubMed

    Le Béchec, Antony; Zindy, Pierre; Sierocinski, Thomas; Petritis, Dimitri; Bihouée, Audrey; Le Meur, Nolwenn; Léger, Jean; Théret, Nathalie

    2008-01-01

    Microarray technology is a widely used approach to gene expression analysis. Many tools for microarray management and data analysis have been developed, and recently new methods have been proposed for deciphering biological pathways by integrating microarray data with other data sources. However, to improve microarray analysis and provide meaningful gene interaction networks, integrated software solutions are still needed. Therefore, we developed M@IA, an environment for DNA microarray data analysis allowing gene network reconstruction. M@IA is a microarray integrated application which includes all of the steps of a microarray study, from MIAME-compliant raw data storage and processing gene expression analysis. Furthermore, M@IA allows automatic gene annotation based on ontology, metabolic/signalling pathways, protein interaction, miRNA and transcriptional factor associations, as well as integrative analysis of gene interaction networks. Statistical and graphical methods facilitate analysis, yielding new hypotheses on gene expression data. To illustrate our approach, we applied M@IA modules to microarray data taken from an experiment on liver tissue. We integrated differentially expressed genes with additional biological information, thus identifying new molecular interaction networks that are associated with fibrogenesis. M@IA is a new application for microarray management and data analysis, offering functional insights into microarray data by the combination of gene expression data and biological knowledge annotation based on interactive graphs. M@IA is an interactive multi-user interface based on a flexible modular architecture and it is freely available for academic users at http://maia.genouest.org. PMID:18430991

  1. Gene expression profiling in peanut using high density oligonucleotide microarrays

    PubMed Central

    Payton, Paxton; Kottapalli, Kameswara Rao; Rowland, Diane; Faircloth, Wilson; Guo, Baozhu; Burow, Mark; Puppala, Naveen; Gallo, Maria

    2009-01-01

    Background Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of these ESTs for oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology. Results We have developed a high-density oligonucleotide microarray for peanut using 49,205 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues. To identify putatively tissue-specific genes and demonstrate the utility of this array for expression profiling in a variety of peanut tissues, we compared transcript levels in pod, peg, leaf, stem, and root tissues. Results from this experiment showed 108 putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to peg, leaf, stem, or root. The transcripts significantly over-represented in pod include genes responsible for seed storage proteins and desiccation (e.g., late-embryogenesis abundant proteins, aquaporins, legumin B), oil production, and cellular defense. Additionally, almost half of the pod-abundant genes represent unknown genes allowing for the possibility of associating putative function to these previously uncharacterized genes. Conclusion The peanut oligonucleotide array represents the majority of publicly available peanut ESTs and can be used as a tool for expression profiling studies in diverse tissues. PMID:19523230

  2. Pro-oncogene Pokemon promotes breast cancer progression by upregulating survivin expression

    PubMed Central

    2011-01-01

    Introduction Pokemon is an oncogenic transcription factor involved in cell growth, differentiation and oncogenesis, but little is known about its role in human breast cancer. In this study, we aimed to reveal the role of Pokemon in breast cancer progression and patient survival and to understand its underlying mechanisms. Methods Tissue microarray analysis of breast cancer tissues from patients with complete clinicopathological data and more than 20 years of follow-up were used to evaluate Pokemon expression and its correlation with the progression and prognosis of the disease. DNA microarray analysis of MCF-7 cells that overexpress Pokemon was used to identify Pokemon target genes. Chromatin immunoprecipitation (ChIP) and site-directed mutagenesis were utilized to determine how Pokemon regulates survivin expression, a target gene. Results Pokemon was found to be overexpressed in 158 (86.8%) of 182 breast cancer tissues, and its expression was correlated with tumor size (P = 0.0148) and lymph node metastasis (P = 0.0014). Pokemon expression led to worse overall (n = 175, P = 0.01) and disease-related (n = 79, P = 0.0134) patient survival. DNA microarray analyses revealed that in MCF-7 breast cancer cells, Pokemon regulates the expression of at least 121 genes involved in several signaling and metabolic pathways, including anti-apoptotic survivin. In clinical specimens, Pokemon and survivin expression were highly correlated (n = 49, r = 0.6799, P < 0.0001). ChIP and site-directed mutagenesis indicated that Pokemon induces survivin expression by binding to the GT boxes in its promoter. Conclusions Pokemon promotes breast cancer progression by upregulating survivin expression and thus may be a potential target for the treatment of this malignancy. PMID:21392388

  3. Microarray Gene Expression Data Society

    NSDL National Science Digital Library

    The Microarray Gene Expression Data Society is an international organization composed of computer scientists, data analysts, and biologists "that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments." Hosted by the European Bioinformatics Institute, this website connects to information about six major Data Society workgroups (e.g. the Ontology Working Group, the Reporting Structure for Biological Investigations Working Groups, the Data Transformation and Normalization Working Group). The Data Society website also offers a News Archive; several downloadable publications from the past few years; a number of PowerPoint presentations from past Society meetings; contact information for Society Board Members; and links to information about upcoming and past Society meetings.

  4. DNA Microarrays An R Tutorial

    E-print Network

    Qiu, Weigang

    ://rstudio.org) SimpleR: an R Tutorial (http://wiener.math.csi.cuny. edu/Statistics/R/simpleR/index.html) Bio;DNA Microarrays An R Tutorial Bi-variate Data Categorical vs Numerical HG-U95Av2 Affymetrix GeneChip Data: B-cell acute lymphoblastic leukemia (ALL) patients, 37 with BCR/ABL gene fusion, 42 with normal

  5. Tissue Microarray Analysis of Hepatocyte Growth Factor\\/Met Pathway Components Reveals a Role for Met, Matriptase, and Hepatocyte Growth Factor Activator Inhibitor 1 in the Progression of Node-negative Breast Cancer1

    Microsoft Academic Search

    Jung Y. Kang; Marisa Dolled-Filhart; Idris Tolgay Ocal; Baljit Singh; Chen-Yong Lin; Robert B. Dickson; David L. Rimm; Robert L. Camp

    Numerous studies have demonstrated that overexpression of Met, the hepatocyte growth factor (HGF) receptor, plays an important role in tumorigenesis. Met activation can either occur through ligand-indepen- dent or -dependent mechanisms, both of which are mediated by a series of proteases and modulators. We studied the protein expression of several components of the HGF\\/Met pathway on a cohort of 330

  6. Differentially Expressed Proteins and Associated Histological and Disease Progression Changes in Cotyledon Tissue of a Resistant and Susceptible Genotype of Brassica napus Infected with Sclerotinia sclerotiorum

    PubMed Central

    Garg, Harsh; Li, Hua; Sivasithamparam, Krishnapillai; Barbetti, Martin J.

    2013-01-01

    Sclerotinia rot caused by Sclerotinia sclerotiorum is one of the most serious diseases of oilseed rape. To understand the resistance mechanisms in the Brassica napus to S. sclerotiorum, comparative disease progression, histological and proteomic studies were conducted of two B. napus genotypes (resistant cv. Charlton, susceptible cv. RQ001-02M2). At 72 and 96 h post inoculation (hpi), lesion size on cotyledons was significantly (P?0.001) smaller in the resistant Charlton. Anatomical investigations revealed impeded fungal growth (at 24 hpi and onwards) and hyphal disintegration only on resistant Charlton. Temporal changes (12, 24, 48 and 72 hpi) in protein profile showed certain enzymes up-regulated only in resistant Charlton, such as those related to primary metabolic pathways, antioxidant defence, ethylene biosynthesis, pathogenesis related proteins, protein synthesis and protein folding, play a role in mediating defence responses against S. sclerotiorum. Similarly a eukaryotic translation initiation factor 5A enzyme with increased abundance in susceptible RQ001-02M2 and decreased levels in resistant Charlton has a role in increased susceptibility to this pathogen. This is the first time that the expression of these enzymes has been shown to be associated with mediating the defence response against S. sclerotinia in cotyledon tissue of a resistant cultivar of B. napus at a proteomics level. This study not only provides important new insights into the resistance mechanisms within B. napus against S. sclerotiorum, but opens the way for novel engineering of new B. napus varieties that over-express these key enzymes as a strategy to enhance resistance and better manage this devastating pathogen. PMID:23776450

  7. Paraffin-Embedded Cell Line Microarray (PECLIMA): Development and Validation of a High-Throughput Method for Antigen Profiling of Cell Lines

    Microsoft Academic Search

    Berta Ferrer; Raquel Bermudo; Timothy Thomson; Iracema Nayach; Marta Soler; Montserrat Sánchez; Mireia Castillo; Julia Calvo; Elias Campo; Pedro L. Fernández

    2005-01-01

    The introduction of high-throughput techniques is increasingly providing abundant information on molecular alterations requiring validation at the posttranscriptional level. Protein expression is now efficiently evaluated in large series of tumors included in tissue microarrays. We propose, describe and validate a technique to elaborate paraffin-embedded cell line microarrays (PECLIMA) from fixed cell cultures, which can be processed like standard surgical pathology

  8. THE ABRF MARG MICROARRAY SURVEY 2005: TAKING THE PULSE ON THE MICROARRAY FIELD

    EPA Science Inventory

    Over the past several years microarray technology has evolved into a critical component of any discovery based program. Since 1999, the Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) has conducted biennial surveys designed to generate a pr...

  9. Gene Expression Microarrays in Cancer Research

    Microsoft Academic Search

    Jian Yan; Weikuan Gu

    The advent of microarray technology has enabled scientists to simultaneously investigate the expression of thousands of genes.\\u000a This technology has been widely used in cancer research to better characterize cancer behaviors at mRNA level and to obtain\\u000a new insights into various stages of carcinogenesis. A microarray-based experiment generally involves three major components:\\u000a microarray manufacturing, sample processing, and data analysis, with

  10. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data

    Microsoft Academic Search

    Paul Spellman; Chris Stoeckert; John Aach; Wilhelm Ansorge; Catherine A. Ball; Helen C. Causton; Terry Gaasterland; Patrick Glenisson; Frank C. P. Holstege; Irene F. Kim; Victor Markowitz; John C. Matese; Helen Parkinson; Alan Robinson; Ugis Sarkans; Steffen Schulze-Kremer; Jason Stewart; Ronald Taylor; Jaak Vilo; Martin Vingron; Alvis Brazma; John Quackenbush

    2001-01-01

    Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum

  11. THE ABRF-MARG MICROARRAY SURVEY 2004: TAKING THE PULSE OF THE MICROARRAY FIELD

    EPA Science Inventory

    Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. The goal of the surve...

  12. 2008 Microarray Research Group (MARG Survey): Sensing the State of Microarray Technology

    EPA Science Inventory

    Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution and transformation, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. Th...

  13. A Meta-Analysis of Microarray Gene Expression in Mouse Stem Cells: Redefining Stemness

    Microsoft Academic Search

    Yvonne J. K. Edwards; Kevin Bryson; David T. Jones; Winston Hide

    2008-01-01

    BackgroundWhile much progress has been made in understanding stem cell (SC) function, a complete description of the molecular mechanisms regulating SCs is not yet established. This lack of knowledge is a major barrier holding back the discovery of therapeutic uses of SCs. We investigated the value of a novel meta-analysis of microarray gene expression in mouse SCs to aid the

  14. Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics

    Microsoft Academic Search

    Julio E Celis; Mogens Kruhøffer; Irina Gromova; Casper Frederiksen; Morten Østergaard; Thomas Thykjaer; Pavel Gromov; Jinsheng Yu; Hildur Pálsdóttir; Nils Magnusson; Torben F Ørntoft

    2000-01-01

    Novel and powerful technologies such as DNA microarrays and proteomics have made possible the analysis of the expression levels of multiple genes simultaneously both in health and disease. In combination, these technologies promise to revolutionize biology, in particular in the area of molecular medicine as they are expected to reveal gene regulation events involved in disease progression as well as

  15. Integrated imaging instrument for self-calibrated fluorescence protein microarrays

    PubMed Central

    Reddington, A. P.; Monroe, M. R.; Ünlü, M. S.

    2013-01-01

    Protein microarrays, or multiplexed and high-throughput assays, monitor multiple protein binding events to facilitate the understanding of disease progression and cell physiology. Fluorescence imaging is a popular method to detect proteins captured by immobilized probes with high sensitivity and specificity. Reliability of fluorescence assays depends on achieving minimal inter- and intra-assay probe immobilization variation, an ongoing challenge for protein microarrays. Therefore, it is desirable to establish a label-free method to quantify the probe density prior to target incubation to calibrate the fluorescence readout. Previously, a silicon oxide on silicon chip design was introduced to enhance the fluorescence signal and enable interferometric imaging to self-calibrate the signal with the immobilized probe density. In this paper, an integrated interferometric reflectance imaging sensor and wide-field fluorescence instrument is introduced for sensitive and calibrated microarray measurements. This platform is able to analyze a 2.5 mm × 3.4 mm area, or 200 spots (100 ?m diameter with 200 ?m pitch), in a single field-of-view. PMID:24182114

  16. Protein-Based Microarray for the Detection of Pathogenic Bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microarrays have been used for gene expression and protein interaction studies, but recently, multianalyte diagnostic assays have employed the microarray platform. We developed a microarray immunoassay for bacteria, with biotinylated capture antibodies on streptavidin slides. To complete the fluor...

  17. Application of Singular Value Decomposition to DNA Microarray

    E-print Network

    Friedland, Shmuel

    Application of Singular Value Decomposition to DNA Microarray Amir Niknejad M.S. Claremont Graduate.1 Missing gene imputation in DNA microarrays . . . . . . . . . . . . 8 1.2 Some biological background and Translation . . . . . . . . . . . . . . . . 12 1.2.3 DNA microarrays (chips

  18. Critical Review of Methods available for Microarray Data Analysis Krithika Ramamoorthy

    E-print Network

    in an intact organism, pathological tissue specimens from patients and serial time points following a stimulus to the cell or organism (1). A typical microarray experiment contains expression levels of thousands of genes by the Affymetrix GeneChip technology and spotted cDNA arrays. The GeneChip contains oligonucleotides of 25 base

  19. Utility of Natural Populations for Microarray Analyses: Isolation of Genes Necessary for Functional Genomic Studies

    Microsoft Academic Search

    Marjorie F. Oleksiak; Kevin J. Kolell; Douglas L. Crawford

    2001-01-01

    How much variation is there in gene expression? How is this variation partitioned within and among populations? How much variation is biologically important? That is, how much of this variation affects longevity, reproductive fitness, or probability of survival? Microarray analyses can be used to accurately quantify the expression of most, if not all, genes expressed in a tissue and thus

  20. The unique genomic properties of sex-biased genes: Insights from avian microarray data

    Microsoft Academic Search

    Judith E Mank; Lina Hultin-Rosenberg; Matthew T Webster; Hans Ellegren

    2008-01-01

    BACKGROUND: In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue. RESULTS: From the 15982 significantly expressed coding regions that have been assigned to either the autosomes or the Z chromosome (12979 in brain,

  1. Yeast Proteomics and Protein Microarrays

    PubMed Central

    Chen, Rui; Snyder, Michael

    2010-01-01

    Our understanding of biological processes as well as human diseases has improved greatly thanks to studies on model organisms such as yeast. The power of scientific approaches with yeast lies in its relatively simple genome, its facile classical and molecular genetics, as well as the evolutionary conservation of many basic biological mechanisms. However, even in this simple model organism, systems biology studies, especially proteomic studies had been an intimidating task. During the past decade, powerful high-throughput technologies in proteomic research have been developed for yeast including protein microarray technology. The protein microarray technology allows the interrogation of protein-protein, protein-DNA, protein-small molecule interaction networks as well as post-translational modification networks in a large-scale, high-throughput manner. With this technology, many groundbreaking findings have been established in studies with the budding yeast Saccharomyces cerevisiae, most of which could have been unachievable with traditional approaches. Discovery of these networks has profound impact on explicating biological processes with a proteomic point of view, which may lead to a better understanding of normal biological phenomena as well as various human diseases. PMID:20728591

  2. BOS TAURUS 60MER OLIGONUCLEOTIDE MICROARRAY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine high-density long oligonucleotide microarrays were developed, tested and optimized. The bovine microarray with ~345,000 features (60mer oligonucleotides) representing 45,383 cattle unique sequences was designed and produced with Maskless Array Synthesizer technology. The 45,383 unique sequenc...

  3. Application of microarray technology in pulmonary diseases

    Microsoft Academic Search

    Argyris Tzouvelekis; George Patlakas; Demosthenes Bouros

    2004-01-01

    Microarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives.

  4. Microarrays: biotechnology's discovery platform for functional genomics

    Microsoft Academic Search

    Mark Schena; Renu A Heller; Thomas P Theriault; Ken Konrad; Eric Lachenmeier; Ronald W Davis

    1998-01-01

    Advances in microarray technology enable massive parallel mining of biological data, with biological chips providing hybridization-based expression monitoring, polymorphism detection and genotyping on a genomic scale. Microarrays containing sequences representative of all human genes may soon permit the expression analysis of the entire human genome in a single reaction. These `genome chips' will provide unprecedented access to key areas of

  5. Oligosaccharide microarrays to decipher the glyco code

    Microsoft Academic Search

    Wengang Chai; Ten Feizi

    2004-01-01

    The oligosaccharide moieties of glycoproteins, glycolipids, proteoglycans and polysaccharides are highly diverse, the reason for this diversity is not yet understood. Neoglycolipid technology allows the generation of oligosaccharide probes with lipid tags from desired sources and is showing promise as a basis for oligosaccharide microarrays. Such microarrays would allow surveys of glycomes and proteomes to be carried out, which would

  6. Empirical Bayes Analysis of a Microarray Experiment

    Microsoft Academic Search

    Bradley Efron; Robert Tibshirani; Storey J. D; Virginia Tusher

    2001-01-01

    Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typi- cal microarray experiment can produce millions of data points, raising serious problems of data reduction, and simultaneous infer- ence. We consider one such experiment in which oligonucleotide arrays were employed to assess the genetic effects of ionizing radiation on seven thousand human

  7. Microarrays and the shadows in Plato's cave

    E-print Network

    Futschik, Matthias E.

    11 Microarrays and the shadows in Plato's cave Matthias E. Futschik Institute for Theoretical Biology Humboldt-University, Berlin, Germany Overview General Introduction Plato and the cave: What can we and data storage Design of experiments Reference design Factorial design Yeast cDNA microarray Plato's Cave

  8. Normalization strategies for cDNA microarrays

    Microsoft Academic Search

    Johannes Schuchhardt; Dieter Beule; Arif Malik; E ryc Wolski; Holger Eickhoff; Hans Lehrach; Hanspeter Herzel

    2000-01-01

    Multiple Arabidopsis thaliana clones from an experi- mental series of cDNA microarrays are evaluated in order to identify essential sources of noise in the spotting and hybridization process. Theoretical and experimental strategies for an improved quantitative evaluation of cDNA microarrays are proposed and tested on a series of differently diluted control clones. Several sources of noise are identified from the

  9. Application of microarray technology in pulmonary diseases

    PubMed Central

    Tzouvelekis, Argyris; Patlakas, George; Bouros, Demosthenes

    2004-01-01

    Microarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives. PMID:15585067

  10. Design of studies using DNA microarrays

    Microsoft Academic Search

    Richard Simon; Michael D. Radmacher; Kevin Dobbin

    2002-01-01

    DNA microarrays are assays that simultaneously provide information about expression levels of thousands of genes and are consequently finding wide use in biomedical research. In order to control the many sources of variation and the many opportunities for misanalysis, DNA microarray studies require careful planning. Different studies have different objectives, and important aspects of design and analysis strategy differ for

  11. DNA microarrays in drug discovery and development

    Microsoft Academic Search

    Christine Debouck; Peter N. Goodfellow

    1999-01-01

    DNA microarrays can be used to measure the expression patterns of thousands of genes in parallel, generating clues to gene function that can help to identify appropriate targets for therapeutic intervention. They can also be used to monitor changes in gene expression in response to drug treatments. Here, we discuss the different ways in which microarray analysis is likely to

  12. Multiple Hypothesis Testing in Microarray Experiments

    Microsoft Academic Search

    Sandrine Dudoit; Juliet Popper Shaffer; Jennifer C. Boldrick

    2003-01-01

    DNA microarrays are part of a new and promising class of biotechnologies that allow the monitoring of expression levels in cells for thousands of genes simultaneously. An important and common question in DNA microarray experiments is the identification of differentially expressed genes, that is, genes whose expression levels are associated with a response or covariate of interest. The biological question

  13. Microarrays Made Simple: "DNA Chips" Paper Activity

    ERIC Educational Resources Information Center

    Barnard, Betsy

    2006-01-01

    DNA microarray technology is revolutionizing biological science. DNA microarrays (also called DNA chips) allow simultaneous screening of many genes for changes in expression between different cells. Now researchers can obtain information about genes in days or weeks that used to take months or years. The paper activity described in this article…

  14. Gene Microarray Analysis using Angular Distribution Decomposition

    E-print Network

    Roberts, Stephen

    Gene Microarray Analysis using Angular Distribution Decomposition Karen Lees1 , Stephen Roberts1 of microarray data to group genes with similar expression profiles. The similarity of expres- sion profiles to define the similarity of gene expression patterns. The pairwise comparisons of exper- imental conditions

  15. Features of cell death in brain and liver, the target tissues of progressive neuronal degeneration of childhood with liver disease (Alpers-Huttenlocher disease)

    Microsoft Academic Search

    Alessandro Simonati; Massimiliano Filosto; Chiara Savio; Giuliano Tomelleri; Paola Tonin; Bernardo Dalla Bernardina; Nicolo' Rizzuto

    2003-01-01

    Alpers-Huttenlocher disease (AHD) is a rare encephalopathy of infancy and childhood characterized by myoclonic seizures and progressive neurological deterioration, usually associated with signs and symptoms of liver dysfunction. There is no biological marker of the disease, and ultimate diagnosis still relies on pathological examination. Features of clinical progression and pathological findings suggest AHD to be secondary to a genetically determined

  16. MARS: Microarray analysis, retrieval, and storage system

    PubMed Central

    Maurer, Michael; Molidor, Robert; Sturn, Alexander; Hartler, Juergen; Hackl, Hubert; Stocker, Gernot; Prokesch, Andreas; Scheideler, Marcel; Trajanoski, Zlatko

    2005-01-01

    Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at . PMID:15836795

  17. Microarray technology to investigate genes associated with papillary thyroid carcinoma.

    PubMed

    Zhu, Xinyong; Yao, Jing; Tian, Wen

    2015-05-01

    DNA microarray data on thyroid tissue from patients with papillary thyroid carcinoma (PTC) and from healthy controls were compared in order to investigate the regulatory genes and uncover the underlying regulatory network in PTC. The DNA microarray data set, GSE3678, was downloaded from Gene Expression Omnibus database. This included seven thyroid tissue samples from patients with PTC and seven samples from healthy controls. Raw data were processed and differentially expressed genes (DEGs) were identified using corresponding R packages. Gene regulation analysis was conducted using TRANSFAC® and TRED. A total of 171 DEGs were obtained. A regulatory network was then established, using 104 of the DEGs. Subsequently, pathway enrichment analyses of the genes were conducted using Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Three differentially expressed transcription factors were identified: Trefoil factor 3, cut?like homeobox 2 and forkhead box protein A2. The most significant pathways involving the 104 DEGs were pathways involved in cancer. Biological process analysis using DAVID, suggested that these genes were associated with the positive regulation of gene expression, gene transcription and metabolic processes. The present study identified a range of genes associated with the development of PTC. The results of the present study were beneficial for understanding the regulatory mechanisms involved in PTC, and for developing clinical diagnostic and therapeutic approaches for this disease. PMID:25586635

  18. Tissues from the irradiated dog/mouse archive

    SciTech Connect

    Gayle Woloschak

    2007-04-01

    The purpose of this project is to organize the databases/information and organize and move the tissues from the long-term dog (4,000 dogs) and mouse (over 30,000 mice) radiation experiments done at Argonne National Laboratory during the 1970's and 80's to Northwestern University. These studies were done with the intention of understanding the effects of exposure to radiation at a variety of different doses, dose-rates, and radiation qualities on end-points such as life-shortening, carcinogenesis, cause of death, shifts in disease incidence and other biological parameters. Organ and tissue samples from these animals including cancers, metastases and other significant degenerative and inflammatory lesions and those in a regular protocol of normal tissues were preserved in paraffin blocks, tissue impressions and sections and represent a great resource for the radiation biology community. These collections are particularly significant since these experiments are not likely to be repeated because of the extreme cost of monies and time for such large-scale animal studies. The long-term goal is to make these tissues and databases available to the wider scientific community so that questions such as tissue sensitivity, early and late effects, low dose and protracted dose responses of normal and tumor tissues, etc. can be examined and defined. Recent advances in biology particularly at the subcellular and molecular level now permit microarray-based gene expression array analyses from paraffin-embedded tissues (where RNA samples are significantly degraded), synchrotron-based studies of metal and other elemental distribution patterns in tissues, PCR-based analyses for mutation detection, and other similar approaches that were not available when the long¬ term animal studies were designed and initiated. Understanding the basis and progression of radiation damage should also permit rational approaches to prevention and mitigation of those damages. Therefore, as stated earlier, these tissues and their related documentation, represent a significant resource for future studies. For this project, we propose to accomplish the following objectives: (1) inventory and organize the tissues, blood smears, wet-tissues and paper-¬based information that is available in the tissue bank at Argonne National Laboratory; (2) convert the existing Oracle database of the mouse studies to MS Access( the dog data is already in this format which is far more user friendly and widely used in business and research) , (3) move the remaining samples and documentation from dogs that had been transferred from ANL to New Mexico (in Dr. F. Hahn's care) to Northwestern University and add these to the inventory; (4) move the tissues and Access database at Argonne National Laboratory to Northwestern University.

  19. DNA Microarrays in Herbal Drug Research

    PubMed Central

    Chavan, Preeti; Joshi, Kalpana; Patwardhan, Bhushan

    2006-01-01

    Natural products are gaining increased applications in drug discovery and development. Being chemically diverse they are able to modulate several targets simultaneously in a complex system. Analysis of gene expression becomes necessary for better understanding of molecular mechanisms. Conventional strategies for expression profiling are optimized for single gene analysis. DNA microarrays serve as suitable high throughput tool for simultaneous analysis of multiple genes. Major practical applicability of DNA microarrays remains in DNA mutation and polymorphism analysis. This review highlights applications of DNA microarrays in pharmacodynamics, pharmacogenomics, toxicogenomics and quality control of herbal drugs and extracts. PMID:17173108

  20. Identification of Novel Cholesteatoma-Related Gene Expression Signatures Using Full-Genome Microarrays

    PubMed Central

    Klenke, Christin; Janowski, Sebastian; Borck, Daniela; Widera, Darius; Ebmeyer, Jörg; Kalinowski, Jörn; Leichtle, Anke; Hofestädt, Ralf; Upile, Tahwinder; Kaltschmidt, Christian; Kaltschmidt, Barbara; Sudhoff, Holger

    2012-01-01

    Background Cholesteatoma is a gradually expanding destructive epithelial lesion within the middle ear. It can cause extensive local tissue destruction in the temporal bone and can initially lead to the development of conductive hearing loss via ossicular erosion. As the disease progresses, sensorineural hearing loss, vertigo or facial palsy may occur. Cholesteatoma may promote the spread of infection through the tegmen of the middle ear and cause meningitis or intracranial infections with abscess formation. It must, therefore, be considered as a potentially life-threatening middle ear disease. Methods and Findings In this study, we investigated differentially expressed genes in human cholesteatomas in comparison to regular auditory canal skin using Whole Human Genome Microarrays containing 19,596 human genes. In addition to already described up-regulated mRNAs in cholesteatoma, such as MMP9, DEFB2 and KRT19, we identified 3558 new cholesteatoma-related transcripts. 811 genes appear to be significantly differentially up-regulated in cholesteatoma. 334 genes were down-regulated more than 2-fold. Significantly regulated genes with protein metabolism activity include matrix metalloproteinases as well as PI3, SERPINB3 and SERPINB4. Genes like SPP1, KRT6B, PRPH, SPRR1B and LAMC2 are known as genes with cell growth and/or maintenance activity. Transport activity genes and signal transduction genes are LCN2, GJB2 and CEACAM6. Three cell communication genes were identified; one CDH19 and two from the S100 family. Conclusions This study demonstrates that the expression profile of cholesteatoma is similar to a metastatic tumour and chronically inflamed tissue. Based on the investigated profiles we present novel protein-protein interaction and signal transduction networks, which include cholesteatoma-regulated transcripts and may be of great value for drug targeting and therapy development. PMID:23285167

  1. Assembly of ordered microsphere arrays: Platforms for microarrays

    NASA Astrophysics Data System (ADS)

    Xu, Wanling

    Microarrays are powerful tools in gene expression assessment, protein profiling, and protein function screening, as well as cell and tissue analysis. With thousands of small array spots assembled in an ordered array, these small devices makes it possible to screen for multiple targets in a fast, parallel, high-throughput manner. The well-developed technology of DNA microarrays, also called DNA chips, has proved successful in all kinds of biological experiments, including the human genome-sequencing project. The development of protein arrays has lagged behind that of DNA arrays mainly because of the greater complexity of proteins. Some parts of the microarray technology can be transplanted into the realm of protein arrays, while others cannot. The challenges from the complexity of protein targets demand more robust and powerful devices. Traditional planar arrays, in which proteins bind directly to a planar surface, have a drawback in that some proteins will be denatured or cluster together after immobilization. Microsphere-based microarrays represent a more advanced strategy. The functional proteins are first attached to microspheres; these microspheres are then immobilized in arrays on a planar surface. In this dissertation, two approaches to assembling arrays of microspheres will be discussed. The hydrodynamic approach uses surface micromachining and Deep Reactive Ion Etching techniques to form an array of channels through a silicon wafer. By drawing fluid containing the microspheres through the channels they become trapped in the channels and thereby immobilized. In the magnetic approach, permalloy films are deposited on a silicon substrate and subsequently patterned to form magnetic attachment sites. An external magnetic field is then applied and the magnetic microspheres then assemble on these sites. Both devices are able to immobilize microspheres in an ordered array, as opposed to coarsely grouping them in array spots. The assembled arrays are robust in that they ensure a resolution rate of almost 100%. In addition, different patterns of array spots with various spacings and diameters can be fabricated to satisfy different requirements. Moreover, the devices are easy to clean and reuse, and the experimental set-ups are relatively simple and portable. All these features make them good platforms for all kinds of microarrays.

  2. Design, construction, characterization, and application of a hyperspectral microarray scanner

    E-print Network

    spectrum between 490 and 900 nm with a spectral resolution of 3 nm for each pixel of the microarray and elimination of unwanted artifacts and greatly improves the accuracy of microarray experiments. Microarray to further in- crease sensitivity, throughput, and accuracy. In a typical microarray experiment,1­4 glass

  3. Contributions to Statistical Problems Related to Microarray Data

    ERIC Educational Resources Information Center

    Hong, Feng

    2009-01-01

    Microarray is a high throughput technology to measure the gene expression. Analysis of microarray data brings many interesting and challenging problems. This thesis consists three studies related to microarray data. First, we propose a Bayesian model for microarray data and use Bayes Factors to identify differentially expressed genes. Second, we…

  4. Exploration and Analysis of DNA Microarray and Protein Array Data

    E-print Network

    Cabrera, Javier

    1 Exploration and Analysis of DNA Microarray and Protein Array Data Dhammika Amaratunga Senior. Multivariate methods (JC) 5. Computational issues and software (JC) Exploration and Analysis of DNA Microarray microarrays DNA microarrays are the most widely used tool to monitor the expression levels of many thousands

  5. Computer vision methods for DNA microarray spotting and quality

    E-print Network

    Cabrera, Javier

    1 Computer vision methods for DNA microarray spotting and quality control Javier Cabrera Rutgers · DNA microarrays · Data processing steps · Spotting the raw image · Spotted image: Microarray Quality the process: DNA ? mRNA ? protein transcription translation #12;4 DNA microarrays One of the most promising

  6. Estimating Dataset Size Requirements for Classifying DNA Microarray Data

    E-print Network

    Poggio, Tomaso

    Estimating Dataset Size Requirements for Classifying DNA Microarray Data S. Mukherjee*+#1 , P words: Gene expression profiling, molecular pattern recognition, DNA microarrays, microarray analysis;1. Introduction Over the last few years the routine use of DNA microarrays has made possible the creation of large

  7. Multidimensional analysis of gene expression reveals TGFB1I1-induced EMT contributes to malignant progression of astrocytomas

    PubMed Central

    Wang, Kuanyu; Zhang, Chuanbao; Wang, Yinyan; Yao, Kun; Yang, Pei; Han, Lei; Kang, Chunsheng; Zhang, Wei; Jiang, Tao

    2014-01-01

    Malignant progression of astrocytoma is a multistep process with the integration of genetic abnormalities including grade progression and subtypes transition. Established biomarkers of astrocytomas, like IDH1 and TP53 mutation, were not associated with malignant progression. To identify new biomarker(s) contributing to malignant progression, we collected 252 samples with whole genome mRNA expression profile [34 normal brain tissue (NBT), 136 grade II astrocytoma (AII) and 82 grade III astrocytoma (AIII)]. Bioinformatics analysis revealed that EMT-associated pathways were most significantly altered along with tumor grades progress with up-regulation of 17 genes. Up-regulation of these genes was further confirmed by RNA-sequencing in 128 samples. Survival analysis revealed that high expression of these genes indicates a poor survival outcome. We focused on TGFB1I1 (TGF-?1 induced transcript 1) whose expression correlation with WHO grades was further validated by qPCR in 6 cell lines of different grades and 49 independent samples (36 AIIs and 13 AIIIs). High expression of TGFB1I1 was found associated with subtype transition and EMT pathways activation. The conclusion was confirmed using immunohistochemistry in tissue microarrays. Studies in vitro and in vivo using TGF-?1 and TGFB1I1 shRNA demonstrated that TGFB1I1 is required for TGF-? stimulated EMT that contributes to malignant progression of astrocytomas. PMID:25333259

  8. Multidimensional analysis of gene expression reveals TGFB1I1-induced EMT contributes to malignant progression of astrocytomas.

    PubMed

    Liu, Yanwei; Hu, Huimin; Wang, Kuanyu; Zhang, Chuanbao; Wang, Yinyan; Yao, Kun; Yang, Pei; Han, Lei; Kang, Chunsheng; Zhang, Wei; Jiang, Tao

    2014-12-30

    Malignant progression of astrocytoma is a multistep process with the integration of genetic abnormalities including grade progression and subtypes transition. Established biomarkers of astrocytomas, like IDH1 and TP53 mutation, were not associated with malignant progression. To identify new biomarker(s) contributing to malignant progression, we collected 252 samples with whole genome mRNA expression profile [34 normal brain tissue (NBT), 136 grade II astrocytoma (AII) and 82 grade III astrocytoma (AIII)]. Bioinformatics analysis revealed that EMT-associated pathways were most significantly altered along with tumor grades progress with up-regulation of 17 genes. Up-regulation of these genes was further confirmed by RNA-sequencing in 128 samples. Survival analysis revealed that high expression of these genes indicates a poor survival outcome. We focused on TGFB1I1 (TGF-?1 induced transcript 1) whose expression correlation with WHO grades was further validated by qPCR in 6 cell lines of different grades and 49 independent samples (36 AIIs and 13 AIIIs). High expression of TGFB1I1 was found associated with subtype transition and EMT pathways activation. The conclusion was confirmed using immunohistochemistry in tissue microarrays. Studies in vitro and in vivo using TGF-?1 and TGFB1I1 shRNA demonstrated that TGFB1I1 is required for TGF-? stimulated EMT that contributes to malignant progression of astrocytomas. PMID:25333259

  9. RNA-seq as a powerful tool for penaeid shrimp genetic progress

    PubMed Central

    Santos, Camilla A.; Blanck, Danielly V.; de Freitas, Patrícia D.

    2014-01-01

    The sequences of all different RNA transcripts present in a cell or tissue that are related to the gene expression and its functional control represent what it is called a transcriptome. The transcripts vary between cells, tissues, ontogenetic and environmental conditions, and the knowledge that can be gained through them is of a solid relevance for genetic applications in aquaculture. Some of the techniques used in transcriptome studies, such as microarrays, are being replaced for next-generation sequencing approaches. RNA-seq emerges as a new possibility for the transcriptome complexity analysis as well as for the candidate genes and polymorphisms identification of penaeid species. Thus, it may also help to understand the determination of complex traits mechanisms and genetic improvement of stocks. In this review, it is first introduced an overview of transcriptome analysis by RNA-seq, followed by a discussion of how this approach may be applied in genetic progress within penaeid stocks. PMID:25221571

  10. Use of lectin microarray to differentiate gastric cancer from gastric ulcer

    PubMed Central

    Huang, Wei-Li; Li, Yang-Guang; Lv, Yong-Chen; Guan, Xiao-Hui; Ji, Hui-Fan; Chi, Bao-Rong

    2014-01-01

    AIM: To investigate the feasibility of lectin microarray for differentiating gastric cancer from gastric ulcer. METHODS: Twenty cases of human gastric cancer tissue and 20 cases of human gastric ulcer tissue were collected and processed. Protein was extracted from the frozen tissues and stored. The lectins were dissolved in buffer, and the sugar-binding specificities of lectins and the layout of the lectin microarray were summarized. The median of the effective data points for each lectin was globally normalized to the sum of medians of all effective data points for each lectin in one block. Formalin-fixed paraffin-embedded gastric cancer tissues and their corresponding gastric ulcer tissues were subjected to Ag retrieval. Biotinylated lectin was used as the primary antibody and HRP-streptavidin as the secondary antibody. The glycopatterns of glycoprotein in gastric cancer and gastric ulcer specimens were determined by lectin microarray, and then validated by lectin histochemistry. Data are presented as mean ± SD for the indicated number of independent experiments. RESULTS: The glycosylation level of gastric cancer was significantly higher than that in ulcer. In gastric cancer, most of the lectin binders showed positive signals and the intensity of the signals was stronger, whereas the opposite was the case for ulcers. Significant differences in the pathological score of the two lectins were apparent between ulcer and gastric cancer tissues using the same lectin. For MPL and VVA, all types of gastric cancer detected showed stronger staining and a higher positive rate in comparison with ulcer, especially in the case of signet ring cell carcinoma and intra-mucosal carcinoma. GalNAc bound to MPL showed a significant increase. A statistically significant association between MPL and gastric cancer was observed. As with MPL, there were significant differences in VVA staining between gastric cancer and ulcer. CONCLUSION: Lectin microarray can differentiate the different glycopatterns in gastric cancer and gastric ulcer, and the lectins MPL and VVA can be used as biomarkers. PMID:24833877

  11. Cluster analysis of microarray data Qizheng Sheng

    E-print Network

    Cluster analysis of microarray data Qizheng Sheng , Yves Moreau§ , Frank De Smet , Kathleen Marchal on various clustering techniques that have been developed for micorarray data analysis. The clustering Sequence Analysis Danish Technical University Kemitorvet, Building 208, Lyngby, Denmark http

  12. Glycan profiling of plant cell wall polymers using microarrays.

    PubMed

    Moller, Isabel E; Pettolino, Filomena A; Hart, Charlie; Lampugnani, Edwin R; Willats, William G T; Bacic, Antony

    2012-01-01

    Plant cell walls are complex matrixes of heterogeneous glycans which play an important role in the physiology and development of plants and provide the raw materials for human societies (e.g. wood, paper, textile and biofuel industries)(1,2). However, understanding the biosynthesis and function of these components remains challenging. Cell wall glycans are chemically and conformationally diverse due to the complexity of their building blocks, the glycosyl residues. These form linkages at multiple positions and differ in ring structure, isomeric or anomeric configuration, and in addition, are substituted with an array of non-sugar residues. Glycan composition varies in different cell and/or tissue types or even sub-domains of a single cell wall(3). Furthermore, their composition is also modified during development(1), or in response to environmental cues(4). In excess of 2,000 genes have Plant cell walls are complex matrixes of heterogeneous glycans been predicted to be involved in cell wall glycan biosynthesis and modification in Arabidopsis(5). However, relatively few of the biosynthetic genes have been functionally characterized (4,5). Reverse genetics approaches are difficult because the genes are often differentially expressed, often at low levels, between cell types(6). Also, mutant studies are often hindered by gene redundancy or compensatory mechanisms to ensure appropriate cell wall function is maintained(7). Thus novel approaches are needed to rapidly characterise the diverse range of glycan structures and to facilitate functional genomics approaches to understanding cell wall biosynthesis and modification. Monoclonal antibodies (mAbs)(8,9) have emerged as an important tool for determining glycan structure and distribution in plants. These recognise distinct epitopes present within major classes of plant cell wall glycans, including pectins, xyloglucans, xylans, mannans, glucans and arabinogalactans. Recently their use has been extended to large-scale screening experiments to determine the relative abundance of glycans in a broad range of plant and tissue types simultaneously(9,10,11). Here we present a microarray-based glycan screening method called Comprehensive Microarray Polymer Profiling (CoMPP) (Figures 1 & 2)(10,11) that enables multiple samples (100 sec) to be screened using a miniaturised microarray platform with reduced reagent and sample volumes. The spot signals on the microarray can be formally quantified to give semi-quantitative data about glycan epitope occurrence. This approach is well suited to tracking glycan changes in complex biological systems(12) and providing a global overview of cell wall composition particularly when prior knowledge of this is unavailable. PMID:23271573

  13. Glycan Profiling of Plant Cell Wall Polymers using Microarrays

    PubMed Central

    Moller, Isabel E.; Pettolino, Filomena A.; Hart, Charlie; Lampugnani, Edwin R.; Willats, William G.T.; Bacic, Antony

    2012-01-01

    Plant cell walls are complex matrixes of heterogeneous glycans which play an important role in the physiology and development of plants and provide the raw materials for human societies (e.g. wood, paper, textile and biofuel industries)1,2. However, understanding the biosynthesis and function of these components remains challenging. Cell wall glycans are chemically and conformationally diverse due to the complexity of their building blocks, the glycosyl residues. These form linkages at multiple positions and differ in ring structure, isomeric or anomeric configuration, and in addition, are substituted with an array of non-sugar residues. Glycan composition varies in different cell and/or tissue types or even sub-domains of a single cell wall3. Furthermore, their composition is also modified during development1, or in response to environmental cues4. In excess of 2,000 genes have Plant cell walls are complex matrixes of heterogeneous glycans been predicted to be involved in cell wall glycan biosynthesis and modification in Arabidopsis5. However, relatively few of the biosynthetic genes have been functionally characterized 4,5. Reverse genetics approaches are difficult because the genes are often differentially expressed, often at low levels, between cell types6. Also, mutant studies are often hindered by gene redundancy or compensatory mechanisms to ensure appropriate cell wall function is maintained7. Thus novel approaches are needed to rapidly characterise the diverse range of glycan structures and to facilitate functional genomics approaches to understanding cell wall biosynthesis and modification. Monoclonal antibodies (mAbs)8,9 have emerged as an important tool for determining glycan structure and distribution in plants. These recognise distinct epitopes present within major classes of plant cell wall glycans, including pectins, xyloglucans, xylans, mannans, glucans and arabinogalactans. Recently their use has been extended to large-scale screening experiments to determine the relative abundance of glycans in a broad range of plant and tissue types simultaneously9,10,11. Here we present a microarray-based glycan screening method called Comprehensive Microarray Polymer Profiling (CoMPP) (Figures 1 & 2)10,11 that enables multiple samples (100 sec) to be screened using a miniaturised microarray platform with reduced reagent and sample volumes. The spot signals on the microarray can be formally quantified to give semi-quantitative data about glycan epitope occurrence. This approach is well suited to tracking glycan changes in complex biological systems12 and providing a global overview of cell wall composition particularly when prior knowledge of this is unavailable. PMID:23271573

  14. Protein Microarrays: Novel Developments and Applications

    Microsoft Academic Search

    Luis Berrade; Angie E. Garcia; Julio A. Camarero

    2011-01-01

    Protein microarray technology possesses some of the greatest potential for providing direct information on protein function\\u000a and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological\\u000a pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical\\u000a pathways and have been used for

  15. Clustering Microarray Data to Determine Normalization Method

    Microsoft Academic Search

    Marie Vendettuoli; Erin Doyle; Heike Hofmann

    \\u000a Most of the scientific journals require published microarray experiments to meet Minimum Information About a Microarray Experiment\\u000a (MIAME) standards. This ensures that other researchers have the necessary information to interpret the results or reproduce\\u000a them. Required MIAME information includes raw experimental data, processed data, and data processing procedures. However,\\u000a the normalization method is often reported inaccurately or not at all.

  16. How Does a DNA Microarray Work?

    NSDL National Science Digital Library

    In this YouTube video, created by Southwest Center for Microsystems Education (SCME), viewers are introduced to the structure of DNA microarrays. Viewers will learn about the physical structure of an array, how it works by utilizing the DNA hybridization process, and how an array analysis is interpreted. This is the second in a series of presentations on DNA microarrays. Supporting materials can be downloaded from the SCME website.

  17. Genome-Wide Microarray Expression and Genomic Alterations by Array-CGH Analysis in Neuroblastoma Stem-Like Cells

    PubMed Central

    Martínez-Soto, Soledad; Legarra, Sheila; Pata-Merci, Noémie; Guegan, Justine; Danglot, Giselle; Bernheim, Alain; Meléndez, Bárbara; Rey, Juan A.; Castresana, Javier S.

    2014-01-01

    Neuroblastoma has a very diverse clinical behaviour: from spontaneous regression to a very aggressive malignant progression and resistance to chemotherapy. This heterogeneous clinical behaviour might be due to the existence of Cancer Stem Cells (CSC), a subpopulation within the tumor with stem-like cell properties: a significant proliferation capacity, a unique self-renewal capacity, and therefore, a higher ability to form new tumors. We enriched the CSC-like cell population content of two commercial neuroblastoma cell lines by the use of conditioned cell culture media for neurospheres, and compared genomic gains and losses and genome expression by array-CGH and microarray analysis, respectively (in CSC-like versus standard tumor cells culture). Despite the array-CGH did not show significant differences between standard and CSC-like in both analyzed cell lines, the microarray expression analysis highlighted some of the most relevant biological processes and molecular functions that might be responsible for the CSC-like phenotype. Some signalling pathways detected seem to be involved in self-renewal of normal tissues (Wnt, Notch, Hh and TGF-?) and contribute to CSC phenotype. We focused on the aberrant activation of TGF-? and Hh signalling pathways, confirming the inhibition of repressors of TGF-? pathway, as SMAD6 and SMAD7 by RT-qPCR. The analysis of the Sonic Hedgehog pathway showed overexpression of PTCH1, GLI1 and SMO. We found overexpression of CD133 and CD15 in SIMA neurospheres, confirming that this cell line was particularly enriched in stem-like cells. This work shows a cross-talk among different pathways in neuroblastoma and its importance in CSC-like cells. PMID:25392930

  18. Probe-Level Analysis of Expression Microarrays Characterizes Isoform-Specific Degradation during Mouse Oocyte Maturation

    PubMed Central

    Salisbury, Jesse; Hutchison, Keith W.; Wigglesworth, Karen; Eppig, John J.; Graber, Joel H.

    2009-01-01

    Background Gene expression microarrays have provided many insights into changes in gene expression patterns between different tissue types, developmental stages, and disease states. Analyses of these data focused primarily measuring the relative abundance of transcripts of a gene, while treating most or all transcript isoforms as equivalent. Differences in the selection between transcript isoforms can, however, represent critical changes to either the protein product or the posttranscriptional regulation of the transcript. Novel analyses on existing microarray data provide fresh insights and new interpretations into transcriptome-wide changes in expression. Methodology A probe-level analysis of existing gene expression arrays revealed differences in mRNA processing, primarily affecting the 3?-untranslated region. Working with the example of microarrays drawn from a transcriptionally silent period of mouse oocyte development, probe-level analysis (implemented here as rmodel) identified genes whose transcript isoforms have differing stabilities. Comparison of micorarrays measuring cDNA generated from oligo-dT and random primers revealed further differences in the polyadenylation status of some transcripts. Additional analysis provided evidence for sequence-targeted cleavage, including putative targeting sequences, as one mechanism of degradation for several hundred transcripts in the maturing oocyte. Conclusions The capability of probe-level analysis to elicit novel findings from existing expression microarray data was demonstrated. The characterization of differences in stability between transcript isoforms in maturing mouse oocytes provided some mechanistic details of degradation. Similar analysis of existing archives of expression microarray data will likely provide similar discoveries. PMID:19834616

  19. Evaluation of Surface Chemistries for Antibody Microarrays

    SciTech Connect

    Seurynck-Servoss, Shannon L.; White, Amanda M.; Baird, Cheryl L.; Rodland, Karin D.; Zangar, Richard C.

    2007-12-01

    Antibody microarrays are an emerging technology that promises to be a powerful tool for the detection of disease biomarkers. The current technology for protein microarrays has been primarily derived from DNA microarrays and is not fully characterized for use with proteins. For example, there are a myriad of surface chemistries that are commercially available for antibody microarrays, but no rigorous studies that compare these different surfaces. Therefore, we have used an enzyme-linked immunosorbent assay (ELISA) microarray platform to analyze 16 different commercially available slide types. Full standard curves were generated for 24 different assays. We found that this approach provides a rigorous and quantitative system for comparing the different slide types based on spot size and morphology, slide noise, spot background, lower limit of detection, and reproducibility. These studies demonstrate that the properties of the slide surface affect the activity of immobilized antibodies and the quality of data produced. Although many slide types can produce useful data, glass slides coated with poly-L-lysine or aminosilane, with or without activation with a crosslinker, consistently produce superior results in the ELISA microarray analyses we performed.

  20. Identifying pathogenic processes by integrating microarray data with prior knowledge

    PubMed Central

    2014-01-01

    Background It is of great importance to identify molecular processes and pathways that are involved in disease etiology. Although there has been an extensive use of various high-throughput methods for this task, pathogenic pathways are still not completely understood. Often the set of genes or proteins identified as altered in genome-wide screens show a poor overlap with canonical disease pathways. These findings are difficult to interpret, yet crucial in order to improve the understanding of the molecular processes underlying the disease progression. We present a novel method for identifying groups of connected molecules from a set of differentially expressed genes. These groups represent functional modules sharing common cellular function and involve signaling and regulatory events. Specifically, our method makes use of Bayesian statistics to identify groups of co-regulated genes based on the microarray data, where external information about molecular interactions and connections are used as priors in the group assignments. Markov chain Monte Carlo sampling is used to search for the most reliable grouping. Results Simulation results showed that the method improved the ability of identifying correct groups compared to traditional clustering, especially for small sample sizes. Applied to a microarray heart failure dataset the method found one large cluster with several genes important for the structure of the extracellular matrix and a smaller group with many genes involved in carbohydrate metabolism. The method was also applied to a microarray dataset on melanoma cancer patients with or without metastasis, where the main cluster was dominated by genes related to keratinocyte differentiation. Conclusion Our method found clusters overlapping with known pathogenic processes, but also pointed to new connections extending beyond the classical pathways. PMID:24758699

  1. NUMERICAL MODELING OF DNA HYBRIDIZATION IN ELECTRONICALLY ACTIVE MICROARRAYS WITH PARTIAL

    E-print Network

    Kassegne, Samuel Kinde

    .......................................................................................................1 1.2 Types of DNA Microarrays............................................................................................14 2.1. DNA Microarray Overview.........................................................................................21 2.3. Dna Microarray Applications

  2. Testing an aflatoxin B1 gene signature in rat archival tissues.

    PubMed

    Merrick, B Alex; Auerbach, Scott S; Stockton, Patricia S; Foley, Julie F; Malarkey, David E; Sills, Robert C; Irwin, Richard D; Tice, Raymond R

    2012-05-21

    Archival tissues from laboratory studies represent a unique opportunity to explore the relationship between genomic changes and agent-induced disease. In this study, we evaluated the applicability of qPCR for detecting genomic changes in formalin-fixed, paraffin-embedded (FFPE) tissues by determining if a subset of 14 genes from a 90-gene signature derived from microarray data and associated with eventual tumor development could be detected in archival liver, kidney, and lung of rats exposed to aflatoxin B1 (AFB1) for 90 days in feed at 1 ppm. These tissues originated from the same rats used in the microarray study. The 14 genes evaluated were Adam8, Cdh13, Ddit4l, Mybl2, Akr7a3, Akr7a2, Fhit, Wwox, Abcb1b, Abcc3, Cxcl1, Gsta5, Grin2c, and the C8orf46 homologue. The qPCR FFPE liver results were compared to the original liver microarray data and to qPCR results using RNA from fresh frozen liver. Archival liver paraffin blocks yielded 30 to 50 ?g of degraded RNA that ranged in size from 0.1 to 4 kB. qPCR results from FFPE and fresh frozen liver samples were positively correlated (p ? 0.05) by regression analysis and showed good agreement in direction and proportion of change with microarray data for 11 of 14 genes. All 14 transcripts could be amplified from FFPE kidney RNA except the glutamate receptor gene Grin2c; however, only Abcb1b was significantly upregulated from control. Abundant constitutive transcripts, S18 and ?-actin, could be amplified from lung FFPE samples, but the narrow RNA size range (25-500 bp length) prevented consistent detection of target transcripts. Overall, a discrete gene signature derived from prior transcript profiling and representing cell cycle progression, DNA damage response, and xenosensor and detoxication pathways was successfully applied to archival liver and kidney by qPCR and indicated that gene expression changes in response to subchronic AFB1 exposure occurred predominantly in the liver, the primary target for AFB1-induced tumors. We conclude that an evaluation of gene signatures in archival tissues can be an important toxicological tool for evaluating critical molecular events associated with chemical exposures. PMID:22545673

  3. Analysis of gene expression profiles as a tool to uncover tumor markers of liver cancer progression in a rat model

    PubMed Central

    VÁSQUEZ-GARZÓN, VERÓNICA R.; BELTRÁN-RAMÍREZ, OLGA; SALCIDO-NEYOY, MARTHA E.; CERVANTE-ANAYA, NANCY; VILLA-TREVIÑO, SAÚL

    2015-01-01

    Establishing a transcriptomic profile of human hepatocellular liver cancer (HCC) progression is a complex undertaking. A rat model of HCC was employed to develop a transcriptomic profile. Using three interventions, preneoplastic lesions appeared after 30 days and they progressed to HCC by 9 months. Preneoplastic and cancer lesions were characterized for transcriptomic analysis, and RNA from total liver homogenates was obtained at 1, 7, 11 and 16 days after the initiation treatment. RNA from dissected persistent preneoplastic lesions, adjacent tissue or cancer tissue was used for 30 days, and 5, 9, 12 and 18 months. The GeneChip® Rat Exon 1.0 ST arrays, Partek software and an Affymetrix console were employed for these analyses. LGALS3BP was differentially expressed at each time point, from the initial period, through the preneoplastic evolution period and until the end of cancer progression period. Twelve differentially expressed genes common to the preneoplastic evolution and to the cancer progression period were detected, which included ABCC3. Validation of the microarrays was confirmed by reverse transcription-quantitative polymerase chain reaction of six genes, including LGALS3BP and ABCC3. Of note, the proteins of these two genes are associated with the multidrug response complex, and evasion of immune surveillance and negative regulation of T cell proliferation. This model is useful for identifying candidate genes, and to validate them with regards to determining their relevance in rat HCC progression. PMID:25798242

  4. Analysis of High-Throughput ELISA Microarray Data

    SciTech Connect

    White, Amanda M.; Daly, Don S.; Zangar, Richard C.

    2011-02-23

    Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

  5. Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray

    PubMed Central

    2010-01-01

    Background Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Results Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties. Conclusion All results suggest that our high-density flax oligo-microarray platform can be used as a very sensitive tool for analyzing gene expression in a large variety of tissues as well as in different cultivars. Moreover, this highly reliable platform can also be used for the quantification of mRNA transcriptional profiling in different flax tissues. PMID:20964859

  6. ampliPHOX colorimetric detection on a DNA microarray for influenza.

    PubMed

    Moulton, Kevin R; Taylor, Amber W; Rowlen, Kathy L; Dawson, Erica D

    2011-01-01

    DNA microarrays have emerged as a powerful tool for pathogen detection. For instance, many examples of the ability to type and subtype influenza virus have been demonstrated. The identification and subtyping of influenza on DNA microarrays has applications in both public health and the clinic for early detection, rapid intervention, and minimizing the impact of an influenza pandemic. Traditional fluorescence is currently the most commonly used microarray detection method. However, as microarray technology progresses towards clinical use, replacing expensive instrumentation with low cost detection technology exhibiting similar performance characteristics to fluorescence will make microarray assays more attractive and cost-effective. The ampliPHOX colorimetric detection technology is intended for research applications, and has a limit of detection within one order of magnitude of traditional fluorescence, with a main advantage being an approximate ten-fold lower instrument cost compared to the confocal microarray scanners required for fluorescence microarray detection. Another advantage is the compact size of the instrument which allows for portability and flexibility, unlike traditional fluorescence instruments. Because the polymerization technology is not as inherently linear as fluorescence detection, however, it is best suited for lower density microarray applications in which a yes/no answer for the presence of a certain sequence is desired, such as for pathogen detection arrays. Currently the maximum spot density compatible with ampliPHOX detection is ˜1800 spots/array. Because of the spot density limitations, higher density microarrays are not suitable for ampliPHOX detection. Here, we present ampliPHOX colorimetric detection technology as a method of signal amplification on a low density microarray developed for the detection and characterization of influenza viruses (FluChip). Although this protocol uses the FluChip (a DNA microarray) as one specific application of ampliPHOX detection, any microarray incorporating biotinylated target can be labeled and detected in a similar manner. The microarray design and biotinylation of the target to be captured are the responsibility of the user. Once the biotinylated target has been captured on the array, ampliPHOX detection can be performed by first tagging the array with a streptavidin-label conjugate (ampliTAG). Upon light exposure using the ampliPHOX Reader instrument, polymerization of a monomer solution (ampliPHY) occurs only in regions containing ampliTAG-labeled targets. The polymer formed can be subsequently stained with a non-toxic solution to improve visual contrast, followed by imaging and analysis using a simple software package (ampliVIEW). The entire FluChip assay from un-extracted sample to result can be performed in about 6 hours, and the ampliPHOX detection steps described above can be completed in about 30 min. PMID:21694688

  7. The use of microarrays in microbial ecology

    SciTech Connect

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer oligonucleotide probes and covers more than 10,000 gene sequences in 150 gene categories involved in carbon, nitrogen, sulfur, and phosphorus cycling, metal resistance and reduction, and organic contaminant degradation. GeoChip can be used as a generic tool for microbial community analysis, and also link microbial community structure to ecosystem functioning. Examples of the application of both arrays in different environmental samples will be described in the two subsequent sections.

  8. Microarrays - A Key Technology for Glycobiology

    NASA Astrophysics Data System (ADS)

    Liu, Yan; Feizi, Ten

    Carbohydrate chains of glycoproteins , glycolipids , and proteoglycans can mediate processes of biological and medical importance through their interactions with complementary proteins. The unraveling of these interactions is a priority therefore in biomedical sciences. Carbohydrate microarray technology is a new development at the frontiers of glycomics that has revolutionized the study of carbohydrate-protein interactions and the elucidation of their specificities in endogenous biological processes, immune defense mechanisms, and microbe-host interactions. In this chapter we briefly touch upon the principles of numerous platforms since the introduction of carbohydrate microarrays in 2002, and we highlight platforms that are beyond proof-of-concept, and have provided new biological information.

  9. A memetic algorithm for discovering negative correlation biclusters of DNA microarray data

    E-print Network

    Hao, Jin-Kao

    A memetic algorithm for discovering negative correlation biclusters of DNA microarray data Wassim; Microarrays data; Negative correlations; Memetic algorithm. 1. Introduction DNA microarray technology permits for specific biological studies and medical applications. In this context, biclustering of DNA microarray data

  10. The Utility of the DNA Microarray Scanner to Simplify the Immunofluorescence Evaluation of Autoimmune Bullous Diseases

    PubMed Central

    Iwamoto, Satori; Iwamoto, Alex T.; Cha, Jisun; Clark, Todd; Lu, Ming; Breen, Catherine; Bhawan, Jag; Falanga, Vincent

    2009-01-01

    A DNA microarray scanner was used as a digital fluorescence microscope to simplify the diagnosis of autoimmune bullous diseases. Frozen sections of skin biopsies were taken from 3 patients with bullous pemphigoid and 1 patient each with lichen planus pemphigoides, linear immunoglobulin (Ig) A disease, and dermatitis herpetiformis. After incubation with cyanine-labeled antibodies, the tissues were scanned at 5-?m resolution using an instrument originally designed to study gene expression. The microarray scanner’s large field of view, unlike that of fluorescence microscopy, allowed a view of the entire specimen, considerably easing the orientation of tissue. All images were diagnostic and included a linear pattern along the basement membrane zone (BMZ) using anti-IgG and anti-C3 in all cases of bullous pemphigoid, a linear pattern of igG along the BMZ in lichen planus pemphigoides, and a linear pattern of IgA along the BMZ in linear IgA dermatosis. IgA deposition along dermal papillary tips was seen in dermatitis herpetiformis, but a granular pattern was indiscernible at the 5-?m resolution. The advantage of the microarray scanner over standard fluorescence microscopy include speed, technical ease, large field of view, potential for visualizing multiple antibodies simultaneously in a tissue section, and convenience of digital image archiving. PMID:19384060

  11. Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies

    PubMed Central

    2013-01-01

    Background The most important challenge of performing insitu transcriptional profiling of the human ocular surface epithelial regions is obtaining samples in sufficient amounts, without contamination from adjacent tissue, as the region of interest is microscopic and closely apposed to other tissues regions. We have effectively collected ocular surface (OS) epithelial tissue samples from the Limbal Epithelial Crypt (LEC), limbus, cornea and conjunctiva of post-mortem cadaver eyes with laser microdissection (LMD) technique for gene expression studies with spotted oligonucleotide microarrays and Gene 1.0 ST arrays. Methods Human donor eyes (4 pairs for spotted oligonucleotide microarrays, 3 pairs for Gene 1.0 ST arrays) consented for research were included in this study with due ethical approval of the Nottingham Research Ethics Committee. Eye retrieval was performed within 36 hours of post-mortem period. The dissected corneoscleral buttons were immersed in OCT media and frozen in liquid nitrogen and stored at ?80°C till further use. Microscopic tissue sections of interest were taken on PALM slides and stained with Toluidine Blue for laser microdissection with PALM microbeam systems. Optimisation of the laser microdissection technique was crucial for efficient and cost effective sample collection. Results The starting concentration of RNA as stipulated by the protocol of microarray platforms was taken as the cut-off concentration of RNA samples in our studies. The area of LMD tissue processed for spotted oligonucleotide microarray study ranged from 86,253 ?m2 in LEC to 392,887 ?m2 in LEC stroma. The RNA concentration of the LMD samples ranged from 22 to 92 pg/?l. The recommended starting concentration of the RNA samples used for Gene 1.0 ST arrays was 6 ng/5 ?l. To achieve the desired RNA concentration the area of ocular surface epithelial tissue sample processed for the Gene 1.0 ST array experiments was approximately 100,0000 ?m2 to 130,0000 ?m2. RNA concentration of these samples ranged from 10.88 ng/12 ?l to 25.8 ng/12 ?l, with the RNA integrity numbers (RIN) for these samples from 3.3 to 7.9. RNA samples with RIN values below 2, that had failed to amplify satisfactorily were discarded. Conclusions The optimised protocol for sample collection and laser microdissection improved the RNA yield of the insitu ocular surface epithelial regions for effective microarray studies on spotted oligonucleotide and affymetrix platforms. PMID:24160452

  12. Photoelectromechanical synthesis of low-cost DNA microarrays

    E-print Network

    Chow, Brian, 1978-

    2008-01-01

    Recent advances in de novo gene synthesis, library construction, and genomic selection for target sequencing using DNA from custom microarrays have demonstrated that microarrays can effectively be used as the world's ...

  13. Genome-wide analyses using bead-based microarrays

    E-print Network

    Dunning, Mark J

    2008-09-04

    Microarrays are now an established tool for biological research and have a wide range of applications. In this thesis I investigate the BeadArray microarray technology developed by Illumina. The design of this technology is unique and gives rise...

  14. Multiple criteria differential expression analysis of microarray data

    E-print Network

    Hero, Alfred O.

    from biological data. ! Data Mining: Algorithms for extracting information from huge datasets using aberrations, gain settings ! Imaging and Extraction ­ misaligned spot grid, segmentation Microarray dataMultiple criteria differential expression analysis of microarray data Alfred O. Hero III University

  15. Mixture Modeling and Outlier Detection in Microarray Data Analysis

    E-print Network

    George, Nysia I.

    2010-01-16

    Microarray technology has become a dynamic tool in gene expression analysis because it allows for the simultaneous measurement of thousands of gene expressions. Uniqueness in experimental units and microarray data platforms, coupled with how gene...

  16. Zebrafish promoter microarrays identify actively transcribed embryonic genes

    E-print Network

    Wardle, Fiona C; Odom, Duncan T; Bell, George W; Yuan, Bingbing; Danford, Timothy W; Wiellette, Elizabeth L; Herbolsheimer, Elizabeth; Sive, Hazel L; Young, Richard A; Smith, James C

    2006-08-04

    Abstract We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody...

  17. Zebrafish promoter microarrays identify actively transcribed embryonic genes

    E-print Network

    Wardle, Fiona C

    We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation ...

  18. Microarray analysis of gene expression during the inflammation and endochondral bone formation stages of rat femur fracture repair

    Microsoft Academic Search

    Charles H. Rundle; Hali Wang; Hongrun Yu; Robert B. Chadwick; Emile I. Davis; Jon E. Wergedal; K.-H. William Lau; Subburaman Mohan; James T. Ryaby; David J. Baylink

    2006-01-01

    Microarray analysis of gene expression was performed in the healing femur fractures of 13-week-old male rats during the inflammatory stage of repair, at 3 days post-fracture, and the endochondral bone formation stage of repair, at 11 days post-fracture. Multiple replicate pairs of fracture tissues paired with unfractured tissues, and unfractured control bones that had the stabilizing K-wire were introduced. This

  19. Lossless compression of microarray images using image-dependent finite-context models.

    PubMed

    Neves, António J R; Pinho, Armando J

    2009-02-01

    The use of microarray expression data in state-of-the-art biology has been well established. The widespread adoption of this technology, coupled with the significant volume of data generated per experiment, in the form of images, has led to significant challenges in storage and query retrieval. In this paper, we present a lossless bitplane-based method for efficient compression of microarray images. This method is based on arithmetic coding driven by image-dependent multibitplane finite-context models. It produces an embedded bitstream that allows progressive, lossy-to-lossless decoding. We compare the compression efficiency of the proposed method with three image compression standards (JPEG2000, JPEG-LS, and JBIG) and also with the two most recent specialized methods for microarray image coding. The proposed method gives better results for all images of the test sets and confirms the effectiveness of bitplane-based methods and finite-context modeling for the lossless compression of microarray images. PMID:19188108

  20. Microarray Probe Design Using -Multi-Objective Evolutionary Algorithms with

    E-print Network

    . As DNA microarrays have been widely used for gene expres- sion profiling and other fields, the importance microarray is widely used to study cell cycle, gene expression profiling, and other DNA-related phenomena of reliable probe design for microarray has been highlighted. First, the probe design for DNA mi- croarray

  1. Selecting Informative Genes from Microarray Dataset by Incorporating Gene Ontology

    E-print Network

    Buffalo, State University of New York

    profiling [13]. A typical DNA microarray study utilizes several DNA microarray chips on different tis- sue in classifying tumor molecularly with the advent of DNA microarray technologies for large-scale transcriptional samples and generates a numerical array with thousands of rows (genes) and tens of columns (experiments/DNA

  2. Applications for Microarrays in Renal Biology and Medicine

    Microsoft Academic Search

    Erwin P. Böttinger; Wenjun Ju; Jiri Zavadil

    2002-01-01

    Groundbreaking recent developments, such as the near completion of human and mouse genome sequencing efforts and the emergence of robust microarray (gene chip) technologies, enabling comprehensive analysis of transcriptomes, provide new opportunities of unprecedented scale for researchers of kidney biology and disease. Combined with advanced computational and mathematical approaches for microarray data analysis, microarray applications promise to revolutionize our understanding

  3. Combining Results of Microarray Experiments: A Rank Aggregation Approach

    Microsoft Academic Search

    Robert P. DeConde; Sarah Hawley; Seth Falcon; Nigel Clegg; Beatrice Knudsen; Ruth Etzioni

    2006-01-01

    As technology for microarray analysis becomes widespread, it is becoming increasingly important to be able to compare and combine the results of experiments that explore the same scientific question. In this article, we present a rank-aggregation approach for combining results from several microarray studies. The motivation for this approach is twofold; first, the final results of microarray studies are typically

  4. Iterated Local Search for Biclustering of Microarray Data

    E-print Network

    Hao, Jin-Kao

    with two most popular algorithms. Key words: Analysis of DNA microarray data, biclustering, evaluation function, iterative local search. 1 Introduction With the fast advances of DNA Microarray technologies or gene interaction, and to understand various genetic diseases. Formally, DNA microarray data is usually

  5. DNA microarray inspection by interference microscopy and A. Dubois

    E-print Network

    DNA microarray inspection by interference microscopy L. Vabrea) and A. Dubois Laboratoire d November 2000; accepted for publication 4 March 2001 DNA microarrays are important new objects of picometers in height. This microscope has been applied to obtain 3D images of DNA microarray spots. We

  6. Mining Subspace Clusters from DNA Microarray Data Using Large Itemset

    E-print Network

    Chang, Ye-In

    Mining Subspace Clusters from DNA Microarray Data Using Large Itemset Techniques Ye-In Chang1 the DNA microarrays could help researchers identify those genes which commonly contribute to a disease of conditions. Since in a DNA microarray, the number of genes is far larger than the number of conditions, those

  7. DNA microarray technologies for measuring proteinDNA interactions

    E-print Network

    Bulyk, Martha L.

    DNA microarray technologies for measuring protein­DNA interactions Martha L Bulyk DNA approach to analyse the in vitro binding of proteins directly to double-stranded DNA microarrays (protein specificities. Recent advances in DNA microarray synthesis technologies have facilitated the definition of DNA

  8. Compressed Sensing DNA Microarrays ECE, Rice University TREE0706

    E-print Network

    Compressed Sensing DNA Microarrays ECE, Rice University TREE0706 Mona A. Sheikh, Olgica Milenkovic. The DNA microarray is one of the most frequently employed technological solutions for microbe detection. To overcome these limitations, it has been proposed that a DNA microarray based on the theory of Compressed

  9. Pattern-based Similarity Search for Microarray Data Haixun Wang

    E-print Network

    Pei, Jian

    - ciently quantify the similarity between two objects in a meaningful way. In DNA microarray analysis microarray analy- sis [1, 8, 7]. A DNA microarray is a two dimensional matrix where entry dij represents near neighbors based on subspace pattern similarity is important to many applications including DNA

  10. DNA MICROARRAY DATA CLUSTERING USING GROWING SELF ORGANIZING NETWORKS

    E-print Network

    Koprinska, Irena

    DNA MICROARRAY DATA CLUSTERING USING GROWING SELF ORGANIZING NETWORKS Kim Jackson and Irena}@it.usyd.edu.au ABSTRACT Recent advances in DNA microarray technology have allowed biologists to simultaneously monitor Neural Gas) for clustering DNA microarray data, comparing them with traditional algorithms. 1

  11. Application of Statistical Learning Theory to DNA Microarray Analysis

    E-print Network

    Poggio, Tomaso

    Application of Statistical Learning Theory to DNA Microarray Analysis by Sayan Mukherjee B Learning Theory to DNA Microarray Analysis by Sayan Mukherjee Submitted to the Department of Brain Sciences in the framework of statistical learning theory, to analyzing DNA microarray data. The rst part of the thesis

  12. Gene Selection and Ranking with Microarray Data Alfred O. Hero

    E-print Network

    Hero, Alfred O.

    Gene Selection and Ranking with Microarray Data Alfred O. Hero Dept. of Electrical Engineering in biotechnology. For example, using gene microarrays, it is now possible to probe a person's gene ex- pression profile over the more than 30,000 genes of the hu- man genome. Signals extracted from gene microarray

  13. Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.

    SciTech Connect

    Rohde, Rachel M.; Timlin, Jerilyn Ann

    2005-11-01

    This report summarizes research performed at Sandia National Laboratories (SNL) in collaboration with the Environmental Protection Agency (EPA) to assess microarray quality on arrays from two platforms of interest to the EPA. Custom microarrays from two novel, commercially produced array platforms were imaged with SNL's unique hyperspectral imaging technology and multivariate data analysis was performed to investigate sources of emission on the arrays. No extraneous sources of emission were evident in any of the array areas scanned. This led to the conclusions that either of these array platforms could produce high quality, reliable microarray data for the EPA toxicology programs. Hyperspectral imaging results are presented and recommendations for microarray analyses using these platforms are detailed within the report.

  14. Discriminatory Mining of Gene Expression Microarray Data

    Microsoft Academic Search

    Zuyi Wang; Yue Wang; Jianping Lu; Sun-yuan Kung; Junying Zhang; Richard Lee; Jianhua Xuan; Javed I. Khan; Robert Clarke

    2003-01-01

    Recent advances in machine learning and pattern recognition methods provide new analytical tools to explore high dimensional gene expression microarray data. Our data mining software, VISual Data Analyzer for cluster discovery (VISDA), reveals many distinguishing patterns among gene expression profiles, which are responsible for the cell's phenotypes. The model-supported exploration of high-dimensional data space is achieved through two complementary schemes:

  15. Shrinkage covariance matrix approach for microarray data

    NASA Astrophysics Data System (ADS)

    Karjanto, Suryaefiza; Aripin, Rasimah

    2013-04-01

    Microarray technology was developed for the purpose of monitoring the expression levels of thousands of genes. A microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints including the high cost of producing microarray chips. As a result, the widely used standard covariance estimator is not appropriate for this purpose. One such technique is the Hotelling's T2 statistic which is a multivariate test statistic for comparing means between two groups. It requires that the number of observations (n) exceeds the number of genes (p) in the set but in microarray studies it is common that n < p. This leads to a biased estimate of the covariance matrix. In this study, the Hotelling's T2 statistic with the shrinkage approach is proposed to estimate the covariance matrix for testing differential gene expression. The performance of this approach is then compared with other commonly used multivariate tests using a widely analysed diabetes data set as illustrations. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.

  16. ANNOTATION OF THE AFFYMETRIX PORCINE GENOME MICROARRAY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Affymetrix Porcine Genome Microarray is minimally annotated. Less than 10% of the probe sets on this array are described with gene names, posing a challenge to biological interpretation of data. Lack of annotation is likely due to limited availability of full-length porcine cDNA sequence. Pr...

  17. Normalization for triple-target microarray experiments

    Microsoft Academic Search

    Marie-laure Martin-magniette; Julie Aubert; Avner Bar-hen; Samira Elftieh; Frederic Magniette; Jean-pierre Renou; Jean-jacques Daudin

    2008-01-01

    BACKGROUND: Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis) allow hybridization up to four samples simultaneously. The two additional dyes are

  18. MICROARRAY DATA ANALYSIS USING MULTIPLE STATISTICAL MODELS

    EPA Science Inventory

    Microarray Data Analysis Using Multiple Statistical Models Wenjun Bao1, Judith E. Schmid1, Amber K. Goetz1, Ming Ouyang2, William J. Welsh2,Andrew I. Brooks3,4, ChiYi Chu3,Mitsunori Ogihara3,4, Yinhe Cheng5, David J. Dix1. 1National Health and Environmental Effects Researc...

  19. Practical DNA Microarray Analysis: An Introduction

    E-print Network

    Spang, Rainer

    DNA versus oligonucleotide microarrays, spotted vs. printed vs. in-situ synthesized chips, one- channel vs statistical tests (t-test, Wilco- xon test) P values from these tests have to be corrected for mul- tiple are nested, the appropriate statistical method is ANO- VA The problem of multiple testing persists #12

  20. On integrating multi-experiment microarray data.

    PubMed

    Tsiliki, Georgia; Vlachakis, Dimitrios; Kossida, Sophia

    2014-05-28

    With the extensive use of microarray technology as a potential prognostic and diagnostic tool, the comparison and reproducibility of results obtained from the use of different platforms is of interest. The integration of those datasets can yield more informative results corresponding to numerous datasets and microarray platforms. We developed a novel integration technique for microarray gene-expression data derived by different studies for the purpose of a two-way Bayesian partition modelling which estimates co-expression profiles under subsets of genes and between biological samples or experimental conditions. The suggested methodology transforms disparate gene-expression data on a common probability scale to obtain inter-study-validated gene signatures. We evaluated the performance of our model using artificial data. Finally, we applied our model to six publicly available cancer gene-expression datasets and compared our results with well-known integrative microarray data methods. Our study shows that the suggested framework can relieve the limited sample size problem while reporting high accuracies by integrating multi-experiment data. PMID:24751870

  1. Bisociative Knowledge Discovery for Microarray Data Analysis

    E-print Network

    Novak, Petra Kralj

    to diverse bioinformatics resources. Preliminary ex- periments with microarray data illustrate the approach and Kyoto Encyclopedia of Genes and Genomes, are sources of biological knowledge. Since the growing amounts. The concept of biso- ciation in science is illustrated in Figure 1. Fig. 1. Koestler's schema of bisociative

  2. Sources of variation in Affymetrix microarray experiments

    Microsoft Academic Search

    Stanislav O. Zakharkin; Kyoungmi Kim; Tapan Mehta; Lang Chen; Stephen Barnes; Katherine E. Scheirer; Rudolph S. Parrish; David B. Allison; Grier P. Page

    2005-01-01

    Background: A typical microarray experiment has many sources of variation which can be attributed to biological and technical causes. Identifying sources of variation and assessing their magnitude, among other factors, are important for optimal experimental design. The objectives of this study were: (1) to estimate relative magnitudes of different sources of variation and (2) to evaluate agreement between biological and

  3. Missing value estimation methods for DNA microarrays

    Microsoft Academic Search

    Olga G. Troyanskaya; Michael Cantor; Gavin Sherlock; Patrick O. Brown; Trevor Hastie; Robert Tibshirani; David Botstein; Russ B. Altman

    2001-01-01

    Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression val- ues. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical cluster- ing and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. Methods

  4. Analysis of Microarray Gene Expression Data

    Microsoft Academic Search

    Tuan D. Pham; Christine Wells; Denis I. Crane

    2006-01-01

    Microarrays provide the biological research community with tremendously rich, sensitive and detailed information on gene expression profiles. Gene expression profiling and gene expression patterns have been found useful for solving a wide variety of important biological and biomedical problems, including the study of metabolic pathways, inference of the functions of unknown genes, diagnosis of diseased states, as well as facilitating

  5. Probe Design for Compressive Sensing DNA Microarrays

    E-print Network

    microarrays, in which each genetic sensor is designed to re- spond to a single target, in a CSM each sensor, experiments show that out- of-equilibrium datasets are usually as accurate as those obtained from equilibrium design I. INTRODUCTION Accurate identification of large numbers of genetic se- quences in an environment

  6. Data Mining Techniques DNA Microarray Data

    E-print Network

    Rocha, Luis

    Data Mining Techniques for DNA Microarray Data Miguel Rocha Isabel Rocha CCTC / CEB Universidade do Minho #12;PRESENTATION STRUCTURE TECHNOLOGY DATA PRE-PROCESSING DATA MINING CLUSTERING CLASSIFICATION CONCLUSIONS #12;TECHNOLOGY DATA PRE-PROCESSING STATISTICAL TESTS DATA MINING CLUSTERING CLASSIFICATION

  7. Basic microarray analysis: grouping and feature reduction

    Microsoft Academic Search

    Soumya Raychaudhuri; Patrick D. Sutphin; Jeffrey T. Chang; Russ B. Altman

    2001-01-01

    DNA microarray technologies are useful for addressing a broad range of biological problems — including the measurement of mRNA expression levels in target cells. These studies typically produce large data sets that contain measurements on thousands of genes under hundreds of conditions. There is a critical need to summarize this data and to pick out the important details. The most

  8. Mixture model analysis of DNA microarray images

    Microsoft Academic Search

    Konstantinos Blekas; Nikolas P. Galatsanos; Aristidis Likas; Isaac E. Lagaris

    2005-01-01

    In this paper, we propose a new methodology for anal- ysis of microarray images. First, a new gridding algorithm is pro- posed for determining the individual spots and their borders. Then, a Gaussian mixture model (GMM) approach is presented for the analysis of the individual spot images. The main advantages of the proposed methodology are modeling flexibility and adaptability to

  9. Discovery and analysis of pancreatic adenocarcinoma genes using cDNA microarrays

    PubMed Central

    Jin, Gang; Hu, Xian-Gui; Ying, Kang; Tang, Yan; Liu, Rui; Zhang, Yi-Jie; Jing, Zai-Ping; Xie, Yi; Mao, Yu-Min

    2005-01-01

    AIM: To study the pathogenetic processes and the role of gene expression by microarray analyses in expediting our understanding of the molecular pathophysiology of pancreatic adenocarcinoma, and to identify the novel cancer-associated genes. METHODS: Nine histologically defined pancreatic head adenocarcinoma specimens associated with clinical data were studied. Total RNA and mRNA were isolated and labeled by reverse transcription reaction with Cy5 and Cy3 for cDNA probe. The cDNA microarrays that represent a set of 4 096 human genes were hybridized with labeled cDNA probe and screened for molecular profiling analyses. RESULTS: Using this methodology, 184 genes were screened out for differences in gene expression level after nine couples of hybridizations. Of the 184 genes, 87 were upregulated and 97 downregulated, including 11 novel human genes. In pancreatic adenocarcinoma tissue, several invasion and metastasis related genes showed their high expression levels, suggesting that poor prognosis of pancreatic adenocarcinoma might have a solid molecular biological basis. CONCLUSION: The application of cDNA microarray technique for analysis of gene expression patterns is a powerful strategy to identify novel cancer-associated genes, and to rapidly explore their role in clinical pancreatic adenocarcinoma. Microarray profiles provide us new insights into the carcinogenesis and invasive process of pancreatic adenocarcinoma. Our results suggest that a highly organized and structured process of tumor invasion exists in the pancreas. PMID:16425432

  10. Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization

    PubMed Central

    2014-01-01

    Background Affymetrix microarray technology allows one to investigate expression of thousands of genes simultaneously upon a variety of conditions. In a popular U133A microarray platform, the expression of 37% of genes is measured by more than one probeset. The discordant expression observed for two different probesets that match the same gene is a widespread phenomenon which is usually underestimated, ignored or disregarded. Results Here we evaluate the prevalence of discordant expression in data collected using Affymetrix HG-U133A microarray platform. In U133A, about 30% of genes annotated by two different probesets demonstrate a substantial correlation between independently measured expression values. To our surprise, sorting the probesets according to the nature of the discrepancy in their expression levels allowed the classification of the respective genes according to their fundamental functional properties, including observed enrichment by tissue-specific transcripts and alternatively spliced variants. On another hand, an absence of discrepancies in probesets that simultaneously match several different genes allowed us to pinpoint non-expressed pseudogenes and gene groups with highly correlated expression patterns. Nevertheless, in many cases, the nature of discordant expression of two probesets that match the same transcript remains unexplained. It is possible that these probesets report differently regulated sets of transcripts, or, in best case scenario, two different sets of transcripts that represent the same gene. Conclusion The majority of absolute gene expression values collected using Affymetrix microarrays may not be suitable for typical interpretative downstream analysis. PMID:25563078

  11. Cell microarrays based on hydrogel microstructures for the application to cell-based biosensor.

    PubMed

    Koh, Won-Gun

    2011-01-01

    Cell-based biosensors constitute a promising field that has numerous applications ranging from pharmaceutical screening to detection of pathogen and toxicant. The trends toward miniaturization of cell-based biosensor continue to spur development of cell microarray integrated into microfluidic devices. For cell-based biosensors to be useful for larger applications, several technical goals must be realized. First, the cell-patterning method used to generate multi-phenotypic array can accommodate multiple cell lines without major losses of cell viability, maintain total isolation of each cell phenotype, provide for the adequate mass transfer of dissolved gases and nutrients, and easy enough to allow for mass production. Second, cells on microarray must be cultured in three-dimensional environment as they do in real tissue to obtain accurate response of cells against target analyte. Third, physiological status of micropatterned cells must be monitored non-invasively. As one solution to satisfy these requirements, we prepare cell microarrays using microfabricated poly(ethylene glycol)(PEG) hydrogel. Arrays of hydrogel microstructures encapsulating one or more different cell phenotypes can be fabricated using photolithography or photoreaction injection molding, and can be incorporated within microfluidic network. Finally, we demonstrate the potential application of cell-containing hydrogel microarrays for toxin detection by monitoring toxin-induced change of cell viability and intercellular enzymatic reaction. PMID:20967627

  12. High-Throughput Nano-Biofilm Microarray for Antifungal Drug Discovery

    PubMed Central

    Srinivasan, Anand; Leung, Kai P.; Lopez-Ribot, Jose L.; Ramasubramanian, Anand K.

    2013-01-01

    ABSTRACT Micro- and nanoscale technologies have radically transformed biological research from genomics to tissue engineering, with the relative exception of microbial cell culture, which is still largely performed in microtiter plates and petri dishes. Here, we present nanoscale culture of the opportunistic fungal pathogen Candida albicans on a microarray platform. The microarray consists of 1,200 individual cultures of 30 nl of C. albicans biofilms (“nano-biofilms”) encapsulated in an inert alginate matrix. We demonstrate that these nano-biofilms are similar to conventional macroscopic biofilms in their morphological, architectural, growth, and phenotypic characteristics. We also demonstrate that the nano-biofilm microarray is a robust and efficient tool for accelerating the drug discovery process: (i) combinatorial screening against a collection of 28 antifungal compounds in the presence of immunosuppressant FK506 (tacrolimus) identified six drugs that showed synergistic antifungal activity, and (ii) screening against the NCI challenge set small-molecule library identified three heretofore-unknown hits. This cell-based microarray platform allows for miniaturization of microbial cell culture and is fully compatible with other high-throughput screening technologies. PMID:23800397

  13. Symptomatic and asymptomatic benign prostatic hyperplasia: Molecular differentiation by using microarrays

    NASA Astrophysics Data System (ADS)

    Prakash, Kulkarni; Pirozzi, Gregorio; Elashoff, Michael; Munger, William; Waga, Iwao; Dhir, Rajiv; Kakehi, Yoshiyuki; Getzenberg, Robert H.

    2002-05-01

    Benign prostatic hyperplasia (BPH) is a disease of unknown etiology that significantly affects the quality of life in aging men. Histologic BPH may present itself either as symptomatic or asymptomatic in nature. To elucidate the molecular differences underlying BPH, gene expression profiles from the prostate transition zone tissue have been analyzed by using microarrays. A set of 511 differentially expressed genes distinguished symptomatic and asymptomatic BPH. This genetic signature separates BPH from normal tissue but does not seem to change with age. These data could provide novel approaches for alleviating symptoms and hyperplasia in BPH.

  14. The Quantum of Initial Transformed Cells Potentially Modulates the Type of Local Inflammation Mechanism Elicited by Surrounding Normal Epithelial Tissues and Systemic Immune Pattern for Tumor Arrest or Progression

    PubMed Central

    Owusu, Lawrence; Wang, Bo; Du, Yue; Li, Weiling; Xin, Yi

    2015-01-01

    The immune/ inflammation system potentially serves to arrest, eliminate or promote tumor development. Nonetheless, factors that dictate the choice are not comprehensively known yet. Using a B16/F1 syngeneic wild type model, we evaluated the essentiality of initial transformed cells' density for overt tumor development, the molecular trends of inflammatory mediators in the normal tumor-adjacent epithelial tissues (NTAT), and how such local events may reflect systematically in the host. Overt tumors developed, within an observatory period of at least 45 days and 90 days at most, only in mice inoculated with cancer cells above a limiting threshold of 1× 103 cells. Immunoblots showed early, intense and transient presence of IL-1?, IFN-?, and both the all-thiol and disulfide forms of HMGB1 in the NTAT of non-tumor bearing mice. However, all-thiol form of HMGB1 and delayed but aberrant IL-6 expression characterized chronic inflammation in tumor bearing hosts. These local epithelial tissue events uniquely reflected in host's systemic cytokines dynamics where stable Th1/Th2 signature (IFN-?/ IL-4) coupled with early Th1 cells polarization (IL-12/ IL-4) evidenced in non-tumor hosts but highly fluctuating Th1/ Th2 profile in tumor hosts, even before tumors became overt. This hypothesizes that the physical quantum of transformed cells that may either spontaneously arise or accrue at a locus may be crucial in orchestrating the mechanism for the type of local epithelial tissue and systemic immune/ inflammatory responses essential for tumor progression or arrest. PMID:25561977

  15. Solitary Bone Plasmacytoma Progressing into Retroperitoneal Plasma Cell Myeloma with No Related End Organ or Tissue Impairment: A Case Report and Review of the Literature

    PubMed Central

    Tikku, Gargi; Jain, Monica; Mridha, Asit; Grover, Rajesh

    2014-01-01

    Solitary bone plasmacytomas and plasma cell myeloma are clonal proliferations of plasma cells. Many patients with solitary bone plasmacytomas develop plasma cell myeloma on follow-up. We present a case of a 70-year-old man who presented with fracture and a lytic lesion in the subtrochanteric region of the left femur and was assigned a diagnosis of solitary bone plasmacytoma. He received local curative radiotherapy. However, 4 months later his serum M protein and ?2-microglobulin levels increased to 2.31 g/dL and 5.965 mg/L, respectively. He complained of abdominal fullness and constipation. Ultrasound and non-contrast CT imaging revealed multiple retroperitoneal masses. Colonoscopic examination was normal. Biopsy of the a retroperitoneal mass confirmed it to be a plasmacytoma. Repeat hemogram, blood urea, serum creatinine, skeletal survey, and bone marrow examination revealed no abnormalities. This is an unusual presentation of plasma cell myeloma, which manifested as multiple huge extramedullary retroperitoneal masses and arose from a solitary bone plasmacytoma, without related end organ or tissue impairment and bone marrow plasmacytosis. The patient succumbed to his disease 8 months after the appearance of the retroperitoneal masses. This case highlights the importance of close monitoring of patients diagnosed with solitary bone plasmacytoma with increased serum M protein and serum ?2-microglobulin levels, so that early therapy can be instituted to prevent conversion to plasma cell myeloma. PMID:25330522

  16. Nestin(+) Tissue-Resident Multipotent Stem Cells Contribute to Tumor Progression by Differentiating into Pericytes and Smooth Muscle Cells Resulting in Blood Vessel Remodeling

    PubMed Central

    Klein, Diana; Meissner, Nicole; Kleff, Veronika; Jastrow, Holger; Yamaguchi, Masahiro; Ergün, Süleyman; Jendrossek, Verena

    2014-01-01

    Tumor vessels with resistance to anti-angiogenic therapy are characterized by the normalization of the vascular structures through integration of mature pericytes and smooth muscle cells (SMC) into the vessel wall, a process termed vessel stabilization. Unfortunately, stabilization-associated vascular remodeling can result in reduced sensitivity to subsequent anti-angiogenic therapy. We show here that blockade of VEGF by bevacizumab induces stabilization of angiogenic tumor blood vessels in human tumor specimen by recruiting Nestin-positive cells, whereas mature vessels down-regulated Nestin-expression. Using xenograft tumors growing on bone-marrow (BM) chimera of C57Bl/6 wildtype and Nestin-GFP transgenic mice, we show for first time that Nestin(+) cells inducing the maturation of tumor vessels do not originate from the BM but presumably reside within the adventitia of adult blood vessels. Complementary ex vivo experiments using explants of murine aortas revealed that Nestin(+) multipotent stem cells (MPSCs) are mobilized from their niche and differentiated into pericytes and SMC through the influence of tumor-cell-secreted factors. We conclude that tissue-resident Nestin(+) cells are more relevant than BM-derived cells for vessel stabilization and therefore have to be considered in future strategies for anti-angiogenic therapy. The identification of proteins mediating recruitment or differentiation of local Nestin(+) cells with potential stem cell character to angiogenic blood vessels may allow the definition of new therapeutic targets to reduce tumor resistance against anti-angiogenic drugs. PMID:25019063

  17. Evaluation of Hepatic Tissue Blood Flow Using Xenon Computed Tomography with Fibrosis Progression in Nonalcoholic Fatty Liver Disease: Comparison with Chronic Hepatitis C

    PubMed Central

    Shigefuku, Ryuta; Takahashi, Hideaki; Kato, Masaki; Yoshida, Yoshihito; Suetani, Keigo; Noguchi, Yohei; Hatsugai, Moriaki; Nakahara, Kazunari; Ikeda, Hiroki; Kobayashi, Minoru; Matsunaga, Kotaro; Matsumoto, Nobuyuki; Okuse, Chiaki; Itoh, Fumio; Maeyama, Shiro; Sase, Shigeru; Suzuki, Michihiro

    2014-01-01

    Aims The present study evaluated the utility of xenon computed tomography (Xe-CT) as a noninvasive diagnostic procedure for the measurement of hepatic tissue blood flow (TBF) in patients with nonalcoholic fatty liver disease (NAFLD) or chronic hepatitis C (CH-C). Methods Xe-CT was performed in 93 patients with NAFLD and in 109 patients with CH-C. Subjects were classified into one of three groups, based on fibrosis stage: group 1, no bridging fibrosis; group 2, bridging fibrosis; and group 3, liver cirrhosis. Correlations between hepatic TBFs in each fibrosis stage were examined. Results In group 1, portal venous TBF (PVTBF), hepatic arterial (HATBF), and total hepatic TBF (THTBF) were significantly lower in patients with in nonalcoholic steatohepatitis (NASH) than in those with CH-C (p < 0.001, p < 0.05, p < 0.001, respectively). In group 2, PVTBF and THTBF were significantly lower in patients with in NASH than in those with CH-C (p < 0.001, p < 0.05, respectively). In group 3, hepatic TBFs were not significantly different when comparing patients with NASH and those with CH-C. Conclusions PVTBF decreased due to fat infiltration. Therefore, hemodynamic changes occur relatively earlier in NAFLD than in CH-C. Patients with NASH should be monitored carefully for portal hypertensive complications in the early fibrosis stage. PMID:24424317

  18. Microarray analysis at single molecule resolution

    PubMed Central

    Mure?an, Leila; Jacak, Jaros?aw; Klement, Erich Peter; Hesse, Jan; Schütz, Gerhard J.

    2010-01-01

    Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state of the art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack in appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of two to 20 micrometers and quantifies the abundance of target molecules by determining average pixel intensities, a novel high resolution approach [1] directly visualizes individual bound molecules as diffraction limited peaks. The now possible quantification via counting is less susceptible to labeling artifacts and background noise. We have developed an approach for the analysis of high-resolution microarray images. It consists first of a single molecule detection step, based on undecimated wavelet transforms, and second, of a spot identification step via spatial statistics approach (corresponding to the segmentation step in the classical microarray analysis). The detection method was tested on simulated images with a concentration range of 0.001 to 0.5 molecules per square micron and signal-to-noise ratio (SNR) between 0.9 and 31.6. For SNR above 15 the false negatives relative error was below 15%. Separation of foreground/background proved reliable, in case foreground density exceeds background by a factor of 2. The method has also been applied to real data from high-resolution microarray measurements. PMID:20123580

  19. Identifying Fishes through DNA Barcodes and Microarrays

    PubMed Central

    Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N.; Weber, Hannes; Blohm, Dietmar

    2010-01-01

    Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products. PMID:20838643

  20. Methods in molecular cardiology: microarray technology

    PubMed Central

    van den Bosch, B.; Doevendans, P.A.; Lips, D.; Smeets, H.J.M.

    2003-01-01

    It has become more and more evident that changes in expression levels of genes can play an important role in cardiovascular diseases. Specific gene expression profiles may explain, for example, the pathophysiology of myocardial hypertrophy and pump failure and may provide clues for therapeutic interventions. Knowledge of gene expression patterns can also be applied for diagnostic and prognostic purposes, in which differences in gene activity can be used for classification. DNA microarray technology has become the method of choice to simultaneously study the expression of many different genes in a single assay. Each microarray contains many thousands of different DNA sequences attached to a glass slide. The amount of messenger RNA, which is a measure of gene activity, is compared for each gene on the microarray by labelling the mRNA with different fluorescently labelled nucleotides (Cy3 or Cy5) for the test and reference samples. After hybridisation to the microarray the relative amounts of a particular gene transcript in the two samples can be determined by measuring the signal intensities for the fluorescent groups (Cy3 and Cy5) and calculating signal ratios. This paper describes the development of in-house microarray technology, using commercially available cDNA collections. Several technical approaches will be compared and an overview of the pitfalls and possibilities will be presented. The technology will be explained in the context of our project to determine gene expression differences between normal, hypertrophic and failing heart. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5Figure 6Figure 7Figure 9 PMID:25696214

  1. NIH Neuroscience Microarray The NIH Neuroscience Microarray Consortium is a group of four facilities chosen for their outstanding

    E-print Network

    Baker, Chris I.

    NIH Neuroscience Microarray Consortium The NIH Neuroscience Microarray Consortium is a group. The Consortium gives NIH-funded neuroscience researchers cost-effective access to state-of-the-art microarray, technical procedures, and data analysis techniques specific to neuroscience research · Manuscript assistance

  2. On-Chip Synthesis of Protein Microarrays from DNA Microarrays via Coupled In Vitro Transcription and Translation for Surface Plasmon

    E-print Network

    - scribed from surface-bound dsDNA on one microarray element (the "generator element"), and translatedOn-Chip Synthesis of Protein Microarrays from DNA Microarrays via Coupled In Vitro Transcription and Translation for Surface Plasmon Resonance Imaging Biosensor Applications Ting H. Seefeld, Aaron R. Halpern

  3. Investigating the biochemical progression of liver disease through fibrosis, cirrhosis, dysplasia, and hepatocellular carcinoma using Fourier transform infrared spectroscopic imaging

    NASA Astrophysics Data System (ADS)

    Sreedhar, Hari; Pant, Mamta; Ronquillo, Nemencio R.; Davidson, Bennett; Nguyen, Peter; Chennuri, Rohini; Choi, Jacqueline; Herrera, Joaquin A.; Hinojosa, Ana C.; Jin, Ming; Kajdacsy-Balla, Andre; Guzman, Grace; Walsh, Michael J.

    2014-03-01

    Hepatocellular carcinoma (HCC) is the most common form of primary hepatic carcinoma. HCC ranks the fourth most prevalent malignant tumor and the third leading cause of cancer related death in the world. Hepatocellular carcinoma develops in the context of chronic liver disease and its evolution is characterized by progression through intermediate stages to advanced disease and possibly even death. The primary sequence of hepatocarcinogenesis includes the development of cirrhosis, followed by dysplasia, and hepatocellular carcinoma.1 We addressed the utility of Fourier Transform Infrared (FT-IR) spectroscopic imaging, both as a diagnostic tool of the different stages of the disease and to gain insight into the biochemical process associated with disease progression. Tissue microarrays were obtained from the University of Illinois at Chicago tissue bank consisting of liver explants from 12 transplant patients. Tissue core biopsies were obtained from each explant targeting regions of normal, liver cell dysplasia including large cell change and small cell change, and hepatocellular carcinoma. We obtained FT-IR images of these tissues using a modified FT-IR system with high definition capabilities. Firstly, a supervised spectral classifier was built to discriminate between normal and cancerous hepatocytes. Secondly, an expanded classifier was built to discriminate small cell and large cell changes in liver disease. With the emerging advances in FT-IR instrumentation and computation there is a strong drive to develop this technology as a powerful adjunct to current histopathology approaches to improve disease diagnosis and prognosis.

  4. Microarray Meta-Analysis of RNA-Binding Protein Functions in Alternative Polyadenylation

    PubMed Central

    Hu, Wenchao; Liu, Yuting; Yan, Jun

    2014-01-01

    Alternative polyadenylation (APA) is a post-transcriptional mechanism to generate diverse mRNA transcripts with different 3?UTRs from the same gene. In this study, we systematically searched for the APA events with differential expression in public mouse microarray data. Hundreds of genes with over-represented differential APA events and the corresponding experiments were identified. We further revealed that global APA differential expression occurred prevalently in tissues such as brain comparing to peripheral tissues, and biological processes such as development, differentiation and immune responses. Interestingly, we also observed widespread differential APA events in RNA-binding protein (RBP) genes such as Rbm3, Eif4e2 and Elavl1. Given the fact that RBPs are considered as the main regulators of differential APA expression, we constructed a co-expression network between APAs and RBPs using the microarray data. Further incorporation of CLIP-seq data of selected RBPs showed that Nova2 represses and Mbnl1 promotes the polyadenylation of closest poly(A) sites respectively. Altogether, our study is the first microarray meta-analysis in a mammal on the regulation of APA by RBPs that integrated massive mRNA expression data under a wide-range of biological conditions. Finally, we present our results as a comprehensive resource in an online website for the research community. PMID:24622240

  5. Improved data normalization methods for reverse phase protein microarray analysis of complex biological samples

    PubMed Central

    Chiechi, Antonella; Mueller, Claudius; Boehm, Kevin M.; Romano, Alessandra; Benassi, Maria Serena; Picci, Piero; Liotta, Lance A.; Espina, Virginia

    2013-01-01

    Reverse phase protein microarrays (RPMA) are designed for quantitative, multiplexed analysis of proteins, and their posttranslational modified forms, from a limited amount of sample. To correct for sample to sample variability due to the number of cells in each lysate and the presence of extracellular proteins or red blood cells, a normalization method is required that is independent of these potentially confounding parameters. We adopted a gene microarray algorithm for use with RPMA to optimize the proteomic data normalization process and developed a systematic approach to RPMA processing and analysis, tailored to the study set. Our approach capitalizes on the gene microarray algorithms geNorm and NormFinder to identify the normalization parameter with the lowest variability across a proteomic sample set. Seven analytes (ssDNA, glyceraldehyde 3-phosphate dehydrogenase, ?/?-tubulin, mitochondrial ribosomal protein L11, ribosomal protein L13a, ?-actin, and total protein) were compared across sample sets including cell lines, tissues subjected to laser capture microdissection, and blood-contaminated tissues. We examined normalization parameters to correct for red blood cell content. We show that single-stranded DNA (ssDNA) is proportional to total non-red blood cell content and is a suitable RPMA normalization parameter. Simple modifications to RPMA processing allow flexibility in using ssDNA- or protein-based normalization molecules. PMID:22946677

  6. Gene expression profiling in developing pig adipose tissue: non-secreted regulatory proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The expression of many genes encoding secreted and non-secreted factors have been studied in human and rodent adipose tissue with cDNA microarrays, but few such studies in adipose tissue from growing pigs have been reported. Total RNA was collected at slaughter from outer subcutaneous adipose tissue...

  7. A quality-controlled microarray method for gene expression profiling.

    PubMed

    Degenkolbe, Thomas; Hannah, Matthew A; Freund, Susanne; Hincha, Dirk K; Heyer, Arnd G; Köhl, Karin I

    2005-11-15

    Gene expression profiling on microarrays is widely used to measure the expression of large numbers of genes in a single experiment. Because of the high cost of this method, feasible numbers of replicates are limited, thus impairing the power of statistical analysis. As a step toward reducing technically induced variation, we developed a procedure of sample preparation and analysis that minimizes the number of sample manipulation steps, introduces quality control before array hybridization, and allows recovery of the prepared mRNA for independent validation of results. Sample preparation is based on mRNA separation using oligo(dT) magnetic beads, which are subsequently used for first-strand cDNA synthesis on the beads. cDNA covalently bound to the magnetic beads is used as template for second-strand cDNA synthesis, leaving the intact mRNA in solution for further analysis. The quality of the synthesized cDNA can be assessed by quantitative polymerase chain reaction using 3'- and 5'-specific primer pairs for housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase. Second-strand cDNA is chemically labeled with fluorescent dyes to avoid dye bias in enzymatic labeling reactions. After hybridization of two differently labeled samples to microarray slides, arrays are scanned and images analyzed automatically with high reproducibility. Quantile-normalized data from five biological replica display a coefficient of variation 45% for 90% of profiled genes, allowing detection of twofold changes with false positive and false negative rates of 10% each. We demonstrate successful application of the procedure for expression profiling in plant leaf tissue. However, the method could be easily adapted for samples from animal including human or from microbial origin. PMID:16213454

  8. Detection of pathogenic Vibrio spp. in shellfish by using multiplex PCR and DNA microarrays.

    PubMed

    Panicker, Gitika; Call, Douglas R; Krug, Melissa J; Bej, Asim K

    2004-12-01

    This study describes the development of a gene-specific DNA microarray coupled with multiplex PCR for the comprehensive detection of pathogenic vibrios that are natural inhabitants of warm coastal waters and shellfish. Multiplex PCR with vvh and viuB for Vibrio vulnificus, with ompU, toxR, tcpI, and hlyA for V. cholerae, and with tlh, tdh, trh, and open reading frame 8 for V. parahaemolyticus helped to ensure that total and pathogenic strains, including subtypes of the three Vibrio spp., could be detected and discriminated. For DNA microarrays, oligonucleotide probes for these targeted genes were deposited onto epoxysilane-derivatized, 12-well, Teflon-masked slides by using a MicroGrid II arrayer. Amplified PCR products were hybridized to arrays at 50 degrees C and detected by using tyramide signal amplification with Alexa Fluor 546 fluorescent dye. Slides were imaged by using an arrayWoRx scanner. The detection sensitivity for pure cultures without enrichment was 10(2) to 10(3) CFU/ml, and the specificity was 100%. However, 5 h of sample enrichment followed by DNA extraction with Instagene matrix and multiplex PCR with microarray hybridization resulted in the detection of 1 CFU in 1 g of oyster tissue homogenate. Thus, enrichment of the bacterial pathogens permitted higher sensitivity in compliance with the Interstate Shellfish Sanitation Conference guideline. Application of the DNA microarray methodology to natural oysters revealed the presence of V. vulnificus (100%) and V. parahaemolyticus (83%). However, V. cholerae was not detected in natural oysters. An assay involving a combination of multiplex PCR and DNA microarray hybridization would help to ensure rapid and accurate detection of pathogenic vibrios in shellfish, thereby improving the microbiological safety of shellfish for consumers. PMID:15574946

  9. Immobilization Techniques for Microarray: Challenges and Applications

    PubMed Central

    Nimse, Satish Balasaheb; Song, Keumsoo; Sonawane, Mukesh Digambar; Sayyed, Danishmalik Rafiq; Kim, Taisun

    2014-01-01

    The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided. PMID:25429408

  10. Examining galectin binding specificity using glycan microarrays.

    PubMed

    Arthur, Connie M; Rodrigues, Lílian Cataldi; Baruffi, Marcelo Dias; Sullivan, Harold C; Heimburg-Molinaro, Jamie; Smith, Dave F; Cummings, Richard D; Stowell, Sean R

    2015-01-01

    Glycan binding proteins (GBPs) possess the unique ability to regulate a wide variety of biological processes through interactions with highly modifiable cell surface glycans. While many studies demonstrate the impact of glycan modification on GBP recognition and activity, the relative contribution of subtle changes in glycan structure on GBP binding can be difficult to define. To overcome limitations in the analysis of GBP-glycan interactions, recent studies utilized glycan microarray platforms containing hundreds of structurally defined glycans. These studies not only provided important information regarding GBP-glycan interactions, but have also resulted in significant insight into the binding specificity and biological activity of the galectin family. We will describe the methods used when employing glycan microarray platforms to examine galectin-glycan binding specificity and function. PMID:25253137

  11. Epigenetics-related genes in prostate cancer: expression profile in prostate cancer tissues, androgen-sensitive and -insensitive cell lines.

    PubMed

    Shaikhibrahim, Zaki; Lindstrot, Andreas; Ochsenfahrt, Jacqueline; Fuchs, Kerstin; Wernert, Nicolas

    2013-01-01

    Epigenetic changes have been suggested to drive prostate cancer (PCa) development and progression. Therefore, in this study, we aimed to identify novel epigenetics-related genes in PCa tissues, and to examine their expression in metastatic PCa cell lines. We analyzed the expression of epigenetics-related genes via a clustering analysis based on gene function in moderately and poorly differentiated PCa glands compared to normal glands of the peripheral zone (prostate proper) from PCa patients using Whole Human Genome Oligo Microarrays. Our analysis identified 12 epigenetics-related genes with a more than 2-fold increase or decrease in expression and a p-value <0.01. In modera-tely differentiated tumors compared to normal glands of the peripheral zone, we found the genes, TDRD1, IGF2, DICER1, ADARB1, HILS1, GLMN and TRIM27, to be upregulated, whereas TNRC6A and DGCR8 were found to be downregulated. In poorly differentiated tumors, we found TDRD1, ADARB and RBM3 to be upregulated, whereas DGCR8, PIWIL2 and BC069781 were downregulated. Our analysis of the expression level for each gene in the metastatic androgen-sensitive VCaP and LNCaP, and -insensitive PC3 and DU-145 PCa cell lines revealed differences in expression among the cell lines which may reflect the different biological properties of each cell line, and the potential role of each gene at different metastatic sites. The novel epigenetics-related genes that we identified in primary PCa tissues may provide further insight into the role that epigenetic changes play in PCa. Moreover, some of the genes that we identified may play important roles in primary PCa and metastasis, in primary PCa only, or in metastasis only. Follow-up studies are required to investigate the functional role and the role that the expression of these genes play in the outcome and progression of PCa using tissue microarrays. PMID:23135352

  12. Microarray-to-microarray transfer of reagents by snapping of two chips for cross-reactivity-free multiplex immunoassays.

    PubMed

    Li, Huiyan; Bergeron, Sébastien; Juncker, David

    2012-06-01

    Whereas microarray and microfluidic technologies have progressed on many fronts, servicing microchips with minute amounts of reagents still constitutes an important challenge for many applications. Recently, chip-to-chip reagent transfer methods were introduced that simplify the delivery of reagents but required manual, visual alignment, custom-built microwells, and only showed the reaction of a single sample with multiple chemicals. Here, we present the snap chip, which uses common glass slides for transfer, back-side alignment for achieving precise alignment in spite of mirroring, and a snap-apparatus for facile transfer of arrays of chemicals at once by snapping the two slides together. We recently established that cross-reactivity was a significant problem in multiplex assays both theoretically and experimentally and found that it can be eliminated by avoiding mixing, but which necessitates delivering each detection antibody to a single spot with the cognate capture antibody. Using the snap chip, multiplexed sandwich immunoassays without mixing were performed: a slide with multiple arrays of 10 different capture antibodies was incubated with a sample, and then all detection antibodies transferred at once by snapping, each to the single cognate spot. All binding curves were established and limits of detection in the pg/mL range were obtained. Snap chips were stored up to 3 months prior to usage. The snap chip, by dissociating microarray production, which requires expensive equipment, from assay execution, which can be achieved using a hand-held alignment apparatus, will allow for multiplex reactions to be performed using a user-friendly kit. This new liquid handling format can be easily adapted to other applications that require transfer of minute amounts of different reagents in parallel. PMID:22536939

  13. Phosphorylated SATB1 is associated with the progression and prognosis of glioma.

    PubMed

    Han, S; Xia, J; Qin, X; Han, S; Wu, A

    2013-01-01

    Special AT-rich sequence-binding protein 1 (SATB1) is a global chromatin organizer and gene regulator, and high expression of SATB1 is associated with progression and poor prognosis in several malignancies. Here, we examine the expression pattern of SATB1 in glioma. Microarray analysis of 127 clinical samples showed that SATB1 mRNA was expressed at lower levels in highly malignant glioblastoma multiforme (GBM) than in low-grade glioma and normal brain tissue. This result was further confirmed by real-time RT-PCR in the clinical samples, three GBM cell lines, primary SU3 glioma cells and tumor cells harvested by laser-capture microdissection. Consistent with the mRNA levels, SATB1 protein expression was downregulated in high-grade glioma, as shown by western blotting. However, phospho-SATB1 levels showed an opposite pattern, with a significant increase in these tumors. Immunohistochemical analysis of phospho-SATB1 expression in tissue microarrays with tumors from 122 glioma cases showed that phospho-SATB1 expression was significantly associated with high histological grade and poor survival by Kaplan-Meier analysis. In vitro transfection analysis showed that phospho-SATB1 DNA binding has a key role in regulating the proliferation and invasion of glioma cells. The effect of SATB1 in glioma cell is mainly histone deacetylase (HDAC1)-dependent. We conclude that phospho-SATB1, but not SATB1 mRNA expression, is associated with the progression and prognosis of glioma. By interaction with HDAC1, phospho-SATB1 contributes to the invasive and proliferative phenotype of GBM cells. PMID:24176859

  14. Microarray gene expression analysis of the human airway in patients exposed to sulfur mustard.

    PubMed

    Najafi, Ali; Masoudi-Nejad, Ali; Imani Fooladi, Abbas Ali; Ghanei, Mostafa; Nourani, Mohamad Reza

    2014-08-01

    There is much data about the acute effects of sulfur mustard gas on humans, animals and cells. But less is known regarding the molecular basics of chronic complications in humans. Basically, mustard gas, as an alkylating agent, causes several chronic problems in the eyes, skin and more importantly in the pulmonary system which is the main cause of death. Although recent proteomic research has been carried out on bronchoalveolar lavage (BAL) and serum, but high-throughput transcriptomics have not yet been applied to chronic airway remodeling. This is the first cDNA-microarray report on the chronic human mustard lung disease, 25 years after exposure during the Iran-Iraq war. Microarray transcriptional profiling indicated that a total of 122 genes were significantly dysregulated in tissues located in the airway of patients. These genes are associated with the extracellular matrix components, apoptosis, stress response, inflammation and mucus secretion. PMID:24823320

  15. Quantitative polymerase chain reaction: validation of microarray results from postmortem brain studies.

    PubMed

    Mimmack, Michael L; Brooking, Justin; Bahn, Sabine

    2004-02-15

    Quantitative polymerase chain reaction (Q-PCR) is now considered the "technique of choice" for validating gene expression changes identified with ribonucleic acid-based expression profiling technologies (especially micro- and macroarray techniques). The identification of altered gene expression profiles with microarrays is best viewed as the first step in the determination of potential disease-associated genes; however, the false-positive rate can be high, particularly with small sample sets and in view of the typically small differences observed in brain expression studies. Quantitative PCR is a rapid and highly sensitive technique for accurate quantification of microarray results; however, careful consideration of experimental design, quality of primer/probe design, internal standards, and normalization procedures are pivotal, particularly when the work involves postmortem tissue. PMID:14960285

  16. Undetected sex chromosome aneuploidy by chromosomal microarray.

    PubMed

    Markus-Bustani, Keren; Yaron, Yuval; Goldstein, Myriam; Orr-Urtreger, Avi; Ben-Shachar, Shay

    2012-11-01

    We report on a case of a female fetus found to be mosaic for Turner syndrome (45,X) and trisomy X (47,XXX). Chromosomal microarray analysis (CMA) failed to detect the aneuploidy because of a normal average dosage of the X chromosome. This case represents an unusual instance in which CMA may not detect chromosomal aberrations. Such a possibility should be taken into consideration in similar cases where CMA is used in a clinical setting. PMID:23034780

  17. Penalized Principal Component Analysis of Microarray Data

    Microsoft Academic Search

    Vladimir Nikulin; Geoffrey J. McLachlan

    2009-01-01

    \\u000a The high dimensionality of microarray data, the expressions of thousands of genes in a much smaller number of samples, presents\\u000a challenges that affect the validity of the analytical results. Hence attention has to be given to some form of dimension reduction\\u000a to represent the data in terms of a smaller number of variables. The latter are often chosen to be

  18. Monitoring gene expression using DNA microarrays

    Microsoft Academic Search

    Christina A Harrington; Carsten Rosenow; Jacques Retief

    2000-01-01

    The concurrent development of high-density array technologies and the complete sequencing of a number of microbial genomes is providing the opportunity to comprehensively and efficiently survey the transcription profile of microorganisms under different conditions and well-defined genotypes. Microarray-based studies are uncovering broad patterns of genetic activity, providing new understanding of gene functions and, in some cases, generating unexpected insight into

  19. Static progressive splinting.

    PubMed

    Schultz-Johnson, Karen

    2002-01-01

    Static progressive splinting is the use of inelastic components to apply torque to a joint in order to statically position it as close to end range as possible. It maximizes total end-range time, thus increasing passive range of motion. As tissue lengthens in response to this carefully applied stress, the clinician or wearer adjusts the joint position to progress tissue at the new maximum tolerable length. Static progressive splinting combines precision in joint position and torque application with patient-controlled stress to create an approach powerful enough to succeed when no other treatment approach does. This article discusses static progressive splinting indications, contraindications, and advantages as well as guidelines for a splinting regimen. It offers many examples of static progressive splinting and makes clear that this approach can be used with any mobilizing splint design. The unique mechanics of this splinting approach are described, and the various methods of achieving static progressive splinting are compared. Offering high levels of patient satisfaction and compliance, static progressive splinting has come to the forefront of clinical practice. PMID:12086027

  20. The classification of cancer stage microarray data.

    PubMed

    Chen, Chi-Kan

    2012-12-01

    Correctly diagnosing the cancer stage is most important for selecting an appropriate cancer treatment option for a patient. Recent advances in microarray technology allow the cancer stage to be predicted using gene expression patterns. The cancer stage is in ordinal scale. In this paper, we employ strict ordinal regressions including cumulative logit model in traditional statistics with data dimensionality reduction, and distribution free approaches of large margin rank boundaries implemented by the support vector machine, as well as an ensemble ranking scheme to model the cancer stage using gene expression microarray data. Predictive genes included in models are selected by univariate feature ranking, and recursive feature elimination. We perform cross-validation experiments to assess and compare classification accuracies of ordinal and non-ordinal algorithms on five cancer stage microarray datasets. We conclude that a strict ordinal classifier trained by a validated approach can predict the cancer stage more accurately than traditional non-ordinal classifiers without considering the order of cancer stages. PMID:22925656

  1. High-Throughput Enzyme Kinetics Using Microarrays

    SciTech Connect

    Guoxin Lu; Edward S. Yeung

    2007-11-01

    We report a microanalytical method to study enzyme kinetics. The technique involves immobilizing horseradish peroxidase on a poly-L-lysine (PLL)- coated glass slide in a microarray format, followed by applying substrate solution onto the enzyme microarray. Enzyme molecules are immobilized on the PLL-coated glass slide through electrostatic interactions, and no further modification of the enzyme or glass slide is needed. In situ detection of the products generated on the enzyme spots is made possible by monitoring the light intensity of each spot using a scientific-grade charged-coupled device (CCD). Reactions of substrate solutions of various types and concentrations can be carried out sequentially on one enzyme microarray. To account for the loss of enzyme from washing in between runs, a standard substrate solution is used for calibration. Substantially reduced amounts of substrate solution are consumed for each reaction on each enzyme spot. The Michaelis constant K{sub m} obtained by using this method is comparable to the result for homogeneous solutions. Absorbance detection allows universal monitoring, and no chemical modification of the substrate is needed. High-throughput studies of native enzyme kinetics for multiple enzymes are therefore possible in a simple, rapid, and low-cost manner.

  2. Microarray analysis in gastric cancer: A review

    PubMed Central

    D’Angelo, Giovanna; Di Rienzo, Teresa; Ojetti, Veronica

    2014-01-01

    Gastric cancer is one of the most common tumors worldwide. Although several treatment options have been developed, the mortality rate is increasing. Lymph node involvement is considered the most reliable prognostic indicator in gastric cancer. Early diagnosis improves the survival rate of patients and increases the likelihood of successful treatment. The most reliable diagnostic method is endoscopic examination, however, it is expensive and not feasible in poorer countries. Therefore, many innovative techniques have been studied to develop a new non-invasive screening test and to identify specific serum biomarkers. DNA microarray analysis is one of the new technologies able to measure the expression levels of a large number of genes simultaneously. It is possible to define the gene expression profile of the tumor and to correlate it with the prognosis and metastasis formation. Several studies in the literature have been published on the role of microarray analysis in gastric cancer and the mechanisms of proliferation and metastasis formation. The aim of this review is to analyze the importance of microarray analysis and its clinical applications to better define the genetic characteristics of gastric cancer and its possible implications in a more decisive treatment. PMID:25232233

  3. Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer

    PubMed Central

    2011-01-01

    Background Na+/I- symporter (NIS)-mediated iodide uptake allows radioiodine therapy for thyroid cancer. NIS is also expressed in breast tumors, raising potential for radionuclide therapy of breast cancer. However, NIS expression in most breast cancers is low and may not be sufficient for radionuclide therapy. We aimed to identify biomarkers associated with NIS expression such that mechanisms underlying NIS modulation in human breast tumors may be elucidated. Methods Published oligonucleotide microarray data within the National Center for Biotechnology Information Gene Expression Omnibus database were analyzed to identify gene expression tightly correlated with NIS mRNA level among human breast tumors. NIS immunostaining was performed in a tissue microarray composed of 28 human breast tumors which had corresponding oligonucleotide microarray data available for each tumor such that gene expression associated with cell surface NIS protein level could be identified. Results and Discussion NIS mRNA levels do not vary among breast tumors or when compared to normal breast tissues when detected by Affymetrix oligonucleotide microarray platforms. Cell surface NIS protein levels are much more variable than their corresponding NIS mRNA levels. Despite a limited number of breast tumors examined, our analysis identified cysteinyl-tRNA synthetase as a biomarker that is highly associated with cell surface NIS protein levels in the ER-positive breast cancer subtype. Conclusions Further investigation on genes associated with cell surface NIS protein levels within each breast cancer molecular subtype may lead to novel targets for selectively increasing NIS expression/function in a subset of breast cancers patients. PMID:21989294

  4. Laser capture microdissection of embryonic cells and preparation of RNA for microarray assays.

    PubMed

    Redmond, Latasha C; Pang, Christopher J; Dumur, Catherine; Haar, Jack L; Lloyd, Joyce A

    2014-01-01

    In order to compare the global gene expression profiles of different embryonic cell types, it is first necessary to isolate the specific cells of interest. The purpose of this chapter is to provide a step-by-step protocol to perform laser capture microdissection (LCM) on embryo samples and obtain sufficient amounts of high-quality RNA for microarray hybridizations. Using the LCM/microarray strategy on mouse embryo samples has some challenges, because the cells of interest are available in limited quantities. The first step in the protocol is to obtain embryonic tissue, and immediately cryoprotect and freeze it in a cryomold containing Optimal Cutting Temperature freezing media (Sakura Finetek), using a dry ice-isopentane bath. The tissue is then cryosectioned, and the microscope slides are processed to fix, stain, and dehydrate the cells. LCM is employed to isolate specific cell types from the slides, identified under the microscope by virtue of their morphology. Detailed protocols are provided for using the currently available ArcturusXT LCM instrument and CapSure(®) LCM Caps, to which the selected cells adhere upon laser capture. To maintain RNA integrity, upon removing a slide from the final processing step, or attaching the first cells on the LCM cap, LCM is completed within 20 min. The cells are then immediately recovered from the LCM cap using a denaturing solution that stabilizes RNA integrity. RNA is prepared using standard methods, modified for working with small samples. To ensure the validity of the microarray data, the quality of the RNA is assessed using the Agilent bioanalyzer. Only RNA that is of sufficient integrity and quantity is used to perform microarray assays. This chapter provides guidance regarding troubleshooting and optimization to obtain high-quality RNA from cells of limited availability, obtained from embryo samples by LCM. PMID:24318813

  5. Increasing the Number of Thyroid Lesions Classes in Microarray Analysis Improves the Relevance of Diagnostic Markers

    PubMed Central

    Fontaine, Jean-Fred; Mirebeau-Prunier, Delphine; Raharijaona, Mahatsangy; Franc, Brigitte; Triau, Stephane; Rodien, Patrice; Goëau-Brissonniére, Olivier; Karayan-Tapon, Lucie; Mello, Marielle; Houlgatte, Rémi; Malthiery, Yves; Savagner, Frédérique

    2009-01-01

    Background Genetic markers for thyroid cancers identified by microarray analysis have offered limited predictive accuracy so far because of the few classes of thyroid lesions usually taken into account. To improve diagnostic relevance, we have simultaneously analyzed microarray data from six public datasets covering a total of 347 thyroid tissue samples representing 12 histological classes of follicular lesions and normal thyroid tissue. Our own dataset, containing about half the thyroid tissue samples, included all categories of thyroid lesions. Methodology/Principal Findings Classifier predictions were strongly affected by similarities between classes and by the number of classes in the training sets. In each dataset, sample prediction was improved by separating the samples into three groups according to class similarities. The cross-validation of differential genes revealed four clusters with functional enrichments. The analysis of six of these genes (APOD, APOE, CLGN, CRABP1, SDHA and TIMP1) in 49 new samples showed consistent gene and protein profiles with the class similarities observed. Focusing on four subclasses of follicular tumor, we explored the diagnostic potential of 12 selected markers (CASP10, CDH16, CLGN, CRABP1, HMGB2, ALPL2, ADAMTS2, CABIN1, ALDH1A3, USP13, NR2F2, KRTHB5) by real-time quantitative RT-PCR on 32 other new samples. The gene expression profiles of follicular tumors were examined with reference to the mutational status of the Pax8-PPAR?, TSHR, GNAS and NRAS genes. Conclusion/Significance We show that diagnostic tools defined on the basis of microarray data are more relevant when a large number of samples and tissue classes are used. Taking into account the relationships between the thyroid tumor pathologies, together with the main biological functions and pathways involved, improved the diagnostic accuracy of the samples. Our approach was particularly relevant for the classification of microfollicular adenomas. PMID:19893615

  6. Adipose Gene Expression Profiles Related to Metabolic Syndrome Using Microarray Analyses in Two Different Models

    PubMed Central

    Yoo, Hye Jin; Hwang, Hwan-Jin; Jung, Tae Woo; Ryu, Ja Young; Hong, Ho Cheol; Choi, Hae Yoon; Baik, Sei Hyun

    2014-01-01

    Background Peroxisome proliferator-activated receptor-? (PPAR-?) agonist has a wide-ranging influence on multiple components of metabolic syndrome. The Otsuka Long-Evans Tokushima Fatty (OLETF) rat is a useful animal model of metabolic syndrome. To determine genes related to metabolic syndrome, we examined overlapping genes that are simultaneously decreased by PPAR-? agonists and increased in OLETF rats using microarrays in two different models. Methods In the first microarray analysis, PPAR-? agonist-treated db/db mice were compared to standard diet-fed db/db mice. In the second microarray analysis, OLETF rats were compared to Long-Evans Tokushima Otsuka (LETO) rats (control of OLETF rats). Results Among the overlapping genes, in the present study, we validated that lipocalin-2 expression was significantly decreased in the visceral adipose tissue of PPAR-? agonist-treated db/db mice compared to standard diet-fed db/db mice and increased in OLETF rats compared to LETO rats using real time reverse transcription polymerase chain reaction. Furthermore, we showed for the first time that lipocalin-2 expression was significantly increased in the visceral adipose tissues of obese humans compared with nonobese humans. In addition, the expression level of lipocalin-2 in human visceral adipose tissue had a significant positive correlation with body mass index, serum interleukin-6, adipocyte fatty acid binding protein levels, and white blood cell count. Conclusion Lipocalin-2 was confirmed to be a significant adipokine affected by PPAR-? agonist and obesity in the present study. Also, for the first time in human visceral adipose tissue, it was determined that the expression of lipocalin-2 from obese humans was significantly increased and correlated with circulating inflammatory markers. PMID:25349823

  7. DNA microarray for detection of gastrointestinal viruses.

    PubMed

    Martínez, Miguel A; Soto-Del Río, María de Los Dolores; Gutiérrez, Rosa María; Chiu, Charles Y; Greninger, Alexander L; Contreras, Juan Francisco; López, Susana; Arias, Carlos F; Isa, Pavel

    2015-01-01

    Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 10(3) virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals. PMID:25355758

  8. Tissue types (image)

    MedlinePLUS

    There are 4 basic types of tissue: connective tissue, epithelial tissue, muscle tissue, and nervous tissue. Connective tissue supports other tissues and binds them together (bone, blood, and lymph tissues). Epithelial tissue ...

  9. ProMAT: protein microarray analysis tool

    SciTech Connect

    White, Amanda M.; Daly, Don S.; Varnum, Susan M.; Anderson, Kevin K.; Bollinger, Nikki; Zangar, Richard C.

    2006-04-04

    Summary: ProMAT is a software tool for statistically analyzing data from ELISA microarray experiments. The software estimates standard curves, sample protein concentrations and their uncertainties for multiple assays. ProMAT generates a set of comprehensive figures for assessing results and diagnosing process quality. The tool is available for Windows or Mac, and is distributed as open-source Java and R code. Availability: ProMAT is available at http://www.pnl.gov/statistics/ProMAT. ProMAT requires Java version 1.5.0 and R version 1.9.1 (or more recent versions) which are distributed with the tool.

  10. Reproducible Clusters from Microarray Research: Whither?

    PubMed Central

    Garge, Nikhil R; Page, Grier P; Sprague, Alan P; Gorman, Bernard S; Allison, David B

    2005-01-01

    Motivation In cluster analysis, the validity of specific solutions, algorithms, and procedures present significant challenges because there is no null hypothesis to test and no 'right answer'. It has been noted that a replicable classification is not necessarily a useful one, but a useful one that characterizes some aspect of the population must be replicable. By replicable we mean reproducible across multiple samplings from the same population. Methodologists have suggested that the validity of clustering methods should be based on classifications that yield reproducible findings beyond chance levels. We used this approach to determine the performance of commonly used clustering algorithms and the degree of replicability achieved using several microarray datasets. Methods We considered four commonly used iterative partitioning algorithms (Self Organizing Maps (SOM), K-means, Clutsering LARge Applications (CLARA), and Fuzzy C-means) and evaluated their performances on 37 microarray datasets, with sample sizes ranging from 12 to 172. We assessed reproducibility of the clustering algorithm by measuring the strength of relationship between clustering outputs of subsamples of 37 datasets. Cluster stability was quantified using Cramer's v2 from a kXk table. Cramer's v2 is equivalent to the squared canonical correlation coefficient between two sets of nominal variables. Potential scores range from 0 to 1, with 1 denoting perfect reproducibility. Results All four clustering routines show increased stability with larger sample sizes. K-means and SOM showed a gradual increase in stability with increasing sample size. CLARA and Fuzzy C-means, however, yielded low stability scores until sample sizes approached 30 and then gradually increased thereafter. Average stability never exceeded 0.55 for the four clustering routines, even at a sample size of 50. These findings suggest several plausible scenarios: (1) microarray datasets lack natural clustering structure thereby producing low stability scores on all four methods; (2) the algorithms studied do not produce reliable results and/or (3) sample sizes typically used in microarray research may be too small to support derivation of reliable clustering results. Further research should be directed towards evaluating stability performances of more clustering algorithms on more datasets specially having larger sample sizes with larger numbers of clusters considered. PMID:16026595

  11. Identification of differentially expressed genes in shrimp ( Penaeus stylirostris ) infected with White spot syndrome virus by cDNA microarrays

    Microsoft Academic Search

    A. K. Dhar; A. Dettori; M. M. Roux; K. R. Klimpel; B. Read

    2003-01-01

    Summary. White spot syndrome virus (WSSV) is currently the most important viral pathogen infecting penaeid shrimp worldwide. Although considerable progress has been made in characterizing the WSSV genome and developing detection methods, information pertaining to host genes involved in WSSV pathogenesis is limited. We examined the potential of cDNA microarray analysis to study gene expression in WSSV-infected shrimp. Shrimp cDNAs

  12. An antibody microarray analysis of serum cytokines in neurodegenerative Parkinsonian syndromes

    PubMed Central

    2012-01-01

    Background Microarray technology may offer a new opportunity to gain insight into disease-specific global protein expression profiles. The present study was performed to apply a serum antibody microarray to screen for differentially regulated cytokines in Parkinson's disease (PD), multiple system atrophy (MSA), progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS). Results Serum samples were obtained from patients with clinical diagnoses of PD (n?=?117), MSA (n?=?31) and PSP/CBS (n?=?38) and 99 controls. Cytokine profiles of sera from patients and controls were analyzed with a semiquantitative human antibody array for 174 cytokines and the expression of 12 cytokines was found to be significantly altered. In a next step, results from the microarray experiment were individually validated by different immunoassays. Immunoassay validation confirmed a significant increase of median PDGF-BB levels in patients with PSP/CBS, MSA and PD and a decrease of median prolactin levels in PD. However, neither PDGF-BB nor prolactin were specific biomarkers to discriminate PSP/CBS, MSA, PD and controls. Conclusions In our unbiased cytokine array based screening approach and validation by a different immunoassay only two of 174 cytokines were significantly altered between patients and controls. PMID:23173604

  13. Mutation analysis of 272 Spanish families affected by autosomal recessive retinitis pigmentosa using a genotyping microarray

    PubMed Central

    Ávila-Fernández, Almudena; Cantalapiedra, Diego; Aller, Elena; Vallespín, Elena; Aguirre-Lambán, Jana; Blanco-Kelly, Fiona; Corton, M.; Riveiro-Álvarez, Rosa; Allikmets, Rando; Trujillo-Tiebas, María José; Millán, José M.; Cremers, Frans P.M.

    2010-01-01

    Purpose Retinitis pigmentosa (RP) is a genetically heterogeneous disorder characterized by progressive loss of vision. The aim of this study was to identify the causative mutations in 272 Spanish families using a genotyping microarray. Methods 272 unrelated Spanish families, 107 with autosomal recessive RP (arRP) and 165 with sporadic RP (sRP), were studied using the APEX genotyping microarray. The families were also classified by clinical criteria: 86 juveniles and 186 typical RP families. Haplotype and sequence analysis were performed to identify the second mutated allele. Results At least one-gene variant was found in 14% and 16% of the juvenile and typical RP groups respectively. Further study identified four new mutations, providing both causative changes in 11% of the families. Retinol Dehydrogenase 12 (RDH12) was the most frequently mutated gene in the juvenile RP group, and Usher Syndrome 2A (USH2A) and Ceramide Kinase-Like (CERKL) were the most frequently mutated genes in the typical RP group. The only variant found in CERKL was p.Arg257Stop, the most frequent mutation. Conclusions The genotyping microarray combined with segregation and sequence analysis allowed us to identify the causative mutations in 11% of the families. Due to the low number of characterized families, this approach should be used in tandem with other techniques. PMID:21151602

  14. Secreted proteins and genes in fetal and neonatal pig adipose tissue and stromal-vascular cells.

    PubMed

    Hausman, G J; Poulos, S P; Richardson, R L; Barb, C R; Andacht, T; Kirk, H C; Mynatt, R L

    2006-07-01

    Although microarray and proteomic studies have indicated the expression of unique and unexpected genes and their products in human and rodent adipose tissue, similar studies of meat animal adipose tissue have not been reported. Thus, total RNA was isolated from stromal-vascular (S-V) cell cultures (n = 4; 2 arrays; 2 cultures/array) from 90-d (79% of gestation) fetuses and adipose tissue from 105-d (92% of gestation) fetuses (n = 2) and neonatal (5-d-old) pigs (n = 2). Duplicate adipose tissue microarrays (n = 4) represented RNA samples from a pig and a fetus. Dye-labeled cDNA probes were hybridized to custom microarrays (70-mer oligonucleotides) representing more than 600 pig genes involved in growth and reproduction. Microarray studies showed significant expression of 40 genes encoding for known adipose tissue secreted proteins in fetal S-V cell cultures and adipose tissue. Expression of 10 genes encoding secreted proteins not known to be expressed by adipose tissue was also observed in neonatal adipose tissue and fetal S-V cell cultures. Additionally, the agouti gene was detected by reverse transcription-PCR in pig S-V cultures and adipose tissue. Proteomic analysis of adipose tissue and fetal and young pig S-V cell culture-conditioned media identified multiple secreted proteins including heparin-like epidermal growth factor-like growth factor and several apolipoproteins. Another adipose tissue secreted protein, plasminogen activator inhibitor-1, was identified by ELISA in S-V cell culture media. A group of 20 adipose tissue secreted proteins were detected or identified using the gene microarray and the proteomic and protein assay approaches including apolipoprotein-A1, apolipoprotein-E, relaxin, brain-derived neurotrophic factor, and IGF binding protein-5. These studies demonstrate, for the first time, the expression of several major secreted proteins in pig adipose tissue that may influence local and central metabolism and growth. PMID:16775050

  15. MicroRNA Expression Variability in Human Cervical Tissues

    PubMed Central

    Pereira, Patrícia M.; Marques, João Paulo; Soares, Ana R.; Carreto, Laura; Santos, Manuel A. S.

    2010-01-01

    MicroRNAs (miRNAs) are short (?22 nt) non-coding regulatory RNAs that control gene expression at the post-transcriptional level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. Cervical cancer is one of the most common cancers in women worldwide and there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform containing probes for mature miRNAs. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL) and 9 low-grade squamous intraepithelial lesion (LSIL) samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, deregulated miRNAs were identified in malignant and pre-malignant cervical tissues after tackling the high expression variability observed. We were also able to identify putative target genes of relevant candidate miRNAs. Our results show that miRNA expression shows natural variability among human samples, which complicates miRNA data profiling analysis. However, such expression noise can be filtered and does not prevent the identification of deregulated miRNAs that play a role in the malignant transformation of cervical squamous cells. Deregulated miRNAs highlight new candidate gene targets allowing for a better understanding of the molecular mechanism underlying the development of this tumour type. PMID:20668671

  16. Kernel-based distance metric learning for microarray data classification

    PubMed Central

    Xiong, Huilin; Chen, Xue-wen

    2006-01-01

    Background The most fundamental task using gene expression data in clinical oncology is to classify tissue samples according to their gene expression levels. Compared with traditional pattern classifications, gene expression-based data classification is typically characterized by high dimensionality and small sample size, which make the task quite challenging. Results In this paper, we present a modified K-nearest-neighbor (KNN) scheme, which is based on learning an adaptive distance metric in the data space, for cancer classification using microarray data. The distance metric, derived from the procedure of a data-dependent kernel optimization, can substantially increase the class separability of the data and, consequently, lead to a significant improvement in the performance of the KNN classifier. Intensive experiments show that the performance of the proposed kernel-based KNN scheme is competitive to those of some sophisticated classifiers such as support vector machines (SVMs) and the uncorrelated linear discriminant analysis (ULDA) in classifying the gene expression data. Conclusion A novel distance metric is developed and incorporated into the KNN scheme for cancer classification. This metric can substantially increase the class separability of the data in the feature space and, hence, lead to a significant improvement in the performance of the KNN classifier. PMID:16774678

  17. A rapid and inexpensive labeling method for microarray gene expression analysis

    E-print Network

    Ouellet, Mario

    2012-01-01

    Global gene expression profiling by DNA microarrays is anBackground DNA microarrays allow global profiling of nucleicDNA microarrays have been devel- oped in the past decade [1,2], differential gene expression profiling

  18. Why we developed the microarray, Patrick BrownSite: DNA Interactive (www.dnai.org)

    NSDL National Science Digital Library

    2008-03-26

    Interviewee: Patrick (Pat) Brown DNAi Location:Applications>Genes and medicine>genetic profiling>Patrick Brown>Why we developed the microarray Why we developed microarrays Pat Brown talks about developing microarray technology for genome-wide analysis.

  19. What's on a microarray, Patrick BrownSite: DNA Interactive (www.dnai.org)

    NSDL National Science Digital Library

    2008-03-26

    Interviewee: Pat Brown DNAi Location:Applications>Genes and medicine>genetic profiling>Patrick Brown>What's on a microarray What's on a microarray Pat Brown talks about how the 30,000 spots on the microarray represent genes.

  20. Making a DNA microarray, Patrick BrownSite: DNA Interactive (www.dnai.org)

    NSDL National Science Digital Library

    2008-03-26

    Interviewee: Pat Brown DNAi Location:Applications>Genes and medicine>genetic profiling>Patrick Brown>Making a microarray Making a microarray Pat Brown discusses the early technology behind the microarray.

  1. A Comparative Study of Normalization Methods Used in Statistical Analysis of Oligonucleotide Microarray Data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Normalization methods used in the statistical analysis of oligonucleotide microarray data were evaluated. The oligonucleotide microarray is considered an efficient analytical tool for analyzing thousands of genes simultaneously in a single experiment. However, systematic variation in microarray, ori...

  2. Site-Specific Immobilization of Biotinylated Proteins for Protein Microarray Analysis

    E-print Network

    Yao, Shao Q

    could vary from approximately 40,000 to as many as 1,000,000. The DNA microarray technology has allowed in an organism, protein microarray, which adopts the same spotting technology used to fabricate DNA microarray

  3. Identification of a Novel Coronavirus from a Beluga Whale by Using a Panviral Microarray ? †

    PubMed Central

    Mihindukulasuriya, Kathie A.; Wu, Guang; St. Leger, Judy; Nordhausen, Robert W.; Wang, David

    2008-01-01

    The emergence of viruses such as severe acute respiratory syndrome coronavirus and Nipah virus has underscored the role of animal reservoirs in human disease and the need for reservoir surveillance. Here, we used a panviral DNA microarray to investigate the death of a captive beluga whale in an aquatic park. A highly divergent coronavirus, tentatively named coronavirus SW1, was identified in liver tissue from the deceased whale. Subsequently, the entire genome of SW1 was sequenced, yielding a genome of 31,686 nucleotides. Phylogenetic analysis revealed SW1 to be a novel virus distantly related to but most similar to group III coronaviruses. PMID:18353961

  4. An Empirical Bayes Adjustment to Multiple p-values For the Detection of Differentially Expressed Genes in Microarray Experiments

    Microsoft Academic Search

    Somnath Datta; Susmita Datta

    2000-01-01

    In recent microarray experiments thousands of gene expressions are simultaneously tested in comparing samples (e.g., tissue types or experimental conditions). Application of a statistical test, such as the t-test, would lead to a p-value for each gene that reflects the amount of statistical evidence present in the data that the given gene is indeed differentially expressed. We show how to

  5. DETERMINING THE ROLE OF ETHYLENE IN THE DEVELOPMENT OF TOMATO IRREGUALR RIPENING DISORDER USING MICROARRAY TECHNOLOGY AND RT-REAL TIME PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to determine the underlying causes of tomato irregular ripening disorder associated with whitefly feeding, microarray hybridization analysis followed by reverse transcription real time PCR validation were used to determine gene regulation in young and old leaf tissue, stems, flowers, roots,...

  6. Protease degradomics: mass spectrometry discovery of protease substrates and the CLIP-CHIP, a dedicated DNA microarray of all human proteases and inhibitors

    Microsoft Academic Search

    Christopher M. Overall; Eric M. Tam; Reinhild Kappelhoff; Andrea Connor; T. Ewart; C. J. Morrison; X. Puente; C. López-Otín; A. Seth

    2004-01-01

    The biological role of most proteases in vivo is largely unknown. Therefore, to develop robust techniques to analyze the protease degradome in cells and tissues and to elucidate their substrate degradomes we have devel- oped a dedicated and complete human protease and inhibitor microarray that we have called the CLIP-CHIP. Oligonucleotides (70-mers) for identifying all 715 human proteases, inactive homologs

  7. Identification and functional analysis of light-responsive unique or paralogous gene family members in rice using a near genomic gene microarray

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using a NSF45K-gene-microarray, we performed expression-profiling experiments on 2-week-old light- and dark-grown rice leaf tissue to identify mutants of light-responsive genes. We identified 356 genes that were at least 8-fold light induced genes at FDR of 1.00E-06. Then, we screened rice T-DNA i...

  8. A New Way to Introduce Microarray Technology in a Lecture/Laboratory Setting by Studying the Evolution of This Modern Technology

    ERIC Educational Resources Information Center

    Rowland-Goldsmith, Melissa

    2009-01-01

    DNA microarray is an ordered grid containing known sequences of DNA, which represent many of the genes in a particular organism. Each DNA sequence is unique to a specific gene. This technology enables the researcher to screen many genes from cells or tissue grown in different conditions. We developed an undergraduate lecture and laboratory…

  9. Tissue Engineering

    Microsoft Academic Search

    Robert Langer; Joseph P. Vacanti

    1993-01-01

    The loss or failure of an organ or tissue is one of the most frequent, devastating, and costly problems in human health care. A new field, tissue engineering, applies the principles of biology and engineering to the development of functional substitutes for damaged tissue. This article discusses the foundations and challenges of this interdisciplinary field and its attempts to provide

  10. Fascin expression is increased in metastatic lesions but does not correlate with progression nor outcome in melanoma.

    PubMed

    Ma, Yafeng; Faller, William J; Sansom, Owen J; Brown, Ewan R; Doig, Tamasin N; Melton, David W; Machesky, Laura M

    2015-04-01

    Levels of the actin bundling protein fascin correlate with invasion and metastasis and reveal prognostic value in many epithelial carcinomas. However, we know very little about the potential role of fascin in melanoma. The purpose of this study is to compare fascin expression in primary melanomas and melanoma metastasis. Fascin expression was examined through the immunohistochemistry of paraffin embedded tissue microarrays including 560 cores of primary tumour and metastasis. Fascin expression was significantly elevated in 48 metastases compared with 254 primary tumours (P=0.034). In 187 patients with primary melanomas, fascin was not correlated with survival (P=0.067), whereas low fascin was significantly correlated with the presence of ulceration (P=0.005). Our results indicate that fascin status does not correlate with progression in melanoma. Upregulated fascin expression was detected in melanoma metastases, but was not correlated to patient outcome. PMID:25535872

  11. Cell Type-dependent Gene Transcription Profile in Three Dimensional Human Skin Tissue Model Exposed to Low Doses of Ionizing Radiation: Implications for Medical Exposures

    SciTech Connect

    Freiin von Neubeck, Claere H.; Shankaran, Harish; Karin, Norman J.; Kauer, Paula M.; Chrisler, William B.; Wang, Xihai; Robinson, Robert J.; Waters, Katrina M.; Tilton, Susan C.; Sowa, Marianne B.

    2012-04-17

    The concern over possible health risks from exposures to low doses of ionizing radiation has been driven largely by the increase in medical exposures, the routine implementation of X-ray backscatter devices for airport security screening, and, most recently, the nuclear incident in Japan. Due to a paucity of direct epidemiological data at very low doses, cancer risk must be estimated from high dose exposure scenarios. However, there is increasing evidence that low and high dose exposures result in different signaling events and may have different mechanisms of cancer induction. We have examined the radiation induced temporal response of an in vitro three dimensional (3D) human skin tissue model using microarray-based transcriptional profiling. Our data shows that exposure to 100 mGy of X-rays is sufficient to affect gene transcription. Cell type specific analysis showed significant changes in gene expression with the levels of > 1400 genes altered in the dermis and > 400 genes regulated in the epidermis. The two cell types rarely exhibited overlapping responses at the mRNA level. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) measurements validated the microarray data in both regulation direction and value. Key pathways identified relate to cell cycle regulation, immune responses, hypoxia, reactive oxygen signaling, and DNA damage repair. We discuss in particular the role of proliferation and emphasizing how the disregulation of cellular signaling in normal tissue may impact progression towards radiation induced secondary diseases.

  12. Leptospiral Outer Membrane Protein Microarray, a Novel Approach to Identification of Host Ligand-Binding Proteins

    PubMed Central

    Matsunaga, James; Haake, David A.

    2012-01-01

    Leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes belonging to the genus Leptospira. The leptospiral life cycle involves transmission via freshwater and colonization of the renal tubules of their reservoir hosts. Infection requires adherence to cell surfaces and extracellular matrix components of host tissues. These host-pathogen interactions involve outer membrane proteins (OMPs) expressed on the bacterial surface. In this study, we developed an Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 OMP microarray containing all predicted lipoproteins and transmembrane OMPs. A total of 401 leptospiral genes or their fragments were transcribed and translated in vitro and printed on nitrocellulose-coated glass slides. We investigated the potential of this protein microarray to screen for interactions between leptospiral OMPs and fibronectin (Fn). This approach resulted in the identification of the recently described fibronectin-binding protein, LIC10258 (MFn8, Lsa66), and 14 novel Fn-binding proteins, denoted Microarray Fn-binding proteins (MFns). We confirmed Fn binding of purified recombinant LIC11612 (MFn1), LIC10714 (MFn2), LIC11051 (MFn6), LIC11436 (MFn7), LIC10258 (MFn8, Lsa66), and LIC10537 (MFn9) by far-Western blot assays. Moreover, we obtained specific antibodies to MFn1, MFn7, MFn8 (Lsa66), and MFn9 and demonstrated that MFn1, MFn7, and MFn9 are expressed and surface exposed under in vitro growth conditions. Further, we demonstrated that MFn1, MFn4 (LIC12631, Sph2), and MFn7 enable leptospires to bind fibronectin when expressed in the saprophyte, Leptospira biflexa. Protein microarrays are valuable tools for high-throughput identification of novel host ligand-binding proteins that have the potential to play key roles in the virulence mechanisms of pathogens. PMID:22961849

  13. Gene Expression Analyses of Subchondral Bone in Early Experimental Osteoarthritis by Microarray

    PubMed Central

    Chen, YuXian; Shen, Jun; Lu, HuaDing; Zeng, Chun; Ren, JianHua; Zeng, Hua; Li, ZhiFu; Chen, ShaoMing; Cai, DaoZhang; Zhao, Qing

    2012-01-01

    Osteoarthritis (OA) is a degenerative joint disease that affects both cartilage and bone. A better understanding of the early molecular changes in subchondral bone may help elucidate the pathogenesis of OA. We used microarray technology to investigate the time course of molecular changes in the subchondral bone in the early stages of experimental osteoarthritis in a rat model. We identified 2,234 differentially expressed (DE) genes at 1 week, 1,944 at 2 weeks and 1,517 at 4 weeks post-surgery. Further analyses of the dysregulated genes indicated that the events underlying subchondral bone remodeling occurred sequentially and in a time-dependent manner at the gene expression level. Some of the identified dysregulated genes that were identified have suspected roles in bone development or remodeling; these genes include Alp, Igf1, Tgf ?1, Postn, Mmp3, Tnfsf11, Acp5, Bmp5, Aspn and Ihh. The differences in the expression of these genes were confirmed by real-time PCR, and the results indicated that our microarray data accurately reflected gene expression patterns characteristic of early OA. To validate the results of our microarray analysis at the protein level, immunohistochemistry staining was used to investigate the expression of Mmp3 and Aspn protein in tissue sections. These analyses indicate that Mmp3 protein expression completely matched the results of both the microarray and real-time PCR analyses; however, Aspn protein expression was not observed to differ at any time. In summary, our study demonstrated a simple method of separation of subchondral bone sample from the knee joint of rat, which can effectively avoid bone RNA degradation. These findings also revealed the gene expression profiles of subchondral bone in the rat OA model at multiple time points post-surgery and identified important DE genes with known or suspected roles in bone development or remodeling. These genes may be novel diagnostic markers or therapeutic targets for OA. PMID:22384228

  14. ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks

    PubMed Central

    2014-01-01

    Background Uncovering the complex transcriptional regulatory networks (TRNs) that underlie plant and animal development remains a challenge. However, a vast amount of data from public microarray experiments is available, which can be subject to inference algorithms in order to recover reliable TRN architectures. Results In this study we present a simple bioinformatics methodology that uses public, carefully curated microarray data and the mutual information algorithm ARACNe in order to obtain a database of transcriptional interactions. We used data from Arabidopsis thaliana root samples to show that the transcriptional regulatory networks derived from this database successfully recover previously identified root transcriptional modules and to propose new transcription factors for the SHORT ROOT/SCARECROW and PLETHORA pathways. We further show that these networks are a powerful tool to integrate and analyze high-throughput expression data, as exemplified by our analysis of a SHORT ROOT induction time-course microarray dataset, and are a reliable source for the prediction of novel root gene functions. In particular, we used our database to predict novel genes involved in root secondary cell-wall synthesis and identified the MADS-box TF XAL1/AGL12 as an unexpected participant in this process. Conclusions This study demonstrates that network inference using carefully curated microarray data yields reliable TRN architectures. In contrast to previous efforts to obtain root TRNs, that have focused on particular functional modules or tissues, our root transcriptional interactions provide an overview of the transcriptional pathways present in Arabidopsis thaliana roots and will likely yield a plethora of novel hypotheses to be tested experimentally. PMID:24739361

  15. Tissue Mechanics

    NSDL National Science Digital Library

    Integrated Teaching and Learning Program,

    Students reflect on their experiences making silly putty (the previous hands-on activity in the unit), especially why changing the borax concentration alters the mechanical properties of silly putty and how this pertains to tissue mechanics. Students learn why engineers must understand tissue mechanics in order to design devices that will be implanted or used inside bodies, to study pathologies of tissues and how this alters tissue function, and to design prosthetics. Finally, students learn about collagen, elastin and proteoglycans and their roles in giving body tissues their unique functions. This prepares them for the culminating design-build-test activity of the unit.

  16. Statistical design and the analysis of gene expression microarray data

    Microsoft Academic Search

    M. KATHLEEN KERR; GARY A. CHURCHILL

    2001-01-01

    Gene expression microarrays are an innovative technology with enormous promise to help geneticists explore and understand the genome. Although the potential of this technology has been clearly demonstrated, many important and interesting statistical questions persist. We relate certain features of microarrays to other kinds of experimental data and argue that classical statistical techniques are appropriate and useful. We advocate greater

  17. Microarray data analysis Gold-mining in a minefield

    E-print Network

    Futschik, Matthias E.

    there is a raised way; and you will see, if you look, a low wall built along the way, like the screen which-out, design and validation Minefield III: Not everything is gold that shines Error detection and correction two-colour) microarrays One-channel (or one-colour) microarrays Goldmines: Clustering of arrays

  18. AVA: visual analysis of gene expression microarray data

    Microsoft Academic Search

    Yihua Zhou; Jingdong Liu

    2003-01-01

    Summary: AV A( Array Visual Analyzer) is a Java program that provides a graphical environment for visualization and analysis of gene expression microarray data. Together with its interactive visualization tools and a variety of built-in data analysis and filtration methods, AVA effectively inte- grates microarray data normalization, quality assessment, and data mining into one application. Availability: The software is freely

  19. The Importance of Normalization on Large and Heterogeneous Microarray Datasets

    EPA Science Inventory

    DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

  20. Experimental Approaches to Microarray Analysis of Tumor Samples

    ERIC Educational Resources Information Center

    Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

    2008-01-01

    Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

  1. Fabricating RNA Microarrays with RNA-DNA Surface Ligation Chemistry

    E-print Network

    Fabricating RNA Microarrays with RNA-DNA Surface Ligation Chemistry Hye Jin Lee, Alastair W. Wark, there are at present only a handful of reports on the fabrication of RNA microarrays in the literature.12-15 These fabrication strategies typically employ modified RNA (e.g., thiol- terminated or biotinylated

  2. A concise guide to cDNA microarray analysis

    Microsoft Academic Search

    P. Hegde; R. Qi; K. Abernathy; C. Gay; S. Dharap; R. Gaspard

    2000-01-01

    Microarray expression analysis has become one of the most widely used functional genomics tools. Efficient application of this technique requires the development of robust and reproducible protocols. We have optimized all aspects of the process, including PCR amplification of target cDNA clones, microarray printing, probe labeling, and hybridization, and we have developed strategies for data normalization and analysis.

  3. ORIGINAL PAPER Allergen microarrays on high-sensitivity silicon slides

    E-print Network

    ORIGINAL PAPER Allergen microarrays on high-sensitivity silicon slides Marina Cretich & Daniela with sensitizations to inhalant allergens. We compared the performance of silicon versus glass substrates that reproducibility of the microarray on glass supports was not different from available data on allergen arrays

  4. Determining gene expression on a single pair of microarrays

    Microsoft Academic Search

    Robert W. Reid; Anthony A. Fodor

    2008-01-01

    BACKGROUND: In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new algorithm called PINC (PINC is Not Cyber-T)

  5. Reliability and reproducibility issues in DNA microarray measurements

    Microsoft Academic Search

    Sorin Draghici; Purvesh Khatri; Aron C. Eklund; Zoltan Szallasi

    2006-01-01

    DNA microarrays enable researchers to monitor the expression of thousands of genes simultaneously. However, the current technology has several limitations. Here we discuss problems related to the sensitivity, accuracy, specificity and reproducibility of microarray results. The existing data suggest that for relatively abundant transcripts the existence and direction (but not the magnitude) of expression changes can be reliably detected. However,

  6. Machine Learning in DNA Microarray Analysis for Cancer Classification

    Microsoft Academic Search

    Sung-Bae Cho; Hong-Hee Won

    2003-01-01

    The development of microarray technology has supplied a large volume of data to many fields. In particular, it has been applied to prediction and diagnosis of cancer, so that it expectedly helps us to exactly predict and diagnose cancer. To precisely classify cancer we have to select genes related to cancer because extracted genes from microarray have many noises. In

  7. The application of DNA microarrays in gene expression analysis

    Microsoft Academic Search

    Nicole L. W van Hal; Oscar Vorst; Adèle M. M. L van Houwelingen; Esther J Kok; A. A. C. M. Peijnenburg; Asaph Aharoni; Arjen J van Tunen; Jaap Keijer

    2000-01-01

    DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed. These comprise array manufacturing and design, array hybridisation, scanning, and data handling. Furthermore, it is discussed

  8. Detection of bacterial pathogens in environmental samples using DNA microarrays

    Microsoft Academic Search

    Douglas R. Call; Monica K. Borucki; Frank J. Loge

    2003-01-01

    Polymerase chain reaction (PCR) is an important tool for pathogen detection, but historically, it has not been possible to accurately identify PCR products without sequencing, Southern blots, or dot-blots. Microarrays can be coupled with PCR where they serve as a set of parallel dot-blots to enhance product detection and identification. Microarrays are composed of many discretely located probes on a

  9. Automatic analysis of DNA microarray images using mathematical morphology

    Microsoft Academic Search

    Jesús Angulo; Jean Serra

    2003-01-01

    Motivation: DNA microarrays are an experimental tech- nology which consists in arrays of thousands of discrete DNA sequences that are printed on glass microscope slides. Image analysis is an important aspect of microarray experiments. The aim of this step is to reduce an image of spots into a table with a measure of the intensity for each spot. Efficient, accurate

  10. Microarray-based gene expression profiles of silkworm brains

    Microsoft Academic Search

    Ling Gan; Xilong Liu; Zhonghuai Xiang; Ningjia He

    2011-01-01

    BACKGROUND: Molecular genetic studies of Bombyx mori have led to profound advances in our understanding of the regulation of development. Bombyx mori brain, as a main endocrine organ, plays important regulatory roles in various biological processes. Microarray technology will allow the genome-wide analysis of gene expression patterns in silkworm brains. RESULTS: We reported microarray-based gene expression profiles in silkworm brains

  11. Significance analysis of microarrays applied to the ionizing radiation response

    Microsoft Academic Search

    V. G. Tusher; Robert Tibshirani; Gilbert Chu

    2001-01-01

    Microarrays can measure the expression of thousands of genes to identify changes in expression between different biological states. Methods are needed to determine the significance of these changes while accounting for the enormous number of genes.We describe a method, Significance Analysis of Microarrays (SAM), that assigns a score to each gene on the basis of change in gene expression relative

  12. GENERATING ENCODED COMPOUND LIBRARIES FOR FABRICATING MICROARRAYS AS A

    E-print Network

    Zhu, Xiangdong

    .] Keywords Chemical microarray; high-throughput screening; one-bead­one-compound (OBOC) synthesis; proteinGENERATING ENCODED COMPOUND LIBRARIES FOR FABRICATING MICROARRAYS AS A HIGH-THROUGHPUT PROTEIN-compound synthesis and employs a novel trilayer bead-partition Received June 23, 2013. Address correspondence to Yung

  13. Comparing microarrays and next-generation sequencing technologies

    E-print Network

    Bae, Jin-Woo

    Comparing microarrays and next- generation sequencing technologies for microbial ecology research of DNA microarrays and next-generation sequencing (NGS) technologies to the field of microbial ecology genomic and metagenomic tools [1]. With the application of these technologies, in particular next-generation

  14. Clustering methods for the analysis of DNA microarray data

    E-print Network

    Tibshirani, Robeert

    Clustering methods for the analysis of DNA microarray data Robert Tibshirani, Trevor Hastie, Mike methods of clustering, and illustrate how they can be used to arrange both the genes and cell lines from a set of DNA microarray experiments. The methods discussed are global clustering techniques including

  15. Clustering methods for the analysis of DNA microarray data

    E-print Network

    Hastie, Trevor

    Clustering methods for the analysis of DNA microarray data Robert Tibshirani, Trevor Hastie, Mike of clustering, and illustrate how they can be used to arrange both the genes and cell lines from a set of DNA microarray experiments. The methods discussed are global clustering techniques including hierarchical, K

  16. Biological Pathway Conducting Microarray-Based Cancer Classification

    Microsoft Academic Search

    Tao Zeng; Fei Luo; Juan Liu

    2009-01-01

    The cancer classification is a major and important study field in the medical research, and DNA microarrays have been proved to provide useful and great information for cancer classification at molecular level, compared with traditional clinical or histopathological information. Bio-markers from microarray gene expression analysis have developed to a new approach for cancer classification but still face the problems such

  17. Antigen microarrays profiling of autoantibodies in rheumatoid arthritis

    Microsoft Academic Search

    W. Huebner; Brian A. Kidd; Beren H. Tomooka; Byung J. Lee; Bonnie Bruce; James F. Fries; G. Sonderstrup; Paul Monach; Jan W. Drijfhout; Walther J. van Venrooij; Paul J. Utz; Mark C. Genovese

    2005-01-01

    Objective. Because rheumatoid arthritis (RA) is a heterogeneous autoimmune disease in terms of disease manifestations, clinical outcomes, and therapeutic re- sponses, we developed and applied a novel antigen microarray technology to identify distinct serum anti- body profiles in patients with RA. Methods. Synovial proteome microarrays, con- taining 225 peptides and proteins that represent candi- date and control antigens, were developed.

  18. Copy number variations are progressively associated with the pathogenesis of colorectal cancer in ulcerative colitis

    PubMed Central

    Shivakumar, Bhadravathi Marigowda; Rotti, Harish; Vasudevan, Thanvanthri Gururajan; Balakrishnan, Aswath; Chakrabarty, Sanjiban; Bhat, Ganesh; Rao, Lakshmi; Pai, Cannanore Ganesh; Satyamoorthy, Kapaettu

    2015-01-01

    AIM: To evaluate the association of known copy number variations (CNVs) in ulcerative colitis (UC) progressing to colorectal cancer. METHODS: Microsatellite instability analysis using the National Cancer Institute’s panel of markers, and CNV association studies using Agilent 2 × 105 k arrays were done in tissue samples from four patient groups with UC: those at low risk (LR) or high risk of developing colorectal cancer, those with premalignant dysplastic lesions, and those with colitis-associated colorectal cancer (CAC). DNA from tissue samples of these groups were independently hybridized on arrays and analyzed. The data obtained were further subjected to downstream bioinformatics enrichment analysis to examine the correlation with CAC progression. RESULTS: Microarray analysis highlighted a progressive increase in the total number of CNVs [LR (n = 178) vs CAC (n = 958), 5.3-fold], gains and losses [LR (n = 37 and 141) vs CAC (n = 495 and 463), 13.4- and 3.3-fold, respectively], size [LR (964.2 kb) vs CAC (10540 kb), 10.9-fold] and the number of genes in such regions [LR (n = 119) vs CAC (n = 455), 3.8-fold]. Chromosome-wise analysis of CNVs also showed an increase in the number of CNVs across each chromosome. There were 38 genes common to all four groups in the study; 13 of these were common to cancer genes from the Genetic Disease Association dataset. The gene set enrichment analysis and ontology analysis highlighted many cancer-associated genes. All the samples in the different groups were microsatellite stable. CONCLUSION: Increasing numbers of CNVs are associated with the progression of UC to CAC, and warrant further detailed exploration. PMID:25605985

  19. Decreased expression of SCUBE2 is associated with progression and prognosis in colorectal cancer.

    PubMed

    Song, Qi; Li, Chuanwei; Feng, Xiaodong; Yu, Ailian; Tang, Huamei; Peng, Zhihai; Wang, Xuechun

    2015-04-01

    Signal peptide-CUB-epidermal growth factor-like domain-containing protein 2 (SCUBE2), a member of the SCUBE protein family, is a secreted and membrane-associated multi-domain glycoprotein. SCUBE2 is known as a novel tumor suppressor and a useful prognostic marker in breast cancer. In the present study, we investigated the expression (including mRNA and protein levels) of SCUBE2 in colorectal cancer (CRC) and adjacent normal tissues, using quantitative real-time PCR, western blot analysis and immunohistochemistry on a tissue microarray. Upregulation of SCUBE2 was achieved by transient transfection in RKO cell lines, and the effects of SCUBE2 on tumor proliferation, invasion, migration and apoptosis were evaluated by a series of functional experiments. The results indicated that SCUBE2 expression was decreased at the transcriptional and translational levels in CRC tissues and significantly associated with clinical stage, the depth of tumor invasion, lymph?node metastasis, distant metastasis and histological grade. Patients with SCUBE2?positive tumors had a lower recurrence rate and better survival than patients with SCUBE2-negative tumors. Moreover, upregulation of SCUBE2 had a limited effect on cell apoptosis but significantly inhibited tumor cell proliferation, migration and invasion in vitro. In conclusion, SCUBE2 plays an important role in suppressing CRC progression and prognosis. Our findings suggested that SCUBE2 may serve as a novel tumor suppressor and a potential therapeutic target for CRC patients. PMID:25672935

  20. Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis

    PubMed Central

    Birsoy, K?vanç; Berry, Ryan; Wang, Tim; Ceyhan, Ozge; Tavazoie, Saeed; Friedman, Jeffrey M.; Rodeheffer, Matthew S.

    2011-01-01

    Obesity is characterized by an expansion of white adipose tissue mass that results from an increase in the size and the number of adipocytes. However, the mechanisms responsible for the formation of adipocytes during development and the molecular mechanisms regulating their increase and maintenance in adulthood are poorly understood. Here, we report the use of leptin-luciferase BAC transgenic mice to track white adipose tissue (WAT) development and guide the isolation and molecular characterization of adipocytes during development using DNA microarrays. These data reveal distinct transcriptional programs that are regulated during murine WAT development in vivo. By using a de novo cis-regulatory motif discovery tool (FIRE), we identify two early gene clusters whose promoters show significant enrichment for NRF2/ETS transcription factor binding sites. We further demonstrate that Ets transcription factors, but not Nrf2, are regulated during early adipogenesis and that Ets2 is essential for the normal progression of the adipocyte differentiation program in vitro. These data identify ETS2 as a functionally important transcription factor in adipogenesis and its possible role in regulating adipose tissue mass in adults can now be tested. Our approach also provides the basis for elucidating the function of other gene networks during WAT development in vivo. Finally these data confirm that although gene expression during adipogenesis in vitro recapitulates many of the patterns of gene expression in vivo, there are additional developmental transitions in pre and post-natal adipose tissue that are not evident in cell culture systems. PMID:21989915

  1. On the Statics for Micro-Array Data Analysis

    NASA Astrophysics Data System (ADS)

    Urushibara, Tomoko; Akasaka, Shizu; Ito, Makiko; Suzuki, Tomonori; Miyazaki, Satoru

    2010-01-01

    Recently after human genome sequence has been determined almost perfectly, more and more researchers have been studying genes in detail. Therefore, we are sure that accumulated gene information for human will be getting more important in the near future to develop customized medicine and to make gene interactions clear. Among plenty of information, micro array might be one of the most important analysis method for genes because it is the technique that can get big amount of the gene expressions data from one time experiment and also can be used for DNA isolation. To get the novel knowledge from micro array data, we need to enrich statistical tools for its data analysis. So far, many mathematical theories and definition have been proposing. However, many of those proposals are tested with strict conditions or customized to data for specific species. In this paper, we reviewed existing typical statistical methods for micro array analysis and discussed the repeatability of the analysis, construction the guideline with more general procedure. First we analyzed the micro array data for TG rats, with statistical methods of family-wise error rate (FWER) control approach and False Discovery Rate (FDR) control approach. As existing report, no significantly different gene could be detected with FWER control approach. On the other hand, we could find several genes significantly with FDR control approach even q=0.5. To find out the reliability of FDR control approach with micro array conditions, we have analyzed 2 more pieces of data from Gene Expression Omnibus (GEO) public database on the web site with SAM in addition to FWER and FDR control approaches. We could find a certain number of significantly different genes with BH method and SAM in the case of q=0.05. However, we have to note that the number and kinds of detected genes are different when we compare our result with the one from the published paper. Even if the same approach is used to analyze the same micro array data, we might get a different result because the distinct definition for micro array data has not been set yet. It means that from the same data we will get different results depending on researchers. We are afraid that this problem will have a big effect on developing new medicines and to progress the next step, like a 2nd screening. So, we suggest that we should have certain guidelines to analyze Micro-Array data validly with statistic method and it will surely be helpful for Micro-Array analysis for medical studies in the future.

  2. Vector edge operators for cDNA microarray spot localization.

    PubMed

    Lukac, Rastislav; Plataniotis, Konstantinos N

    2007-10-01

    This paper introduces a vector-based framework for edge detection and spot localization in cDNA microarray data. Since cDNA microarray images can be viewed as vector fields, both their spectral and spatial characteristics should be used to determine edges, discontinuities and structural elements. Building upon the powerful nature of nonlinear operators, the proposed vector edge operators can effectively localize microarray spots outperforming the commonly used scalar edge detectors. Moreover, due to the utilization of the principle of robust statistics, vector edge detectors are relatively immune to the noise present in microarray images. Simulation studies reported in this paper indicate that the proposed framework yields excellent performance and it can be readily incorporated in the cDNA microarray processing pipeline. PMID:17707611

  3. Gene Expression Studies Using Microarrays: Principles, Problems, and Prospects

    NSDL National Science Digital Library

    PhD David Murphy (University of Bristol Research Centre for Neuroendocrinology)

    2002-12-01

    Anumber of mammalian genomes having been sequenced, an important next step is to catalog the expression patterns of all transcription units in health and disease by use of microarrays. Such discovery programs are crucial to our understanding of the gene networks that control developmental, physiological, and pathological processes. However, despite the excitement, the full promise of microarray technology has yet to be realized, as the superficial simplicity of the concept belies considerable problems. Microarray technology is very new; methodologies are still evolving, common standards have yet to be established, and many problems with experimental design and variability have still to be fully understood and overcome. This review will describe the time course of a microarray experimentÂ?RNA isolation from sample, target preparation, hybridization to the microarray probe, data capture, and bioinformatic analysis. For each stage, the advantages and disadvantages of competing techniques are compared, and inherent sources of error are identified and discussed.

  4. Dickkopf-1 expression increases early in prostate cancer development and decreases during progression from primary tumor to metastasis

    PubMed Central

    Hall, Christopher L.; Daignault, Stephanie D.; Shah, Rajal B.; Pienta, Kenneth J.; Keller, Evan T.

    2012-01-01

    BACKGROUND Prostate cancer (PCa) frequently metastasizes to the bone and induces osteoblastic lesions. We previously demonstrated through over-expression of the Wnt inhibitor dickkopf-1 (DKK-1) that Wnts contribute to the osteoblastic component of PCa osseous lesions in vivo. METHODS To test the clinical significance of DKK-1 expression during PCa progression, tissue microarrays were stained for DKK-1 protein by immunohistochemistry. RESULTS DKK-1 expression index (EI) was found to increase in PIN and primary lesions compared to non-neoplastic tissue (106±10 vs. 19±6, respectively, where the EI is the product of the percent expression and staining intensity). DKK-1 expression was also found to be higher in all PCa metastatic lesions (56±21 EI) compared to non-neoplastic tissues but was significantly decreased vs. primary PCa lesions (p<0.008). The decline in DKK-1 correlated with a shift of ?-catenin staining from the nucleus to the cytoplasm suggesting possible mechanism for the observed decrease in DKK-1 levels during PCa progression. Within metastatic lesions, DKK-1 expression was least abundant in PCa bone metastases relative to all soft tissue PCa metastatic lesions except lymph node metastases. High DKK-1 expression within PCa metastases was further associated with shorter over-all patient survival. CONCLUSIONS Taken together, these data demonstrate that elevated DKK-1 expression is an early event in PCa and that as PCa progresses DKK-1 expression declines, particularly in advanced bone metastases. The decline of DKK-1 in bone metastases can unmask Wnts’ osteoblastic activity. These data support a model in which DKK-1 is a molecular switch that transitions the phenotype of PCa osseous lesions from osteolytic to osteoblastic. PMID:18561248

  5. The overexpression membrane type 1 matrix metalloproteinase is associated with the progression and prognosis in breast cancer

    PubMed Central

    Li, Yongping; Cai, Guohong; Yuan, Shifang; Jun, Yi; Li, Nanlin; Wang, Ling; Chen, Feng; Ling, Rui; Yun, Jun

    2015-01-01

    Membrane type 1 matrix metalloproteinase (MT1-MMP) has been demonstrated to play an important role in tumor progression. The aim of the present study was to analyze the expression of MT1-MMP in breast cancer and its correlation with clinicopathologic characteristics, including the survival of breast cancer patients. In our results, MT-MMP1 was up-expressed in breast cancer tissues compared with ductal hyperplasia tissues in microarray data (GSE2429). MT1-MMP mRNA and protein expression was markedly higher in breast cancer tissues than in normal breast tissues (P=0.005 and P=0.037, respectively). Using immunohistochemistry, high levels of MT1-MMP protein were positively correlated with the status of clinical stage (I-II vs. III-IV; P=0.043), lymph node metastasis (absence vs. presence; P=0.024), and distant metastasis (No vs. Yes; P=0.017) of breast cancer patients. Patients with higher MT1-MMP expression had a significantly shorter overall survival time than did patients with low MT1-MMP expression. Multivariate analysis indicated that the level of MT1-MMP expression was an independent prognostic indicator (P<0.001) for the survival of patients with breast cancer. In conclusions, MT1-MMP plays an important role on breast cancer aggressiveness and prognosis and may act as a promising target for prognostic prediction. PMID:25755834

  6. Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray

    PubMed Central

    Skreka, Konstantinia; Zywicki, Marek; Karbiener, Michael; Hüttenhofer, Alexander; Scheideler, Marcel; Rederstorff, Mathieu

    2012-01-01

    Mammalian transcriptomes mainly consist of non protein coding RNAs. These ncRNAs play various roles in all cells and are involved in multiple regulation pathways. More recently, ncRNAs have also been described as valuable diagnostic tools. While RNA-seq approaches progressively replace microarray-based technologies for high-throughput expression profiling, they are still not routinely used in diagnostic. Microarrays, on the other hand, are more widely used for diagnostic profiling, especially for very small ncRNA (e.g., miRNAs), employing locked nucleic acid (LNA) arrays. However, LNA microarrays are quite expensive for high-throughput studies targeting longer ncRNAs, while DNA arrays do not provide satisfying results for the analysis of small RNAs. Here, we describe a mixed DNA/LNA microarray platform, where directly labeled small and longer ncRNAs are hybridized on LNA probes or custom DNA probes, respectively, enabling sensitive and specific analysis of a complex RNA population on a unique array in one single experiment. The DNA/LNA system, requiring relatively low amounts of total RNA, which complies with diagnostic references, was successfully applied to the analysis of differential ncRNA expression in mouse embryonic stem cells and adult brain cells. PMID:22778910

  7. MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data

    PubMed Central

    2013-01-01

    Background MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing and represent critical regulators of cell and tissue differentiation. Microarray expression profiling of miRNAs is an effective means of acquiring genome-level information of miRNA activation and inhibition, as well as the potential regulatory role that these genes play within a biological system. As with mRNA expression profiling arrays, miRNA microarrays come in a variety of platforms from numerous manufacturers, and there are a multitude of techniques available for reducing and analyzing these data. Results In this paper, we present an analysis of a typical two-color miRNA microarray experiment using publicly available packages from R and Bioconductor, the open-source software project for the analysis of genomic data. Covered topics include visualization, normalization, quality checking, differential expression, cluster analysis, miRNA target identification, and gene set enrichment analysis. Many of these tools carry-over from the analysis of mRNA microarrays, but with some notable differences that require special attention. The paper is presented as a “compendium” which, along with the accompanying R package MmPalateMiRNA, contains all of the experimental data and source code to reproduce the analyses contained in the paper. Conclusions The compendium presented in this paper will provide investigators with an access point for applying the methods available in R and Bioconductor for analysis of their own miRNA array data. PMID:23298515

  8. Microarray analysis of genes differentially expressed in HepG2 cells cultured in simulated microgravity: preliminary report

    NASA Technical Reports Server (NTRS)

    Khaoustov, V. I.; Risin, D.; Pellis, N. R.; Yoffe, B.; McIntire, L. V. (Principal Investigator)

    2001-01-01

    Developed at NASA, the rotary cell culture system (RCCS) allows the creation of unique microgravity environment of low shear force, high-mass transfer, and enables three-dimensional (3D) cell culture of dissimilar cell types. Recently we demonstrated that a simulated microgravity is conducive for maintaining long-term cultures of functional hepatocytes and promote 3D cell assembly. Using deoxyribonucleic acid (DNA) microarray technology, it is now possible to measure the levels of thousands of different messenger ribonucleic acids (mRNAs) in a single hybridization step. This technique is particularly powerful for comparing gene expression in the same tissue under different environmental conditions. The aim of this research was to analyze gene expression of hepatoblastoma cell line (HepG2) during early stage of 3D-cell assembly in simulated microgravity. For this, mRNA from HepG2 cultured in the RCCS was analyzed by deoxyribonucleic acid microarray. Analyses of HepG2 mRNA by using 6K glass DNA microarray revealed changes in expression of 95 genes (overexpression of 85 genes and downregulation of 10 genes). Our preliminary results indicated that simulated microgravity modifies the expression of several genes and that microarray technology may provide new understanding of the fundamental biological questions of how gravity affects the development and function of individual cells.

  9. IPO8 and FBXL10: New Reference Genes for Gene Expression Studies in Human Adipose Tissue

    Microsoft Academic Search

    Carmen Hurtado del Pozo; Rosa M. Calvo; Gregorio Vesperinas-García; Javier Gómez-Ambrosi; Gema Frühbeck; Ramón Corripio-Sánchez; Miguel A. Rubio; Maria-Jesus Obregon; Maria J. Obregon

    2010-01-01

    Housekeeping genes frequently used in gene expression studies are highly regulated in human adipose tissue. To ensure a correct interpretation of results, it is critical to select appropriate reference genes. Subcutaneous (SC) and omental (OM) adipose tissue expression was analyzed from lean and obese subjects using whole genome complementary DNA (cDNA) microarrays to identify stably expressed genes and commercial TaqMan

  10. Microarrays for Pathogen Detection and Analysis

    PubMed Central

    2011-01-01

    DNA microarrays have emerged as a viable platform for detection of pathogenic organisms in clinical and environmental samples. These microbial detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies like high-throughput sequencing. While pathogen detection arrays have been used primarily in a research context, several groups are aggressively working to develop arrays for clinical diagnostics, food safety testing, environmental monitoring and biodefense. Statistical algorithms that can analyze data from microbial detection arrays and provide easily interpretable results are absolutely required in order for these efforts to succeed. In this article, we will review the most promising array designs and analysis algorithms that have been developed to date, comparing their strengths and weaknesses for pathogen detection and discovery. PMID:21930658

  11. Digital microarray analysis for digital artifact genomics

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger; Handley, James; Williams, Deborah

    2013-06-01

    We implement a Spatial Voting (SV) based analogy of microarray analysis for digital gene marker identification in malware code sections. We examine a famous set of malware formally analyzed by Mandiant and code named Advanced Persistent Threat (APT1). APT1 is a Chinese organization formed with specific intent to infiltrate and exploit US resources. Manidant provided a detailed behavior and sting analysis report for the 288 malware samples available. We performed an independent analysis using a new alternative to the traditional dynamic analysis and static analysis we call Spatial Analysis (SA). We perform unsupervised SA on the APT1 originating malware code sections and report our findings. We also show the results of SA performed on some members of the families associated by Manidant. We conclude that SV based SA is a practical fast alternative to dynamics analysis and static analysis.

  12. DNA microarrays on a mesospaced surface

    NASA Astrophysics Data System (ADS)

    Hong, Bong Jin; Park, Joon Won

    2004-12-01

    A dendron having nine carboxylic acid groups at the end of the branches and a protected amine at the apex was allowed to form a molecular layer on the aminosilylated surface through multipoint ionic attraction. It was found that a compact and smooth monolayer was obtained at appropriate condition. The film quality was maintained successfully after deprotecting CBZ group with trimethylsilyl iodide. The surface density of the primary amine after the deprotection was measured with fluorometry, and 0.1-0.2 amine group per 1 nm2 was observed. This implies that the spacing between the amine functional groups is 24-34 Å in hexagonal close packing (hcp) model. In addition, DNA microarrays were fabricated successfully on the dendron-modified surface.

  13. MicroRNA-224 negatively regulates p21 expression during late neoplastic progression in inflammatory bowel disease

    PubMed Central

    Olaru, Alexandru V.; Yamanaka, Sumitaka; Vazquez, Christine; Mori, Yuriko; Cheng, Yulan; Abraham, John M.; Bayless, Theodore M.; Harpaz, Noam; Meltzer, Stephen J.

    2014-01-01

    Background The development of colon cancer represents a major complication in patients with inflammatory bowel disease (IBD). The importance of microRNAs (miRs) in carcinogenesis is becoming clearer, as miRs have been implicated in the regulation of cancer-related cellular processes to include apoptosis, differentiation, cell cycle progression, and immune function. In the current study, we sought to identify miR dysregulation specific to progression along the normal-inflammation-cancer axis in colonic specimens from IBD patients. Methods MiR microarrays and quantitative RT-PCR were used to detect and confirm dysregulated miRs. Receiver-operating characteristic curve analysis was applied to evaluate the potential utility of miR-224 as a neoplastic disease marker in IBD. For miR-224 target mRNA identification, mRNA microarrays were employed in combination with bioinformatic analyses, Western blotting, and luciferase activity measurements. Results We identified 30 miRs that were differentially expressed between chronically inflamed mucosae and cancers arising in IBD. MiR-224 levels increased successively at each stage of IBD progression and accurately discriminated cancers from normal or chronically inflamed IBD tissues. Moreover, mRNA arrays combined with bioinformatic analyses suggested participation of miR-224 in cell cycle regulation. Subsequently, cell cycle experiments indicated that miR-224 regulates the G1/S checkpoint. Finally, in silico prediction analyses, confirmed by Western blotting and luciferase assays, identified p21 as a specific direct mRNA target of miR-224. Conclusions These findings reveal miR dysregulation specific to IBD-associated colorectal carcinoma. MiR-224 is overexpressed in IBD-cancers and targets p21, a key cell cycle regulator. Moreover, these results establish the participation of miR-224 in IBD-carcinogenesis. PMID:23399735

  14. A lesson for cancer research: placental microarray gene analysis in preeclampsia

    PubMed Central

    Louwen, Frank; Muschol-Steinmetz, Cornelia; Reinhard, Joscha; Reitter, Anke; Yuan, Juping

    2012-01-01

    Tumor progression and pregnancy share many common features, such as immune tolerance and invasion. The invasion of trophoblasts in the placenta into the uterine wall is essential for fetal development, and is thus precisely regulated. Its deregulation has been implicated in preeclampsia, a leading cause for maternal and perinatal mortality and morbidity. Pathogenesis of preeclampsia remains to be defined. Microarray-based gene profiling has been widely used for identifying genes responsible for preeclampsia. In this review, we have summarized the recent data from the microarray studies with preeclamptic placentas. Despite the complex of gene signatures, suggestive of the heterogeneity of preeclampsia, these studies identified a number of differentially expressed genes associated with preeclampsia. Interestingly, most of them have been reported to be tightly involved in tumor progression. We have discussed these interesting genes and analyzed their potential molecular functions in preeclampsia, compared with their roles in malignancy development. Further investigations are warranted to explore the involvement in molecular network of each identified gene, which may provide not only novel strategies for prevention and therapy for preeclampsia but also a better understanding of cancer cells. The trophoblastic cells, with their capacity for proliferation and differentiation, apoptosis and survival, migration, angiogenesis and immune modulation by exploiting similar molecular pathways, make them a compelling model for cancer research. PMID:22929622

  15. Molecular mechanisms of osteoarthritis using gene microarrays.

    PubMed

    Cui, Shuo; Zhang, Xinying; Hai, Sen; Lu, Hong; Chen, Yongcai; Li, Chao; Tong, Pengfei; Lu, Fei; Yuan, Zhengjiang

    2015-01-01

    This study aimed to investigate the molecular mechanisms of osteoarthritis (OA) by microarray analysis. Three gene expression datasets GSE1919, 19664 and 55235 were downloaded from the Gene Expression Omnibus, and data of OA samples and healthy controls were used. After data preprocessing, differential expression analysis between the OA group and controls was performed using LIMMA (Linear Models for Microarray Data) package and genes with |log2FC (fold change)|>1 and P<0.05 were screened as DEGs (differentially expressed genes). The screened DEGs were then subject to functional annotation and pathway enrichment analysis using DAVID (Database for Annotation Visualization and Integrated Discovery). Next, gene-set enrichment analysis was performed using Enrichment map Cytoscape plug-in, followed by detecting sub-networks using clusterONE. Finally, risk subpathways were screened using iSubpathwayMiner package. A total of 141 DEGs were screened, including 52 up-regulated ones and 89 down-regulated ones. These DEGs were enriched in 48 GO terms that were mainly related to locomotory behavior, taxis, adhesion, and 11 pathways that were related to cytokine-cytokine receptor interaction, ECM-receptor interaction, focal adhesion, as well as several signaling pathways. The enrichment map enriched gene-sets mainly related to cell death and apoptosis, and extracellular components. The risk pathways up-regulated DEGs were exclusively related to arachidonic acid metabolism and glycosphingolipid biosynthesis, and the top two risk pathways were tyrosine metabolism for the down-regulated ones. From this study we conclude that genes involved in cell death and apoptosis, as well as cell-extracellular matrix interaction, may be essential for OA pathogenesis by altering multiple signaling pathways. PMID:25468726

  16. The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

    SciTech Connect

    Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

    2010-01-27

    Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.

  17. Microarray profiling reveals that placental transcriptomes of early-onset HELLP syndrome and preeclampsia are similar

    PubMed Central

    Varkonyi, T; Nagy, B; Fule, T; Tarca, AL; Karaszi, K; Schonleber, J; Hupuczi, P; Mihalik, N; Kovalszky, I; Rigo, J; Meiri, H; Papp, Z; Romero, R; Than, NG

    2013-01-01

    Background The involvement of the placenta in the pathogenesis of preeclampsia and HELLP syndrome is well established, and placental lesions also similar in these two syndromes. Here we aimed to examine the placental transcriptome and to identify candidate biomarkers in early-onset preeclampsia and HELLP syndrome. Methods Placental specimens were obtained at C-sections from women with early-onset preeclampsia and HELLP syndrome, and from controls who delivered preterm or at term. After histopathological examination, fresh-frozen placental specimens were used for microarray profiling and validation by qRT-PCR. Differential expression was analysed using log-linear models while adjusting for gestational age. Gene ontology and pathway analyses were used to interpret gene expression changes. Tissue microarrays were constructed from paraffin-embedded placental specimens and immunostained. Results Placental gene expression was gestational age-dependent among preterm and term controls. Out of the 350 differentially expressed genes in preeclampsia and 554 genes in HELLP syndrome, 224 genes (including LEP, CGB, LHB, INHA, SIGLEC6, PAPPA2, TREM1, and FLT1) changed in the same direction (elevated or reduced) in both syndromes. Many of these encode proteins that have been implicated as biomarkers for preeclampsia. Enrichment analyses revealed similar biological processes, cellular compartments and biological pathways enriched in early-onset preeclampsia and HELLP syndrome; however, some processes and pathways (e.g., cytokine-cytokine receptor interaction) were over-represented only in HELLP syndrome. Conclusion High-throughput transcriptional and tissue microarray expression profiling revealed that placental transcriptomes of early-onset preeclampsia and HELLP syndrome largely overlap, underlying a potential common cause and pathophysiologic processes in these syndromes. However, gene expression changes may also suggest a more severe placental pathology and pronounced inflammatory response in HELLP syndrome than in preeclampsia. PMID:20541258

  18. Microarrays for identifying binding sites and probing structure of RNAs

    PubMed Central

    Kierzek, Ryszard; Turner, Douglas H.; Kierzek, Elzbieta

    2015-01-01

    Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure–function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs. PMID:25505162

  19. Novel microarrays for simultaneous serodiagnosis of multiple antiviral antibodies.

    PubMed

    Sivakumar, Ponnurengam Malliappan; Moritsugu, Nozomi; Obuse, Sei; Isoshima, Takashi; Tashiro, Hideo; Ito, Yoshihiro

    2013-01-01

    We developed an automated diagnostic system for the detection of virus-specific immunoglobulin Gs (IgGs) that was based on a microarray platform. We compared efficacies of our automated system with conventional enzyme immunoassays (EIAs). Viruses were immobilized to microarrays using a radical cross-linking reaction that was induced by photo-irradiation. A new photoreactive polymer containing perfluorophenyl azide (PFPA) and poly(ethylene glycol) methacrylate was prepared and coated on plates. Inactivated measles, rubella, mumps, Varicella-Zoster and recombinant Epstein-Barr viruse antigen were added to coated plates, and irradiated with ultraviolet light to facilitate immobilization. Virus-specific IgGs in healthy human sera were assayed using these prepared microarrays and the results obtained compared with those from conventional EIAs. We observed high correlation (0.79-0.96) in the results between the automated microarray technique and EIAs. The microarray-based assay was more rapid, involved less reagents and sample, and was easier to conduct compared with conventional EIA techniques. The automated microarray system was further improved by introducing reagent storage reservoirs inside the chamber, thereby conserving the use of expensive reagents and antibodies. We considered the microarray format to be suitable for rapid and multiple serological diagnoses of viral diseases that could be developed further for clinical applications. PMID:24367491

  20. Differential Expression of Genes within the Cochlea as Defined by a Custom Mouse Inner Ear Microarray

    PubMed Central

    Morris, Ken A.; Snir, Einat; Pompeia, Celine; Koroleva, Irina V.; Kachar, Bechara; Hayashizaki, Yoshihide; Carninci, Piero; Soares, M. Bento

    2005-01-01

    Microarray analyses have contributed greatly to the rapid understanding of functional genomics through the identification of gene networks as well as gene discovery. To facilitate functional genomics of the inner ear, we have developed a mouse inner-ear-pertinent custom microarray chip (CMA-IE1). Nonredundant cDNA clones were obtained from two cDNA library resources: the RIKEN subtracted inner ear set and the NIH organ of Corti library. At least 2000 cDNAs unique to the inner ear were present on the chip. Comparisons were performed to examine the relative expression levels of these unique cDNAs within the organ of Corti, lateral wall, and spiral ganglion. Total RNA samples were obtained from the three cochlear-dissected fractions from adult CF-1 mice. The total RNA was linearly amplified, and a dendrimer-based system was utilized to enhance the hybridization signal. Differentially expressed genes were verified by comparison to known gene expression patterns in the cochlea or by correlation with genes and gene families deduced to be present in the three tissue types. Approximately 22–25% of the genes on the array had significant levels of expression. A number of differentially expressed genes were detected in each tissue fraction. These included genes with known functional roles, hypothetical genes, and various unknown or uncharacterized genes. Four of the differentially expressed genes found in the organ of Corti are linked to deafness loci. None of these are hypothetical or unknown genes. PMID:15735932

  1. Insights from the clustering of microarray data associated with the heart disease

    PubMed Central

    Perumal, Venkatesan; Mahalingam, Vasantha

    2013-01-01

    Heart failure (HF) is the major of cause of mortality and morbidity in the developed world. Gene expression profiles of animal model of heart failure have been used in number of studies to understand human cardiac disease. In this study, statistical methods of analysing microarray data on cardiac tissues from dogs with pacing induced HF were used to identify differentially expressed genes between normal and two abnormal tissues. The unsupervised techniques principal component analysis (PCA) and cluster analysis were explored to distinguish between three different groups of 12 arrays and to separate the genes which are up regulated in different conditions among 23912 genes in heart failure canines' microarray data. It was found that out of 23912 genes, 1802 genes were differentially expressed in the three groups at 5% level of significance and 496 genes were differentially expressed at 1% level of significance using one way analysis of variance (ANOVA). The genes clustered using PCA and clustering analysis were explored in the paper to understand HF and a small number of differentially expressed genes related to HF were identified. PMID:24023417

  2. General assessment of copy number variation in normal and tumor tissues of the domestic dog (Canis lupus familiaris).

    PubMed

    Gurgul, Artur; ?ukowski, Kacper; ?laska, Brygida; Semik, Ewelina; Pawlina, Klaudia; Z?bek, Tomasz; Jasielczuk, Igor; Bugno-Poniewierska, Monika

    2014-08-01

    In recent years, characterization of a copy number variation (CNV) of the genomic DNA has provided evidence for the relationship of this type of genetic variation with the occurrence of a broad spectrum of diseases, including cancer lesions. Copy number variants (CNVs) also occur in the genomes of healthy individuals as a result of abnormal recombination processes in germ cells and have a hereditary character contributing to the natural genetic diversity. Recent image analysis methods and advanced computational techniques allow for identification of CNVs using SNPs genotyping microarrays based on the analysis of signal intensity observed for markers located in the specific genomic regions. In this study we used CanineHD BeadChip assay (Illumina) to identify both natural and cancer-induced CNVs in the genomes of different dog breeds and in different cancer types occurring in this species. The obtained results showed that structural aberrations are a common phenomenon arising during a tumor progression and are more complex and widespread in tumors of mesenchymal tissue origin than in epithelial tissue originating tumors. The tumor derived CNVs, in comparison to healthy samples, were characterized by larger sizes of regions, higher number of amplifications, and in some cases encompassed genes with potential effect on tumor progression. PMID:24573641

  3. Triple-target microarray experiments: a novel experimental strategy

    PubMed Central

    Forster, Thorsten; Costa, Yael; Roy, Douglas; Cooke, Howard J; Maratou, Klio

    2004-01-01

    Background High-throughput, parallel gene expression analysis by means of microarray technology has become a widely used technique in recent years. There are currently two main dye-labelling strategies for microarray studies based on custom-spotted cDNA or oligonucleotides arrays: (I) Dye-labelling of a single target sample with a particular dye, followed by subsequent hybridisation to a single microarray slide, (II) Dye-labelling of two different target samples with two different dyes, followed by subsequent co-hybridisation to a single microarray slide. The two dyes most frequently used for either method are Cy3 and Cy5. We propose and evaluate a novel experiment set-up utilising three differently labelled targets co-hybridised to one microarray slide. In addition to Cy3 and Cy5, this incorporates Alexa 594 as a third dye-label. We evaluate this approach in line with current data processing and analysis techniques for microarrays, and run separate analyses on Alexa 594 used in single-target, dual-target and the intended triple-target experiment set-ups (a total of 18 microarray slides). We follow this by pointing out practical applications and suitable analysis methods, and conclude that triple-target microarray experiments can add value to microarray research by reducing material costs for arrays and related processes, and by increasing the number of options for pragmatic experiment design. Results The addition of Alexa 594 as a dye-label for an additional – third – target sample works within the framework of more commonplace Cy5/Cy3 labelled target sample combinations. Standard normalisation methods are still applicable, and the resulting data can be expected to allow identification of expression differences in a biological experiment, given sufficient levels of biological replication (as is necessary for most microarray experiments). Conclusion The use of three dye-labelled target samples can be a valuable addition to the standard repertoire of microarray experiment designs. The method enables direct comparison between two experimental populations as well as measuring these two populations in relation to a third reference sample, allowing comparisons within the slide and across slides. These benefits are only offset by the added level of consideration required in the experimental design and data processing of a triple-target study design. Common methods for data processing and analysis are still applicable, but there is scope for the development of custom models for triple-target data. In summary, we do not consider the triple-target approach to be a new standard, but a valuable addition to the existing microarray study toolkit. PMID:15018645

  4. Fruity-Glows: Pictures of Health on a Microarray Canvas

    NSDL National Science Digital Library

    Arizona Science Center

    2012-01-01

    In this activity, learners apply the concepts of pixilation and pointillism to the world of biomedical science. They learn how DNA microarrays and supercomputers help in disease detection by organizing large amounts of data points from our human genome. Learners discover that categories of disease can be sorted based on color-coded expression level patterns on microarrays. In particular, learners evaluate what genes are turned on and off in a patient suffering from a particular disease. Learners use Cheerios stacks to create microarrays and simulate the gene matching (hybridization) process that happens in cells.

  5. Tissue Processing

    Cancer.gov

    Tissue samples, also called biospecimens, are tissue and fluid samples taken from the human body that can be used for research. Biospecimens from cancer patients are critical to cancer research because they contain an extraordinary amount of biological information, written in the language of cells. Genes and proteins in biospecimens can identify the biological characteristics of cancer cells.

  6. Progressive Insurance

    Microsoft Academic Search

    Paul Farris

    Since the late 1980s, Progressive Casualty Insurance Company has maintained a stronghold on the nonstandard auto-insurance market (auto insurance for high-risk drivers). Progressive’s goals in the 1990s are to expand its insurance coverage to include standard and preferred customers (drivers with clean driving records and no accidents). The company never advertised before 1994; as a result, consumer awareness has been

  7. Transcriptome architecture across tissues in the pig

    PubMed Central

    Ferraz, André LJ; Ojeda, Ana; López-Béjar, Manel; Fernandes, Lana T; Castelló, Anna; Folch, Josep M; Pérez-Enciso, Miguel

    2008-01-01

    Background Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor – joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome. PMID:18416811

  8. Fabrication and characterization of RNA aptamer microarrays for the study of proteinaptamer

    E-print Network

    Fabrication and characterization of RNA aptamer microarrays for the study of protein of reproducibly fabricating and maintaining stable and uniform RNA microarrays. Since RNA molecules are more developed for DNA microarrays cannot be directly trans- ferred to RNA microarray fabrication. Currently

  9. Statistical Analysis of DNA Microarray Data in Cancer Research Jianqing Fan1

    E-print Network

    Fan, Jianqing

    Statistical Analysis of DNA Microarray Data in Cancer Research Jianqing Fan1 andYi Ren2 Abstract. Preprocessing and Normalization for cDNA Microarrays The quality of microarray data is paramount important array platforms are available: commercial Affyme- trix GeneChip, oligonucleotide microarrays, cDNA

  10. Overexpression of E2F mRNAs Associated with Gastric Cancer Progression Identified by the Transcription Factor and miRNA Co-Regulatory Network Analysis

    PubMed Central

    Zhang, XiaoTian; Ni, ZhaoHui; Duan, ZiPeng; Xin, ZhuoYuan; Wang, HuaiDong; Tan, JiaYi; Wang, GuoQing; Li, Fan

    2015-01-01

    Gene expression is regulated at the transcription and translation levels; thus, both transcription factors (TFs) and microRNAs (miRNA) play roles in regulation of gene expression. This study profiled differentially expressed mRNAs and miRNAs in gastric cancer tissues to construct a TF and miRNA co-regulatory network in order to identify altered genes in gastric cancer progression. A total of 70 cases gastric cancer and paired adjacent normal tissues were subjected to cDNA and miRNA microarray analyses. We obtained 887 up-regulated and 93 down-regulated genes and 41 down-regulated and 4 up-regulated miRNAs in gastric cancer tissues. Using the Transcriptional Regulatory Element Database, we obtained 105 genes that are regulated by the E2F family of genes and using Targetscan, miRanda, miRDB and miRWalk tools, we predicted potential targeting genes of these 45 miRNAs. We then built up the E2F-related TF and miRNA co-regulatory gene network and identified 9 hub-genes. Furthermore, we found that levels of E2F1, 2, 3, 4, 5, and 7 mRNAs associated with gastric cancer cell invasion capacity, and has associated with tumor differentiation. These data showed Overexpression of E2F mRNAs associated with gastric cancer progression. PMID:25646628

  11. Imaging combined autoimmune and infectious disease microarrays

    NASA Astrophysics Data System (ADS)

    Ewart, Tom; Raha, Sandeep; Kus, Dorothy; Tarnopolsky, Mark

    2006-09-01

    Bacterial and viral pathogens are implicated in many severe autoimmune diseases, acting through such mechanisms as molecular mimicry, and superantigen activation of T-cells. For example, Helicobacter pylori, well known cause of stomach ulcers and cancers, is also identified in ischaemic heart disease (mimicry of heat shock protein 65), autoimmune pancreatitis, systemic sclerosis, autoimmune thyroiditis (HLA DRB1*0301 allele susceptibility), and Crohn's disease. Successful antibiotic eradication of H.pylori often accompanies their remission. Yet current diagnostic devices, and test-limiting cost containment, impede recognition of the linkage, delaying both diagnosis and therapeutic intervention until the chronic debilitating stage. We designed a 15 minute low cost 39 antigen microarray assay, combining autoimmune, viral and bacterial antigens1. This enables point-of-care serodiagnosis and cost-effective narrowly targeted concurrent antibiotic and monoclonal anti-T-cell and anti-cytokine immunotherapy. Arrays of 26 pathogen and 13 autoimmune antigens with IgG and IgM dilution series were printed in triplicate on epoxysilane covalent binding slides with Teflon well masks. Sera diluted 1:20 were incubated 10 minutes, washed off, anti-IgG-Cy3 (green) and anti-IgM-Dy647 (red) were incubated for 5 minutes, washed off and the slide was read in an ArrayWoRx(e) scanning CCD imager (Applied Precision, Issaquah, WA). As a preliminary model for the combined infectious disease-autoimmune diagnostic microarray we surveyed 98 unidentified, outdated sera that were discarded after Hepatitis B antibody testing. In these, significant IgG or IgM autoantibody levels were found: dsDNA 5, ssDNA 11, Ro 2, RNP 7, SSB 4, gliadin 2, thyroglobulin 13 cases. Since control sera showed no autoantibodies, the high frequency of anti-DNA and anti-thyroglobulin antibodies found in infected sera lend increased support for linkage of infection to subsequent autoimmune disease. Expansion of the antigen set with synthetic peptide sequences should reveal the shared bacterial/human epitopes involved.

  12. Semantic Subgroup Discovery: Using Ontologies in Microarray Data Analysis

    E-print Network

    Novak, Petra Kralj

    suggest the general practitioner how to select individuals for population screening, concerning high riskSemantic Subgroup Discovery: Using Ontologies in Microarray Data Analysis Nada Lavrac, Petra Kralj also current directions in creative knowledge discovery through bisociative data analysis, illustrated

  13. Classifying microarray cancer datasets using nearest subspace classification

    E-print Network

    sub- space, which is defined as the minimum reconstruction error across all subspaces. Furthermore, we Introduction DNA microarrays have provided researchers with a new tool for discovering the underlying causes

  14. IDENTIFYING AND MONITORING ENVIRONMENTAL TOXICITY USING CERIODAPHNIA MICROARRAYS - PHASE I

    EPA Science Inventory

    The current U.S. Environmental Protection Agency (EPA) SBIR solicitation states that “technology is needed to better identify and monitor sources of pollution and protect water quality.” Microarrays may be particularly well suited to identifying environmental toxic...

  15. Biocompatible polymer microarrays for cellular high-content screening 

    E-print Network

    Pernagallo, Salvatore

    2010-11-25

    The global aim of this thesis was to study the use of microarray technology for the screening and identification of biocompatible polymers, to understand physiological phenomena, and the design of biomaterials, implant ...

  16. Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray

    PubMed Central

    Zhu, Heng; Hu, Shaohui; Jona, Ghil; Zhu, Xiaowei; Kreiswirth, Nate; Willey, Barbara M.; Mazzulli, Tony; Liu, Guozhen; Song, Qifeng; Chen, Peng; Cameron, Mark; Tyler, Andrea; Wang, Jian; Wen, Jie; Chen, Weijun; Compton, Susan; Snyder, Michael

    2006-01-01

    To monitor severe acute respiratory syndrome (SARS) infection, a coronavirus protein microarray that harbors proteins from SARS coronavirus (SARS-CoV) and five additional coronaviruses was constructed. These microarrays were used to screen ?400 Canadian sera from the SARS outbreak, including samples from confirmed SARS-CoV cases, respiratory illness patients, and healthcare professionals. A computer algorithm that uses multiple classifiers to predict samples from SARS patients was developed and used to predict 206 sera from Chinese fever patients. The test assigned patients into two distinct groups: those with antibodies to SARS-CoV and those without. The microarray also identified patients with sera reactive against other coronavirus proteins. Our results correlated well with an indirect immunofluorescence test and demonstrated that viral infection can be monitored for many months after infection. We show that protein microarrays can serve as a rapid, sensitive, and simple tool for large-scale identification of viral-specific antibodies in sera. PMID:16537477

  17. Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostate Cancer

    E-print Network

    Gerstein, Mark

    Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostate Cancer Sunita R array data from localized and metastatic prostate cancer. Comparison of metastatic cancer and localized pathways that were significantly dysregulated (P prostate cancer metastasis. The pathway

  18. Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Gba1 Mutant Mouse Model Treated with Velaglucerase alfa or Imiglucerase

    PubMed Central

    Oh, Sunghee; Sun, Ying; Jia, Li; Keddache, Mehdi; Grabowski, Gregory A

    2013-01-01

    Gaucher disease type 1, an inherited lysosomal storage disorder, is caused by mutations in GBA1 leading to defective glucocerebrosidase (GCase) function and consequent excess accumulation of glucosylceramide/glucosylsphingosine in visceral organs. Enzyme replacement therapy (ERT) with the biosimilars, imiglucerase (imig) or velaglucerase alfa (vela) improves/reverses the visceral disease. Comparative transcriptomic effects (microarray and mRNA-Seq) of no ERT and ERT (imig or vela) were done with liver, lung, and spleen from mice having Gba1 mutant alleles, termed D409V/null. Disease-related molecular effects, dynamic ranges, and sensitivities were compared between mRNA-Seq and microarrays and their respective analytic tools, i.e. Mixed Model ANOVA (microarray), and DESeq and edgeR (mRNA-Seq). While similar gene expression patterns were observed with both platforms, mRNA-Seq identified more differentially expressed genes (DEGs) (?3-fold) than the microarrays. Among the three analytic tools, DESeq identified the maximum number of DEGs for all tissues and treatments. DESeq and edgeR comparisons revealed differences in DEGs identified. In 9V/null liver, spleen and lung, post-therapy transcriptomes approximated WT, were partially reverted, and had little change, respectively, and were concordant with the corresponding histological and biochemical findings. DEG overlaps were only 8–20% between mRNA-Seq and microarray, but the biological pathways were similar. Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were most altered with the Gaucher disease process. Imig and vela differentially affected specific disease pathways. Differential molecular responses were observed in direct transcriptome comparisons from imig- and vela-treated tissues. These results provide cross-validation for the mRNA-Seq and microarray platforms, and show differences between the molecular effects of two highly structurally similar ERT biopharmaceuticals. PMID:24124461

  19. Proteomics. Tissue-based map of the human proteome.

    PubMed

    Uhlén, Mathias; Fagerberg, Linn; Hallström, Björn M; Lindskog, Cecilia; Oksvold, Per; Mardinoglu, Adil; Sivertsson, Åsa; Kampf, Caroline; Sjöstedt, Evelina; Asplund, Anna; Olsson, IngMarie; Edlund, Karolina; Lundberg, Emma; Navani, Sanjay; Szigyarto, Cristina Al-Khalili; Odeberg, Jacob; Djureinovic, Dijana; Takanen, Jenny Ottosson; Hober, Sophia; Alm, Tove; Edqvist, Per-Henrik; Berling, Holger; Tegel, Hanna; Mulder, Jan; Rockberg, Johan; Nilsson, Peter; Schwenk, Jochen M; Hamsten, Marica; von Feilitzen, Kalle; Forsberg, Mattias; Persson, Lukas; Johansson, Fredric; Zwahlen, Martin; von Heijne, Gunnar; Nielsen, Jens; Pontén, Fredrik

    2015-01-23

    Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body. PMID:25613900

  20. Analysis of Temporal-spatial Co-variation within Gene Expression Microarray Data in an Organogenesis Model

    NASA Astrophysics Data System (ADS)

    Ehler, Martin; Rajapakse, Vinodh; Zeeberg, Barry; Brooks, Brian; Brown, Jacob; Czaja, Wojciech; Bonner, Robert F.

    The gene networks underlying closure of the optic fissure during vertebrate eye development are poorly understood. We used a novel clustering method based on Laplacian Eigenmaps, a nonlinear dimension reduction method, to analyze microarray data from laser capture microdissected (LCM) cells at the site and developmental stages (days 10.5 to 12.5) of optic fissure closure. Our new method provided greater biological specificity than classical clustering algorithms in terms of identifying more biological processes and functions related to eye development as defined by Gene Ontology at lower false discovery rates. This new methodology builds on the advantages of LCM to isolate pure phenotypic populations within complex tissues and allows improved ability to identify critical gene products expressed at lower copy number. The combination of LCM of embryonic organs, gene expression microarrays, and extracting spatial and temporal co-variations appear to be a powerful approach to understanding the gene regulatory networks that specify mammalian organogenesis.

  1. Emerging Use of Gene Expression Microarrays in Plant Physiology

    PubMed Central

    Difazio, Stephen P.

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry. PMID:18629133

  2. Growing applications and advancements in microarray technology and analysis tools

    Microsoft Academic Search

    Justine K. Peeters; Peter J. Van der Spek

    2005-01-01

    In today's field of genomics, traditional gene-by-gene approach is not adequate to meet the demand of processing information\\u000a generated from mapping the complex biology of the human genome. More global views of analyzing the magnitude of information\\u000a are necessary, such as with microarrays. Microarray technology today is rapidly uncovering broad patterns of genetic activity\\u000a and showing insight into gene functions,

  3. Computational Intelligence Techniques for Classification in Microarray Analysis

    Microsoft Academic Search

    Juan F. De Paz; Javier Bajo; Sara Rodríguez; Juan M. Corchado

    \\u000a During the last few years there has been a growing need for using computational intelligence techniques to analyze microarray\\u000a data. The aim of the system presented in this study is to provide innovative decision support techniques for classifying data\\u000a from microarrays and for extracting knowledge about the classification process. The computational intelligence techniques\\u000a used in this chapter follow the case-based

  4. Data Complexity in Clustering Analysis of Gene Microarray Expression Profiles

    Microsoft Academic Search

    Feng Luo; Latifur Khan

    The increasing application of microarray technology is generating large amounts of high dimensional gene expression data.\\u000a Genes participating in the same biological process tend to have similar expression patterns, and clustering is one of the\\u000a most useful and efficient methods for identifying these patterns. Due to the complexity of microarray profiles, there are\\u000a some limitations in directly applying traditional clustering

  5. Detection and Characterization of Uncultivated Microorganisms Using Microarrays

    Microsoft Academic Search

    Terry J. Gentry; Zhili He; Jizhong Zhou

    Microarrays have unprecedented potential for the high-throughput detection and characterization of uncultivated microorganisms.\\u000a Several different types of arrays have been developed or adapted for the interrogation of microbial genomes and monitoring\\u000a microbial population dynamics and\\/or activity in relation to various microbial processes such as bioremediation and biogeochemical\\u000a cycling. Even though the number of such microarray studies has increased dramatically over

  6. cDNA microarray screening in food safety

    Microsoft Academic Search

    Sashwati Roy; Chandan K. Sen

    2006-01-01

    The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and

  7. Profiling In Situ Microbial Community Structure with an Amplification Microarray

    PubMed Central

    Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

    2013-01-01

    The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3?) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

  8. Evaluation of DNA microarray results with quantitative gene expression platforms

    Microsoft Academic Search

    Roger D Canales; Yuling Luo; James C Willey; Bradley Austermiller; Catalin C Barbacioru; Cecilie Boysen; Kathryn Hunkapiller; Roderick V Jensen; Charles R Knight; Kathleen Y Lee; Yunqing Ma; Botoul Maqsodi; Adam Papallo; Elizabeth Herness Peters; Karen Poulter; Patricia L Ruppel; Raymond R Samaha; Leming Shi; Wen Yang; Lu Zhang; Federico M Goodsaid

    2006-01-01

    We have evaluated the performance characteristics of three quantitative gene expression technologies and correlated their expression measurements to those of five commercial microarray platforms, based on the MicroArray Quality Control (MAQC) data set. The limit of detection, assay range, precision, accuracy and fold-change correlations were assessed for 997 TaqMan Gene Expression Assays, 205 Standardized RT (Sta)RT-PCR assays and 244 QuantiGene

  9. Genomic and microarray approaches to coral reef conservation biology

    Microsoft Academic Search

    S. Forêt; K. S. Kassahn; L. C. Grasso; D. C. Hayward; A. Iguchi; E. E. Ball; D. J. Miller

    2007-01-01

    New technologies based on DNA microarrays and comparative genomics hold great promise for providing the background biological\\u000a information necessary for effective coral reef conservation and management. Microarray analysis has been used in a wide range\\u000a of applications across the biological sciences, most frequently to examine simultaneous changes in the expression of large\\u000a numbers of genes in response to experimental manipulation

  10. Emerging use of gene expression microarrays in plant physiology.

    PubMed

    Wullschleger, Stan D; Difazio, Stephen P

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry. PMID:18629133

  11. Astronomical algorithms for automated analysis of tissue protein expression in breast cancer

    PubMed Central

    Ali, H R; Irwin, M; Morris, L; Dawson, S-J; Blows, F M; Provenzano, E; Mahler-Araujo, B; Pharoah, P D; Walton, N A; Brenton, J D; Caldas, C

    2013-01-01

    Background: High-throughput evaluation of tissue biomarkers in oncology has been greatly accelerated by the widespread use of tissue microarrays (TMAs) and immunohistochemistry. Although TMAs have the potential to facilitate protein expression profiling on a scale to rival experiments of tumour transcriptomes, the bottleneck and imprecision of manually scoring TMAs has impeded progress. Methods: We report image analysis algorithms adapted from astronomy for the precise automated analysis of IHC in all subcellular compartments. The power of this technique is demonstrated using over 2000 breast tumours and comparing quantitative automated scores against manual assessment by pathologists. Results: All continuous automated scores showed good correlation with their corresponding ordinal manual scores. For oestrogen receptor (ER), the correlation was 0.82, P<0.0001, for BCL2 0.72, P<0.0001 and for HER2 0.62, P<0.0001. Automated scores showed excellent concordance with manual scores for the unsupervised assignment of cases to ‘positive' or ‘negative' categories with agreement rates of up to 96%. Conclusion: The adaptation of astronomical algorithms coupled with their application to large annotated study cohorts, constitutes a powerful tool for the realisation of the enormous potential of digital pathology. PMID:23329232

  12. A Novel Androgen Receptor Splice Variant Is Upregulated during Prostate Cancer Progression and Promotes Androgen-depletion-resistant Growth

    PubMed Central

    Guo, Zhiyong; Yang, Xi; Sun, Feng; Jiang, Richeng; Linn, Douglas E.; Chen, Hege; Chen, Hegang; Kong, Xiangtian; Melamed, Jonathan; Tepper, Clifford G.; Kung, Hsing-Jien; Brodie, Angela M. H.; Edwards, Joanne; Qiu, Yun

    2009-01-01

    The androgen receptor (AR) plays a key role in progression to incurable androgen-ablation resistant prostate cancer (PCA). We have identified three novel AR splice variants lacking the ligand binding domain (designated as AR3, AR4 and AR5) in hormone insensitive PCA cells. AR3, one of the major splice variants expressed in human prostate tissues, is constitutively active and its transcriptional activity is not regulated by androgens or antiandrogens. Immunohistochemistry analysis on tissue microarrays containing 429 human prostate tissue samples shows that AR3 is significantly upregulated during PCA progression and AR3 expression level is correlated with the risk of tumor recurrence after radical prostatectomy. Overexpression of AR3 confers ablation-independent growth of PCA cells while specific knock-down of AR3 expression (without altering AR level) in hormone resistant PCA cells attenuates their growth under androgen-depleted conditions in both cell culture and xenograft models, suggesting an indispensable role of AR3 in ablation-independent growth of PCA cells. Furthermore, AR3 may play a distinct yet essential role in ablation-independent growth through regulating a unique set of genes including AKT1, which are not regulated by the prototype AR. Our data suggest that aberrant expression of AR splice variants may be a novel mechanism underlying ablation-independence during PCA progression and AR3 may serve as a prognostic marker to predict patient outcome in response to hormonal therapy. Given that these novel AR splice variants are not inhibited by currently available anti-androgen drugs, development of new drugs targeting these AR isoforms may potentially be effective for treatment of ablation-resistant PCA. PMID:19244107

  13. The Perils of SNP Microarray Testing: Uncovering Unexpected Consanguinity

    PubMed Central

    Tarini, Beth A.; Konczal, Laura; Goldenberg, Aaron J.; Goldman, Edward B.; McCandless, Shawn E.

    2013-01-01

    Background While single nucleotide polymorphism (SNP) chromosomal microarrays identify areas of small genetic deletions/duplications, they can also reveal regions of homozygosity indicative of consanguinity. As more non-geneticists order SNP microarrays, they must prepare for the potential ethical, legal and social issues that result from revelation of unanticipated consanguinity. Patient An infant with multiple congenital anomalies underwent SNP microarray testing. Results The results of the SNP microarray revealed several large regions of homozygosity that indicated identity by descent most consistent with a second or third degree relative mating (e.g., uncle/ niece, half brother/sister, first cousins). Mother was not aware of the test's potential to reveal consanguinity. When informed of the test results, she reluctantly admitted to being raped by her half-brother around the time of conception. Conclusions During the pre-testing consent process, providers should inform parents that SNP microarray testing could reveal consanguinity. Providers must also understand the psychological implications, as well as the legal and moral obligations, that accompany SNP microarray results that indicate consanguinity. PMID:23827427

  14. Evaluating concentration estimation errors in ELISA microarray experiments

    SciTech Connect

    Daly, Don S.; White, Amanda M.; Varnum, Susan M.; Anderson, Kevin K.; Zangar, Richard C.

    2005-01-26

    Enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to predict a protein concentration in a sample. Deploying ELISA in a microarray format permits simultaneous prediction of the concentrations of numerous proteins in a small sample. These predictions, however, are uncertain due to processing error and biological variability. Evaluating prediction error is critical to interpreting biological significance and improving the ELISA microarray process. Evaluating prediction error must be automated to realize a reliable high-throughput ELISA microarray system. Methods: In this paper, we present a statistical method based on propagation of error to evaluate prediction errors in the ELISA microarray process. Although propagation of error is central to this method, it is effective only when comparable data are available. Therefore, we briefly discuss the roles of experimental design, data screening, normalization and statistical diagnostics when evaluating ELISA microarray prediction errors. We use an ELISA microarray investigation of breast cancer biomarkers to illustrate the evaluation of prediction errors. The illustration begins with a description of the design and resulting data, followed by a brief discussion of data screening and normalization. In our illustration, we fit a standard curve to the screened and normalized data, review the modeling diagnostics, and apply propagation of error.

  15. Unsupervised SVM-based gridding for DNA microarray images.

    PubMed

    Bariamis, Dimitris; Maroulis, Dimitris; Iakovidis, Dimitris K

    2010-09-01

    This paper presents a novel method for unsupervised DNA microarray gridding based on support vector machines (SVMs). Each spot is a small region on the microarray surface where chains of known DNA sequences are attached. The goal of microarray gridding is the separation of the spots into distinct cells. The positions of the spots on a DNA microarray image are first detected using image analysis operations and then a set of soft-margin linear SVM classifiers is used to estimate the optimal layout of the grid lines in the image. Each grid line is the separating line produced by one of the SVM classifiers, which maximizes the margin between two consecutive rows or columns of spots. The classifiers are trained using the spot locations as training vectors. The proposed method was evaluated on reference microarray images containing more than two million spots in total. The results illustrate its robustness in the presence of artifacts, noise and weakly expressed spots, as well as image rotation. The comparison to state of the art methods for microarray gridding reveals the superior performance of the proposed method. In 96.4% of the cases, the spots reside completely inside their respective grid cells. PMID:19879109

  16. Design and analysis of mismatch probes for long oligonucleotide microarrays

    SciTech Connect

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  17. Novel 3-Dimensional Dendrimer Platform for Glycolipid Microarray

    PubMed Central

    Zhang, Jian; Zhou, Xichun

    2011-01-01

    Glycolipids are important biological molecules that modulate cellular recognitions and pathogen adhesions. In this paper, we report a sensitive glycolipid microarray for non-covalently immobilizing glycolipids on a microarray substrate and we perform a set of immunoassays to explore glycolipid-protein interactions. This substrate utilizes a three-dimensional hydrazide-functionalized dendrimer monolayer attached onto a microscopic glass surface, which possesses the characteristics to adsorb glycoliplids non-covalently and facilitates multivalent attributes on the substrate surface. In the proof-of-concept experiments, gangliosides such as GM1, FucGM1, GM3, GD1b, GT1b, and GQ1b, and a lipoarabinomannan were tested on the substrate and interrogated with toxins and antibodies. The resulting glycolipid microarrays exhibited hypersensitivity and specificity for detection of glycolipid-protein interactions. In particular, a robust and specific binding of a pentameric cholera toxin B subunit to the GM1 glycolipid spotted on the array has demonstrated its superiority in sensitivity and specificity. In addition, this glycolipid microarray substrate was used to detect lipoarabinomannan in buffer within a limit-of-detection of 125 ng/mL. Furthermore, Mycobacterium tuberculosis (Mtb) Lipoarabinomannan was tested in human urine specimens on this platform, which can effectively identify urine samples either infected or not infected with Mtb. The results of this work suggest the possibility of using this glycolipid microarray platform to fabricate glycoconjugate microarrays, which includes free glycans and glycolipids and potential application in detection of pathogen and toxin. PMID:21820887

  18. Bayesian pathway analysis of cancer microarray data.

    PubMed

    Korucuoglu, Melike; Isci, Senol; Ozgur, Arzucan; Otu, Hasan H

    2014-01-01

    High Throughput Biological Data (HTBD) requires detailed analysis methods and from a life science perspective, these analysis results make most sense when interpreted within the context of biological pathways. Bayesian Networks (BNs) capture both linear and nonlinear interactions and handle stochastic events in a probabilistic framework accounting for noise making them viable candidates for HTBD analysis. We have recently proposed an approach, called Bayesian Pathway Analysis (BPA), for analyzing HTBD using BNs in which known biological pathways are modeled as BNs and pathways that best explain the given HTBD are found. BPA uses the fold change information to obtain an input matrix to score each pathway modeled as a BN. Scoring is achieved using the Bayesian-Dirichlet Equivalent method and significance is assessed by randomization via bootstrapping of the columns of the input matrix. In this study, we improve on the BPA system by optimizing the steps involved in "Data Preprocessing and Discretization", "Scoring", "Significance Assessment", and "Software and Web Application". We tested the improved system on synthetic data sets and achieved over 98% accuracy in identifying the active pathways. The overall approach was applied on real cancer microarray data sets in order to investigate the pathways that are commonly active in different cancer types. We compared our findings on the real data sets with a relevant approach called the Signaling Pathway Impact Analysis (SPIA). PMID:25036210

  19. Bayesian Pathway Analysis of Cancer Microarray Data

    PubMed Central

    Korucuoglu, Melike; Isci, Senol; Ozgur, Arzucan; Otu, Hasan H.

    2014-01-01

    High Throughput Biological Data (HTBD) requires detailed analysis methods and from a life science perspective, these analysis results make most sense when interpreted within the context of biological pathways. Bayesian Networks (BNs) capture both linear and nonlinear interactions and handle stochastic events in a probabilistic framework accounting for noise making them viable candidates for HTBD analysis. We have recently proposed an approach, called Bayesian Pathway Analysis (BPA), for analyzing HTBD using BNs in which known biological pathways are modeled as BNs and pathways that best explain the given HTBD are found. BPA uses the fold change information to obtain an input matrix to score each pathway modeled as a BN. Scoring is achieved using the Bayesian-Dirichlet Equivalent method and significance is assessed by randomization via bootstrapping of the columns of the input matrix. In this study, we improve on the BPA system by optimizing the steps involved in “Data Preprocessing and Discretization”, “Scoring”, “Significance Assessment”, and “Software and Web Application”. We tested the improved system on synthetic data sets and achieved over 98% accuracy in identifying the active pathways. The overall approach was applied on real cancer microarray data sets in order to investigate the pathways that are commonly active in different cancer types. We compared our findings on the real data sets with a relevant approach called the Signaling Pathway Impact Analysis (SPIA). PMID:25036210

  20. Tissue Debridement

    Microsoft Academic Search

    Michael Soudry; Alexander Lerner

    \\u000a The major factor determining the outcome in high-energy combat injuries to the limbs is the severity and extension of the\\u000a soft tissue damage. Primary radical debridement is a crucial phase in the management of patients after open high-energy injuries.\\u000a Inadequate tissue debridement remains the major cause of acute and chronic infection after severe trauma. Often, this important\\u000a first surgical procedure