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Avatar DNA Nanohybrid System in Chip-on-a-Phone

SCIENTIFIC REPORTS 2014年第1期4卷 4879-4879页

作者： Park, Dae-Hwan Han, Chang Jo Shul, Yong-Gun Choy, Jin-Ho Ewha Womans Univ Dept Chem & Nano Sci Ctr Intelligent NanoBio Mat CINBM Ewha Global Top 5 Program 2011 Seoul 120750 South Korea Ewha Womans Univ Dept Bioinspired Sci Seoul 120750 South Korea Yonsei Univ Dept Chem & Biomol Engn Seoul 120749 South Korea

Long admired for informational role and recognition function in multidisciplinary science, DNA nanohybrids have been emerging as ideal materials for molecular nanotechnology and genetic information code. Here, we designed an optical machine-readable DNA icon on microarray, Avatar DNA, for automatic identification and data capture such as Quick Response and ColorZip codes. Avatar icon is made of telepathic DNA-DNA hybrids inscribed on chips, which can be identified by camera of smartphone with application software. Information encoded in base-sequences can be accessed by connecting an off-line icon to an on-line web-server network to provide message, index, or URL from database library. Avatar DNA is then converged with nano-bio-info-cogno science: each building block stands for inorganic nanosheets, nucleotides, digits, and pixels. This convergence could address item-level identification that strengthens supply-chain security for drug counterfeits. It can, therefore, provide molecular-level vision through mobile network to coordinate and integrate data management channels for visual detection and recording.

关键词： DNA folding NANOtechnology research microarray technology AUTOMATIC identification SMARTPHONES AVATARS (Virtual reality) MOBILE apps SOFTWARE

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Gαs Protein Expression Is an Independent Predictor of Recurrence in Prostate Cancer

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JOURNAL OF IMMUNOLOGY RESEARCH 2014年第1期2014卷 301376-301376页

作者： Wang, Lijuan Jin, Guihua He, Chenchen Guo, Xijing Zhou, Xia Li, Meng Ying, Xia Wang, Le Wu, Huili Zhu, Qing Xi An Jiao Tong Univ Affiliated Hosp 1 Coll Med Dept Med Oncol Xian 710061 Peoples R China

Background. T393C polymorphism in the gene GNAS1, which encodes the G-protein alpha s subunit (G.. s) of heterotrimeric G protein, is significantly associated with the clinical outcome of patients suffering from several cancers. However, studies on the role and protein expression of G.. s subunit in prostate cancer were still unavailable. Methods. The immunohistochemical staining was used to assess G.. s expression through tissue microarray procedure of 56 metastatic PCas, 291 localized PCas, and 67 benign hyperplasia (BPH). G.. s expression was semiquantitatively scored and evaluated the correlation with pathologic parameters and biochemical recurrence of prostate-specific antigen (PSA). Results. G.. s expression was localized in nuclear and cytoplasm in prostate cancer cells and downregulated in metastatic PCa compared to localized PCa and BPH (P < 0.001). G alpha s was inversely associated with PSA level and Gleason scores;patients with low expression of G.. s had adverse clincopathological features. In multivariable Cox regression analysis, high G alpha s expression and Gleason scores were independent predictors of both PSA progression-free and overall survival. Conclusions. G.. s down-expression is associated with adverse pathologic features and clinical PSA biochemical recurrence of prostate cancer. G.. s is an independent predictor to help determine the risk of PSA progression and death.

关键词： PROTEIN expression GENETICS ALTERNATIVE treatment for cancer HYPERPLASIA microarray technology GENETIC aspects

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Effects and Mechanism of Bufei Yishen Formula in a Rat Chronic Obstructive Pulmonary Disease Model

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014年第6期2014卷 381976-381976页

作者： Li, Jiansheng Yang, Liping Yao, Qin Li, Ya Tian, Yange Li, Suyun Jiang, Suli Wang, Ying Li, Xinmin Guo, Zheng Henan Univ Tradit Chinese Med Zhengzhou 450008 Peoples R China Harbin Med Univ Coll Bioinformat Sci & Technol Harbin 150086 Peoples R China Henan Univ TCM Affiliated Hosp 1 Resp Dis Inst Zhengzhou 450000 Peoples R China Univ Elect Sci & Technol China Sch Life Sci Bioinformat Ctr Chengdu 610054 Peoples R China

Bufei Yishen Formula (BYF) has been used for centuries in Asia to effectively treat patients with chronic obstructive pulmonary disease (COPD). This study established a COPD animal model in rats, wherein three groups (control, COPD, and BYF) were used to evaluate the mechanism(s) and curative effect of BYF. Pulmonary function and histomorphology demonstrated that BYF had an evident effect on COPD. Gene microarray was then exploited to analyze the effects of BYF on COPD. ClueGO analysis of differentially expressed genes indicated that BYF improved COPD by regulating expression of interleukins, myosin filament assembly components, and mitochondrial electron transport-related molecules. Moreover, ELISA revealed that expression of several interleukins (IL1 beta, IL6, IL8, andIL10) was reduced in peripheral blood and bronchoalveolar lavage fluid by BYF treatment. It was concluded that BYF has therapeutic effects on COPD in rats through its effects on interleukin expression and/or secretion. Furthermore, pharmacological or targeted expression of two differentially expressed genes, F2R and Sprik1, might be useful in novel COPD therapies. This study provides the basis for mechanisms of BYF on COPD and new therapeutic drug targets.

关键词： OBSTRUCTIVE lung diseases -- Treatment CHINESE medicine ANIMAL experimentation BIOLOGICAL models ENZYME-linked immunosorbent assay EXPERIMENTAL design GENE expression GENES HERBAL medicine INTERLEUKINS RATS RESPIRATORY measurements RNA T-test (Statistics) DATA analysis -- Software microarray technology DESCRIPTIVE statistics ADMINISTRATION of drugs DOSAGE of drugs THERAPEUTIC use

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Effect of Huanglian Jiedu Decoction on Thoracic Aorta Gene Expression in Spontaneous Hypertensive Rats

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014年第1期2014卷 565784-565784页

作者： Yue, Gui-Hua Zhuo, Shao-Yuan Xia, Meng Zhang, Zhuo Gao, Yi-Wen Luo, Yuan Guangxi Univ Chinese Med Nanning 530001 Peoples R China Guangxi Univ Chinese Med Affiliated Ruikang Hosp Nanning 530001 Peoples R China

Objective. Hypertension is one of the most common cardiovascular disorders with high mortality. Here we explored the antihypertension effects of Huanglian Jiedu Decoction (HJD) on thoracic aorta gene expression in spontaneous hypertensive rats. Methods. A rat model of spontaneous hypertension was used. The gene change profile of thoracic aorta after JHD treatment was assessed by GeneChip(GC) analysis using the Agilent Whole Rat Genome Oligo microarray. Results. Hypertension induced 441 genes upregulated and 417 genes downregulated compared with the normal control group. Treatment of HJD resulted in 76 genes downregulated and 20 genes upregulated. GC data analysis showed that the majority of change genes were involved in immune system process, developmental process, and cell death. Conclusion. Hypertension altered expression of many genes that regulate various biological functions. HJD significantly reduced hypertension and altered the gene expression profiles of SHR rats. These changing genes were involved in many cellular functions such as regulating smooth muscle contraction, Ca(2+) homeostasis, and NO pathway. This study provides the potential novel insights into hypertension and antihypertension effects of HJD.

关键词： HYPERTENSION -- Prevention ANIMAL experimentation BIOLOGICAL models BLOOD pressure measurement GENE expression GENES HERBAL medicine CHINESE medicine RATS RESEARCH -- Finance T-test (Statistics) DATA analysis -- Software microarray technology DESCRIPTIVE statistics THORACIC aorta ADMINISTRATION of drugs DOSAGE of drugs

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Tissue microarray in a subset of South African patients with DLBCL

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TRANSFUSION AND APHERESIS SCIENCE 2013年第2期49卷 120-132页

作者： Sissolak, Gerhard Wood, Lucille Smith, Lynette Chan, John (Wing C) Armitage, James Jacobs, Peter Univ Stellenbosch Tygerberg Acad Hosp Fac Hlth Sci Div Clin Haematol ZA-7600 Stellenbosch South Africa Univ Nebraska Med Ctr Omaha NE USA Univ Stellenbosch Tygerberg Acad Hosp Fac Hlth Sci Div Haematol Pathol ZA-7600 Stellenbosch South Africa

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

关键词： microarray technology LYMPHOMAS CHEMOTHERAPY (Cancer) B cells -- Tumors RITUXIMAB IMMUNOGLOBULINS THERAPEUTIC use

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Regular gridding and segmentation for microarray images

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COMPUTERS & ELECTRICAL ENGINEERING 2013年第7期39卷 2173-2182页

作者： Helmy, A. K. El-taweel, Gh. S. Natl Author Remote Sensing & Space Sci Cairo Egypt Suez Canal Univ Fac Comp & Informat Ismailia Egypt

In this paper, we propose a new regular gridding and segmentation approach for microarray image. Initially, the microarray images are preprocessed using Stationary Wavelet Transform (SWT), followed by a hard thresholding filtering technique to get a de-noised microarray image. Then, we use autocorrelation to enhance the self-similarity of the image profile to get a regular gridding. Fuzzy Gaussian Mixture Model (FGMM) is used for spot segmentation. This approach has the capabilities of fitting data as generalized GMM but it can reduce about half of their computational time. Comparing probability based GMM with distance based FGMM, the latter outperforms the former in terms of computational efficiency, Due to the nature of the fast computation and nonlinear fitting of the FGMM approach. The proposed approach was evaluated using images from the Stanford microarray Database (SMD), proved more accurate in intensity computation and more reliable means for estimating gene expression than conventional methods. (C) 2013 Elsevier Ltd. All rights reserved.

关键词： SEGMENTATION (Image processing) microarray technology COMPUTATIONAL grids (Computer systems) WAVELET transforms CORRELATION (Statistics) CLUSTER analysis (Statistics)

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microRNA-144: the 'what' and 'how' of remote ischemic conditioning?

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BASIC RESEARCH IN CARDIOLOGY 2014年第5期109卷 429-429页

作者： Przyklenk, Karin Wayne State Univ Sch Med Cardiovasc Res Inst Detroit MI 48201 USA Wayne State Univ Sch Med Dept Physiol Detroit MI 48201 USA Wayne State Univ Sch Med Dept Emergency Med Detroit MI 48201 USA

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The ordered acquisition of Class II and Class I mutations directs formation of human t(8;21) acute myelogenous leukemia stem cell

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EXPERIMENTAL HEMATOLOGY 2014年第11期42卷 955-965页

作者： Shima, Takahiro Miyamoto, Toshihiro Kikushige, Yoshikane Yuda, Junichiro Tochigi, Taro Yoshimoto, Goichi Kato, Koji Takenaka, Katsuto Iwasaki, Hiromi Mizuno, Shinichi Goto, Noriko Akashi, Koichi Kyushu Univ Grad Sch Med Dept Med & Biosyst Sci Grad Sch Med Sci Fukuoka 8120054 Japan Kyushu Univ Grad Sch Med Ctr Cellular & Mol Med Grad Sch Med Sci Fukuoka 8120054 Japan Kanazawa Univ Canc Res Inst Kanazawa Ishikawa 9201192 Japan

The cellular properties of leukemia stem cells (LSCs) are achieved at least through Class I and Class II mutations that generate signals for enhanced proliferation and impaired differentiation, respectively. Here we show that in t(8;21) acute myelogenous leukemia (AML), hematopoietic stem cells (HSCs) transform into LSCs via definitively-ordered acquisition of Class II (AML1/ETO) and then Class I (c-KIT mutant) abnormalities. Six t(8;21) AML patients with c-KIT mutants maintaining > 3 years of complete remission were analyzed. At diagnosis, all single LSCs had both AML1/ETO and c-KIT mutations. However, in remission, 16 out of 1,728 CD34(+)CD38(-) HSCs and 89 out of 7,187 single HSC-derived myeloerythroid colonies from these patients had AML1/ETO, whose breakpoints were identical to those found in LSCs. These cells had wild-type c-KIT, which expressed AML1/ETO at a low level, and could differentiate into mature blood cells, suggesting that they may be the persistent preleukemic stem cells. microarray analysis suggested that mutated c-KIT signaling provides LSCs with enhanced survival and proliferation. Thus, in t(8;21) AML, the acquisition of AML1/ETO is not sufficient, and the subsequent upregulation of AML1/ETO and the additional c-KIT mutant signaling are critical steps for transformation into LSCs. (C) 2014 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc.

关键词： Acute myeloid leukemia Mutation (Biology) Cancer stem cells Cancer cells -- Proliferation Cancer remission microarray technology Oncology

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Brief Report: Interferon- Induction and Detection of Anti-Ro, Anti-La, Anti-Sm, and Anti-RNP Autoantibodies by Autoantigen microarray Analysis in Juvenile Dermatomyositis

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ARTHRITIS AND RHEUMATISM 2013年第9期65卷 2424-2429页

作者： Balboni, Imelda Niewold, Timothy B. Morgan, Gabrielle Limb, Cindy Eloranta, Maija-Leena Ronnblom, Lars Utz, Paul J. Pachman, Lauren M. Stanford Univ Stanford CA 94305 USA Mayo Clin Rochester MN USA Ann & Robert H Lurie Childrens Res Ctr Chicago IL USA Uppsala Univ Uppsala Sweden Univ Uppsala Hosp Uppsala Sweden Childrens Res Ctr Chicago IL USA Northwestern Univ Feinberg Sch Med Chicago IL 60611 USA

Objective To evaluate serum interferon- (IFN) activity in the context of autoantibody profiles in patients with juvenile dermatomyositis (JDM). Methods Sera from 36 patients with JDM were analyzed. Autoantibody profiles were determined by probing microarrays, which were fabricated with approximate to 80 distinct autoantigens, with serum and a Cy3-conjugated secondary antibody. Arrays were scanned and analyzed to determine antigen reactivity. Serum IFN activity was measured using a functional reporter cell assay. Sera were assayed alone or in combination with cellular material released from necrotic U937 cells to stimulate peripheral blood mononuclear cells from healthy donors in vitro, and IFN production in culture was measured by a dissociation-enhanced lanthanide fluoroimmunoassay (DELFIA). Results Reactivity against at least 1 of 41 autoantigens on the microarray, including Ro 52, Ro 60, La, Sm, and RNP, was observed in 75% of the serum samples from patients with JDM. IFN activity was detected in 7 samples by reporter cell assay. The reporter cell assay showed a significant association of reactivity against Ro, La, Sm, and proliferating cell nuclear antigen with serum IFN activity (P = 0.005). Significance Analysis of microarrays (SAM) identified increased reactivity against Sm, RNP, Ro 52, U1-C, and Mi-2 in these sera. Sixteen samples induced IFN production as measured by DELFIA, and there was a significant association of reactivity against Ro, La, Sm, and RNP with the induction of IFN by serum and necrotic cell material (P = 0.034). SAM identified increased reactivity against Ro 60 in these sera. Conclusion These data support the hypothesis that nucleic acid-associated autoantibodies, including the Ro/La and Sm/RNP complexes, may stimulate the production of active IFN in children with JDM.

关键词： ACADEMIC medical centers AUTOANTIBODIES DERMATOMYOSITIS INTERFERONS FINANCING of research DATA analysis software microarray technology CHILDREN

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Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts

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GENETICS RESEARCH 2013年第1期95卷 14-29页

作者： Purdom, E. Restall, C. Busuttil, R. A. Schluter, H. Boussioutas, A. Thompson, E. W. Anderson, R. L. Speed, T. P. Haviv, I. Univ Calif Berkeley Dept Stat Berkeley CA 94720 USA Peter MacCallum Canc Ctr Metastasis Res Lab Melbourne Vic Australia St Vincents Hosp Dept Surg Melbourne Vic Australia St Vincents Inst Melbourne Vic Australia Univ Melbourne Fac Med Dent & Hlth Sci Dept Pathol Melbourne Vic 3010 Australia Walter & Eliza Hall Inst Med Res Bioinformat Div Melbourne Vic Australia Bar Ilan Univ Fac Med Galilee Zfat Israel

Gene expression profiling using microarrays and xenograft transplants of human cancer cell lines are both popular tools to investigate human cancer. However, the undefined degree of cross hybridization between the mouse and human genomes hinders the use of microarrays to characterize gene expression of both the host and the cancer cell within the xenograft. Since an increasingly recognized aspect of cancer is the host response (or cancer-stroma interaction), we describe here a bioinformatic manipulation of the Affymetrix profiling that allows interrogation of the gene expression of both the mouse host and the human tumour. Evidence of microenvironmental regulation of epithelial mesenchymal transition of the tumour component in vivo is resolved against a background of mesenchymal gene expression. This tool could allow deeper insight to the mechanism of action of anti-cancer drugs, as typically novel drug efficacy is being tested in xenograft systems.

关键词： EPITHELIAL cells microarray technology XENOGRAFTS GENE expression MESENCHYME -- Tumors CANCER cells CELL lines

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