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Affolter VK. Dermatopathology - the link between ancillary techniques and clinical lesions. Vet Dermatol 2016; 28:134-e28. [DOI: 10.1111/vde.12345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Verena K. Affolter
- Department of Pathology, Microbiology, Immunology; School of Veterinary Medicine; University California Davis; One Shields Avenue, VM3A, Room 4206 Davis CA 95616 USA
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2
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Kumar R, Weigel S, Meyer R, Niemeyer CM, Fuchs H, Hirtz M. Multi-color polymer pen lithography for oligonucleotide arrays. Chem Commun (Camb) 2016; 52:12310-12313. [DOI: 10.1039/c6cc07087f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Multi-color patterning by polymer pen lithography (PPL) was used to fabricate covalently immobilized fluorophore and oligonucleotide arrays with up to five different components. These can easily be translated for presentation of multiple protein types to a single cell.
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Affiliation(s)
- R. Kumar
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF)
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
- Physical Institute & Center for Nanotechnology (CeNTech)
| | - S. Weigel
- Institute of Biological Interfaces (IBG-1)
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - R. Meyer
- Institute of Biological Interfaces (IBG-1)
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - C. M. Niemeyer
- Institute of Biological Interfaces (IBG-1)
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - H. Fuchs
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF)
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
- Physical Institute & Center for Nanotechnology (CeNTech)
| | - M. Hirtz
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF)
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
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3
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Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Xu D, Nguyen HT. Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). BMC Genomics 2015; 16:148. [PMID: 25880563 PMCID: PMC4351908 DOI: 10.1186/s12864-015-1316-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/03/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most devastating pathogen of soybean. Many gene expression profiling studies have been conducted to investigate the responses of soybean to the infection by this pathogen using primarily the first-generation soybean genome array that covered approximately 37,500 soybean transcripts. However, no study has been reported yet using the second-generation Affymetrix soybean whole-genome transcript array (Soybean WT array) that represents approximately 66,000 predicted soybean transcripts. RESULTS In the present work, the gene expression profiles of two soybean plant introductions (PIs) PI 437654 and PI 567516C (both resistant to multiple SCN HG Types) and cultivar Magellan (susceptible to SCN) were compared in the presence or absence of the SCN inoculum at 3 and 8 days post-inoculation using the Soybean WT array. Data analysis revealed that the two resistant soybean lines showed distinctive gene expression profiles from each other and from Magellan not only in response to the SCN inoculation, but also in the absence of SCN. Overall, 1,413 genes and many pathways were revealed to be differentially regulated. Among them, 297 genes were constitutively regulated in the two resistant lines (compared with Magellan) and 1,146 genes were responsive to the SCN inoculation in the three lines, with 30 genes regulated both constitutively and by SCN. In addition to the findings similar to those in the published work, many genes involved in ethylene, protein degradation, and phenylpropanoid pathways were also revealed differentially regulated in the present study. GC-rich elements (e.g., GCATGC) were found over-represented in the promoter regions of certain groups of genes. These have not been observed before, and could be new defense-responsive regulatory elements. CONCLUSIONS Different soybean lines showed different gene expression profiles in the presence and absence of the SCN inoculum. Both inducible and constitutive gene expression may contribute to resistance to multiple SCN HG Types in the resistant soybean PI lines. Ethylene, protein degradation, and phenylpropanoid pathways, as well as many other pathways reported previously, may play important roles in mediating the soybean-SCN interactions. The revealed genes, pathways, and promoter elements can be further explored to regulate or engineer soybean for resistance to SCN.
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Affiliation(s)
- Jinrong Wan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Tri Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Yongqing Jiao
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
- Current address: Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, 430062, China.
| | - Trupti Joshi
- Department of Computer Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Hongxin Zhang
- Department of Computer Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Dong Xu
- Department of Computer Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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4
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Mujawar LH, Kuerten JGM, Siregar DP, van Amerongen A, Norde W. Influence of the relative humidity on the morphology of inkjet printed spots of IgG on a non-porous substrate. RSC Adv 2014. [DOI: 10.1039/c4ra01327a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
During the drying of inkjet printed droplets, the solute particles (IgG-Alexa-635 molecules) in the drop may distribute unevenly on the substrate, resulting in a “coffee-stain” spot morphology.
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Affiliation(s)
- Liyakat Hamid Mujawar
- Food and Biobased Research, Biomolecular Sensing and Diagnostics
- Wageningen University and Research Centre
- 6708 AA Wageningen, The Netherlands
- Laboratory of Physical Chemistry and Colloid Science
- Wageningen University
| | - J. G. M. Kuerten
- Department of Mechanical Engineering
- Eindhoven University of Technology
- 5600 MB Eindhoven, The Netherlands
- Faculty EEMCS
- University of Twente
| | - D. P. Siregar
- Department of Mechanical Engineering
- Eindhoven University of Technology
- 5600 MB Eindhoven, The Netherlands
| | - Aart van Amerongen
- Food and Biobased Research, Biomolecular Sensing and Diagnostics
- Wageningen University and Research Centre
- 6708 AA Wageningen, The Netherlands
| | - Willem Norde
- Laboratory of Physical Chemistry and Colloid Science
- Wageningen University
- 6703 HB Wageningen, The Netherlands
- University Medical Center Groningen
- University of Groningen
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5
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Voelker AE, Viswanathan R. Synthesis of a Suite of Bioorthogonal Glutathione S-Transferase Substrates and Their Enzymatic Incorporation for Protein Immobilization. J Org Chem 2013; 78:9647-58. [DOI: 10.1021/jo401278x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alden E. Voelker
- Department of Chemistry, Case Western Reserve University, Millis Science Center: Rm
216, 2074 Adelbert Road, Cleveland, Ohio 44106-7078, United States
| | - Rajesh Viswanathan
- Department of Chemistry, Case Western Reserve University, Millis Science Center: Rm
216, 2074 Adelbert Road, Cleveland, Ohio 44106-7078, United States
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6
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Chang TY, Huang M, Yanik AA, Tsai HY, Shi P, Aksu S, Yanik MF, Altug H. Large-scale plasmonic microarrays for label-free high-throughput screening. LAB ON A CHIP 2011; 11:3596-602. [PMID: 21901194 DOI: 10.1039/c1lc20475k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Microarrays allowing simultaneous analysis of thousands of parameters can significantly accelerate screening of large libraries of pharmaceutical compounds and biomolecular interactions. For large-scale studies on diverse biomedical samples, reliable, label-free, and high-content microarrays are needed. In this work, using large-area plasmonic nanohole arrays, we demonstrate for the first time a large-scale label-free microarray technology with over one million sensors on a single microscope slide. A dual-color filter imaging method is introduced to dramatically increase the accuracy, reliability, and signal-to-noise ratio of the sensors in a highly multiplexed manner. We used our technology to quantitatively measure protein-protein interactions. Our platform, which is highly compatible with the current microarray scanning systems can enable a powerful screening technology and facilitate diagnosis and treatment of diseases.
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Affiliation(s)
- Tsung-Yao Chang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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8
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Zhao S, Chen A, Revzin A, Pan T. Stereomask lithography (SML): a universal multi-object micro-patterning technique for biological applications. LAB ON A CHIP 2011; 11:224-30. [PMID: 21113523 DOI: 10.1039/c0lc00275e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The advent of biological micro-patterning techniques has given new impetus to many areas of biological research, including quantitative biochemical analysis, tissue engineering, biosensing, and regenerative medicine. Derived from photolithography or soft lithography, current bio-patterning approaches have yet to completely address the needs of out-of-cleanroom, universal applicability, high feature resolution, as well as multi-object placement, though many have shown great promise to precisely pattern one specific biomaterial. In this paper, we present a novel versatile biological lithography technique to achieve integrated multi-object patterning with high feature resolution and high adaptability to various biomaterials, referred to as stereomask lithography (SML). Successive patterning of multiple objects is enabled by using unique three-dimensional masks (i.e., the stereomasks), which lay out current micropatterns while protecting pre-existing biological features on the substrate. Furthermore, high-precision reversible alignment among multiple bio-objects is achieved by adopting a peg-in-hole design between the substrate and stereomasks. We demonstrate that the SML technique is capable of constructing a complex biological microenvironment with various bio-functional components at the single-cell resolution, which to the best of our knowledge has not been realized before.
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Affiliation(s)
- Siwei Zhao
- Micro-Nano Innovations (MiNI) Laboratory, Department of Biomedical Engineering, University of California, Davis, CA, USA
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9
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Min EH, Ting SRS, Billon L, Stenzel MH. Thermo-responsive glycopolymer chains grafted onto honeycomb structured porous films via RAFT polymerization as a thermo-dependent switcher for lectin Concanavalin a conjugation. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/pola.24129] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Qiu J, Cui X. Evaluation of a statistical equivalence test applied to microarray data. J Biopharm Stat 2010; 20:240-66. [PMID: 20309757 DOI: 10.1080/10543400903572738] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Microarray technology is commonly used to identify differentially expressed (DE) genes across conditions. A related issue that has rarely been discussed but is equally important is to identify commonly expressed genes or constantly expressed genes across different organs, tissues, or species. A common practice in the literature for such studies is to apply the differential expression analysis and conclude that a gene is unchanged if there is no statistical evidence to conclude for differential expression. However, genes that are not statistically significantly DE could be (1) truly non-DE genes or (2) truly DE genes not detected by the statistical test of differential expression due to lack of power resulted from high noise level or lack of replication. Therefore, the practice of treating non-statistically significantly DE genes as non-DE genes has the risk of including genes that are truly DE without controlling such errors. We argue that if one wants to identify genes that are truly non-DE, one needs to show statistical evidence through valid statistical tests with the appropriate type I error rate control. In this paper, we consider the identification of non-DE genes through statistical equivalence tests under the framework of multiple testing. In particular, we consider the average equivalence criterion and study the power and false discovery rate (FDR) of the standard average equivalence test, the "two one-sided tests" (TOST), through extensive simulation studies based on real microarray data sets. We study the effects of various factors that can affect the power and FDR of the equivalence test including the proportion of non-DE genes. We also compare the ROC curves of the equivalence test with those of the naive method of selecting genes that are not statistically significant DE.
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Affiliation(s)
- Jing Qiu
- Department of Statistics, University of Missouri, Columbia, Missouri, USA.
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11
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Choudhuri S. Looking back to the future: From the development of the gene concept to toxicogenomics. Toxicol Mech Methods 2009; 19:263-77. [DOI: 10.1080/15376510902855529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Barbulovic-Nad I, Lucente M, Sun Y, Zhang M, Wheeler AR, Bussmann M. Bio-Microarray Fabrication Techniques—A Review. Crit Rev Biotechnol 2008; 26:237-59. [PMID: 17095434 DOI: 10.1080/07388550600978358] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Microarrays with biomolecules (e.g., DNA and proteins), cells, and tissues immobilized on solid substrates are important tools for biological research, including genomics, proteomics, and cell analysis. In this paper, the current state of microarray fabrication is reviewed. According to spot formation techniques, methods are categorized as "contact printing" and "non-contact printing." Contact printing is a widely used technology, comprising methods such as contact pin printing and microstamping. These methods have many advantages, including reproducibility of printed spots and facile maintenance, as well as drawbacks, including low-throughput fabrication of arrays. Non-contact printing techniques are newer and more varied, comprising photochemistry-based methods, laser writing, electrospray deposition, and inkjet technologies. These technologies emerged from other applications and have the potential to increase microarray fabrication throughput; however, there are several challenges in applying them to microarray fabrication, including interference from satellite drops and biomolecule denaturization.
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Affiliation(s)
- Irena Barbulovic-Nad
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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13
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Genomics. Genomics 2008. [DOI: 10.3109/9781420067064-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Li T, Guo L, Wang Z. Microarray based Raman spectroscopic detection with gold nanoparticle probes. Biosens Bioelectron 2008; 23:1125-30. [DOI: 10.1016/j.bios.2007.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 11/01/2007] [Accepted: 11/02/2007] [Indexed: 11/15/2022]
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15
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Abstract
The emergence of microarray technology as a novel tool in molecular biology has led to significant progress in many biomedical disciplines, including gerontology. Both cDNA and oligonucleotide-based DNA microarrays are now widely used to identify the basic physiological mechanisms of aging and to uncover the molecular mechanisms underlying the biological effects of anti-aging drugs. Two different protocols covering both cDNA and oligonucleotide microarray platforms, with radioactive and nonradioactive (fluorescent) labeling, are detailed in the manuscript. These in-depth protocols provide a background for the technical aspects of everyday work with DNA microarrays.
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Affiliation(s)
- Sergey V Anisimov
- Neuronal Survival Unit, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
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16
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Andersson M, Berg M, Fossum C, Jensen-Waern M. Development of a microarray for studying porcine cytokine production in blood mononuclear cells and intestinal biopsies. ACTA ACUST UNITED AC 2007; 54:161-8. [PMID: 17381682 DOI: 10.1111/j.1439-0442.2007.00906.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A microarray for demonstration of a limited number of porcine cytokines was initiated. Polymerase chain reaction (PCR) products were synthesized for four house-keeping genes, cyclophilin, beta-actin, hypoxanthine phosphoribosyltransferase (HPRT) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and the following cytokines: interleukin (IL)-1beta, IL-4, IL-6, IL-8, IL-10, IL-12 p35, IL-12 p40, IL-18, interferon (IFN)-alpha, IFN-beta, IFN-gamma, tumour necrosis factor (TNF)-alpha, macrophage inhibition factor (MIF) and granulocyte/macrophage colony-stimulating factor (GM-CSF). Cytokine production was induced by incubation of porcine peripheral blood mononuclear cells (PBMC) with Concanavalin A (ConA) or oligodeoxynucleotide (ODN) 2216. RNA was isolated after 6 or 24 h from stimulated cells or unstimulated control cells and from intestinal biopsies. Cytokine expression was analysed using a 3-DNA Array 350(TM) labelling kit from Genisphere. Data were normalized using external control genes and analysed with the genepix pro 5.0 software. All the cytokines could be induced in PBMC and expressed on the array and the cytokines IL-6 and IFN-alpha were also analysed at protein level. All but one cytokine were expressed in samples from intestinal biopsies. Densitometric analyses of PCR products of the house-keeping genes were performed to validate the results from the microarray. Thus, this microarray will enable analyses of the cytokine profile during local and systemic infections in the pig.
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Affiliation(s)
- M Andersson
- Department of Clinical Sciences, Section of Comparative Physiology and Medicine, Swedish University of Agricultural Sciences, Box 7018, SE 75007 Uppsala, Sweden.
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17
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Ducray F, Honnorat J, Lachuer J. Principes et intérêts pour l’étude des maladies neurologiques et technologie des puces ADN. Rev Neurol (Paris) 2007; 163:409-20. [PMID: 17452943 DOI: 10.1016/s0035-3787(07)90417-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
INTRODUCTION DNA microarray is a powerful technology which can rapidly provide a high throughput and detailed view of the entire genome and transcriptome. In this review we discuss the basic principles behind gene expression microarrays, CGH arrays and DNA microarray genotyping, and their potential applications to neurological diseases. STATE OF THE ART Microarray gene expression profiling is a reliable technology that has already been used with great success in the molecular classification of cancer. It is a very promising technology in the field of Neurooncology. One of the interesting characteristics of DNA microarrays is also that they can be used in a non-hypothesis-driven manner to discover new genomic characteristics that will enable to establish new pathophysiological hypotheses. Such a strategy has already yielded interesting new insights in the study of multiple sclerosis, Alzheimer disease or neuromuscular diseases. With DNA microarray genotyping it is now possible to detect mutations in many genes simultaneously. CONCLUSIONS In Neurooncology DNA microarrays should help to establish a more accurate classification of brain tumors and recent studies have shown how gene expression profiling of brain tumors allows to uncover previously unrecognized patient subsets that differ in their survival. The applications of microarrays for the study of neurological diseases, like multiple sclerosis, Alzheimer disease or neuromuscular diseases are also promising both for generating new pathophysiological hypotheses and for enabling new molecular classifications. DNA microarray genotyping is a powerful technology that should help to discover genetic factors associated with multifactorial neurological disorders and help to diagnose complex neurogenetic diseases. This technology should also facilitate the realization of pharmacogenomic studies in neurological diseases.
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Affiliation(s)
- F Ducray
- Service de Neurologie B, Hôpital Neurologique Pierre Wertheimer, Lyon
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18
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Cui X, Affourtit J, Shockley KR, Woo Y, Churchill GA. Inheritance patterns of transcript levels in F1 hybrid mice. Genetics 2006; 174:627-37. [PMID: 16888332 PMCID: PMC1602077 DOI: 10.1534/genetics.106.060251] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic analysis of transcriptional regulation is a rapidly emerging field of investigation that promises to shed light on the regulatory networks that control gene expression. Although a number of such studies have been carried out, the nature and extent of the heritability of gene expression traits have not been well established. We describe the inheritance of transcript levels in liver tissue in the first filial (F1) generation of mice obtained from reciprocal crosses between the common inbred strains A/J and C57BL/6J. We obtain estimates of genetic and technical variance components from these data and demonstrate that shrinkage estimators can increase detectable heritability. Estimates of heritability vary widely from transcript to transcript, with one-third of transcripts showing essentially no heritability (<0.01) and one-quarter showing very high heritability (>0.50). Roughly half of all transcripts are differentially expressed between the two parental strains. Most transcripts show an additive pattern of inheritance. Dominance effects were observed for 20% of transcripts and a small number of transcripts were identified as showing an overdominance mode of inheritance. In addition, we identified 314 transcripts with expression levels that differ between the reciprocal F1 animals. These genes may be related to maternal effect.
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Affiliation(s)
- Xiangqin Cui
- Department of Biostatistics, Section on Statistical Genetics, Department of Medicine, Genetic and Translational Medicine Division, University of Alabama, Alabama 35294, USA.
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19
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Bally M, Halter M, Vörös J, Grandin HM. Optical microarray biosensing techniques. SURF INTERFACE ANAL 2006. [DOI: 10.1002/sia.2375] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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McCabe AF, Eliasson C, Prasath RA, Hernandez-Santana A, Stevenson L, Apple I, Cormack PAG, Graham D, Smith WE, Corish P, Lipscomb SJ, Holland ER, Prince PD. SERRS labelled beads for multiplex detection. Faraday Discuss 2006; 132:303-8; discussion 309-19. [PMID: 16833125 DOI: 10.1039/b506942d] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Beads labelled using surface enhanced resonance Raman scattering (SERRS) are highly sensitive and specific tags, with potential applications in biological assays, including molecular diagnostics. The beads consist of a nucleus containing dye labelled silver-nanoparticle aggregates surrounded by a polymer core. The nuclei generate strong SERRS signals. To illustrate the coding advantage created by the sharp, molecularly specific SERRS signals, four specially designed SERRS dyes have been used as labels and three of these have been combined in a multiplex analysis. These dyes use specific groups such as benzotriazole and 8-hydroxyquinoline to improve binding to the surface of the silver particles. The aggregation state of the particles is held constant by the polymer core, this nucleus also contains many dye labels, yielding a very high Raman scattering intensity for each bead. To functionalise these beads for use in biological assays an outer polymer shell can be added, which allows the attachment of oligonucleotide probes. Oligonucleotide modified beads can then be used for detection of specific oligonucleotide targets. The specificity of SERRS will allow for the detection of multiple targets within a single assay.
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Affiliation(s)
- Ailie F McCabe
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, UK
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Eberhard S, Jain M, Im CS, Pollock S, Shrager J, Lin Y, Peek AS, Grossman AR. Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii. Curr Genet 2005; 49:106-24. [PMID: 16333659 DOI: 10.1007/s00294-005-0041-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 10/24/2005] [Accepted: 10/25/2005] [Indexed: 01/08/2023]
Abstract
The availability of genome sequences makes it possible to develop microarrays that can be used for profiling gene expression over developmental time, as organisms respond to environmental challenges, and for comparison between wild-type and mutant strains under various conditions. The desired characteristics of microarrays (intense signals, hybridization specificity and extensive coverage of the transcriptome) were not fully met by the previous Chlamydomonas reinhardtii microarray: probes derived from cDNA sequences (approximately 300 bp) were prone to some nonspecific cross-hybridization and coverage of the transcriptome was only approximately 20%. The near completion of the C. reinhardtii nuclear genome sequence and the availability of extensive cDNA information have made it feasible to improve upon these aspects. After developing a protocol for selecting a high-quality unigene set representing all known expressed sequences, oligonucleotides were designed and a microarray with approximately 10,000 unique array elements (approximately 70 bp) covering 87% of the known transcriptome was developed. This microarray will enable researchers to generate a global view of gene expression in C. reinhardtii. Furthermore, the detailed description of the protocol for selecting a unigene set and the design of oligonucleotides may be of interest for laboratories interested in developing microarrays for organisms whose genome sequences are not yet completed (but are nearing completion).
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Affiliation(s)
- Stephan Eberhard
- Department of Plant Biology, The Carnegie Institution, 260 Panama Street, Stanford, CA, 94305, USA.
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Gibson B, Huntington S, Rubanov S, Olivero P, Digweed-Lyytikäinen K, Canning J, Love J. Exposure and characterization of nano-structured hole arrays in tapered photonic crystal fibers using a combined FIB/SEM technique. OPTICS EXPRESS 2005; 13:9023-9028. [PMID: 19498937 DOI: 10.1364/opex.13.009023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This paper presents a technique to expose and characterize nano-structured hole arrays in tapered photonic crystal fibers. Hole array structures are examined with taper outer diameters ranging from 12.9 microm to 1.6 microm. A combined focused ion beam milling and scanning electron microscope system was used to expose and characterize the arrayed air-silica structures. Results from this combined technique are presented which resolve hole-to-hole pitch sizes and hole diameters in the order of 120 nm and 60 nm, respectively.
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Shimanuki M, Shimamura K, Hirai S, Nishiuchi T, Suzuki K, Kodama H. Polyethylene glycol-mediated enhancement of the hybridization rate on cDNA microarrays. Anal Biochem 2005; 344:284-6. [PMID: 15979558 DOI: 10.1016/j.ab.2005.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 05/13/2005] [Accepted: 05/16/2005] [Indexed: 11/29/2022]
Affiliation(s)
- Mamiko Shimanuki
- Graduate School of Science and Technology, Chiba University, 1-33 Yayoi-cho, Inage-Ku, Chiba 263-8522, Japan
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Christman KL, Maynard HD. Protein micropatterns using a pH-responsive polymer and light. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:8389-93. [PMID: 16114947 DOI: 10.1021/la050646a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein and peptide microarrays are popular candidates for medical diagnostics because of the possibility for high sensitivity and simultaneous marker screening. To realize the potential of these arrays, new strategies for ligand patterning are needed. We report a method for patterning proteins that utilizes a pH-responsive polymer, deep ultraviolet (DUV) light, and a photoacid generator (PAG). Poly(3,3'-diethoxypropyl methacrylate) (PDEPMA) contains reactive acetal side chains which are converted to aldehydes following treatment with acid. PDEPMA was spin-coated onto Si-SiO(2) substrates and was either chemically deprotected with 1 M HCl or photochemically deprotected by exposure to DUV in the presence of triphenylsulfonium triflate. Conversion to aldehyde groups was confirmed with Purpald and by reaction with a green fluorescent hydroxylamine. Protein microarrays were demonstrated by incubating photochemically patterned surfaces with an aldehyde-reactive biotin followed by red fluorescent streptavidin. This methodology provides a new substrate for the precise patterning of both peptides and proteins for various biological applications including medical sensors.
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Affiliation(s)
- Karen L Christman
- Department of Chemistry and Biochemistry and California Nanosystems Institute, 607 E. Charles E. Young Drive, Los Angeles, California 90095-1569, USA
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Dannecker C. Response to the letter “DNA microarrays will be instrumental in the future diagnosis of cervical dysplasia and neoplasia”, by P. K. Wright (doi:10.1093/annonc/mdi109): prospective and controlled trials are required to evaluate the relevance of DNA microarrays with regard to diagnosis and therapy of cervical neoplasia. Ann Oncol 2005. [DOI: 10.1093/annonc/mdi117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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