",isbn:"978-1-83962-547-3",printIsbn:"978-1-83962-546-6",pdfIsbn:"978-1-83962-548-0",doi:null,price:0,priceEur:0,priceUsd:0,slug:null,numberOfPages:0,isOpenForSubmission:!1,hash:"e5ba02fedd7c87f0ab66414f3b07de0c",bookSignature:"Dr. John P. Tiefenbacher",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/10765.jpg",keywords:"Managing Urbanization, Managing Development, Managing Resource Use, Drought Management, Flood Management, Water Quality Monitoring, Air Quality Monitoring, Ecological Monitoring, Modeling Extreme Natural Events, Ecological Restoration, Restoring Environmental Flows, Environmental Management Perspectives",numberOfDownloads:18,numberOfWosCitations:0,numberOfCrossrefCitations:0,numberOfDimensionsCitations:0,numberOfTotalCitations:0,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"January 12th 2021",dateEndSecondStepPublish:"February 9th 2021",dateEndThirdStepPublish:"April 10th 2021",dateEndFourthStepPublish:"June 29th 2021",dateEndFifthStepPublish:"August 28th 2021",remainingDaysToSecondStep:"2 months",secondStepPassed:!0,currentStepOfPublishingProcess:4,editedByType:null,kuFlag:!1,biosketch:"A geospatial scholar working at the interface of natural and human systems, collaborating internationally on innovative studies about hazards and environmental challenges. Dr. Tiefenbacher has published more than 200 papers on a diverse array of topics that examine perception and behaviors with regards to the application of pesticides, releases of toxic chemicals, environments of the U.S.-Mexico borderlands, wildlife hazards, and the geography of wine.",coeditorOneBiosketch:null,coeditorTwoBiosketch:null,coeditorThreeBiosketch:null,coeditorFourBiosketch:null,coeditorFiveBiosketch:null,editors:[{id:"73876",title:"Dr.",name:"John P.",middleName:null,surname:"Tiefenbacher",slug:"john-p.-tiefenbacher",fullName:"John P. Tiefenbacher",profilePictureURL:"https://mts.intechopen.com/storage/users/73876/images/system/73876.jfif",biography:"Dr. John P. Tiefenbacher (Ph.D., Rutgers, 1992) is a professor of Geography at Texas State University. His research has focused on various aspects of hazards and environmental management. 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From chapter submission and review, to approval and revision, copyediting and design, until final publication, I work closely with authors and editors to ensure a simple and easy publishing process. I maintain constant and effective communication with authors, editors and reviewers, which allows for a level of personal support that enables contributors to fully commit and concentrate on the chapters they are writing, editing, or reviewing. I assist authors in the preparation of their full chapter submissions and track important deadlines and ensure they are met. I help to coordinate internal processes such as linguistic review, and monitor the technical aspects of the process. As an ASM I am also involved in the acquisition of editors. 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1. Introduction
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In the past two decades, our understanding in biology, materials science and nanotechnology has expanded rapidly. The inevitable intersection of these three disciplines has set in motion the development of an emerging research area, nanobiotechnology or nanobiomedical science, which offers exciting and abundant opportunities for discovering new processes and phenomena. In particular, the advances in the synthesis and characterization of nanoscale materials allow scientists to understand and control the interactions between nanomaterials (e.g., nanowires, nanofibers, nanoparticles, nanobelts or nanoribbons, and nanotubes) and biological entities (e.g., nucleic acid, proteins, or cells) at molecular or cellular levels. These advances promise major achievements in the life sciences.
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By way of an example, the research on magnetic nanomaterials (Skomski, 2003) has attracted a lot of attention because of their numerous applications including magnetic separation of biomolecules (Nam et al., 2003), as biocompatible contrast agents for magnetic resonance imaging (MRI) (Wang et al., 2001; Berry & Curtis 2003; Pankhurst et al., 2003; Tartaj et al., 2003; Nitin et al., 2004; Lee et al., 2007), magnetic recording (Darques et al., 2009), spintronic devices and magnetic sensing (Thurn-Albrecht et al., 2000; Allwood et al., 2002; Redl et al., 2003). Relatively large, near-monodisperse spherical iron oxide (Fe3O4, magnetite) nanoparticles with average core diameters of 200–1000 nm are commercially available (e.g., Feridex), some of them are used as contrast agents for in vivo clinical MRI. These relatively large magnetite nanoparticles can be obtained by a structural refinement process of bulk materials or a recrystallization from small nanoparticles. In respect to biological applications, the particles’ surface is usually coated with dextran as a biocompatible, protective layer. Biodegradable magnetic nanoparticles can be labeled intracellularly towards cellular and molecular imaging, and also used for targeted drug carrier together with controlled release capabilities (Lübbe et al., 2001), and radio frequency therapy of tumours via hyperthermia (Fortin et al., 2007). There are indications that the size, shape, structure, and the functional surfaces (e.g., amine, hydroxyl, poly(ethylene glycol), etc.), texture and porosity of many biocompatible nanomaterials are important parameters which influence the rate of cell attachment, internalization, uptake and vascular dynamics (Corot et al., 2006; Wilhelm & Gazeau 2008; Mitragotri & Lahann 2009; Park et al., 2009).
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The properties of one-dimensional (1-D) nanowires toward biological systems are attracting increasing attention recently (Fang & Kelley 2009; Cohen-Karni et al., 2009). Generally, nanomaterials having elongated shapes and correspondingly increased surface area are more effective in vivo due to the geometrically enhanced multivalent interaction between ligands and receptors (Mitragotri & Lahann 2009). In comparison to the zero-dimensional nanoparticles, 1-D nanowires provide more parallel-aligned surface functionalities per molecular structure, which are suitable for multivalent molecular recognition on cell surfaces. Potential application of the magnetic nanowires may offer endothelium surface magnetic labeling because of their steric hindrance in passing into the extra-vascular space. Macrophage cells may take up the nanowires more rapidly than nanoparticles by their differences in mass. It is of current interest to investigate the cell labeling efficacy with 1-D nanomaterials, cytotoxicity, stability in different cell compartments, and fate of the materials. Recently, Park et al. reported 1-D magnetic nanoworms for in vivo tumor targeting (Park et al., 2009). Superparamagnetic iron oxide nanoworms that have a long dimension of ~70 nm and thickness of ~30 nm have been used for targeting xenograft tumors. The nanoworms exhibit superior in vivo tumor-targeting ability than nanoparticles (mean diameter ~30 nm). The authors conclude that the blood half-life of a targeting molecules-nanomaterial ensemble is a key consideration when selecting the appropriate ligand and nanoparticle chemistry for tumor targeting.
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Although different magnetic nanowires have been fabricated by solution methods—a bottom-up approach (versus a top-down aprroach which produces nanostructures by refinement of bulk materials) (Xia et al., 1999; Stephanopoulos et al., 2005)—and characterized by various techniques (Whitney et al., 1993; Meier et al., 1996; Doudin et al., 1996; Ferré et al., 1997; Fert & Piraux 1999; García & Miltat 2002; Nielsch et al., 2002; Chen et al.(a), 2003; Chen et al.(b), 2003; Love et al., 2003; Ponhan & Maensiri 2009), however, the effective preparation, cytotoxicity, as well as cell labelling efficacy of different cell types using relatively rigid, long magnetic nanowires have been seldomly investigated. Therefore, we have recently investigated rigid 1-D magnetic nanostructures as effective contrast agents for MRI, and discovered the preparation of Mn-Fe oxide nanowires with amine-functional peripheries, which are formed by a self-assembling organization of their corresponding small MnFe2O4 nanoparticles — a process of assembling approach using cystamine as the linker. This approach, which utilizes chemicals and supramolecular driving forces to arrange small components into an ordered conformation, represents an effective and inexpensive way to achieve more complex and functional nanoarchitectures. Herein, the properties of Mn-Fe nanowires with lengths ranging from 400-1000 nm and widths ranging from 8-35 nm for MRI contrast and the potential of macrophage cell uptake are also reported (Leung et al., 2008; Leung et al., 2009).
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2. Approach
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2.1. Synthesis of the nanostructures
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Spontaneous organization of small individual nanostructures into large and well-defined nanowires, represents (Tang et al., 2002; Grubbs 2007) a facile way to obtain useful nanomaterials for magnetic devices (Hangarter et al., 2007; Wu et al., 2007). The key to prepare our target 1-D Mn-Fe nanowires for cell labeling and MRI contrast could be achieved in such a way that small building blocks — MnFe2O4 nanoparticles which were prepared by co-precipitation at elevated temperature (Sousa et al., 2001; Aquino et al., 2002; Deng et al., 2005), were rationally organized into Mn-Fe nanowires with larger lengths in relatively high yields. We have found out that suitable amount of linker — cystamine (NH2CH2CH2S–SCH2CH2NH2) could induce the organization of the as-synthesized MnFe2O4 nanoparticles into novel amine-functionalized Mn-Fe nanowires in good yields under basic condition and magnetic stirring for 24 hours. The precipitate was separated by centrifugation and washed with water/ethanol mixture to afford the 1-D Mn-Fe nanostructures.
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2.2. Characterization of the nanostructures
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The morphology of as-prepared MnFe2O4 nanoparticles was characterized by high-resolution TEM, revealing their morphologies with an average diameter of 5 nm (Figure 1A). One drop of sample in ethanol suspension was added to the holey carbon-coated
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Figure 1.
High-resolution transmission electron microscopic images of (A) MnFe2O4 nanoparticles; (B) nanoneedles; (C) nanorods; and (D) nanowires.
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copper grid and was allowed to evaporate to dryness. For the prepared Mn-Fe nanostructures, TEM images revealed that they were in substantial amounts (Figures 1B-D). The nanoneedles possessed (Figure 1B) an average length of 400 nm and width of 8 nm; while the nanorods possessed (Figure 1C) an average length of 800 nm and width of 30 nm. For the nanowires, they possessed (Figure 1D) an average length of 1 μm and width of 35 nm.
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Figure 2.
Energy-dispersive X-ray spectroscopic analyses (on copper grid) of (A) MnFe2O4 nanoparticles and (B) Mn-Fe nanowires. The obseved signals for Cu originated from the copper grid.
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In addition to the TEM characterization, inductively coupled plasma-optical emission spectroscopy (ICP-OES) and energy-dispersive X-ray (EDX) spectroscopy were employed for the determination of elemental contents (Mn, Fe, S, O and N) of the nanoarchitectures (Table 1, Figure 2). EDX measurements were performed by locating a region (~20 nm × 20 nm) with substantial amount of materials on copper grid without carbon coating. By comparing between the EDX spectra of the MnFe2O4 nanoparticles (Figure 2A) and nanowires (Figure 2B), the spectrum of the nanowires revealed additional signals of sulfur and nitrogen as well as enhanced signals of carbon, originating from the attached cystamine linker. The observed EDX signal of copper, which originates from the TEM sample grid, has been omitted in the calculations of the elemental contents present in our nanostructures. The X-ray diffraction (XRD) analysis revealed that the MnFe2O4 nanoparticles exhibited several peaks corresponding to the characteristic interplanar spacings 220, 311, 400, 511 and 400 of the spinel structure with 2θ 31.5, 35.0, 42.4, 56.2 and 61.7, respectively. These results are similar to the reported values in the literature (Aquino et al., 2002).
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ICP-OES samples were dissolved in 2% HCl solution with a few drops of SnCl2 solution. Iron absorption was observed at 238.20 nm while the manganese absorption was observed at 257.61 nm. Although the separate measurements (Table 1) by ICP-OES and EDX occurred with the errors that are less than 1%, there existed relatively large errors (0.3–48%) when comparing the results obtained in both methods. Generally, ICP-OES is regarded as an accurate method to determine the metal ion concentrations while EDX spectroscopy is an evaluation of the existence of elements in a specific area on sample grid surface. The ratio of Mn:Fe is approximately 1:2. From the MnFe2O4 nanoparticles to the nanowires, there was a trend in the quantitative ICP-OES measurements that both the Mn and Fe metal contents decrease slightly. Moreover, the sulfur and nitrogen contents originated from the cystamine linker appeared in the EDX measurement of the 1-D nanoarchitectures. These increased organic characteristics indicate that the amounts of linker play a crucial role in controlling the sizes of the nanostructures.
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Figure 3.
VSM spectra of (A) MnFe2O4 nanoparticles and (B) Mn-Fe nanowires showing the difference in magnetic response.
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The magnetic properties of the nanomaterials have been investigated using a vibrating sample magnetometer (VSM). The VSM spectra (M-H) of magnetization (emu/g) versus magnetic field (Oe) are examined. Figure 3A shows a hysteresis loop of typical MnFe2O4 nanoparticles measured by sweeping the external field between –10000 to 10000 Oe at room temperature. The magnetization curve shows no remanemce or coercivity at room temperature, demonstrating the superparamagnetic character. Superparamagnetism is the responsiveness to an applied magnetic field without retaining any magnetism after removal of the applied magnetic field. The saturated magnetization value of MnFe2O4 nanoparticles is determined to be 43.7 emu/g. On the other hand, Figure 3B shows a hysteresis loop of Mn-Fe nanowires measured by sweeping the external field between –10000 to 10000 Oe at room temperature. The magnetization curve shows that the coercivity and remanence are small at room temperature (Figure 3B inset). The saturated magnetization value of Mn-Fe nanowires is determined to be 9.0 emu/g. The decreased saturated magnetization value is in part due to the increasing thickness of organic coating layer of the nanowires. Other reasons are the presence of a magnetic dead or anti-ferromagnetic organic layer on the nanowire’s periphery.
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For high-density information storage, the superparamagnetic relaxation of magnetization direction in tiny magnetic data bits has to be avoided in order to keep the digital data stored for a desired period of time. For biomedical applications such as magnetic resonance imaging, hyperthermia, drug delivery, and catalysis, in contrast, superparamagnetic property of materials would be essential from which the materials do not retain any magnetization in the absence of an externally applied magnetic field. In our system, soft magnetized nanowires have been employed as contrast agents for magnetic resonance imaging.
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Table 1.
Summarized results of ICP-OES and EDX measurements
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2.3. Magnetic resonance imaging
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For magnetic resonance imaging (MRI), the capability of nanoarchitectures to influence the T2 relaxation time was studied using a clinical 1.5 T whole-body MR system (Sonata, Siemens Symphony, Erlangen, Germany) with a standard human knee coil radio frequency coil for excitation and signal reception. Nanoarchitectures were diluted in distilled water at nanowire concentrations of 100, 10, 1 and 0.1 µg/mL. For MR measurements, the nanomaterial suspensions (1 mL) were filled in 2 mL Eppendorf vials each. These vials were placed in a water bath. Sonication was applied for 10 min prior to MRI using at 35 kHz in water at ambient temperature. The imaging sequence was a standard Carr-Purcell-Meiboom-Gill pulse sequence with the following parameters: TR = 2000 milisecond, TE range 30-960 milisecond, 32 echoes, FOV = 134 × 67 mm2, matrix = 128 × 64, slice thickness 5 mm, NEX = 3. T2 relaxation times were calculated by a linear fit of the logarithmic ROI signal amplitudes versus TE.
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When a cylindrical magnetic nanorod segment is disk-shaped, its magnetization axis lies perpendicular to the rod axis. It also follows that if the segment is longer than its width, its axis of magnetization is parallel to the nanorod axis (Ferré et al., 1997). Therefore, the magnetic properties of nanostructures can be tuned over a wide range by tuning the aspect ratio of the magnetic block and its composition (Fert & Piraux 1999). Experimentally, the T2 relaxivities (r2) for nanoneedles, nanorods, and nanowires were determined to be 20.81 ± 0.58, 8.10 ± 0.31, and 6.62 ± 0.42 mM-1sec-1, respectively (Figure 4). These values are at the lower end of the relaxivity of other iron oxide nanoparticle derivatives, such as VSOP-C184 has a r2 of 33 mM-1sec-1 and SHU-555C (Supravist) has a r2 of 38 mM-1sec-1 (Wang et al., 2001; Nitin et al., 2004; Lee et al., 2007; Lu et al., 2007; Lee et al., 2008). It is interesting to notice that though the iron concentration of nanoneedles is not very different to the other nanostructures, it has significantly higher MR relaxivity than the other nanostructures. It is known that MR relaxivity depends in part on the crystal lattice of the iron oxide. Our results suggest that the nanoneedles with higher MR relaxivity are majorly composed of iron oxide crystal lattice similar to those of the nanoparticles (Wang et al., 2001). The development of larger 1-D nanostructures leaded to lower MR relaxivities. Despite the slightly weaker MR relaxivity of the nanostructures developed in the current study, it is expected that the unique shape of these nanostructures can find applications for cell labeling, as drug carrier, magnetic separation of labeled cells and other biological entities, and also in the application of magnetic targeting (Alexiou et al., 2000; Pankhurst et al., 2003; Tartaj et al., 2003; Berry & Curtis 2003). It may be possible to further modify the systems with the aim to increase their relaxivities. It has been reported that the doping of Mn into Fe3O4 can also increase the MR
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Figure 4.
Spin echo MR image of the Mn-Fe nanostructure suspensions obtained at 1.5 Tesla with time of repetition (TR) 2000 millisecond and time of echo (TE) of 960 millisecond. All the Mn-Fe nanostructures with concentration of 100 µg/mL decrease the MRI signal to background signal (dark contrast). Mn-Fe nanostructures with concentration of 10 µg/mL decrease the MRI signal substantially, though less so with nanorods. Compared to the water signal, contrast due to 1 µg/mL nanostructures is just detectable.
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relaxivity as compared with the pure iron oxide counterpart (Lee et al., 2007). For in vivo tissue contrast, the weaker MR relaxivity can be compensated by using T2* MRI sequence and higher magnetic field such as 3 Tesla or 7 Tesla.
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The nanowires were incubated with RAW264.7 cells followed by Prussian blue staining. The results indicated that the Mn-Fe nanowires were effectively incorporated into RAW264.7 cells without the addition of any transfecting agent (e.g., liposomes) (Figure 5). Figures 5B–5D reveal the optical microscopic images of the RAW264.7 cells incubated with nanowires for 2 hours at the concentration of 10, 50, 100 µg/mL respectively. As increasing
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Figure 5.
Optical microscope images of the Raw264.7 cells [Original magnification: 100×]: (A) Control cells without the labeling of nanowires. (B)–(D) Cells incubated with nanowires for 2 hours at the concentration of 10, 50, 100 µg/mL, respectively. Prussian blue staining was carried out. As increasing the labeling concentration with nanowires, increased amounts of the nanowire uptake are observed as shown in the blue-stained part inside the cells. For (C) and (D), the cell labeling efficacies with the nanowires are approximately 100%.
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the labeling concentration with nanowires, increased amounts of the nanowire uptake were observed as in the blue-stained part inside the cells. At the nanowire concentrations of 50 and 100 µg/mL (Figures 5C and 5D), the cell labeling efficacies with the nanowires were approximately 100%.
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TEM analysis was also performed to confirm the location of nanowires inside the RAW264.7 cells. For the TEM analysis, specimens were fixed in 2.5% glutaraldehyde and 2% paraformaldehyde in 0.1 M cacodylate buffer (pH 7.2) containing 0.05% CaCl2 for 2 hours at room temperature, followed by post-fixation in 2% osmium tetroxide in the same buffer solution for 2 hours at room temperature. After dehydration and embedded in Spurr’s resin, ultra-thin sections (80 nm) were cut before examined under a FEI/Philips Tecnai 12 TEM operated at 80 kV. TEM results demonstrated that the nanowires were located within the lyzosome and cell vesicles (Figure 6). No obvious sub-cellular superstructure injury and cell apoptosis was observed. However, modest amount of the nanoparticles were observed inside the lyzosome and cell vesicles, a result which indicates that the nanostructures might be susceptible to enzymatic degradation in the slightly acidic lyzosome environment. It is also expected that some nanowires incorporated in the cells were fragmented or partially cut during the preparation of the ultra-thin section for TEM.
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Figure 6.
TEM images of the nanowires-labeled RAW264.7cells. The arrow denotes some of the nanowires present in the lysosomes and vesicles.
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It has been demonstrated that certain biocompatible synthetic materials with amine functional peripheries could enhance the degree of cell adhesion and transfection (Pollard et al., 1998; Wang et al., 2009). As a result, our reported Mn-Fe nanostructures which contain free amines would be beneficial not only to the macrophage cells but also can extend their labeling efficacy to other cell lines.
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To assess the biocompatibility of the nanostructures, after RAW264.7 cells incubated with 0.1, 1, 10, 50, 100 µg/mL nanowires for 2 hours, Trypan blue exclusion assay (Sigma T6146) was performed to assess the viability of the cells. To assess the cell proliferation potential post labeling, RAW264.7 cells were cultured in 96-well plate at the density of 2500 cell/well with DMEM including 10% FCS. After labeling cells with 0.1, 1, 10, 50 or 100 µg/mL nanowires for 2 hours, nanowires were removed from the plate and PBS was used to rinse the residual nanostructures. Fresh DMEM including 10% FCS was added again for normal cell growth. 3-[4,5-Dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide (MTT) assay was performed to detect the proliferation of the nanowire-labeled RAW264.7 cells.
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The Trypan blue exclusion assay results and MTT assay results are shown in Figure 7. RAW264.7 cell viability was not significantly affected from the labeling concentration of 0.1 up to 50 µg/mL with nanowires, and no apparent growth inhibition of RAW264.7 cells was observed after labeling up to 50 µg/mL of nanowires (inclusive). These results revealed the satisfactory safety profiles of these nanostructures.
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Figure 7.
The Trypan blue exclusion assay and MTT assay results. RAW264.7 cells were incubated with 0.1, 1, 10, 50, 100 µg/mL of nanowires for 2 hours. Satisfactory biocompatibility is shown from the concentration of 0.1 to 50 µg/mL. At 100 µg/mL, cell death and cell proliferation inhibition was observed.
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3. Conclusion
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In summary, the manganese-doped iron oxide nanoparticles are capable to organize into one-dimensional magnetic Mn-Fe nanostructures of different sizes with cystamine. The use of these materials which are employed as the cell-labeling agent for magnetic resonance imaging (MRI), has been explored. All nanoarchitectures demonstrate remarkable magnetic resonance T2 relaxivities. The cell viability test and growth curve reveal the satisfactory safety profiles of these nanostructures. This method represents an efficient and facile way to prepare novel functional nanoarchitectures for potential use in magnetic separation of labeled cells and other biological entities, magnetic resonance imaging, carriers of therapeutic molecules and magnetic targeting, and radio frequency therapy of tumours via hyperthermia (Alexiou et al., 2000; Berry & Curtis 2003; Pankhurst et al., 2003; Tartaj et al., 2003). Eventually, nanoarchitectures of specific sizes can be potentially obtained by this method and used as MRI contrast agents. The labeling efficacies of these nanostructures can be investigated with different cell types such as inflammation cells and liver cells (Du et al., 2007), etc. The comparative study on the use of both magnetic nanoparticles and nanowires as effective, biocompatible MRI contrast agents for different cell lines should be further investigated.
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\n\t\n',keywords:null,chapterPDFUrl:"https://cdn.intechopen.com/pdfs/8897.pdf",chapterXML:"https://mts.intechopen.com/source/xml/8897.xml",downloadPdfUrl:"/chapter/pdf-download/8897",previewPdfUrl:"/chapter/pdf-preview/8897",totalDownloads:2423,totalViews:165,totalCrossrefCites:2,totalDimensionsCites:7,hasAltmetrics:0,dateSubmitted:null,dateReviewed:null,datePrePublished:null,datePublished:"February 1st 2010",dateFinished:null,readingETA:"0",abstract:null,reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/8897",risUrl:"/chapter/ris/8897",book:{slug:"nanowires-science-and-technology"},signatures:"Ken Cham-Fai Leung and Yi-Xiang J. Wang",authors:[{id:"7095",title:"Prof",name:"Ken",middleName:null,surname:"Leung",fullName:"Ken Leung",slug:"ken-leung",email:"cfleung@cuhk.edu.hk",position:null,institution:null},{id:"120959",title:"PhD.",name:"Yi-Xiang",middleName:null,surname:"Wang",fullName:"Yi-Xiang Wang",slug:"yi-xiang-wang",email:"yixiang_wang@cuhk.edu.hk",position:null,institution:{name:"Chinese University of Hong Kong",institutionURL:null,country:{name:"China"}}}],sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Approach",level:"1"},{id:"sec_2_2",title:"2.1. Synthesis of the nanostructures",level:"2"},{id:"sec_3_2",title:"2.2. Characterization of the nanostructures",level:"2"},{id:"sec_4_2",title:"2.3. Magnetic resonance imaging",level:"2"},{id:"sec_6",title:"3. 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Center of Novel Functional Molecules, Department of Chemistry and Department of Diagnostic Radiology and Organ Imaging, Prince of Wales Hospital The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, P. R. China
'},{corresp:null,contributorFullName:"J. Wang Yi-Xiang",address:null,affiliation:'
Center of Novel Functional Molecules, Department of Chemistry and Department of Diagnostic Radiology and Organ Imaging, Prince of Wales Hospital The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, P. R. China
'}],corrections:null},book:{id:"3156",title:"Nanowires",subtitle:"Science and Technology",fullTitle:"Nanowires Science and Technology",slug:"nanowires-science-and-technology",publishedDate:"February 1st 2010",bookSignature:"Nicoleta Lupu",coverURL:"https://cdn.intechopen.com/books/images_new/3156.jpg",licenceType:"CC BY-NC-SA 3.0",editedByType:"Edited by",editors:[{id:"6995",title:"Dr.",name:"Nicoleta",middleName:null,surname:"Lupu",slug:"nicoleta-lupu",fullName:"Nicoleta Lupu"}],productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"},chapters:[{id:"8883",title:"Nickel Silicide Nanowire Growth and Applications",slug:"nickel-silicide-nanowire-growth-and-applications",totalDownloads:5075,totalCrossrefCites:1,signatures:"Joondong Kim",authors:[{id:"7322",title:"Dr.",name:"Joondong",middleName:null,surname:"Kim",fullName:"Joondong Kim",slug:"joondong-kim"}]},{id:"8884",title:"Syntheses of Silver Nanowires in Liquid Phase",slug:"syntheses-of-silver-nanowires-in-liquid-phase",totalDownloads:14243,totalCrossrefCites:8,signatures:"Xinling Tang and Masaharu Tsuji",authors:[{id:"8684",title:"Prof.",name:"Masaharu",middleName:null,surname:"Tsuji",fullName:"Masaharu Tsuji",slug:"masaharu-tsuji"}]},{id:"8885",title:"Growth of Nanowire and Nanobelt Based Oxides by Thermal Oxidation with Gallium",slug:"growth-of-nanowire-and-nanobelt-based-oxides-by-thermal-oxidation-with-gallium",totalDownloads:4084,totalCrossrefCites:2,signatures:"Qing Yang, Takahito Yasuda, Hitonori Kukino, Miyoko Tanaka and Hirokazu Tatsuoka",authors:[{id:"7615",title:"Professor",name:"Hirokazu",middleName:null,surname:"Tatsuoka",fullName:"Hirokazu Tatsuoka",slug:"hirokazu-tatsuoka"},{id:"26060",title:"Prof.",name:"Qing",middleName:null,surname:"Yang",fullName:"Qing Yang",slug:"qing-yang"},{id:"120913",title:"Prof.",name:"Miyoko",middleName:null,surname:"Tanaka",fullName:"Miyoko Tanaka",slug:"miyoko-tanaka"}]},{id:"8886",title:"Nano-Cones Formed on a Surface of Semiconductors by Laser Radiation: Technology, Model and Properties",slug:"nano-cones-formed-on-a-surface-of-semiconductors-by-laser-radiation-technology-model-and-properties",totalDownloads:2856,totalCrossrefCites:1,signatures:"Artur Medvid’",authors:[{id:"7220",title:"Prof.",name:"Artur",middleName:null,surname:"Medvid'",fullName:"Artur Medvid'",slug:"artur-medvid'"}]},{id:"8887",title:"Magnetic Properties of Nanowires guided by Carbon Nanotubes",slug:"magnetic-properties-of-nanowires-guided-by-carbon-nanotubes",totalDownloads:3767,totalCrossrefCites:0,signatures:"Miguel A. 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Zoloff Michoff, Patricio Vélez, Sergio A. Dassie and Ezequiel P. M. Leiva",authors:[{id:"7474",title:"Prof.",name:"Ezequiel",middleName:null,surname:"Leiva",fullName:"Ezequiel Leiva",slug:"ezequiel-leiva"},{id:"7475",title:"Dr.",name:"Martin",middleName:"Eduardo",surname:"Zoloff Michoff",fullName:"Martin Zoloff Michoff",slug:"martin-zoloff-michoff"},{id:"121000",title:"Prof.",name:"Patricio",middleName:null,surname:"Velez",fullName:"Patricio Velez",slug:"patricio-velez"},{id:"121004",title:"Prof.",name:"Sergio Alberto",middleName:null,surname:"Dassie",fullName:"Sergio Alberto Dassie",slug:"sergio-alberto-dassie"}]},{id:"8905",title:"Modelling Metallic Nanowires Breakage for Statistical Studies: Ni Case as Example",slug:"modelling-metallic-nanowires-breakage-for-statistical-studies-ni-case-as-example",signatures:"Samuel Peláez, Carlo Guerrero, Ricardo Paredes, Pedro A. 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C. Bell, D. T. Zimmerman, and N. M. Wereley",authors:[{id:"121029",title:"Dr.",name:"Richard C.",middleName:null,surname:"Bell",fullName:"Richard C. Bell",slug:"richard-c.-bell"},{id:"121030",title:"Prof.",name:"D. T.",middleName:null,surname:"Zimmerman",fullName:"D. T. Zimmerman",slug:"d.-t.-zimmerman"},{id:"121033",title:"Dr.",name:"Norman M.",middleName:null,surname:"Wereley",fullName:"Norman M. Wereley",slug:"norman-m.-wereley"}]},{id:"8912",title:"The Applications of Metallic Nanowires for Live Cell Studies",slug:"the-applications-of-metallic-nanowires-for-live-cell-studies",signatures:"Chiung-Wen Kuo and Peilin Chen",authors:[{id:"7620",title:"Dr.",name:"Peilin",middleName:null,surname:"Chen",fullName:"Peilin Chen",slug:"peilin-chen"},{id:"121034",title:"Prof.",name:"Chiung-Wen",middleName:null,surname:"Kuo",fullName:"Chiung-Wen Kuo",slug:"chiung-wen-kuo"}]}]}]},onlineFirst:{chapter:{type:"chapter",id:"73614",title:"Epigenetic Studies of Atopic Dermatitis",doi:"10.5772/intechopen.94092",slug:"epigenetic-studies-of-atopic-dermatitis",body:'\n
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1. Introduction
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Atopic dermatitis (AD) is a chronic recurrent inflammation of the skin, characterized by impairment of the epidermal barrier that entailing its further dysfunction. The predisposition to IgE-mediated hypertension contributes to such a malfunction, realized in sensitization to surrounding allergens. [1] This pathology is also characterized by infiltration and accumulation of type 2 T helper cells (Th2) and eosinophils. [2] Atopic dermatitis is a multifactorial disease. The main triggers are various genetically predetermined defects of the epidermal barrier and the immune system influenced by environment [1].
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Thus, the study of tissues and cells transcriptome involved in the pathogenesis of the disease is one of the best options for detecting molecular signs of complex diseases such as AD. [3] In one of these studies, it was found that the expression of a large number of genes which were responsible for terminal differentiation of keratinocytes was reduced in case of AD compared with healthy controls. These genes include filaggrin (FLG), loricrin (LOR), involucrin, late cornified envelope protein LCE2B, and genes encoding the S100 family of proteins. [4] This study showed that AD is associated with impaired keratinization processes in the epidermis, and confirmed another profile study by Sugiura et al., where suppression of LOR and FLG expression was determined in the lesional skin. [5] With the help of RNA sequencing technology by which transcriptomes of intact and damaged skin of patients with moderate and severe AD were compared, an increased expression of the TREM-1 signaling pathway, as well as IL-36, was revealed. [6] The laser capture microdissection method once again confirmed that the expression of genes encoding skin barrier proteins, including FLG, LOR, CLDN4 and CLDN8, is reduced in affected atopic skin; and, on the contrary, the expression of cytokines Th2 and Th17 genes, such as CCL22, CCL26, TSLP, and IL-22 etc., is increased [7].
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Loss of function mutations in the gene encoding FLG are one of the most significant genetic risk factors for AD. A transcriptome profiling study realized by RNA sequencing revealed differentially expressed genes involved in the extracellular reactions, lipid metabolism, and stress response. In FLG-deficient skin, the stress response mediated by type I interferon (IFN) was expressed [8].
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However, genetic changes solely do not fully shed light on the molecular mechanisms involved in the pathogenesis of AD. Therefore, epigenetic mechanisms involved in the genomic adaptation according to environmental conditions may possibly explain how environmental exposure affects the risk of allergy development.
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Epigenetic mechanisms, in particular methylation, play a key role in immune regulation and are influenced by a variety of environmental factors leading to persistent molecular changes in genes. The methylation process involves the addition of a methyl group to the cytosine (C5 position; 5-methylcytosine, 5mC). DNA methylation occurs primarily in the context of CpG dinucleotides and is the main epigenetic modification involved in the regulation of chromatin structure and gene expression [9].
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2. Targeted methylation studies
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2.1 DNA methyltransferase studies
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The main enzymes responsible for the methylation process in humans are DNA methyltransferases 1, 3a, and 3b (DNMT1, DNMT3a, and DNMT3b). It is generally accepted that DNMT3a and DNMT3b are de novo methyltransferases that form a model of DNA methylation at early stages of development, as well as its changes during cell differentiation. [10] DNA methyltransferase 1 (DNMT1) maintains the methylated state of DNA by attaching methyl groups to one of the DNA strands at the sites where the other complementary strand is methylated [9].
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In the context of the AD study, only DNA methyltransferase-1 (DNMT-1), an enzyme that catalyzes the methylation of cytosine bases in CpG islands, has so far been considered. Nakamura et al. for the first time carried out an indirect assessment of methylation status in patients with atopic dermatitis by measuring the expression of messenger RNA (mRNA) of DNA methyltransferase-1 in peripheral blood mononuclear cells (PBMC) by quantitative RT-PCR. Although the expression level of DNMT-1 mRNA had a tendency to decrease in patients with atopic dermatitis compared with healthy controls, there were no significant differences between these groups. [11] However, in the group of patients with AD, the IgE level was also taken into account. It was found that the level of DNMT-1 mRNA was significantly lower in the high IgE group compared to the control group.
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It is common knowledge that many local factors, such as skin impairment, play an important role in the development of AD. [12, 13] However, Th2-infiltration in response to penetration of allergens and production of cytokines by infiltrated cells (for example, IL-4 and IL-5) plays the key role in the development of IgE-mediated response and chronic inflammation involving eosinophils. [14, 15, 16] It is assumed that in these processes DNA hypomethylation contributes to the hyperreactivity of Th2 cells in response to allergens and, as a consequence, cytokine-mediated IgE production. It has also been suggested that IL-4-mediated IgE production in patients with high serum IgE levels is associated with DNA hypomethylation in B cells. [16, 17] In this study the decrease in DNMT-1 expression in PBMCs in patients with high IgE levels also confirmed the concept that AD is promoted by lower DNMT-1 levels.
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On the other hand, the lack of significant differences while comparing DNMT-1 expression between groups with high and low IgE levels, along with no correlation between DNMT-1 expression and serum IgE levels in the respective patients, indicates that DNMT-1 cannot be a factor that solely affects serum IgE. To clarify this issue, more studies are needed in which DMNT-1 levels would be assessed in patients without AD but with high serum IgE levels.
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2.2 \nFCER1G\n methylation studies
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Based on the opinion that overexpression of the high-affinity IgE receptor on monocytes and dendritic cells contributes to the pathogenesis of AD, a group of scientists studied the epigenetic mechanism of deregulation of high-affinity IgE receptors – FcεRI [18].
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Liang et al. measured the methylation level of total DNA of monocytes from 10 patients with AD and 10 healthy people from the control group. Bisulfite sequencing was used as the main method to determine the methylation status of the FCER1G promoter region. To determine the functional significance of methylation changes in FcεRI expression, targeted methylation of the sequence and a demethylating agent, 5-azacytidine (5-aza), were used. The levels of FcεRIγ mRNA and FcεRI protein were determined using RT-PCR RT, Western blotting, and flow cytometry, respectively.
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Thus, total hypomethylation in CD14+ monocytes in patients with AD was revealed, as well as locus-specific hypomethylation of the FCER1G promoter region in comparison with healthy controls. In addition, hypomethylation of FCER1G contributed to its increased expression. Targeted methylation in combination with a reporter luciferase assay confirmed this association between methylation and expression. Moreover, treatment of monocytes of healthy people with 5-azacytidine caused a decrease in methylation levels and induction of FcεRIγ transcription and expression of surface FcεRI. The authors showed that demethylation of specific regulatory elements at the FCER1G locus promotes an increase in FcεRI expression in monocytes in patients with AD, which, in turn, leads to an enhanced allergic response.
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Atopic monocytes with high FcεRI levels are thought to play an important role in the pathogenesis of AD. This is due to the fact that monocytes carrying FcεRI can differentiate into inflammatory dendritic epidermal cells (IDECs), which intensify allergic inflammatory reactions in the skin by stimulating T cells, and are also involved in the transition to the chronic course of AD with a predominance of Th2. [19, 20] In this study, it was shown for the first time that changes in the epigenetic regulation of the FCER1G gene can explain the pathological activation of FcεRI on patient monocytes.
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2.3 \nTSLP methylation studies\n
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Thymic stromal lymphopoietin (TSLP) plays an important role in maintaining T-cell homeostasis and, apparently, is of great importance in the development of allergic symptoms, especially in atopic dermatitis and asthma. [21, 22] Human TSLP is overexpressed in keratinocytes of patients with acute and chronic AD. However, the mechanism of such TSLP expression remains unclear. The question is whether TSLP expression is regulated by modification of aberrant DNA methylation of TSLP promoter in keratinocytes of AD patients [23].
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It is known that the TSLP protein cannot be found in healthy skin, in skin lesions in patients with nickel contact dermatitis or in patients with disseminated lupus erythematosus, as well as in intact skin in patients with AD; however, increased levels of TSLP expression are observed in both acute and chronic atopic skin lesions. [21, 24] TSLP overexpression in keratinocytes can activate myeloid dendritic cells by enhancing the surface expression of CD54, CD80, CD83, CD86 molecules and MHC class II molecules on myeloid dendritic cells [25], which lead to Th2-inflammatory reactions [24].
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Luo et al. measured the levels of mRNA and TSLP protein in samples of affected skin from 10 atopic children and 10 healthy people from the control group, using quantitative RT-PCR and immunohistochemistry. [26] Bisulfite sequencing was performed to determine the methylation status of the TSLP promoter; 5-aza, a DNA methyltransferase inhibitor, was used to determine the effect of DNA methylation on TSLP expression.
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As a result, the levels of expression of mRNA and TSLP protein relative to β-actin were significantly higher in affected skin regions of patients with AD compared with healthy controls. In addition, hypomethylation of the promoter region of the TSLP gene containing 16 CG pairs was found in the affected skin regions. Upon treatment of HaCaT cell line keratinocytes with 5-aza, the methylation level of the TSLP promoter decreased significantly, while its transcription increased.
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It can be concluded that DNA demethylation of the specific regulatory region of the TSLP gene may contribute to the overexpression of TSLP in the affected skin regions in atopic patients. This suggests that aberrant epigenetic modifications play an important role in the pathogenesis of this disease.
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In another study, the authors tried to reveal the effect of prenatal smoking on DNA methylation in case of atopic disorders. [27] Methylation differences associated with exposure to tobacco smoke were initially identified with the use of Illumina Infinium 27 K methylation kits in 14 children in a Taiwanese study cohort. Information on the course of the disease and possible risk factors was collected. Cord blood levels of cotinine were measured in order to represent prenatal smoking. CpG loci, in which statistically significant differences in methylation were found, were validated by methylation-dependent fragment separation (MDFS). Differential methylation in three genes (TSLP, GSTT1, and CYB5R3) was detected during the experiment. Among these, only the TSLP gene showed a significant difference in the percentage of promoter methylation after testing with MDFS. The TSLP gene was further investigated in a larger sample group (150 children) which completed a follow-up study. The TSLP 5’-CpG island (5’CGI) methylation status has been found to be significantly associated with prenatal exposure to smoke and atopic dermatitis. The degree of the TSLP 5’CGI methylation was inversely correlated with the expression levels of the TSLP protein.
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Thus, it can be assumed that changes in TSLP 5’CGI methylation decrease the regulatory function of the immune system and cause the development of Th2-type allergic inflammation in case of atopic dermatitis. The methylation status of TSLP 5’CGI was also found to differ depending on cotinine levels, and hypomethylated TSLP 5’CGI was positively associated with atopic dermatitis. Moreover, the degree of TSLP 5’CGI methylation and the level of TSLP protein showed an inverse correlation. This means that severe exposure to smoke can lead to TSLP 5’CGI hypomethylation. Therefore, hypomethylated TSLP 5’CGI is associated with increased gene expression and increased TSLP protein concentration. An increased level of TSLP protein may also activate Langerhans epidermal cells, contributing to the AD development. TSLP was also highly expressed in the lesional skin of atopic patients [24].
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The results of Wang et al. study suggest that prenatal exposure to tobacco smoke is associated with a risk of atopic dermatitis, possibly through DNA methylation.
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2.4 \nMICAL3\n methylation studies
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Cho et al. conducted a research to assess the role of 25-hydroxyvitamin D (25[OH]D) deficiency in cord blood in comparison with postnatal 25[OH]D levels in AD development during the first 3 years of life and found out how 25[OH]D deficiency affects the DNA methylation profile of cord blood leukocytes. [28]
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Severe 25[OH]D deficiency in cord blood was associated with a higher risk of atopic dermatitis diagnosing precisely at the age from 2 to 3. Comparison of differentially methylated CpG sites in accordance with moderate and insufficient 25[OH]D levels in cord blood revealed the common MICAL3 gene for groups with and without pathology. MICAL3 was hypomethylated in the case of low 25[OH]D levels.
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Since MICAL3 is a member of the MICAL family of flavoprotein monooxygenases involved in axon control and actin remodeling through oxidation of its molecules or production of reactive oxygen species (ROS) [29], ROS, induced by increased expression of MICAL3, can then suppress the antioxidant defense of the fetus, leading to subsequent AD development during the first 3 years of life. This process probably also affects the severity of the disease, since a correlation has been established between the expression of MICAL3 mRNA and the severity index of atopic dermatitis. In addition, MICAL3 expression levels were associated with 25[OH]D levels in cord blood regardless of the presence of AD.
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To reproduce the mechanism of atopic dermatitis associated with ROS, using the example of MICAL3, another gene was chosen, 8-oxoguanine-DNA glycosylase (OGG1), which, as is known from data on mRNA expression, contributes to the development of allergic diseases in combination with oxidative stress reactions. [30] Accordingly, in atopic children with 25[OH]D deficiency in cord blood, the expression of OGG1 mRNA was 5.22 times higher than in healthy children with a sufficient level of 25[OH]D. OGG1 expression levels were found to be inversely related to 25[OH]D levels and atopic dermatitis severity index. In addition, there is a significant correlation between the expression levels of MICAL3 and OGG1. However, studies showing that MICAL3 and OGG1 are directly related have not yet been conducted.
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2.5 \nHBD-1\n methylation studies
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Noh et al. described patterns of DNA methylation of human β-defensin-1 (HBD-1), a unique antimicrobial peptide expressed in various tissues, including the skin. [31] HBD-1 may be associated with a variety of innate immune system defects in the AD pathogenesis. A possible mechanism for the decrease in HBD-1 gene expression in atopic dermatitis was investigated, and the HBD-1 transcription restoration in undifferentiated normal epidermal keratinocytes after treatment with a DNA methyltransferase inhibitor was shown.
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Suppression of HBD-1 in undifferentiated NHEK cells has been shown to be regulated by an epigenetic inactivation mechanism involving methylation of DNA 14 CpG dinucleotide in the 5′-region of HBD-1. In dermatitis-affected skin, the frequency of methylation at the CpG 3 and CpG 4 sites within the HBD-1 promoter was significantly higher than in healthy skin.
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To identify specific CpG sites that play a significant role in HBD-1 expression in NHEK cells, bisulfite genomic sequencing of the region upstream of the proximal site of the HBD-1 promoter was performed and methylation profiles of 6 CpG dinucleotides (from CpG 3 to CpG 8) were determined. Since the single nucleotide polymorphism (rs2978863) is located at the CpG 8 locus within the HBD-1 promoter region (GenBank accession no. NC_000008.11) in the NHEK cell line, the other five CpG dinucleotides (CpG 3–7) were subjected to bisulfite sequencing analysis. Studying the methylation profile of the HBD-1 promoter revealed detectable demethylation at the CpG 3 and CpG 4 loci in 2-deoxy-5-azacytidine-treated NHEK cells compared with untreated control cells. Such differentially methylated single CpG units in the HBD-1 promoter may play a special role in the regulation of HBD-1 transcription of the NHEK cell line.
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Thus, epigenetic modulation of the HBD-1 promoter, that is, DNA methylation in two separate CpG units, can affect HBD-1 expression in vitro. In the affected skin, both CpG sites were hypermethylated. The failure of skin innate immunity leading to increased colonization of S. aureus in atopic patients may be due to an epigenetic predisposition of constitutively expressed HBD-1.
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3. Genome-wide DNA methylation
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3.1 In naive CD4+\n
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Both atopic dermatitis and psoriasis are characterized by a targeted immune response via polarized CD4+ T cells. During the polarization of naive CD4+ T cells, DNA methylation plays an important role in the regulation of gene transcription. Taken into consideration the similarity of immune response of atopic dermatitis and psoriasis, Han et al. conducted a study of the global DNA methylation profile in naive CD4+ T cells in patients with AD and psoriasis, as well as in healthy people using the ChIP-seq method. DNA hypomethylation (more than 4 times) was found in T-cell samples isolated from patients with psoriasis and healthy people in 26 genome sites ranging in size from 10 to 70 kb. These regions were mostly pericentromeric on 10 different chromosomes and randomly overlaid with various defining epigenome signals, such as histone modifications and binding sites for transcription factors (according to the ENCODE project), which implied the potential influence of epigenetic regulation in the development of psoriasis [32].
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To determine whether naive CD4+ T cells from patients with AD or psoriasis have DNA methylation patterns different from those of healthy people, complex genome-wide CpG methylation profiling was performed. The uniquely mapped regions coincided with strong histone modification signals such as H3K4Me1, H3K27Ac, and H3K4Me3, as well as with transcription factor binding sites in various cell lines.
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It appears that hypomethylation in some pericentromeric regions of naive CD4+ T cells may be a sign of psoriasis, but not atopic dermatitis. It is not yet clear what exact role epigenetic changes of these regions play in the development of T cells. However, these data show for the first time the importance of such changes in the development of immune-mediated skin diseases [33].
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The X chromosome encodes many of immune genes, which show a higher hypermethylation pattern than other genes. It is known that abnormalities, such as inactivation of the X chromosome, can contribute to the impairment of self-structures recognition and, ultimately, lead to autoimmunity. [34] In addition, DNA methylation is involved in the initiation of the X chromosome inactivation, as well as in the stable maintenance of the gene silencing state. [35] These studies suggest that DNA methylation may affect gene expression on the X chromosome or the development of T cells in psoriasis. It was found that DNA methylation is dramatically increased in the promoter region of genes on the X chromosome in patients with psoriasis. The binding sites for CDPCR3, GATA3, BRN2, and other transcription factors were identified as slightly enriched. The data obtained on epigenome changes in T cells show that naive CD4+ T cells may be involved in the development of atopic dermatitis or psoriasis even before antigenic stimulation. This may be due to the effects of various environmental factors.
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3.2 Tissue-specific patterns
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To determine the tissue-specific differences in DNA methylation associated with AD, the research group of Rodriguez et al. examined the DNA of whole blood, T cells, B cells, as well as the affected and unaffected epidermis of atopic patients and healthy people from the control group. [36] To identify functional associations, they studied the expression profiles of epidermal mRNA.
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Whole-genome methylation analysis was performed using Human Methylation27 BeadCheap. The results for epidermal tissue were different from those for blood cells. To determine the intraindividual and interindividual differences in DNA methylation, the researchers identified a pairwise correlation of methylated regions in the same tissue in samples from patients of similar sex and age, as well as between different tissues in the same person. In whole blood, T cells, and B cells, there were no significant differences in genome DNA methylation in the pathology group as compared with and the control group, and in general, intraindividual differences in DNA methylation were greater than those between individuals. A clear link was shown in case of comparing similar tissue in different individuals for different CpG sites, which partially correlated with altered levels of gene transcripts, mainly related to the processes of epidermal differentiation (S100A genes) and reactions of the innate immune response - thus, this study confirms the high the level of tissue specificity for DNA methylation patterns.
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Regarding differentially methylated CpG islands in the epidermal tissue, 9 regions were identified as reliably associated with atopic dermatitis: in the CFLAR, GPR55, MMP7, LOC283487, SH2D2A, and ERP27 genes, these regions were hypomethylated, and in the LRRC8C, S100A5, and EBP49 genes, these regions were hypermethylated.
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Based on analysis of whole genome mRNA expression (using HumanHT-12v3 Expression BeadChip), significant differences were revealed in seven transcripts when comparing samples of the affected skin of patients with AD and the skin of healthy people.
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From nine selected pairs of differentially methylated regions / differentially expressed transcripts using the EpiTYPER system and quantitative PCR, the following combinations associated with the development of AD were successfully validated: KRT6A/KRT6A and KRT6A/KRT6B (encode keratin); IFI27/IFI27, OAS2/OAS2 (belong to the family of proteins regulated by IFN), GDPD3/GDPD3 and S100A5/S100A2. In most of these pairs, an inverse correlation was observed, that is, higher levels of methylation were associated with lower expression of the relevant gene, and vice versa. Such dependence is usually observed in CpG islands near the sites of transcription initiation, where DNA methylation is associated with prolonged silencing of the relevant gene.
\n
Olisova et al. carried out a genome-wide study of DNA methylation using the Illumina Infinium Human Methylation450 BeadChip technology. [37] When comparing the affected and unaffected skin areas in atopic patients, no difference in the methylation profile was found. This suggests that epigenetic changes affected the entire skin as a whole, although they have not yet appeared in clinically intact skin areas. However, when comparing the affected skin with the skin of healthy volunteers, differentially methylated genes of the TSS200 and TSS1500 regions were isolated, whose protein products were involved in the pathogenesis of atopic dermatitis and related processes: steroid hormone biosynthesis and cell metabolism (HSD17B14, HSD17B), epithelial differentiation (KRT31, LCE3D), regulation of DNA-dependent transcription and RNA processing (DMBX1, MTO1, SNORD93, WDR36), immune response and activation of lymphocytes (AIM2, CD300E, CLEC1A, DEFB135, IL23A), activation of transforming growth factor β1 (LTBP1), cellular proliferation and apoptosis (SERPINB3, EPR1).
\n
\n
\n
3.3 Replicated methylation
\n
Another genome-wide epigenetic study examined differences in DNA methylation in atopic dermatitis together with herpetic eczema (HE), and revealed how methylation changes in patients with atopic dermatitis, complicated or uncomplicated HE. [38]
\n
490 significantly differentially methylated CpG sites were identified. Many of these were associated with indicators of disease severity, especially with the level of eosinophils (431/490 sites). One CpG region was replicated and was significantly differentially methylated based severity and phenotype.
\n
The authors found replication for one CpG region associated with total serum IgE in the IL4 gene, as well as possible replication for four CpG regions associated with HE in the IL13 and IL4 genes. It has also been shown that eosinophil levels play an important role in methylation patterns in people with AD, which via molecular mechanisms can lead to phenotypic changes.
\n
\n
\n
\n
4. Epigenetic regulation of immune system factors
\n
It is known that abnormal epigenetic regulation of immune factors and skin barriers contribute to the pathogenesis of AD. During the development of immune system cells, epigenetic mechanisms are involved in specific changes in the variants of immune response. [39] Here are some examples.
\n
Regulatory T cells (Tregs) play an important role in early immune programming and the formation of an adequate immune response in relation to pro-allergic or tolerant conditions. Tregs are best characterized by the expression of transcription factor 3 (Foxp3), which is important for the induction and stability of Tregs. [40] Foxp3 is controlled by DNA methylation of its transcriptional regulatory regions. Naturally induced by TGF-β Foxp3+ Tregs indicate stable expression of Foxp3, which is associated with selective demethylation of an evolutionarily conserved element at the Foxp3 locus - a Treg-specific demethylated region. Inhibition of DNA methylation by azacytidine, even in the absence of exogenous TGF-β, not only promotes induction of Foxp3 expression de novo during priming, but also ensures stability of Foxp3 expression upon restimulation. Importantly, stable Foxp3 expression was detected only in cells with an increased level of TSDR demethylation. [41] Research suggests that prenatal environmental factors can alter DNA methylation at the FOXP3 locus in cord blood. Babies with low Tregs identified by TSDR demethylation at birth may have a higher risk of AD developing or sensitization to food allergens in the first 3 years of life [42].
\n
In the neonatal immune system, epigenetic regulation can be shifted away from Th1-mediated immunity in order to prevent dangerous cellular immune responses to the developing fetus. The IFN-γ gene (IFNG), a prototype Th1 cytokine gene whose activity is regulated during fetal development, is hypermethylated in the promoter regions of resting neonatal CD4+ cells compared to adult ones. [43] Similarly, the availability of chromatin at the TBX21 locus, a major regulator of Th1 clone committing, is attenuated in neonatal CD4+ cells compared to mature cells, and a decrease of transcription factor level in peripheral T cells suppresses IFN-γ production. [44] After birth, exposure to a variety of microorganisms and the formation of microbiota contributes to the essential activation of Th1 immune responses through epigenetic modifications. In a mouse model it was shown that prenatal administration of gram-negative bacteria leads to histone H4 acetylation at the IFNG gene and the associated increase in IFN-γ production in the offspring [45].
\n
MicroRNAs (miRNAs) are short, single-stranded RNA molecules that function with their associated proteins and cause the degradation of targeted mRNAs, inhibiting their translation. miRNAs play an important role in a wide range of biological processes, including proliferation, differentiation, determination of cell development, apoptosis, signal transduction, and organ development. Some miRNAs are expressed specifically for each type of cells and tissues and contribute to the maintenance of cell identity. Tissue-specific miRNAs function at various levels of gene regulation, ranging from control of targeted effector genes, incompatible with the differentiated state, to control over the levels of transcriptional regulators and alternative pre-mRNA splicing. This multilevel regulation of miRNAs influences the gene expression program of differentiated cells. [46] miRNAs, including miR-21, miR-146, and miR-223, activated in patients with allergic disorders, are also activated in the skin of patients with AD. [47] A study by Herberth et al. showed that maternal exposure to tobacco during pregnancy correlated with high levels of miRNA-223 and low Treg cell levels, which predisposed children to atopic dermatitis during the first 3 years of life. [48] Sonkoly et al. found that miR-155 was one of the most activated miRNAs in lesional skin samples from atopic patients in comparison with skin samples from healthy people. It has been found that local exposure of relevant allergens to intact skin of patients with AD induces miR-155 expression. miR-155 suppresses cytotoxic T lymphocyte – associated protein 4 - CTLA-4, which negatively regulates the function of T cells. This suppression of CTLA-4, in turn, enhances the T cell proliferative response, which can then lead to a long-term chronic inflammatory state [47].
\n
\n
\n
5. Conclusion
\n
There is not much evidence on the role of epigenetic mechanisms of innate and adaptive immunity regulation in the pathogenesis of atopic diseases, as these mechanisms have been studied recently. The described candidate genes involved in pathological processes such as dysfunction of the epidermal barrier, enhanced transmission of Th2 immunity signals, weakened innate immune responses, etc. play an important role in the pathogenesis of AD. Epigenetic studies also indicate modifications in genes involved in these mechanisms. Dysfunction of the epithelial barrier and immune response reactions together trigger the development of atopic dermatitis.
\n
New insights on epigenetic and immunological markers associated with the risk of development of atopic dermatitis will help to create new prognostic approaches in the management of patients with atopic pathology. In this regard, it is important to have a complete understanding of the pathogenic mechanisms of an allergic disease.
\n
\n
Conflict of interest
The authors declare no conflict of interest.
\n',keywords:"atopic dermatitis, epigenetics, DNA methylation, genome-wide methylation analysis, immune system",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/73614.pdf",chapterXML:"https://mts.intechopen.com/source/xml/73614.xml",downloadPdfUrl:"/chapter/pdf-download/73614",previewPdfUrl:"/chapter/pdf-preview/73614",totalDownloads:64,totalViews:0,totalCrossrefCites:0,dateSubmitted:"July 8th 2020",dateReviewed:"September 18th 2020",datePrePublished:"November 23rd 2020",datePublished:null,dateFinished:"October 14th 2020",readingETA:"0",abstract:"Since the pathogenesis of atopic dermatitis could not be explained only by a population genetic and phenotypic profiles, epigenetic regulator factors have been considered. Epigenetics is the study of inherited changes in gene expression that are not related to changes in its nucleotide sequence. One of the main classical regulatory mechanisms in human cells is DNA methylation. It is not clear how permanent modifications caused by this process are and whether it is possible to affect them by changing the activity of enzymes that trigger remodeling reactions. In this chapter we analyze all recent studies in this field. We focus more on methylation of innate and adaptive immune factors, with an emphasis on T-lymphocyte genes such as CD3, CD4, and CD8.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/73614",risUrl:"/chapter/ris/73614",signatures:"Vladimir Sobolev, Elizaveta Bystritskaya and Oxana Svitich",book:{id:"10306",title:"Atopic Dermatitis - Essential Issues",subtitle:null,fullTitle:"Atopic Dermatitis - Essential Issues",slug:null,publishedDate:null,bookSignature:"Prof. Celso Pereira",coverURL:"https://cdn.intechopen.com/books/images_new/10306.jpg",licenceType:"CC BY 3.0",editedByType:null,editors:[{id:"66336",title:"Prof.",name:"Celso",middleName:null,surname:"Pereira",slug:"celso-pereira",fullName:"Celso Pereira"}],productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"}},authors:null,sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Targeted methylation studies",level:"1"},{id:"sec_2_2",title:"2.1 DNA methyltransferase studies",level:"2"},{id:"sec_3_2",title:"2.2 \nFCER1G\n methylation studies",level:"2"},{id:"sec_4_2",title:"2.3 \nTSLP methylation studies\n",level:"2"},{id:"sec_5_2",title:"2.4 \nMICAL3\n methylation studies",level:"2"},{id:"sec_6_2",title:"2.5 \nHBD-1\n methylation studies",level:"2"},{id:"sec_8",title:"3. Genome-wide DNA methylation",level:"1"},{id:"sec_8_2",title:"3.1 In naive CD4+\n",level:"2"},{id:"sec_9_2",title:"3.2 Tissue-specific patterns",level:"2"},{id:"sec_10_2",title:"3.3 Replicated methylation",level:"2"},{id:"sec_12",title:"4. Epigenetic regulation of immune system factors",level:"1"},{id:"sec_13",title:"5. Conclusion",level:"1"},{id:"sec_17",title:"Conflict of interest",level:"1"}],chapterReferences:[{id:"B1",body:'\nMartin MJ, Estravís M, García-Sánchez A, et al. Genetics and Epigenetics of Atopic Dermatitis: An Updated Systematic Review. 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The X chromosome in immune functions: when a chromosome makes the difference. Nat Rev Immunol 2010; 10: 594-604.\n'},{id:"B35",body:'\nKaslow DC, Migeon BR. DNA methylation stabilizes X chromosome inactivation in eutherians but not in marsupials: evidence for multistep maintenance of mammalian X dosage compensation. Proceedings of the National Academy of Sciences 1987; 84: 6210-6214.\n'},{id:"B36",body:'\nRodríguez E, Baurecht H, Wahn AF, et al. An Integrated Epigenetic and Transcriptomic Analysis Reveals Distinct Tissue-Specific Patterns of DNA Methylation Associated with Atopic Dermatitis. Journal of Investigative Dermatology 2014; 134: 1873-1883.\n'},{id:"B37",body:'\nOlisova OYu, Kochergin NG, Kayumova LN, et al. Skin DNA methylation profile in atopic dermatitis patients: A case–control study. Exp Dermatol 2020; 29: 184-189.\n'},{id:"B38",body:'\nBoorgula MP, Taub MA, Rafaels N, et al. Replicated methylation changes associated with eczema herpeticum and allergic response. Clin Epigenet 2019; 11: 122.\n'},{id:"B39",body:'\nLiang Y, Chang C, Lu Q. The Genetics and Epigenetics of Atopic Dermatitis—Filaggrin and Other Polymorphisms. Clinic Rev Allerg Immunol 2016; 51: 315-328.\n'},{id:"B40",body:'\nFontenot JD, Rasmussen JP, Williams LM, et al. Regulatory T Cell Lineage Specification by the Forkhead Transcription Factor Foxp3. Immunity 2005; 22: 329-341.\n'},{id:"B41",body:'\nPolansky JK, Kretschmer K, Freyer J, et al. DNA methylation controls Foxp3 gene expression. Eur J Immunol 2008; 38: 1654-1663.\n'},{id:"B42",body:'\nHinz D, Bauer M, Röder S, et al. Cord blood Tregs with stable FOXP3 expression are influenced by prenatal environment and associated with atopic dermatitis at the age of one year. Allergy 2012; 67: 380-389.\n'},{id:"B43",body:'\nWhite GP, Watt PM, Holt BJ, et al. Differential Patterns of Methylation of the IFN-γ Promoter at CpG and Non-CpG Sites Underlie Differences in IFN-γ Gene Expression Between Human Neonatal and Adult CD45RO − T Cells. J Immunol 2002; 168: 2820-2827.\n'},{id:"B44",body:'\nKaminuma O, Kitamura F, Miyatake S, et al. T-box 21 transcription factor is responsible for distorted TH2 differentiation in human peripheral CD4+ T cells. Journal of Allergy and Clinical Immunology 2009; 123: 813-823.e3.\n'},{id:"B45",body:'\nBrand S, Teich R, Dicke T, et al. Epigenetic regulation in murine offspring as a novel mechanism for transmaternal asthma protection induced by microbes. Journal of Allergy and Clinical Immunology 2011; 128: 618-625.e7.\n'},{id:"B46",body:'\nMakeyev EV, Maniatis T. Multilevel Regulation of Gene Expression by MicroRNAs. Science 2008; 319: 1789-1790.\n'},{id:"B47",body:'\nSonkoly E, Janson P, Majuri M-L, et al. MiR-155 is overexpressed in patients with atopic dermatitis and modulates T-cell proliferative responses by targeting cytotoxic T lymphocyte–associated antigen 4. Journal of Allergy and Clinical Immunology 2010; 126: 581-589.e20.\n'},{id:"B48",body:'\nHerberth G, Bauer M, Gasch M, et al. Maternal and cord blood miR-223 expression associates with prenatal tobacco smoke exposure and low regulatory T-cell numbers. Journal of Allergy and Clinical Immunology 2014; 133: 543-550.e4.\n'}],footnotes:[],contributors:[{corresp:"yes",contributorFullName:"Vladimir Sobolev",address:"vlsobolew@gmail.com",affiliation:'
I. Mechnikov Research Institute for Vaccines and Sera, Russian Federation
Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Federation
I. Mechnikov Research Institute for Vaccines and Sera, Russian Federation
Sechenov University, Russian Federation
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BKCI is a part of Web of Science Core Collection (WoSCC) and the world’s leading citation index with multidisciplinary content from the top tier international and regional journals, conference proceedings, and books. The Book Citation Index includes over 104,500 editorially selected books, with 10,000 new books added each year. Containing more than 53.2 million cited references, coverage dates back from 2005 to present. The Book Citation Index is multidisciplinary, covering disciplines across the sciences, social sciences, and arts & humanities.
Produced by the Web Of Science group, BIOSIS Previews research database provides researchers with the most current sources of life sciences information, including journals, conferences, patents, books, review articles, and more. Researchers can also access multidisciplinary coverage via specialized indexing such as MeSH disease terms, CAS registry numbers, Sequence Databank Numbers and Major Concepts.
Produced by the Web Of Science group, Zoological Record is the world’s oldest continuing database of animal biology. It is considered the world’s leading taxonomic reference, and with coverage back to 1864, has long acted as the world’s unofficial register of animal names. The broad scope of coverage ranges from biodiversity and the environment to taxonomy and veterinary sciences.
Provides a simple way to search broadly for scholarly literature. Includes peer-reviewed papers, theses, books, abstracts and articles, from academic publishers, professsional societies, preprint repositories, universities and other scholarly organizations. Google Scholar sorts articles by weighing the full text of each article, the author, the publication in which the article appears, and how often the article has been cited in other scholarly literature, so that the most relevant results are returned on the first page.
Microsoft Academic is a project exploring how to assist human conducting scientific research by leveraging machine’s cognitive power in memory, computation, sensing, attention, and endurance. Re-launched in 2016, the tool features an entirely new data structure and search engine using semantic search technologies. The Academic Knowledge API offers information retrieval from the underlying database using REST endpoints for advanced research purposes.
The national library of the United Kingdom includes 150 million manuscripts, maps, newspapers, magazines, prints and drawings, music scores, and patents. Online catalogues, information and exhibitions can be found on its website. The library operates the world's largest document delivery service, providing millions of items a year to national and international customers.
The digital NSK portal is the central gathering place for the digital collections of the National and University Library (NSK) in Croatia. It was established in 2016 to provide access to the Library’s digital and digitized material collections regardless of storage location. The digital NSK portal enables a unified search of digitized material from the NSK Special Collections - books, visual material, maps and music material. From the end of 2019, all thematic portals are available independently: Digital Books, Digitized Manuscripts, Digitized Visual Materials, Digital Music Materials and Digitized Cartographic Materials (established in 2017). Currently available only in Croatian.
The official DOI (digital object identifier) link registration agency for scholarly and professional publications. Crossref operates a cross-publisher citation linking system that allows a researcher to click on a reference citation on one publisher’s platform and link directly to the cited content on another publisher’s platform, subject to the target publisher’s access control practices. This citation-linking network covers millions of articles and other content items from several hundred scholarly and professional publishers.
Dimensions is a next-generation linked research information system that makes it easier to find and access the most relevant information, analyze the academic and broader outcomes of research, and gather insights to inform future strategy. Dimensions delivers an array of search and discovery, analytical, and research management tools, all in a single platform. Developed in collaboration with over 100 leading research organizations around the world, it brings together over 128 million publications, grants, policy, data and metrics for the first time, enabling users to explore over 4 billion connections between them.
The primary aim of DOAB (Directory of Open Access Books) is to increase discoverability of Open Access books. Metadata will be harvestable in order to maximize dissemination, visibility and impact. Aggregators can integrate the records in their commercial services and libraries can integrate the directory into their online catalogues, helping scholars and students to discover the books.
OAPEN is dedicated to open access, peer-reviewed books. OAPEN operates two platforms, the OAPEN Library (www.oapen.org), a central repository for hosting and disseminating OA books, and the Directory of Open Access Books (DOAB, www.doabooks.org), a discovery service for OA books.
OpenAIRE aims at promoting and implementing the directives of the European Commission (EC) and the European Research Council on the promotion and funding of science and research. OpenAIRE supports the Open Access Mandate and the Open Research Data Pilot developed as part of the Horizon 2020 projects.
An integrated information service combining reference databases, subscription management, online journals, books and linking services. Widely used by libraries, schools, government institutions, medical institutions, corporations and others.
SFX® link resolver gives patrons and librarians a wealth of features that optimize management of and access to resources. It provides patrons with a direct route to electronic full-text records through OpenURL linking, delivers alternative links for further resource discovery, access to journals, and more. Released in 2001 as the first OpenURL resolver, SFX is continuously enhanced to support the newest industry developments and meet the evolving needs of customers. The records include a mix of scholarly material – primarily articles and e-books – but also conference proceedings, newspaper articles, and more.
A non-profit, membership, computer library service and research organization dedicated to the public purposes of furthering access to the world's information and reducing information costs. More than 41,555 libraries in 112 countries and territories around the world use OCLC services to locate, acquire, catalogue, lend and preserve library materials.
The world’s largest collection of open access research papers. CORE's mission is to aggregate all open access research outputs from repositories and journals worldwide and make them available to the public. In this way CORE facilitates free unrestricted access to research for all.
Perlego is a digital online library focusing on the delivery of academic, professional and non-fiction eBooks. It is a subscription-based service that offers users unlimited access to these texts for the duration of their subscription, however IntechOpen content integrated on the platform will always be available for free. They have been billed as “the Spotify for Textbooks” by the Evening Standard. Perlego is based in London but is available to users worldwide.
MyScienceWork provides a suite of data-driven solutions for research institutions, scientific publishers and private-sector R&D companies. MyScienceWork's comprehensive database includes more than 90 million scientific publications and 12 million patents.
CNKI (China National Knowledge Infrastructure) is a key national information construction project under the lead of Tsinghua University, and supported by PRC Ministry of Education, PRC Ministry of Science, Propaganda Department of the Communist Party of China and PRC General Administration of Press and Publication. CNKI has built a comprehensive China Integrated Knowledge Resources System, including journals, doctoral dissertations, masters' theses, proceedings, newspapers, yearbooks, statistical yearbooks, ebooks, patents, standards and so on. CNKI keeps integrating new contents and developing new products in 2 aspects: full-text academic resources, software on digitization and knowledge management. Began with academic journals, CNKI has become the largest and mostly-used academic online library in China.
As one of the largest digital content platform in China,independently developed by CNPIEC, CNPeReading positions herself as “One Platform,Vast Content, Global Services”. Through their new cooperation model and service philosophy, CNPeReading provides integrated promotion and marketing solutionsfor upstream publishers, one-stop, triune, recommendation, online reading and management servicesfor downstream institutions & libraries.
ERIC (Education Resources Information Center), sponsored by the Institute of Education Sciences (IES) of the U.S. Department of Education, provides access to education literature to support the use of educational research and information to improve practice in learning, teaching, educational decision-making, and research. The ERIC website is available to the public for searching more than one million citations going back to 1966.
The ACM Digital Library is a research, discovery and networking platform containing: The Full-Text Collection of all ACM publications, including journals, conference proceedings, technical magazines, newsletters and books. A collection of curated and hosted full-text publications from select publishers.
BASE (Bielefeld Academic Search Engine) is one of the world's most voluminous search sengines especially for academic web resources, e.g. journal articles, preprints, digital collections, images / videos or research data. BASE facilitates effective and targeted searches and retrieves high quality, academically relevant results. Other than search engines like Google or Bing BASE searches the deep web as well. The sources which are included in BASE are intellectually selected (by people from the BASE team) and reviewed. That's why data garbage and spam do not occur.
Zentralblatt MATH (zbMATH) is the world’s most comprehensive and longest-running abstracting and reviewing service in pure and applied mathematics. It is edited by the European Mathematical Society (EMS), the Heidelberg Academy of Sciences and Humanities and FIZ Karlsruhe. zbMATH provides easy access to bibliographic data, reviews and abstracts from all areas of pure mathematics as well as applications, in particular to natural sciences, computer science, economics and engineering. It also covers history and philosophy of mathematics and university education. All entries are classified according to the Mathematics Subject Classification Scheme (MSC 2020) and are equipped with keywords in order to characterize their particular content.
IDEAS is the largest bibliographic database dedicated to Economics and available freely on the Internet. Based on RePEc, it indexes over 3,100,000 items of research, including over 2,900,000 that can be downloaded in full text. RePEc (Research Papers in Economics) is a large volunteer effort to enhance the free dissemination of research in Economics which includes bibliographic metadata from over 2,000 participating archives, including all the major publishers and research outlets. IDEAS is just one of several services that use RePEc data.
As the authoritative source for chemical names, structures and CAS Registry Numbers®, the CAS substance collection, CAS REGISTRY®, serves as a universal standard for chemists worldwide. Covering advances in chemistry and related sciences over the last 150 years, the CAS content collection empowers researchers, business leaders, and information professionals around the world with immediate access to the reliable information they need to fuel innovation.
BKCI is a part of Web of Science Core Collection (WoSCC) and the world’s leading citation index with multidisciplinary content from the top tier international and regional journals, conference proceedings, and books. The Book Citation Index includes over 104,500 editorially selected books, with 10,000 new books added each year. Containing more than 53.2 million cited references, coverage dates back from 2005 to present. The Book Citation Index is multidisciplinary, covering disciplines across the sciences, social sciences, and arts & humanities.
Produced by the Web Of Science group, BIOSIS Previews research database provides researchers with the most current sources of life sciences information, including journals, conferences, patents, books, review articles, and more. Researchers can also access multidisciplinary coverage via specialized indexing such as MeSH disease terms, CAS registry numbers, Sequence Databank Numbers and Major Concepts.
Produced by the Web Of Science group, Zoological Record is the world’s oldest continuing database of animal biology. It is considered the world’s leading taxonomic reference, and with coverage back to 1864, has long acted as the world’s unofficial register of animal names. The broad scope of coverage ranges from biodiversity and the environment to taxonomy and veterinary sciences.
Provides a simple way to search broadly for scholarly literature. Includes peer-reviewed papers, theses, books, abstracts and articles, from academic publishers, professsional societies, preprint repositories, universities and other scholarly organizations. Google Scholar sorts articles by weighing the full text of each article, the author, the publication in which the article appears, and how often the article has been cited in other scholarly literature, so that the most relevant results are returned on the first page.
Microsoft Academic is a project exploring how to assist human conducting scientific research by leveraging machine’s cognitive power in memory, computation, sensing, attention, and endurance. Re-launched in 2016, the tool features an entirely new data structure and search engine using semantic search technologies. The Academic Knowledge API offers information retrieval from the underlying database using REST endpoints for advanced research purposes.
The national library of the United Kingdom includes 150 million manuscripts, maps, newspapers, magazines, prints and drawings, music scores, and patents. Online catalogues, information and exhibitions can be found on its website. The library operates the world's largest document delivery service, providing millions of items a year to national and international customers.
The digital NSK portal is the central gathering place for the digital collections of the National and University Library (NSK) in Croatia. It was established in 2016 to provide access to the Library’s digital and digitized material collections regardless of storage location. The digital NSK portal enables a unified search of digitized material from the NSK Special Collections - books, visual material, maps and music material. From the end of 2019, all thematic portals are available independently: Digital Books, Digitized Manuscripts, Digitized Visual Materials, Digital Music Materials and Digitized Cartographic Materials (established in 2017). Currently available only in Croatian.
The official DOI (digital object identifier) link registration agency for scholarly and professional publications. Crossref operates a cross-publisher citation linking system that allows a researcher to click on a reference citation on one publisher’s platform and link directly to the cited content on another publisher’s platform, subject to the target publisher’s access control practices. This citation-linking network covers millions of articles and other content items from several hundred scholarly and professional publishers.
Dimensions is a next-generation linked research information system that makes it easier to find and access the most relevant information, analyze the academic and broader outcomes of research, and gather insights to inform future strategy. Dimensions delivers an array of search and discovery, analytical, and research management tools, all in a single platform. Developed in collaboration with over 100 leading research organizations around the world, it brings together over 128 million publications, grants, policy, data and metrics for the first time, enabling users to explore over 4 billion connections between them.
The primary aim of DOAB (Directory of Open Access Books) is to increase discoverability of Open Access books. Metadata will be harvestable in order to maximize dissemination, visibility and impact. Aggregators can integrate the records in their commercial services and libraries can integrate the directory into their online catalogues, helping scholars and students to discover the books.
OAPEN is dedicated to open access, peer-reviewed books. OAPEN operates two platforms, the OAPEN Library (www.oapen.org), a central repository for hosting and disseminating OA books, and the Directory of Open Access Books (DOAB, www.doabooks.org), a discovery service for OA books.
OpenAIRE aims at promoting and implementing the directives of the European Commission (EC) and the European Research Council on the promotion and funding of science and research. OpenAIRE supports the Open Access Mandate and the Open Research Data Pilot developed as part of the Horizon 2020 projects.
An integrated information service combining reference databases, subscription management, online journals, books and linking services. Widely used by libraries, schools, government institutions, medical institutions, corporations and others.
SFX® link resolver gives patrons and librarians a wealth of features that optimize management of and access to resources. It provides patrons with a direct route to electronic full-text records through OpenURL linking, delivers alternative links for further resource discovery, access to journals, and more. Released in 2001 as the first OpenURL resolver, SFX is continuously enhanced to support the newest industry developments and meet the evolving needs of customers. The records include a mix of scholarly material – primarily articles and e-books – but also conference proceedings, newspaper articles, and more.
A non-profit, membership, computer library service and research organization dedicated to the public purposes of furthering access to the world's information and reducing information costs. More than 41,555 libraries in 112 countries and territories around the world use OCLC services to locate, acquire, catalogue, lend and preserve library materials.
The world’s largest collection of open access research papers. CORE's mission is to aggregate all open access research outputs from repositories and journals worldwide and make them available to the public. In this way CORE facilitates free unrestricted access to research for all.
Perlego is a digital online library focusing on the delivery of academic, professional and non-fiction eBooks. It is a subscription-based service that offers users unlimited access to these texts for the duration of their subscription, however IntechOpen content integrated on the platform will always be available for free. They have been billed as “the Spotify for Textbooks” by the Evening Standard. Perlego is based in London but is available to users worldwide.
MyScienceWork provides a suite of data-driven solutions for research institutions, scientific publishers and private-sector R&D companies. MyScienceWork's comprehensive database includes more than 90 million scientific publications and 12 million patents.
CNKI (China National Knowledge Infrastructure) is a key national information construction project under the lead of Tsinghua University, and supported by PRC Ministry of Education, PRC Ministry of Science, Propaganda Department of the Communist Party of China and PRC General Administration of Press and Publication. CNKI has built a comprehensive China Integrated Knowledge Resources System, including journals, doctoral dissertations, masters' theses, proceedings, newspapers, yearbooks, statistical yearbooks, ebooks, patents, standards and so on. CNKI keeps integrating new contents and developing new products in 2 aspects: full-text academic resources, software on digitization and knowledge management. Began with academic journals, CNKI has become the largest and mostly-used academic online library in China.
As one of the largest digital content platform in China,independently developed by CNPIEC, CNPeReading positions herself as “One Platform,Vast Content, Global Services”. Through their new cooperation model and service philosophy, CNPeReading provides integrated promotion and marketing solutionsfor upstream publishers, one-stop, triune, recommendation, online reading and management servicesfor downstream institutions & libraries.
ERIC (Education Resources Information Center), sponsored by the Institute of Education Sciences (IES) of the U.S. Department of Education, provides access to education literature to support the use of educational research and information to improve practice in learning, teaching, educational decision-making, and research. The ERIC website is available to the public for searching more than one million citations going back to 1966.
The ACM Digital Library is a research, discovery and networking platform containing: The Full-Text Collection of all ACM publications, including journals, conference proceedings, technical magazines, newsletters and books. A collection of curated and hosted full-text publications from select publishers.
BASE (Bielefeld Academic Search Engine) is one of the world's most voluminous search sengines especially for academic web resources, e.g. journal articles, preprints, digital collections, images / videos or research data. BASE facilitates effective and targeted searches and retrieves high quality, academically relevant results. Other than search engines like Google or Bing BASE searches the deep web as well. The sources which are included in BASE are intellectually selected (by people from the BASE team) and reviewed. That's why data garbage and spam do not occur.
Zentralblatt MATH (zbMATH) is the world’s most comprehensive and longest-running abstracting and reviewing service in pure and applied mathematics. It is edited by the European Mathematical Society (EMS), the Heidelberg Academy of Sciences and Humanities and FIZ Karlsruhe. zbMATH provides easy access to bibliographic data, reviews and abstracts from all areas of pure mathematics as well as applications, in particular to natural sciences, computer science, economics and engineering. It also covers history and philosophy of mathematics and university education. All entries are classified according to the Mathematics Subject Classification Scheme (MSC 2020) and are equipped with keywords in order to characterize their particular content.
IDEAS is the largest bibliographic database dedicated to Economics and available freely on the Internet. Based on RePEc, it indexes over 3,100,000 items of research, including over 2,900,000 that can be downloaded in full text. RePEc (Research Papers in Economics) is a large volunteer effort to enhance the free dissemination of research in Economics which includes bibliographic metadata from over 2,000 participating archives, including all the major publishers and research outlets. IDEAS is just one of several services that use RePEc data.
As the authoritative source for chemical names, structures and CAS Registry Numbers®, the CAS substance collection, CAS REGISTRY®, serves as a universal standard for chemists worldwide. Covering advances in chemistry and related sciences over the last 150 years, the CAS content collection empowers researchers, business leaders, and information professionals around the world with immediate access to the reliable information they need to fuel innovation.
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He registered 2 patents, wrote 12 international books, published more than 90 SCI journal papers and 45 conference presentations, and served as the technique committee member as well as chair in many international conferences and the editor in BMC Genomics as well as in Current Issues in Molecular Biology, and also a reviewer for more than 25 SCI cited journals. He received several awards, including State Prize awarded from the Academy of Science, Egypt (2004); Young Arab Researcher Prize awarded from Schuman Foundation, Jordan (2005); State Excellence Prize from the Academy of Science, Egypt (2011 and 2018); and Cairo University Prizes (2007, 2010, and 2014). He served as an expert for African Regional Center for Technology, Dakar, Senegal, plus a visiting professor at Pan African University, African Union, Nairobi, Kenya. He was appointed acting vice president of the Academy of Science and Technology from November 2013 to November 2014, Egypt. 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