\r\n\t(i) Quantum dots of very high-quality optical applications, Quantum dot light-emitting diodes (QD-LED) and ‘QD-White LED’, Quantum dot photodetectors (QDPs), Quantum dot solar cells (Photovoltaics).
\r\n
\r\n\t(ii) Quantum Computing (quantum bits or ‘qubits’), (vii) The Future of Quantum Dots (broad range of real-time applications, magnetic quantum dots & graphene quantum dots), Superconducting Loop, Quantum Entanglement, Quantum Fingerprints.
\r\n
\r\n\t(iii) Biomedical and Environmental Applications (to study intracellular processes, tumor targeting, in vivo observation of cell trafficking, diagnostics and cellular imaging at high resolutions), Bioconjugation, Cell Imaging, Photoelectrochemical Immunosensor, Membranes and Bacterial Cells, Resonance Energy-Transfer Processes, Evaluation of Drinking Water Quality, Water and Wastewater Treatment, Pollutant Control.
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1. Introduction
1.1 History of R-loops
R-loops are three-stranded nucleic acid structures consisting of a DNA–RNA hybrid and a displaced single-stranded (ss) DNA. They were first described in 1976 by Thomas et al., who observed a hybridized form of ribosomal RNA and ribosomal DNA of Saccharomyces cerevisiae 26S [1]. Structurally, RNA–DNA hybrids adopt an A-form structure [2, 3]. The structure of an R-loop formed with RNA polymerase or CRISPR-Cas9 shows that R-loops have a helical RNA–DNA hybrid structure and a dissociated ssDNA [4, 5, 6, 7].
1.2 Biological functions of R-loops
RNA–DNA hybrids can be formed from GC-rich clusters during transcription or primer synthesis of DNA replication [2, 8]. Because nucleic acid strands are stabilized when they form a double-stranded conformation, the nascent RNA is hybridized to the template DNA strand when the double-stranded (ds)DNA is denatured during replication or transcription [2]. Therefore, R-loops can form at any time when there is a chance that RNA can be annealed with its template DNA. The thread-back model proposes that R-loop formation stems from the annealing of RNA with DNA when the DNA left behind the transcriptome is negatively supercoiled and unwound [9]. Previous studies support this model [10, 11, 12, 13]. Incomplete transcription elongation and termination also induce RNA–DNA hybrid formation, and the denaturation of duplex DNA by negative supercoiling increases R-loop formation.
R-loops have multiple roles in diverse biological reactions (Figure 1). First, R-loops induce genetic rearrangements in B-cells during immunoglobulin class switching [14]. R-loop formation is promoted by transcription through switched immunoglobulin loci, and the R-loop provides a ssDNA substrate for activation-induced deaminase (AID), which converts cytosine to uracil in both DNA strands. Uracil is subsequently removed by uracil glycosylase, and apurinic/apyrimidinic endonuclease makes nicks at the abasic sites and induces DNA double-strand breaks. During DNA double-strand break repair, the immunoglobulin locus is rearranged to change the level of antibodies generated. R-loops can also regulate both the activation and termination of transcription. Most human promoters are associated with CpG islands [15]. Ginno et al. demonstrated that R-loops are located at promoter sites that have CpG islands and proposed that R-loops protect the template DNA strand from gene-silencing methylation [16]. R-loop stabilization at the promoter region also regulates transcription. Flowering Locus C (FLC) is a transcription repressor of Arabidopsis thaliana that is regulated by COOLAIR through antisense transcription. Sun et al. found that the homeodomain protein AtNDX stabilizes R-loops by binding their displaced ssDNA at the COOLAIR promoter, thus inhibiting COOLAIR transcription and regulating FLC expression [17]. Antisense transcription-mediated R-loop formation at the Vimentin (VIM) promoter induces local chromatin decondensation and enhances gene expression [18]. R-loops also play a role in chromatin organization. For example, they are tightly linked to H3 S10 phosphorylation, which is a mark of chromatin condensation [19]. R-loops regulate both transcription initiation and termination [20]. Skourti-Stathaki et al. proposed a pause-dependent transcription termination mechanism mediated by R-loops and H3K9me2. R-loops are formed in transcription termination regions containing GC-rich sequences and facilitate antisense RNA transcription, inducing dsRNA for RNA interference factors, and they recruit G9a/GLP for the methylation of H3K9 along with HP1γ, which terminates transcription [21]. In addition to research by Skourti-Stathaki and colleagues, other studies suggest that R-loops can regulate transcription termination by RNA polymerase pausing [22, 23]. R-loops also occur at telomeres. Telomeric-repeat-containing RNAs (TERRAs) are noncoding RNAs transcribed from eukaryotic telomeres [24]. During telomerase-mediated telomere elongation in rat1–1 mutant Saccharomyces cerevisiae, TERRAs form RNA–DNA hybrids and inhibit telomerase function [25]. In addition, the THO complex maintains yeast telomeres by suppressing R-loops generated by TERRAs [26].
Figure 1.
The causes and consequences of R-loop formation.
1.3 R-loops, genomic instability, and human diseases
Despite the multiple roles of R-loops in normal cellular processes described above, they are also considered a form of DNA damage that can threaten genomic maintenance and integrity. In particular, the displaced ssDNA in an R-loop can increase genomic instability because it is a good endonuclease substrate [13, 27]. R-loops also induce replication stress. When the displaced ssDNA is broken, the replication fork stops at the R-loop. The RNA–DNA hybrid itself can block the progression of replication forks, and DNA polymerases may become trapped at R-loops [13, 28, 29]. Such replication stresses will activate DNA repair pathways, which might cause chromosome rearrangement [29].
Genomic instability that stems from R-loops may also contribute to some human diseases. Although there is no apparent evidence that R-loops are directly associated with disease, efforts to show causality between R-loops and disease have increased [30]. Some genetic disorders are caused by gene-specific repeats. R-loop formation is highly probable in tandem repeat sequences with high GC content and could change the repeat length. In particular, trinucleotide repeat expansion is a major cause of neurological and neuromuscular diseases, such as Huntington’s disease and fragile X syndrome [31, 32]. It has been proposed that R-loops are associated with other neurological disorders, including amyotrophic lateral sclerosis, Aicardi-Goutières syndrome, and Prader-Willi syndrome [33, 34, 35]. R-loops also appear to be associated with cancer. BRCA genes, which are involved in DNA double-strand break repair via homologous recombination, are intimately associated with breast and ovarian cancer, and BRCA2 prevents R-loop accumulation [36, 37]. VIM is a member of the intermediate filament family and associated with different types of cancer. In colon cancer, the VIM promoter is hypermethylated and VIM expression is silenced. In normal cells, the gene is activated by R-loop formation in the promoter region, raising the possibility that transcription regulation by R-loops related to cancer development [18].
1.4 R-loop prevention and elimination
As described above, R-loops can cause genomic instability unless they are resolved, so they must be properly regulated. Several proteins are involved in R-loop prevention or elimination, such as RNase H, DNA TOP1, and Sen1 [38]. For example, RNase H directly removes R-loops by specifically degrading the RNA in RNA–DNA hybrid structures [39]. RNA helicases also resolve R-loops by unwinding RNA–DNA hybrid structures [40]. Because negative supercoiling promotes R-loop formation, topoisomerases play a key role in preventing R-loops [41]. In the case of replication fork stalling due to R-loops, FANCD2 recruits RNA processing enzymes such as hnRNP U and DDX47 to resolve R-loops at the stalled fork [42].
2. In vivo R-loop assays
Visualizing R-loop formation is important for understanding R-loop metabolism. Because R-loops basically consist of nucleic acids, distinguishing R-loop from ds- and ss-DNA or RNA using existing DNA staining or visualization methods is challenging. S9.6 is an antibody specific to an RNA–DNA hybrid, which was developed in 1986 and rapidly advanced R-loop-related research [43]. This antibody is commonly used to detect R-loops both in vivo and in vitro [44, 45, 46, 47].
Currently, the most popular R-loop characterization technique is DNA–RNA immunoprecipitation sequencing (DRIP-seq), in which RNA–DNA hybrid strands are immunoprecipitated with S9.6 and then sequenced (Figure 2, [47, 48]). DRIP-seq was first adopted for profiling CpG island promoters, where R-loops are predominantly formed [16]. This method revealed that genes containing terminal GC-rich sequences form R-loops at their 3′-end, suggesting that R-loops contribute to efficient transcription termination [20]. The DRIP-seq technique has been further improved; S1 nuclease treatment prior to DRIP-seq can stabilize the DNA–RNA hybrid because S1 removes the displaced ssDNA, thus improving the resolution [49]. In conventional DRIP-seq, it is assumed that the content of R-loops or RNA–DNA hybrids does not vary depending on cell type and growth condition. For appropriate comparison, quantitative differential DNA–RNA immunoprecipitation sequence (qDRIP-seq) uses synthetic RNA–DNA hybrids as internal standards and facilitates comparison between different conditions with high resolution and sensitivity [50]. Although DRIP-seq is a very robust and well-characterized technique, it can only measure the ensemble average level of R-loops. However, single-molecule R-loop footprinting (SMRF-seq) can reveal the R-loop population via chemical reactivity of ssDNA at the single-molecule level. Malig et al. developed SMRF-sequencing based on non-denaturing bisulfite conversion [51, 52]. Sodium bisulfite treatment converts unpaired cytosines to uracils on ssDNA. In R-loops, only one strand is unpaired and exposed to bisulfite, whereas the complementary strand is protected by RNA. Thus, the PCR product of the displaced single strand in an R-loop has a converted sequence of cytosines to thymines, which is a footprint of the R-loop. PCR products are rapidly sequenced using a single-molecule real-time sequencing technique [53]. This approach enables characterization of the individual footprints of R-loops on long-range genomes at high resolution, even at the single-molecule level.
Figure 2.
The flow chart of DRIP-seq. Step 1: whole-genomic DNA containing R-loops is extracted from cells. Step 2: extracted genomic DNA is fragmented by various types of restriction enzymes. Step 3: R-loops containing RNA–DNA hybrids are precipitated with S9.6 antibodies. Step 4: S9.6 antibodies are eliminated by proteinase K treatment, and R-loops are purified by phenol-chloroform extraction followed by ethanol precipitation. Step 5: precipitated R-loops are sequenced.
Fluorescently labeled S9.6 can be used as an R-loop probe in microscope imaging at the cellular level (Figure 3a). The brief procedure is following. K562 cells were pelleted after trypsinization for detaching cells from the plate. Supernatant was discarded to approximately 300 ul, and cell pellets were resuspended. 5 ml of 37°C pre-warmed 75 mM KCl solution was added in a drop-wise manner while the resuspended cells were slowly agitated. After the cells were incubated at 37°C for 14 min, five or six drops of fresh ice-cold fixative solution (3,1 methanol:acetic acid) were added to the cells, which were centrifuged again. Supernatant was discarded to approximately 300 ul, and cell pellets were resuspended. The cells were treated on ice with 5 ml of ice-cold fixative solution in a drop-wise manner. After washed once with fixative solution, the cells were spread onto a clean slide followed by 1 min incubation in 95°C steam for drying. The slide was immediately treated with blocking buffer (1x PBS, 5% BSA, 0.5% Triton X-100) and incubated at room temperature for 1 hr. The slide was successively treated with S9.6 antibody (1500) in blocking buffer at 4°C overnight. After residual S9.6 antibody was washed three times with washing buffer (1x PBS supplemented with 0.1% Triton X-100), the slide was treated with mouse AlexaFluor 594-conjugated secondary antibody at room temperature for 1 hr. The unbound secondary antibody was washed three times with washing buffer, and then the cells were stained with 4,6 diamidino-2-phenylindole (DAPI) and mounted using Vectashield (Vector Laboratories). Finally, the cells were imaged using a fluorescence microscope.
Figure 3.
Flow chart of in vivo immunofluorescence imaging using S9.6 for R-loop visualization. (a) Flow chart ofin vivo immunofluorescence imaging using S9.6 for R-loop visualization. (b) Cellular images of S9.6 labeled with fluorescent secondary antibodies. RNase H1 overexpression significantly reduces the S9.6 signal due to elimination of R-loops.
The use of immunofluorescence with S9.6 can allow visualization of the intracellular locations of RNA–DNA hybrids, even in mitochondria [54, 55, 56]. Furthermore, R-loop detection by S9.6 is ensured by RNase H1 overexpression (Figure 3b). R-loops can also be visualized via R-loop associated proteins with diverse modifications. Prendergast et al. subcloned the RNA binding domain (RBD) of RNase H1 fused to DsRed fluorescent protein to monitor intracellular R-loop dynamics [57]. Hodroj et al. enhanced green fluorescent protein (eGFP)-fused Ddx19 RNA helicase that specifically binds RNA–DNA hybrids. The fluorescent signal of eGFP-Ddx19 indicates R-loop formation inside cells. In addition, it does not form foci when RBD-mutated Ddx19 and phosphorylation site-mutated Ddx19 are used [58].
3. In vitro approaches
In addition to in vivo methods, several biochemical assays have been developed to study R-loops. Classically, R-loops are formed from transcription in a supercoiled plasmid by phage RNA polymerases (RNAPs) such as T3 or T7 [59]. Because R-loops have a three-strand structure, they have lower mobility than DNA duplexes in gel electrophoresis, so band shift or smearing occurs between supercoiled and relaxed plasmids during this procedure [53, 60]. Because RNase H digests ssRNA, dsRNA, and RNA–DNA hybrids, RNase H treatment eliminates the mobility shift of plasmids observed with gel electrophoresis [61, 62]. In addition, R-loops can be detected by isotope (e.g. 32P) or fluorescently labeled RNA, which is formed with isotope or fluorescently labeled ribonucleoside triphosphates during transcription. The labeled RNA is used to confirm if the plasmid mobility shift actually results from R-loops [53, 60]. In contrast, S9.6 is also used in electrophoresis mobility shift assay (EMSA) and Western blot with oligomers (Figure 4a). EMSA in Figure 4a was performed with fluorescently labeled R-loop and homoduplex DNA with synthesized oligomers (Table 1) following the previous protocol [55]. The oligomers were mixed for R-loop and homoduplex DNA as shown in Table 2, and the mixture was heated at 95°C and then slowly cooled down to room temperature. 10 nM R-loop or duplex DNA was mixed to S9.6 (10, 30 and 50 nM) in reaction buffer (10 mM HEPES [pH 7.5], 1 mM DTT, and 5% glycerol). The reactant was incubated in the dark at room temperature for 20 min. The R-loop formation and the binding of S9.6 to R-loop were analyzed with 5% non-denaturing polyacrylamide gel electrophoresis and imaged by Typhoon RGB (GE Healthcare) system. In EMSA using the oligomers, R-loops show band shift from dsDNA resulting from low mobility due to its triple-strand structure. Further band shift is observed following treatment with S9.6, which binds to RNA–DNA hybrids [50, 55]. In Western blotting, RNA–DNA hybrid interactors can be validated using S9.6 and target protein immunoprecipitation [45].
Figure 4.
In vitro EMSA (electrophoresis mobility shift assay) for R-loop identification. (a) EMSA image for identifying R-loops in vitro. Fluorescently labeled oligomers were hybridized to form duplex DNA and R-loop structures. The R-loops shifted upward because of their lower mobility compared with same-length duplex DNA due to its molecular weight and the displaced ssDNA (lane 1 vs. lane 3). Because S9.6 specifically binds to R-loops, S9.6 treatment further super-shifts R-loops but not duplexes (lane 2 vs. lanes 4, 5, and 6). The black triangle represents the increasing concentration of S9.6 antibody (10, 30, and 50 nM). (b) Simplified diagram of R-loop visualization using fluorescently labeled catalytically-inactive RNase H1 or RBD. In addition to the S9.6 antibody, catalytically-inactive RNase H1 and RBD with fluorescence dye can also be used to visualize R-loops.
Oligomer name
Sequences
DNA 1
5’-GCC GTC GCA TGA CGC TGC CGA ATT CTA CCA CGC GAT TCA TAC CTG TCG TGC CAG CTG CTT TGC CCA CCT GCA GGT TCA CCT CGT CCC TGG C-3′
[Cy3] and [Cy5] indicate the labeling of Cy3 and Cy5 fluorescent dyes, respectively.
Substrate name
Mixture recipe (total 20 μl in reaction buffer)
Homoduplex
DNA 1: 6 μM, DNA 2: 5 μM
R-Loop
DNA 1: 6 μM, DNA 3: 5 μM, RNA 1: 5 μM
Table 2.
Hybridization of oligomers for EMSA.
Purified RBD-DsRed specifically binds to RNA-containing structures, enabling its use as a probe of R-loops (Figure 4b). DNA fibers can be spread on a surface to distinguish the positions of R-loop regions with the purified RBD-DsRed. Various tags combining the RBD of RNase H1 have been used in microscopic fluorescent imaging, EMSA, and DRIP-seq to identify R-loops [63]. Crossely et al. designed and purified different types of RNase H1 that contains RBD and full amino acid sequences [50]. However, the RNase H1 used in their research has a D210N mutation that renders it catalytically inactive. Their construct successfully recognizes R-loops and RNA–DNA hybrids without degradation of RNA in EMSA. The GFP-labeled catalytic mutant RNase H1 thoroughly colocalized with R-loop-containing oligos within the cells.
Atomic force microscopy (AFM) scans a sample on a mica surface using a cantilever to yield a topographic image of the sample [64]. AFM has revealed diverse types of nucleic acids structures and DNA-protein complex formations [65, 66, 67]. AFM is also applied for visualizing R-loop formation. Carrasco-Salas et al. used AFM to observe three distinct structures derived from R-loops: blobs, spurs, and loops [68]. The specific R-loop structures depend on the sequence of non-template strand that is displaced in the R-loop, which suggests that non-template strand organization is an intrinsic characteristic of R-loops.
4. Single-molecule approaches for R-loop studies
Although R-loop formation, function, and fate have been extensively studied using biochemical assays and cell-based imaging as described above, those approaches still have limitations related to probing molecular details due to the ensemble average effect. Such hurdles can be overcome with single-molecule techniques that enable researchers to 1) observe individual molecules without an ensemble average effect, 2) mechanically manipulate biomolecules, and 3) directly observe biomolecular interactions [69]. Several single-molecule techniques have been utilized for R-loop studies. Lee et al. used protein-induced fluorescence enhancement (PIFE) to observe R-loop formation during T7 RNA polymerase transcription [70]. PIFE is a phenomenon in which a protein sometimes enhances the intensity of fluorescent dyes on other biomolecules [71]. PIFE assays exploit this intensity enhancement to measure the distance and interaction between non-tagged proteins and fluorescent dyes on target molecules, such as DNA. Fluorescent tagging of proteins is inefficient and may disturb protein activity; however, in PIFE assays there is no need to tag proteins [72]. The authors demonstrated that a G-quadruplex on the non-template strand stabilizes the R-loop, which enhances transcription elongation.
In addition to PIFE, single-molecule FRET (smFRET) has been widely used for probing the conformational dynamics of biomolecules (Figure 5a) [73, 74]. FRET requires two dyes (donor and acceptor) with spectral overlap for donor emission and acceptor absorption. In FRET, only the donor dye is excited, while the acceptor dye emits fluorescence through energy transfer when both dyes are in close proximity, as the energy transfer efficiency depends on the distance between them. R-loops are also studied using smFRET, during which the target DNA or RNA and RNA polymerases are fluorescently labeled with FRET donors and acceptors (Figure 5a, [75]). For smFRET experiments, one DNA oligomer with both FRET donor (Cy3) and acceptor (Cy5) and its complementary oligomer with biotin were hybridized. The hybridized DNA was anchored on the surface of a quartz slide coated with polyethylene glycol (PEG) via biotin-streptavidin interaction. Transcription was initiated by injecting 8 nM T7 RNA polymerases and 2 mM of rNTPs in imaging buffer (40 mM Tris–HCl [pH 8.0], 50 mM KCl, 5 mM NaOH, 20 mM MgCl2, 1 mM DTT, 2 mM spermidine, 3 mM Trolox, 5 mM PCA, and 4 units/ml PCD). Total internal reflection fluorescence (TIRF) microscopy equipped with an electron-multiplying CCD camera was used for fluorescence imaging. Donor (Cy3) and acceptor (Cy5) dyes were excited by 532-nm and 633-nm lasers, respectively. smFRET experiments revealed that R-loop formation precedes and facilitates G-quadruplex formation, which is extremely stable even after R-loop resolution. Using smFRET, we can examine R-loop formation induced by dsDNA denaturation, collision between RNAP and obstacles such as protein roadblocks or DNA lesions, and G-quadruplex formation of displaced ssDNA during R-loop formation [70, 75].
Figure 5.
Single-molecule R-loop visualization techniques. (a) Schematic of single-molecule FRET. Hybridized oligomers are anchored on the biotinylated polyethylene glycol surface via biotin-streptavidin linkage. Donor (green) and acceptor (red) dyes in a duplex DNA display low FRET due to the long distance between the two dyes. However, when an R-loop is formed during the transcription by RNAP (yellow), the dissociated ssDNA emits high FRET. (b) Schematic of single-molecule DNA curtain. For DNA curtain assay, the slide surface with nanometric diffusion barriers was coated with a biotinylated lipid bilayer, which is made of DOPC (1,2-dioleoyl-sn-glycero-phosphocholine), 0.5% biotinylated-DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(cap biotinyl)), and 8% mPEG 2000-DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000]). A Cy5-labeled R-loop was inserted into lambda phage DNA, which has biotin at one end. The lambda phage DNA was anchored on the lipid bilayer via biotin-streptavidin linkage in BSA buffer (40 mM Tris–HCl [pH 8.0], 50 mM NaCl, 2 mM MgCl2, and 0.4% BSA). TonEBP with 3x FLAG was labeled with anti-FLAG conjugated quantum dot. Under hydrodynamic flow, DNA curtain was formed in reaction buffer (10 mM HEPES [pH 7.5] and 50 mM NaCl), and R-loops were imaged by Cy5 fluorescence under TIRF microscopy. Then quantum dot-labeled TonEBP was incubated with the lambda DNA, and its binding to the R-loop was imaged. DNA molecules containing an R-loop are unidirectionally stretched on the biotinylated lipid-coated slide (sky blue) and aligned at the chromium nano-barrier (gray) due to the fluidity of lipid bilayer. The interaction between TonEBP (blue) and R-loops (red), in which RNA is labeled with a fluorescent dye, can be visualized in real time. (c) Schematic of magnetic tweezers. The magnetic field exerts and measures both force and torque on the magnetic bead (black). The interaction between Mdf (violet) linked to both duplex DNA and RNAP (yellow) during R-loop formation can be measured based on the length change of DNA under a constant force using magnetic tweezers.
In addition to R-loop formation, sensing R-loops is important for downstream processes, including R-loop resolution. In particular, how R-loop-binding proteins recognize R-loops in long genomic DNA is unclear. R-loop search mechanisms have been investigated with a novel single-molecule fluorescence imaging technique called DNA curtain (Figure 5b, [76, 77]). In this assay, DNA molecules are anchored on a lipid bilayer and aligned at nanometric diffusion barriers. Owing to the fluidity of the surface lipid bilayer, DNA molecules are unidirectionally stretched under hydrodynamic flow. DNA curtains can be used to identify sequence-dependent binding of proteins to DNA. Moreover, they allow us to visualize the movement of a protein along a single DNA molecule in real time. To study the search mechanism, an R-loop is inserted into a specific location of lambda phage DNA and fluorescently imaged with Cy5-labeled RNA in the R-loop. Then, the R-loop-binding protein is tagged with a fluorescent nanoparticle called a quantum dot (Qdot), which has a different emission wavelength from Cy5. Two-color imaging of both Cy5 and Qdot in the DNA curtain allows the R-loop search mechanism of the R-loop-binding protein. Kang et al. reported that tonicity enhancer-binding protein (TonEBP) plays important roles in R-loop sensing and recruitment of downstream proteins [55]. Using the DNA curtain approach, they revealed that TonEBP preferentially binds R-loops through both three-dimensional collision and one-dimensional diffusion. This dual-search mechanism facilitates rapid searches for R-loop throughout the long human genome. Furthermore, the quantitative analysis on one-dimensional diffusion shows that TonEBP diffuses along DNA by sliding rather than hopping. In EMSAs, TonEBP preferentially binds R-loops, D-loops, and bubble DNA structures over duplex DNA. The substances for which TonEBP has a high affinity all contain displaced ssDNA structures. These results indicate that TonEBP preferentially binds displaced ssDNA, thus recognizing R-loops on duplex DNA.
Magnetic tweezers assay can measure both the tension and topological features of a single supercoiled DNA. In this approach, a linear DNA molecule is torsionally constrained by tethering the DNA ends to the slide surface and a magnetic bead that is rotated to induce DNA supercoiling (Figure 5c). Portmen et al. used magnetic tweezers to elucidate the R-loop formation mechanism by the transcription-coupled repair factor Mfd during transcription based on topologically changing the DNA [78]. For the magnetic tweezers assay, 4.6 kbp long DNA containing a promoter site was ligated with biotinylated handle at one end and digoxigenin handle at the other hand. Digoxigenin end was anchored on an anti-digoxigenin-coated glass coverslip, and biotinylated end was attached to a 1 μm diameter superparamagnetic bead. Transcription reaction was done in reaction buffer (40 mM HEPES [pH 8.0], 100 mM KCl, 8 mM MgCl2, 0.5 mg/ml BSA, and 1 mM DTT) supplemented with 300 pM RNA polymerases, 500 nM Mfd, 50 nM GreB, 1 mM rATP, 100 μM rCTP, 100 μM rUTP, and 100 μM rGTP. They found that R-loop formation was mediated by the Mfd-RNAP complex, which compacted and supercoiled the template DNA during transcription. Mfd simultaneously binds both RNAP and DNA and results in tripartite supercoiled domains. The negative supercoiling in the tripartite domains serves as a substrate for R-loop formation.
With advances in single-molecule imaging technology, we can investigate R-loops and related factors that cannot be observed in traditional ensemble assays. The convergence of single-molecule techniques and R-loop research will pave the way to more thorough investigation of R-loops with higher spatiotemporal resolution.
5. Conclusions
R-loops are involved in various cellular activities but can threaten genomic stability. Detecting these structures is important for understanding their metabolism and underlying mechanism. This chapter described the formation, roles, and regulation of R-loops and related diseases and explored in vivo and in vitro methods for R-loop detection and visualization, including single-molecule techniques. The most classical methods for R-loop are based on the S9.6 antibody. However, novel techniques that do not require this antibody have been developed. In particular, single-molecule R-loop imaging techniques have accelerated research. We expect that more advanced techniques for R-loops with high sensitivity and resolution will be developed in the future.
Acknowledgments
This work was supported by the National Research Foundation (grant number: NRF-2020R1A2B5B01001792) and the Institute for Basic Science (IBS-R022-D1).
Conflict of interest
The authors declare no conflict of interest.
\n',keywords:"R-loop, genetic instability, R-loop sensing, and single-molecule imaging",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/81016.pdf",chapterXML:"https://mts.intechopen.com/source/xml/81016.xml",downloadPdfUrl:"/chapter/pdf-download/81016",previewPdfUrl:"/chapter/pdf-preview/81016",totalDownloads:29,totalViews:0,totalCrossrefCites:0,dateSubmitted:"January 20th 2022",dateReviewed:"February 10th 2022",datePrePublished:"March 29th 2022",datePublished:null,dateFinished:"March 29th 2022",readingETA:"0",abstract:"An R-loop is a triple-stranded nucleic acid structure consisting of a DNA–RNA hybrid and a displaced single-stranded DNA. R-loops are associated with diverse biological reactions, such as immune responses and gene regulation, and dysregulated R-loops can cause genomic instability and replication stress. Therefore, investigating the formation, regulation, and elimination of R-loops is important for understanding the molecular mechanisms underlying biological processes and diseases related to R-loops. Existing research has primarily focused on R-loop detection. In this chapter, we introduce a variety of biochemical and biophysical techniques for R-loop sensing and visualization both in vivo and in vitro, including single-molecule imaging. These methods can be used to investigate molecular mechanisms underlying R-loop search and identification.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/81016",risUrl:"/chapter/ris/81016",signatures:"Na Young Cheon, Subin Kim and Ja Yil Lee",book:{id:"11349",type:"book",title:"Gene Expression",subtitle:null,fullTitle:"Gene Expression",slug:null,publishedDate:null,bookSignature:"Dr. Fumiaki Uchiumi",coverURL:"https://cdn.intechopen.com/books/images_new/11349.jpg",licenceType:"CC BY 3.0",editedByType:null,isbn:"978-1-80355-622-2",printIsbn:"978-1-80355-621-5",pdfIsbn:"978-1-80355-623-9",isAvailableForWebshopOrdering:!0,editors:[{id:"47235",title:"Dr.",name:"Fumiaki",middleName:null,surname:"Uchiumi",slug:"fumiaki-uchiumi",fullName:"Fumiaki Uchiumi"}],productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"}},authors:null,sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_1_2",title:"1.1 History of R-loops",level:"2"},{id:"sec_2_2",title:"1.2 Biological functions of R-loops",level:"2"},{id:"sec_3_2",title:"1.3 R-loops, genomic instability, and human diseases",level:"2"},{id:"sec_4_2",title:"1.4 R-loop prevention and elimination",level:"2"},{id:"sec_6",title:"2. In vivo R-loop assays",level:"1"},{id:"sec_7",title:"3. In vitro approaches",level:"1"},{id:"sec_8",title:"4. Single-molecule approaches for R-loop studies",level:"1"},{id:"sec_9",title:"5. Conclusions",level:"1"},{id:"sec_10",title:"Acknowledgments",level:"1"},{id:"sec_13",title:"Conflict of interest",level:"1"}],chapterReferences:[{id:"B1",body:'Thomas M, White RL, Davis RW. Hybridization of RNA to double-stranded DNA: Formation of R-loops. Proceedings of the National Academy of Sciences of the United States of America. 1976;73(7):2294-2298. DOI: 10.1073/pnas.73.7.2294'},{id:"B2",body:'Roberts RW, Crothers DM. 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DOI: 10.1615/CritRevEukaryotGeneExpr.v26.i1.70'},{id:"B67",body:'Bustamante C, Vesenka J, Tang CL, Rees W, Guthold M, Keller R. Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry. 1992;31(1):22-26. DOI: 10.1021/bi00116a005'},{id:"B68",body:'Carrasco-Salas Y, Malapert A, Sulthana S, Molcrette B, Chazot-Franguiadakis L, Bernard P, et al. The extruded non-template strand determines the architecture of R-loops. Nucleic Acids Research. 2019;47(13):6783-6795. DOI: 10.1093/nar/gkz341'},{id:"B69",body:'Kim SO, Jackman JA, Mochizuki M, Yoon BK, Hayashi T, Cho NJ. Correlating single-molecule and ensemble-average measurements of peptide adsorption onto different inorganic materials. Physical Chemistry Chemical Physics. 2016;18(21):14454-14459. DOI: 10.1039/c6cp01168c'},{id:"B70",body:'Lee CY, McNerney C, Ma K, Zhao W, Wang A, Myong S. R-loop induced G-quadruplex in non-template promotes transcription by successive R-loop formation. Nature Communications. 2020;11(1):3392. DOI: 10.1038/s41467-020-17176-7'},{id:"B71",body:'Hwang H, Kim H, Myong S. Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(18):7414-7418. DOI: 10.1073/pnas.1017672108'},{id:"B72",body:'Hwang H, Myong S. Protein induced fluorescence enhancement (PIFE) for probing protein-nucleic acid interactions. Chemical Society Reviews. 2014;43(4):1221-1229. DOI: 10.1039/c3cs60201j'},{id:"B73",body:'Ha T. Single-molecule fluorescence resonance energy transfer. Methods. 2001;25(1):78-86. DOI: 10.1006/meth.2001.1217'},{id:"B74",body:'Roy R, Hohng S, Ha T. A practical guide to single-molecule FRET. Nature Methods. 2008;5(6):507-516. DOI: 10.1038/nmeth.1208'},{id:"B75",body:'Lim G, Hohng S. Single-molecule fluorescence studies on cotranscriptional G-quadruplex formation coupled with R-loop formation. Nucleic Acids Research. 2020;48(16):9195-9203. DOI: 10.1093/nar/gkaa695'},{id:"B76",body:'Collins BE, Ye LF, Duzdevich D, Greene EC. DNA curtains: Novel tools for imaging protein-nucleic acid interactions at the single-molecule level. Methods in Cell Biology. 2014;123:217-234. DOI: 10.1016/B978-0-12-420138-5.00012-4'},{id:"B77",body:'Greene EC, Wind S, Fazio T, Gorman J, Visnapuu ML. DNA curtains for high-throughput single-molecule optical imaging. Methods in Enzymology. 2010;472:293-315. DOI: 10.1016/S0076-6879(10)72006-1'},{id:"B78",body:'Portman JR, Brouwer GM, Bollins J, Savery NJ, Strick TR. Cotranscriptional R-loop formation by Mfd involves topological partitioning of DNA. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(15):e2019630118. DOI: 10.1073/pnas.2019630118'}],footnotes:[],contributors:[{corresp:null,contributorFullName:"Na Young Cheon",address:null,affiliation:'
Department of Biological Sciences, Ulsan National Institute of Science and Technology, Republic of Korea
Department of Biological Sciences, Ulsan National Institute of Science and Technology, Republic of Korea
'},{corresp:"yes",contributorFullName:"Ja Yil Lee",address:"biojayil@unist.ac.kr",affiliation:'
Department of Biological Sciences, Ulsan National Institute of Science and Technology, Republic of Korea
Center for Genomic Integrity, Institute for Basic Science, Republic of Korea
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Usually, teamwork assessment software and Internet applications for several hierarchy level teams are included in the field of Management Information Systems (MIS). However, some assessment tasks in teams with several levels of hierarchy and assessment may be performed in an educational context, and the existing applications for the assessment and evaluation of teams with several levels of hierarchy are not applications dedicated to the assessment of students in an educational context. The “Cluster” application is able to present the course material, to train the students in teams as well as to present individual and team assessment tasks. The application’s special functionalities enable it to assess the teams at several levels of hierarchy, which constitute the hierarchical aggregate assessment process. In effect, the members of the teams may have appointments of team member, team leader and team administrator that supervises team leaders. This application can therefore evaluate simultaneously different knowledge and skills in the same assessment task based on the hierarchical position of the team member. The summative evaluation of the application consists of work to submit as well as objective examinations in HTML format, while the formative evaluation is composed of assessment grid computer forms of self-assessment and peer assessment. The application contains two mutually exclusive modes, the assessor mode and the student mode. The assessor mode allows the teacher to create courses, manage students, form the teams and also assess the students and the teams in a summative manner. The student mode allows the students to follow courses, write exams, submit homework, perform in teams and submit self- and peers formative assessment. The theoretical consideration of the project establishes the link between hierarchical aggregate assessment applications and management information systems (MIS). The application is an electronic portfolio (e-portfolio) management system in the competency-based learning and an Internet test administration system in the mastery learning approach. The aim of the chapter is to introduce the reader to the field of hierarchical aggregate assessment and to show how to implement complex assessment tasks with several levels of hierarchy into an Internet software application.",signatures:"Martin Lesage, Gilles Raîche, Martin Riopel, Frédérick Fortin and\nDalila Sebkhi",authors:[{id:"174960",title:"Ph.D. Student",name:"Martin",surname:"Lesage",fullName:"Martin Lesage",slug:"martin-lesage",email:"lesagelm@hotmail.com"},{id:"175173",title:"Prof.",name:"Gilles",surname:"Raîche",fullName:"Gilles Raîche",slug:"gilles-raiche",email:"raiche.gilles@uqam.ca"},{id:"175174",title:"Prof.",name:"Martin",surname:"Riopel",fullName:"Martin Riopel",slug:"martin-riopel",email:"riopel.martin@uqam.ca"},{id:"175175",title:"Mrs.",name:"Dalila",surname:"Sebkhi",fullName:"Dalila Sebkhi",slug:"dalila-sebkhi",email:"dalilasebkhi@hotmail.com"},{id:"175176",title:"Mr.",name:"Frédérick",surname:"Fortin",fullName:"Frédérick Fortin",slug:"frederick-fortin",email:"fredfortin80@gmail.com"}],book:{id:"4792",title:"E-Learning",slug:"e-learning-instructional-design-organizational-strategy-and-management",productType:{id:"1",title:"Edited Volume"}}}],collaborators:[{id:"80248",title:"Dr.",name:"Ileana",surname:"Hamburg",slug:"ileana-hamburg",fullName:"Ileana Hamburg",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"86020",title:"Dr.",name:"Nicoleta",surname:"Gudanescu Nicolau",slug:"nicoleta-gudanescu-nicolau",fullName:"Nicoleta Gudanescu Nicolau",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:{name:"Universitatea Hyperion din Bucureşti",institutionURL:null,country:{name:"Romania"}}},{id:"174960",title:"Ph.D. Student",name:"Martin",surname:"Lesage",slug:"martin-lesage",fullName:"Martin Lesage",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/174960/images/4176_n.jpg",biography:null,institutionString:null,institution:{name:"University of Quebec at Montreal",institutionURL:null,country:{name:"Canada"}}},{id:"175173",title:"Prof.",name:"Gilles",surname:"Raîche",slug:"gilles-raiche",fullName:"Gilles Raîche",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:{name:"University of Quebec at Montreal",institutionURL:null,country:{name:"Canada"}}},{id:"175175",title:"Mrs.",name:"Dalila",surname:"Sebkhi",slug:"dalila-sebkhi",fullName:"Dalila Sebkhi",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"175176",title:"Mr.",name:"Frédérick",surname:"Fortin",slug:"frederick-fortin",fullName:"Frédérick Fortin",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"175290",title:"Prof.",name:"Ahmad",surname:"Rafi",slug:"ahmad-rafi",fullName:"Ahmad Rafi",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/175290/images/4268_n.jpg",biography:"Dr. Ahmad Rafi is an architect and a Professor in the Faculty of Creative Multimedia at Multimedia University (MMU), Malaysia. He is currently the Vice President (Academic), MMU. He is also the Deputy Chairman 2, Creative Content Industry Guild (CCIG), Malaysia and certified Multimedia Professional by CCIG. He was the Dean of Institute for Postgraduate Studies, MMU (2013 – 2014). He was the Deputy Rector of Academic Affairs at the National Academy of Arts, Culture and Heritage (ASWARA), a university under the Ministry of Information, Communication and Culture, Malaysia (2010 – 2012). He obtained a Bachelor degree in Architecture (BArch., Honours), Master of Science in Computer-Aided Building Design (MSc. in CABD) and Ph.D. in the area of architectural animation and virtual reality from the University of Strathclyde, Glasgow, Scotland, UK in 1998. He was the Dean of Faculty of Creative Multimedia, Chairman of Centre for Interpretation and Expression (CIE) (2000 – 2006) and Director of Research and Development (R&D) Collaborations (2008 – 2009), MMU. He is also the chairman of Creative Content Industry Recognition Framework (CCIRF), CCIG. His research includes virtual reality, virtual heritage, 3D animation, architectural visualisation, educational technology, and multimedia. He has published more than 100 internationally multi-disciplinary refereed conference papers, journal articles and books.\n\nHe also contributes in several local and international reviewing committees including guest editor and reviewer for Automation in Construction International Research Journal, Open House International Journal, International Journal of Educational Technology and Society, International Journal of Computer Games Technology, International Journal of Engineering Education, CAADRIA (Asia & Australasia), CAAD Futures, eCAADe (Europe), G-CAD (USA), CyberGames International Conference (Australia), international research panel for King Fahd University of Petroleum and Minerals (Saudi Arabia), e‐Content Fund, e-Science Fund, Techno Fund, InnoFund and Creative Industry Life-long Learning (CILL) Programme (Ministry of Science, Technology and Innovation - MOSTI, Malaysia), Multimedia Grant Scheme (MGS) (Malaysia), Bumiputera Content Industry Initiative Fund (BCi2) Fund (Malaysia), Fundamental and Exploratory Research Grants (FRGS and ERGS), and Higher Institution Centre of Excellence (HiCOE) (Ministry of Education – MoE, Malaysia), Malaysian Examinations Council (Chair for ICT) and to name a few. He has pioneered into the development of Bachelor, Master of Multimedia and Ph.D. degree programmes in the country targeted for producing world-class ‘content developers’ in the Multimedia Super Corridor (MSC), Malaysia over the last 16 years.",institutionString:null,institution:{name:"Multimedia University",institutionURL:null,country:{name:"Malaysia"}}},{id:"175291",title:"Dr.",name:"Khairulanuar",surname:"Samsudin",slug:"khairulanuar-samsudin",fullName:"Khairulanuar Samsudin",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"175292",title:"Mr.",name:"Hafizul Fahri",surname:"Hanafi",slug:"hafizul-fahri-hanafi",fullName:"Hafizul Fahri Hanafi",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"175303",title:"Dr.",name:"Kueichih",surname:"Chuang",slug:"kueichih-chuang",fullName:"Kueichih Chuang",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:{name:"National Yunlin University of Science and Technology",institutionURL:null,country:{name:"Taiwan"}}}]},generic:{page:{slug:"OA-publishing-fees",title:"Open Access Publishing Fees",intro:"
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As a gold Open Access publisher, an Open Access Publishing Fee is payable on acceptance following peer review of the manuscript. In return, we provide high quality publishing services and exclusive benefits for all contributors. IntechOpen is the trusted publishing partner of over 140,000 international scientists and researchers.
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The Open Access Publishing Fee (OAPF) is payable only after your book chapter, monograph or journal article is accepted for publication.
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OAPF Publishing Options
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1,400 GBP Chapter - Edited Volume
\n\t
850 GBP Chapter - Book Series Topic (Annual Volume)
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10,000 GBP Monograph - Long Form
\n\t
4,000 GBP Compacts Monograph - Short Form
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850 GBP Journal Article (Across Portfolio)
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During the launching phase journals do not charge an APC, rather they will be funded by IntechOpen.
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*These prices do not include Value-Added Tax (VAT). Residents of European Union countries need to add VAT based on the specific rate in their country of residence. Institutions and companies registered as VAT taxable entities in their own EU member state will not pay VAT as long as provision of the VAT registration number is made during the application process. This is made possible by the EU reverse charge method.
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Services included are:
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An online manuscript tracking system to facilitate your work
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Personal contact and support throughout the publishing process from your dedicated Author Service Manager
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Assurance that your manuscript meets the highest publishing standards
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English language copyediting and proofreading, including the correction of grammatical, spelling, and other common errors
\n\t
XML Typesetting and pagination - web (PDF, HTML) and print files preparation
\n\t
Discoverability - electronic citation and linking via DOI
\n\t
Permanent and unrestricted online access to your work
\n
\n\n
What isn't covered by the Open Access Publishing Fee?
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If your manuscript:
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Exceeds the number of pages defined by the publishing guidelines, an additional fee per page may be required
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If a manuscript requires Heavy Editing or Language Polishing, this will incur additional fees.
\n
\n\n
Your Author Service Manager will inform you of any items not covered by the OAPF and provide exact information regarding those additional costs before proceeding.
\n\n
Open Access Funding
\n\n
To explore funding opportunities and learn more about how you can finance your IntechOpen publication, go to our Open Access Funding page. IntechOpen offers expert assistance to all of its Authors. We can support you in approaching funding bodies and institutions in relation to publishing fees by providing information about compliance with the Open Access policies of your funder or institution. We can also assist with communicating the benefits of Open Access in order to support and strengthen your funding request and provide personal guidance through your application process. You can contact us at funders@intechopen.com for further details or assistance.
\n\n
For Authors who are still unable to obtain funding from their institutions or research funding bodies for individual projects, IntechOpen does offer the possibility of applying for a Waiver to offset some or all processing feed. Details regarding our Waiver Policy can be found here.
\n\n
Added Value of Publishing with IntechOpen
\n\n
Choosing to publish with IntechOpen ensures the following benefits:
\n\n
\n\t
Indexing and listing across major repositories, see details ...
\n\t
Long-term archiving
\n\t
Visibility on the world's strongest OA platform
\n\t
Live Performance Metrics to track readership and the impact of your chapter
\n\t
Dissemination and Promotion
\n
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Benefits of Publishing with IntechOpen
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\n\t
Proven world leader in Open Access book publishing with over 10 years experience
\n\t
+5,700 OA books published
\n\t
Most competitive prices in the market
\n\t
Fully compliant with OA funding requirements
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Optimized processes that assure your research is made available to the scientific community without delay
\n\t
Personal support during every step of the publication process
\n\t
+184,650 citations in Web of Science databases
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Currently strongest OA platform with over 175 million downloads
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They show broad diversity of mineral associations, with Vesuvius and Vulcano being also among the world localities richest in mineral species. Volcanic systems, which show recession over a longer period, show fumarolic development from the high-temperature alkaline halide/sulphate, calcic sulphate or sulphidic parageneses, synchronous with or immediately following the eruptions, through medium-temperature ammonium minerals, metal chlorides, or fluoride associations to the late low-temperature paragenesis dominated by sulphur, gypsum, alunogen, and other hydrous sulphates. The situation can be different in the systems that are not recessing but show fluctuations in activity, illustrated by the example of Vulcano where the high-temperature association appears intermittently. A full survey of the mineral groups and species is given in respect to their importance and appearance in fumarolic associations.",book:{id:"5311",slug:"updates-in-volcanology-from-volcano-modelling-to-volcano-geology",title:"Updates in Volcanology",fullTitle:"Updates in Volcanology - From Volcano Modelling to Volcano Geology"},signatures:"Tonči Balić-Žunić, Anna Garavelli, Sveinn Peter Jakobsson, Kristjan\nJonasson, Athanasios Katerinopoulos, Konstantinos Kyriakopoulos\nand Pasquale Acquafredda",authors:[{id:"183593",title:"Dr.",name:"Tonci",middleName:null,surname:"Balic-Zunic",slug:"tonci-balic-zunic",fullName:"Tonci Balic-Zunic"},{id:"183700",title:"Prof.",name:"Anna",middleName:null,surname:"Garavelli",slug:"anna-garavelli",fullName:"Anna Garavelli"},{id:"183701",title:"Dr.",name:"Sveinn Peter",middleName:null,surname:"Jakobsson",slug:"sveinn-peter-jakobsson",fullName:"Sveinn Peter Jakobsson"},{id:"183702",title:"Prof.",name:"Athanasios",middleName:null,surname:"Katerinopoulos",slug:"athanasios-katerinopoulos",fullName:"Athanasios Katerinopoulos"},{id:"188833",title:"Dr.",name:"Kristjan",middleName:null,surname:"Jonasson",slug:"kristjan-jonasson",fullName:"Kristjan Jonasson"},{id:"188834",title:"Dr.",name:"Konstantinos",middleName:null,surname:"Kyriakopoulos",slug:"konstantinos-kyriakopoulos",fullName:"Konstantinos Kyriakopoulos"},{id:"188835",title:"Dr.",name:"Pasquale",middleName:null,surname:"Acquafredda",slug:"pasquale-acquafredda",fullName:"Pasquale Acquafredda"}]},{id:"51105",doi:"10.5772/63486",title:"How Polygenetic are Monogenetic Volcanoes: Case Studies of Some Complex Maar‐Diatreme Volcanoes",slug:"how-polygenetic-are-monogenetic-volcanoes-case-studies-of-some-complex-maar-diatreme-volcanoes",totalDownloads:1939,totalCrossrefCites:5,totalDimensionsCites:15,abstract:"The increasing number of field investigations and various controlled benchtop and large‐scale experiments have permitted the evaluation of a large number of processes involved in the formation of maar‐diatreme volcanoes, the second most common type of small‐volume subaerial volcanoes on Earth. A maar‐diatreme volcano is recognized by a volcanic crater that is cut into country rocks and surrounded by a low‐height ejecta rim composed of pyroclastic deposits of few meters to up to 200 m thick above the syn‐eruptive surface level. The craters vary from 0.1 km to up to 5 km wide and vary in depth from a few dozen meters to up to 300 m deep. Their irregular morphology reflects the simple or complex volcanic and cratering processes involved in their formation. The simplicity or complexity of the crater or the entire maar itself is usually observed in the stratigraphy of the surrounding ejecta rings. The latter are composed of sequences of successive alternating and contrastingly bedded phreatomagmatic‐derived dilute pyroclastic density currents (PDC) and fallout depositions, with occasional interbedded Strombolian‐derived spatter materials or scoria fall units, exemplifying the changes in the eruptive styles during the formation of the volcano. The entire stratigraphic sequence might be preserved as a single eruptive package (small or very thick) in which there is no stratigraphic gap or significant discordance indicative of a potential break during the eruption. A maar with a single eruptive deposit is quantified as monogenetic maar, meaning that it was formed by a single eruptive vent from which only a small and ephemeral magma erupted over a short period of time. The stratigraphy may also display several packages of deposits separated either by contrasting discordance surfaces or paleosoils, which reflect multiple phases or episodes of eruptions within the same maar. Such maars are characterized as complex polycyclic maars if the length of time between the eruptive events is relatively short (days to years). For greater length of time (thousands to millions of years), the complex maar will be quantified as polygenetic. These common depositional breaks interpreted as signs of temporal interruption of the eruptions for various timescales also indicate deep magma system processes; hence magmas of different types might erupt during the formation of both simple and complex maars. The feeding dikes can interact with groundwater and form closely distributed small craters. The latter can coalesce to form a final crater with various shapes depending on the distance between them. This observation indicates the significant role of the magmatic plumbing system on the formation and growth of complex and polygenetic maar‐diatreme volcanoes.",book:{id:"5311",slug:"updates-in-volcanology-from-volcano-modelling-to-volcano-geology",title:"Updates in Volcanology",fullTitle:"Updates in Volcanology - From Volcano Modelling to Volcano Geology"},signatures:"Boris Chako Tchamabé, Gabor Kereszturi, Karoly Németh and\nGerardo Carrasco‐Núñez",authors:[{id:"51162",title:"Dr.",name:"Károly",middleName:null,surname:"Németh",slug:"karoly-nemeth",fullName:"Károly Németh"},{id:"62029",title:"Dr.",name:"Gabor",middleName:null,surname:"Kereszturi",slug:"gabor-kereszturi",fullName:"Gabor Kereszturi"},{id:"182834",title:"Dr.",name:"Boris",middleName:null,surname:"Chako Tchamabé",slug:"boris-chako-tchamabe",fullName:"Boris Chako Tchamabé"},{id:"183809",title:"Dr.",name:"Gerardo",middleName:null,surname:"Carrasco-Núñez",slug:"gerardo-carrasco-nunez",fullName:"Gerardo Carrasco-Núñez"}]},{id:"49656",doi:"10.5772/61974",title:"Optical Satellite Remote Sensing of the Coastal Zone Environment — An Overview",slug:"optical-satellite-remote-sensing-of-the-coastal-zone-environment-an-overview",totalDownloads:2463,totalCrossrefCites:7,totalDimensionsCites:15,abstract:"Optical remote-sensing data are a powerful source of information for monitoring the coastal environment. Due to the high complexity of coastal environments, where different natural and anthropogenic phenomenon interact, the selection of the most appropriate sensor(s) is related to the applications required, and the different types of resolutions available (spatial, spectral, radiometric, and temporal) need to be considered. The development of specific techniques and tools based on the processing of optical satellite images makes possible the production of information useful for coastal environment management, without any destructive impacts. This chapter will highlight different subjects related to coastal environments: shoreline change detection, ocean color, water quality, river plumes, coral reef, alga bloom, bathymetry, wetland mapping, and coastal hazards/vulnerability. The main objective of this chapter is not an exhaustive description of the image processing methods/algorithms employed in coastal environmental studies, but focus in the range of applications available. Several limitations were identified. The major challenge still is to have remote-sensing techniques adopted as a routine tool in assessment of change in the coastal zone. Continuing research is required into the techniques employed for assessing change in the coastal environment.",book:{id:"5104",slug:"environmental-applications-of-remote-sensing",title:"Environmental Applications of Remote Sensing",fullTitle:"Environmental Applications of Remote Sensing"},signatures:"Ana C. Teodoro",authors:[{id:"18485",title:"Dr.",name:"Ana",middleName:null,surname:"Teodoro",slug:"ana-teodoro",fullName:"Ana Teodoro"}]},{id:"49851",doi:"10.5772/62122",title:"Detection of Tree Crowns in Very High Spatial Resolution Images",slug:"detection-of-tree-crowns-in-very-high-spatial-resolution-images",totalDownloads:3240,totalCrossrefCites:8,totalDimensionsCites:13,abstract:"The requirements for advanced knowledge on forest resources have led researchers to develop efficient methods to provide detailed information about trees. Since 1999, orbital remote sensing has been providing very high resolution (VHR) image data. The new generation of satellite allows individual tree crowns to be visually identifiable. The increase in spatial resolution has also had a profound effect in image processing techniques and has motivated the development of new object-based procedures to extract information. Tree crown detection has become a major area of research in image analysis considering the complex nature of trees in an uncontrolled environment. This chapter is subdivided into two parts. Part I offers an overview of the state of the art in computer detection of individual tree crowns in VHR images. Part II presents a new hybrid approach developed by the authors that integrates geometrical-optical modeling (GOM), marked point processes (MPP), and template matching (TM) to individually detect tree crowns in VHR images. The method is presented for two different applications: isolated tree detection in an urban environment and automatic tree counting in orchards with an average performance rate of 82% for tree detection and above 90% for tree counting in orchards.",book:{id:"5104",slug:"environmental-applications-of-remote-sensing",title:"Environmental Applications of Remote Sensing",fullTitle:"Environmental Applications of Remote Sensing"},signatures:"Marilia Ferreira Gomes and Philippe Maillard",authors:[{id:"177110",title:"Dr.",name:"Philippe",middleName:null,surname:"Maillard",slug:"philippe-maillard",fullName:"Philippe Maillard"},{id:"177172",title:"Ph.D.",name:"Marilia",middleName:"Ferreira",surname:"Gomes",slug:"marilia-gomes",fullName:"Marilia Gomes"}]}],mostDownloadedChaptersLast30Days:[{id:"66703",title:"P-Wave Teleseismic Tomography: Evidence of Imprints of Deccan Mantle Plume below the Kachchh Rift Zone, Gujarat, India",slug:"p-wave-teleseismic-tomography-evidence-of-imprints-of-deccan-mantle-plume-below-the-kachchh-rift-zon",totalDownloads:2602,totalCrossrefCites:2,totalDimensionsCites:2,abstract:"The Indian plate had experienced the Deccan volcanism at 65 Ma when it moved over the Re-union hotspot, which has altered lithospheric structure below the Kachchh rift zone (KRZ). To quantify the influence of Deccan volcanism on the crust-mantle, the present chapter focuses on the delineation of the upper mantle structure below the KRZ, through the modeling of crust corrected P-residuals and P-wave teleseismic tomography. The crust corrected normalized P-residuals suggest dominant negative residuals associated with the central KRZ, indicating crustal and lithospheric thinning below the KRZ. A low velocity down to a depth of 170 km below the central KRZ is detected through the teleseismic tomography using these P-residuals. However, these residuals also show positive values for the surrounding un-rifted zones. Note that a low shear velocity zone extending from 100–120 km to 170–220 km depth beneath the central KRZ has already been revealed by the modeling of P-RFs. This reduction in seismic velocity in the upper mantle could be explained by the presence of trapped carbonatite/partial melts related to the Deccan volcanism. The influx of volatile CO2 emanating from the carbonatite melts in the asthenosphere might be generating lower crustal earthquakes occurring in the KRZ.",book:{id:"7677",slug:"forecasting-volcanic-eruptions",title:"Forecasting Volcanic Eruptions",fullTitle:"Forecasting Volcanic Eruptions"},signatures:"Prantik Mandal",authors:[{id:"279344",title:"Dr.",name:"Prantik",middleName:null,surname:"Mandal",slug:"prantik-mandal",fullName:"Prantik Mandal"}]},{id:"49608",title:"Remote Sensing of Mountain Glaciers and Related Hazards",slug:"remote-sensing-of-mountain-glaciers-and-related-hazards",totalDownloads:2386,totalCrossrefCites:1,totalDimensionsCites:5,abstract:"Mountain glaciers are highly sensitive to temperature and precipitation fluctuations and active geomorphic agents in shaping the landforms of glaciated regions which are direct imprints of past glaciations, providing reliable evidence of the evolution of the past Cryosphere and contain important information on climatic variables. But most importantly, glaciers have aroused a lot of concern in terms of glacier area changes, thickness change, mass balance and their consequences on water resources as well as related hazards. The contribution of glacier mass loss to global sea-level rise and increasing number of glacier-related hazards are the most important and current socioeconomic concerns. Therefore, understanding the dynamics of the changes and constant monitoring of glaciers are essential for studying climate, water resource management and hydropower and also to predict and evade glacier-related hazards. The recent advances in the techniques of earth observations have proved as a boon for investigating glaciers and glacier-related hazards. Remote sensing technology enables extraction of glacier parameters such as albedo/reflectance/scattering, glacier area, glacier zones and facies, equilibrium line, glacier thickness, volume, mass balance, velocity and glacier topography. The present chapter explores the prospective of remote sensing technology for understanding and surveying glaciers formed at high, inaccessible mountains and glacier-induced hazards.",book:{id:"5104",slug:"environmental-applications-of-remote-sensing",title:"Environmental Applications of Remote Sensing",fullTitle:"Environmental Applications of Remote Sensing"},signatures:"Pratima Pandey, Alagappan Ramanathan and Gopalan\nVenkataraman",authors:[{id:"18342",title:"Prof.",name:"Ramanathan",middleName:null,surname:"Alagappan",slug:"ramanathan-alagappan",fullName:"Ramanathan Alagappan"},{id:"177179",title:"Dr.",name:"Pratima",middleName:null,surname:"Pandey",slug:"pratima-pandey",fullName:"Pratima Pandey"},{id:"178231",title:"Prof.",name:"Gopalan",middleName:null,surname:"Venkataraman",slug:"gopalan-venkataraman",fullName:"Gopalan Venkataraman"}]},{id:"60548",title:"Volcanic Glass and its Uses as Adsorbent",slug:"volcanic-glass-and-its-uses-as-adsorbent",totalDownloads:1601,totalCrossrefCites:1,totalDimensionsCites:3,abstract:"Volcanic glasses are an amorphous phyllosilicates formed by the fast cooling of the magma. The physicochemical properties of volcanic glasses are directly related to their chemical composition. Thus, the rhyolitic magma, which presents the highest SiO2 percentage, displays a high viscosity, which leads to explosive eruptions by the ex-solution of H2O, CO2, and SO2, when the pressure diminishes generates a macroporous structure with interesting applications in construction, as abrasive, acoustic, filter as well as in the agriculture field. The macroporosity of volcanic glass allows to host large molecules as biomolecules, tensoactives, or dyes. On the other hand, the existence of hydroxyl groups in this amorphous aluminosilicate also favors the adsorption of cations and anions, so the volcanic glass is an economical adsorbent to retain heavy metals or radioactive cations.",book:{id:"6104",slug:"volcanoes-geological-and-geophysical-setting-theoretical-aspects-and-numerical-modeling-applications-to-industry-and-their-impact-on-the-human-health",title:"Volcanoes",fullTitle:"Volcanoes - Geological and Geophysical Setting, Theoretical Aspects and Numerical Modeling, Applications to Industry and Their Impact on the Human Health"},signatures:"Juan Antonio Cecilia, Miguel Armando Autie-Pérez, Juan Manuel\nLabadie-Suarez, Enrique Rodríguez Castellón and Antonia Infantes\nMolina",authors:[{id:"126325",title:"Dr.",name:"Enrique",middleName:null,surname:"Rodríguez-Castellón",slug:"enrique-rodriguez-castellon",fullName:"Enrique Rodríguez-Castellón"}]},{id:"57502",title:"The Characteristics of Volcanic Eruption in Indonesia",slug:"the-characteristics-of-volcanic-eruption-in-indonesia",totalDownloads:1846,totalCrossrefCites:1,totalDimensionsCites:1,abstract:"This chapter discusses the unique characteristics of the volcanic eruptions in Indonesia. We know that Indonesia has 147 volcanoes and 76 of them are active volcanoes and spread along the islands of Java, Lesser Sunda, Sumatra, and Celebes. The characteristics of Indonesian volcanoes are quite unique in terms of the formation process, eruption phenomenon, and the resulting natural disasters. Most volcanoes in Indonesia consist of stratovolcanoes, but this does not mean that the resulting eruptions are always explosive and they have a long period. This can be seen from the activity of Semeru that always erupts effusively every day, Sinabung that has a very short eruption period, Tangkuban Perahu eruption that occurs suddenly with the lack of early signs, and Merapi and Kelud that have eruption period that is getting shorter. Based on the results of our study it can be known that the types of volcanic eruption are influenced by the structure of the constituent rocks of the volcanoes. However, the presence of external control factors in the form of large-scale earthquakes will affect their periodicity. The large earthquakes can affect the stability of the magma chamber that can trigger a premature eruption.",book:{id:"6104",slug:"volcanoes-geological-and-geophysical-setting-theoretical-aspects-and-numerical-modeling-applications-to-industry-and-their-impact-on-the-human-health",title:"Volcanoes",fullTitle:"Volcanoes - Geological and Geophysical Setting, Theoretical Aspects and Numerical Modeling, Applications to Industry and Their Impact on the Human Health"},signatures:"Eko Hariyono and Liliasari S",authors:[{id:"214360",title:"Dr.",name:"Eko",middleName:null,surname:"Hariyono",slug:"eko-hariyono",fullName:"Eko Hariyono"},{id:"219699",title:"Prof.",name:"Liliasari",middleName:null,surname:"S",slug:"liliasari-s",fullName:"Liliasari S"}]},{id:"51105",title:"How Polygenetic are Monogenetic Volcanoes: Case Studies of Some Complex Maar‐Diatreme Volcanoes",slug:"how-polygenetic-are-monogenetic-volcanoes-case-studies-of-some-complex-maar-diatreme-volcanoes",totalDownloads:1939,totalCrossrefCites:5,totalDimensionsCites:15,abstract:"The increasing number of field investigations and various controlled benchtop and large‐scale experiments have permitted the evaluation of a large number of processes involved in the formation of maar‐diatreme volcanoes, the second most common type of small‐volume subaerial volcanoes on Earth. A maar‐diatreme volcano is recognized by a volcanic crater that is cut into country rocks and surrounded by a low‐height ejecta rim composed of pyroclastic deposits of few meters to up to 200 m thick above the syn‐eruptive surface level. The craters vary from 0.1 km to up to 5 km wide and vary in depth from a few dozen meters to up to 300 m deep. Their irregular morphology reflects the simple or complex volcanic and cratering processes involved in their formation. The simplicity or complexity of the crater or the entire maar itself is usually observed in the stratigraphy of the surrounding ejecta rings. The latter are composed of sequences of successive alternating and contrastingly bedded phreatomagmatic‐derived dilute pyroclastic density currents (PDC) and fallout depositions, with occasional interbedded Strombolian‐derived spatter materials or scoria fall units, exemplifying the changes in the eruptive styles during the formation of the volcano. The entire stratigraphic sequence might be preserved as a single eruptive package (small or very thick) in which there is no stratigraphic gap or significant discordance indicative of a potential break during the eruption. A maar with a single eruptive deposit is quantified as monogenetic maar, meaning that it was formed by a single eruptive vent from which only a small and ephemeral magma erupted over a short period of time. The stratigraphy may also display several packages of deposits separated either by contrasting discordance surfaces or paleosoils, which reflect multiple phases or episodes of eruptions within the same maar. Such maars are characterized as complex polycyclic maars if the length of time between the eruptive events is relatively short (days to years). For greater length of time (thousands to millions of years), the complex maar will be quantified as polygenetic. These common depositional breaks interpreted as signs of temporal interruption of the eruptions for various timescales also indicate deep magma system processes; hence magmas of different types might erupt during the formation of both simple and complex maars. The feeding dikes can interact with groundwater and form closely distributed small craters. The latter can coalesce to form a final crater with various shapes depending on the distance between them. This observation indicates the significant role of the magmatic plumbing system on the formation and growth of complex and polygenetic maar‐diatreme volcanoes.",book:{id:"5311",slug:"updates-in-volcanology-from-volcano-modelling-to-volcano-geology",title:"Updates in Volcanology",fullTitle:"Updates in Volcanology - From Volcano Modelling to Volcano Geology"},signatures:"Boris Chako Tchamabé, Gabor Kereszturi, Karoly Németh and\nGerardo Carrasco‐Núñez",authors:[{id:"51162",title:"Dr.",name:"Károly",middleName:null,surname:"Németh",slug:"karoly-nemeth",fullName:"Károly Németh"},{id:"62029",title:"Dr.",name:"Gabor",middleName:null,surname:"Kereszturi",slug:"gabor-kereszturi",fullName:"Gabor Kereszturi"},{id:"182834",title:"Dr.",name:"Boris",middleName:null,surname:"Chako Tchamabé",slug:"boris-chako-tchamabe",fullName:"Boris Chako Tchamabé"},{id:"183809",title:"Dr.",name:"Gerardo",middleName:null,surname:"Carrasco-Núñez",slug:"gerardo-carrasco-nunez",fullName:"Gerardo Carrasco-Núñez"}]}],onlineFirstChaptersFilter:{topicId:"658",limit:6,offset:0},onlineFirstChaptersCollection:[],onlineFirstChaptersTotal:0},preDownload:{success:null,errors:{}},subscriptionForm:{success:null,errors:{}},aboutIntechopen:{},privacyPolicy:{},peerReviewing:{},howOpenAccessPublishingWithIntechopenWorks:{},sponsorshipBooks:{sponsorshipBooks:[],offset:8,limit:8,total:0},allSeries:{pteSeriesList:[{id:"14",title:"Artificial Intelligence",numberOfPublishedBooks:9,numberOfPublishedChapters:89,numberOfOpenTopics:6,numberOfUpcomingTopics:0,issn:"2633-1403",doi:"10.5772/intechopen.79920",isOpenForSubmission:!0},{id:"7",title:"Biomedical Engineering",numberOfPublishedBooks:12,numberOfPublishedChapters:104,numberOfOpenTopics:3,numberOfUpcomingTopics:0,issn:"2631-5343",doi:"10.5772/intechopen.71985",isOpenForSubmission:!0}],lsSeriesList:[{id:"11",title:"Biochemistry",numberOfPublishedBooks:32,numberOfPublishedChapters:318,numberOfOpenTopics:4,numberOfUpcomingTopics:0,issn:"2632-0983",doi:"10.5772/intechopen.72877",isOpenForSubmission:!0},{id:"25",title:"Environmental Sciences",numberOfPublishedBooks:1,numberOfPublishedChapters:12,numberOfOpenTopics:4,numberOfUpcomingTopics:0,issn:"2754-6713",doi:"10.5772/intechopen.100362",isOpenForSubmission:!0},{id:"10",title:"Physiology",numberOfPublishedBooks:11,numberOfPublishedChapters:141,numberOfOpenTopics:4,numberOfUpcomingTopics:0,issn:"2631-8261",doi:"10.5772/intechopen.72796",isOpenForSubmission:!0}],hsSeriesList:[{id:"3",title:"Dentistry",numberOfPublishedBooks:8,numberOfPublishedChapters:129,numberOfOpenTopics:2,numberOfUpcomingTopics:0,issn:"2631-6218",doi:"10.5772/intechopen.71199",isOpenForSubmission:!0},{id:"6",title:"Infectious Diseases",numberOfPublishedBooks:13,numberOfPublishedChapters:113,numberOfOpenTopics:3,numberOfUpcomingTopics:1,issn:"2631-6188",doi:"10.5772/intechopen.71852",isOpenForSubmission:!0},{id:"13",title:"Veterinary Medicine and Science",numberOfPublishedBooks:11,numberOfPublishedChapters:106,numberOfOpenTopics:3,numberOfUpcomingTopics:0,issn:"2632-0517",doi:"10.5772/intechopen.73681",isOpenForSubmission:!0}],sshSeriesList:[{id:"22",title:"Business, Management and Economics",numberOfPublishedBooks:1,numberOfPublishedChapters:19,numberOfOpenTopics:3,numberOfUpcomingTopics:0,issn:"2753-894X",doi:"10.5772/intechopen.100359",isOpenForSubmission:!0},{id:"23",title:"Education and Human Development",numberOfPublishedBooks:0,numberOfPublishedChapters:5,numberOfOpenTopics:1,numberOfUpcomingTopics:1,issn:null,doi:"10.5772/intechopen.100360",isOpenForSubmission:!0},{id:"24",title:"Sustainable Development",numberOfPublishedBooks:0,numberOfPublishedChapters:15,numberOfOpenTopics:5,numberOfUpcomingTopics:0,issn:null,doi:"10.5772/intechopen.100361",isOpenForSubmission:!0}],testimonialsList:[{id:"6",text:"It is great to work with the IntechOpen to produce a worthwhile collection of research that also becomes a great educational resource and guide for future research endeavors.",author:{id:"259298",name:"Edward",surname:"Narayan",institutionString:null,profilePictureURL:"https://mts.intechopen.com/storage/users/259298/images/system/259298.jpeg",slug:"edward-narayan",institution:{id:"3",name:"University of Queensland",country:{id:null,name:"Australia"}}}},{id:"13",text:"The collaboration with and support of the technical staff of IntechOpen is fantastic. The whole process of submitting an article and editing of the submitted article goes extremely smooth and fast, the number of reads and downloads of chapters is high, and the contributions are also frequently cited.",author:{id:"55578",name:"Antonio",surname:"Jurado-Navas",institutionString:null,profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002bRisIQAS/Profile_Picture_1626166543950",slug:"antonio-jurado-navas",institution:{id:"720",name:"University of Malaga",country:{id:null,name:"Spain"}}}}]},series:{item:{id:"6",title:"Infectious Diseases",doi:"10.5772/intechopen.71852",issn:"2631-6188",scope:"This series will provide a comprehensive overview of recent research trends in various Infectious Diseases (as per the most recent Baltimore classification). Topics will include general overviews of infections, immunopathology, diagnosis, treatment, epidemiology, etiology, and current clinical recommendations for managing infectious diseases. Ongoing issues, recent advances, and future diagnostic approaches and therapeutic strategies will also be discussed. This book series will focus on various aspects and properties of infectious diseases whose deep understanding is essential for safeguarding the human race from losing resources and economies due to pathogens.",coverUrl:"https://cdn.intechopen.com/series/covers/6.jpg",latestPublicationDate:"June 25th, 2022",hasOnlineFirst:!0,numberOfPublishedBooks:13,editor:{id:"131400",title:"Prof.",name:"Alfonso J.",middleName:null,surname:"Rodriguez-Morales",slug:"alfonso-j.-rodriguez-morales",fullName:"Alfonso J. Rodriguez-Morales",profilePictureURL:"https://mts.intechopen.com/storage/users/131400/images/system/131400.png",biography:"Dr. Rodriguez-Morales is an expert in tropical and emerging diseases, particularly zoonotic and vector-borne diseases (especially arboviral diseases). He is the president of the Travel Medicine Committee of the Pan-American Infectious Diseases Association (API), as well as the president of the Colombian Association of Infectious Diseases (ACIN). He is a member of the Committee on Tropical Medicine, Zoonoses, and Travel Medicine of ACIN. He is a vice-president of the Latin American Society for Travel Medicine (SLAMVI) and a Member of the Council of the International Society for Infectious Diseases (ISID). Since 2014, he has been recognized as a Senior Researcher, at the Ministry of Science of Colombia. He is a professor at the Faculty of Medicine of the Fundacion Universitaria Autonoma de las Americas, in Pereira, Risaralda, Colombia. He is an External Professor, Master in Research on Tropical Medicine and International Health, Universitat de Barcelona, Spain. He is also a professor at the Master in Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima, Peru. In 2021 he has been awarded the “Raul Isturiz Award” Medal of the API. Also, in 2021, he was awarded with the “Jose Felix Patiño” Asclepius Staff Medal of the Colombian Medical College, due to his scientific contributions to COVID-19 during the pandemic. He is currently the Editor in Chief of the journal Travel Medicine and Infectious Diseases. 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He also obtained an MSc in Molecular and Genetic Medicine, and a Ph.D. in Clinical Immunology and Human Genetics from the University of Sheffield, UK. He also completed a short-term fellowship in Pediatric Clinical Immunology and Bone Marrow Transplantation at Newcastle General Hospital, England. Dr. Rezaei is a Full Professor of Immunology and Vice Dean of International Affairs and Research, at the School of Medicine, Tehran University of Medical Sciences, and the co-founder and head of the Research Center for Immunodeficiencies. He is also the founding president of the Universal Scientific Education and Research Network (USERN). Dr. Rezaei has directed more than 100 research projects and has designed and participated in several international collaborative projects. He is an editor, editorial assistant, or editorial board member of more than forty international journals. He has edited more than 50 international books, presented more than 500 lectures/posters in congresses/meetings, and published more than 1,100 scientific papers in international journals.",institutionString:"Tehran University of Medical Sciences",institution:{name:"Tehran University of Medical Sciences",country:{name:"Iran"}}},{id:"180733",title:"Dr.",name:"Jean",middleName:null,surname:"Engohang-Ndong",slug:"jean-engohang-ndong",fullName:"Jean Engohang-Ndong",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/180733/images/system/180733.png",biography:"Dr. Jean Engohang-Ndong was born and raised in Gabon. After obtaining his Associate Degree of Science at the University of Science and Technology of Masuku, Gabon, he continued his education in France where he obtained his BS, MS, and Ph.D. in Medical Microbiology. He worked as a post-doctoral fellow at the Public Health Research Institute (PHRI), Newark, NJ for four years before accepting a three-year faculty position at Brigham Young University-Hawaii. Dr. Engohang-Ndong is a tenured faculty member with the academic rank of Full Professor at Kent State University, Ohio, where he teaches a wide range of biological science courses and pursues his research in medical and environmental microbiology. Recently, he expanded his research interest to epidemiology and biostatistics of chronic diseases in Gabon.",institutionString:"Kent State University",institution:{name:"Kent State University",country:{name:"United States of America"}}},{id:"188773",title:"Prof.",name:"Emmanuel",middleName:null,surname:"Drouet",slug:"emmanuel-drouet",fullName:"Emmanuel Drouet",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/188773/images/system/188773.png",biography:"Emmanuel Drouet, PharmD, is a Professor of Virology at the Faculty of Pharmacy, the University Grenoble-Alpes, France. As a head scientist at the Institute of Structural Biology in Grenoble, Dr. Drouet’s research investigates persisting viruses in humans (RNA and DNA viruses) and the balance with our host immune system. He focuses on these viruses’ effects on humans (both their impact on pathology and their symbiotic relationships in humans). He has an excellent track record in the herpesvirus field, and his group is engaged in clinical research in the field of Epstein-Barr virus diseases. He is the editor of the online Encyclopedia of Environment and he coordinates the Universal Health Coverage education program for the BioHealth Computing Schools of the European Institute of Science.",institutionString:null,institution:{name:"Grenoble Alpes University",country:{name:"France"}}},{id:"131400",title:"Prof.",name:"Alfonso J.",middleName:null,surname:"Rodriguez-Morales",slug:"alfonso-j.-rodriguez-morales",fullName:"Alfonso J. Rodriguez-Morales",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/131400/images/system/131400.png",biography:"Dr. Rodriguez-Morales is an expert in tropical and emerging diseases, particularly zoonotic and vector-borne diseases (especially arboviral diseases). He is the president of the Travel Medicine Committee of the Pan-American Infectious Diseases Association (API), as well as the president of the Colombian Association of Infectious Diseases (ACIN). He is a member of the Committee on Tropical Medicine, Zoonoses, and Travel Medicine of ACIN. He is a vice-president of the Latin American Society for Travel Medicine (SLAMVI) and a Member of the Council of the International Society for Infectious Diseases (ISID). Since 2014, he has been recognized as a Senior Researcher, at the Ministry of Science of Colombia. He is a professor at the Faculty of Medicine of the Fundacion Universitaria Autonoma de las Americas, in Pereira, Risaralda, Colombia. He is an External Professor, Master in Research on Tropical Medicine and International Health, Universitat de Barcelona, Spain. He is also a professor at the Master in Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima, Peru. In 2021 he has been awarded the “Raul Isturiz Award” Medal of the API. Also, in 2021, he was awarded with the “Jose Felix Patiño” Asclepius Staff Medal of the Colombian Medical College, due to his scientific contributions to COVID-19 during the pandemic. He is currently the Editor in Chief of the journal Travel Medicine and Infectious Diseases. His Scopus H index is 47 (Google Scholar H index, 68).",institutionString:"Institución Universitaria Visión de las Américas, Colombia",institution:null},{id:"332819",title:"Dr.",name:"Chukwudi Michael",middleName:"Michael",surname:"Egbuche",slug:"chukwudi-michael-egbuche",fullName:"Chukwudi Michael Egbuche",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/332819/images/14624_n.jpg",biography:"I an Dr. Chukwudi Michael Egbuche. I am a Senior Lecturer in the Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka.",institutionString:null,institution:{name:"Nnamdi Azikiwe University",country:{name:"Nigeria"}}},{id:"284232",title:"Mr.",name:"Nikunj",middleName:"U",surname:"Tandel",slug:"nikunj-tandel",fullName:"Nikunj Tandel",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/284232/images/8275_n.jpg",biography:'Mr. Nikunj Tandel has completed his Master\'s degree in Biotechnology from VIT University, India in the year of 2012. He is having 8 years of research experience especially in the field of malaria epidemiology, immunology, and nanoparticle-based drug delivery system against the infectious diseases, autoimmune disorders and cancer. He has worked for the NIH funded-International Center of Excellence in Malaria Research project "Center for the study of complex malaria in India (CSCMi)" in collaboration with New York University. The preliminary objectives of the study are to understand and develop the evidence-based tools and interventions for the control and prevention of malaria in different sites of the INDIA. Alongside, with the help of next-generation genomics study, the team has studied the antimalarial drug resistance in India. Further, he has extended his research in the development of Humanized mice for the study of liver-stage malaria and identification of molecular marker(s) for the Artemisinin resistance. At present, his research focuses on understanding the role of B cells in the activation of CD8+ T cells in malaria. Received the CSIR-SRF (Senior Research Fellow) award-2018, FIMSA (Federation of Immunological Societies of Asia-Oceania) Travel Bursary award to attend the IUIS-IIS-FIMSA Immunology course-2019',institutionString:"Nirma University",institution:{name:"Nirma University",country:{name:"India"}}},{id:"334383",title:"Ph.D.",name:"Simone",middleName:"Ulrich",surname:"Ulrich Picoli",slug:"simone-ulrich-picoli",fullName:"Simone Ulrich Picoli",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/334383/images/15919_n.jpg",biography:"Graduated in Pharmacy from Universidade Luterana do Brasil (1999), Master in Agricultural and Environmental Microbiology from Federal University of Rio Grande do Sul (2002), Specialization in Clinical Microbiology from Universidade de São Paulo, USP (2007) and PhD in Sciences in Gastroenterology and Hepatology (2012). She is currently an Adjunct Professor at Feevale University in Medicine and Biomedicine courses and a permanent professor of the Academic Master\\'s Degree in Virology. She has experience in the field of Microbiology, with an emphasis on Bacteriology, working mainly on the following topics: bacteriophages, bacterial resistance, clinical microbiology and food microbiology.",institutionString:null,institution:{name:"Universidade Feevale",country:{name:"Brazil"}}},{id:"229220",title:"Dr.",name:"Amjad",middleName:"Islam",surname:"Aqib",slug:"amjad-aqib",fullName:"Amjad Aqib",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/229220/images/system/229220.png",biography:"Dr. Amjad Islam Aqib obtained a DVM and MSc (Hons) from University of Agriculture Faisalabad (UAF), Pakistan, and a PhD from the University of Veterinary and Animal Sciences Lahore, Pakistan. Dr. Aqib joined the Department of Clinical Medicine and Surgery at UAF for one year as an assistant professor where he developed a research laboratory designated for pathogenic bacteria. Since 2018, he has been Assistant Professor/Officer in-charge, Department of Medicine, Manager Research Operations and Development-ORIC, and President One Health Club at Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan. He has nearly 100 publications to his credit. His research interests include epidemiological patterns and molecular analysis of antimicrobial resistance and modulation and vaccine development against animal pathogens of public health concern.",institutionString:"Cholistan University of Veterinary and Animal Sciences",institution:null},{id:"62900",title:"Prof.",name:"Fethi",middleName:null,surname:"Derbel",slug:"fethi-derbel",fullName:"Fethi Derbel",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/62900/images/system/62900.jpeg",biography:"Professor Fethi Derbel was born in 1960 in Tunisia. He received his medical degree from the Sousse Faculty of Medicine at Sousse, University of Sousse, Tunisia. He completed his surgical residency in General Surgery at the University Hospital Farhat Hached of Sousse and was a member of the Unit of Liver Transplantation in the University of Rennes, France. He then worked in the Department of Surgery at the Sahloul University Hospital in Sousse. Professor Derbel is presently working at the Clinique les Oliviers, Sousse, Tunisia. His hospital activities are mostly concerned with laparoscopic, colorectal, pancreatic, hepatobiliary, and gastric surgery. He is also very interested in hernia surgery and performs ventral hernia repairs and inguinal hernia repairs. He has been a member of the GREPA and Tunisian Hernia Society (THS). During his residency, he managed patients suffering from diabetic foot, and he was very interested in this pathology. For this reason, he decided to coordinate a book project dealing with the diabetic foot. Professor Derbel has published many articles in journals and collaborates intensively with IntechOpen Access Publisher as an editor.",institutionString:"Clinique les Oliviers",institution:null},{id:"300144",title:"Dr.",name:"Meriem",middleName:null,surname:"Braiki",slug:"meriem-braiki",fullName:"Meriem Braiki",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/300144/images/system/300144.jpg",biography:"Dr. Meriem Braiki is a specialist in pediatric surgeon from Tunisia. She was born in 1985. She received her medical degree from the University of Medicine at Sousse, Tunisia. She achieved her surgical residency training periods in Pediatric Surgery departments at University Hospitals in Monastir, Tunis and France.\r\nShe is currently working at the Pediatric surgery department, Sidi Bouzid Hospital, Tunisia. Her hospital activities are mostly concerned with laparoscopic, parietal, urological and digestive surgery. She has published several articles in diffrent journals.",institutionString:"Sidi Bouzid Regional Hospital",institution:null},{id:"229481",title:"Dr.",name:"Erika M.",middleName:"Martins",surname:"de Carvalho",slug:"erika-m.-de-carvalho",fullName:"Erika M. de Carvalho",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/229481/images/6397_n.jpg",biography:null,institutionString:null,institution:{name:"Oswaldo Cruz Foundation",country:{name:"Brazil"}}},{id:"186537",title:"Prof.",name:"Tonay",middleName:null,surname:"Inceboz",slug:"tonay-inceboz",fullName:"Tonay Inceboz",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/186537/images/system/186537.jfif",biography:"I was graduated from Ege University of Medical Faculty (Turkey) in 1988 and completed his Med. PhD degree in Medical Parasitology at the same university. I became an Associate Professor in 2008 and Professor in 2014. I am currently working as a Professor at the Department of Medical Parasitology at Dokuz Eylul University, Izmir, Turkey.\n\nI have given many lectures, presentations in different academic meetings. I have more than 60 articles in peer-reviewed journals, 18 book chapters, 1 book editorship.\n\nMy research interests are Echinococcus granulosus, Echinococcus multilocularis (diagnosis, life cycle, in vitro and in vivo cultivation), and Trichomonas vaginalis (diagnosis, PCR, and in vitro cultivation).",institutionString:"Dokuz Eylül University",institution:{name:"Dokuz Eylül University",country:{name:"Turkey"}}},{id:"71812",title:"Prof.",name:"Hanem Fathy",middleName:"Fathy",surname:"Khater",slug:"hanem-fathy-khater",fullName:"Hanem Fathy Khater",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/71812/images/1167_n.jpg",biography:"Prof. Khater is a Professor of Parasitology at Benha University, Egypt. She studied for her doctoral degree, at the Department of Entomology, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, USA. She has completed her Ph.D. degrees in Parasitology in Egypt, from where she got the award for “the best scientific Ph.D. dissertation”. She worked at the School of Biological Sciences, Bristol, England, the UK in controlling insects of medical and veterinary importance as a grant from Newton Mosharafa, the British Council. Her research is focused on searching of pesticides against mosquitoes, house flies, lice, green bottle fly, camel nasal botfly, soft and hard ticks, mites, and the diamondback moth as well as control of several parasites using safe and natural materials to avoid drug resistances and environmental contamination.",institutionString:null,institution:{name:"Banha University",country:{name:"Egypt"}}},{id:"99780",title:"Prof.",name:"Omolade",middleName:"Olayinka",surname:"Okwa",slug:"omolade-okwa",fullName:"Omolade Okwa",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/99780/images/system/99780.jpg",biography:"Omolade Olayinka Okwa is presently a Professor of Parasitology at Lagos State University, Nigeria. She has a PhD in Parasitology (1997), an MSc in Cellular Parasitology (1992), and a BSc (Hons) Zoology (1990) all from the University of Ibadan, Nigeria. She teaches parasitology at the undergraduate and postgraduate levels. She was a recipient of a Commonwealth fellowship supported by British Council tenable at the Centre for Entomology and Parasitology (CAEP), Keele University, United Kingdom between 2004 and 2005. She was awarded an Honorary Visiting Research Fellow at the same university from 2005 to 2007. \nShe has been an external examiner to the Department of Veterinary Microbiology and Parasitology, University of Ibadan, MSc programme between 2010 and 2012. She is a member of the Nigerian Society of Experimental Biology (NISEB), Parasitology and Public Health Society of Nigeria (PPSN), Science Association of Nigeria (SAN), Zoological Society of Nigeria (ZSN), and is Vice Chairperson of the Organisation of Women in Science (OWSG), LASU chapter. She served as Head of Department of Zoology and Environmental Biology, Lagos State University from 2007 to 2010 and 2014 to 2016. She is a reviewer for several local and international journals such as Unilag Journal of Science, Libyan Journal of Medicine, Journal of Medicine and Medical Sciences, and Annual Research and Review in Science. \nShe has authored 45 scientific research publications in local and international journals, 8 scientific reviews, 4 books, and 3 book chapters, which includes the books “Malaria Parasites” and “Malaria” which are IntechOpen access publications.",institutionString:"Lagos State University",institution:{name:"Lagos State University",country:{name:"Nigeria"}}},{id:"273100",title:"Dr.",name:"Vijay",middleName:null,surname:"Gayam",slug:"vijay-gayam",fullName:"Vijay Gayam",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/273100/images/system/273100.jpeg",biography:"Dr. Vijay Bhaskar Reddy Gayam is currently practicing as an internist at Interfaith Medical Center in Brooklyn, New York, USA. He is also a Clinical Assistant Professor at the SUNY Downstate University Hospital and Adjunct Professor of Medicine at the American University of Antigua. He is a holder of an M.B.B.S. degree bestowed to him by Osmania Medical College and received his M.D. at Interfaith Medical Center. His career goals thus far have heavily focused on direct patient care, medical education, and clinical research. He currently serves in two leadership capacities; Assistant Program Director of Medicine at Interfaith Medical Center and as a Councilor for the American\r\nFederation for Medical Research. As a true academician and researcher, he has more than 50 papers indexed in international peer-reviewed journals. He has also presented numerous papers in multiple national and international scientific conferences. His areas of research interest include general internal medicine, gastroenterology and hepatology. He serves as an editor, editorial board member and reviewer for multiple international journals. His research on Hepatitis C has been very successful and has led to multiple research awards, including the 'Equity in Prevention and Treatment Award” from the New York Department of Health Viral Hepatitis Symposium (2018) and the 'Presidential Poster Award” awarded to him by the American College of Gastroenterology (2018). He was also awarded 'Outstanding Clinician in General Medicine” by Venus International Foundation for his extensive research expertise and services, perform over and above the standard expected in the advancement of healthcare, patient safety and quality of care.",institutionString:"Interfaith Medical Center",institution:{name:"Interfaith Medical Center",country:{name:"United States of America"}}},{id:"93517",title:"Dr.",name:"Clement",middleName:"Adebajo",surname:"Meseko",slug:"clement-meseko",fullName:"Clement Meseko",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/93517/images/system/93517.jpg",biography:"Dr. Clement Meseko obtained DVM and PhD degree in Veterinary Medicine and Virology respectively. He has worked for over 20 years in both private and public sectors including the academia, contributing to knowledge and control of infectious disease. 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This topic will closely deal with all emerging trends in this discipline.",coverUrl:"https://cdn.intechopen.com/series_topics/covers/15.jpg",keywords:"Phenolic Compounds, Essential Oils, Modification of Biomolecules, Glycobiology, Combinatorial Chemistry, Therapeutic peptides, Enzyme Inhibitors"},{id:"17",title:"Metabolism",scope:"Metabolism is frequently defined in biochemistry textbooks as the overall process that allows living systems to acquire and use the free energy they need for their vital functions or the chemical processes that occur within a living organism to maintain life. Behind these definitions are hidden all the aspects of normal and pathological functioning of all processes that the topic ‘Metabolism’ will cover within the Biochemistry Series. Thus all studies on metabolism will be considered for publication.",coverUrl:"https://cdn.intechopen.com/series_topics/covers/17.jpg",keywords:"Biomolecules Metabolism, Energy Metabolism, Metabolic Pathways, Key Metabolic Enzymes, Metabolic Adaptation"},{id:"18",title:"Proteomics",scope:"With the recognition that the human genome cannot provide answers to the etiology of a disorder, changes in the proteins expressed by a genome became a focus in research. Thus proteomics, an area of research that detects all protein forms expressed in an organism, including splice isoforms and post-translational modifications, is more suitable than genomics for a comprehensive understanding of the biochemical processes that govern life. The most common proteomics applications are currently in the clinical field for the identification, in a variety of biological matrices, of biomarkers for diagnosis and therapeutic intervention of disorders. From the comparison of proteomic profiles of control and disease or different physiological states, which may emerge, changes in protein expression can provide new insights into the roles played by some proteins in human pathologies. Understanding how proteins function and interact with each other is another goal of proteomics that makes this approach even more intriguing. Specialized technology and expertise are required to assess the proteome of any biological sample. Currently, proteomics relies mainly on mass spectrometry (MS) combined with electrophoretic (1 or 2-DE-MS) and/or chromatographic techniques (LC-MS/MS). MS is an excellent tool that has gained popularity in proteomics because of its ability to gather a complex body of information such as cataloging protein expression, identifying protein modification sites, and defining protein interactions. The Proteomics topic aims to attract contributions on all aspects of MS-based proteomics that, by pushing the boundaries of MS capabilities, may address biological problems that have not been resolved yet.",coverUrl:"https://cdn.intechopen.com/series_topics/covers/18.jpg",keywords:"Mono- and Two-Dimensional Gel Electrophoresis (1-and 2-DE), Liquid Chromatography (LC), Mass Spectrometry/Tandem Mass Spectrometry (MS; MS/MS), Proteins"}],annualVolumeBook:{},thematicCollection:[],selectedSeries:null,selectedSubseries:null},seriesLanding:{item:null},libraryRecommendation:{success:null,errors:{},institutions:[]},route:{name:"chapter.detail",path:"/chapters/12029",hash:"",query:{},params:{id:"12029"},fullPath:"/chapters/12029",meta:{},from:{name:null,path:"/",hash:"",query:{},params:{},fullPath:"/",meta:{}}}},function(){var e;(e=document.currentScript||document.scripts[document.scripts.length-1]).parentNode.removeChild(e)}()