Sediment budget of the Sundarban forests, after Rogers
\\n\\n
These books synthesize perspectives of renowned scientists from the world’s most prestigious institutions - from Fukushima Renewable Energy Institute in Japan to Stanford University in the United States, including Columbia University (US), University of Sidney (AU), University of Miami (USA), Cardiff University (UK), and many others.
\\n\\nThis collaboration embodied the true essence of Open Access by simplifying the approach to OA publishing for Academic editors and authors who contributed their research and allowed the new research to be made available free and open to anyone anywhere in the world.
\\n\\nTo celebrate the 50 books published, we have gathered them at one location - just one click away, so that you can easily browse the subjects of your interest, download the content directly, share it or read online.
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IntechOpen and Knowledge Unlatched formed a partnership to support researchers working in engineering sciences by enabling an easier approach to publishing Open Access content. Using the Knowledge Unlatched crowdfunding model to raise the publishing costs through libraries around the world, Open Access Publishing Fee (OAPF) was not required from the authors.
\n\nInitially, the partnership supported engineering research, but it soon grew to include physical and life sciences, attracting more researchers to the advantages of Open Access publishing.
\n\n\n\nThese books synthesize perspectives of renowned scientists from the world’s most prestigious institutions - from Fukushima Renewable Energy Institute in Japan to Stanford University in the United States, including Columbia University (US), University of Sidney (AU), University of Miami (USA), Cardiff University (UK), and many others.
\n\nThis collaboration embodied the true essence of Open Access by simplifying the approach to OA publishing for Academic editors and authors who contributed their research and allowed the new research to be made available free and open to anyone anywhere in the world.
\n\nTo celebrate the 50 books published, we have gathered them at one location - just one click away, so that you can easily browse the subjects of your interest, download the content directly, share it or read online.
\n\n\n\n\n'}],latestNews:[{slug:"intechopen-supports-asapbio-s-new-initiative-publish-your-reviews-20220729",title:"IntechOpen Supports ASAPbio’s New Initiative Publish Your Reviews"},{slug:"webinar-introduction-to-open-science-wednesday-18-may-1-pm-cest-20220518",title:"Webinar: Introduction to Open Science | Wednesday 18 May, 1 PM CEST"},{slug:"step-in-the-right-direction-intechopen-launches-a-portfolio-of-open-science-journals-20220414",title:"Step in the Right Direction: IntechOpen Launches a Portfolio of Open Science Journals"},{slug:"let-s-meet-at-london-book-fair-5-7-april-2022-olympia-london-20220321",title:"Let’s meet at London Book Fair, 5-7 April 2022, Olympia London"},{slug:"50-books-published-as-part-of-intechopen-and-knowledge-unlatched-ku-collaboration-20220316",title:"50 Books published as part of IntechOpen and Knowledge Unlatched (KU) Collaboration"},{slug:"intechopen-joins-the-united-nations-sustainable-development-goals-publishers-compact-20221702",title:"IntechOpen joins the United Nations Sustainable Development Goals Publishers Compact"},{slug:"intechopen-signs-exclusive-representation-agreement-with-lsr-libros-servicios-y-representaciones-s-a-de-c-v-20211123",title:"IntechOpen Signs Exclusive Representation Agreement with LSR Libros Servicios y Representaciones S.A. de C.V"},{slug:"intechopen-expands-partnership-with-research4life-20211110",title:"IntechOpen Expands Partnership with Research4Life"}]},book:{item:{type:"book",id:"10379",leadTitle:null,fullTitle:"Bioethanol Technologies",title:"Bioethanol Technologies",subtitle:null,reviewType:"peer-reviewed",abstract:"Bioethanol Technologies explores the conceptual and methodological approaches for understanding bioethanol technologies and future perspectives. The book comprehensively covers the global scenario of ethanol production from both food and non-food crops and other sources. This book is a useful resource for those involved with biofuels in general and bioethanol in particular, including energy engineers, researchers, consultants, analysts, policy makers, and professionals in the industry supply chain. This book:
Genome sequencing, assembling and annotation have been major priorities in plant genetics research during the past 20 years. The release of draft reference genomes have typically constituted major milestones and have proven to be invaluable for the analysis and characterization of genome architecture, genes and their expression, diversity and evolution [1–5]. The expansion of sequence information in a growing number of taxa has contributed to comparative studies and the implementation of molecular breeding and biotechnology approaches for crop improvement [6, 7]. The construction of the first plant genomes was made possible by applying considerable resources, coordination and effort to enabling automated Sanger-based sequencing technologies and computational algorithms. Starting in 2005, a series of technological revolutions in DNA sequencing, driven in large part by the goal of affordable personalized genome sequencing, radically changed the sequencing model. First, new technologies drastically increased throughput while reducing costs and times in data collection. Additional technologies then enabled long single-molecule reads and algorithms that were more suitable to resolve complex genomes [8, 9].
In addition to these advances, the genomics community has benefited from the development and implementation of complementary mapping technologies and methods that have facilitated the scaffolding of sequences and integration to genetic maps. This review provides a historical and technical perspective of methods and technologies applied to genome reference assembly in plants as well as current advances and future directions.
The construction of reference genomes was initially enabled by technological advances in sequencing using the Sanger method [10]. During the 1980s and 1990s, the introduction of thermal cycle sequencing, single-tube reactions and fluorescence-tagged terminator chemistry [11] facilitated the development of high-capacity sequencing platforms. Additional improvements in parallelization, base quality assessment, read length and cost-effectiveness were achieved by the development of automatic base-calling and capillary electrophoresis [12, 13]. With no major modifications made in the past years, automated high-throughput Sanger sequencing is performed by parallel reactions that include a mixture of the DNA template, primer, DNA polymerase, and deoxynucleotides (dNTPs). A proportion of dideoxynucleotide terminators (ddNTP) are included in the reaction, each labelled with a different fluorescent dye. DNA molecules are extended from templates using a thermal cycling reaction and terminated by random incorporation of the labelled ddNTPs, which are detected by laser excitation of the fluorescent labels after capillary-based electrophoresis. The differences in dye excitation profiles are recorded and translated by a computer to generate the sequence. Primary analysis software then calls nucleotides from the raw sequences, assigning a corresponding quality score at each position [6, 14].
The complete sequencing of the first bacterial genomes [15,16] as well as the creation of initiatives aimed at sequencing the genomes of
The second Sanger sequence assembly strategy, clone-by-clone, was successfully deployed in projects aimed at complex eukaryotic genomes. In clone-by-clone genome assembly, shotgun sequencing is performed in libraries derived from individual genomic large-insert clones, selected in a minimum tile path according to physical and genetic map information [24, 25]. The most common type of large-insert clone is the bacterial artificial chromosome (BAC), which can stably carry genomic inserts ranging from 100 to 300 kb and is relatively easy to maintain and purify. Accordingly, this method is usually referred to as BAC-by-BAC, although additional vector systems have been used in assembly projects, including yeast artificial chromosomes (YACs), P1 artificial chromosomes (PAC), transformation-competent artificial chromosomes (TACs), cosmids and fosmids. The two major genomic shotgun-sequencing approaches, WGS and BAC-by-BAC, had advantages and disadvantages when applied to Sanger-based sequencing platforms, depending on the genome of interest. The clone-by-clone approach benefited from working in small units, effectively reducing complexity and computational requirements. This approach minimized problems associated with the misassembly of highly repetitive DNA and therefore provided a better, more complete assembly in plants and other complex eukaryotic genomes. WGS projects were computationally intensive and were less effective bridging repetitive regions in complex genomes but benefited from considerably lower cost, time and logistics [14].
The first completed reference plant genome was from the model system
The second published plant genome reference was rice (
The draft reference genome of Maize, one of the most important crops in the world, is considered the last major published plant genome project based primarily on a Sanger BAC-by-BAC strategy [29]. At 2.3 Gb and spanning 10 chromosomes, the nuclear genome of maize is considerably larger than that of rice and Arabidopsis, approximately 3/4 the size of the human genome. A set of 16,848 minimally overlapping BAC clones, derived from an integrated physical and genetic map, were selected and end-sequenced. The assembly was performed after adding additional data derived from cDNA sequences and sequences from subtractive libraries with methyl-filtered DNA and high C0t techniques, resulting in a whole-genome assembly (B73 RefGen_v1) made of 2,048 Mb in 125,325 sequence contigs and 61,161 scaffolds [29]. Unlike the completed genomes of rice and Arabidopsis, most sequenced BACs in the first version of the maize draft genome are unfinished. Gaps and low-quality regions in BACs were not systematically closed by PCR sequencing or other target approaches. Therefore, while the BACs used in the minimum tiling path were mapped, the order and orientation of individual contigs within a single BAC could be incorrect. Subsequent versions of the genome have been improved by targeting gaps and adding alternative sequencing strategies described later in this review.
Finally, it is important to mention that a significant number of plant genome sequencing initiatives have used WGS strategies, which provide a considerable reduction in time and cost associated with cloning, construction, mapping and selection. Sanger WGS genome projects included those of poplar tree, grape, and papaya [30–32]. Later refinements to the process enabled the sequencing of
The high cost and logistics of plant projects based on clone-by-clone Sanger sequencing required extensive funding, the creation of large collaborative consortia and several years of fingerprinting and sequencing work. The cost of the project by the Arabidopsis Genome Initiative has been estimated at US$70 million [36]. The International Rice Genome Sequencing Project (IRGSP), which included groups from 11 different nations, took over 5 years to complete. During its early stages, IRGSP had estimated that the project would take 10 years and cost a staggering US$200 million [37]. The Maize draft genome was accomplished by multiple laboratories at an estimated cost of tens of millions in a joint NSF/DOE/USDA program. It is worth noticing that, while the cost and time required to accomplish Sanger WGS projects are in fact lower than those based on a clone-by-clone approach, they are still considerable for today’s standards. The sequencing of the 1.1-Gb soybean genome, the largest published plant genome based on a Sanger WGS approach, provides an example of such a cost. It was completed in less than two years although it took a group of 18 institutions several million dollars to generate and assemble more than 15 million Sanger reads from multiple libraries with average sizes ranging from 3.3 kb to 135 kb [35].
Besides cost and time considerations, these early Sanger-only projects posed considerable technical challenges. Despite the extensive resources deployed towards the sequencing of the Arabidopsis and rice genomes, which are usually considered as finished, as well as other projects mentioned in this review, they all have representation gaps. A considerable number of gaps correspond to regions that are “unclonable” under the conditions used to prepare BAC and other genomic libraries. Although many of these regions correspond to tandem repeats such as telomeric sequences and other repetitive regions, it may also include gene space [29]. Moreover, the maximum length of quality Sanger reads, usually 800–900 bp, as well as technical issues associated with the sequencing of DNA stretches with strong secondary structures or extensive homopolymers, create conditions for additional sequencing gaps, even in regions with physical coverage.
Finally, most plant genomes are characterized by elevated proportions of highly repetitive DNA and by the presence of segmental duplications or full genome duplications due to polyploidization events [38], which can be problematic during assembly. The 1C genome content in Maize, for example, is smaller than in humans but it consists of higher proportions and larger tracks of high-copy elements such as retrotransposable elements [29, 38]. At least some of the differences between the assembled and estimated genomes of the Maize line B73 could be attributed to the assembly-based collapse of highly similar long terminal repeats (LTRs) at the end of retrotransposons. It is important to note that all the Sanger-only initiatives corresponded to plant species with genomes that were considerably smaller than the average 5.8-Gb plant genome. Plant genomes have a considerably wider size range than in mammals, and in some important crops (e.g. wheat), nuclear genomes can be more than 15 Gb long, well beyond the practical realm of Sanger sequencing. Although BAC-by-BAC approaches can reduce complexity by more than 10,000 fold, Sanger-based assembly remains difficult and prohibitively expensive in plant genomes of moderate or large size. The WGS approach is even more sensitive to the complexity of plant genomes as it increases the potential for assembly artefacts due to haplotype and homeolog collapse in regions with high identity. Reductions in time and cost in WGS projects are achieved at the expense of assembly fidelity in repetitive regions and expanded need for computational resources.
As indicated above, successful whole-genome sequencing projects have been achieved with the use of Sanger technology. However, such projects require dealing with several complicating factors, including high costs and relatively long turnaround times to completion. The emergence of next-generation sequencing (NGS) technologies has changed this paradigm, both by reducing costs and increasing sequencing throughputs, while at the same time introducing complexity related to the relative short reads of NGS reads. Several NGS technologies have emerged in the past 7 to 8 years [for reviews, see refs. 39–41]. All follow a relatively uniform approach to library construction and sequencing. To complete sequencing: (1) universal adapters are ligated at the end of single DNA molecule templates; (2) adapter-ligated DNA templates are amplified via PCR to create a cluster of identical isoforms and (3) clusters are loaded on sequencers and nucleotide incorporations occur in parallel on millions of clusters. These generate an amplified signal that is recognized by the platform and translated into a base call.
The most widely used NGS technology nowadays is the one commercialized by Illumina [42], whose high-throughput instrument, the HiSeq4000, can produce up to 1.5 Tb of sequencing data in approximately 3.5 days.. In the Illumina sequencing platform, sequencing templates generated during library construction are immobilized on a solid surface, and a “bridge PCR” approach allows for the localized amplification of millions of single DNA molecules, thus generating millions of clusters, each containing thousands of copies of the original DNA molecules [43]. Sequencing then is performed using a sequencing-by-synthesis approach where single-base extension allows the incorporation of a fluorescently labelled nucleotide (a blocking chemical moiety at the 3’ hydroxyl end allows the incorporation of one base only). Once incorporated, the label is detected and the resulting signal subsequently translated into a base call. Finally, the fluorescent dye and the blocking 3’ agent are cleaved, allowing the next single base incorporation event to occur. Through the use of alternating cycles of base incorporation, image capture and dye cleavage, the Illumina sequencing technology can produce reads that are up to 300 bp in length. The relatively high error rate (~0.1% or 10 times higher than Sanger sequencing) [39] can be compensated by very high sequencing coverage, thus allowing random errors at any given base position to be ignored below a certain frequency threshold. The relative short read of Illumina sequencing reads can be explained by several noise factors accumulating after each cycle, including phasing, where imperfect single-base incorporation and imperfect cleavage of the dye and 3’ hydroxyl blocking moiety lead to the accumulation of copies of various lengths within a cluster, and the subsequent increase of signal-to-noise ratio after each cycle [44].
According to Michael and Van Buren [45], over 100 plants genomes have been sequenced since 2000, out of which 63% are genomes from various crop species. As indicated above, different Sanger sequencing strategies have been applied with varying degrees of success on several plant genomes. However, the most successful Sanger-based genome assemblies have been obtained from relatively small genomes (Arabidopsis, rice), while
The domesticated tomato genome [60] represents an example of Sanger/NGS hybrid genome assembly. A total of 30,800 BAC clones from three different BAC libraries were shotgun-sequenced and end-sequenced, generating a total of 3.3 Gb of Sanger reads. In addition, 454/Roche shotgun and mate-pair sequencing was performed, both on BAC pools and whole-genome DNA preparation, using different insert sizes and generating a total of 21 Gb of NGS data. The
Because of the relatively cheap costs involved, a large number of plant genomes have been sequenced and assembled using NGS technologies alone. This includes the assembly of the complex tetraploid genome of cultivated cotton (
An example of a smaller, relatively less complex genome assembly is that of the crop species
While a large number of genomes have been sequenced with NGS technologies alone, the relatively short reads of the major NGS platforms that have been used in those assembly projects, combined with the general complexity of most of those genomes, generally require the use of alternative methods to facilitate the assembly or confirm its integrity. These methods rely on the use of various types of NGS libraries, such as mate-pair large inserts, or the use of Sanger-derived sequencing data such as EST or BAC-based shotgun reads. However, scaffolding of NGS contigs, based on using pairing information between NGS reads originating from the same DNA fragment, generally leads to unresolved gaps between contigs, often due to the presence of large repeat regions whose size exceed the length and resolution of short NGS reads. As a result, significant portions of any given scaffold contain large batches of unknown sequences, and of unknown length. To address these issues and improve plant genome assemblies, researchers have developed a series of multifaceted solutions, combining alignment to known public data, such as ESTs or BAC ends, or, when available, reference genomes from related species, integration of physical and genetic map data, or new technologies. Some of these approaches have been described in the next chapter.
NGS assembly strategies based on the use of short reads cannot solve long and identical transposable elements abundantly present in most plant genomes. The use of long reads is expected to address some of those shortcomings and improve the overall quality of
A distinct strategy to long-read assembly, namely, the Illumina TruSeq Synthetic Long-Read (SLR) strategy [68], is also expected to improve the quality of assemblies generated with short reads only. In SLR libraries, genomic DNA is fragmented to ~10 kb and individual indexed Illumina libraries are generated in parallel from highly diluted pools of sheared DNA fragments. After Illumina sequencing and data deconvolution, the original ~10 kb fragments can be reassembled, effectively reducing the complexity level of the assembly and generating very-high quality synthetic long reads that can subsequently be assembled together or used for haplotype resolution.
The use of long reads in
The emergence of NGS technologies has rapidly led researchers to develop methods and assays for variant discovery in various plant genomes. Some studies have shown that Single nucleotide polymorphisms (SNPs) can be discovered in parental inbred lines using next-generation sequencing [69]. Entire mapping populations also have been simultaneously sequenced and genotyped, in a process known as “genotyping-by-sequencing” (GBS) [70, 71], discovering in the process extensive lists of segregating markers within the mapped population [72, 73], that can be completed by using known reference maps or sequences to impute missing marker data from individual haplotypes. Various reduced-representation methods have been employed for NGS-derived SNP discovery in plant species where whole-genome shotgun sequencing still remains too expensive for sequencing more than a few individuals [71]. These methods include the use of restriction enzyme digestion–based assays with methyl-sensitive restriction endonucleases [74, 75], or methods based on sequence capture approaches [76], to sequence and map gene-rich portions of a genome, and allowing the anchoring of SNPs in a relatively unambiguous manner.
More recently, ultradense linkage maps have been created from genotyping by whole genome sequencing of a genetic mapping population. It has been used to place whole-genome sequencing contigs into a map, thus anchoring, and ordering, sequencing of contigs [77]. Such an approach requires using a genetic linkage map as a framework, into which SNPs derived from the whole genome sequencing assembly can be integrated into a genetic framework derived from low coverage whole-genome sequencing data from a segregating population. The genetic position of the sequence-derived SNPs can then be used to assign chromosomal locations to the contigs harboring them. Such an approach has been used in the context of a whole-genome assembly project in barley where genetic anchoring was applied to a whole-genome assembly [78]. SNPs discovered by sequencing individuals from two mapping populations at low coverage (~1×) were placed into genetic maps that had been previously constructed through different means, including SNP array data and GBS, or made from the whole-genome shotgun sequencing data of the population. Their genetic positions then were used to assign chromosomal locations, and integrate into the combined physical and genetic genome framework, approximately two-thirds of all whole-genome shotgun sequencing contigs. While highly effective in plants, where mapping populations are often readily available, it must be noted that such an approach is limited by the overall recombination landscape, and the subsequent relationship between physical and genetic distance within a particular region of the genome [76]. Recombination events in plants often occur in distal regions of the chromosomes, and peri-centromeric regions may require very large mapping populations to improve their resolution. In addition, recent studies have suggested that specific features of the genome, such as chromosomal inversion, translocation and duplication varying between the two parents used to generate the mapping population, may lead to errors and potentially confound genome assemblies.
A large number of genome assemblies have been generated with the help of physical maps and the use of a BAC-by-BAC sequencing approach. While laborious and costly, this approach still remains relevant as it offers multiple advantages over a whole-genome sequencing approach, especially in terms of assembling sequencing reads conserved in the context of a whole-genome assembly but mapping exclusively to a defined portion of a genome in the context of an individual clone assembly. Lonardi
Optical mapping is a single-molecule approach that produces fingerprints using ordered restriction maps [82] or specific nick sites [83]. After enzymatic treatment and subsequent incorporation of fluorescent labels, the DNA molecules are stretched on a glass surface or in a nanochannel array and directly imaged to locate regions corresponding to the restriction sites or nick sites within the molecule. Distances between those sites are then inferred to produce an optical map of the DNA molecule. Two commercial platforms currently are available, namely, the Opgen Argus [84] and the BioNano Genomics Irys [85] systems. Using such techniques, very large DNA molecules, in the Mb range, can be interrogated for the presence and location of short recognition sites (whose sequence will vary with the enzyme being used to treat the DNA). Consensus optical maps then can be created by determining the overlap, under highly redundant conditions, between optical maps of single DNA molecules. Such consensus maps have to take into account the possibility of errors inherent to this type of technology, including star activity and false enzyme cuts, or the possibility of chimeric maps when joining, for example, optically mapped molecules containing paralogous genomic regions.
Optical maps can be used for multiple applications, including comparative genomics and structural variation detection, as well as the development of optical map-guided genome assemblies, where the optical map is aligned and compared to
High-throughput Chromosome capture (Hi-C) is a method that uses cross-linking of DNA-binding protein to DNA followed by restriction digestion and self-ligation of protein-bound DNA fragments, to probe genome-wide three-dimensional chromatin interactions between chromosomal regions bound to the same proteins (such as enhancer and promoter regions) [88]. There is a statistically higher probability that those regions are located on the same chromosome rather than on different chromosomes, as expected within the context of chromosomes located in distinct three-dimensional spaces within the nucleus. As a result, a vast majority of Hi-C read pairs (where each paired reads correspond to reads that may be millions of bases apart from each other on the same chromosome) can be used to determine what two contigs can be linked together on the same chromosome, based on the Hi-C paired reads they each contain.
Burton
Two companies, namely, 10X Genomics [92] (Pleasanton, CA) and Dovetail Genomics [93] (Santa Cruz, CA), recently presented new ways to assemble short reads delivered by the Illumina technology. The GemCode instrument from 10X Genomics is a microfluidic device used to partition very long DNA molecules (typically 50 kb or more) into oil-based droplets and to prepare Illumina-compatible libraries in combination with “gel beads”, each containing a unique 14-bp indexing barcode. Once sequencing is performed, in-house software deconvolutes the barcodes and reconstructs the sequence of the original DNA subfragments as to where they originate from on the original long DNA molecule. In contrast to 10X Genomics, Dovetail Genomics approach does not necessarily require an instrument but requires larger amount of starting material for preparing samples. Dovetail’s approach works essentially by
Reference genomes are now available for a significant number of plant species. The emergence of NGS technologies has made it possible to sequence genomes not only from economically important crop species but also from nonstandard model and special plants whose genomes otherwise might not have been sequenced due to the requirements for large funds, instrumentation and personnel that was witnessed in earlier pre-NGS days. While great progress has been made, assembling such genomes still remains challenging due to their inherent complexity and the relative absence of long-range connectivity, lost during DNA fragmentation and short-read sequencing. As a result, plant genome assemblies tend to be highly fragmented, and focused essentially on unique “gene-rich” regions, while large fractions of the genomes, namely, complex repeat and conserved regions, remain unassembled. Researchers have come up with creative ways to address those shortcomings, including the use of mate-pair NGS libraries, the complementation of physical assemblies with genetic maps, or the use of new technologies for sequencing, physical mapping or scaffolding. It is hoped that the routine use of such novel approaches will help in elucidating the biological aspects of genomes by allowing true comparative and structural analysis between species, strains, tissue or environment.
The authors would like to acknowledge Gregory May for his support and contribution to this book chapter.
Tidal energy influences deltaic components, regulates morphodynamic processes and facilitates onshore sedimentation worldwide [1, 2, 3]. Regular inundation of the intertidal terrain sustains the Ganga-Brahmaputra (G-B) deltaic plain. Since the pre-colonial era, the unified G-B delta region in both India and Bangladesh, witnessed construction of earthen embankments along the tidal channels, rivers, coastal stretches and also within the deltaic plain to prevent flooding, salinity intrusion and land erosion [4, 5]. Referred to by the Dutch term ‘polder’, there are low-lying floodplain tracts which are enclosed by the dykes and used for rice cultivation and aquaculture in Bangladesh [2]. These partly-engineered structures not only restrain standard range of tidal flooding but also seize large areas of formerly intertidal landscape. Over the years, the entangled network of rivers fuelling life to the vast stretch of mangrove forests in both India and Bangladesh Sundarbans, has been reduced and the fresh water discharge has been deterred since the rivers got disconnected due to upstream interferences like large barrage and dam installations [5, 6]. In addition, more complex human interventions due to increased population, irrigation, economic activities in terms of flow of goods and requirement for maintaining larger scale infrastructure have magnified the fragilities of the delta over time. For past centuries, a number of embankments have been built in the south-western side (the Indian Sundarban) totaling to about 3638 km in length [6, 7]. In Bangladesh Sundarban, emerging, more than 129 polders have been constructed in the upstream areas encompassing 13,000 km2 of land or, about 44 percent of the total area in deltaic Bangladesh [6, 8].
Several researches in past few years have documented substantial lowering of coastal tracts indicating greater risk of submergence by sea-level rise and amplified inundation by storm surges [2, 7, 9]. This elevation loss is attributed to the sedimentation within embanked channels conjoined with sediment compaction within intertidal platform and removal of forest biomass [2, 9]. Middlekoop
Created by the confluence of the Ganges, Meghna and Brahmaputra rivers and their myriad distributaries, the Sundarbans constitutes the southern end of the Ganga- Brahmaputra delta in Bangladesh and West Bengal (India). The geographically undivided Sundarban tract (Figure 1) stretches approximately 260 km. west–east along the Bay of Bengal from the Hugli River estuary at the western segment in India to the Meghna River at the east in Bangladesh. Situated at the littoral fringe of the world’s largest deltaic landscape and shrouded by magnificent thicket of mangroves, the Sundarbans has a total area of roughly 10,200 km2, about 60 percent of which is in Bangladesh and 40 percent in India [6]. This intertidal region receives saline influx from the Bay of Bengal twice a day, whilst is also bathed with freshwater flow from the Ganga-Brahmaputra-Meghna River System [12]. Constituted by total 102 islands, the Sundarban Biosphere Reserve (SBR) in India is bordered by 54 inhabited islands to the north with a repugnantly contrasting human-modified landscape and the rest are within the mangrove Reserve Forest area. In Bangladesh the mangroves are sheltered in the Sundarban Reserve Forest which is starkly surrounded by polders, shrimp farms and settlement to the north.
The integrated indo-Bangladesh Sundarbans. Image details: True color image, (Landsat TM, 1992).
Constructed primarily by fluvial processes, the delta is now maintained almost exclusively by tidal actions and contributed by acute water-surface gradients along the interconnecting tidal channels. The major fluvial systems has either disjoined or migrated to the east and eliminated the most direct fluvial input at the Indian section of the delta due to the Farakka barrage or the Ganges Treaty which was operationalized between India and Bangladesh in 1975. Inevitably, it decreased the perennial flow by diverting a maximum 1133 cumec of water through the feeder canal through Bhagirathi-Hugli river system of West Bengal (India) [6]. Due to this upstream diversion, the distributaries of the Bhagirathi-Hugli have either been disconnected by siltation or dried. Presently freshwater in the rivers contributing to Sundarban is negligible or mostly absent except during monsoon months [6]. In eastern section (Bangladesh) Gorai-Modhumoti-Passur river systems still contribute substantially unlike the Mathabhanga-Kapotaksha-Sibsa river system which once was significant but deteriorated subsequently.
Coupled with this severe shortage in fresh water discharge from upstream, especially at the Bengal section, incessant embanking at the downstream water courses has notably affected the salinity regimes in the rivers and creeks of the lower section of the delta including Sundarbans. The lower-gradient fluvio-tidal section in the south-east (Bangladesh) is advancing into the sea with comparatively steady-state channels contrary to the fluvially discarded tidal section in the south-west (India) which is accreting vertically but also declining irreversibly in certain sections [6, 13]. However, periodic flooding of the land surface during the tidal cycle coupled with enormous sediment delivery during the monsoon (wet season) promotes sediment accumulation and heterogeneous surface elevation gain through time [9, 14]. Sediment transport is landward and to the south-west in the Bengal section (India) [13]. Indeed, the flood defensive structures have terminated the pathways of sediment conveyance and inland sediment transport for much of the lower delta region, especially at the south-west section. Thriving at the southern end of the G-B delta and constituting about 47 percent of the deltaic coastline, the Sundarbans as a complex socio-ecological system with i) extended fluvio-deltaic plains, ii) agriculture and shrimp farming and iii) tide-dominated morphodynamic processes, is the focus area of the chapter.
At the dawn of colonial period the Sundarbans was sparsely populated teeming with profuse flora and fauna as pointed out by Hunter in an essay published in his book ‘A Statistical Account of Bengal’ [15]. The East India Company presented an image of the tracts that were not under the government’s lease and thus, they conferred tenure and activated their revenue-yielding process through the conversion of inaccessible ‘wastelands’ into paddy lands as early as 1770s [16, 17]. At this time, they also noticed the dilapidated condition of the hitherto built ‘public’ embankments or mud bunds which were supposed to be maintained by
According to Hunter [15] a major part of reclamation work included in keeping out the lateral flow of saline water and thus, bringing the marsh lands under rice cultivation. In availing this method, all the inlets from the channels were embanked, and smaller channels called
In almost all shallow and active tide-dominated platforms like the southern part of G-B delta, tidal inlets or creeks play a crucial role in governing local morphodynamic behavior and maintaining equilibrium at the landscape level. The equilibrium is achieved by the dynamic interplays among the landscape components which are materials, processes and forms. When the river influx and tidal forcing, averaged over a seasonal cycle are sufficiently steady, tidal channels can evolve towards near-stable morphology. In high discharge phases during wet seasons sediment export is promoted by high transport capacity of rivers which reduces tidal deformation. In contrast, stunted river discharge as a sequel of dry seasons, advocates flooding and facilitates sediment imports only from the estuarine mouth [14]. Hence, the tidal motion balances the delta morphology at the landscape scale as the sediment import during low flow balances sediment export during maximum flow within a seasonal cycle [14, 27]. In fact, the tidal distributaries or creeks, exhibit lesser migration rates and also, are not easily flooded by the river because of opposing non-linear interactivity between river discharge and the tide [28]. This results in more uniform and balanced distribution of discharge across the channels. Historical satellite imagery from the Sundarban mangrove forest depicts that the tidal-channel network in the region has been quasi stable since the 1970s with <2 percent net change in the length of waterways and meager changes in channel widths. Indeed, morphological equilibrium of the tidal inlets is not only dependent on the freshwater discharge, but also sediment transport coupled with grain size characteristics, tidal prism and tidal asymmetry i.e. high energy short duration flood tides, and low energy long duration ebb tides [29].
The bi-directional flow associated with tidal rise and fall, generating huge volume of water inland with amplitude reaching more than 4–7 m during spring tides, is called tidal prism. As the tidal oscillations conduct sediment from the shelf across the delta plain, up to 120 km towards hinterland the tidal prism retains substantial suspended sediment concentrations [30]. Suspended sediment amount may be estimated by the widely applied form:
where, Qs represents suspended sediment discharge (kg s−1) and Q indicates water discharge (m3 s−1). With the propagation of tidal wave up channel non-linear frictional distortions and relative depths of channel beds induce differences in magnitude and duration between flood and ebb tidal waves, also known as tidal asymmetry [33, 34]. The tidal approach of within G-B delta of south-western section (India) depicts pronounced flood dominance and rising tide turns the estuarine channels into sediment sink. Sediment convergence takes place at the turbidity maximum zone (Figure 2) where sediments are trapped by outrushing freshwater discharge and onshore tidal deluge. The sediments typically precipitate as velocities decline at the end of the transport path along the upstream reaches of the tidal channels or on the intertidal mangrove platform and small creeks and the process is further sustained by relatively low flow velocity of the falling tide [30, 35]. This tidal pumping [33] is imperative in facilitating vertical accretion in the plains which receive little or no sediment influx from upstream barring Hugli (India) and Baleshwari river (Bangladesh). Sediment deposition at the Sundarbans mangrove platform is measured up to 96x106 tons per year which is 10 percent of the annual sediment content of the Ganga-Brahmaputra-Meghna river system [6].
(a) Sediment transport pattern within the tide-dominated estuarine landscape, after ozCoasts (
A unit-scale analysis [2] at 48 stations of deltaic Bangladesh, reports that the annual sediment content of the Ganga-Brahmaputra-Meghna river system (~1.1 Gt yr.−1) is competent to aggrade the entire deltaic system at rates of >0.5 cm yr.−1, provided there is an effective riparian energy enabling dispersal of sediment to various reaches of the delta and also, substantial tidal exchanges carrying the sediment inland supplementing to vertical accretion of the delta. Through their seasonal investigations Rogers
Province | Surface area (km2) | Storage (106 t a−1) | Percent of total sediment discharge of the Ganga and the Brahmaputra* |
---|---|---|---|
Bangladesh | 4800 | 62.4 | 6.2 |
India | 3000 | 13–32 | 1.3–3.2 |
Total | 8000 | 77.4–96.4 | 8–10 |
As implied by the studies of Hale
On other hand, Syavitski
Based on the model of Syvitski
Reclamation of the landscape (Figure 3) with hard, consolidated embankment causes wave and current deflection from the base of the wall causing basal scouring and subsequent subsidence and overtopping. As the cross-sectional area is reduced due to exclusion of intertidal part by reclamation, sedimentation takes place on the channel bed and thereby, raises its elevation [39]. On the flip side, the interior part of islands remains sediment starved and thus subsides due to compaction and de-watering [40, 41]. This develops a reverse gradient with lower central position. Once flooded, water enters into the island and is unable to drain back to the channels (Figure 4b).
Embankments and polders in the indo-Bangladesh Sundarbans [
(a) Typical south-western deltaic landscape with embankment, (b) cross-section of the delta plain: River bed lies above the land behind embankment, (c) post-cyclone (‘Amphan’, 2020) damages of earthen embankment in Indian Sundarban.
Formerly, widespread sedimentation could be possible in the active stretches as the tidal distributaries tended to migrate or witness landward transgression across the plain for maintaining their position within coastal energy gradient [38]. But unplanned construction of these flood defensive walls have hindered the channel migration process and reduced the capacity of small channels to navigate into the larger one. Estuarine transgression, however, is a two-stage process in which lateral erosion of the seaward margins of salt marshes and upper mudflats is balanced by vertical accretion on their surfaces so that their landward margins frontier forward. But the embankments are standing between these two processes, permitting the erosion to take place to seaward preventing the accretion to landward [41]. Moreover, a number of interior creeks and estuaries are exposed to unprecedented siltation, especially at the western part of the lower delta stretch, as a consequence of reduction in tidal spill [42].
Four types of embankments are commonly built at the south-western section of the delta: i) 2 m high earthen wall bordering small tidal channels, ii) 2 m high earthen wall with brick pitching on island margins, iii) 3 m high wall with brick pitching on wave exposed coastal tracts, iv) 3.67 m high wall with boulder pitching on eroding stretches [6]. On other hand the tidal creeks of Sundarbans are classed as meso-macro tidal having amplitude ranging from 2 to 5.5 m. The incoming tidal waves during spring tides and wet months often achieve the height of more than 3 m (often 4 m) to overtop the barrier and thereby, enter into the agricultural lands [40]. Clearly, this positive feedback loop discards the embankments as a protective wall from saline water. Further, deep foundation of embankments impairs the dynamic interconnection between ground water table and river by retarding influent and effluent seepage [43]. The embankment on the bank is affected by the hydrostatic pressure causing uplift and dislodgement of such structures. The scouring of the bank along the concave side of meander and heavy weight of overlying structure often leads to collapse of the banks.
Beginning in the late 1960s and continuing to the early 1980s, ~5000 km2 of the low-lying tidal delta plain of Bangladesh section was embanked and converted to densely inhabited, agricultural islands i.e., polders. From this section of Bangladesh Wilson
Standard polder system of the south-eastern section (Bangladesh) of the delta. Siltation within tidal channels result in formation of
Year | Poldered Area | Natural Area | ||||
---|---|---|---|---|---|---|
1973 | 2003 | 2013 | 1973 | 2003 | 2013 | |
Length of tidal channels outside of polders (km) | 1891 | 783 | 782 | 1964 | 1987 | 1981 |
Length of tidal channels obstructed by polders (km) | 0 | 1108 | 1108 | 0 | 0 | 0 |
Length of tidal channels outside of polders with >50% obstruction [ | 0 | 355 | 420 | 0 | 0 | 0 |
−59% | 1% | |||||
45% | 54% | 0% |
Summary of results from GIS analysis (1973–2013), after Wilson
The massive shrinkage in inter-tidal areas by the artificial barriers affected natural ability of the system to respond to and dissipate flood energy. In many parts of the delta, the land behind the barriers is now lower than the inter-tidal areas or channel beds: an apparent sign that the system dynamics has been disrupted (Figure 4). Construction of marginal levees increases channel depth and accentuates flood dominance which further, aggravate sedimentation at the channel bed as the channel tries to restore its equilibrium [46]. The major waterways lose their original widths. Consequently, the ‘conduit’ channel beds procure substantial elevation by infilling processes as opposed to the land behind the embankments. In the state of morphological equilibrium, length of a resonant macro-tidal estuary like the Hugli (Indian section), tends to equal a quarter of the tidal wavelength (L) [46, 47], i.e. 0.25 L. As explained by Bandyopadhyay (1997), the tidal wavelength (L) is determined by the following equation:
Where, T is tidal period (constant in a given locality), g is gravitational acceleration (a constant) and D is mean depth of the estuary (the only variable). Reclamation by restricting the area of tidal spill through marginal embankments increases the mean depth and leaves the estuary out of equilibrium to which it tries to return by active in-channel sedimentation and bank erosion to decrease mean depth [5]. With its length 0.17 (i.e. less than a quarter) of its tidal wavelength, this is the situation of the Hugli estuary [5].
Post-storm (category-I cyclone ‘Aila’, 2009) investigation of Auerbach
On other hand, there has been substantial channel infilling by interlaminated silt and mud in association with reduced tidal prism and current velocities outside polder walls. The combination of these geomorphic responses has led to many channel beds becoming shallower than polder elevations, which exacerbates water-logging in polders [2, 13]. Wilson
Mangrove swamps, with interspersed tidal channels flanked by the estuary, serve as a depocentre for fine sediment. It is important to note that, interaction between fresh water and saline tidal water at the mineral-rich turbidity maximum zone leads to flocculation or aggregation of clay or silt particles, followed by the settlement of macro-flocs [26, 50]. Diurnal and semi-diurnal tidal deluge deforms significantly inside the mesh of mangrove trees and intertwining roots. As the sediment-laden tidal water enters to the platform, the flow speed is slackened by the dense distribution of aerial roots and further, turbulence is generated by flow around the trees and roots. The turbulence induces eddy formation leading to collision of particles and development of flocs. Here, settling of flocculated sediments takes a shorter time (<30 minutes) during the flood-ebb transition. Settling is also enabled by sticking of microbial mucus and percolation of water through animal burrows on the swamp floor [50]. Hence, sediment trapping on the floor plays a dominant role in building new land and further, sheltering mangrove ecosystem.
Reversing tidal flows complement exchange of materials, such as nutrients, dissolved oxygen, mangrove litter etc. between mangrove areas and coastal waters [36]. In addition, viviparous germination of mangroves in association with unique propagule dispersal and subsequent, seedling establishment processes are supported by the gentle slope of bottom substrate, loose bottom sediments and water inundation into the swamp area and channels during the tidal period. Mangrove propagules have an obligate dispersal phase for several weeks before the radicle extends for root development. The dispersal depends on their buoyancy, longevity and action of tides and currents. After the period of obligate dispersal the healthy propagules anchor at the soft, muddy slope of channel banks and swamps. Mangrove propagules are not only the key to mangrove propagation and regeneration, but also are significant storage potentials to atmospheric carbon [51]. Moreover, species-level zonation and distribution of mangroves are attributable to the dispersal and seedling anchorage patterns. For instance, freshly fallen gray mangrove propagules, such as
The mangrove environment should be understood as a component of the total ecosystem that comprises the river basin, river, and estuarine and coastal waters, forming an ecohydrology system that should be considered holistically [17]. Physical processes within the mangrove swamps of the Sundarbans, especially, processes of water movement, are imperative in maintaining the functional characteristics of the mangrove ecosystem and building new land. Water circulation and the dispersion of material in mangrove swamps control both the aquatic and terrestrial biodiversity and nourish mangrove colonies. Frequency of tidal inundation, volume of tidal prism, duration of flooding at long time scales and salinity gradients determine species-level structural and phenological variability of mangrove forests [36]. But the brick dykes along the water bodies have fragmented the network of tidal channels and mangrove areas in the lower stretch of the delta, especially at the south-western section. As the embankments disjoin forest-river alliance in the buffer and transition areas of the Sundarban Biosphere Reserve (SBR, India), it inevitably, influence the tidal inundation pattern at the core area forest swamps. As mentioned before, inflated tidal prism within the enclosed tidal channel further reduces sediment entrainment towards the forest swamps, instead deposit it on the channel bed giving it a higher elevation. Hence, the swamp elevation gets lowered by sediment deprivation over time which, in turn, affects the zonation pattern of mangroves. Looy
Representative vegetation profile along a mud bank without embankment [
Excavation of burrows or ‘bioturbation’ by fiddler crabs (genus
Embankment structures, surrounding the islands, hinder free dispersal of mangrove propagules and thereby, affect mangrove regeneration in the Indian Sundarban (IRS 1D, LISS-III, 2002).
The embanked and poldered landscape is incompetent to withstand the current pace of sea-level rise and storm surges. Even, implementation of management plan is seemingly complicated at the present form of social and political alignments in both the countries. However, there prevails severe lack of researches about environmentally and socially suitable management aspects. Wilson
The role of mangroves in protecting coasts against storms and coastal erosion has been widely acknowledged. Sea level rise and tidal hydraulics entanglements often result in erosion of sea-facing islands and estuary margins and thereby curtail the land area progressively. Indeed, conservation and restoration of mangrove forests are crucial in order to protect the island as well as prevent the surge of sediment input inland. At this juncture, planting mangroves on the artificially built sediment terraces alternated by brick blocks on the embankment slopes might occupy some amount of sediment as well as protect the banks. However, Aamir and Sharma [55] have experimented with the novel ‘Porcupine system’ which regulates flow energy at a definite reach of river, prevents scouring at the bottom river bank and induces sedimentation. A Porcupine is a unit with six bars which are joined by iron nuts and bolts giving it a tetrahedral frame. In real sense, the frame acts as a substitute of a tree in effectuating turbulence generation and resisting sediment entrainment by flow of water (Figure 8). The technique, however, might be applicable in poldered tracts by linking the area with the surrounding tidal channel through a narrow conduit. Once a part of the excessive sediment-laden water is passed to the depressed polder area the porcupine frames on the depressed area could retard the flow energy and facilitate sediment accumulation. Indeed, the height and spacing between the Porcupine frames need to be relative to the amount of incoming water within a tidal cycle.
(a) Sediment deposition around porcupine units in river Brahmaputra, (b) three-dimensional sketch of a porcupine unit, after Aamir and Sharma [
Already established earthen walls pressurize the soft, compressible riverine soils and the collapsing tendency temporarily brings disastrous impacts on the livelihoods of the region. Geotextile as a state-of-the-art geosynthetic-reinforced structure is considered to be one of the useful and cost-effective environmental applications, especially for embankment management [56, 57]. Geotextiles are flexible and permeable continuous sheets of woven, non-woven or knitted fibers or yarns. Geogrids which are uniformly placed array of apertures between their longitudinal and transverse elements, permit direct contact between soil particles on either side of the sheet. Geocells are relatively thick, three-dimensional networks constructed from strips of polymeric sheet. The strips are conjoined to form interconnected cells which are filled with soil and sometimes concrete (Figure 9). Geotextile layers intensify the embankment stability by virtue of two primary functions: tensile reinforcement and as a drainage element reducing pore pressures [58].
Different types of geosynthetic methods to control stability and settlement of embankments. (a) Two-layered geotextiles with folded ends, (b) embankment with vertical piles or geogrids and (c) embankment with geocells [
Apart from the aforementioned methods, plantation of long-rooted vetiver grass (Figure 10) (
Naturally grown clump of vetiver grass at Kuakata, Bangladesh. Image courtesy: Islam [
Estuarine stretch of the G-B delta plain is considered to be a broad system with nature-wetland subsystem and human-social sub-system being interconnected to one another. Embankment as a product of the human-social processes plays a key role in governing the steady-state of the entire system. The ever escalating population has left this fragile plain densely settled. Furthermore, as livelihood generation and increasing demand for food are two key concerns behind agriculture, the inhabitants of this region perform a consistent task of protecting their lands from being swallowed by saline water. Embankments, in fact, made cultivation in apparent saline soil possible since historical past. The system is, however, disturbed and the functions of different components of the landscape are modified due to the stark separation between the two subsystems. While embankment breaching is seemingly destructive to the land use and livelihoods of the inhabitants, the long-term impacts of these walls by far more dubious to the deltaic physical and ecological processes. This chapter documents here, i) changing tidal inundation pattern and morphodynamic characteristics within the tidal channels or primary creeks due to the artificial structures, ii) shifting of sediment deposition and channel infilling as contrasted to previously intertidal deltaic plain and iii) gradual alteration to mangrove functionalities and habitat with respect to seedling establishment, swamp flooding and fragmentation. Most of the suspended sediment that is imported landward on flood tides is instead deposited within channels, resulting in the infilling and closure of >600 km of intertidal channels and emergence of ~90 km2 of new land in the southwest delta [13]. Current researches as representative of mean annual sedimentation in the central fluvial-tidal G-B delta indicates that the cumulative vertical accretion rate (2.3 cm y−1) is over two times higher than sedimentation within the natural intertidal setting of the Sundarbans [61]. Explicitly, the chapter attempts to reassess the previous studies and searches for feasible and sustainable routes to delimit the degree of nature-society conflicts in this embanked landscape.
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He performed post-doctoral studies at Max-Planck Institute, Germany, and University of Florence, Italy in addition to making several scientific visits abroad. He currently works as a Full Professor of Biochemistry in the Faculty of Pharmacy, Anadolu University, Turkey. Dr. Beydemir has published over a hundred scientific papers spanning protein biochemistry, enzymology and medicinal chemistry, reviews, book chapters and presented several conferences to scientists worldwide. He has received numerous publication awards from various international scientific councils. He serves in the Editorial Board of several international journals. Dr. Beydemir is also Rector of Bilecik Şeyh Edebali University, Turkey.",institutionString:null,institution:{name:"Anadolu University",institutionURL:null,country:{name:"Turkey"}}},editorTwo:{id:"13652",title:"Prof.",name:"Deniz",middleName:null,surname:"Ekinci",slug:"deniz-ekinci",fullName:"Deniz Ekinci",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002aYLT1QAO/Profile_Picture_1634557223079",biography:"Dr. Deniz Ekinci obtained a BSc in Chemistry in 2004, MSc in Biochemistry in 2006, and PhD in Biochemistry in 2009 from Atatürk University, Turkey. He studied at Stetson University, USA, in 2007-2008 and at the Max Planck Institute of Molecular Cell Biology and Genetics, Germany, in 2009-2010. Dr. Ekinci currently works as a Full Professor of Biochemistry in the Faculty of Agriculture and is the Head of the Enzyme and Microbial Biotechnology Division, Ondokuz Mayıs University, Turkey. He is a member of the Turkish Biochemical Society, American Chemical Society, and German Genetics society. Dr. Ekinci published around ninety scientific papers, reviews and book chapters, and presented several conferences to scientists. He has received numerous publication awards from several scientific councils. Dr. Ekinci serves as the Editor in Chief of four international books and is involved in the Editorial Board of several international journals.",institutionString:null,institution:{name:"Ondokuz Mayıs University",institutionURL:null,country:{name:"Turkey"}}},editorThree:null},{id:"17",title:"Metabolism",coverUrl:"https://cdn.intechopen.com/series_topics/covers/17.jpg",isOpenForSubmission:!0,editor:{id:"138626",title:"Dr.",name:"Yannis",middleName:null,surname:"Karamanos",slug:"yannis-karamanos",fullName:"Yannis Karamanos",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002g6Jv2QAE/Profile_Picture_1629356660984",biography:"Yannis Karamanos, born in Greece in 1953, completed his pre-graduate studies at the Université Pierre et Marie Curie, Paris, then his Masters and Doctoral degree at the Université de Lille (1983). He was associate professor at the University of Limoges (1987) before becoming full professor of biochemistry at the Université d’Artois (1996). He worked on the structure-function relationships of glycoconjugates and his main project was the investigations on the biological roles of the de-N-glycosylation enzymes (Endo-N-acetyl-β-D-glucosaminidase and peptide-N4-(N-acetyl-β-glucosaminyl) asparagine amidase). From 2002 he contributes to the understanding of the Blood-brain barrier functioning using proteomics approaches. He has published more than 70 papers. His teaching areas are energy metabolism and regulation, integration and organ specialization and metabolic adaptation.",institutionString:null,institution:{name:"Artois University",institutionURL:null,country:{name:"France"}}},editorTwo:null,editorThree:null},{id:"18",title:"Proteomics",coverUrl:"https://cdn.intechopen.com/series_topics/covers/18.jpg",isOpenForSubmission:!0,editor:{id:"200689",title:"Prof.",name:"Paolo",middleName:null,surname:"Iadarola",slug:"paolo-iadarola",fullName:"Paolo Iadarola",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002bSCl8QAG/Profile_Picture_1623568118342",biography:"Paolo Iadarola graduated with a degree in Chemistry from the University of Pavia (Italy) in July 1972. He then worked as an Assistant Professor at the Faculty of Science of the same University until 1984. In 1985, Prof. Iadarola became Associate Professor at the Department of Biology and Biotechnologies of the University of Pavia and retired in October 2017. Since then, he has been working as an Adjunct Professor in the same Department at the University of Pavia. His research activity during the first years was primarily focused on the purification and structural characterization of enzymes from animal and plant sources. During this period, Prof. Iadarola familiarized himself with the conventional techniques used in column chromatography, spectrophotometry, manual Edman degradation, and electrophoresis). Since 1995, he has been working on: i) the determination in biological fluids (serum, urine, bronchoalveolar lavage, sputum) of proteolytic activities involved in the degradation processes of connective tissue matrix, and ii) on the identification of biological markers of lung diseases. In this context, he has developed and validated new methodologies (e.g., Capillary Electrophoresis coupled to Laser-Induced Fluorescence, CE-LIF) whose application enabled him to determine both the amounts of biochemical markers (Desmosines) in urine/serum of patients affected by Chronic Obstructive Pulmonary Disease (COPD) and the activity of proteolytic enzymes (Human Neutrophil Elastase, Cathepsin G, Pseudomonas aeruginosa elastase) in sputa of these patients. More recently, Prof. Iadarola was involved in developing techniques such as two-dimensional electrophoresis coupled to liquid chromatography/mass spectrometry (2DE-LC/MS) for the proteomic analysis of biological fluids aimed at the identification of potential biomarkers of different lung diseases. He is the author of about 150 publications (According to Scopus: H-Index: 23; Total citations: 1568- According to WOS: H-Index: 20; Total Citations: 1296) of peer-reviewed international journals. He is a Consultant Reviewer for several journals, including the Journal of Chromatography A, Journal of Chromatography B, Plos ONE, Proteomes, International Journal of Molecular Science, Biotech, Electrophoresis, and others. He is also Associate Editor of Biotech.",institutionString:null,institution:{name:"University of Pavia",institutionURL:null,country:{name:"Italy"}}},editorTwo:{id:"201414",title:"Dr.",name:"Simona",middleName:null,surname:"Viglio",slug:"simona-viglio",fullName:"Simona Viglio",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002bRKDHQA4/Profile_Picture_1630402531487",biography:"Simona Viglio is an Associate Professor of Biochemistry at the Department of Molecular Medicine at the University of Pavia. She has been working since 1995 on the determination of proteolytic enzymes involved in the degradation process of connective tissue matrix and on the identification of biological markers of lung diseases. She gained considerable experience in developing and validating new methodologies whose applications allowed her to determine both the amount of biomarkers (Desmosine and Isodesmosine) in the urine of patients affected by COPD, and the activity of proteolytic enzymes (HNE, Cathepsin G, Pseudomonas aeruginosa elastase) in the sputa of these patients. Simona Viglio was also involved in research dealing with the supplementation of amino acids in patients with brain injury and chronic heart failure. She is presently engaged in the development of 2-DE and LC-MS techniques for the study of proteomics in biological fluids. The aim of this research is the identification of potential biomarkers of lung diseases. She is an author of about 90 publications (According to Scopus: H-Index: 23; According to WOS: H-Index: 20) on peer-reviewed journals, a member of the “Società Italiana di Biochimica e Biologia Molecolare,“ and a Consultant Reviewer for International Journal of Molecular Science, Journal of Chromatography A, COPD, Plos ONE and Nutritional Neuroscience.",institutionString:null,institution:{name:"University of Pavia",institutionURL:null,country:{name:"Italy"}}},editorThree:null}]},overviewPageOFChapters:{paginationCount:42,paginationItems:[{id:"82914",title:"Glance on the Critical Role of IL-23 Receptor Gene Variations in Inflammation-Induced Carcinogenesis",doi:"10.5772/intechopen.105049",signatures:"Mohammed El-Gedamy",slug:"glance-on-the-critical-role-of-il-23-receptor-gene-variations-in-inflammation-induced-carcinogenesis",totalDownloads:12,totalCrossrefCites:0,totalDimensionsCites:0,authors:null,book:{title:"Chemokines Updates",coverURL:"https://cdn.intechopen.com/books/images_new/11672.jpg",subseries:{id:"18",title:"Proteomics"}}},{id:"82875",title:"Lipidomics as a Tool in the Diagnosis and Clinical Therapy",doi:"10.5772/intechopen.105857",signatures:"María Elizbeth Alvarez Sánchez, Erick Nolasco Ontiveros, Rodrigo Arreola, Adriana Montserrat Espinosa González, Ana María García Bores, Roberto Eduardo López Urrutia, Ignacio Peñalosa Castro, María del Socorro Sánchez Correa and Edgar Antonio Estrella Parra",slug:"lipidomics-as-a-tool-in-the-diagnosis-and-clinical-therapy",totalDownloads:7,totalCrossrefCites:0,totalDimensionsCites:0,authors:null,book:{title:"Fatty Acids - Recent Advances",coverURL:"https://cdn.intechopen.com/books/images_new/11669.jpg",subseries:{id:"17",title:"Metabolism"}}},{id:"82440",title:"Lipid Metabolism and Associated Molecular Signaling Events in Autoimmune Disease",doi:"10.5772/intechopen.105746",signatures:"Mohan Vanditha, Sonu Das and Mathew John",slug:"lipid-metabolism-and-associated-molecular-signaling-events-in-autoimmune-disease",totalDownloads:17,totalCrossrefCites:0,totalDimensionsCites:0,authors:null,book:{title:"Fatty Acids - Recent Advances",coverURL:"https://cdn.intechopen.com/books/images_new/11669.jpg",subseries:{id:"17",title:"Metabolism"}}},{id:"82483",title:"Oxidative Stress in Cardiovascular Diseases",doi:"10.5772/intechopen.105891",signatures:"Laura Mourino-Alvarez, Tamara Sastre-Oliva, Nerea Corbacho-Alonso and Maria G. 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She is also the Global Harmonization Initiative (GHI)",institutionString:"Australian College of Business & Technology",institution:{name:"Kobe College",institutionURL:null,country:{name:"Japan"}}}]},{type:"book",id:"6820",title:"Keratin",subtitle:null,coverURL:"https://cdn.intechopen.com/books/images_new/6820.jpg",slug:"keratin",publishedDate:"December 19th 2018",editedByType:"Edited by",bookSignature:"Miroslav Blumenberg",hash:"6def75cd4b6b5324a02b6dc0359896d0",volumeInSeries:2,fullTitle:"Keratin",editors:[{id:"31610",title:"Dr.",name:"Miroslav",middleName:null,surname:"Blumenberg",slug:"miroslav-blumenberg",fullName:"Miroslav Blumenberg",profilePictureURL:"https://mts.intechopen.com/storage/users/31610/images/system/31610.jpg",biography:"Miroslav Blumenberg, Ph.D., was born in Subotica and received his BSc in Belgrade, Yugoslavia. He completed his Ph.D. at MIT in Organic Chemistry; he followed up his Ph.D. with two postdoctoral study periods at Stanford University. Since 1983, he has been a faculty member of the RO Perelman Department of Dermatology, NYU School of Medicine, where he is codirector of a training grant in cutaneous biology. Dr. Blumenberg’s research is focused on the epidermis, expression of keratin genes, transcription profiling, keratinocyte differentiation, inflammatory diseases and cancers, and most recently the effects of the microbiome on the skin. He has published more than 100 peer-reviewed research articles and graduated numerous Ph.D. and postdoctoral students.",institutionString:null,institution:{name:"New York University Langone Medical Center",institutionURL:null,country:{name:"United States of America"}}}]},{type:"book",id:"7978",title:"Vitamin A",subtitle:null,coverURL:"https://cdn.intechopen.com/books/images_new/7978.jpg",slug:"vitamin-a",publishedDate:"May 15th 2019",editedByType:"Edited by",bookSignature:"Leila Queiroz Zepka, Veridiana Vera de Rosso and Eduardo Jacob-Lopes",hash:"dad04a658ab9e3d851d23705980a688b",volumeInSeries:3,fullTitle:"Vitamin A",editors:[{id:"261969",title:"Dr.",name:"Leila",middleName:null,surname:"Queiroz Zepka",slug:"leila-queiroz-zepka",fullName:"Leila Queiroz Zepka",profilePictureURL:"https://mts.intechopen.com/storage/users/261969/images/system/261969.png",biography:"Prof. Dr. Leila Queiroz Zepka is currently an associate professor in the Department of Food Technology and Science, Federal University of Santa Maria, Brazil. 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He is especially interested in the genetic differentiation pattern and speciation process that correlate to the flashing pattern and mating behavior of some fireflies in Japan. He then worked for Olympus Corporation, a Japanese manufacturer of optics and imaging products, where he was involved in the development of luminescence technology and produced a bioluminescence microscope that is currently being used for gene expression analysis in chronobiology, neurobiology, and developmental biology. 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The applications of this research cover many related fields, such as biotechnology and medicine, where, for example, Bioinformatics contributes to faster drug design, DNA analysis in forensics, and DNA sequence analysis in the field of personalized medicine. Personalized medicine is a type of medical care in which treatment is customized individually for each patient. Personalized medicine enables more effective therapy, reduces the costs of therapy and clinical trials, and also minimizes the risk of side effects. Nevertheless, advances in personalized medicine would not have been possible without bioinformatics, which can analyze the human genome and other vast amounts of biomedical data, especially in genetics. The rapid growth of information technology enabled the development of new tools to decode human genomes, large-scale studies of genetic variations and medical informatics. The considerable development of technology, including the computing power of computers, is also conducive to the development of bioinformatics, including personalized medicine. In an era of rapidly growing data volumes and ever lower costs of generating, storing and computing data, personalized medicine holds great promises. Modern computational methods used as bioinformatics tools can integrate multi-scale, multi-modal and longitudinal patient data to create even more effective and safer therapy and disease prevention methods. Main aspects of the topic are: Applying bioinformatics in drug discovery and development; Bioinformatics in clinical diagnostics (genetic variants that act as markers for a condition or a disease); Blockchain and Artificial Intelligence/Machine Learning in personalized medicine; Customize disease-prevention strategies in personalized medicine; Big data analysis in personalized medicine; Translating stratification algorithms into clinical practice of personalized medicine.",annualVolume:11403,isOpenForSubmission:!0,coverUrl:"https://cdn.intechopen.com/series_topics/covers/7.jpg",editor:{id:"351533",title:"Dr.",name:"Slawomir",middleName:null,surname:"Wilczynski",fullName:"Slawomir Wilczynski",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0033Y000035U1loQAC/Profile_Picture_1630074514792",institutionString:null,institution:{name:"Medical University of Silesia",institutionURL:null,country:{name:"Poland"}}},editorTwo:null,editorThree:null,editorialBoard:[{id:"5886",title:"Dr.",name:"Alexandros",middleName:"T.",surname:"Tzallas",fullName:"Alexandros Tzallas",profilePictureURL:"https://mts.intechopen.com/storage/users/5886/images/system/5886.png",institutionString:"University of Ioannina, Greece & Imperial College London",institution:{name:"University of Ioannina",institutionURL:null,country:{name:"Greece"}}},{id:"257388",title:"Distinguished Prof.",name:"Lulu",middleName:null,surname:"Wang",fullName:"Lulu Wang",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002bRX6kQAG/Profile_Picture_1630329584194",institutionString:"Shenzhen Technology University",institution:{name:"Shenzhen Technology University",institutionURL:null,country:{name:"China"}}},{id:"225387",title:"Prof.",name:"Reda R.",middleName:"R.",surname:"Gharieb",fullName:"Reda R. Gharieb",profilePictureURL:"https://mts.intechopen.com/storage/users/225387/images/system/225387.jpg",institutionString:"Assiut University",institution:{name:"Assiut University",institutionURL:null,country:{name:"Egypt"}}}]},{id:"8",title:"Bioinspired Technology and Biomechanics",keywords:"Bioinspired Systems, Biomechanics, Assistive Technology, Rehabilitation",scope:'Bioinspired technologies take advantage of understanding the actual biological system to provide solutions to problems in several areas. Recently, bioinspired systems have been successfully employing biomechanics to develop and improve assistive technology and rehabilitation devices. The research topic "Bioinspired Technology and Biomechanics" welcomes studies reporting recent advances in bioinspired technologies that contribute to individuals\' health, inclusion, and rehabilitation. Possible contributions can address (but are not limited to) the following research topics: Bioinspired design and control of exoskeletons, orthoses, and prostheses; Experimental evaluation of the effect of assistive devices (e.g., influence on gait, balance, and neuromuscular system); Bioinspired technologies for rehabilitation, including clinical studies reporting evaluations; Application of neuromuscular and biomechanical models to the development of bioinspired technology.',annualVolume:11404,isOpenForSubmission:!0,coverUrl:"https://cdn.intechopen.com/series_topics/covers/8.jpg",editor:{id:"144937",title:"Prof.",name:"Adriano",middleName:"De Oliveira",surname:"Andrade",fullName:"Adriano Andrade",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002bRC8QQAW/Profile_Picture_1625219101815",institutionString:null,institution:{name:"Federal University of Uberlândia",institutionURL:null,country:{name:"Brazil"}}},editorTwo:null,editorThree:null,editorialBoard:[{id:"49517",title:"Prof.",name:"Hitoshi",middleName:null,surname:"Tsunashima",fullName:"Hitoshi Tsunashima",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002aYTP4QAO/Profile_Picture_1625819726528",institutionString:null,institution:{name:"Nihon University",institutionURL:null,country:{name:"Japan"}}},{id:"425354",title:"Dr.",name:"Marcus",middleName:"Fraga",surname:"Vieira",fullName:"Marcus Vieira",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0033Y00003BJSgIQAX/Profile_Picture_1627904687309",institutionString:null,institution:{name:"Universidade Federal de Goiás",institutionURL:null,country:{name:"Brazil"}}},{id:"196746",title:"Dr.",name:"Ramana",middleName:null,surname:"Vinjamuri",fullName:"Ramana Vinjamuri",profilePictureURL:"https://mts.intechopen.com/storage/users/196746/images/system/196746.jpeg",institutionString:"University of Maryland, Baltimore County",institution:{name:"University of Maryland, Baltimore County",institutionURL:null,country:{name:"United States of America"}}}]},{id:"9",title:"Biotechnology - Biosensors, Biomaterials and Tissue Engineering",keywords:"Biotechnology, Biosensors, Biomaterials, Tissue Engineering",scope:"The Biotechnology - Biosensors, Biomaterials and Tissue Engineering topic within the Biomedical Engineering Series aims to rapidly publish contributions on all aspects of biotechnology, biosensors, biomaterial and tissue engineering. We encourage the submission of manuscripts that provide novel and mechanistic insights that report significant advances in the fields. Topics can include but are not limited to: Biotechnology such as biotechnological products and process engineering; Biotechnologically relevant enzymes and proteins; Bioenergy and biofuels; Applied genetics and molecular biotechnology; Genomics, transcriptomics, proteomics; Applied microbial and cell physiology; Environmental biotechnology; Methods and protocols. Moreover, topics in biosensor technology, like sensors that incorporate enzymes, antibodies, nucleic acids, whole cells, tissues and organelles, and other biological or biologically inspired components will be considered, and topics exploring transducers, including those based on electrochemical and optical piezoelectric, thermal, magnetic, and micromechanical elements. Chapters exploring biomaterial approaches such as polymer synthesis and characterization, drug and gene vector design, biocompatibility, immunology and toxicology, and self-assembly at the nanoscale, are welcome. Finally, the tissue engineering subcategory will support topics such as the fundamentals of stem cells and progenitor cells and their proliferation, differentiation, bioreactors for three-dimensional culture and studies of phenotypic changes, stem and progenitor cells, both short and long term, ex vivo and in vivo implantation both in preclinical models and also in clinical trials.",annualVolume:11405,isOpenForSubmission:!0,coverUrl:"https://cdn.intechopen.com/series_topics/covers/9.jpg",editor:{id:"126286",title:"Dr.",name:"Luis",middleName:"Jesús",surname:"Villarreal-Gómez",fullName:"Luis Villarreal-Gómez",profilePictureURL:"https://mts.intechopen.com/storage/users/126286/images/system/126286.jpg",institutionString:null,institution:{name:"Autonomous University of Baja California",institutionURL:null,country:{name:"Mexico"}}},editorTwo:null,editorThree:null,editorialBoard:[{id:"35539",title:"Dr.",name:"Cecilia",middleName:null,surname:"Cristea",fullName:"Cecilia Cristea",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002aYQ65QAG/Profile_Picture_1621007741527",institutionString:null,institution:{name:"Iuliu Hațieganu University of Medicine and Pharmacy",institutionURL:null,country:{name:"Romania"}}},{id:"40735",title:"Dr.",name:"Gil",middleName:"Alberto Batista",surname:"Gonçalves",fullName:"Gil Gonçalves",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002aYRLGQA4/Profile_Picture_1628492612759",institutionString:null,institution:{name:"University of Aveiro",institutionURL:null,country:{name:"Portugal"}}},{id:"211725",title:"Associate Prof.",name:"Johann F.",middleName:null,surname:"Osma",fullName:"Johann F. 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