**Author details**

Roohi Sharifah Ahmad1 \* and Pho Robert Wan Heng2 \*Address all correspondence to<EMAIL_ADDRESS>1 Universiti Putra Malaysia, Serdang, Selangor, Malaysia 2 National University of Singapore, Singapore


3.2.1. Analysis of Güzeloba Mosque in Terms of Configuration

As retrieved from the archives of Muratpa¸sa Municipality, the Güzeloba Mosque's layout plan includes only the mosque itself (Figure 10). The toilets and living quarters accommodating the mosque personnel, which is under construction in the north of the mosque, are not included in the layout plan, and the parking areas in the south and south-west of the mosque are not available.

When the floor plans were examined, we detected that the shops on the south side of the mosque were not included in the licensed architectural projects (Figure 11).

Figure 12 shows the south façade in the construction permit of the mosque and the current use. In the floor plans and sections of the construction permit, where the shops are located, there was Quran school for women, a condolence house, and a multi-purpose hall. Quran learning activities were taking place in a different part of the mosque.

During the architectural project in the Güzeloba mosque, it was observed that the market and glassware units had problems, such as loading goods, since no solution was offered for the service needs of the businesses. In addition, the expansion of the trade units towards the mosque garden could not be prevented, and the marketplace image was formed by the exhibition of the products sold up to the garden wall, causing a negative appearance in terms of urban aesthetics (Figure 13).

**Figure 10.** Layout plan of Güzeloba Mosque.

**Figure 11.** Basement floor plan of Guzeloba Mosque.

**Figure 12.** The Guzeloba Mosque's south façade, drawn in the construction permit/south façade in the current use.

**Figure 13.** The Guzeloba Mosque's south façade drawn in the construction permit/south façade in the current use.


2.4.4. Module Visualize and Hub Genes

We performed genes trend expression analysis of four modules of interest (Figure 12). Interestingly, by analyzing the trend expression of genes in sienna3 module, we found that they are specifically expressed only in the stem, which suggests that they play an important role in the stem. Through further analysis of this module, several hub genes were discovered, such as beta-glucosidase and granule-bound starch synthase (*GBSSI*). This indicates that the specific expression of these polysaccharide-related genes in stems may be related to the content of polysaccharides in stems significantly higher than in other tissues.

In the blue module, Do\_S shows specific expression in this module, several hub genes were detected in each important module, with each gene interacting with many other genes. These genes include bHLH, beta-glucosidase, alpha-L-fucosidase, and other genes related to *Dendrobium* polysaccharide and secondary metabolism. In salmon4 module, Do\_S shows specific expression in this module, hub genes include *CCR*4 (cinnamoyl -CoA reductase), bZIP, and MYB transcription factors were identified. In lightsteelblue1, a large number of genes were annotated to *ketohexokinase* (*KHK*). *KHK*, also known as fructokinase, which is a key enzyme in fructose metabolism. Fructose is a kind of plant polysaccharide, which suggests that this module is related to polysaccharide biosynthesis.

**Figure 12.** Expression profile and transcriptional regulatory network associated with the tissue-specific modules. (**a**), (**c**), (**e**), and (**g**) heatmaps showing genes in module that were significantly over-represented in Dm\_L, Dm\_R, Dm\_S, Do\_L, Do\_R, Do\_S, Dh\_L, Dh\_R, Dh\_S and predicted transcriptional regulatory

network associated with the gene sets showing expression patterns at Dm\_L, Dm\_R, Dm\_S, Do\_L, Do\_R, Do\_S, Dh\_L, Dh\_R, and Dh\_S. Heatmaps show the expression profile of all the co-expressed genes (number given on the top) in the modules (labelled on top). Candidate hub genes are shown in rectangular shapes. Purple in figure (**b**, **d** and **h**) represents genes related to polysaccharides. Red in figure (**d** and **f**) represents genes related to secondary metabolites. The shapes, from big to small, indicate the weights from big to small. Green in figure d represents bHLH transcription factors. Green in figure (**f**) represents bZIP transcription factors and yellow represents MYB transcription factors.

#### **3. Discussion**

Traditional biological research focuses on elucidating the effects of individual functional elements (such as DNA, mRNA, and protein) on life activities at the molecular level. Although those methods are of great significance for revealing the genetic mechanisms of specific traits, it can only partially explain the cause of a certain life activities. With the rapid development of sequencing technology, traditional biological research cannot fully and effectively explore the biological significance contained in massive data. As a research method of systems biology, the network is widely used in the exploration of life sciences with the help of data of genome, transcriptome, and metabolome. Compared with other regulatory networks, WGCNA can screen for genes related to specific traits and perform modular classification from large samples to obtain highly biologically significant co-expression modules, which has proven to be an efficient data mining method [35].

WGCNA has been widely used in plants in recent years. In order to obtain key expression modules and key hub genes related to drought resistance in *Brassica napus* L., WGCNA was used to analyze *Brassica napus* transcriptome data in multiple samples (48 transcriptome data), the well-watered and droughted networks contained 17 and 20 modules, respectively, suggesting that there are additional expression patterns in the droughted network because of rearrangement of the transcriptome in response to the drought treatment. [36]. In the study of *Fragaria* L. flowers [37], researchers generated different tissue- and stage-transcriptomic profiling of woodland strawberry (*Fragaria vesca*) flower development, they discovered a developing receptacle-specific module exhibiting similar molecular features to those of young floral meristems and hub genes of the strawberry homologs of a number of meristem regulators, including LOST MERISTEM and WUSCHEL in the developing receptacle network. [37]. Analysis of the pollen transcriptome of three male sterile lines using weighted gene co-expression network analysis revealed that two modules were significantly associated with male sterility and many hub genes that were differentially expressed in the sterile lines [38]. Farcuh et al. used WGCNA to investigate sugar metabolism during leaf and fruit development of two Japanese plum varieties, and identified 11 key sugar metabolism-related genes, the results showed that sugar metabolism was reprogrammed in a non-climacteric bud mutant of a climacteric plum fruit and showed an increase in sorbitol synthesis [39]. In *Ginkgo biloba*, a total of 12 gene modules were revealed to be involved in flavonoid metabolism structural genes and transcription factors by constructing co-expression networks, they reveal that some hub genes operate during the biosynthesis by identifying transcription factors (TFs) and structure genes and seven key hub genes were also identified by analyzing the correlation between gene expression level and flavonoids content [40]. Through these studies, it was found that many of the hub genes obtained by WGCNA analysis were indeed very important genes. In order to obtain the hub gene related to the synthesis and regulation of Dendrobium polysaccharides and alkaloids, we also performed WGCNA analysis.

Therefore, we constructed a *Dendrobium* gene co-expression network using a WGCNA approach and identified co-expression modules using transcriptome data from three kinds of *Dendrobium* species and three different tissues. Correlation analysis between co-expression modules and two traits (species and tissues) was carried out, and four highly significant active ingredients-related modules (*p*-value < 0.05) were identified. These modules consist of highly connected functional genes, and different modules appear to be involved in individual functions [41]. Meanwhile, KEGG pathway enrichment analysis of modules associated with polysaccharide and secondary metabolism indicated that these pathways in different *Dendrobium* species and different tissues are related to each other at the transcriptomic level. In sienna3 module, we found that several hub genes related to polysaccharide biosynthesis, such as *KHK* (*ketohexokinase*) which is a key enzyme in fructose metabolism. In the expression trend of this module, the stem has a clear advantage, indicating that the polysaccharide content is indeed concentrated on the *Dendrobium* stem, which is consistent with our previous determination of the polysaccharide content. Meanwhile, in blue module, we found that not only the hub genes related to polysaccharide, but also related to secondary metabolism. In the expression trend, we found that the stem of *Dendrobium o*ffi*cinale* to be the highest. This result is consistent with the trend in the determination of polysaccharides and alkaloids. The results also indicated that one component can be regulated by multiple modules, and one module can simultaneously be associated with multiple components.

Module hub genes are generally considered representative of a given module in a biological network. Previous studies reported that MYB-bHLH-WDR (MBW) ternary complexes comprise the essential regulatory machinery for catechin and anthocyanin biosynthesis [42]. In the present study, transcription factors MYB and bHLH were identified as hub genes in modules related to secondary metabolism. In addition, several genes involved in polysaccharide and secondary metabolism biosynthesis (*CCR4: cinnamoyl -CoA reductase* and *KHK: ketohexokinase*) were identified in modules. MYB transcription factors play an important role in the regulation of phenylpropane biosynthesis. Phenylpropane synthesis is upstream of the regulation of flavonoid biosynthesis, indicating that MYB is also an important transcription factor for the synthesis of flavonoids. In gentian, both GtMYBP3 and GtMYBP4 can activate the gene expression of flavonol synthesis, and then significantly increase the flavonol content in seedlings [43]. Ginkgo GbMYBF2 inhibits the expression of *CHS* (*chalcone synthase*), *F3H* (*flavanone 3-hydroxylase)*, *FLS* (*flavonol synthase*, Flavonol synthase and ANS genes) on the phenylpropane synthesis pathway, thereby reducing the content of flavonoids and anthocyanins [44]. *Salvia miltiorrhiza* SmMYB39 affects the synthesis of rosmarinic acid by regulating the expression of key enzyme genes of the phenylpropane metabolic pathway [45]. Current studies indicate that plant bHLH transcription factors are involved in regulating various signal transduction and anabolic pathways, such as light signal transduction, hormone synthesis, glandular and root hair development, and stress [46–49].

In this study, the WGCNA method was used for the first time in *Dendrobium*, and the modules related to specific tissues and genes related to specific traits were identified. Hub genes were further analyzed to find related genes and predict gene functions [30]. Combining the WGCNA method and RNA-Seq data can be used to better mine the genes and transcription factors related to traits. In strawberry, modules related to tissue specificity such as torus were found in strawberry, and 7 hub genes were identified in torus tissue [37]; in tomato, genes related to vitamin C biosynthesis were found [50]; co-expression modules related to acidity and genes related to anthocyanin synthesis were found in apple [33,51]. In addition, specific modules in other tissues such as roots, leaves, flowers, and fruits at other periods can be excavated to find relevant metabolic processes and important genes and potential transcription factors.


**3.4 Compaction**

The filler materials used in the pasting compost at 20% volume rate are viewed in **Figure 6**. Shale particles contained high porosity reaching 7.8% in the compost. The

**Figure 7.** *Relative compaction changes of paste fill with Şırnak limestone, asphaltite slime char, and Şırnak shale after load indentation.*

limestone's water absorption values were lower with asphaltite slime at about 2–3.5%. The filler mixing combinations are given in **Table 7**.

The effect of fly ash and Şırnak asphaltite and shale on compost density with asphalt mixing is illustrated in **Figure 7**.

In this study, the mechanical properties of local limestone and mine waste stone of Şırnak asphaltite slime and shale are used as filler for the purpose of asphalt sludge filler paste production. The waste slime asphaltite and Şırnak char are ground below 4 mm at the coarser part of 5% weight ratio. Şırnak shale and 15% Silopi fly ash are prepared as a binder cementing matter of sludge mixture of paste. The pressed blocks were manufactured in 50 50 10 mm like pile blocks, 10 mm thick bending strength, impact resistance, friction, abrasion loss, compaction distance were determined by the experiments. The ability of paste in the pile blocks to compact loss asphalt bitumen and water desorption are analyzed.

These experiments show that local rock cement mixtures and elaborate the application of cementing technique with silica fume used and it prevents the coating applied to moisturize the strengthening of historic buildings Sirnak region as a result and is determined to carry out the consolidation.

#### **3.5 Shear load and compression strength analysis**

It is determined that the 90°C temperature accelerates the melting of asphalt bitumen. These technological applications can be further developed with the evaluability of local natural stone powder in paste backfill. The strength of sludge paste pile blocks produced is reduced 7.2 to 6.4 MPa. Lower asphalt weight increased mechanical strength of pasted pile block with compaction been advantageous. Thus, the ideal compacting load of 100 kg tight aggregates with the block and pasted block resistance of the produced slag mixture may arise from 8.3 to 9.2 MPa.

*Hazardous Waste Granule Composting by Cycled Retort Using Microwave Radiated… DOI: http://dx.doi.org/10.5772/intechopen.101676*

**Figure 8.** *Compression strength of paste fill material rocks.*

#### **Figure 9.** *Point load I strength of paste fill material rocks.*

The results are shown in **Figures 8** and **9**. Indentation tests of the rock types were determined by a drill machine at 10 mm bit diameter due to the correlation of rock strengths underground mining cavity conditions.

#### **3.6 Paste fill block production and compaction analysis**

Asphalt and fly ash binders are raised to 10–45% weight ratio at different mixtures and 20% wet hazardous sludge and strength properties of prepared mixture paste with asphalt melted compost.

The water/binder (w/B) ratio is decided to be 20%/10–45% as a result of preliminary experiments. Pasting 5% melted asphalt is sufficient. The amount of each series fly ash composting fines are sorted asphalt and sludge in pile blocks and determined the compressive strength after drying blocks.

#### **Figure 10.**

*Char addition weight of pile paste blocks with paste fill vs. UCS test results: 1. Shale 2. Sirnak limestone 3. Sirnak limestone.*

#### **4. Conclusions**

Fly ash fine-texture and sludge mixing were homogeneous and the contamination act of sludge decreased at half amount rate by addition of 20% fly ash addition to paste mixture. The char carbon will also ten times decrease the metal contamination to water sources. The texture of low asphalt and emulsified hıgh bitumen content lowered the compaction resistance by increasing structure strength.

Especially the compact loading resistivity increased over 1500 kg for 70 mm barrel loading on which the resistance is kept as high as 20 mm displacement as high. Sand content of sludge was lower than the limestone so that this gradation provided high durability and less cracking during compaction loading final product briquettes and lower abrasion resistance.

**Figure 10** shows the 1000 kg loading was suitable for long durability and optımum briquetting outputs. The stability was varied depending on the amount of fly ash and Şırnak asphaltite slime contained in the pasting relative to the pore contents in the micro-structural texture of asphalt compost. The pore density will decrease by low asphalt content and compaction resulting in the development of impermeable surface on the compost briquettes consequently.

The apparent uniaxial compressive strength test of Şırnak limestone showed sufficient substrate gradation and porous texture with high Los Angeles values of 67% at 4.5 mm granules. The gradation was suitable for high compaction ability and Şırnak limestone exhibited low porosity and water sorption 0.8%.

The higher compaction over 1000 kg provided sufficient permeability and compression strength values and higher shear resistance with lower cracking over time period of dynamical stress loads related to landfill application.

#### **Symbols**

*Hazardous Waste Granule Composting by Cycled Retort Using Microwave Radiated… DOI: http://dx.doi.org/10.5772/intechopen.101676*


**1. Introduction**

The ocean is the biggest ecosystem of our planet. Plenty of organisms live in the ocean, and new species are discovered every year. As well, being the oldest ecosystem, marine organisms have evolved for a longer time than terrestrial living beings, and thus have different and sometimes better mechanisms of defense. These are represented by specific compounds, like toxins found in fish and algae and other bioactive substances found in sponges or tunicates. Usually, the real producers of these compounds are microorganisms such as bacteria, cyanobacteria, or dinoflagellates. The interesting properties of some of these metabolites have attracted the attention of the scientific community. As they are usually scarce and difficult to obtain in large amounts, total synthesis has emerged in the last decades as a necessary tool to tackle this problem. It has helped to clarify the structure of some intriguing compounds, and to obtain higher amounts of them in order to perform proper biological studies. Total synthesis is still a crucial tool, as even with today's advanced NMR techniques, misassignment of the structure of biologically relevant macrolides is a common issue [1].

Polyketides are a diverse class of metabolites, comprising linear as well as macrolide compounds with a range of biological activities. Some of them have promising potential as drug candidates [2]. Common sources of this class of compounds are dinoflagellates of the genus *Amphidinium* [3]. To understand how to access the macrolide core present in these and other structures within natural products, we encourage the reader to review general macrolactonization methods [4].

On the other hand, oxygenated heterocycles are common motifs in marine bioactive compounds, and therefore the development of methods for their synthesis also requires attention. The most common are six-membered oxacycles, tetrahydropyrans, and thus numerous works focus on their synthesis [5,6]. Oxepanes and tetrahydrofurans also appear in a very large number of marine natural products with interesting properties. Oxepanecontaining marine compounds were recently reviewed by our group [7]. Total syntheses of marine and non-marine products containing 2,3,5-trisubstituted tetrahydrofurans (such as kumausallene or petromyroxol) have been recently reviewed by Fernandes [8,9].

Continuing our interest for marine heterocyclic compounds, here we provide an overview, from 2013 to October 2021, of tetrahydrofuran-containing marine polyketides.

**Citation:** Fernández-Peña, L.; Díez-Poza, C.; González-Andrés, P.;Barbero, A. The Tetrahydrofuran Motif in Polyketide Marine Drugs. *Mar. Drugs* **2022**, *20*, 120. https://doi.org/10.3390/ md20020120

Academic Editor: Vassilios Roussis

Received: 2 January 2022 Accepted: 1 February 2022 Published: 3 February 2022

**Publisher's Note:** MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

**Copyright:** © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

The compilation of literature on THF-containing macrolides up to 2012 was covered in an excellent review [10]. Macrolides is such a fertile field that some particular families of compounds have already been reviewed, such as haterumalides and biselides [11], or more recently, mandelalides [12]. In recent years, numerous synthetic approaches to the polyketide family continue to emerge, and here we offer an overview of them.

#### **2. Polyketide Marine Drugs Containing Tetrahydrofuran Rings**


**5. ECM proteolysis and the generation of synaptic signaling molecules**

Endogenous ECM-modulating enzymes regulate synaptic function in the juvenile and adult brain [25,26]. Such enzymes can exert their function by either altering the extracellular milieu via digestion of the ECM or by generating proteolytic fragments that may act as signaling molecules. An important group of such enzymes are the metalloproteases of the ADAMTSfamily (a disintegrin and metalloproteinase with thrombospondin motifs). Within this family, ADAMTS-4/-5 are particularly interesting, as they are known for their ability to digest aggrecan and brevican. Therefore, they have been termed previously aggrecanase-1/-2. The current terminology, however, better reflects the ability of these enzymes to digest all members of the lectican family. Interestingly, their activity is increased after epileptic seizures and regulates homeostatic plasticity [27]. However, their impact on synaptic plasticity remains elusive and is subject of current research. The best-studied extracellular protease is the matrix metalloprotease 9 (MMP9). The activity-dependent expression of MMP9 influences synaptic plasticity by regulating spine enlargement and synaptic potentiation [25]. Recently, a molec‐ ular signaling cascade regulating synaptic plasticity has been identified based on the MMP-9 dependent cleavage of neuroligin-1 [28]. This study has demonstrated that focal activation of a single spine by glutamate uncaging is sufficient to cleave neuroligin-1. Moreover, the activity of MMP9 has been shown to be NMDA-receptor dependent and hence implemented locally input-specific forms of synaptic plasticity. Thereby, extracellular MMP-9 triggers a specific retrograde regulation of presynaptic efficacy by targeting postsynaptic neuroligin-1 [26,28]. Similarly, the brain-specific serine protease neurotrypsin is regulated in an activity-dependent manner and requires concomitant activation of the postsynaptic neuron [29]. Proteolytic cleavage of agrin by neurotrypsin unmasks a signaling molecule harboring a single laminin G3 domain. This 22 kDa molecule can further regulate spine morphology and de-novo synapse generation. Together, this suggests that proteolysis of components of the ECM by exoenzymes not only modify the structural rigidity, but also activates instructive signal molecules that locally modulate synaptic functions [25]. This may temporally restore local divisions of "juvenile" environments as a major constituent of the balance between plasticity and tenacity in the mature brain.

We have shown that the ECM in the adult brain is a plastic structural scaffold shaped by network activity. Depending on the current activity level, the ECM can incorporate secreted components or release signaling messengers by proteolytic cleavage. Cleaved products can trigger signaling through diverse ECM receptors and modulate the activities of transmitter receptor, ion channels, or integrin signaling impacting on plastic shaping of individual synapses.