**8. Basin Modeling**

The natural geological bodies of the formation level—where the processes of oil and gas formation that took place (and/or are taking place) are oil and gas source formations or horizons (OGSH)—are responsible for the oil and gas potential of various regions. The total oil and gas-producing potential of a particular oil and gas basin (OGB) should be estimated by the amount of OM contained in OGSH. The OGSH are characterized by certain concentrations of OM, types of OM, and a certain volume, i.e., thickness and area of development, as well as the maturity of OM (catagenesis). In order for OGSH (or their combination) to become a focus of oil and gas formation (OGF), the minimum values of HC migration densities from them should be at least 50 thousand tons/km2 (50 million nm3/km2) under ideal accumulation conditions (the immediate vicinity of the reservoir and its optimal thickness). In general, the border focal density of migration can be assumed to be 100 thousand tons/km2 (100 million m3/km2). In order to identify the localization of OGF, it is necessary to determine the area of development and the thickness of the OGSH

as well as the concentration of OM (Corg) in them; it is also necessary to identify the degree of catagenesis of OM, and with the use of the created models of the generation-migration of HC, to calculate the scale of migration for the type of OM corresponding to this OGSH.

On the territory of the TP SB, the Domanik-Tournaisian formation and the Silurian formations (29% and 25% for oil, respectively) play the main role in terms of the scale of oil and gas formation; Lower Permian formations (12% for oil and 22% for gas) can be attributed to less significant ones.

The Domanik-Tournaisian formation was continued from the continent to the sea on the basis of facies constructions and seismic data, according to the results of which reef bodies were identified, outlining the zone of the pre-reef facies of the sublatitudinal strike. Thin layers of domanikoid rocks are found in the section of the clay-carbonate deposits of well No. 1—Pakhancheskaya, which is typical for some areas of the reef facies near the reef body [50]. These interlayers are enriched with OM and are not of interest from the standpoint of large-scale oil and gas formation, but they indicate the relative proximity of the development of domanikoids of the formation scale. The thickness of the Domanik OGSH increases in general from west to east—from 20 to 300 m—as the age range of the formation expands. The average concentrations of Corg vary in the range of 0.6–1.5%. In the work area, the Domanik-Tournaisian OGSH is characterized by the following degrees of catagenesis of OM: MK21 and MK22 [49].

The mudstones of the Lower Ordovician and Upper Cambrian are characterized by shallow-sea facies formation conditions and sapropel organic matter. At the same time, a large proportion of algal OM is noted in Ordovician samples. The degree of transformation of rocks according to bituminology remains relatively low, but the correctness of these definitions is questionable, especially given the large spread of analysis results.

The modern geothermal regime of the TP SB is characterized by the relatively low intensity of the thermal field; the average geothermal gradients in the section do not usually exceed 2.5 ◦C/100 m [25]. In the TPB, the so-called abbreviated ("subdonets") zonality of the catagenesis of OM [49] was established due to the intense geothermal regime in the past (paleogradients of the order of 5 ◦C/100 m), which is characteristic of Paleozoic basins. Table 1 shows the paleodepth dimension of such a scale compared with measurements of the reflectivity of vitrinite Ra (measurements carried out in oil) and Ro (measurements carried out in air) (Table 1) [49,50].

**Table 1.** The dimension of the Paleozoic catagenetic scale of the Timan–Pechora basin and its comparison with the optical indicators of vitrinite [35,36].

The scheme of the distribution of the centers of oil and gas generation of hydrocarbons in the water area of the Timan–Pechora basin is shown in Figure 10.

**Figure 10.** The main centers of generation of the north of the TPP and the directions of migration.

The thicknesses of the OGSH of the Silurian complex in the work area vary in the range of 50–400 m, while the direction of thickness changes and their gradients are aligned with the seismic map of the total thicknesses of O2-D1. Average concentrations of Corg in the OGSH (S1-2) vary in the range of 0.25–0.60% (isocarbs 0.3; 0.5). The organic matter in the Silurian OGSH is characterized by the degree of catagenesis of MK3 (Figure 11).

**Figure 11.** Scheme of catagenesis of OM on the roof of Silurian deposits.

In most of the territory of the TBP, the catagenetic scale has a shortened, so-called subdonets character corresponding to the maximum paleogradient of 5 ◦C/100 m. The scale is justified by numerous data on the definitions of the reflectivity of vitrinite.

The data of analytical geochemical studies made it possible to create a basin model for the studied region. The modeling of the processes of generation, migration, and accumulation of hydrocarbons was carried out using the TemisFlow software package. The geological history of the basin is modeled with backstripping technology, which involves restoring the history of the basin's dives by sequentially removing structural horizons. The modeling of the geochemical history is carried out based on the kinetic model of hydrocarbon transformation based on the work of the French Institute of Petroleum (IFP). The applied modeling method makes it possible to link disparate geochemical and structural materials to assess the qualitative characteristics of oil and gas source rocks and the degree of realization of their potential, as well as to obtain approximate but reasonable quantitative data on the scale of generation and migration of hydrocarbons.

As a result of the work carried out to assess the oil and gas source potential in the Lower-Middle Paleozoic section of the MKM, the main prospects for the formation of possible hydrocarbon accumulations are associated with Silurian oil-producing strata. It was not possible to separate the Lower and Upper Silurian deposits at the research site, and the characteristics of their oil and gas production potential are given together.

To the west of the fault separating the structures of the Pechora–Kolva Aulacogen from the Malozemelsko–Kolguevskaya monocline, a band of the absence of oil and gas source strata is mapped. The scale of the thicknesses of the OGSH of the Silurian complex in the work area is 50–400 m, while the direction of change in thicknesses and their gradients are aligned with the seismic map of the total thicknesses of O2-D1. Average concentrations of Corg in the OGSH (S1-2) vary in the range of 0.25–0.60%.

To create the model, the constructed structural maps for the main reflecting horizons and thickness maps between them were used, the degree of erosion as a result of large interruptions in sedimentation was estimated, and prospective source strata, forecast reservoirs, and fluid barriers of the lower structural floor of the MKM were estimated (Figure 12).

At the initial stage of the work, the 1D modeling method was also used to evaluate the catagenetic transformation of the OM according to deep-drilling data. The modeling of the temperature history of catagenetic changes in rocks was based on T.K. Bazhenova's opinion that in Paleozoic basins, there was a reduced catagenetic zonality due to an increased paleogradient of temperatures of up to 4.5–5.0 ◦C/100 m, as well as data on the modern thermal gradient for mobile foundation blocks (which was the MKM) at 2.4–2.7 ◦C/100 m [6,46].

To assess the reliability of fluid traps and the generation potential of oil source rocks, the results of the logging data analysis for deep wells extrapolated to the territory of the entire site were used. The surfaces of fluid traps and oil source rocks were calculated by the method of convergence in the gap between the main structural horizons, by a proportional division of the thickness between the main deep surfaces. The correction of the depth reference was made based on the borehole data, where it is possible. To assess erosion, it was assumed that the maximum apparent thickness of the eroded complex was almost equal to the thickness of the complex before erosion. Furthermore, the amount of erosion was calculated as the difference between the maximum thickness and the current thickness. At the same time, the paleoterrain at the time of the formation of the analyzed complex was noted, and the thickness of the filling of paleotroughs was excluded from the calculation, for which the correlation of additional horizons was performed [40,48,50].

**Figure 12.** Structural map of the foundation (RH VI) with tectonic zoning [41].

The basin model was carried out on the basis of the data on the geochemical characteristics (including lithology, type of organic matter, and the history of immersion).

It was revealed that the organic matter in the Silurian OGSH in the work area is characterized by a degree of catagenesis from MK2 to MK3, while only in the extreme northern periphery is it up to MK4-5. The main center of generation is shown in Figure 13.

The identification and substantiation of oil source strata in the modeling process was a difficult task due to the small size of the work area and its marginal position in the oil and gas basin. Belonging to the reservoir, fluid trap or oil source strata was determined based on the lithological characteristics of the strata and the content of Corg. Bundles in the Upper Silurian and Upper Devonian Domanik deposits have been tested as oil and gas source strata [3,47,49].

The Upper Silurian deposits in the work area are a layer of clay-carbonate interlayer, which was studied in natural outcrops along the Dolgaya River. An analysis of the GC curve of well No. 1—Naryan–Marsky allowed us to take the thickness of the interlayers with the

oil source potential as 1/3 of the total thickness of the Upper Silurian deposits. The Lower Devonian sediments developed locally; they do not have widespread distribution. Their development is associated with the most loaded sections of the pre-Timan structural stage.

**Figure 13.** (**a**) Scheme of catagenetic zonality of Upper Silurian deposits [47]; (**b**) Scheme of the development of the center of generation and the migration direction of the HC of the Malozemelsko– Kolguevskaya monocline and the zones of its junction with adjacent territories [42].


**3.1. Next generation sequencing**

The NGS technique produces millions of short sequences (typical read length of 125 bp), which represent many unconnected small pieces of a genome or transcriptome, in each flow cell of the sequencing platform per sequence run. With these short sequences, one may *de novo* construct transcripts or genomes, characterize sequence variation (i.e., single nucleotide variation (SNV), insertion, and deletion), quantify sequence architecture (i.e., sequence repeats, copy numbers, and gene expression), and most importantly provide a sequence reference to expand discoveries from one species to another. Over the past decade, the sequence length of NGS (specifically Illumina technology) has significantly increased from 35 bp to current commonly produced 125 bp (Illumina HiSeq), and new long single sequence technology platforms are delivering sequence lengths of up to 40 kb in size (e.g., Pacific Bioscience RSII at 20 kb) that are changing the paradigm for whole genome *de novo* assembly.

different *Xiphophorus* interspecies hybrids have been shown to be melanoma inducible after exposure to DNA damaging agents such as UVB light. Some of these inducible melanoma models involve hybridization of *X. maculatus* and *X. couchianus* with a following backcross of the F1 hybrid to the *X. couchianus* parent. Both the heavy pigmented backcross progeny and F1 hybrids can develop melanoma after UVB or MNU exposure in their early life stage [16–20]. Genomes of aquatic disease models serve as bridges to link phenotypic changes to genetic responses and allow physiological and pathophysiological discoveries from animal models to be applied to human disease research. The sequencing of model system genomes offers researchers great resources for biomedical research. Genome sequences allow researchers to (a) find sequence variation among genomes and transcriptomes between different species and populations; (b) compare genetic response between different phenotypes, development stages, disease conditions, drug treatment, etc.; and (c) discover gene/gene and gene/environment

For *Xiphophorus,* genome sequencing, assembly, and annotation for 3 *Xiphophorus* species (*X. maculatus*, *X. couchianus*, and *X. hellerii*) were accomplished in 2014 ([3, 21] and unpublished data). In the post-*Xiphophorus* genome era, these genomes resources have strengthened the *Xiphophorus* melanoma models by establishing high similarity in gene expression patterns for *Xiphophorus* and human melanoma tumors. The genome assemblies for both parents of an interspecific disease model are now allowing regulatory dissection of melanoma relevant gene expression in hybrids and after tumor-inducing treatments [22]. The gene expression features that characterize metastatic melanoma progression in humans closely mimic those found in *Xiphophorus* melanoma tumors (unpublished data). For the purpose of screening potential antimelanoma compounds, a mutant *Xmrk* gene has been used to make a transgenic medaka (*Oryzias latipes*) fish model that develops melanoma very early after hatching [23, 24]. Whole transgenic melanoma medaka at 3–4 weeks post hatch are being utilized to characterize melanoma disease markers and for use in screening of small compounds for inhibitors of melanoma progression. In this way, several aquatic models systems represent a direct connection from "fish tank" discovery to "bedside" therapeutic application (for additional information on this topic, see https://dpcpsi.nih.gov/sites/default/files/orip/document/

The NGS technique produces millions of short sequences (typical read length of 125 bp), which represent many unconnected small pieces of a genome or transcriptome, in each flow cell of the sequencing platform per sequence run. With these short sequences, one may *de novo* construct transcripts or genomes, characterize sequence variation (i.e., single nucleotide variation (SNV), insertion, and deletion), quantify sequence architecture (i.e., sequence repeats, copy numbers, and gene expression), and most importantly provide a sequence reference to expand discoveries from one species to another. Over the past decade, the

interactions and use these findings to direct medical applications.

64 Next Generation Sequencing - Advances, Applications and Challenges

zebrafish\_workshop\_final\_report\_orip\_website.pdf).

**3.** *Xiphophorus* **genome assembly**

**3.1. Next generation sequencing**

It is beyond the scope of this chapter to examine all of the current and upcoming sequencing technologies, and thus we focus on the most common NGS platform that is currently being employed to establish genomic and transcriptomic resources in aquatic models systems.

The Illumina genome analyzer platform is currently the most widely used NGS system accounting for over 70% of the NGS market [25]. In Figure 1, we illustrate the basic steps of Illumina sequencing technology. The sequencing process starts with preparation of a library. The DNA (for genomic sequencing) or cDNA (for RNA sequencing) sample is sheared, usually by physical, enzymatic, or chemical method, into short fragments predetermined to be a specific size, and then sequencing adaptors are ligated to both ends of each short fragment by annealing. The fragments are then loaded onto a flow cell. The flow cell has oligonucleotides bound to the surface of the flow cell, and their sequences are complementary to the adaptors such that the free end of the fragment is attached to the flow cell via base pairing. A PCR step converts the initial fragment to its complementary sequence, and now both the forward strand and the reverse strand of fragments are bound to the surface of the flow cell (Figure 1). To amplify the signal, PCR is repeated for several rounds resulting in a cluster of copies around the initial copy of a fragment. Cyclic sequencing of these fragment clusters is very similar to Sanger sequencing and utilizes a sequence-by-synthesis process. One of two unique primers is attached to the free end of the bound fragments, and then nucleotides that each carries a different fluorescent reporter tag and a reversible terminator are flowed onto the flow cell. Since each nucleotide contains an elongation terminator, only a single nucleotide can be incorporated into newly synthesized sequences per sequencing cycle. After the nucleotide incorporation, laser sources excite the fluorescent reporter, and an optical sensor scans the entire flow cell to capture colors that represent newly added bases in every cluster. This optical information is converted to a base call for each growing sequence. At the end of each cycle, the terminator is removed and the next cycle continues until the desired sequence length is attained. In paired-end sequencing, after the forward strand sequence is attained, another sequence primer initiates the sequencing of the reverse strand of each fragment.

This massively parallel sequencing platform allows high throughput sequencing. Each flow cell contains 8 lanes with each lane producing 250 million reads (i.e., up to 500 GB/flow cell) with length of each sequence read ranging from 35 bp to 250 (Illumina HiSeq-2500) or 300 bp (Illumina MiSeq). Each sequencing adaptor has incorporated into it a unique barcode in the format of oligonucleotides. Thus, multiple samples from different sources can be pooled together in one lane, and this greatly facilitates the sequencing throughput.

Before subsequent sequence assembly or reference sequence alignment, a quality control step is usually necessary to attain sequences that best represent the biology being studied. A short sequencing result file contains two types of "contaminants" that can hinder the sequence assembly and result in misrepresentation of actual nucleotide sequence: adaptor sequence and low quality base calls. For paired-end sequencing, the length of DNA fragment between the

**Figure 1.** Outline of Illumina genome analyzer sequencing process. (1) Adaptors are annealed to the ends of sequence fragments. (2) Fragments bind to primer-loaded flow cell and bridge PCR reactions amplify each bound fragment to produce clusters of fragments. (3) During each sequencing cycle, one fluorophore attached nucleotide is added to the growing strands. Laser excites the fluorophores in all the fragments that are being sequenced and an optic scanner col‐ lects the signals from each fragment cluster. Then the sequencing terminator is removed and the next sequencing cycle starts.

two adaptor sequences is defined as "insertion size." When the desired sequencing length is longer than insertion size, the short sequencing can contain adaptor sequence in it. This artificial sequence must be trimmed off, so as not to produce significant sequence error in sequence assemblies. Another contaminant, the low quality base call, has many sources, from equipment to sequencing glitches. The quality of a base call is defined as Phred quality score (*Q*Phred score). If we assign *P* as base calling error probabilities [26], then

$$Q\_{\text{Phrod}} = -10 \log\_{10} P$$

To retain the most usable as high-quality sequencing reads, the adaptor sequences are first clipped off, subsequently trim off low-quality base calls at the end of sequencing reads, and finally filter out sequence reads that contain a certain percentage of base calls that are below a defined *Q*Phred score. Several tool software packages are available that can be utilized to perform the read filtering steps (e.g., fastx\_toolkit: http://hannonlab.cshl.edu/fastx\_toolkit/).


**1. Introduction**

Skin, the major portion of the integumentary system, is the human body's largest organ. It spans approximately 2 m2 and is 0.075–0.15 mm thick in the average adult [1]. It acts as the first line of defense to shield the human body from ultraviolet radiation, infection by pathogens, and chemical irritants [2]. Furthermore, skin plays a key role in thermoregulation, immunological function, and maintaining body water balance.

Schade and Marchionini first introduced the term "acid mantle" to describe the slight acidification of the uppermost layer of human skin [3]. The acid mantle is characterized by a pH value of 4–6, as a result of amino acids, fatty acids, sebum secreted by the sebaceous gland, and lactate excreted from sweat. All of these compounds are acidic and when present together on the human skin, become a barrier that prevents bacterial colonization. Another critical skin barrier is the lipid barrier, the extracellular lipid matrix of the stratum corneum (SC) [4], which is composed of free fatty acids, cholesterol and ceramides and functions as a hydrophobic barrier for human skin [5]. A skin barrier schematic is provided in Figure 1.

**Figure 1.** The scheme of the skin barrier. Lipid barrier sits atop the acid mantle and displays a pH value of 4–6. Pathogens can be various bacteria. Slight acidic environment is a disadvantage for bacterial colonization.

Most human-pathogen bacteria are inhibited by the acidic milieu on the surface of normal human skin, but this shield is disturbed when skin is wounded. The tissue beneath skin has a physiological pH of 7.4 [6], which raises the overall pH value at the wound site and provides advantages for bacterial colonization. Bacterial contaminants in wounds, e.g., *Staphylococcus aureus*, interfere with the normal wound healing process.

There are four phases in normal wound healing [7,8]: hemostasis, inflammation, proliferation, and remodeling. During hemostasis the wound is filled with fibrin and coagulated blood. Clots are formed to stop bleeding and seal the wound site until tissues are repaired. During inflammation, histamine is produced by basophils and mast cells to increase capillary permeability, which allows leukocytes such as neutrophils to migrate to the infected wound site and remove dead cells and pathogens. However, a failure in eliminating pathogens or the remaining high pH environment can be primary reasons for chronic wound development. During proliferation, epithelial cells increase in number, granulation tissue forms, and angiogenesis occurs. Healthy granulation tissues should be pink in color and uneven in texture. The final phase, remodeling, may take years to complete. The wound matrix undergoes degradation by metalloproteinases and new extracellular matrix (ECM) is created during remodeling. Scar tissue can form due to degradation or ECM generation disruption. While the alkaline milieu activates protease, which facilitates the removal of damaged components, excessive amounts of protease eventually destroy newly constructed tissue [9]. Moreover, alkaline pH values are usually found in chronic wounds, and are associated with an increased risk of bacterial colonization [10].

pH value is a critical factor in the wound healing process and could offer important physiological condition information regarding skin status and infection. It assists physicians with clinically relevant diagnosis and patient wounds care. It can be used, for instance, to determine whether wounds are infected, becoming chronic, provide monitored, real-time wound status, and ultimately facilitate proper treatment in a more timely manner.

Recently, multiple innovative and elegant smart wound dressings combined with either pH sensors or drug control-released carriers have been extensively studied [11–15]. With these promising technologies, wound monitoring procedures can be visualized and designed for use in clinics and at home. The first step in clinically managing and in self-managing wounds is to understand wound status. Advances in and implementation of such technologies may alter the course of wound care and improve quality of life.

The role of pH value in evaluating skin and wound status will be systematically discussed in this review. We will emphasize its clinical application and highlight significant research that leverages pH to promote precise diagnoses leading to the development of impactful medical devices. We will also discuss pH-related di fferences in caring for adult skin versus neonatal skin, which is thin and requires more rigorous e fforts for e ffective care.