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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 14240

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Dr. Mikhail P. Ponomarenko

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Institute of Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia
Interests: DNA sequence analysis; mutation; single-nucleotide polymorphism (SNP); quantitative sequence-activity relationships; DNA-protein affinity; TATA-binding protein binding site (TATA box); genome-wide prediction in silico; experimental verification; in vitro; in vivo; hereditary disease

Special Issue Information

Dear Colleagues,

Developmental biology investigates ontogenesis that is how step-by-step, single cells (e.g., animal zygotes) turn into multicellular organisms of proper shape, size and structure, which altogether provide all functions during whole life cycle. Molecular mechanisms of both signal transduction and gene regulation networks are elementary basis of ontogenesis within biological organization hierarchy, where they interfere with each other from cellular processes (e.g., differentiation and migration) through morphogenesis up to whole life cycle. As for embryogenesis, among the top achievements of both experimental and computational approaches, which are mutually enriching one another to reconstruct the Drosophila segment polarity gene-network, that is a well-established molecular mechanism of the fruit fly initializing segmentation during 3 hours just after fertilization until embryo of 14 para-segmental units. Respecting to morphogenesis, one of the breakthroughs of combined experimental-computational techniques focused on gene-network of synthesis, diffusion and active transport of auxin in Arabidopsis is certainly the high-resolution 3D-map of cell cycle stages from the root meristem up to the layers of completely differentiated cells. In the matter of life cycle, amongst the greatest successes of the computational models using the experimental signaling network in-between all the 959 cells including all the 302 nerve cells of Caenorhabditis elegans is indisputably accepted a real-time in silico simulator of how nematodes find food and avoid obstacles. In reference to evolutionary limitations within developmental biology, the recent cross-kingdom comparison between animals, plants and fungi integrated the developmental hourglass concept into a modern paradigm of transcriptome ontogenetic switches. Apropos normal development, everything develops normally, whereas developmental abnormalities - premature aging, neurodegeneration, tumorigenesis, induced pluripotent cells, wound healing, post-traumatic repair, regeneration, assisted reproductive technologies, stress-induced epigenetic reprogramming, - which have just become challenges for the post-genome experimental-computational biology, are waiting for their pioneers able to contribute predictive preventive personalized participatory (4P) medicine.

Dr. Mikhail P. Ponomarenko
Guest Editor

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Keywords

animal
plant
fungus
biological organization hierarchy
evolutionary limitations
fertilization
zygote
cell cycle
stem cell
meristem
cell layer
tissue
embryo
multicellular organism
ontogenesis
morphogenesis
life cycle
molecular mechanism
signal transduction
gene regulation
gene-networks
cellular process
differentiation
migration
segmentation
high-resolution 3D-map
real-time in silico simulator
developmental hourglass
transcriptome ontogenetic switch
developmental abnormality
premature aging
neurodegeneration
tumorigenesis
atherogenesis
autoimmunity
induced pluripotent cell
wound healing
regeneration
assisted reproductive technologies
epigenetic reprogramming
predictive preventive personalized participatory (4P) medicine

Published Papers (11 papers)

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Editorial

Jump to: Research

4 pages, 195 KiB

Open AccessEditorial

Developmental Biology: Computational and Experimental Approaches

by Mikhail Ponomarenko

Int. J. Mol. Sci. 2023, 24(13), 10435; https://doi.org/10.3390/ijms241310435 - 21 Jun 2023

Viewed by 901

Abstract

Developmental biology studies ontogenesis, the individual development of an organism from the time of fertilization in sexual reproduction or its expelling from the maternal organism in asexual reproduction to the end of an organism’s life, with all phenotypical characters typical of this biological [...] Read more.

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

Research

Jump to: Editorial

39 pages, 11069 KiB

Open AccessArticle

Molecular Basis for the Involvement of Mammalian Serum Albumin in the AGE/RAGE Axis: A Comprehensive Computational Study

by Daria A. Belinskaia, Richard O. Jenkins and Nikolay V. Goncharov

Int. J. Mol. Sci. 2024, 25(6), 3204; https://doi.org/10.3390/ijms25063204 - 11 Mar 2024

Viewed by 470

Abstract

In mammals, glycated serum albumin (gSA) contributes to the pathogenesis of many metabolic diseases by activating the receptors (RAGE) for advanced glycation end products (AGEs). Many aspects of the gSA–RAGE interaction remain unknown. The purpose of the present paper was to study the interaction of glycated human albumin (gHSA) with RAGE using molecular modeling methods. Ten models of gHSA modified with different lysine residues to carboxymethyl-lysines were prepared. Complexes of gHSA–RAGE were obtained by the macromolecular docking method with subsequent molecular dynamics simulation (MD). According to the MD, the RAGE complexes with gHSA glycated at Lys233, Lys64, Lys525, Lys262 and Lys378 are the strongest. Three-dimensional models of the RAGE dimers with gHSA were proposed. Additional computational experiments showed that the binding of fatty acids (FAs) to HSA does not affect the ability of Lys525 (the most reactive lysine) to be glycated. In contrast, modification of Lys525 reduces the affinity of albumin for FA. The interspecies differences in the molecular structure of albumin that may affect the mechanism of the gSA–RAGE interaction were discussed. The obtained results will help us to learn more about the molecular basis for the involvement of serum albumin in the AGE/RAGE axis and improve the methodology for studying cellular signaling pathways involving RAGE. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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18 pages, 3815 KiB

Open AccessArticle

Loss of ERβ Disrupts Gene Regulation in Primordial and Primary Follicles

by Eun Bee Lee, V. Praveen Chakravarthi, Ryan Mohamadi, Vinesh Dahiya, Kevin Vo, Anamika Ratri, Patrick E. Fields, Courtney A. Marsh and M. A. Karim Rumi

Int. J. Mol. Sci. 2024, 25(6), 3202; https://doi.org/10.3390/ijms25063202 - 11 Mar 2024

Viewed by 607

Abstract

Loss of ERβ increases primordial follicle growth activation (PFGA), leading to premature ovarian follicle reserve depletion. We determined the expression and gene regulatory functions of ERβ in dormant primordial follicles (PdFs) and activated primary follicles (PrFs) using mouse models. PdFs and PrFs were isolated from 3-week-old Erβ knockout (Erβ^null) mouse ovaries, and their transcriptomes were compared with those of control Erβ^fl/fl mice. We observed a significant (≥2-fold change; FDR p-value ≤ 0.05) deregulation of approximately 5% of genes (866 out of 16,940 genes, TPM ≥ 5) in Erβ^null PdFs; ~60% (521 out of 866) of the differentially expressed genes (DEGs) were upregulated, and 40% were downregulated, indicating that ERβ has both transcriptional enhancing as well as repressing roles in dormant PdFs. Such deregulation of genes may make the Erβ^null PdFs more susceptible to increased PFGA. When the PdFs undergo PFGA and form PrFs, many new genes are activated. During PFGA of Erβ^fl/fl follicles, we detected a differential expression of ~24% genes (4909 out of 20,743; ≥2-fold change; FDR p-value ≤ 0.05; TPM ≥ 5); 56% upregulated and 44% downregulated, indicating the gene enhancing and repressing roles of Erβ-activated PrFs. In contrast, we detected a differential expression of only 824 genes in Erβ^null follicles during PFGA (≥2-fold change; FDR p-value ≤ 0.05; TPM ≥ 5). Moreover, most (~93%; 770 out of 824) of these DEGs in activated Erβ^null PrFs were downregulated. Such deregulation of genes in Erβ^null activated follicles may impair their inhibitory role on PFGA. Notably, in both Erβ^null PdFs and PrFs, we detected a significant number of epigenetic regulators and transcription factors to be differentially expressed, which suggests that lack of ERβ either directly or indirectly deregulates the gene expression in PdFs and PrFs, leading to increased PFGA. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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11 pages, 1895 KiB

Open AccessCommunication

BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function

by Igor V. Deyneko

Int. J. Mol. Sci. 2024, 25(3), 1903; https://doi.org/10.3390/ijms25031903 - 05 Feb 2024

Viewed by 500

Abstract

The concept of cis-regulatory modules located in gene promoters represents today’s vision of the organization of gene transcriptional regulation. Such modules are a combination of two or more single, short DNA motifs. The bioinformatic identification of such modules belongs to so-called NP-hard problems with extreme computational complexity, and therefore, simplifications, assumptions, and heuristics are usually deployed to tackle the problem. In practice, this requires, first, many parameters to be set before the search, and second, it leads to the identification of locally optimal results. Here, a novel method is presented, aimed at identifying the cis-regulatory elements in gene promoters based on an exhaustive search of all the feasible modules’ configurations. All required parameters are automatically estimated using positive and negative datasets. To be computationally efficient, the search is accelerated using a multidimensional hash function, allowing the search to complete in a few hours on a regular laptop (for example, a CPU Intel i7, 3.2 GH, 32 Gb RAM). Tests on an established benchmark and real data show better performance of BestCRM compared to the available methods according to several metrics like specificity, sensitivity, AUC, etc. A great practical advantage of the method is its minimum number of input parameters—apart from positive and negative promoters, only a desired level of module presence in promoters is required. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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15 pages, 3428 KiB

Open AccessArticle

Cancer Associated PRDM9: Implications for Linking Genomic Instability and Meiotic Recombination

by Paris Ladias, Georgios S. Markopoulos, Charilaos Kostoulas, Ioanna Bouba, Sofia Markoula and Ioannis Georgiou

Int. J. Mol. Sci. 2023, 24(22), 16522; https://doi.org/10.3390/ijms242216522 - 20 Nov 2023

Viewed by 1016

Abstract

The PR domain-containing 9 or PRDM9 is a gene recognized for its fundamental role in meiosis, a process essential for forming reproductive cells. Recent findings have implicated alterations in the PRDM9, particularly its zinc finger motifs, in the onset and progression of cancer. This association is manifested through genomic instability and the misregulation of genes critical to cell growth, proliferation, and differentiation. In our comprehensive study, we harnessed advanced bioinformatic mining tools to delve deep into the intricate relationship between PRDM9F and cancer. We analyzed 136,752 breakpoints and found an undeniable association between specific PRDM9 motifs and the occurrence of double-strand breaks, a phenomenon evidenced in every cancer profile examined. Utilizing R statistical querying and the Regioner package, 55 unique sequence variations of PRDM9 were statistically correlated with cancer, from a pool of 1024 variations. A robust analysis using the Enrichr tool revealed prominent associations with various cancer types. Moreover, connections were noted with specific phenotypic conditions and molecular functions, underlining the pervasive influence of PRDM9 variations in the biological spectrum. The Reactome tool identified 25 significant pathways associated with cancer, offering insights into the mechanistic underpinnings linking PRDM9 to cancer progression. This detailed analysis not only confirms the pivotal role of PRDM9 in cancer development, but also unveils a complex network of biological processes influenced by its variations. The insights gained lay a solid foundation for future research aimed at deciphering the mechanistic pathways of PRDM9, offering prospects for targeted interventions and innovative therapeutic approaches in cancer management. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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19 pages, 1506 KiB

Open AccessArticle

The New General Biological Property of Stem-like Tumor Cells (Part II: Surface Molecules, Which Belongs to Distinctive Groups with Particular Functions, Form a Unique Pattern Characteristic of a Certain Type of Tumor Stem-like Cells)

by Daria D. Petrova, Evgeniya V. Dolgova, Anastasia S. Proskurina, Genrikh S. Ritter, Vera S. Ruzanova, Yaroslav R. Efremov, Ekaterina A. Potter, Svetlana S. Kirikovich, Evgeniy V. Levites, Oleg S. Taranov, Alexandr A. Ostanin, Elena R. Chernykh, Nikolay A. Kolchanov and Sergey S. Bogachev

Int. J. Mol. Sci. 2022, 23(24), 15800; https://doi.org/10.3390/ijms232415800 - 13 Dec 2022

Cited by 3 | Viewed by 1281

Abstract

An ability of poorly differentiated cells of different genesis, including tumor stem-like cells (TSCs), to internalize extracellular double-stranded DNA (dsDNA) fragments was revealed in our studies. Using the models of Krebs-2 murine ascites carcinoma and EBV-induced human B-cell lymphoma culture, we demonstrated that dsDNA internalization into the cell consists of several mechanistically distinct phases. The primary contact with cell membrane factors is determined by electrostatic interactions. Firm contacts with cell envelope proteins are then formed, followed by internalization into the cell of the complex formed between the factor and the dsDNA probe bound to it. The key binding sites were found to be the heparin-binding domains, which are constituents of various cell surface proteins of TSCs—either the C1q domain, the collagen-binding domain, or domains of positively charged amino acids. These results imply that the interaction between extracellular dsDNA fragments and the cell, as well as their internalization, took place with the involvement of glycocalyx components (proteoglycans/glycoproteins (PGs/GPs) and glycosylphosphatidylinositol-anchored proteins (GPI-APs)) and the system of scavenger receptors (SRs), which are characteristic of TSCs and form functional clusters of cell surface proteins in TSCs. The key provisions of the concept characterizing the principle of organization of the “group-specific” cell surface factors of TSCs of various geneses were formulated. These factors belong to three protein clusters: GPs/PGs, GIP-APs, and SRs. For TSCs of different tumors, these clusters were found to be represented by different members with homotypic functions corresponding to the general function of the cluster to which they belong. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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18 pages, 2421 KiB

Open AccessArticle

Mother–Fetus Immune Cross-Talk Coordinates “Extrinsic”/“Intrinsic” Embryo Gene Expression Noise and Growth Stability

by Tatyana Ivanovna Babochkina, Ludmila Alekseevna Gerlinskaya, Margarita Vladimirovna Anisimova, Galina Vladimirovna Kontsevaya, Natalia Aleksandrovna Feofanova, Aliya Konstantinovna Stanova, Mikhail Pavlovich Moshkin and Yuri Mikhailovich Moshkin

Int. J. Mol. Sci. 2022, 23(20), 12467; https://doi.org/10.3390/ijms232012467 - 18 Oct 2022

Cited by 1 | Viewed by 1322

Abstract

Developmental instability (DI) is thought to be inversely related to a capacity of an organism to buffer its development against random genetic and environmental perturbations. DI is represented by a trait’s inter- and intra-individual variabilities. The inter-individual variability (inversely referred to as canalization) indicates the capability of organisms to reproduce a trait from individual to individual. The intra-individual variability reflects an organism’s capability to stabilize a trait internally under the same conditions, and, for symmetric traits, it is expressed as fluctuating asymmetry (FA). When representing a trait as a random variable conditioned on environmental fluctuations, it is clear that, in statistical terms, the DI partitions into “extrinsic” (canalization) and “intrinsic” (FA) components of a trait’s variance/noise. We established a simple statistical framework to dissect both parts of a symmetric trait variance/noise using a PCA (principal component analysis) projection of the left/right measurements on eigenvectors followed by GAMLSS (generalized additive models for location scale and shape) modeling of eigenvalues. The first eigenvalue represents “extrinsic” and the second—“intrinsic” DI components. We applied this framework to investigate the impact of mother–fetus major histocompatibility complex (MHC)-mediated immune cross-talk on gene expression noise and developmental stability. We showed that “intrinsic” gene noise for the entire transcriptional landscape could be estimated from a small subset of randomly selected genes. Using a diagnostic set of genes, we found that allogeneic MHC combinations tended to decrease “extrinsic” and “intrinsic” gene noise in C57BL/6J embryos developing in the surrogate NOD-SCID and BALB/c mothers. The “intrinsic” gene noise was negatively correlated with growth (embryonic mass) and the levels of placental growth factor (PLGF), but not vascular endothelial growth factor (VEGF). However, it was positively associated with phenotypic growth instability and noise in PLGF. In mammals, the mother–fetus MHC interaction plays a significant role in development, contributing to the fitness of the offspring. Our results demonstrate that a positive impact of distant MHC combinations on embryonic growth could be mediated by the reduction of “intrinsic” gene noise followed by the developmental stabilization of growth. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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17 pages, 1106 KiB

Open AccessArticle

Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing

by Dmitry Oshchepkov, Irina Chadaeva, Rimma Kozhemyakina, Svetlana Shikhevich, Ekaterina Sharypova, Ludmila Savinkova, Natalya V. Klimova, Anton Tsukanov, Victor G. Levitsky and Arcady L. Markel

Int. J. Mol. Sci. 2022, 23(20), 12269; https://doi.org/10.3390/ijms232012269 - 14 Oct 2022

Cited by 6 | Viewed by 1809

Abstract

Studies on hereditary fixation of the tame-behavior phenotype during animal domestication remain relevant and important because they are of both basic research and applied significance. In model animals, gray rats Rattus norvegicus bred for either an enhancement or reduction in defensive response to humans, for the first time, we used high-throughput RNA sequencing to investigate differential expression of genes in tissue samples from the tegmental region of the midbrain in 2-month-old rats showing either tame or aggressive behavior. A total of 42 differentially expressed genes (DEGs; adjusted p-value < 0.01 and fold-change > 2) were identified, with 20 upregulated and 22 downregulated genes in the tissue samples from tame rats compared with aggressive rats. Among them, three genes encoding transcription factors (TFs) were detected: Ascl3 was upregulated, whereas Fos and Fosb were downregulated in tissue samples from the brains of tame rats brain. Other DEGs were annotated as associated with extracellular matrix components, transporter proteins, the neurotransmitter system, signaling molecules, and immune system proteins. We believe that these DEGs encode proteins that constitute a multifactorial system determining the behavior for which the rats have been artificially selected. We demonstrated that several structural subtypes of E-box motifs—known as binding sites for many developmental TFs of the bHLH class, including the ASCL subfamily of TFs—are enriched in the set of promoters of the DEGs downregulated in the tissue samples of tame rats’. Because ASCL3 may act as a repressor on target genes of other developmental TFs of the bHLH class, we hypothesize that the expression of TF gene Ascl3 in tame rats indicates longer neurogenesis (as compared to aggressive rats), which is a sign of neoteny and domestication. Thus, our domestication model shows a new function of TF ASCL3: it may play the most important role in behavioral changes in animals. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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16 pages, 33222 KiB

Open AccessArticle

Formation of Unique Placental Seed Capsules in the Maturation Process of the Tomato Fruit

by Inna A. Chaban, Alexander A. Gulevich and Ekaterina N. Baranova

Int. J. Mol. Sci. 2022, 23(19), 11101; https://doi.org/10.3390/ijms231911101 - 21 Sep 2022

Cited by 2 | Viewed by 2392

Abstract

The morphological and anatomical study of the seed formation features in a juicy tomato fruit was carried out. The ovules, which form on the placenta, have been shown to be gradually enveloped by the protrusions of placental tissue that arises simultaneously with them. As a result of this process, each seed is enclosed in an individual capsule. These seed capsules have been shown in vivo to be airtight and air-filled. Tomato seeds, as has been shown in this study, develop inside these capsules until the full maturity of the fruit and do not come into contact with the detached and moldered cells of the placenta protrusions, which convert into a gel (pulp). Using scanning electron microscopy, it was possible to reveal the details of a ribbon-like “pubescence” formation of the tomato seed, as well as to understand the mechanism of cracking of the outer layer cells in the seed coat, associated with the detection of calcium oxalate crystals in these cells. The unique outer layer of the tomato seed coat seems to play the role of a scaffold that maintains a constant volume of the protective capsule. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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9 pages, 1016 KiB

Open AccessArticle

In Silico Study of piRNA Interactions with the SARS-CoV-2 Genome

by Aigul Akimniyazova, Oxana Yurikova, Anna Pyrkova, Aizhan Rakhmetullina, Togzhan Niyazova, Alma-Gul Ryskulova and Anatoliy Ivashchenko

Int. J. Mol. Sci. 2022, 23(17), 9919; https://doi.org/10.3390/ijms23179919 - 31 Aug 2022

Cited by 4 | Viewed by 1520

Abstract

A prolonged pandemic with numerous human casualties requires a rapid search for means to control the various strains of SARS-CoV-2. Since only part of the human population is affected by coronaviruses, there are probably endogenous compounds preventing the spread of these viral pathogens. It has been shown that piRNA (PIWI-interacting RNAs) interact with the mRNA of human genes and can block protein synthesis at the stage of translation. Estimated the effects of piRNA on SARS-CoV-2 genomic RNA (gRNA) in silico. A cluster of 13 piRNA binding sites (BS) in the SARS-CoV-2 gRNA region encoding the oligopeptide was identified. The second cluster of BSs 39 piRNAs also encodes the oligopeptide. The third cluster of 24 piRNA BS encodes the oligopeptide. Twelve piRNAs were identified that strongly interact with the gRNA. Based on the identified functionally important endogenous piRNAs, synthetic piRNAs (spiRNAs) are proposed that will suppress the multiplication of the coronavirus even more strongly. These spiRNAs and selected endogenous piRNAs have little effect on human 17494 protein-coding genes, indicating a low probability of side effects. The piRNA and spiRNA selection methodology created for the control of SARS-CoV-2 (NC_045512.2) can be used to control all strains of SARS-CoV-2. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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15 pages, 5853 KiB

Open AccessArticle

Plant_SNP_TATA_Z-Tester: A Web Service That Unequivocally Estimates the Impact of Proximal Promoter Mutations on Plant Gene Expression

by Dmitry Rasskazov, Irina Chadaeva, Ekaterina Sharypova, Karina Zolotareva, Bato Khandaev, Petr Ponomarenko, Nikolay Podkolodnyy, Natalya Tverdokhleb, Oleg Vishnevsky, Anton Bogomolov, Olga Podkolodnaya, Ludmila Savinkova, Elena Zemlyanskaya, Vadimir Golubyatnikov, Nikolay Kolchanov and Mikhail Ponomarenko

Int. J. Mol. Sci. 2022, 23(15), 8684; https://doi.org/10.3390/ijms23158684 - 04 Aug 2022

Cited by 9 | Viewed by 1410

Abstract

Synthetic targeted optimization of plant promoters is becoming a part of progress in mainstream postgenomic agriculture along with hybridization of cultivated plants with wild congeners, as well as marker-assisted breeding. Therefore, here, for the first time, we compiled all the experimental data—on mutational effects in plant proximal promoters on gene expression—that we could find in PubMed. Some of these datasets cast doubt on both the existence and the uniqueness of the sought solution, which could unequivocally estimate effects of proximal promoter mutation on gene expression when plants are grown under various environmental conditions during their development. This means that the inverse problem under study is ill-posed. Furthermore, we found experimental data on in vitro interchangeability of plant and human TATA-binding proteins allowing the application of Tikhonov’s regularization, making this problem well-posed. Within these frameworks, we created our Web service Plant_SNP_TATA_Z-tester and then determined the limits of its applicability using those data that cast doubt on both the existence and the uniqueness of the sought solution. We confirmed that the effects (of proximal promoter mutations on gene expression) predicted by Plant_SNP_TATA_Z-tester correlate statistically significantly with all the experimental data under study. Lastly, we exemplified an application of Plant_SNP_TATA_Z-tester to agriculturally valuable mutations in plant promoters. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches)

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