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25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series

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

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 7610

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Prof. Dr. Yuriy L. Orlov

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The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
Interests: computer genomics; bioinformatics; digital medicine (e-Health); gene expression regulation; ChIP-seq
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Prof. Dr. Nikolay A. Kolchanov

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Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
Interests: bioinformatics; systems biology; genetics; genomics; gene networks
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Prof. Dr. Ming Chen

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Guest Editor

College of Life Sciences, Zhejiang University, Hangzhou 310058, China
Interests: bioinformatics; systems biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This is Commemorative Special Issue collecting research manuscripts and reviews on genetics and bioinformatics from the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (ICG SB RAS) in Novosibirsk, Russia (https://www.icgbio.ru/). We present memorial papers on the mathematical biology and bioinformatics school foundation, as well as historical views on the development of this science field. In 2023, we celebrate the 25^th anniversary of the Bioinformatics of Genome Regulation and Structure conference series. The first international meeting of the “Bioinformatics of Genome Regulation and Structure/Systems Biology” (BGRS/SB) conference series was held in Novosibirsk in 1998, organized at the ICG SB RAS. BGRS is the longest-running biannual conference series gathering scientists, bioinformaticians, medical doctors, and geneticists in Novosibirsk (https://bgrssb.icgbio.ru/2022/). The key science topic is the regulation of gene expression at the transcriptional level. In this Special Issue, we aim to commemorate the international science meetings on genetics organized by the Institute of Cytology and Genetics, such as memorial the Belyaev conference on genetics and evolution «Belyaev Readings-2017» http://conf.bionet.nsc.ru/belyaev100/en). The full member of the USSR Academy of Sciences Professor Dmitry K. Belyaev (1917–1985) was the founder and first director of the Institute. D. K. Belyaev was an outstanding scientist, evolutionist and geneticist who investigated the background on the genetics of behaviour and the domestication of wild animals. This Special Issue aims to present an overview of new trends in animal genetics based on next-generation sequencing technologies for understanding neurobiology mechanisms. We will present the research works conducted by Prof. Vladimir K. Shumny on plant genetics, Prof. Vadim A. Ratner on mathematical biology, and Dr. Vitaly A. Likhoshvai on gene network theory.

Overall, this IJMS Special Issue shall continue the trends set by earlier IJMS Special Issues and other collections of advances in computer genomics and bioinformatics following recent bioinformatics events and young scientists’ developments in Russia («Systems biology and bioinformatics» (SBB) School series).

MDPI has already published several successful Special Issues on the bioinformatics of gene expression, including the following:

"Molecular Mechanisms of Gene Expression: “Bioinformatics of Gene Regulations and Structure”" (2020) and "Bioinformatics of Gene Regulations and Structure - 2022".

In the research perspectives part of this Special Issue, we will focus on bioinformatics and systems biology approaches to genomics and biotechnology problems. The central problems include the analysis of molecular mechanisms of gene expression regulations, analysis of transcription regulation, and network interactions.

Topics of interest to this Special Issue include the following:

Invited memorial reviews on the foundation of bioinformatics schools;
Analysis of the regulation of gene expression;
Applications of bioinformatics to omics technologies;
Gene networks and associative networks analysis;
Protein structure analysis and biophysical models;
Interdisciplinary research in computational genomics of model organisms—plants, animals, bacteria;
Systems biology approaches for gene expression analysis, including Machine Learning and AI.

The BGRS conference series has its own history of initiating successful Special Issues on bioinformatics with IJMS:

as well as "New Sights into Bioinformatics of Gene Regulations and Structure": https://www.mdpi.com/journal/ijms/special_issues/MVA479KFR7

Research on bioinformatics topic is in high demand at IJMS. We welcome novel research on bioinformatics education that extends the discussion beyond the frames of the anniversary of the BGRS conference series.

Prof. Dr. Yuriy L. Orlov
Prof. Dr. Nikolay A. Kolchanov
Prof. Dr. Ming Chen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

bioinformatics
systems biology
human genomics
mathematical genetics
genomics of model organisms
gene expression regulation
fundamental biomedicine
gene networks
bioinformatics education
Bioinformatics of Genome Regulation and Structure conference series
Institute of Cytology and Genetics SB RAS

Published Papers (9 papers)

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Research

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22 pages, 4202 KiB

Open AccessArticle

Synergistic Effect of Dietary Supplementation with Sodium Butyrate, β-Glucan and Vitamins on Growth Performance, Cortisol Level, Intestinal Microbiome and Expression of Immune-Related Genes in Juvenile African Catfish (Clarias gariepinus)

by Martyna Arciuch-Rutkowska, Joanna Nowosad, Łukasz Gil, Urszula Czarnik and Dariusz Kucharczyk

Int. J. Mol. Sci. 2024, 25(9), 4619; https://doi.org/10.3390/ijms25094619 - 24 Apr 2024

Viewed by 301

Abstract

The effect of dietary supplementation with sodium butyrate, β-glucan and vitamins (A, D3, E, K, C) on breeding indicators and immune parameters of juvenile African catfish was examined. The fish were fed with unenriched (group C) and enriched feed with a variable proportion of sodium butyrate/β-glucan, and constant content of vitamins (W1–W3). After the experiment, blood and the middle gut were collected. The microbiome of the gut was determined using Next Generation Sequencing (NGS). Liver tissue was collected for determination of expression of immune-related genes (HSP70, IL-1β, TNFα). W2 and W3 were characterized by the most favorable values of breeding indicators (p < 0.05). The highest blood cortisol concentration was in group C (71.25 ± 10.45 ng/mL), and significantly the lowest in W1 (46.03 ± 7.01 ng/ mL) (p < 0.05). The dominance of Cetobacterium was observed in all study groups, with the largest share in W3 (65.25%) and W1 (61.44%). Gene expression showed an increased number of HSP70 genes in W1. IL-1β and TNFα genes peaked at W3. The W3 variant turns out to be the most beneficial supplementation, due to the improvement of breeding and immunological parameters. The data obtained can be used to create a preparation for commercial use in the breeding of this species. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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17 pages, 2894 KiB

Open AccessArticle

A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior

by Irina Chadaeva, Rimma Kozhemyakina, Svetlana Shikhevich, Anton Bogomolov, Ekaterina Kondratyuk, Dmitry Oshchepkov, Yuriy L. Orlov and Arcady L. Markel

Int. J. Mol. Sci. 2024, 25(9), 4613; https://doi.org/10.3390/ijms25094613 - 23 Apr 2024

Viewed by 300

Abstract

The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms underlying these changes remain poorly understood. The present study deals with an analysis of the transcriptomes from four brain regions of gray rats (Rattus norvegicus), serving as an experimental model object of domestication. We compared gene expression profiles in the hypothalamus, hippocampus, periaqueductal gray matter, and the midbrain tegmental region between tame domesticated and aggressive gray rats and revealed subdivisions of differentially expressed genes by principal components analysis that explain the main part of differentially gene expression variance. Functional analysis (in the DAVID (Database for Annotation, Visualization and Integrated Discovery) Bioinformatics Resources database) of the differentially expressed genes allowed us to identify and describe the key biological processes that can participate in the formation of the different behavioral patterns seen in the two groups of gray rats. Using the STRING- DB (search tool for recurring instances of neighboring genes) web service, we built a gene association network. The genes engaged in broad network interactions have been identified. Our study offers data on the genes whose expression levels change in response to artificial selection for behavior during animal domestication. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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13 pages, 6706 KiB

Open AccessArticle

Identification of Genomic Signatures for Colorectal Cancer Survival Using Exploratory Data Mining

by Justin J. Hummel, Danlu Liu, Erin Tallon, John Snyder, Wesley Warren, Chi-Ren Shyu, Jonathan Mitchem and Rene Cortese

Int. J. Mol. Sci. 2024, 25(6), 3220; https://doi.org/10.3390/ijms25063220 - 12 Mar 2024

Viewed by 609

Abstract

Clinicopathological presentations are critical for establishing a postoperative treatment regimen in Colorectal Cancer (CRC), although the prognostic value is low in Stage 2 CRC. We implemented a novel exploratory algorithm based on artificial intelligence (explainable artificial intelligence, XAI) that integrates mutational and clinical features to identify genomic signatures by repurposing the FoundationOne Companion Diagnostic (F1CDx) assay. The training data set (n = 378) consisted of subjects with recurrent and non-recurrent Stage 2 or 3 CRC retrieved from TCGA. Genomic signatures were built for identifying subgroups in Stage 2 and 3 CRC patients according to recurrence using genomic parameters and further associations with the clinical presentation. The summarization of the top-performing genomic signatures resulted in a 32-gene genomic signature that could predict tumor recurrence in CRC Stage 2 patients with high precision. The genomic signature was further validated using an independent dataset (n = 149), resulting in high-precision prognosis (AUC: 0.952; PPV = 0.974; NPV = 0.923). We anticipate that our genomic signatures and NCCN guidelines will improve recurrence predictions in CRC molecular stratification. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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31 pages, 6945 KiB

Open AccessArticle

Brain-Region-Specific Genes Form the Major Pathways Featuring Their Basic Functional Role: Their Implication in Animal Chronic Stress Model

by Vladimir Babenko, Olga Redina, Dmitry Smagin, Irina Kovalenko, Anna Galyamina and Natalia Kudryavtseva

Int. J. Mol. Sci. 2024, 25(5), 2882; https://doi.org/10.3390/ijms25052882 - 01 Mar 2024

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Abstract

The analysis of RNA-Sec data from murine bulk tissue samples taken from five brain regions associated with behavior and stress response was conducted. The focus was on the most contrasting brain region-specific genes (BRSG) sets in terms of their expression rates. These BRSGs are identified as genes with a distinct outlying (high) expression rate in a specific region compared to others used in the study. The analysis suggested that BRSG sets form non-randomly connected compact gene networks, which correspond to the major neuron-mediated functional processes or pathways in each brain region. The number of BRSGs and the connection rate were found to depend on the heterogeneity and coordinated firing rate of neuron types in each brain region. The most connected pathways, along with the highest BRSG number, were observed in the Striatum, referred to as Medium Spiny Neurons (MSNs), which make up 95% of neurons and exhibit synchronous firing upon dopamine influx. However, the Ventral Tegmental Area/Medial Raphe Nucleus (VTA/MRN) regions, although primarily composed of monoaminergic neurons, do not fire synchronously, leading to a smaller BRSG number. The Hippocampus (HPC) region, on the other hand, displays significant neuronal heterogeneity, with glutamatergic neurons being the most numerous and synchronized. Interestingly, the two monoaminergic regions involved in the study displayed a common BRSG subnetwork architecture, emphasizing their proximity in terms of axonal throughput specifics and high-energy metabolism rates. This finding suggests the concerted evolution of monoaminergic neurons, leading to unique adaptations at the genic repertoire scale. With BRSG sets, we were able to highlight the contrasting features of the three groups: control, depressive, and aggressive mice in the animal chronic stress model. Specifically, we observed a decrease in serotonergic turnover in both the depressed and aggressive groups, while dopaminergic emission was high in both groups. There was also a notable absence of dopaminoceptive receptors on the postsynaptic membranes in the striatum in the depressed group. Additionally, we confirmed that neurogenesis BRSGs are specific to HPC, with the aggressive group showing attenuated neurogenesis rates compared to the control/depressive groups. We also confirmed that immune-competent cells like microglia and astrocytes play a crucial role in depressed phenotypes, including mitophagy-related gene Prkcd. Based on this analysis, we propose the use of BRSG sets as a suitable framework for evaluating case–control group-wise assessments of specific brain region gene pathway responses. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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19 pages, 5696 KiB

Open AccessArticle

Altered N6-Methyladenosine Modification Patterns and Transcript Profiles Contributes to Cognitive Dysfunction in High-Fat Induced Diabetic Mice

by Zhaoming Cao, Yu An and Yanhui Lu

Int. J. Mol. Sci. 2024, 25(4), 1990; https://doi.org/10.3390/ijms25041990 - 06 Feb 2024

Viewed by 716

Abstract

N6-methyladenosine (m⁶A) constitutes the paramount post-transcriptional modification within eukaryotic mRNA. This modification is subjected to stimulus-dependent regulation within the central nervous system of mammals, being influenced by sensory experiences, learning processes, and injuries. The patterns of m⁶A methylation within the hippocampal region of diabetes cognitive impairment (DCI) has not been investigated. A DCI model was established by feeding a high-fat diet to C57BL/6J mice. m⁶A and RNA sequencing was conducted to profile the m⁶A-tagged transcripts in the hippocampus. Methylated RNA immunoprecipitation with next-generation sequencing and RNA sequencing analyses yielded differentially m⁶A-modified and expressed genes in the hippocampus of DCI mice, which were enriched in pathways involving synaptic transmission and axonal guidance. Mechanistic analyses revealed a remarkable change in m⁶A modification levels through alteration of the mRNA expression of m⁶A methyltransferases (METTL3 and METTL14) and demethylase (FTO) in the hippocampus of DCI mice. We identified a co-mediated specific RNA regulatory strategy that broadens the epigenetic regulatory mechanism of RNA-induced neurodegenerative disorders associated with metabolic and endocrine diseases. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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29 pages, 3383 KiB

Open AccessArticle

Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks

by Oleg V. Vishnevsky, Andrey V. Bocharnikov and Elena V. Ignatieva

Int. J. Mol. Sci. 2024, 25(2), 1011; https://doi.org/10.3390/ijms25021011 - 13 Jan 2024

Viewed by 763

Abstract

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments, multiple regression models were constructed, demonstrating a significant dependence of the peak scores on the presence in the peak sequences of not only highly significant target motifs but also less significant motifs corresponding to the binding sites of the partner transcription factors. A significant correlation was shown between the presence of the target motifs FOXA2 and the partner motifs HNF4G, which found experimental confirmation in the scientific literature, demonstrating the important contribution of the partner transcription factors to the binding of the target transcription factor to DNA and, consequently, their important contribution to the peak score. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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17 pages, 3590 KiB

Open AccessArticle

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

by Anton Bogomolov, Karina Zolotareva, Sergey Filonov, Irina Chadaeva, Dmitry Rasskazov, Ekaterina Sharypova, Nikolay Podkolodnyy, Petr Ponomarenko, Ludmila Savinkova, Natalya Tverdokhleb, Bato Khandaev, Ekaterina Kondratyuk, Olga Podkolodnaya, Elena Zemlyanskaya, Nikolay A. Kolchanov and Mikhail Ponomarenko

Int. J. Mol. Sci. 2024, 25(1), 607; https://doi.org/10.3390/ijms25010607 - 03 Jan 2024

Viewed by 931

Abstract

The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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13 pages, 3823 KiB

Open AccessArticle

Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species

by Xiaofan He, Xiaopeng Zhang, Yantian Deng, Rui Yang, Long-Xi Yu, Shangang Jia and Tiejun Zhang

Int. J. Mol. Sci. 2023, 24(24), 17334; https://doi.org/10.3390/ijms242417334 - 11 Dec 2023

Viewed by 912

Abstract

Plant mitochondria are crucial for species evolution, phylogenetics, classification, and identification as maternal genetic material. However, the presence of numerous repetitive sequences, complex structures, and a low number of genes in the mitochondrial genome has hindered its complete assembly and related research endeavors. In this study, we assembled two mitochondrial genomes of alfalfa varieties of Zhongmu No.1 (299,123 bp) and Zhongmu No.4 (306,983 bp), based on a combination of PacBio, Illumina, and Hi-C sequences. The comparison of genome assemblies revealed that the same number of mitochondrial genes, including thirty-three protein-coding genes, sixteen tRNA genes, and three rRNA genes existed in the two varieties. Additionally, large fragments of repetitive sequences were found underlying frequent mitochondrial recombination events. We observed extensive transfer of mitochondrial fragments into the nuclear genome of Zhongmu No.4. Analysis of the cox1 and rrn18s genes in 35 Medicago accessions revealed the presence of population-level deletions and substitutions in the rrn18s gene. We propose that mitochondrial structural reorganizations may contribute to alfalfa evolution. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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20 pages, 1217 KiB

Open AccessReview

Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation

by Ivan S. Petrushin, Nadezhda V. Filinova and Daria I. Gutnik

Int. J. Mol. Sci. 2024, 25(2), 750; https://doi.org/10.3390/ijms25020750 - 06 Jan 2024

Cited by 1 | Viewed by 1390

Abstract

Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato—a critical food crop worldwide—highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the “geocaulosphere”, which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant–bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed. Full article

(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)

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