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Bioinformatics: From Gene to Networks
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Bioinformatics: From Gene to Networks

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (20 October 2023) | Viewed by 14553

Special Issue Editors

Dr. Larissa A. Balabanova

E-Mail Website
Guest Editor
1. Department of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia
2. Basic Department of Bioeconomics and Food Security, Far Eastern Federal University, Vladivostok 690022, Russia
Interests: functional genetics and genomics; comparative genomics; protein structure-function and interactions; molecular modeling; development of biomolecules assays; synthetic biology; recombinant protein production; microbiology; biotechnology
Dr. Yuri N. Shkryl

E-Mail Website
Guest Editor
Department of Bioengineering, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences. Vladivostok 690022, Russia
Interests: genetic engineering; genome editing; expression systems; plant biotechnology; nanobiotechnology; metabolomes and regulatory systems; development of synthetic vaccines; gene expression profiles

Special Issue Information

Dear Colleagues,

This Special Issue is devoted to research in the field of biology, biotechnology, agriculture, and medicine using in silico analysis of biological data.

Currently, there is no field of biological sciences that does not involve bioinformatics, particularly at the molecular level. The applied areas of bioinformatics are based on the analysis of accumulated data on DNA, RNA and protein sequences, protein structures, gene expression profiles, and biochemical pathways that have been experimentally confirmed to be involved into metabolic processes (and, consequently, phenotypic traits of organisms). Functional, structural and comparative genomics, oligonucleotide-based and recombinant DNA technologies, and medical informatics are most advanced of biological approaches, covered by bioinformatics. The identification of single genes and their functions allows us to predict the structures and functions of proteins, and their involvement into metabolic pathway networks. By the means of bioinformatics, it is possible to measure the levels of gene expression in different cells or tissiues, construct expression vectors, provide addressed gene editing, develop models for pathogenesis, and design drugs for medical treatment.

In this Special Issue, we invite submissions exploring cutting-edge research and recent advances in the fields of all interdisciplinary sciences using bioinformatics. Both theoretical and experimental studies are welcome, as well as comprehensive review and survey papers.

Dr. Larissa A. Balabanova
Dr. Yuri N. Shkryl
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. Applied Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). 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

  • genetic diversity and phylogenetic relashionships
  • genome sequencing and mining
  • gene function prediction and single-cell transcriptomics
  • protein-protein interaction networks and molecular modeling
  • metabolic pathways and regulatory systems
  • heterologous expression and recombinant protein production
  • mutations and genetically modified organisms
  • biomarker discovery and molecular imaging/targeting
  • assembly of gene therapy vectors and recombinant vaccines
  • drug designing and biotechnology

Published Papers (6 papers)

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Research

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13 pages, 4973 KiB  
Article
TFNetPropX: A Web-Based Comprehensive Analysis Tool for Exploring Condition-Specific RNA-Seq Data Using Transcription Factor Network Propagation
by Ji Hwan Moon and Minsik Oh
Appl. Sci. 2023, 13(20), 11399; https://doi.org/10.3390/app132011399 - 17 Oct 2023
Viewed by 1180
Abstract
Understanding condition-specific biological mechanisms from RNA-seq data requires comprehensive analysis of gene expression data, from the gene to the network level. However, this requires computational expertise, which limits the accessibility of data analysis for understanding biological mechanisms. Therefore, the development of an easy-to-use [...] Read more.
Understanding condition-specific biological mechanisms from RNA-seq data requires comprehensive analysis of gene expression data, from the gene to the network level. However, this requires computational expertise, which limits the accessibility of data analysis for understanding biological mechanisms. Therefore, the development of an easy-to-use and comprehensive analysis system is essential. In response to this issue, we present TFNetPropX, a user-friendly web-based platform designed to perform gene-level, gene-set-level, and network-level analysis of RNA-seq data under two different conditions. TFNetPropX performs comprehensive analysis, from DEG analysis to network propagation, to predict TF-affected genes with a single request, and provides users with an interactive web-based visualization of the results. To demonstrate the utility of our system, we performed analysis on two TF knockout RNA-seq datasets and effectively reproduced biologically significant findings. We believe that our system will make it easier for biological researchers to gain insights from different perspectives, allowing them to develop diverse hypotheses and analyses. Full article
(This article belongs to the Special Issue Bioinformatics: From Gene to Networks)
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8 pages, 270 KiB  
Communication
Closely-Spaced Repetitions of CAMTA Trans-Factor Binding Sites in Promoters of Model Plant MEP Pathway Genes
by Piotr Szymczyk
Appl. Sci. 2023, 13(17), 9680; https://doi.org/10.3390/app13179680 - 27 Aug 2023
Cited by 1 | Viewed by 1219
Abstract
Previous research has demonstrated the presence of two closely spaced repetitions of the rapid stress-responsive cis-active element RSRE (G/A/C)CGCG(C/G/T) in the 5′UTR of S. miltiorrhiza2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase (MECPS) gene. The product of MECPS activity, represented by 2C-methyl-D-erithrytol 2,4-cyclodiphosphate [...] Read more.
Previous research has demonstrated the presence of two closely spaced repetitions of the rapid stress-responsive cis-active element RSRE (G/A/C)CGCG(C/G/T) in the 5′UTR of S. miltiorrhiza2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase (MECPS) gene. The product of MECPS activity, represented by 2C-methyl-D-erithrytol 2,4-cyclodiphosphate (MECPD), indicates its retrograde regulatory role and activates CAMTA trans-factors. Since the complete activation of CAMTA trans-factors requires the cooperative interaction of CAMTA3 with CAMTA2 or CAMTA4, the closely spaced RSREs recognized by CAMTA trans-factors could be used to promote CAMTA trans-factor dimerization. The present study aims to evaluate if the occurrence of these two closely spaced RSREs in the 5′UTR is specific to S. miltiorrhiza or could be observed in other MECPS genes. An analysis of nineteen MECPS gene sequences from seven selected model plants indicated the closely spaced repetition of RSREs in the 5′UTR region of two maize (Zea mays) MECPS genes, Zm00001d051458 and Zm00001d017608. This observation suggests the potential autoregulatory function of MECPD in relation to the MECPS transcription rate. Moreover, an analysis of eighty-five promoter regions of other plastidial methyl-D-erythritol phosphate (MEP) pathway genes indicated such closely spaced RSREs in the proximal promoter of Zea mays2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (CMS) (Zm00001d012197) and Oryza sativa4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) (Os03t0732000-00). Full article
(This article belongs to the Special Issue Bioinformatics: From Gene to Networks)
29 pages, 1144 KiB  
Article
A Special Structural Based Weighted Network Approach for the Analysis of Protein Complexes
by Peter Juma Ochieng, József Dombi, Tibor Kalmár and Miklós Krész
Appl. Sci. 2023, 13(11), 6388; https://doi.org/10.3390/app13116388 - 23 May 2023
Viewed by 1448
Abstract
The detection and analysis of protein complexes is essential for understanding the functional mechanism and cellular integrity. Recently, several techniques for detecting and analysing protein complexes from Protein–Protein Interaction (PPI) dataset have been developed. Most of those techniques are inefficient in terms of [...] Read more.
The detection and analysis of protein complexes is essential for understanding the functional mechanism and cellular integrity. Recently, several techniques for detecting and analysing protein complexes from Protein–Protein Interaction (PPI) dataset have been developed. Most of those techniques are inefficient in terms of detecting, overlapping complexes, exclusion of attachment protein in complex core, inability to detect inherent structures of underlying complexes, have high false-positive rates and an enrichment analysis. To address these limitations, we introduce a special structural-based weighted network approach for the analysis of protein complexes based on a Weighted Edge, Core-Attachment and Local Modularity structures (WECALM). Experimental results indicate that WECALM performs relatively better than existing algorithms in terms of accuracy, computational time, and p-value. A functional enrichment analysis also shows that WECALM is able to identify a large number of biologically significant protein complexes. Overall, WECALM outperforms other approaches by striking a better balance of accuracy and efficiency in the detection of protein complexes. Full article
(This article belongs to the Special Issue Bioinformatics: From Gene to Networks)
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11 pages, 2517 KiB  
Article
Explorative Supercooling Technology for Prevention of Freeze Damages in Vaccines
by Shawn Jun, Youngbok Ko and Seung Hyun Lee
Appl. Sci. 2022, 12(6), 3173; https://doi.org/10.3390/app12063173 - 20 Mar 2022
Cited by 1 | Viewed by 2876
Abstract
Most freeze-sensitive vaccines are stored between 2 °C and 8 °C upon manufacturing and until they are eventually administered in intermediate vaccine stores and health facilities. This so-called “cold chain” of vaccine distribution is strictly regulated at these specific temperatures to avoid freeze [...] Read more.
Most freeze-sensitive vaccines are stored between 2 °C and 8 °C upon manufacturing and until they are eventually administered in intermediate vaccine stores and health facilities. This so-called “cold chain” of vaccine distribution is strictly regulated at these specific temperatures to avoid freeze damage. Liquid formulations of particular vaccines (e.g., aluminum-adsorbed tetanus toxoid (TT)) will irreversibly lose their immunogenicity once frozen. Using an oscillating magnetic field (OMF), supercooling can inhibit ice crystal nucleation effectively; water is susceptible to influence by a strong magnetic field, allowing normal water dynamics even in subzero freezing conditions. This recently developed technology—composed of a custom-designed electromagnet unit producing an optimal field strength (50 mT) at a specific frequency (1 Hz)—was successfully used to inhibit the formation of ice crystals in aluminum adjuvant TT vaccines, therefore preventing any visible damage in the vaccines’ microscopic structure. Despite being subject to temperatures far below their freezing point (up to −14 °C) for up to seven days, the TT vaccines showed no freeze damage on physical appearances. Results were further validated using shake tests and light microscopy. As storage and freeze-protection become more critical during times of increased vaccination efforts—particularly against COVID-19—this supercooling technology can be a promising solution to distribution problems by removing concern for temperature abuse or shock-induced freezing. Full article
(This article belongs to the Special Issue Bioinformatics: From Gene to Networks)
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15 pages, 3255 KiB  
Article
ErbB4 Is a Potential Key Regulator of the Pathways Activated by NTRK-Fusions in Thyroid Cancer
by Andrey Kechin, Viktoriya Borobova, Alexander Kel, Anatoliy Ivanov and Maxim Filipenko
Appl. Sci. 2022, 12(5), 2506; https://doi.org/10.3390/app12052506 - 28 Feb 2022
Cited by 1 | Viewed by 1946
Abstract
NTRK gene fusions are drivers of tumorigenesis events that specific Trk-inhibitors can target. Current knowledge of the downstream pathways activated has been previously limited to the pathways of regulator proteins phosphorylated directly by Trk receptors. Here, we aimed to detect genes whose expression [...] Read more.
NTRK gene fusions are drivers of tumorigenesis events that specific Trk-inhibitors can target. Current knowledge of the downstream pathways activated has been previously limited to the pathways of regulator proteins phosphorylated directly by Trk receptors. Here, we aimed to detect genes whose expression is increased in response to the activation of these pathways. We identified and analyzed differentially expressed genes in thyroid cancer samples with NTRK1 or NTRK3 gene fusions, and without any NTRK fusions, versus normal thyroid gland tissues, using data from the Cancer Genome Atlas, the DESeq2 tool, and the Genome Enhancer and geneXplain platforms. Searching for the genes activated only in samples with an NTRK fusion as opposed to those without NTRK fusions, we identified 29 genes involved in nervous system development, including AUTS2, DTNA, ERBB4, FLRT2, FLRT3, RPH3A, and SCN4A. We found that genes regulating the expression of the upregulated genes (i.e., upstream regulators) were enriched in the “signaling by ERBB4” pathway. ERBB4 was also one of three genes encoding master regulators whose expression was increased only in samples with an NTRK fusion. Moreover, the algorithm searching for positive feedback loops for gene promoters and transcription factors (a so-called “walking pathways” algorithm) identified the ErbB4 protein as the key master regulator. ERBB4 upregulation (p-value = 0.004) was confirmed in an independent sample of ETV6-NTRK3-positive FFPE specimens. Thus, ErbB4 is the potential key regulator of the pathways activated by NTRK gene fusions in thyroid cancer. These results are preliminary and require additional biochemical validation. Full article
(This article belongs to the Special Issue Bioinformatics: From Gene to Networks)
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Review

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23 pages, 1847 KiB  
Review
Plant Exosomal Vesicles: Perspective Information Nanocarriers in Biomedicine
by Yury Shkryl, Zhargalma Tsydeneshieva, Anton Degtyarenko, Yulia Yugay, Larissa Balabanova, Tatiana Rusapetova and Victor Bulgakov
Appl. Sci. 2022, 12(16), 8262; https://doi.org/10.3390/app12168262 - 18 Aug 2022
Cited by 17 | Viewed by 4335
Abstract
Exosomal nanoparticles (exosomes or nanovesicles) are biogenic membrane vesicles secreted by various cell types and represent a conservative mechanism of intercellular and interspecies communication in pro- and eukaryotic organisms. By transporting specific proteins, nucleic acids, and low molecular weight metabolites, the exosomes are [...] Read more.
Exosomal nanoparticles (exosomes or nanovesicles) are biogenic membrane vesicles secreted by various cell types and represent a conservative mechanism of intercellular and interspecies communication in pro- and eukaryotic organisms. By transporting specific proteins, nucleic acids, and low molecular weight metabolites, the exosomes are involved in the regulation of developmental processes, activation of the immune system, and the development of a protective response to stress. Recently, the plant nanovesicles, due to an economical and affordable source of their production, have attracted a lot of attention in the biomedical field. Being a natural transport system, the plant exosomes represent a promising platform in biomedicine for the delivery of molecules of both endogenous and exogenous origin. This review presents current data on the biogenesis of plant exosomes and their composition, as well as mechanisms of their loading with various therapeutic compounds, which are determining factors for their possible practical use. We believe that further research in this area will significantly expand the potential of targeted therapy, particularly targeted gene regulation via the small RNAs, due to the use of plant exosomes in clinical practice. Full article
(This article belongs to the Special Issue Bioinformatics: From Gene to Networks)
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