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Biomolecules
Special Issues
Biomolecular Approaches to Regulate RNA Expression and Functions
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Biomolecular Approaches to Regulate RNA Expression and Functions

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Nucleic Acids".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 10374

Special Issue Editors

Prof. Dr. Shizuka Uchida

E-Mail Website
Guest Editor
Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark
Interests: bioinformatics; cardiovascular system; circRNA; database; epitranscriptomics; lncRNA; miRNA; non-coding RNA
Special Issues, Collections and Topics in MDPI journals
Dr. Mirolyuba Ilieva

E-Mail Website
Guest Editor
Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark
Interests: non-coding RNAs; stem cell biology; neuroscience
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As exemplified by mRNA vaccines against COVID-19, RNA holds vast potential for therapeutic usages. Decades of research has uncovered that only few percent of RNA correspond to the exons of protein-coding genes, leaving majority of transcripts as non-protein-coding. These non-protein-coding transcripts are collectively called, non-coding RNAs (ncRNAs), which includes ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). Given that over 90% of human genome are transcribed as RNA, the research to record expression and understand the functions of ncRNAs have intensified in recent years. Not only within a cell but RNA actively participates in a cell-to-cell communication as in the form of exosomal RNA. Unlike the traditional understanding of exact copy of the genomic DNA, RNA itself can be modified by a variety of enzymes that affect the fates of RNA and its metabolism, including RNA stability, binding to other macromolecules, subcellular localization, and translation. Given the accumulated evidence for the versatility of RNA, this special issue calls for papers related to modulating RNA expression and/or functions using biomolecules. We welcome original research and review manuscripts to further broaden the understanding of RNA.

Prof. Dr. Shizuka Uchida
Dr. Mirolyuba Ilieva
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. Biomolecules is an international peer-reviewed open access monthly 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 2700 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.

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Published Papers (4 papers)

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Research

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11 pages, 2873 KiB  
Article
Modeling Human Lung Cells Exposure to Wildfire Uncovers Aberrant lncRNAs Signature
by Piercen K. Nguyen, Yeongkwon Son, Juli Petereit, Andrey Khlystov and Riccardo Panella
Biomolecules 2023, 13(1), 155; https://doi.org/10.3390/biom13010155 - 12 Jan 2023
Viewed by 1924
Abstract
Emissions generated by wildfires are a growing threat to human health and are characterized by a unique chemical composition that is tightly dependent on geographic factors such as fuel type. Long noncoding RNAs (lncRNAs) are a class of RNA molecules proven to be [...] Read more.
Emissions generated by wildfires are a growing threat to human health and are characterized by a unique chemical composition that is tightly dependent on geographic factors such as fuel type. Long noncoding RNAs (lncRNAs) are a class of RNA molecules proven to be critical to many biological processes, and their condition-specific expression patterns are emerging as prominent prognostic and diagnostic biomarkers for human disease. We utilized a new air-liquid interface (ALI) direct exposure system that we designed and validated in house to expose immortalized human tracheobronchial epithelial cells (AALE) to two unique wildfire smokes representative of geographic regions (Sierra Forest and Great Basin). We conducted an RNAseq analysis on the exposed cell cultures and proved through both principal component and differential expression analysis that each smoke has a unique effect on the LncRNA expression profiles of the exposed cells when compared to the control samples. Our study proves that there is a link between the geographic origin of wildfire smoke and the resulting LncRNA expression profile in exposed lung cells and also serves as a proof of concept for the in-house designed ALI exposure system. Our study serves as an introduction to the scientific community of how unique expression patterns of LncRNAs in patients with wildfire smoke-related disease can be utilized as prognostic and diagnostic tools, as the current roles of LncRNA expression profiles in wildfire smoke-related disease, other than this study, are completely uncharted. Full article
(This article belongs to the Special Issue Biomolecular Approaches to Regulate RNA Expression and Functions)
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13 pages, 1797 KiB  
Article
The Photobiomodulation of MAO-A Affects the Contractile Activity of Smooth Muscle Gastric Tissues
by Charilaos Xenodochidis, Dessislava Staneva, Bela Vasileva, Milena Draganova, George Miloshev, Milena Georgieva and Plamen Zagorchev
Biomolecules 2023, 13(1), 32; https://doi.org/10.3390/biom13010032 - 24 Dec 2022
Cited by 1 | Viewed by 1651
Abstract
Nowadays, the utilized electromagnetic radiation (ER) in modalities such as photobiomodulation (PBM) finds broader applications in medical practice due to the promising results suggested by numerous reports. To date, the published data do not allow for the in-depth elucidation of the molecular mechanisms [...] Read more.
Nowadays, the utilized electromagnetic radiation (ER) in modalities such as photobiomodulation (PBM) finds broader applications in medical practice due to the promising results suggested by numerous reports. To date, the published data do not allow for the in-depth elucidation of the molecular mechanisms through which ER impacts the human organism. Furthermore, there is a total lack of evidence justifying the relation between the enzymatic activity of monoamine oxidase A (MAO-A) and the effect of 5-hydroxytryptamine (5-HT) on the spontaneous contractile activity of smooth muscle gastric tissues exposed to various light sources. We found that exposure of these tissues to lamps, emitting light with wavelengths of 254 nm and 350 nm, lasers, emitting light with 532 nm and 808 nm, and light-emitting diodes (LEDs) with ER at a wavelength of 660 nm, increased the 5-HT effect on the contractility. On the other hand, LEDs at 365 nm and 470 nm reduced it. The analysis of MAO-A enzymatic activity after exposure to the employed light emitters endorsed these findings. Furthermore, MAOA gene expression studies confirmed the possibility of its optogenetic regulation. Therefore, we concluded that the utilized emitters could alternate the functions of significant neuromediators by modulating the activity and gene transcription levels of enzymes that degrade them. Our investigations will help to disclose the selective conditions upon which PBM can effectively treat gastrointestinal and neurological disorders. Full article
(This article belongs to the Special Issue Biomolecular Approaches to Regulate RNA Expression and Functions)
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Review

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11 pages, 884 KiB  
Review
Micro RNAs—The Small Big Players in Hepatitis E Virus Infection: A Comprehensive Review
by Elitsa Golkocheva-Markova
Biomolecules 2022, 12(11), 1543; https://doi.org/10.3390/biom12111543 - 22 Oct 2022
Cited by 2 | Viewed by 1739
Abstract
The molecular mechanism of hepatitis E virus (HEV) pathology is still unclear. The micro RNAs (miRNAs), of host or viral origin, interfere with virus replication and host environment in order to create an appropriate condition for the production of mature HEV progeny. Understanding [...] Read more.
The molecular mechanism of hepatitis E virus (HEV) pathology is still unclear. The micro RNAs (miRNAs), of host or viral origin, interfere with virus replication and host environment in order to create an appropriate condition for the production of mature HEV progeny. Understanding the biogenesis and the interference of miRNAs with HEV will help to revile the mechanism of viral pathogenesis. Full article
(This article belongs to the Special Issue Biomolecular Approaches to Regulate RNA Expression and Functions)
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17 pages, 3117 KiB  
Review
Pancreatic Cancer Research beyond DNA Mutations
by Hiromichi Sato, Kazuki Sasaki, Tomoaki Hara, Yoshiko Tsuji, Yasuko Arao, Chihiro Otsuka, Yumiko Hamano, Mirei Ogita, Shogo Kobayashi, Eric di Luccio, Takaaki Hirotsu, Yuichiro Doki, Hidetoshi Eguchi, Taroh Satoh, Shizuka Uchida and Hideshi Ishii
Biomolecules 2022, 12(10), 1503; https://doi.org/10.3390/biom12101503 - 17 Oct 2022
Cited by 5 | Viewed by 3976
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is caused by genetic mutations in four genes: KRAS proto-oncogene and GTPase (KRAS), tumor protein P53 (TP53), cyclin-dependent kinase inhibitor 2A (CDKN2A), and mothers against decapentaplegic homolog 4 (SMAD4), also called [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) is caused by genetic mutations in four genes: KRAS proto-oncogene and GTPase (KRAS), tumor protein P53 (TP53), cyclin-dependent kinase inhibitor 2A (CDKN2A), and mothers against decapentaplegic homolog 4 (SMAD4), also called the big 4. The changes in tumors are very complex, making their characterization in the early stages challenging. Therefore, the development of innovative therapeutic approaches is desirable. The key to overcoming PDAC is diagnosing it in the early stages. Therefore, recent studies have investigated the multifaced characteristics of PDAC, which includes cancer cell metabolism, mesenchymal cells including cancer-associated fibroblasts and immune cells, and metagenomics, which extend to characterize various biomolecules including RNAs and volatile organic compounds. Various alterations in the KRAS-dependent as well as KRAS-independent pathways are involved in the refractoriness of PDAC. The optimal combination of these new technologies is expected to help treat intractable pancreatic cancer. Full article
(This article belongs to the Special Issue Biomolecular Approaches to Regulate RNA Expression and Functions)
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