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Bioengineering
Special Issues
Molecular Diagnostics in Postgenomic Era
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Molecular Diagnostics in Postgenomic Era

A special issue of Bioengineering (ISSN 2306-5354).

Deadline for manuscript submissions: closed (28 October 2022) | Viewed by 14489

Special Issue Editors

Dr. Petra Korać

E-Mail Website
Guest Editor
Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
Interests: tumor biology; molecular pathology; medical genetics; cell biology; genomics
Special Issues, Collections and Topics in MDPI journals
Dr. Maja Matulić

E-Mail Website
Guest Editor
Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102, 10000 Zagreb, Croatia
Interests: tumor cell; urokinase plasminogen activator; cell signaling

Special Issue Information

Dear Colleagues,

In recent years, we have become increasingly aware of the molecular diagnostics importance in establishing tumor diagnosis, following the progression of the disease, choosing the right therapy, and public health management for screening purposes. As all methods used in molecular diagnostics arise from research in an exciting field of molecular biology, we are witnessing the development of very sophisticated methods that translate to standardized and validated tests.

Therefore, this Special Issue on “Molecular Diagnostics in Postgenomic Era” will focus on original research papers and comprehensive reviews dealing with the application of molecular techniques in cancer diagnostics, but also research papers covering translational research and hypotheses proposing newly developed molecular tests.

Topics include but are not limited to:

  • Detection and application of molecular markers for establishing precise diagnosis;
  • Screening tests available or in development for risk assessment;
  • Molecular tests and markers used for decision making in a field of precise therapy;
  • Gene therapy;
  • Future methods for molecular diagnostics based on genetic engineering techniques;
  • Translational research establishing new biomarkers for cancer diagnosis and treatment;
  • Development of new protocols for molecular diagnostics based on 3D cell cultures.

Dr. Petra Korać
Prof. Dr. Maja Matulić
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. Bioengineering 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.

Keywords

  • screening tests
  • biomarkers
  • genetic engineering techniques
  • 3D cell cultures
  • translational research

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (5 papers)

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Research

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11 pages, 2351 KiB  
Article
Development of a Rapid, Accurate, and On-Site Detection Protocol for Red Imported Fire Ants, Solenopsis invicta (Hymenoptera: Formicidae)
by A-Young Kim and Young Ho Koh
Bioengineering 2022, 9(9), 434; https://doi.org/10.3390/bioengineering9090434 - 2 Sep 2022
Viewed by 1495
Abstract
A rapid, accurate, and on-site molecular diagnostic protocol for red imported fire ants (Solenopsis invicta, Si) was developed using loop-mediated isothermal amplification (LAMP) assays. Si11977 (GenBank accession no. MK986826) was confirmed to be a Si-specific gene. Four-primer Si11977-LAMP [...] Read more.
A rapid, accurate, and on-site molecular diagnostic protocol for red imported fire ants (Solenopsis invicta, Si) was developed using loop-mediated isothermal amplification (LAMP) assays. Si11977 (GenBank accession no. MK986826) was confirmed to be a Si-specific gene. Four-primer Si11977-LAMP (4pSi-LAMP) and six-primer Si11977-LAMP (6pSi-LAMP) assays specifically detected Si. The reaction time of 6pSi-LAMP assays was reduced by 5 min compared with 4pSi-LAMP assays. The optimal amount of polymerase and the detection limit for the 6pSi-LAMP assays were 0.1 unit/μL and 5 fg/μL, respectively. In addition, a method for extracting genomic DNA from ant tissues within 2 to 3 min and a protocol for performing on-site LAMP assays using a car heating mug and a LAMP observation box were described. The on-site Si detection protocol used in this study was possible within 30 min from DNA extraction to species identification. Full article
(This article belongs to the Special Issue Molecular Diagnostics in Postgenomic Era)
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21 pages, 1401 KiB  
Article
Identification of Radiation-Induced miRNA Biomarkers Using the CGL1 Cell Model System
by Jayden Peterson, Christopher D. McTiernan, Christopher Thome, Neelam Khaper, Simon J. Lees, Douglas R. Boreham, Tze Chun Tai and Sujeenthar Tharmalingam
Bioengineering 2022, 9(5), 214; https://doi.org/10.3390/bioengineering9050214 - 16 May 2022
Cited by 4 | Viewed by 2732
Abstract
MicroRNAs (miRNAs) have emerged as a potential class of biomolecules for diagnostic biomarker applications. miRNAs are small non-coding RNA molecules, produced and released by cells in response to various stimuli, that demonstrate remarkable stability in a wide range of biological fluids, in extreme [...] Read more.
MicroRNAs (miRNAs) have emerged as a potential class of biomolecules for diagnostic biomarker applications. miRNAs are small non-coding RNA molecules, produced and released by cells in response to various stimuli, that demonstrate remarkable stability in a wide range of biological fluids, in extreme pH fluctuations, and after multiple freeze–thaw cycles. Given these advantages, identification of miRNA-based biomarkers for radiation exposures can contribute to the development of reliable biological dosimetry methods, especially for low-dose radiation (LDR) exposures. In this study, an miRNAome next-generation sequencing (NGS) approach was utilized to identify novel radiation-induced miRNA gene changes within the CGL1 human cell line. Here, irradiations of 10, 100, and 1000 mGy were performed and the samples were collected 1, 6, and 24 h post-irradiation. Corroboration of the miRNAome results with RT-qPCR verification confirmed the identification of numerous radiation-induced miRNA expression changes at all doses assessed. Further evaluation of select radiation-induced miRNAs, including miR-1228-3p and miR-758-5p, as well as their downstream mRNA targets, Ube2d2, Ppp2r2d, and Id2, demonstrated significantly dysregulated reciprocal expression patterns. Further evaluation is needed to determine whether the candidate miRNA biomarkers identified in this study can serve as suitable targets for radiation biodosimetry applications. Full article
(This article belongs to the Special Issue Molecular Diagnostics in Postgenomic Era)
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21 pages, 7783 KiB  
Article
Design, Spectral Characteristics, Photostability, and Possibilities for Practical Application of BODIPY FL-Labeled Thioterpenoid
by Galina B. Guseva, Elena V. Antina, Mikhail B. Berezin, Anastassia S. Smirnova, Roman S. Pavelyev, Ilmir R. Gilfanov, Oksana G. Shevchenko, Svetlana V. Pestova, Evgeny S. Izmest’ev, Svetlana A. Rubtsova, Olga V. Ostolopovskaya, Sergey V. Efimov, Vladimir V. Klochkov, Ilfat Z. Rakhmatullin, Ayzira F. Timerova, Ilya A. Khodov, Olga A. Lodochnikova, Daut R. Islamov, Pavel V. Dorovatovskii, Liliya E. Nikitina and Sergei V. Boichukadd Show full author list remove Hide full author list
Bioengineering 2022, 9(5), 210; https://doi.org/10.3390/bioengineering9050210 - 12 May 2022
Cited by 4 | Viewed by 2832
Abstract
This paper presents the design and a comparative analysis of the structural and solvation factors on the spectral and biological properties of the BODIPY biomarker with a thioterpene fragment. Covalent binding of the thioterpene moiety to the butanoic acid residue of meso-substituted [...] Read more.
This paper presents the design and a comparative analysis of the structural and solvation factors on the spectral and biological properties of the BODIPY biomarker with a thioterpene fragment. Covalent binding of the thioterpene moiety to the butanoic acid residue of meso-substituted BODIPY was carried out to find out the membranotropic effect of conjugate to erythrocytes, and to assess the possibilities of its practical application in bioimaging. The molecular structure of the conjugate was confirmed via X-ray, UV/vis-, NMR-, and MS-spectra. It was found that dye demonstrates high photostability and high fluorescence quantum yield (to ~100%) at 514–519 nm. In addition, the marker was shown to effectively penetrate the erythrocytes membrane in the absence of erythrotoxicity. The conjugation of BODIPY with thioterpenoid is an excellent way to increase affinity dyes to biostructures, including blood components. Full article
(This article belongs to the Special Issue Molecular Diagnostics in Postgenomic Era)
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14 pages, 472 KiB  
Article
A Systematic Approach to Diagnostic Laboratory Software Requirements Analysis
by Thomas Krause, Elena Jolkver, Paul Mc Kevitt, Michael Kramer and Matthias Hemmje
Bioengineering 2022, 9(4), 144; https://doi.org/10.3390/bioengineering9040144 - 28 Mar 2022
Cited by 4 | Viewed by 3056
Abstract
Genetics plays an ever-increasing role in medical diagnostics. The requirements for laboratory diagnostics are constantly changing due to new emerging diagnostic procedures, methodologies, devices, and regulatory requirements. Standard software already available for laboratories often cannot keep up with the latest developments or is [...] Read more.
Genetics plays an ever-increasing role in medical diagnostics. The requirements for laboratory diagnostics are constantly changing due to new emerging diagnostic procedures, methodologies, devices, and regulatory requirements. Standard software already available for laboratories often cannot keep up with the latest developments or is focused on research rather than process automation. Although the software utilized in diagnostic laboratories is subject to regulatory requirements, there is no well-defined formal procedure for software development. Reference models have been developed to formalize these solutions, but they do not facilitate the initial requirements analysis or the development process itself. A systematic requirements engineering process is however not only essential to ensure the quality of the final product but is also required by regulations such as the European In Vitro Diagnostic Regulation and international standards such as IEC 62304. This paper shows, by example, the systematic requirements analysis of a system for qPCR-based (quantitative polymerase chain reaction) gene expression analysis. Towards this goal, a multi-step research approach was employed, which included literature review, user interviews, and market analysis. Results revealed the complexity of the field with many requirements to be considered for future implementation. Full article
(This article belongs to the Special Issue Molecular Diagnostics in Postgenomic Era)
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Review

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25 pages, 851 KiB  
Review
miRNA in Molecular Diagnostics
by Maja Matulić, Paula Gršković, Andreja Petrović, Valerija Begić, Suzana Harabajsa and Petra Korać
Bioengineering 2022, 9(9), 459; https://doi.org/10.3390/bioengineering9090459 - 9 Sep 2022
Cited by 7 | Viewed by 3237
Abstract
MicroRNAs are a class of small non-coding RNA molecules that regulate gene expression on post-transcriptional level. Their biogenesis consists of a complex series of sequential processes, and they regulate expression of many genes involved in all cellular processes. Their function is essential for [...] Read more.
MicroRNAs are a class of small non-coding RNA molecules that regulate gene expression on post-transcriptional level. Their biogenesis consists of a complex series of sequential processes, and they regulate expression of many genes involved in all cellular processes. Their function is essential for maintaining the homeostasis of a single cell; therefore, their aberrant expression contributes to development and progression of many diseases, especially malignant tumors and viral infections. Moreover, they can be associated with certain states of a specific disease, obtained in the least invasive manner for patients and analyzed with basic molecular methods used in clinical laboratories. Because of this, they have a promising potential to become very useful biomarkers and potential tools in personalized medicine approaches. In this review, miRNAs biogenesis, significance in cancer and infectious diseases, and current available test and methods for their detection are summarized. Full article
(This article belongs to the Special Issue Molecular Diagnostics in Postgenomic Era)
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