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Special Issue "Research Advances in Cell Methods"

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A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: 31 January 2024 | Viewed by 3716

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Prof. Dr. Jan G. Hengstler

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Guest Editor

Leibniz-Research Centre, Toxicology, (IfADo), 44139 Dortmund, Germany
Interests: liver physiology; chronic liver diseases; toxicology; functional imaging
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, entitled “Research Advances in Cell Methods”, welcomes the submission of high-quality research articles and review articles in the cutting-edge fields of cell methods. This Special Issue aims to illustrate, through selected works, frontier research in cell methods; therefore, we encourage distinguished researchers from all over the world, working in all related fields, to contribute. Relevant research topics include (but are not limited to) the following:

Methods for cell culture and manipulation;
Methods for protein engineering, expression, and purification;
Techniques for manipulation of gene expression;
Omics: genomics, epigenomics, transcriptomics, proteomics, metabolomics, etc.;
Bioimaging and optogenetic technologies;
Immunological techniques;
Computational and bioinformatic methods；
Other cell technique areas within the scope of this Special Issue.

Successful papers will be published on an ongoing basis with full open access. We look forward to receiving your contributions.

Prof. Dr. Jan G. Hengstler
Guest Editor

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. Cells 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 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.

Published Papers (3 papers)

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Research

17 pages, 2268 KiB

Open AccessArticle

Early Detection of Pre-Cancerous and Cancerous Cells Using Raman Spectroscopy-Based Machine Learning

and

Cells 2023, 12(14), 1909; https://doi.org/10.3390/cells12141909 - 21 Jul 2023

Viewed by 794

Abstract

Cancer is the most common and fatal disease around the globe, with an estimated 19 million newly diagnosed patients and approximately 10 million deaths annually. Patients with cancer struggle daily due to difficult treatments, pain, and financial and social difficulties. Detecting the disease in its early stages is critical in increasing the likelihood of recovery and reducing the financial burden on the patient and society. Currently used methods for the diagnosis of cancer are time-consuming, producing discomfort and anxiety for patients and significant medical waste. The main goal of this study is to evaluate the potential of Raman spectroscopy-based machine learning for the identification and characterization of precancerous and cancerous cells. As a representative model, normal mouse primary fibroblast cells (NFC) as healthy cells; a mouse fibroblast cell line (NIH/3T3), as precancerous cells; and fully malignant mouse fibroblasts (MBM-T) as cancerous cells were used. Raman spectra were measured from three different sites of each of the 457 investigated cells and analyzed by principal component analysis (PCA) and linear discriminant analysis (LDA). Our results showed that it was possible to distinguish between the normal and abnormal (precancerous and cancerous) cells with a success rate of 93.1%; this value was 93.7% when distinguishing between normal and precancerous cells and 80.2% between precancerous and cancerous cells. Moreover, there was no influence of the measurement site on the differentiation between the different examined biological systems. Full article

(This article belongs to the Special Issue Research Advances in Cell Methods)

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21 pages, 12683 KiB

Open AccessArticle

AMCSMMA: Predicting Small Molecule–miRNA Potential Associations Based on Accurate Matrix Completion

and

Cells 2023, 12(8), 1123; https://doi.org/10.3390/cells12081123 - 10 Apr 2023

Viewed by 982

Abstract

Exploring potential associations between small molecule drugs (SMs) and microRNAs (miRNAs) is significant for drug development and disease treatment. Since biological experiments are expensive and time-consuming, we propose a computational model based on accurate matrix completion for predicting potential SM–miRNA associations (AMCSMMA). Initially, a heterogeneous SM–miRNA network is constructed, and its adjacency matrix is taken as the target matrix. An optimization framework is then proposed to recover the target matrix with the missing values by minimizing its truncated nuclear norm, an accurate, robust, and efficient approximation to the rank function. Finally, we design an effective two-step iterative algorithm to solve the optimization problem and obtain the prediction scores. After determining the optimal parameters, we conduct four kinds of cross-validation experiments based on two datasets, and the results demonstrate that AMCSMMA is superior to the state-of-the-art methods. In addition, we implement another validation experiment, in which more evaluation metrics in addition to the AUC are introduced and finally achieve great results. In two types of case studies, a large number of SM–miRNA pairs with high predictive scores are confirmed by the published experimental literature. In summary, AMCSMMA has superior performance in predicting potential SM–miRNA associations, which can provide guidance for biological experiments and accelerate the discovery of new SM–miRNA associations. Full article

(This article belongs to the Special Issue Research Advances in Cell Methods)

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21 pages, 3950 KiB

Open AccessArticle

Comparative and Temporal Characterization of LPS and Blue-Light-Induced TLR4 Signal Transduction and Gene Expression in Optogenetically Manipulated Endothelial Cells

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Cells 2023, 12(5), 697; https://doi.org/10.3390/cells12050697 - 22 Feb 2023

Cited by 3 | Viewed by 1455

Abstract

In endothelial cells (ECs), stimulation of Toll-like receptor 4 (TLR4) by the endotoxin lipopolysaccharide (LPS) induces the release of diverse pro-inflammatory mediators, beneficial in controlling bacterial infections. However, their systemic secretion is a main driver of sepsis and chronic inflammatory diseases. Since distinct and rapid induction of TLR4 signaling is difficult to achieve with LPS due to the specific and non-specific affinity to other surface molecules and receptors, we engineered new light-oxygen-voltage-sensing (LOV)-domain-based optogenetic endothelial cell lines (opto-TLR4-LOV LECs and opto-TLR4-LOV HUVECs) that allow fast, precise temporal, and reversible activation of TLR4 signaling pathways. Using quantitative mass-spectrometry, RT-qPCR, and Western blot analysis, we show that pro-inflammatory proteins were not only expressed differently, but also had a different time course when the cells were stimulated with light or LPS. Additional functional assays demonstrated that light induction promoted chemotaxis of THP-1 cells, disruption of the EC monolayer and transmigration. In contrast, ECs incorporating a truncated version of the TLR4 extracellular domain (opto-TLR4 ΔECD2-LOV LECs) revealed high basal activity with fast depletion of the cell signaling system upon illumination. We conclude that the established optogenetic cell lines are well suited to induce rapid and precise photoactivation of TLR4, allowing receptor-specific studies. Full article

(This article belongs to the Special Issue Research Advances in Cell Methods)

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