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Feature Papers in Methods and Protocols 2025
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Feature Papers in Methods and Protocols 2025

A special issue of Methods and Protocols (ISSN 2409-9279).

Deadline for manuscript submissions: 31 December 2025 | Viewed by 2465

Special Issue Editor

Prof. Dr. Fernando Albericio

E-Mail Website
Guest Editor
1. School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
2. Department of Organic Chemistry, University of Barcelona, Barcelona, Spain
Interests: antimicrobial peptides; solid-phase chemistry; combinatorial chemistry; drug delivery systems; peptide drug conjugates; orthogonal chemistry; drug discovery; biomaterials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are glad to announce this Special Issue on “Feature Papers in Methods and Protocols 2025”. In this Special Issue, we will collect articles from top researchers describing new approaches or new cutting-edge developments to tackle questions in the fields of life sciences, chemistry, and biomedical sciences. In particular, we encourage submissions in the emerging fields of “Omics and High Throughput”, “Public Health Research”, “Synthetic and Systems Biology” and “Tissue Engineering and Organoids”. Our aim is to encourage scientists to publish new protocols based on established techniques, as well as significant improvements and developments of cutting-edge methods. For all articles, background information necessary to understand the underlying principles, full experimental details, and comparison with available protocols/methods must be provided. Scientists are encouraged to provide accompanying video demonstrations, which will be published online, for ease of reproducibility.

You are welcome to send short proposals for the submission of feature papers to our Managing Editor Ms. Eunice Fu(eunice.fu@mdpi.com) or Editorial Office (mps@mdpi.com) before submission. All papers will be subjected to thorough and rigorous peer review.

We look forward to receiving your excellent work.

Prof. Dr. Fernando Albericio
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. Methods and Protocols 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 1800 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

  • cell biology
  • biochemistry
  • chemistry
  • nanotechnology
  • biotechnology
  • imaging
  • applied computation and bioinformatics
  • genomics
  • proteomics
  • developmental biology
  • model organisms
  • pharmacology
  • structural biology/chemistry
  • biophysics
  • tissue engineering
  • public health

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

Published Papers (4 papers)

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Research

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12 pages, 2410 KiB  
Article
Exploring the Chorioallantoic Membrane (CAM) as a Platform for Burn Wound Modelling and Analysis
by Rita Araújo, Maria Guerra-Gomes, Joana Barros and Pedro Gomes
Methods Protoc. 2025, 8(4), 79; https://doi.org/10.3390/mps8040079 - 10 Jul 2025
Viewed by 219
Abstract
Burn wounds present a significant challenge to both the medical and scientific communities, contributing to the global economic burden on healthcare systems. Due to the complexity and highly variability of burn injuries, along with intricate pathophysiological mechanisms, the development of appropriate and effective [...] Read more.
Burn wounds present a significant challenge to both the medical and scientific communities, contributing to the global economic burden on healthcare systems. Due to the complexity and highly variability of burn injuries, along with intricate pathophysiological mechanisms, the development of appropriate and effective treatment strategies remains particularly demanding. The development of robust pre-clinical models that recapitulate specific molecular and cellular events underlying burn injury are essential to advance the understanding of associated biological mechanisms and facilitate the screening of innovative therapeutic interventions. While conventional in vivo models can replicate the key aspects of human burn wound pathology, they are often associated with ethical, logistical, and cost-related limitations. In this context, this study aims to explore the potential of the chicken chorioallantoic membrane (CAM) as an alternative model for burn wound research. Thus, we describe a reproducible and ethically favorable protocol for establishing standardized burn injuries on the CAM and provide a comprehensive evaluation of tissue responses through macroscopic, morphometric, and histological analyses. Our findings support the CAM as a viable pre-clinical platform for the study of burn wound healing and for the early-stage screening of candidate therapeutic agents. Full article
(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2025)
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19 pages, 2714 KiB  
Article
A Model-Based Approach to Neuronal Electrical Activity and Spatial Organization Through the Neuronal Actin Cytoskeleton
by Ali H. Rafati, Sâmia Joca, Regina T. Vontell, Carina Mallard, Gregers Wegener and Maryam Ardalan
Methods Protoc. 2025, 8(4), 76; https://doi.org/10.3390/mps8040076 - 7 Jul 2025
Viewed by 237
Abstract
The study of neuronal electrical activity and spatial organization is essential for uncovering the mechanisms that regulate neuronal electrophysiology and function. Mathematical models have been utilized to analyze the structural properties of neuronal networks, predict connectivity patterns, and examine how morphological changes impact [...] Read more.
The study of neuronal electrical activity and spatial organization is essential for uncovering the mechanisms that regulate neuronal electrophysiology and function. Mathematical models have been utilized to analyze the structural properties of neuronal networks, predict connectivity patterns, and examine how morphological changes impact neural network function. In this study, we aimed to explore the role of the actin cytoskeleton in neuronal signaling via primary cilia and to elucidate the role of the actin network in conjunction with neuronal electrical activity in shaping spatial neuronal formation and organization, as demonstrated by relevant mathematical models. Our proposed model is based on the polygamma function, a mathematical application of ramification, and a geometrical definition of the actin cytoskeleton via complex numbers, ring polynomials, homogeneous polynomials, characteristic polynomials, gradients, the Dirac delta function, the vector Laplacian, the Goldman equation, and the Lie bracket of vector fields. We were able to reflect the effects of neuronal electrical activity, as modeled by the Van der Pol equation in combination with the actin cytoskeleton, on neuronal morphology in a 2D model. In the next step, we converted the 2D model into a 3D model of neuronal electrical activity, known as a core-shell model, in which our generated membrane potential is compatible with the neuronal membrane potential (in millivolts, mV). The generated neurons can grow and develop like an organoid brain based on the developed mathematical equations. Furthermore, we mathematically introduced the signal transduction of primary cilia in neurons. Additionally, we proposed a geometrical model of the neuronal branching pattern, which we described as ramification, that could serve as an alternative mathematical explanation for the branching pattern emanating from the neuronal soma. In conclusion, we highlighted the relationship between the actin cytoskeleton and the signaling processes of primary cilia. We also developed a 3D model that integrates the geometric organization unique to neurons, which contains soma and branches, such that the mathematical model represents the interaction between the actin cytoskeleton and neuronal electrical activity in generating action potentials. Next, we could generalize the model into a cluster of neurons, similar to an organoid brain model. This mathematical framework offers promising applications in artificial intelligence and advancements in neural networks. Full article
(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2025)
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22 pages, 3360 KiB  
Article
Experimental Investigation of the Effect of Solvent Type and Its Concentration on the Performance of ES-SAGD
by Sajjad Esmaeili, Brij Maini, Zain Ul Abidin and Apostolos Kantzas
Methods Protoc. 2025, 8(2), 39; https://doi.org/10.3390/mps8020039 - 8 Apr 2025
Cited by 1 | Viewed by 529
Abstract
Steam-assisted gravity drainage (SAGD) is a widely used thermal enhanced oil recovery (EOR) technique in North America, particularly in high-permeability oil sand reservoirs. While effective, its economic viability has declined due to low oil prices and high greenhouse gas (GHG) emissions from the [...] Read more.
Steam-assisted gravity drainage (SAGD) is a widely used thermal enhanced oil recovery (EOR) technique in North America, particularly in high-permeability oil sand reservoirs. While effective, its economic viability has declined due to low oil prices and high greenhouse gas (GHG) emissions from the steam generation. To improve cost-effectiveness and reduce emissions, solvent-assisted SAGD techniques have been explored. Expanding Solvent-SAGD (ES-SAGD) involves co-injecting light hydrocarbons like propane or butane with steam to enhance oil viscosity reduction. This approach lowers the steam–oil ratio by combining solvent dissolution effects with thermal effects. However, the high cost of solvents, particularly butane, challenges its commercial feasibility. Propane is cheaper but less effective, while butane improves performance but remains expensive. This research aims to optimize ES-SAGD by using a propane–butane mixture to achieve efficient performance at a lower cost than pure butane. A linear sand pack is used to evaluate different propane/butane compositions, maintaining constant operational conditions and a solvent concentration of 15 vol.%. Temperature monitoring provides insights into steam chamber growth. Results show that solvent injection significantly enhances ES-SAGD performance compared to conventional SAGD. Performance improves with increasing butane concentration, up to 80% butane in the C3–C4 mixture at the test pressure and ambient temperature. Propane alone results in the lowest system temperature, while conventional SAGD reaches the highest temperature. These findings highlight the potential of optimized solvent mixtures to improve ES-SAGD efficiency while reducing costs and GHG emissions. Full article
(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2025)
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Review

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11 pages, 749 KiB  
Review
The PROMISE of Precision Medicine in Myocardial Infarction with Non-Obstructive Coronary Arteries
by Giulia La Vecchia, Vincenzo Scarica, Ludovica Leo and Rocco A. Montone
Methods Protoc. 2025, 8(3), 44; https://doi.org/10.3390/mps8030044 - 27 Apr 2025
Cited by 1 | Viewed by 601
Abstract
Myocardial infarction with non-obstructive coronary arteries (MINOCA) is a working diagnosis encompassing several pathophysiological mechanisms with specific treatments and different prognoses. Despite the absence of obstructive coronary artery disease, MINOCA has proven to be associated with a significant risk of mortality, angina burden, [...] Read more.
Myocardial infarction with non-obstructive coronary arteries (MINOCA) is a working diagnosis encompassing several pathophysiological mechanisms with specific treatments and different prognoses. Despite the absence of obstructive coronary artery disease, MINOCA has proven to be associated with a significant risk of mortality, angina burden, and socioeconomic costs. However, due to the heterogeneous nature of this clinical condition and the absence of randomized clinical trials, evidence supporting a standardized diagnostic algorithm and the clinical management of these patients is lacking. The PROMISE trial is the first randomized clinical trial evaluating the effectiveness of a precision medicine approach strategy in improving the outcomes and quality of life of patients with MINOCA, offering new insights into personalized treatment strategies. This review article discusses the promise of a precision medicine approach in patients with MINOCA, highlighting the potential innovations and challenges of a personalized medicine strategy in MINOCA. Full article
(This article belongs to the Special Issue Feature Papers in Methods and Protocols 2025)
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