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Analytical Methods in Biomedical and Environmental Applications: A Molecular Approach

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 19950

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Guest Editor
Faculty of Electrical Engineering and Computer Science, Transilvania University of Brasov, 500068 Brasov, Romania
Interests: electrochemical and optical (bio)sensors for environmental applications; nanomaterials functionalization and synthesis; biomolecular interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Analytical methods, mainly used for (bio)medical and environmental science applications toward molecular detection, comprise both labeled (fluorescence, nuclear, etc.) and label-free detection techniques, such as electrical, electrochemical, optical, piezoelectric, or thermal detection. Scientists, along with industry, are continuously looking for new and improved analytical methods.

For this Special Issue, “Analytical Methods in Biomedical and Environmental Applications: A Molecular Approach”, we invite manuscripts dealing with the development of new methods to lead to the identification and quantification of important (bio)molecules from different types of samples. The problem to be solved is not only the detection of very small amounts of analyte, but also how to deal with complex matrices such as food, biological, or environmental samples. Tailoring of material and molecular structures, mechanisms, kinetics, and thermodynamics analyses is also of great interest alongside computational studies.

Dr. Melinda David
Dr. Monica Florescu
Guest Editors

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • analytical methods
  • molecular
  • fluorescence
  • nuclear
  • electrical
  • electrochemical
  • optical
  • piezoelectric
  • thermal detection

Published Papers (12 papers)

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Research

17 pages, 5649 KiB  
Article
Carbon Inks-Based Screen-Printed Electrodes for Qualitative Analysis of Amino Acids
by Teodor Adrian Enache, Monica Enculescu, Mihaela-Cristina Bunea, Estibaliz Armendariz Zubillaga, Edurne Tellechea, Maite Aresti, María Lasheras, Aaron C. Asensio and Victor C. Diculescu
Int. J. Mol. Sci. 2023, 24(2), 1129; https://doi.org/10.3390/ijms24021129 - 06 Jan 2023
Cited by 2 | Viewed by 1548
Abstract
Due to the great significance of amino acids, a substantial number of research studies has been directed toward the development of effective and reliable platforms for their evaluation, detection, and identification. In order to support these studies, a new electrochemical platform based on [...] Read more.
Due to the great significance of amino acids, a substantial number of research studies has been directed toward the development of effective and reliable platforms for their evaluation, detection, and identification. In order to support these studies, a new electrochemical platform based on PANI/ZnO nanowires’ modified carbon inks screen-printed electrodes was developed for qualitative analysis of electroactive amino acids, with emphasis on tyrosine (Tyr) and tryptophan (Trp). A comparative investigation of the carbon ink before and after modification with the PANI/ZnO was performed by scanning electron microscopy and by Raman spectroscopy, confirming the presence of PANI and ZnO nanowires. Electrochemical investigations by cyclic voltammetry and electrochemical impedance spectroscopy have shown a higher charge-transfer rate constant, which is reflected into lower charge-transfer resistance and higher capacitance values for the PANI/ZnO modified ink when compared to the simple carbon screen-printed electrode. In order to demonstrate the electrochemical performances of the PANI/ZnO nanowires’ modified carbon inks screen-printed electrodes for amino acids analysis, differential pulse voltammograms were obtained in individual and mixed solutions of electroactive amino acids. It has been shown that the PANI/ZnO nanowires’ modified carbon inks screen-printed electrodes allowed for tyrosine and tryptophan a peak separation of more than 100 mV, enabling their screening and identification in mixed solutions, which is essential for the electrochemical analysis of proteins within the proteomics research field. Full article
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8 pages, 10504 KiB  
Article
A Simple Protocol for Sample Preparation for Scanning Electron Microscopic Imaging Allows Quick Screening of Nanomaterials Adhering to Cell Surface
by Anca Emanuela Minuti, Luminita Labusca, Dumitru-Daniel Herea, George Stoian, Horia Chiriac and Nicoleta Lupu
Int. J. Mol. Sci. 2023, 24(1), 430; https://doi.org/10.3390/ijms24010430 - 27 Dec 2022
Cited by 2 | Viewed by 2580
Abstract
Preparing biological specimens for scanning electron microscopy (SEM) can be difficult to implement, as it requires specialized equipment and materials as well as the training of dedicated personnel. Moreover, the procedure often results in damage to the samples to be analyzed. This work [...] Read more.
Preparing biological specimens for scanning electron microscopy (SEM) can be difficult to implement, as it requires specialized equipment and materials as well as the training of dedicated personnel. Moreover, the procedure often results in damage to the samples to be analyzed. This work presents a protocol for the preparation of biological samples to evaluate the adherence of nanomaterials on the cell surface using SEM. To this end, we used silicon wafers as a substrate to grow cells and replaced difficult steps such as the critical point drying of the samples in order to make the method quicker and easier to perform. The new protocol was tested using two different types of cells, i.e., human osteosarcoma cells and adipose-derived mesenchymal stem cells, and it proved that it can grossly preserve cell integrity in order to be used to estimate nanomaterials’ interaction with cell surfaces. Full article
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18 pages, 4035 KiB  
Article
Detection and Characterization of Nodularin by Using Label-Free Surface-Enhanced Spectroscopic Techniques
by Ioana Andreea Brezeștean, Ana Maria Raluca Gherman, Alia Colniță, Nicoleta Elena Dina, Csilla Müller Molnár, Daniel Marconi, Vasile Chiș, Ioan-Leontin David and Simona Cîntă-Pînzaru
Int. J. Mol. Sci. 2022, 23(24), 15741; https://doi.org/10.3390/ijms232415741 - 12 Dec 2022
Cited by 2 | Viewed by 1380
Abstract
Nodularin (NOD) is a potent toxin produced by Nodularia spumigena cyanobacteria. Usually, NOD co-exists with other microcystins in environmental waters, a class of cyanotoxins secreted by certain cyanobacteria species, which makes identification difficult in the case of mixed toxins. Herein we report a [...] Read more.
Nodularin (NOD) is a potent toxin produced by Nodularia spumigena cyanobacteria. Usually, NOD co-exists with other microcystins in environmental waters, a class of cyanotoxins secreted by certain cyanobacteria species, which makes identification difficult in the case of mixed toxins. Herein we report a complete theoretical DFT-vibrational Raman characterization of NOD along with the experimental drop-coating deposition Raman (DCDR) technique. In addition, we used the vibrational characterization to probe SERS analysis of NOD using colloidal silver nanoparticles (AgNPs), commercial nanopatterned substrates with periodic inverted pyramids (KlariteTM substrate), hydrophobic Tienta® SpecTrimTM slides, and in-house fabricated periodic nanotrenches by nanoimprint lithography (NIL). The 532 nm excitation source provided more well-defined bands even at LOD levels, as well as the best performance in terms of SERS intensity. This was reflected by the results obtained with the KlariteTM substrate and the silver-based colloidal system, which were the most promising detection approaches, providing the lowest limits of detection. A detection limit of 8.4 × 10−8 M was achieved for NOD in solution by using AgNPs. Theoretical computation of the complex vibrational modes of NOD was used for the first time to unambiguously assign all the specific vibrational Raman bands. Full article
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12 pages, 1754 KiB  
Article
Neomycin, but Not Neamine, Blocks Angiogenic Factor Induced Nitric Oxide Release through Inhibition of Akt Phosphorylation
by Raphaël Trouillon, Dong-Ku Kang, Soo-Ik Chang and Danny O’Hare
Int. J. Mol. Sci. 2022, 23(23), 15277; https://doi.org/10.3390/ijms232315277 - 03 Dec 2022
Cited by 1 | Viewed by 1463
Abstract
Angiogenesis, the growth of new blood vessels, is a critical factor of carcinogenesis. Neomycin and neamine, two drugs blocking the nuclear translocation of angiogenin (ANG), have been proven to inhibit tumour growth in vivo. However, the high toxicity of neomycin prevents its therapeutic [...] Read more.
Angiogenesis, the growth of new blood vessels, is a critical factor of carcinogenesis. Neomycin and neamine, two drugs blocking the nuclear translocation of angiogenin (ANG), have been proven to inhibit tumour growth in vivo. However, the high toxicity of neomycin prevents its therapeutic use, thus indicating that the less toxic neamine may be a better candidate. Endothelial cells were cultured on a biocompatible multiple microelectrode array (MMA). The release of NO evoked by ANG or vascular endothelial growth factor (VEGF) was detected electrochemically. The effects of neomycin and neamine on ANG- and VEGF-induced NO releases have been investigated. Neomycin totally blocks NO release for concentrations down to the pM range, probably through the inhibition of the Akt kinase phosphorylation, as revealed by confocal microscopy. On the other hand, both ANG- and VEGF-induced NO releases were not significantly hindered by the presence of high concentrations of neamine. The inhibition of the Akt pathway and NO release are expected to lead to a severe decrease in tissue growth and repair, thus indicating a possible cause for the toxicity of neomycin. Furthermore, the data presented here show that ANG- and VEGF-induced NO releases are not dependent on the nuclear translocation of angiogenin, as these events were not abolished by the presence of neamine. Full article
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16 pages, 4193 KiB  
Article
Assessing the Efficiency of Triangular Gold Nanoparticles as NIR Photothermal Agents In Vitro and Melanoma Tumor Model
by Sorina Suarasan, Andreea Campu, Adriana Vulpoi, Manuela Banciu and Simion Astilean
Int. J. Mol. Sci. 2022, 23(22), 13724; https://doi.org/10.3390/ijms232213724 - 08 Nov 2022
Cited by 3 | Viewed by 1401
Abstract
Photothermal therapy (PTT) is gaining a lot of interest as a cancer treatment option with minimal side effects due to the efficient photothermal agents employed. They are based on nanomaterials that, upon laser irradiation, absorb photon energy and convert it into heat to [...] Read more.
Photothermal therapy (PTT) is gaining a lot of interest as a cancer treatment option with minimal side effects due to the efficient photothermal agents employed. They are based on nanomaterials that, upon laser irradiation, absorb photon energy and convert it into heat to induce hyperthermia, which destroys the cancer cells. Here, the unique light-to-heat conversion features of three different gold nanotriangular nanoparticles (AuNTs) are evaluated with respect to their absorption properties to select the most efficient nanoheater with the highest potential to operate as an efficient photothermal agent. AuNTs with LSPR response in- and out- of resonance with the 785 nm near-infrared (NIR) excitation wavelength are investigated. Upon 15 min laser exposure, the AuNTs that exhibit a plasmonic response in resonance with the 785 nm laser line show the highest photothermal conversion efficacy of 80%, which correlates with a temperature increase of 22 °C. These photothermal properties are well-preserved in agarose-based skin biological phantoms that mimic the melanoma tumoral tissue and surrounding healthy tissue. Finally, in vitro studies on B16.F10 melanoma cells prove by fluorescence staining and MTT assay that the highest phototoxic effect after NIR laser exposure is induced by AuNTs with LSPR response in resonance with the employed laser line, thus demonstrating their potential implementation as efficient photothermal agents in PTT. Full article
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25 pages, 15926 KiB  
Article
Cheminformatics Study on Structural and Bactericidal Activity of Latest Generation β-Lactams on Widespread Pathogens
by Ana Maria Raluca Gherman, Nicoleta Elena Dina and Vasile Chiș
Int. J. Mol. Sci. 2022, 23(20), 12685; https://doi.org/10.3390/ijms232012685 - 21 Oct 2022
Viewed by 1374
Abstract
Raman spectra of oxacillin (OXN), carbenicillin (CBC), and azlocillin (AZL) are reported for the first time together with their full assignment of the normal modes, as calculated using Density Functional Theory (DFT) methods with the B3LYP exchange-correlation functional coupled to the 6-31G(d) and [...] Read more.
Raman spectra of oxacillin (OXN), carbenicillin (CBC), and azlocillin (AZL) are reported for the first time together with their full assignment of the normal modes, as calculated using Density Functional Theory (DFT) methods with the B3LYP exchange-correlation functional coupled to the 6-31G(d) and 6-311+G(2d,p) basis sets. Molecular docking studies were performed on five penicillins, including OXN, CBC, and AZL. Subsequently, their chemical reactivity and correlated efficiency towards specific pathogenic strains were revealed by combining frontier molecular orbital (FMO) data with molecular electrostatic potential (MEP) surfaces. Their bactericidal activity was tested and confirmed on a couple of species, both Gram-positive and Gram-negative, by using the disk diffusion method. Additionally, a surface-enhanced Raman spectroscopy (SERS)—principal component analysis (PCA)-based resistogram of A. hydrophila is proposed as a clinically relevant insight resulting from the synergistic cheminformatics and vibrational study on CBC and AZL. Full article
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11 pages, 1381 KiB  
Article
Photoluminescent Histidine-Stabilized Gold Nanoclusters as Efficient Sensors for Fast and Easy Visual Detection of Fe Ions in Water Using Paper-Based Portable Platform
by Alexandru-Milentie Hada, Markus Zetes, Monica Focsan, Simion Astilean and Ana-Maria Craciun
Int. J. Mol. Sci. 2022, 23(20), 12410; https://doi.org/10.3390/ijms232012410 - 17 Oct 2022
Cited by 2 | Viewed by 1403
Abstract
Herein is presented a novel and efficient portable paper-based sensing platform using paper-incorporated histidine stabilized gold nanoclusters (His-AuNCs), for the sensitive and selective detection of Fe ions from low-volume real water samples based on photoluminescence (PL) quenching. Highly photoluminescent colloidal His-AuNCs are obtained [...] Read more.
Herein is presented a novel and efficient portable paper-based sensing platform using paper-incorporated histidine stabilized gold nanoclusters (His-AuNCs), for the sensitive and selective detection of Fe ions from low-volume real water samples based on photoluminescence (PL) quenching. Highly photoluminescent colloidal His-AuNCs are obtained via a novel microwave-assisted method. The His-AuNCs-based sensor reveals a limit of detection (LOD) as low as 0.2 μM and a good selectivity towards Fe ions, in solution. Further, the fabricated portable sensing device based on paper impregnated with His-AuNCs proves to be suitable for the easy detection of hazardous Fe levels from real water samples, under UV light exposure, through evaluating the level of PL quenching on paper. Photographic images are thereafter captured with a smartphone camera and the average blue intensity ratio (I/I0) of the His-AuNCs-paper spots is plotted against [Fe2+] revealing a LOD of 3.2 μM. Moreover, selectivity and competitivity assays performed on paper-based sensor prove that the proposed platform presents high selectivity and accuracy for the detection of Fe ions from water samples. To validate the platform, sensing assays are performed on real water samples from local sources, spiked with 35 μM Fe ions (i.e., Fe2+). The obtained recoveries prove the high sensitivity and accuracy of the proposed His-AuNCs-paper-based sensor pointing towards its applicability as an easy-to-use, fast, quantitative and qualitative sensor suitable for on-site detection of toxic levels of Fe ions in low-volume real water samples. Full article
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15 pages, 2953 KiB  
Article
Portable Plasmonic Paper-Based Biosensor for Simple and Rapid Indirect Detection of CEACAM5 Biomarker via Metal-Enhanced Fluorescence
by Laurentiu Susu, Adriana Vulpoi, Simion Astilean and Monica Focsan
Int. J. Mol. Sci. 2022, 23(19), 11982; https://doi.org/10.3390/ijms231911982 - 09 Oct 2022
Viewed by 1479
Abstract
Rapid, simple, and sensitive analysis of relevant proteins is crucial in many research areas, such as clinical diagnosis and biomarker detection. In particular, clinical data on cancer biomarkers show great promise in forming reliable predictions for early cancer diagnostics, although the current analytical [...] Read more.
Rapid, simple, and sensitive analysis of relevant proteins is crucial in many research areas, such as clinical diagnosis and biomarker detection. In particular, clinical data on cancer biomarkers show great promise in forming reliable predictions for early cancer diagnostics, although the current analytical systems are difficult to implement in regions of limited recourses. Paper-based biosensors, in particular, have recently received great interest because they meet the criteria for point-of-care (PoC) devices; the main drawbacks with these devices are the low sensitivity and efficiency in performing quantitative measurements. In this work, we design a low-cost paper-based nanosensor through plasmonic calligraphy by directly drawing individual plasmonic lines on filter paper using a ballpoint pen filled with gold nanorods (AuNR) as the colloidal ink. The plasmonic arrays were further successively coated with negatively and positively charged polyelectrolyte layers employed as dielectric spacers to promote the enhancement of the emission of carboxyl-functionalized quantum dots (QD)—previously conjugated with specific antibodies—for indirect detection of the carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5). The efficiency, sensitivity, as well as the specificity of our portable nanosensor were validated by recording the luminescence of the QD@Ab complex when different concentrations of CEACAM5 were added dropwise onto the calligraphed plasmonic arrays. Full article
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13 pages, 2749 KiB  
Article
ATR-FTIR Biosensors for Antibody Detection and Analysis
by Olivier Suys, Allison Derenne and Erik Goormaghtigh
Int. J. Mol. Sci. 2022, 23(19), 11895; https://doi.org/10.3390/ijms231911895 - 07 Oct 2022
Cited by 8 | Viewed by 2191
Abstract
Quality control of drug products is of paramount importance in the pharmaceutical world. It ensures product safety, efficiency, and consistency. In the case of complex biomolecules such as therapeutic proteins, small variations in bioprocess parameters can induce substantial variations in terms of structure, [...] Read more.
Quality control of drug products is of paramount importance in the pharmaceutical world. It ensures product safety, efficiency, and consistency. In the case of complex biomolecules such as therapeutic proteins, small variations in bioprocess parameters can induce substantial variations in terms of structure, impacting the drug product quality. Conditions for obtaining highly reproducible grafting of 11-mercaptoundecanoic acid were determined. On that basis, we developed an easy-to-use, cost effective, and timesaving biosensor based on ATR-FTIR spectroscopy able to detect immunoglobulins during their production. A germanium crystal, used as an internal reflection element (IRE) for FTIR spectroscopy, was covalently coated with immunoglobulin-binding proteins. This thereby functionalized surface could bind only immunoglobulins present in complex media such as culture media or biopharmaceutical products. The potential subsequent analysis of their structure by ATR-FTIR spectroscopy makes this biosensor a powerful tool to monitor the production of biotherapeutics and assess important critical quality attributes (CQAs) such as high-order structure and aggregation level. Full article
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15 pages, 3104 KiB  
Article
Walnut Shell Biowaste Valorization via HTC Process for the Removal of Some Emerging Pharmaceutical Pollutants from Aqueous Solutions
by Anca Andreea Țurcanu, Ecaterina Matei, Maria Râpă, Andra Mihaela Predescu, Andrei-Constantin Berbecaru, George Coman and Cristian Predescu
Int. J. Mol. Sci. 2022, 23(19), 11095; https://doi.org/10.3390/ijms231911095 - 21 Sep 2022
Cited by 1 | Viewed by 1551
Abstract
This research emphasizes the performance of some eco-friendly carbon materials as hydrochars (HC) obtained by the hydrothermal carbonization (HTC) process applied to walnut shell (WS) biowaste. These materials display promising properties that can be used for environmental applications such as emerging pharmaceutical pollutant [...] Read more.
This research emphasizes the performance of some eco-friendly carbon materials as hydrochars (HC) obtained by the hydrothermal carbonization (HTC) process applied to walnut shell (WS) biowaste. These materials display promising properties that can be used for environmental applications such as emerging pharmaceutical pollutant retention from water sources. Thus, three hydrochars coded HCWS1, HCWS2, and HCWS3 were obtained using a dynamic autoclave in specific conditions—temperature of 220 °C, autogenous pressure, 1:10 biomass–water weight ratio—and for three different reaction times, 1 h, 6 h, and 12 h. The HCWSs were characterized by means of ATR-FTIR and SEM-EDS analyses and tested as possible adsorbents to assess the removal efficiencies of some emerging pharmaceutical pollutants (paracetamol and methylene blue) by UV–VIS spectrophotometry. Kinetic and adsorption studies were carried out. The best results were obtained for the HCWS3 hydrochar. Further perspectives include an activation step of the hydrochars and their testing on other emerging pharmaceutical pollutants. Full article
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16 pages, 5232 KiB  
Article
The Development of Honey Recognition Models Based on the Association between ATR-IR Spectroscopy and Advanced Statistical Tools
by Maria David, Ariana Raluca Hategan, Camelia Berghian-Grosan and Dana Alina Magdas
Int. J. Mol. Sci. 2022, 23(17), 9977; https://doi.org/10.3390/ijms23179977 - 01 Sep 2022
Cited by 13 | Viewed by 1480
Abstract
The newly developed prediction models, having the aim to classify Romanian honey samples by associating ATR-FTIR spectral data and the statistical method, PLS-DA, led to reliable differentiations among the samples, in terms of botanical and geographical origin and harvesting year. Based on this [...] Read more.
The newly developed prediction models, having the aim to classify Romanian honey samples by associating ATR-FTIR spectral data and the statistical method, PLS-DA, led to reliable differentiations among the samples, in terms of botanical and geographical origin and harvesting year. Based on this approach, 105 out of 109 honey samples were correctly attributed, leading to true positive rates of 95% and 97% accuracy for the harvesting differentiation model. For the botanical origin classification, 83% of the investigated samples were correctly predicted, when four honey varieties were simultaneously discriminated. The geographical assessment was achieved in a percentage of 91% for the Transylvanian samples and 85% of those produced in other regions, with overall accuracy of 88% in the cross-validation procedure. The signals, based on which the best classification models were achieved, allowed the identification of the most significant compounds for each performed discrimination. Full article
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15 pages, 2843 KiB  
Article
Proof of Concept for the Detection with Custom Printed Electrodes of Enterobactin as a Marker of Escherichia coli
by Alexandra Canciu, Andreea Cernat, Mihaela Tertis, Silvia Botarca, Madalina Adriana Bordea, Joseph Wang and Cecilia Cristea
Int. J. Mol. Sci. 2022, 23(17), 9884; https://doi.org/10.3390/ijms23179884 - 31 Aug 2022
Cited by 3 | Viewed by 1448
Abstract
The rapid and decentralized detection of bacteria from biomedical, environmental, and food samples has the capacity to improve the conventional protocols and to change a predictable outcome. Identifying new markers and analysis methods represents an attractive strategy for the indirect but simpler and [...] Read more.
The rapid and decentralized detection of bacteria from biomedical, environmental, and food samples has the capacity to improve the conventional protocols and to change a predictable outcome. Identifying new markers and analysis methods represents an attractive strategy for the indirect but simpler and safer detection of pathogens that could replace existing methods. Enterobactin (Ent), a siderophore produced by Escherichia coli or other Gram-negative bacteria, was studied on different electrode materials to reveal its electrochemical fingerprint—very useful information towards the detection of the bacteria based on this analyte. The molecule was successfully identified in culture media samples and a future goal is the development of a rapid antibiogram. The presence of Ent was also assessed in wastewater and treated water samples collected from the municipal sewage treatment plant, groundwater, and tap water. Moreover, a custom configuration printed on a medical glove was employed to detect the target in the presence of another bacterial marker, namely pyocyanin (PyoC), that being a metabolite specific of another pathogen bacterium, namely Pseudomonas aeruginosa. Such new mobile and wearable platforms offer considerable promise for rapid low-cost on-site screening of bacterial contamination. Full article
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