Journal Description
International Journal of Molecular Sciences
International Journal of Molecular Sciences
is an international, peer-reviewed, open access journal providing an advanced forum for biochemistry, molecular and cell biology, molecular biophysics, molecular medicine, and all aspects of molecular research in chemistry, and is published semimonthly online by MDPI. The Australian Society of Plant Scientists (ASPS), Epigenetics Society, European Calcium Society (ECS), European Chitin Society (EUCHIS), Spanish Society for Cell Biology (SEBC) and others are affiliated with IJMS and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, MEDLINE, Embase, CAPlus / SciFinder, and other databases.
- Journal Rank: JCR - Q1 (Biochemistry & Molecular Biology) / CiteScore - Q1 (Inorganic Chemistry)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.3 days after submission; acceptance to publication is undertaken in 2.6 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Testimonials: See what our editors and authors say about the IJMS.
- Companion journals for IJMS include: Biophysica, Obesities, Stresses and Lymphatics.
Impact Factor:
5.6 (2022);
5-Year Impact Factor:
6.2 (2022)
Latest Articles
Targeting the Multiple Complex Processes of Hypoxia-Ischemia to Achieve Neuroprotection
Int. J. Mol. Sci. 2024, 25(10), 5449; https://doi.org/10.3390/ijms25105449 (registering DOI) - 17 May 2024
Abstract
Hypoxic-ischemic encephalopathy (HIE) is a major cause of newborn brain damage stemming from a lack of oxygenated blood flow in the neonatal period. Twenty-five to fifty percent of asphyxiated infants who develop HIE die in the neonatal period, and about sixty percent of
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Hypoxic-ischemic encephalopathy (HIE) is a major cause of newborn brain damage stemming from a lack of oxygenated blood flow in the neonatal period. Twenty-five to fifty percent of asphyxiated infants who develop HIE die in the neonatal period, and about sixty percent of survivors develop long-term neurological disabilities. From the first minutes to months after the injury, a cascade of events occurs, leading to blood-brain barrier (BBB) opening, neuronal death and inflammation. To date, the only approach proposed in some cases is therapeutic hypothermia (TH). Unfortunately, TH is only partially protective and is not applicable to all neonates. This review synthesizes current knowledge on the basic molecular mechanisms of brain damage in hypoxia-ischemia (HI) and on the different therapeutic strategies in HI that have been used and explores a major limitation of unsuccessful therapeutic approaches.
Full article
(This article belongs to the Special Issue Molecular Basis and Advances of Targeted Therapy for Brain Endothelial Dysfunction)
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Open AccessArticle
The Association between Salivary Metabolites and Gingival Bleeding Score in Healthy Subjects: A Pilot Study
by
Rita Antonelli, Elena Ferrari, Mariana Gallo, Tecla Ciociola, Elena Calciolari, Alberto Spisni, Marco Meleti and Thelma A. Pertinhez
Int. J. Mol. Sci. 2024, 25(10), 5448; https://doi.org/10.3390/ijms25105448 (registering DOI) - 17 May 2024
Abstract
Periodontal diseases, including gingivitis and periodontitis, are among the most prevalent diseases in humans. Gingivitis is the mildest form of periodontal disease, characterized by inflammation of the gingiva caused by the accumulation of dental plaque. Salivary diagnostics are becoming increasingly popular due to
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Periodontal diseases, including gingivitis and periodontitis, are among the most prevalent diseases in humans. Gingivitis is the mildest form of periodontal disease, characterized by inflammation of the gingiva caused by the accumulation of dental plaque. Salivary diagnostics are becoming increasingly popular due to the variation in saliva composition in response to pathological processes. We used a metabolomics approach to investigate whether a specific saliva metabolic composition could indicate preclinical stage of gingivitis. 1H-NMR spectroscopy was used to obtain the salivary metabolite profiles of 20 healthy subjects. Univariate/multivariate statistical analysis evaluated the whole saliva metabolite composition, and the Full-Mouth Bleeding Score (FMBS) was employed as a classification parameter. Identifying a signature of specific salivary metabolites could distinguish the subjects with high FMBS scores but still within the normal range. This set of metabolites may be due to the enzymatic activities of oral bacteria and be associated with the early stages of gingival inflammation. Although this analysis is to be considered exploratory, it seems feasible to establish an FMBS threshold that distinguishes between the absence and presence of early inflammatory alterations at the salivary level.
Full article
(This article belongs to the Special Issue Molecular Mechanisms of Oral and Gastrointestinal Bacterial Interaction)
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Open AccessCommunication
Discovery of Pathogenic Variants Associated with Idiopathic Recurrent Pregnancy Loss Using Whole-Exome Sequencing
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Jeong Yong Lee, JaeWoo Moon, Hae-Jin Hu, Chang Soo Ryu, Eun Ju Ko, Eun Hee Ahn, Young Ran Kim, Ji Hyang Kim and Nam Keun Kim
Int. J. Mol. Sci. 2024, 25(10), 5447; https://doi.org/10.3390/ijms25105447 (registering DOI) - 17 May 2024
Abstract
Idiopathic recurrent pregnancy loss (RPL) is defined as at least two pregnancy losses before 20 weeks of gestation. Approximately 5% of pregnant couples experience idiopathic RPL, which is a heterogeneous disease with various causes including hormonal, chromosomal, and intrauterine abnormalities. Although how pregnancy
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Idiopathic recurrent pregnancy loss (RPL) is defined as at least two pregnancy losses before 20 weeks of gestation. Approximately 5% of pregnant couples experience idiopathic RPL, which is a heterogeneous disease with various causes including hormonal, chromosomal, and intrauterine abnormalities. Although how pregnancy loss occurs is still unknown, numerous biological factors are associated with the incidence of pregnancy loss, including genetic variants. Whole-exome sequencing (WES) was conducted on blood samples from 56 Korean patients with RPL and 40 healthy controls. The WES data were aligned by means of bioinformatic analysis, and the detected variants were annotated using machine learning tools to predict the pathogenicity of protein alterations. Each indicated variant was confirmed using Sanger sequencing. A replication study was also conducted in 112 patients and 114 controls. The Variant Effect Scoring Tool, Combined Annotation Dependent Depletion tool, Sorting Intolerant from Tolerant annotation tool, and various databases detected 10 potential variants previously associated with spontaneous abortion genes in patients by means of a bioinformatic analysis of WES data. Several variants were detected in more than one patient. Interestingly, several of the detected genes were functionally clustered, including some with a secretory function (mucin 4; MUC4; rs200737893 G>A and hyaluronan-binding protein 2; HABP2; rs542838125 G>T), in which growth arrest-specific 2 Like 2 (GAS2L2; rs140842796 C>T) and dynamin 2 (DNM2; rs763894364 G>A) are functionally associated with cell protrusion and the cytoskeleton. ATP Binding Cassette Subfamily C Member 6 (ABCC6) was the only gene with two variants. HABP2 (rs542838125 G>T), MUC4 (rs200737893 G>A), and GAS2L2 (rs140842796 C>T) were detected in only the patient group in the replication study. The combination of WES and machine learning tools is a useful method to detect potential variants associated with RPL. Using bioinformatic tools, we found 10 potential variants in 9 genes. WES data from patients are needed to better understand the causes of RPL.
Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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Open AccessArticle
Inhibition of Drp1–Filamin Protein Complex Prevents Hepatic Lipid Droplet Accumulation by Increasing Mitochondria–Lipid Droplet Contact
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Kohei Ariyoshi, Kazuhiro Nishiyama, Yuri Kato, Xinya Mi, Tomoya Ito, Yasu-Taka Azuma, Akiyuki Nishimura and Motohiro Nishida
Int. J. Mol. Sci. 2024, 25(10), 5446; https://doi.org/10.3390/ijms25105446 (registering DOI) - 17 May 2024
Abstract
Lipid droplet (LD) accumulation in hepatocytes is one of the major symptoms associated with fatty liver disease. Mitochondria play a key role in catabolizing fatty acids for energy production through β-oxidation. The interplay between mitochondria and LD assumes a crucial role in lipid
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Lipid droplet (LD) accumulation in hepatocytes is one of the major symptoms associated with fatty liver disease. Mitochondria play a key role in catabolizing fatty acids for energy production through β-oxidation. The interplay between mitochondria and LD assumes a crucial role in lipid metabolism, while it is obscure how mitochondrial morphology affects systemic lipid metabolism in the liver. We previously reported that cilnidipine, an already existing anti-hypertensive drug, can prevent pathological mitochondrial fission by inhibiting protein–protein interaction between dynamin-related protein 1 (Drp1) and filamin, an actin-binding protein. Here, we found that cilnidipine and its new dihydropyridine (DHP) derivative, 1,4-DHP, which lacks Ca2+ channel-blocking action of cilnidipine, prevent the palmitic acid-induced Drp1–filamin interaction, LD accumulation and cytotoxicity of human hepatic HepG2 cells. Cilnidipine and 1,4-DHP also suppressed the LD accumulation accompanied by reducing mitochondrial contact with LD in obese model and high-fat diet-fed mouse livers. These results propose that targeting the Drp1–filamin interaction become a new strategy for the prevention or treatment of fatty liver disease.
Full article
(This article belongs to the Special Issue Mitochondrial Remodeling and the Targeting Strategies for Disease Treatment)
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Open AccessArticle
Genome-Wide DNA Methylation in Early-Onset-Dementia Patients Brain Tissue and Lymphoblastoid Cell Lines
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Oscar Ramos-Campoy, Aina Comas-Albertí, David Hervás, Sergi Borrego-Écija, Beatriz Bosch, Juan Sandoval, Laura Fort-Aznar, Fermín Moreno-Izco, Guadalupe Fernández-Villullas, Laura Molina-Porcel, Mircea Balasa, Albert Lladó, Raquel Sánchez-Valle and Anna Antonell
Int. J. Mol. Sci. 2024, 25(10), 5445; https://doi.org/10.3390/ijms25105445 - 16 May 2024
Abstract
Epigenetics, a potential underlying pathogenic mechanism of neurodegenerative diseases, has been in the scope of several studies performed so far. However, there is a gap in regard to analyzing different forms of early-onset dementia and the use of Lymphoblastoid cell lines (LCLs). We
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Epigenetics, a potential underlying pathogenic mechanism of neurodegenerative diseases, has been in the scope of several studies performed so far. However, there is a gap in regard to analyzing different forms of early-onset dementia and the use of Lymphoblastoid cell lines (LCLs). We performed a genome-wide DNA methylation analysis on sixty-four samples (from the prefrontal cortex and LCLs) including those taken from patients with early-onset forms of Alzheimer’s disease (AD) and frontotemporal dementia (FTD) and healthy controls. A beta regression model and adjusted p-values were used to obtain differentially methylated positions (DMPs) via pairwise comparisons. A correlation analysis of DMP levels with Clariom D array gene expression data from the same cohort was also performed. The results showed hypermethylation as the most frequent finding in both tissues studied in the patient groups. Biological significance analysis revealed common pathways altered in AD and FTD patients, affecting neuron development, metabolism, signal transduction, and immune system pathways. These alterations were also found in LCL samples, suggesting the epigenetic changes might not be limited to the central nervous system. In the brain, CpG methylation presented an inverse correlation with gene expression, while in LCLs, we observed mainly a positive correlation. This study enhances our understanding of the biological pathways that are associated with neurodegeneration, describes differential methylation patterns, and suggests LCLs are a potential cell model for studying neurodegenerative diseases in earlier clinical phases than brain tissue.
Full article
(This article belongs to the Special Issue Molecular Mechanism in the Pathogenesis of Alzheimer’s Disease and Related Neurodegenerative Diseases)
Open AccessArticle
Natural Sunlight-Mediated Emodin Photoinactivation of Aeromonas hydrophila
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Gelana Urgesa, Liushen Lu, Jinwei Gao, Lichun Guo, Ting Qin, Bo Liu, Jun Xie and Bingwen Xi
Int. J. Mol. Sci. 2024, 25(10), 5444; https://doi.org/10.3390/ijms25105444 - 16 May 2024
Abstract
Aeromonas hydrophila can be a substantial concern, as it causes various diseases in aquaculture. An effective and green method for inhibiting A. hydrophila is urgently required. Emodin, a naturally occurring anthraquinone compound, was exploited as a photo-antimicrobial agent against A. hydrophila. At
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Aeromonas hydrophila can be a substantial concern, as it causes various diseases in aquaculture. An effective and green method for inhibiting A. hydrophila is urgently required. Emodin, a naturally occurring anthraquinone compound, was exploited as a photo-antimicrobial agent against A. hydrophila. At the minimum inhibitory concentration of emodin (256 mg/L) to inactivate A. hydrophilia in 30 min, an 11.32% survival rate was observed under 45 W white compact fluorescent light irradiation. In addition, the antibacterial activity under natural sunlight (0.78%) indicated its potential for practical application. Morphological observations demonstrated that the cell walls and membranes of A. hydrophila were susceptible to damage by emodin when exposed to light irradiation. More importantly, the photoinactivation of A. hydrophila was predominantly attributed to the hydroxyl radicals and superoxide radicals produced by emodin, according to the trapping experiment and electron spin resonance spectroscopy. Finally, a light-dependent reactive oxygen species punching mechanism of emodin to photoinactivate A. hydrophila was proposed. This study highlights the potential use of emodin in sunlight-mediated applications for bacterial control, thereby providing new possibilities for the use of Chinese herbal medicine in aquatic diseases prevention.
Full article
(This article belongs to the Special Issue Antimicrobial Agents: Natural Products or Synthetic Compounds)
Open AccessEditorial
Molecular Mechanisms of Bacterial Communication and Their Biocontrol
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Corinne Barbey and Xavier Latour
Int. J. Mol. Sci. 2024, 25(10), 5443; https://doi.org/10.3390/ijms25105443 - 16 May 2024
Abstract
A bacterium’s ability to colonize and adapt to an ecological niche is highly dependent on its capacity to perceive and analyze its environment and its ability to interact with its hosts and congeners [...]
Full article
(This article belongs to the Special Issue Molecular Mechanisms of Bacterial Communication and Their Control)
Open AccessArticle
Microbial Detoxification of Sediments Underpins Persistence of Zostera marina Meadows
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Yuki Nakashima, Takumi Sonobe, Masashi Hanada, Goushi Kitano, Yoshimitsu Sonoyama, Katsumi Iwai, Takashi Kimura and Masataka Kusube
Int. J. Mol. Sci. 2024, 25(10), 5442; https://doi.org/10.3390/ijms25105442 - 16 May 2024
Abstract
Eelgrass meadows have attracted much attention not only for their ability to maintain marine ecosystems as feeding grounds for marine organisms but also for their potential to store atmospheric and dissolved CO2 as blue carbon. This study comprehensively evaluated the bacterial and
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Eelgrass meadows have attracted much attention not only for their ability to maintain marine ecosystems as feeding grounds for marine organisms but also for their potential to store atmospheric and dissolved CO2 as blue carbon. This study comprehensively evaluated the bacterial and chemical data obtained from eelgrass sediments of different scales along the Japanese coast to investigate the effect on the acclimatization of eelgrass. Regardless of the eelgrass habitat, approximately 1% Anaerolineales, Babeliales, Cytophagales, and Phycisphaerales was present in the bottom sediment. Sulfate-reducing bacteria (SRB) were present at 3.69% in eelgrass sediment compared to 1.70% in bare sediment. Sulfur-oxidizing bacteria (SOB) were present at 2.81% and 1.10% in the eelgrass and bare sediment, respectively. Bacterial composition analysis and linear discriminant analysis revealed that SOB detoxified H2S in the eelgrass meadows and that the larger-scale eelgrass meadows had a higher diversity of SOB. Our result indicated that there were regional differences in the system that detoxifies H2S in eelgrass meadows, either microbial oxidation mediated by SOB or O2 permeation via the physical diffusion of benthos. However, since bacterial flora and phylogenetic analyses cannot show bias and/or causality due to PCR, future kinetic studies on microbial metabolism are expected.
Full article
(This article belongs to the Special Issue Next-Generation Sequencing and Whole-Genome Sequencing in Molecular Research)
Open AccessReview
Postbiotics as Metabolites and Their Biotherapeutic Potential
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Emília Hijová
Int. J. Mol. Sci. 2024, 25(10), 5441; https://doi.org/10.3390/ijms25105441 - 16 May 2024
Abstract
This review highlights the role of postbiotics, which may provide an underappreciated avenue doe promising therapeutic alternatives. The discovery of natural compounds obtained from microorganisms needs to be investigated in the future in terms of their effects on various metabolic disorders and molecular
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This review highlights the role of postbiotics, which may provide an underappreciated avenue doe promising therapeutic alternatives. The discovery of natural compounds obtained from microorganisms needs to be investigated in the future in terms of their effects on various metabolic disorders and molecular pathways, as well as modulation of the immune system and intestinal microbiota in children and adults. However, further studies and efforts are needed to evaluate and describe new postbiotics. This review provides available knowledge that may assist future research in identifying new postbiotics and uncovering additional mechanisms to combat metabolic diseases.
Full article
(This article belongs to the Special Issue Bioactive Compounds for the Prevention and Treatment of Human Diseases)
Open AccessArticle
SCLpred-ECL: Subcellular Localization Prediction by Deep N-to-1 Convolutional Neural Networks
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Maryam Gillani and Gianluca Pollastri
Int. J. Mol. Sci. 2024, 25(10), 5440; https://doi.org/10.3390/ijms25105440 - 16 May 2024
Abstract
The subcellular location of a protein provides valuable insights to bioinformaticians in terms of drug designs and discovery, genomics, and various other aspects of medical research. Experimental methods for protein subcellular localization determination are time-consuming and expensive, whereas computational methods, if accurate, would
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The subcellular location of a protein provides valuable insights to bioinformaticians in terms of drug designs and discovery, genomics, and various other aspects of medical research. Experimental methods for protein subcellular localization determination are time-consuming and expensive, whereas computational methods, if accurate, would represent a much more efficient alternative. This article introduces an ab initio protein subcellular localization predictor based on an ensemble of Deep N-to-1 Convolutional Neural Networks. Our predictor is trained and tested on strict redundancy-reduced datasets and achieves 63% accuracy for the diverse number of classes. This predictor is a step towards bridging the gap between a protein sequence and the protein’s function. It can potentially provide information about protein–protein interaction to facilitate drug design and processes like vaccine production that are essential to disease prevention.
Full article
(This article belongs to the Section Molecular Biology)
Open AccessArticle
Identification of Genes Crucial for Biological Processes in Breast Cancer Liver Metastasis Relapse
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Tyler Kwok, Suneetha Yeguvapalli and Kumaraswamy Naidu Chitrala
Int. J. Mol. Sci. 2024, 25(10), 5439; https://doi.org/10.3390/ijms25105439 - 16 May 2024
Abstract
Breast cancer, when advancing to a metastatic stage, involves the liver, impacting over 50% of cases and significantly diminishing survival rates. Presently, a lack of tailored therapeutic protocols for breast cancer liver metastasis (BCLM) underscores the need for a deeper understanding of molecular
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Breast cancer, when advancing to a metastatic stage, involves the liver, impacting over 50% of cases and significantly diminishing survival rates. Presently, a lack of tailored therapeutic protocols for breast cancer liver metastasis (BCLM) underscores the need for a deeper understanding of molecular patterns governing this complication. Therefore, by analyzing differentially expressed genes (DEGs) between primary breast tumors and BCLM lesions, we aimed to shed light on the diversities of this process. This research investigated breast cancer liver metastasis relapse by employing a comprehensive approach that integrated data filtering, gene ontology and KEGG pathway analysis, overall survival analysis, identification of the alteration in the DEGs, visualization of the protein–protein interaction network, Signor 2.0, identification of positively correlated genes, immune cell infiltration analysis, genetic alternation analysis, copy number variant analysis, gene-to-mRNA interaction, transcription factor analysis, molecular docking, and identification of potential treatment targets. This study’s integrative approach unveiled metabolic reprogramming, suggesting altered PCK1 and LPL expression as key in breast cancer metastasis recurrence.
Full article
(This article belongs to the Special Issue 25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series)
Open AccessArticle
Soluble Neuropilin-1 Is Elevated in Sepsis and Correlates with Organ Dysfunction and Long-Term Mortality in Critical Illness
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Philipp Hohlstein, Eileen Schumacher, Samira Abu Jhaisha, Jule K. Adams, Maike R. Pollmanns, Carolin V. Schneider, Karim Hamesch, Katarina Horvathova, Theresa H. Wirtz, Frank Tacke, Christian Trautwein, Ralf Weiskirchen and Alexander Koch
Int. J. Mol. Sci. 2024, 25(10), 5438; https://doi.org/10.3390/ijms25105438 - 16 May 2024
Abstract
Critical illness and sepsis may cause organ failure and are recognized as mortality drivers in hospitalized patients. Neuropilin-1 (NRP-1) is a multifaceted transmembrane protein involved in the primary immune response and is expressed in immune cells such as T and dendritic cells. The
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Critical illness and sepsis may cause organ failure and are recognized as mortality drivers in hospitalized patients. Neuropilin-1 (NRP-1) is a multifaceted transmembrane protein involved in the primary immune response and is expressed in immune cells such as T and dendritic cells. The soluble form of NRP-1 (sNRP-1) acts as an antagonist to NRP-1 by scavenging its ligands. The aim of this study was to determine the value of sNRP-1 as a biomarker in critical illness and sepsis. We enrolled 180 critically ill patients admitted to a medical intensive care unit and measured serum sNRP-1 concentrations at admission, comparing them to 48 healthy individuals. Critically ill and septic patients showed higher levels of sNRP-1 compared to healthy controls (median of 2.47 vs. 1.70 nmol/L, p < 0.001). Moreover, sNRP-1 was also elevated in patients with sepsis compared to other critical illness (2.60 vs. 2.13 nmol/L, p = 0.01), irrespective of disease severity or organ failure. In critically ill patients, sNRP-1 is positively correlated with markers of kidney and hepatic dysfunction. Most notably, critically ill patients not surviving in the long term (one year after admission) showed higher concentrations of sNRP-1 at the time of ICU admission (p = 0.036), with this association being dependent on the presence of organ failure. Critically ill and septic patients exhibit higher serum concentrations of circulating sNRP-1, which correlates to organ failure, particularly hepatic and kidney dysfunction.
Full article
(This article belongs to the Special Issue The Road to Tolerance: Mechanism of Immune Homeostasis in Health and Disease)
Open AccessArticle
Amaranth’s Growth and Physiological Responses to Salt Stress and the Functional Analysis of AtrTCP1 Gene
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Shengcai Liu, Zixian An and Zhongxiong Lai
Int. J. Mol. Sci. 2024, 25(10), 5437; https://doi.org/10.3390/ijms25105437 - 16 May 2024
Abstract
Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is
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Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50–200 mmol·L−1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L−1, while it was promoted at 50 mmol·L−1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L−1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth’s growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene.
Full article
(This article belongs to the Section Molecular Plant Sciences)
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The Synergistic Effect of Reduced Graphene Oxide and Proteasome Inhibitor in the Induction of Apoptosis through Oxidative Stress in Breast Cancer Cell Lines
by
Rafał Krętowski, Beata Szynaka, Agata Jabłońska-Trypuć, Anna Kiełtyka-Dadasiewicz and Marzanna Cechowska-Pasko
Int. J. Mol. Sci. 2024, 25(10), 5436; https://doi.org/10.3390/ijms25105436 - 16 May 2024
Abstract
Reduced graphene oxide (rGO) and a proteasome inhibitor (MG-132) are some of the most commonly used compounds in various biomedical applications. However, the mechanisms of rGO- and MG-132-induced cytotoxicity remain unclear. The aim of this study was to investigate the anticancer effect of
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Reduced graphene oxide (rGO) and a proteasome inhibitor (MG-132) are some of the most commonly used compounds in various biomedical applications. However, the mechanisms of rGO- and MG-132-induced cytotoxicity remain unclear. The aim of this study was to investigate the anticancer effect of rGO and MG-132 against ZR-75-1 and MDA-MB-231 breast cancer cell lines. The results demonstrated that rGO, MG-132 or a mix (rGO + MG-132) induced time- and dose-dependent cytotoxicity in ZR-75-1 and MDA-MB-231 cells. Apart from that, we found that treatment with rGO and MG-132 or the mix increased apoptosis, necrosis and induction of caspase-8 and caspase-9 activity in both breast cancer cell lines. Apoptosis and caspase activation were accompanied by changes in the ultrastructure of mitochondria in ZR-75-1 and MDA-MB-231 cells incubated with rGO. Additionally, in the analyzed cells, we observed the induction of oxidative stress, accompanied by increased apoptosis and cell necrosis. In conclusion, oxidative stress induces apoptosis in the tested cells. At the same time, both mitochondrial and receptor apoptosis pathways are activated. These studies provided new information on the molecular mechanisms of apoptosis in the ZR-75-1 and MDA-MB-231 breast cancer cell lines.
Full article
(This article belongs to the Special Issue Nanotechnology in the Treatment and Diagnosis of Cancer: Opportunities and Challenges)
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Open AccessArticle
Preharvest Elicitors as a Tool to Enhance Bioactive Compounds and Quality of Both Peel and Pulp of Yellow Pitahaya (Selenicereus megalanthus Haw.) at Harvest and during Postharvest Storage
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Alex Erazo-Lara, María Emma García-Pastor, Pedro Antonio Padilla-González, Daniel Valero and María Serrano
Int. J. Mol. Sci. 2024, 25(10), 5435; https://doi.org/10.3390/ijms25105435 - 16 May 2024
Abstract
Yellow pitahaya is a tropical fruit that has gained popularity in recent years. Natural elicitors are compounds that can stimulate the resistance and quality of fruits. The objective of this study was to evaluate the effects of natural elicitors, methyl salicylate (MeSa), methyl
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Yellow pitahaya is a tropical fruit that has gained popularity in recent years. Natural elicitors are compounds that can stimulate the resistance and quality of fruits. The objective of this study was to evaluate the effects of natural elicitors, methyl salicylate (MeSa), methyl jasmonate (JaMe), salicylic acid (SA) and oxalic acid (OA) at concentrations of 0.1 mM (MeSa and JaMe) and 5 mM (SA and OA), applied to the yellow pitahaya fruits under greenhouse conditions. After full blossom, four applications were made with a frequency of 15 days. At the time of harvest and after storage, the following variables were evaluated: firmness (whole fruit), total soluble solids (TSS), total acidity (TA), phenolics and carotenoids (in the pulp), while phenolics, carotenoids, macronutrients and micronutrients were determined in the peel. The results showed MeSa advanced the fruit maturation, according to higher TSS, lower TA and firmness than MeJa-treated fruits, for which a delayed ripening process was shown. All treatments induced a higher polyphenolic concentration during storage. Regarding the alternative use of the peel as a by-product, the application of natural elicitors significantly increased the content of polyphenols, carotenoids, macronutrients and micronutrients in the peel, especially MeSa, which can be used as a bioactive compound in the food industry. In conclusion, the results indicate that natural elicitors can be an alternative to improve the quality and shelf life of yellow pitahaya fruits.
Full article
(This article belongs to the Special Issue Melatonin and γ-Aminobutyric Acid (GABA) Applied as Pre- or Post-harvest Treatments Affect Vegetable and Fruit Quality Properties and Antioxidant Systems)
Open AccessArticle
Prediction of Paratope–Epitope Pairs Using Convolutional Neural Networks
by
Dong Li, Fabrizio Pucci and Marianne Rooman
Int. J. Mol. Sci. 2024, 25(10), 5434; https://doi.org/10.3390/ijms25105434 - 16 May 2024
Abstract
Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such as in disease diagnosis and treatment. However,
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Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such as in disease diagnosis and treatment. However, there are currently no reliable methods for predicting the antibodies that recognize a specific antigen region (or epitope) and, conversely, epitopes that recognize the binding region of a given antibody (or paratope). To fill this gap, we developed ImaPEp, a machine learning-based tool for predicting the binding probability of paratope–epitope pairs, where the epitope and paratope patches were simplified into interacting two-dimensional patches, which were colored according to the values of selected features, and pixelated. The specific recognition of an epitope image by a paratope image was achieved by using a convolutional neural network-based model, which was trained on a set of two-dimensional paratope–epitope images derived from experimental structures of antibody–antigen complexes. Our method achieves good performances in terms of cross-validation with a balanced accuracy of 0.8. Finally, we showcase examples of application of ImaPep, including extensive screening of large libraries to identify paratope candidates that bind to a selected epitope, and rescoring and refining antibody–antigen docking poses.
Full article
(This article belongs to the Collection Feature Papers in Molecular Informatics)
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Open AccessArticle
Enzymatic Synthesis and Structural Modeling of Bio-Based Oligoesters as an Approach for the Fast Screening of Marine Biodegradation and Ecotoxicity
by
Anamaria Todea, Ioan Bîtcan, Marco Giannetto, Iulia Ioana Rădoi, Raffaele Bruschi, Monia Renzi, Serena Anselmi, Francesca Provenza, Tecla Bentivoglio, Fioretta Asaro, Emanuele Carosati and Lucia Gardossi
Int. J. Mol. Sci. 2024, 25(10), 5433; https://doi.org/10.3390/ijms25105433 - 16 May 2024
Abstract
Given the widespread use of esters and polyesters in products like cosmetics, fishing nets, lubricants and adhesives, whose specific application(s) may cause their dispersion in open environments, there is a critical need for stringent eco-design criteria based on biodegradability and ecotoxicity evidence. Our
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Given the widespread use of esters and polyesters in products like cosmetics, fishing nets, lubricants and adhesives, whose specific application(s) may cause their dispersion in open environments, there is a critical need for stringent eco-design criteria based on biodegradability and ecotoxicity evidence. Our approach integrates experimental and computational methods based on short oligomers, offering a screening tool for the rapid identification of sustainable monomers and oligomers, with a special focus on bio-based alternates. We provide insights into the relationships between the chemical structure and properties of bio-based oligomers in terms of biodegradability in marine environments and toxicity in benchmark organisms. The experimental results reveal that the considered aromatic monomers (terephthalic acid and 2,5-furandicarboxylic acid) accumulate under the tested conditions (OECD 306), although some slight biodegradation is observable when the inoculum derives from sites affected by industrial and urban pollution, which suggests that ecosystems adapt to non-natural chemical pollutants. While clean seas are more susceptible to toxic chemical buildup, biotic catalytic activities offer promise for plastic pollution mitigation. Without prejudice to the fact that biodegradability inherently signifies a desirable trait in plastic products, nor that it automatically grants them a sustainable “license”, this study is intended to facilitate the rational design of new polymers and materials on the basis of specific uses and applications.
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(This article belongs to the Special Issue Research Progress of Biodegradable Materials)
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Open AccessArticle
Assessment of the Effect on Periodontitis of Antibiotic Therapy and Bacterial Lysate Treatment
by
Diana Larisa Ancuţa, Diana Mihaela Alexandru, Florin Muselin, Romeo Teodor Cristina and Cristin Coman
Int. J. Mol. Sci. 2024, 25(10), 5432; https://doi.org/10.3390/ijms25105432 - 16 May 2024
Abstract
Periodontitis is an inflammatory process that starts with soft tissue inflammation caused by the intervention of oral bacteria. By modulating local immunity, it is possible to supplement or replace current therapeutic methods. The aim of this study was to compare the effects of
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Periodontitis is an inflammatory process that starts with soft tissue inflammation caused by the intervention of oral bacteria. By modulating local immunity, it is possible to supplement or replace current therapeutic methods. The aim of this study was to compare the effects of an immunostimulatory treatment with the antibiotherapy usually applied to periodontitis patients. On a model of periodontitis induced in 30 rats (divided into three equal groups) with bacterial strains selected from the human oral microbiome (Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum and Streptococcus oralis), we administered antibiotics, bacterial lysates and saline for 10 days. Clinically, no significant lesions were observed between the groups, but hematologically, we detected a decrease in lymphocyte and neutrophil counts in both the antibiotic and lysate-treated groups. Immunologically, IL-6 remained elevated compared to the saline group, denoting the body’s effort to compensate for bone loss due to bacterial action. Histopathologically, the results show more pronounced oral tissue regeneration in the antibiotic group and a reduced inflammatory reaction in the lysate group. We can conclude that the proposed bacterial lysate has similar effects to antibiotic therapy and can be considered an option in treating periodontitis, thus eliminating the unnecessary use of antibiotics.
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(This article belongs to the Special Issue Periodontitis: Advances in Mechanisms, Treatment and Prevention)
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Open AccessArticle
Pregestational Prediabetes Induces Maternal Hypothalamic–Pituitary–Adrenal (HPA) Axis Dysregulation and Results in Adverse Foetal Outcomes
by
Mathuli Ngema, Nombuso D. Xulu, Phikelelani S. Ngubane and Andile Khathi
Int. J. Mol. Sci. 2024, 25(10), 5431; https://doi.org/10.3390/ijms25105431 - 16 May 2024
Abstract
Maternal type 2 diabetes mellitus (T2DM) has been shown to result in foetal programming of the hypothalamic–pituitary–adrenal (HPA) axis, leading to adverse foetal outcomes. T2DM is preceded by prediabetes and shares similar pathophysiological complications. However, no studies have investigated the effects of maternal
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Maternal type 2 diabetes mellitus (T2DM) has been shown to result in foetal programming of the hypothalamic–pituitary–adrenal (HPA) axis, leading to adverse foetal outcomes. T2DM is preceded by prediabetes and shares similar pathophysiological complications. However, no studies have investigated the effects of maternal prediabetes on foetal HPA axis function and postnatal offspring development. Hence, this study investigated the effects of pregestational prediabetes on maternal HPA axis function and postnatal offspring development. Pre-diabetic (PD) and non-pre-diabetic (NPD) female Sprague Dawley rats were mated with non-prediabetic males. After gestation, male pups born from the PD and NPD groups were collected. Markers of HPA axis function, adrenocorticotropin hormone (ACTH) and corticosterone, were measured in all dams and pups. Glucose tolerance, insulin and gene expressions of mineralocorticoid (MR) and glucocorticoid (GR) receptors were further measured in all pups at birth and their developmental milestones. The results demonstrated increased basal concentrations of ACTH and corticosterone in the dams from the PD group by comparison to NPD. Furthermore, the results show an increase basal ACTH and corticosterone concentrations, disturbed MR and GR gene expression, glucose intolerance and insulin resistance assessed via the Homeostasis Model Assessment (HOMA) indices in the pups born from the PD group compared to NPD group at all developmental milestones. These observations reveal that pregestational prediabetes is associated with maternal dysregulation of the HPA axis, impacting offspring HPA axis development along with impaired glucose handling.
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(This article belongs to the Section Molecular Endocrinology and Metabolism)
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Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins
by
Jinhao Su, Kaifeng Liu, Huizi Cui, Tianze Shen, Xueqi Fu and Weiwei Han
Int. J. Mol. Sci. 2024, 25(10), 5430; https://doi.org/10.3390/ijms25105430 - 16 May 2024
Abstract
Sweetness in food delivers a delightful sensory experience, underscoring the crucial role of sweeteners in the food industry. However, the widespread use of sweeteners has sparked health concerns. This underscores the importance of developing and screening natural, health-conscious sweeteners. Our study represents a
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Sweetness in food delivers a delightful sensory experience, underscoring the crucial role of sweeteners in the food industry. However, the widespread use of sweeteners has sparked health concerns. This underscores the importance of developing and screening natural, health-conscious sweeteners. Our study represents a groundbreaking venture into the discovery of such sweeteners derived from egg and soy proteins. Employing virtual hydrolysis as a novel technique, our research entailed a comprehensive screening process that evaluated biological activity, solubility, and toxicity of the derived compounds. We harnessed cutting-edge machine learning methodologies, specifically the latest graph neural network models, for predicting the sweetness of molecules. Subsequent refinements were made through molecular docking screenings and molecular dynamics simulations. This meticulous research approach culminated in the identification of three promising sweet peptides: DCY(Asp-Cys-Tyr), GGR(Gly-Gly-Arg), and IGR(Ile-Gly-Arg). Their binding affinity with T1R2/T1R3 was lower than −15 kcal/mol. Using an electronic tongue, we verified the taste profiles of these peptides, with IGR emerging as the most favorable in terms of taste with a sweetness value of 19.29 and bitterness value of 1.71. This study not only reveals the potential of these natural peptides as healthier alternatives to traditional sweeteners in food applications but also demonstrates the successful synergy of computational predictions and experimental validations in the realm of flavor science.
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(This article belongs to the Section Molecular Informatics)
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