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International Journal of Molecular Sciences

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Journals Active Journals Find a Journal Proceedings Series Topics Information For Authors For Reviewers For Editors For Librarians For Publishers For Societies For Conference Organizers Open Access Policy Institutional Open Access Program Special Issues Guidelines Editorial Process Research and Publication Ethics Article Processing Charges Awards Testimonials Author Services Initiatives Sciforum MDPI Books Preprints.org Scilit SciProfiles Encyclopedia JAMS Proceedings Series About Overview Contact Careers News Press Blog Sign In / Sign Up Submit     8.1 4.9 Journals IJMS Extracellular Interactors of the IGF System: Impact on Cancer Hallmarks and Therapeutic Approaches Extracellular Interactors of the IGF System: Impact on Cancer Hallmarks and Therapeutic Approaches The Relationship between Circadian Rhythm and Cancer Disease The Relationship between Circadian Rhythm and Cancer Disease Exploring the Immunological Profile in Breast Cancer: Recent Advances in Diagnosis and Prognosis through Circulating Tumor Cells Exploring the Immunological Profile in Breast Cancer: Recent Advances in Diagnosis and Prognosis through Circulating Tumor Cells Molecularly Imprinted Drug Carrier for Lamotrigine—Design, Synthesis, and Characterization of Physicochemical Parameters Molecularly Imprinted Drug Carrier for Lamotrigine—Design, Synthesis, and Characterization of Physicochemical Parameters Radiocarbon Flux Measurements Provide Insight into Why a Pyroligneous Acid Product Stimulates Plant Growth Radiocarbon Flux Measurements Provide Insight into Why a Pyroligneous Acid Product Stimulates Plant Growth 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 and Molecular Biology) / CiteScore - Q1 (Inorganic Chemistry) Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 18.1 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the first half of 2024). 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, Lymphatics and SynBio. Impact Factor: 4.9 (2023); 5-Year Impact Factor: 5.6 (2023) subject Imprint Information    get_app Journal Flyer     Open Access     ISSN: 1422-0067 Latest Articles 10 pages, 2112 KiB   Open AccessPerspective The Role of Collagens in Atopic Dermatitis by Krzysztof Szalus and Magdalena Trzeciak Int. J. Mol. Sci. 2024, 25(14), 7647; https://doi.org/10.3390/ijms25147647 (registering DOI) - 12 Jul 2024 Abstract Atopic dermatitis (AD) is a chronic inflammatory skin disease affecting both children and adults. The clinical picture of AD manifests in typical skin lesions, such as localized eczema and dry skin, with dominant, persistent itching that leads to sleep disturbances. The pathophysiology of [...] Read more. Atopic dermatitis (AD) is a chronic inflammatory skin disease affecting both children and adults. The clinical picture of AD manifests in typical skin lesions, such as localized eczema and dry skin, with dominant, persistent itching that leads to sleep disturbances. The pathophysiology of AD has been extensively investigated with respect to epigenetic and genetic factors, skin barrier defects, as well as immunological and microbial disorders. However, to date, the involvement of extracellular matrix (ECM) elements has received limited attention. Collagen, a major component of the ECM, may serve as a therapeutic target for the future treatment of AD. This paper summarizes the role of collagens, which are the most abundant components of the extracellular matrix in AD. Full article (This article belongs to the Section Molecular Immunology) ►▼ Show Figures

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17 pages, 888 KiB   Open AccessArticle Leptin Is Associated with Testosterone, Nutritional Markers, and Vascular Muscular Dysfunction in Chronic Kidney Disease by Crina Claudia Rusu, Ina Kacso, Diana Moldovan, Alina Potra, Dacian Tirinescu, Maria Ticala, Remus Orasan, Cristian Budurea, Florin Anton, Ana Valea, Cosmina Ioana Bondor and Mara Carsote Int. J. Mol. Sci. 2024, 25(14), 7646; https://doi.org/10.3390/ijms25147646 (registering DOI) - 12 Jul 2024 Abstract Chronic kidney disease (CKD) causes specific hormonal disturbances, such as variations in leptin and testosterone levels and function. These disturbances can promote errors in signaling interaction and cellular information processing and can be implicated in the pathogenesis of atherosclerosis. This study investigates the [...] Read more. Chronic kidney disease (CKD) causes specific hormonal disturbances, such as variations in leptin and testosterone levels and function. These disturbances can promote errors in signaling interaction and cellular information processing and can be implicated in the pathogenesis of atherosclerosis. This study investigates the factors that affect leptin in CKD patients and examines how leptin is related to markers of vascular disease. We conducted a cross-sectional study of 162 patients with CKD in pre-dialysis and dialysis stages. We recorded clinical and laboratory data, including leptin, testosterone, and subclinical atherosclerosis markers like brachial–ankle pulse wave velocity (ba PWV) in pre-dialysis CKD patients and flow-mediated vasodilation (FMD) and nitroglycerin-mediated vasodilation (NMD) in hemodialysis (HD) patients. Leptin was significantly correlated with testosterone in CKD pre-dialysis stages (p < 0.001) and also in HD (p = 0.026), with adipose tissue mass in pre-dialysis stages (p < 0.001), and also in HD (p < 0.001). In women HD patients, leptin correlated with NMD (p = 0.039; r = −0.379); in all HD patients, leptin correlated with C reactive protein (p = 0.007; r = 0.28) and parathormone (p = 0.039; r = −0.220). Our research emphasizes the connection between leptin, adipose tissue, and testosterone in all stages of CKD. Leptin was associated with NMD in HD women and correlated with inflammatory syndrome and parathyroid hormone in all HD patients. Full article (This article belongs to the Special Issue Hormone Signaling in Human Health and Diseases, 2nd Edition) ►▼ Show Figures

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15 pages, 4501 KiB   Open AccessArticle Preparation and Epitope Identification of Monoclonal Antibodies against the NS6 Protein of Porcine Deltacoronavirus (PDCoV) by Huiguang Wu, Xian Sun, Chen Li, Sihan Xie and Zhenhai Chen Int. J. Mol. Sci. 2024, 25(14), 7645; https://doi.org/10.3390/ijms25147645 (registering DOI) - 12 Jul 2024 Abstract Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that causes substantial economic losses in the swine industry worldwide. The PDCoV NS6 protein is an accessory protein that plays a pivotal role in the viral life cycle and immune evasion. However, the functions of [...] Read more. Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that causes substantial economic losses in the swine industry worldwide. The PDCoV NS6 protein is an accessory protein that plays a pivotal role in the viral life cycle and immune evasion. However, the functions of NS6 and its role in PDCoV pathogenesis remain largely unknown. In this study, we prepared a monoclonal antibody (mAb) 5-A11 that specifically recognizes the PDCoV NS6 protein. The mAb 5-A11 exhibited high specificity for PDCoV, with no cross-reactivity with several major porcine pathogenic viruses. Furthermore, the epitope recognized by mAb 5-A11 was precisely mapped to residues 70EYGSIYGKDFI80 of the NS6 protein using Western blot analysis. Notably, this epitope is highly conserved among different PDCoV isolates. Substantial variations were observed when comparing this epitope with the corresponding regions in the NS6 proteins of other δ coronaviruses, suggesting potential differences in the structure, function, and antigenicity of their NS6 proteins. Our findings provide valuable tools and insights for further elucidating the functions of the NS6 protein and its role in PDCoV pathogenesis, as well as for developing diagnostic and therapeutic strategies against PDCoV infection. Full article (This article belongs to the Section Molecular Immunology) ►▼ Show Figures

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14 pages, 3171 KiB   Open AccessArticle Comparative Analysis of Mitochondria Surrounding the Intercalated Discs in Heart Diseases—An Ultrastructural Pilot Study by Rebecca Schönmehl, Daniel H. Mendelsohn, Lina Winter, Steffen Pabel, Tanja Niedermair, Katja Evert, Wing-Hoi Cheung, Ronald Man Yeung Wong, Volker H. Schmitt, Karsten Keller, Friedrich Barsch, Alexander Dietl, Jan F. Gummert, René Schramm, Samuel Sossalla and Christoph Brochhausen Int. J. Mol. Sci. 2024, 25(14), 7644; https://doi.org/10.3390/ijms25147644 (registering DOI) - 12 Jul 2024 Abstract Background: Mitochondria play a crucial role in adapting to fluctuating energy demands, particularly in various heart diseases. This study investigates mitochondrial morphology near intercalated discs in left ventricular (LV) heart tissues, comparing samples from patients with sinus rhythm (SR), atrial fibrillation (AF), dilated [...] Read more. Background: Mitochondria play a crucial role in adapting to fluctuating energy demands, particularly in various heart diseases. This study investigates mitochondrial morphology near intercalated discs in left ventricular (LV) heart tissues, comparing samples from patients with sinus rhythm (SR), atrial fibrillation (AF), dilated cardiomyopathy (DCM), and ischemic cardiomyopathy (ICM). Methods: Transmission electron microscopy was used to analyze mitochondria within 0–3.5 μm and 3.5–7 μm of intercalated discs in 9 SR, 10 AF, 9 DCM, and 8 ICM patient samples. Parameters included mean size in µm2 and elongation, count, percental mitochondrial area in the measuring frame, and a conglomeration score. Results: AF patients exhibited higher counts of small mitochondria in the LV myocardium, resembling SR. DCM and ICM groups had fewer, larger, and often hydropic mitochondria. Accumulation rates and percental mitochondrial area were similar across groups. Significant positive correlations existed between other defects/size and hydropic mitochondria and between count/area and conglomeration score, while negative correlations between count and size/other defects and between hydropic mitochondria and count could be seen as well. Conclusion: Mitochondrial parameters in the LV myocardium of AF patients were similar to those of SR patients, while DCM and ICM displayed distinct changes, including a decrease in number, an increase in size, and compromised mitochondrial morphology. Further research is needed to fully elucidate the pathophysiological role of mitochondrial morphology in different heart diseases, providing deeper insights into potential therapeutic targets and interventions. Full article (This article belongs to the Special Issue Research of Mitochondrial Function, Structure, Dynamics and Intracellular Organization: 3rd Edition) ►▼ Show Figures

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attachment Supplementary material: Supplementary File 1 (ZIP, 1162 KiB) 14 pages, 5462 KiB   Open AccessArticle The Effect of Alternative Splicing Sites on Mirtron Formation and Arm Selection of Precursor microRNAs by Luca Gál, Anita Schamberger, Gerda Wachtl and Tamás I. Orbán Int. J. Mol. Sci. 2024, 25(14), 7643; https://doi.org/10.3390/ijms25147643 (registering DOI) - 12 Jul 2024 Abstract Mirtrons represent a subclass of microRNAs (miRNAs) that rely on the splicing machinery for their maturation. However, the molecular details of this Drosha-independent processing are still not fully understood; as an example, the Microprocessor complex cannot process the mirtronic pre-miRNA from the transcript [...] Read more. Mirtrons represent a subclass of microRNAs (miRNAs) that rely on the splicing machinery for their maturation. However, the molecular details of this Drosha-independent processing are still not fully understood; as an example, the Microprocessor complex cannot process the mirtronic pre-miRNA from the transcript even if splice site mutations are present. To investigate the influence of alternative splicing sites on mirtron formation, we generated Enhanced Green Fluorescent Protein (EGFP) reporters containing artificial introns to compare the processing of canonical miRNAs and mirtrons. Although mutations of both splice sites generated a complex pattern of alternative transcripts, mirtron formation was always severely affected as opposed to the normal processing of the canonical hsa-mir-33b miRNA. However, we also detected that while its formation was also hindered, the mirtron-derived hsa-mir-877-3p miRNA was less affected by certain mutations than the hsa-mir-877-5p species. By knocking down Drosha, we showed that this phenomenon is not dependent on Microprocessor activity but rather points toward the potential stability difference between the miRNAs from the different arms. Our results indicate that when the major splice sites are mutated, mirtron formation cannot be rescued by nearby alternative splice sites, and stability differences between 5p and 3p species should also be considered for functional studies of mirtrons. Full article (This article belongs to the Section Molecular Biology) ►▼ Show Figures

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attachment Supplementary material: Supplementary File 1 (ZIP, 688 KiB) 25 pages, 2287 KiB   Open AccessArticle Long Non-Coding RNAs and Alzheimer’s Disease: Towards Personalized Diagnosis by Maria I. Mosquera-Heredia, Oscar M. Vidal, Luis C. Morales, Carlos Silvera-Redondo, Ernesto Barceló, Ricardo Allegri, Mauricio Arcos-Burgos, Jorge I. Vélez and Pilar Garavito-Galofre Int. J. Mol. Sci. 2024, 25(14), 7641; https://doi.org/10.3390/ijms25147641 (registering DOI) - 11 Jul 2024 Abstract Alzheimer’s disease (AD), a neurodegenerative disorder characterized by progressive cognitive decline, is the most common form of dementia. Currently, there is no single test that can diagnose AD, especially in understudied populations and developing countries. Instead, diagnosis is based on a combination of [...] Read more. Alzheimer’s disease (AD), a neurodegenerative disorder characterized by progressive cognitive decline, is the most common form of dementia. Currently, there is no single test that can diagnose AD, especially in understudied populations and developing countries. Instead, diagnosis is based on a combination of medical history, physical examination, cognitive testing, and brain imaging. Exosomes are extracellular nanovesicles, primarily composed of RNA, that participate in physiological processes related to AD pathogenesis such as cell proliferation, immune response, and neuronal and cardiovascular function. However, the identification and understanding of the potential role of long non-coding RNAs (lncRNAs) in AD diagnosis remain largely unexplored. Here, we clinically, cognitively, and genetically characterized a sample of 15 individuals diagnosed with AD (cases) and 15 controls from Barranquilla, Colombia. Advanced bioinformatics, analytics and Machine Learning (ML) techniques were used to identify lncRNAs differentially expressed between cases and controls. The expression of 28,909 lncRNAs was quantified. Of these, 18 were found to be differentially expressed and harbored in pivotal genes related to AD. Two lncRNAs, ENST00000608936 and ENST00000433747, show promise as diagnostic markers for AD, with ML models achieving > 95% sensitivity, specificity, and accuracy in both the training and testing datasets. These findings suggest that the expression profiles of lncRNAs could significantly contribute to advancing personalized AD diagnosis in this community, offering promising avenues for early detection and follow-up. Full article (This article belongs to the Special Issue MicroRNA and Non-coding RNA: From Basic Research to Potential Clinical Application) ►▼ Show Figures

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29 pages, 2202 KiB   Open AccessReview The Structure–Antiproliferative Activity Relationship of Pyridine Derivatives by Ana-Laura Villa-Reyna, Martin Perez-Velazquez, Mayra Lizett González-Félix, Juan-Carlos Gálvez-Ruiz, Dulce María Gonzalez-Mosquera, Dora Valencia, Manuel G. Ballesteros-Monreal, Milagros Aguilar-Martínez and Mario-Alberto Leyva-Peralta Int. J. Mol. Sci. 2024, 25(14), 7640; https://doi.org/10.3390/ijms25147640 (registering DOI) - 11 Jul 2024 Abstract Pyridine, a compound with a heterocyclic structure, is a key player in medicinal chemistry and drug design. It is widely used as a framework for the design of biologically active molecules and is the second most common heterocycle in FDA-approved drugs. Pyridine is [...] Read more. Pyridine, a compound with a heterocyclic structure, is a key player in medicinal chemistry and drug design. It is widely used as a framework for the design of biologically active molecules and is the second most common heterocycle in FDA-approved drugs. Pyridine is known for its diverse biological activity, including antituberculosis, antitumor, anticoagulant, antiviral, antimalarial, antileishmania, anti-inflammatory, anti-Alzheimer’s, antitrypanosomal, antimalarial, vasodilatory, antioxidant, antimicrobial, and antiproliferative effects. This review, spanning from 2022 to 2012, involved the meticulous identification of pyridine derivatives with antiproliferative activity, as indicated by their minimum inhibitory concentration values (IC50) against various cancerous cell lines. The aim was to determine the most favorable structural characteristics for their antiproliferative activity. Using computer programs, we constructed and calculated the molecular descriptors and analyzed the electrostatic potential maps of the selected pyridine derivatives. The study found that the presence and positions of the -OMe, -OH, -C=O, and NH2 groups in the pyridine derivatives enhanced their antiproliferative activity over the cancerous cellular lines studied. Conversely, pyridine derivatives with halogen atoms or bulky groups in their structures exhibited lower antiproliferative activity. Full article (This article belongs to the Special Issue Computational Approaches in Drug Design: Novel Methodologies and Applications) attachment Supplementary material: Supplementary File 1 (ZIP, 3018 KiB) 23 pages, 5380 KiB   Open AccessArticle Multi-Omics Characterization of E3 Regulatory Patterns in Different Cancer Types by Zhongyan Li, Jingting Wan, Shangfu Li, Yun Tang, Yang-Chi-Dung Lin, Jie Ni, Xiaoxuan Cai, Jinhan Yu, Hsien-Da Huang and Tzong-Yi Lee Int. J. Mol. Sci. 2024, 25(14), 7639; https://doi.org/10.3390/ijms25147639 (registering DOI) - 11 Jul 2024 Abstract Ubiquitination, a post-translational modification, refers to the covalent attachment of ubiquitin molecules to substrates. This modification plays a critical role in diverse cellular processes such as protein degradation. The specificity of ubiquitination for substrates is regulated by E3 ubiquitin ligases. Dysregulation of ubiquitination [...] Read more. Ubiquitination, a post-translational modification, refers to the covalent attachment of ubiquitin molecules to substrates. This modification plays a critical role in diverse cellular processes such as protein degradation. The specificity of ubiquitination for substrates is regulated by E3 ubiquitin ligases. Dysregulation of ubiquitination has been associated with numerous diseases, including cancers. In our study, we first investigated the protein expression patterns of E3 ligases across 12 cancer types. Our findings indicated that E3 ligases tend to be up-regulated and exhibit reduced tissue specificity in tumors. Moreover, the correlation of protein expression between E3 ligases and substrates demonstrated significant changes in cancers, suggesting that E3-substrate specificity alters in tumors compared to normal tissues. By integrating transcriptome, proteome, and ubiquitylome data, we further characterized the E3-substrate regulatory patterns in lung squamous cell carcinoma. Our analysis revealed that the upregulation of the SKP2 E3 ligase leads to excessive degradation of BRCA2, potentially promoting tumor cell proliferation and metastasis. Furthermore, the upregulation of E3 ubiquitin–protein ligase TRIM33 was identified as a biomarker associated with a favorable prognosis by inhibiting the cell cycle. This work exemplifies how leveraging multi-omics data to analyze E3 ligases across various cancers can unveil prognosis biomarkers and facilitate the identification of potential drug targets for cancer therapy. Full article (This article belongs to the Special Issue Advances in Proteomics in Cancer) attachment Supplementary material: Supplementary File 1 (ZIP, 373 KiB) 17 pages, 1215 KiB   Open AccessArticle FGL2/FcγRIIB Signalling Mediates Arterial Shear Stress-Mediated Endothelial Cell Apoptosis: Implications for Coronary Artery Bypass Vein Graft Pathogenesis by Molly L. Jackson, Andrew R. Bond, Raimondo Ascione, Jason L. Johnson and Sarah J. George Int. J. Mol. Sci. 2024, 25(14), 7638; https://doi.org/10.3390/ijms25147638 (registering DOI) - 11 Jul 2024 Abstract The sudden exposure of venous endothelial cells (vECs) to arterial fluid shear stress (FSS) is thought to be a major contributor to coronary artery bypass vein graft failure (VGF). However, the effects of arterial FSS on the vEC secretome are poorly characterised. We [...] Read more. The sudden exposure of venous endothelial cells (vECs) to arterial fluid shear stress (FSS) is thought to be a major contributor to coronary artery bypass vein graft failure (VGF). However, the effects of arterial FSS on the vEC secretome are poorly characterised. We propose that analysis of the vEC secretome may reveal potential therapeutic approaches to suppress VGF. Human umbilical vein endothelial cells (HUVECs) pre-conditioned to venous FSS (18 h; 1.5 dynes/cm2) were exposed to venous or arterial FSS (15 dynes/cm2) for 24 h. Tandem Mass Tagging proteomic analysis of the vEC secretome identified significantly increased fibroleukin (FGL2) in conditioned media from HUVECs exposed to arterial FSS. This increase was validated by Western blotting. Application of the NFκB inhibitor BAY 11-7085 (1 µM) following pre-conditioning reduced FGL2 release from vECs exposed to arterial FSS. Exposure of vECs to arterial FSS increased apoptosis, measured by active cleaved caspase-3 (CC3) immunocytochemistry, which was likewise elevated in HUVECs treated with recombinant FGL2 (20 ng/mL) for 24 h under static conditions. To determine the mechanism of FGL2-induced apoptosis, HUVECs were pre-treated with a blocking antibody to FcγRIIB, a receptor FGL2 is proposed to interact with, which reduced CC3 levels. In conclusion, our findings indicate that the exposure of vECs to arterial FSS results in increased release of FGL2 via NFκB signalling, which promotes endothelial apoptosis via FcγRIIB signalling. Therefore, the inhibition of FGL2/FcγRIIB signalling may provide a novel approach to reduce arterial FSS-induced vEC apoptosis in vein grafts and suppress VGF. Full article (This article belongs to the Special Issue Molecular Mechanisms of Endothelial Dysfunction 3.0) attachment Supplementary material: Supplementary File 1 (ZIP, 3515 KiB) 14 pages, 1368 KiB   Open AccessArticle CRISPR/dCas9-Mediated DNA Methylation Editing on emx2 in Chinese Tongue Sole (Cynoglossus semilaevis) Testis Cells by Yanxu Sun, Hong-Yan Wang, Binghua Liu, Bowen Yue, Qian Liu, Yuyan Liu, Ivana F. Rosa, Lucas B. Doretto, Shenglei Han, Lei Lin, Xiaoling Gong and Changwei Shao Int. J. Mol. Sci. 2024, 25(14), 7637; https://doi.org/10.3390/ijms25147637 (registering DOI) - 11 Jul 2024 Abstract DNA methylation is a key epigenetic mechanism orchestrating gene expression networks in many biological processes. Nonetheless, studying the role of specific gene methylation events in fish faces challenges. In this study, we validate the regulation of DNA methylation on empty spiracles homeobox 2 [...] Read more. DNA methylation is a key epigenetic mechanism orchestrating gene expression networks in many biological processes. Nonetheless, studying the role of specific gene methylation events in fish faces challenges. In this study, we validate the regulation of DNA methylation on empty spiracles homeobox 2 (emx2) expression with decitabine treatment in Chinese tongue sole testis cells. We used the emx2 gene as the target gene and developed a new DNA methylation editing system by fusing dnmt3a with catalytic dead Cas9 (dCas9) and demonstrated its ability for sequence-specific DNA methylation editing. Results revealed that utilizing dCas9-dnmt3a to target emx2 promoter region led to increased DNA methylation levels and decreased emx2 expression in Chinese tongue sole testis cells. More importantly, the DNA methylation editing significantly suppressed the expression of MYC proto-oncogene, bHLH transcription factor (myc), one target gene of emx2. Furthermore, we assessed the off-target effects of dCas9-dnmt3a and confirmed no significant impact on the predicted off-target gene expression. Taken together, we developed the first DNA methylation editing system in marine species and demonstrated its effective editing ability in Chinese tongue sole cells. This provides a new strategy for both epigenetic research and molecular breeding of marine species. Full article (This article belongs to the Section Molecular Biology) ►▼ Show Figures

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attachment Supplementary material: Supplementary File 1 (ZIP, 211 KiB) 19 pages, 3407 KiB   Open AccessArticle Genome-Wide Identification of Seven in Absentia E3 Ubiquitin Ligase Gene Family and Expression Profiles in Response to Different Hormones in Uncaria rhynchophylla by Jinxu Lan, Conglong Lian, Yingying Shao, Suiqing Chen, Ying Lu, Lina Zhu, Detian Mu and Qi Tang Int. J. Mol. Sci. 2024, 25(14), 7636; https://doi.org/10.3390/ijms25147636 (registering DOI) - 11 Jul 2024 Abstract SINA (Seven in absentia) E3 ubiquitin ligases are a family of RING (really interesting new gene) E3 ubiquitin ligases, and they play a crucial role in regulating plant growth and development, hormone response, and abiotic and biotic stress. However, there is little research [...] Read more. SINA (Seven in absentia) E3 ubiquitin ligases are a family of RING (really interesting new gene) E3 ubiquitin ligases, and they play a crucial role in regulating plant growth and development, hormone response, and abiotic and biotic stress. However, there is little research on the SINA gene family in U. rhynchophylla. In this study, a total of 10 UrSINA genes were identified from the U. rhynchophylla genome. The results of multiple sequence alignments and chromosomal locations show that 10 UrSINA genes were unevenly located on 22 chromosomes, and each UrSINA protein contained a SINA domain at the N-terminal and RING domains at the C-terminal. Synteny analysis showed that there are no tandem duplication gene pairs and there are four segmental gene pairs in U. rhynchophylla, contributing to the expansion of the gene family. Furthermore, almost all UrSINA genes contained the same gene structure, with three exons and two introns, and there were many cis-acting elements relating to plant hormones, light responses, and biotic and abiotic stress. The results of qRT-PCR show that most UrSINA genes were expressed in stems, with the least expression in roots; meanwhile, most UrSINA genes and key enzyme genes were responsive to ABA and MeJA hormones with overlapping but different expression patterns. Co-expression analysis showed that UrSINA1 might participate in the TIA pathway under ABA treatment, and UrSINA5 and UrSINA6 might participate in the TIA pathway under MeJA treatment. The mining of UrSINA genes in the U. rhynchophylla provided novel information for understanding the SINA gene and its function in plant secondary metabolites, growth, and development. Full article (This article belongs to the Special Issue Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants 2.0) attachment Supplementary material: Supplementary File 1 (ZIP, 6903 KiB) 19 pages, 8095 KiB   Open AccessArticle Transcriptomic and Metabolomic Insights into ABA-Related Genes in Cerasus humilis under Drought Stress by Yu Liu, Chenxue Zhao, Xuedong Tang, Lianjun Wang and Ruixue Guo Int. J. Mol. Sci. 2024, 25(14), 7635; https://doi.org/10.3390/ijms25147635 (registering DOI) - 11 Jul 2024 Abstract Cerasus humilis, a small shrub of the Cerasus genus within the Rosaceae family, is native to China and renowned for its highly nutritious and medicinal fruits, robust root system, and remarkable drought resistance. This study primarily employed association transcriptome and metabolome analyses [...] Read more. Cerasus humilis, a small shrub of the Cerasus genus within the Rosaceae family, is native to China and renowned for its highly nutritious and medicinal fruits, robust root system, and remarkable drought resistance. This study primarily employed association transcriptome and metabolome analyses to assess changes in abscisic acid (ABA) levels and identify key regulatory genes in C. humilis subjected to varying degrees of drought stress. Notably, we observed distinct alterations in transcription factors across different drought intensities. Specifically, our transcriptome data indicated noteworthy shifts in GATA, MYB, MYC, WRKY, C2H2, and bHLH transcription factor families. Furthermore, combined transcriptomic and metabolomic investigations demonstrated significant enrichment of metabolic pathways, such as ‘Carbon metabolism’, ‘Biosynthesis of amino acids’, ‘Biosynthesis of cofactors’, ‘Phenylpropanoid biosynthesis’, ‘Starch and sucrose metabolism’, and ‘Plant hormone signal transduction’ under moderate (Mod) or severe (Sev) drought conditions. A total of 11 candidate genes involved in ABA biosynthesis and signaling pathways were identified. The down-regulated genes included secoisolariciresinol dehydrogenase-like and PYL2. Conversely, genes including FAD-dependent urate hydroxylase-like, cytochrome P450 97B2, carotenoid cleavage dioxygenase 4 (CCD4), SnRK2.2, ABI 5-like protein 5, PP2C 51, and SnRK2.3, were up-regulated under Mod or Sev drought stress. This study lays the genetic foundation for ABA biosynthesis to enhance drought tolerance and provides genetic resources for plant genetic engineering and breeding efforts. Full article (This article belongs to the Special Issue Regulation of Transcription Factor–Hormone Networks in Plants) ►▼ Show Figures

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24 pages, 866 KiB   Open AccessReview Unveiling Versatile Applications and Toxicity Considerations of Graphitic Carbon Nitride by Alexandra Paulína Drdanová, Timea Ema Krajčovičová, Miroslav Gál, Katarína Nemčeková, Zuzana Imreová, Jozef Ryba, Monika Naumowicz, Tomáš Homola, Tomáš Mackuľak and Veronika Svitková Int. J. Mol. Sci. 2024, 25(14), 7634; https://doi.org/10.3390/ijms25147634 (registering DOI) - 11 Jul 2024 Abstract Metal-free, low-cost, organic photocatalytic graphitic carbon nitride (g-C3N4) has become a promising and impressive material in numerous scientific fields due to its unique physical and chemical properties. As a semiconductor with a suitable band gap of ~2.7 eV, g-C [...] Read more. Metal-free, low-cost, organic photocatalytic graphitic carbon nitride (g-C3N4) has become a promising and impressive material in numerous scientific fields due to its unique physical and chemical properties. As a semiconductor with a suitable band gap of ~2.7 eV, g-C3N4 is an active photocatalytic material even after irradiation with visible light. However, information regarding the toxicity of g-C3N4 is not extensively documented and there is not a comprehensive understanding of its potential adverse effects on human health or the environment. In this context, the term “toxicity” can be perceived in both a positive and a negative light, depending on whether it serves as a benefit or poses a potential risk. This review shows the applications of g-C3N4 in sensorics, electrochemistry, photocatalysis, and biomedical approaches while pointing out the potential risks of its toxicity, especially in human and environmental health. Finally, the future perspective of g-C3N4 research is addressed, highlighting the need for a comprehensive understanding of the toxicity of this material to provide safe and effective applications in various fields. Full article (This article belongs to the Section Molecular Toxicology) 14 pages, 1244 KiB   Open AccessReview Interoceptive Processing in Functional Gastrointestinal Disorders by Katerina Karaivazoglou, Ioanna Aggeletopoulou and Christos Triantos Int. J. Mol. Sci. 2024, 25(14), 7633; https://doi.org/10.3390/ijms25147633 (registering DOI) - 11 Jul 2024 Abstract Functional gastrointestinal disorders (FGIDs) are characterized by chronic gastrointestinal symptoms in the absence of overt pathology and affect a significant percentage of the worldwide population. They are commonly accompanied by co-morbid psychiatric symptomatology and are associated with significant suffering and great healthcare services [...] Read more. Functional gastrointestinal disorders (FGIDs) are characterized by chronic gastrointestinal symptoms in the absence of overt pathology and affect a significant percentage of the worldwide population. They are commonly accompanied by co-morbid psychiatric symptomatology and are associated with significant suffering and great healthcare services utilization. There is growing evidence that dysregulation of the gut–brain axis and disturbances in the processing of afferent interoceptive signals lie at the heart of these disorders. In this context, the aim of the current review was to detect and critically review original articles focusing on the role of interoception in the pathophysiology of FGIDs. Our search yielded 38 relevant studies. FGID patients displayed increased visceral sensitivity, enhanced attention to gastrointestinal interoceptive cues, and greater emotional arousal when coping with gut-derived sensations. Neuroimaging studies have shown significant structural and functional changes in regions of the interoceptive network, while molecular and genetic studies have revealed significant associations between interoceptive signaling and deficits in excitatory neurotransmission, altered endocrine and immune physiological pathways, and aberrant expression of transient receptor potential channel genes. Finally, there were emerging data suggesting that interoception-based interventions may reduce physical symptoms and improve quality of life and should be integrated into FGID clinical management practices. Full article (This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics) attachment Supplementary material: Supplementary File 1 (ZIP, 890 KiB) 16 pages, 1436 KiB   Open AccessArticle Copper Is Accumulated as Copper Sulfide Particles, and Not Bound to Glutathione, Phytochelatins or Metallothioneins, in the Marine Alga Ulva compressa (Chlorophyta) by Stephanie Romero, Alberto González, Héctor Osorio, Rodrigo Segura and Alejandra Moenne Int. J. Mol. Sci. 2024, 25(14), 7632; https://doi.org/10.3390/ijms25147632 (registering DOI) - 11 Jul 2024 Abstract To analyze the mechanism of copper accumulation in the marine alga Ulva compressa, it was cultivated with 10 μM of copper, with 10 μM of copper and increasing concentrations of a sulfide donor (NaHS) for 0 to 7 days, and with 10 [...] Read more. To analyze the mechanism of copper accumulation in the marine alga Ulva compressa, it was cultivated with 10 μM of copper, with 10 μM of copper and increasing concentrations of a sulfide donor (NaHS) for 0 to 7 days, and with 10 μM of copper and a concentration of the sulfide acceptor (hypotaurine) for 5 days. The level of intracellular copper was determined as well as the level of glutathione (GSH) and phytochelatins (PCs) and the expression of metallothioneins (UcMTs). The level of intracellular copper in the algae treated with copper increased at day 1, slightly increased until day 5 and remained unchanged until day 7. The level of copper in the algae cultivated with copper and 100 or 200 μM of NaHS continuously increased until day 7 and the copper level was higher in the algae cultivated with 200 μM of NaHS compared to 100 μM of NaHS. In contrast, the level of intracellular copper decreased in the algae treated with copper and hypotaurine. The level of intracellular copper did not correlate with the level of GSH or with the expression of UcMTs, and PCs were not detected in response to copper, or copper and NaHS. Algae treated with copper and with copper and 200 μM of NaHS for 5 days were visualized by TEM and the elemental composition of electrondense particles was analyzed by EDXS. The algae treated with copper showed electrondense particles containing copper and sulfur, but not nitrogen, and they were mainly located in the chloroplast, but also in the cytoplasm. The algae treated with copper and NaHS showed a higher level of electrondense particles containing copper and sulfur, but not nitrogen, and they were located in the chloroplast, and in the cytoplasm. Thus, copper is accumulated as copper sulfide insoluble particles, and not bound to GSH, PCs or UcMTs, in the marine alga U. compressa. Full article (This article belongs to the Special Issue Advance in Plant Abiotic Stress) 26 pages, 2969 KiB   Open AccessReview Adjuvant Properties of Caffeic Acid in Cancer Treatment by Nicole Cortez, Cecilia Villegas, Viviana Burgos, Jaime R. Cabrera-Pardo, Leandro Ortiz, Iván González-Chavarría, Vaderament-A. Nchiozem-Ngnitedem and Cristian Paz Int. J. Mol. Sci. 2024, 25(14), 7631; https://doi.org/10.3390/ijms25147631 (registering DOI) - 11 Jul 2024 Abstract Caffeic acid (CA) is a polyphenol belonging to the phenylpropanoid family, commonly found in plants and vegetables. It was first identified by Hlasiwetz in 1867 as a breakdown product of caffetannic acid. CA is biosynthesized from the amino acids tyrosine or phenylalanine through [...] Read more. Caffeic acid (CA) is a polyphenol belonging to the phenylpropanoid family, commonly found in plants and vegetables. It was first identified by Hlasiwetz in 1867 as a breakdown product of caffetannic acid. CA is biosynthesized from the amino acids tyrosine or phenylalanine through specific enzyme-catalyzed reactions. Extensive research since its discovery has revealed various health benefits associated with CA, including its antioxidant, anti-inflammatory, and anticancer properties. These effects are attributed to its ability to modulate several pathways, such as inhibiting NFkB, STAT3, and ERK1/2, thereby reducing inflammatory responses, and activating the Nrf2/ARE pathway to enhance antioxidant cell defenses. The consumption of CA has been linked to a reduced risk of certain cancers, mitigation of chemotherapy and radiotherapy-induced toxicity, and reversal of resistance to first-line chemotherapeutic agents. This suggests that CA could serve as a useful adjunct in cancer treatment. Studies have shown CA to be generally safe, with few adverse effects (such as back pain and headaches) reported. This review collates the latest information from Google Scholar, PubMed, the Phenol-Explorer database, and ClinicalTrials.gov, incorporating a total of 154 articles, to underscore the potential of CA in cancer prevention and overcoming chemoresistance. Full article (This article belongs to the Special Issue Molecular Studies of Natural Compounds and Plant Extracts 2.0) ►▼ Show Figures

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attachment Supplementary material: Supplementary File 1 (ZIP, 106 KiB) 22 pages, 24639 KiB   Open AccessArticle Adipokines—A Cohort Prospective Study in Children with Severe Burns by Silviu Constantin Badoiu, Dan Mircea Enescu, Raluca Tatar, Daniela Miricescu, Iulia-Ioana Stanescu-Spinu, Maria Greabu, Anca Magdalena Coricovac, Silvia Elena Badoiu and Viorel Jinga Int. J. Mol. Sci. 2024, 25(14), 7630; https://doi.org/10.3390/ijms25147630 (registering DOI) - 11 Jul 2024 Abstract Burns generate every year an important burden of morbidity, being a major global public health problem through prolonged hospitalization, complications, and increased mortality. This study’s purpose was to evaluate the serum levels of three adipokines and to establish significant correlations with other circulating [...] Read more. Burns generate every year an important burden of morbidity, being a major global public health problem through prolonged hospitalization, complications, and increased mortality. This study’s purpose was to evaluate the serum levels of three adipokines and to establish significant correlations with other circulating molecules and with some clinical parameters. We evaluated 32 children with severe burns (over 25% total burned surface area—TBSA) at 48 h, day 10, and day 21 post burn, and 21 controls. The serum levels of adiponectin, resistin, leptin, tumor necrosis factor-α (TNF-α), plasminogen activator inhibitor-1 (PAI-1), and C-reactive protein (CRP) (among nine other biochemical parameters) were detected by Multiplex technique. Significant statistical differences were obtained for resistin and leptin compared to the control group, in different moments of measurements. Adiponectin serum levels presented statistically significant correlations with hot liquid mechanism of burn, the Revised Baux score, TBSA, resistin, PAI-1, CRP, TNF-α, and triglycerides (TGLs) serum levels. Resistin serum levels presented statistically significant correlations with adiponectin, CRP, PAI-1, leptin, and TNF-α. Additionally, we found statistically significant correlations between leptin serum levels and length of hospitalization, TNF-α, resistin, adiponectin, and PAI-1 serum levels. In severely burned children, adiponectin, resistin, and leptin specifically correlate with clinical parameters and with proteins involved in the systemic inflammatory response and the hypermetabolic response. Full article (This article belongs to the Special Issue Molecular and Biochemical Aspects in Burns) ►▼ Show Figures

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attachment Supplementary material: Supplementary File 1 (ZIP, 242 KiB) 14 pages, 3293 KiB   Open AccessArticle Characterization of the ddt1 Mutant in Rice and Its Impact on Plant Height Reduction and Water Use Efficiency by Banpu Ruan, Yaohuang Jiang, Yingying Ma, Menghao Zhou, Fei Chen, Yanli Zhang, Yanchun Yu and Limin Wu Int. J. Mol. Sci. 2024, 25(14), 7629; https://doi.org/10.3390/ijms25147629 (registering DOI) - 11 Jul 2024 Abstract Rice (Oryza sativa L.), a fundamental global staple, nourishes over half of the world’s population. The identification of the ddt1 mutant in rice through EMS mutagenesis of the indica cultivar Shuhui527 revealed a dwarf phenotype, characterized by reduced plant height, smaller grain [...] Read more. Rice (Oryza sativa L.), a fundamental global staple, nourishes over half of the world’s population. The identification of the ddt1 mutant in rice through EMS mutagenesis of the indica cultivar Shuhui527 revealed a dwarf phenotype, characterized by reduced plant height, smaller grain size, and decreased grain weight. Detailed phenotypic analysis and map-based cloning pinpointed the mutation to a single-base transversion in the LOC_Os03g04680 gene, encoding a cytochrome P450 enzyme, which results in a premature termination of the protein. Functional complementation tests confirmed LOC_Os03g04680 as the DDT1 gene responsible for the observed phenotype. We further demonstrated that the ddt1 mutation leads to significant alterations in gibberellic acid (GA) metabolism and signal transduction, evidenced by the differential expression of key GA-related genes such as OsGA20OX2, OsGA20OX3, and SLR1. The mutant also displayed enhanced drought tolerance, as indicated by higher survival rates, reduced water loss, and rapid stomatal closure under drought conditions. This increased drought resistance was linked to the mutant’s improved antioxidant capacity, with elevated activities of antioxidant enzymes and higher expression levels of related genes. Our findings suggest that DDT1 plays a crucial role in regulating both plant height and drought stress responses. The potential for using gene editing of DDT1 to mitigate the dwarf phenotype while retaining improved drought resistance offers promising avenues for rice improvement. Full article (This article belongs to the Special Issue Rice Molecular Breeding and Genetics: 3rd Edition) ►▼ Show Figures

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15 pages, 940 KiB   Open AccessReview Microvascular Dysfunction across the Spectrum of Heart Failure Pathology: Pathophysiology, Clinical Features and Therapeutic Implications by Giulia La Vecchia, Isabella Fumarulo, Andrea Caffè, Mario Chiatto, Rocco A. Montone and Nadia Aspromonte Int. J. Mol. Sci. 2024, 25(14), 7628; https://doi.org/10.3390/ijms25147628 (registering DOI) - 11 Jul 2024 Abstract Coronary microvascular dysfunction (CMD) plays a crucial role across the spectrum of heart failure (HF) pathology, contributing to disease development, progression, and outcomes. The pathophysiological mechanisms linking CMD to HF are complex and still not completely understood and include chronic inflammation, oxidative stress, [...] Read more. Coronary microvascular dysfunction (CMD) plays a crucial role across the spectrum of heart failure (HF) pathology, contributing to disease development, progression, and outcomes. The pathophysiological mechanisms linking CMD to HF are complex and still not completely understood and include chronic inflammation, oxidative stress, and neurohormonal activation. Despite the diagnostic and prognostic relevance in patients with HF, there is no specific therapeutic strategy targeting CMD to date. Moreover, the diagnosis of this clinical condition is challenging. In this review article, we aim to discuss the different clinical pathogenetic mechanisms linking CMD to HF across the different spectra of these diseases, their prognostic relevance, and the possible therapeutic targets along with the remaining knowledge gaps in the field. Full article (This article belongs to the Special Issue Advances in Heart Diseases: Molecular Pathogenesis, Biomarkers and Therapies) ►▼ Show Figures

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20 pages, 3943 KiB   Open AccessReview Small Peptides: Orchestrators of Plant Growth and Developmental Processes by Shuaiqi Lu and Fei Xiao Int. J. Mol. Sci. 2024, 25(14), 7627; https://doi.org/10.3390/ijms25147627 (registering DOI) - 11 Jul 2024 Abstract Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, [...] Read more. Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, maturation, and stress responses. As vital mediators of intercellular signaling, SPs have garnered significant attention in plant biology research. This comprehensive review delves into SPs’ structure, classification, and identification, providing a detailed understanding of their significance. Additionally, we summarize recent findings on the biological functions and signaling pathways of prominent SPs that regulate plant growth and development. This review also offers a perspective on future research directions in peptide signaling pathways. 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