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
Molecular Orientation Behavior of Lyotropic Liquid Crystal–Carbon Dot Hybrids in Microfluidic Confinement
Int. J. Mol. Sci. 2024, 25(10), 5520; https://doi.org/10.3390/ijms25105520 (registering DOI) - 18 May 2024
Abstract
Lyotropic liquid crystals represent an important class of anisotropic colloid systems. Their integration with optically active nanoparticles can provide us with responsive luminescent media that offer new fundamental and applied solutions for biomedicine. This paper analyzes the molecular-level behavior of such composites represented
[...] Read more.
Lyotropic liquid crystals represent an important class of anisotropic colloid systems. Their integration with optically active nanoparticles can provide us with responsive luminescent media that offer new fundamental and applied solutions for biomedicine. This paper analyzes the molecular-level behavior of such composites represented by tetraethylene glycol monododecyl ether and nanoscale carbon dots in microfluidic channels. Microfluidic confinement allows for simultaneously applying multiple factors, such as flow dynamics, wall effects, and temperature, for the precise control of the molecular arrangement in such composites and their resulting optical properties. The microfluidic behavior of composites was characterized by a set of analytical and modeling tools such as polarized and fluorescent microscopy, dynamic light scattering, and fluorescent spectroscopy, as well as image processing in Matlab. The composites were shown to form tunable anisotropic intermolecular structures in microchannels with several levels of molecular ordering. A predominant lamellar structure of the composites was found to undergo additional ordering with respect to the microchannel axis and walls. Such an alignment was controlled by applying shear and temperature factors to the microfluidic environment. The revealed molecular behavior of the composite may contribute to the synthesis of hybrid organized media capable of polarized luminescence for on-chip diagnostics and biomimetics.
Full article
(This article belongs to the Section Physical Chemistry and Chemical Physics)
►
Show Figures
Open AccessArticle
Cytosine Deaminase-Overexpressing hTERT-Immortalized Human Adipose Stem Cells Enhance the Inhibitory Effects of Fluorocytosine on Tumor Growth in Castration Resistant Prostate Cancer
by
Jae Heon Kim, Hee Jo Yang, Sang Hun Lee and Yun Seob Song
Int. J. Mol. Sci. 2024, 25(10), 5519; https://doi.org/10.3390/ijms25105519 (registering DOI) - 18 May 2024
Abstract
A promising de novo approach for the treatment of Castration-resistant prostate cancer (CRPC) exploits cell-mediated enzyme prodrug therapy comprising cytosine deaminase (CD) and fluorouracil (5-FC). The aim of this study was to determine the potential of bacterial CD-overexpressing hTERT-immortalized human adipose stem cells
[...] Read more.
A promising de novo approach for the treatment of Castration-resistant prostate cancer (CRPC) exploits cell-mediated enzyme prodrug therapy comprising cytosine deaminase (CD) and fluorouracil (5-FC). The aim of this study was to determine the potential of bacterial CD-overexpressing hTERT-immortalized human adipose stem cells (hTERT-ADSC.CD) to suppress CRPC. A lentiviral vector encoding a bacterial CD gene was used to transfect and to generate the hTERT-ADSC.CD line. The ability of the cells to migrate selectively towards malignant cells was investigated in vitro. PC3 and hTERT-ADSC.CD cells were co-cultured in order to establish. hTERT-ADSC.CD and 1 × 106 PC3 cells were administered to nude mice via intracardiac and subcutaneous injections, respectively, and 5-FC was given for 14 days. hTERT-ADSC.CD were successfully engineered. Enhanced in vitro hTERT-ADSC.CD cytotoxicity and suicide effect were evident following administration of 5 μM 5-FC. hTERT-ADSC.CD, together with 5-FC, augmented the numbers of PC3 cells undergoing apoptosis. In comparison to controls administered hTERT-ADSC.CD monotherapy, hTERT-ADSC.CD in combination with 5-FC demonstrated a greater suppressive effect on tumor. In CPRC-bearing mice, tumor suppression was enhanced by the combination of CD-overexpressing ADSC and the prodrug 5-FC. Stem cells exhibiting CD gene expression are a potential novel approach to treatment for CRPC.
Full article
(This article belongs to the Special Issue Cancer Suicide Gene Therapy)
Open AccessArticle
Differential Transcription Profiling Reveals the MicroRNAs Involved in Alleviating Damage to Photosynthesis under Drought Stress during the Grain Filling Stage in Wheat
by
Ruixiang Zhou, Yuhang Song, Xinyu Xue, Ruili Xue, Haifang Jiang, Yi Zhou, Xueli Qi and Yuexia Wang
Int. J. Mol. Sci. 2024, 25(10), 5518; https://doi.org/10.3390/ijms25105518 (registering DOI) - 18 May 2024
Abstract
To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat (Triticum aestivum L.) cultivar, miRNA transcriptome sequencing of the flag leaves of Zhengmai 1860, drought-sensitive variety Zhoumai 18, and drought-resistant variety Bainong 207 was performed
[...] Read more.
To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat (Triticum aestivum L.) cultivar, miRNA transcriptome sequencing of the flag leaves of Zhengmai 1860, drought-sensitive variety Zhoumai 18, and drought-resistant variety Bainong 207 was performed during the grain filling stage. We also observed changes in the chloroplast ultrastructure, phytohormone levels, and antioxidant- and photosynthesis-related physiological indicators in three wheat varieties. The results showed that the flag leaves of the drought-tolerant variety Zhengmai 1860 had higher chlorophyll contents and net photosynthetic rates than those of Zhoumai 18 under drought stress during the grain filling stage; in addition, the chloroplast structure was more complete. However, there was no significant difference between Zhengmai 1860 and Bainong 207. MiRNA transcriptome analysis revealed that the differential expression of the miRNAs and mRNAs exhibited variable specificity. The KEGG pathway enrichment results indicated that most of the genes were enriched in the MAPK signaling pathway, plant hormone signal transduction, photosynthetic antennae protein, and amino acid and carbohydrate metabolism. In the drought-tolerant cultivar Zhengmai 1860, tae-miR408 was targeted to regulate the allene oxide synthase (AOS) gene, inhibit its expression, reduce the AOS content, and decrease the synthesis of jasmonic acid (JA) and abscisic acid (ABA). The results of this study suggest that Zhengmai 1860 could improve the photosynthetic performance of flag leaves by inhibiting the expression of genes involved in the JA pathway through miRNAs under drought conditions. Moreover, multiple miRNAs may target chlorophyll, antioxidant enzymes, phytohormone signal transduction, and other related pathways; thus, it is possible to provide a more theoretical basis for wheat molecular breeding.
Full article
(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)
►▼
Show Figures
Figure 1
Open AccessArticle
Combined Metabolite and Transcriptomic Profiling Unveil a Potential Gene Network Involved in the Triterpenoid Metabolism of Rose roxburghii
by
Liangqun Li, Mei Peng, Yanfang Yan, Tingfei Deng, Qiancheng Liang, Xian Tao, Haodong Li, Juan Yang, Guandi He, Sanwei Yang, Xiaojun Pu and Xiaosheng Yang
Int. J. Mol. Sci. 2024, 25(10), 5517; https://doi.org/10.3390/ijms25105517 (registering DOI) - 18 May 2024
Abstract
Rose roxburghii, a horticulturally significant species within the Rosa genus of the Rosaceae family, is renowned for its abundance of secondary metabolites and ascorbate, earning it the title ‘king of vitamin C’. Despite this recognition, the mechanisms underlying the biosynthesis and regulation
[...] Read more.
Rose roxburghii, a horticulturally significant species within the Rosa genus of the Rosaceae family, is renowned for its abundance of secondary metabolites and ascorbate, earning it the title ‘king of vitamin C’. Despite this recognition, the mechanisms underlying the biosynthesis and regulation of triterpenoid compounds in R. roxburghii remain largely unresolved. In this study, we conducted high-performance liquid chromatography profiling across various organs of R. roxburghii, including fruit, root, stem, and leaves, revealing distinct distributions of triterpenoid compounds among different plant parts. Notably, the fruit exhibited the highest total triterpenoid content, followed by root and stem, with leaf containing the lowest levels, with leaf containing the lowest levels. Transcriptomic analysis unveiled preferential expression of members from the cytochrome P450 (CYP) and glycosyltransferase (UGT) families, likely contributing to the higher accumulation of both ascorbate and triterpenoid compounds in the fruits of R. roxburghii compared to other tissues of R. roxburghii. Transcriptomic analysis unveiled a potential gene network implicated in the biosynthesis of both ascorbate and triterpenoid compounds in R. roxburghii. These findings not only deepen our understanding of the metabolic pathways in this species but also have implications for the design of functional foods enriched with ascorbate and triterpenoids in R. roxburghii.
Full article
(This article belongs to the Special Issue Advance in Plant Abiotic Stress)
►▼
Show Figures
Figure 1
Open AccessArticle
Fatty Acids and Their Lipogenic Enzymes in Anorexia Nervosa Clinical Subtypes
by
Nhien Nguyen, D. Blake Woodside, Eileen Lam, Oswald Quehenberger, J. Bruce German and Pei-an Betty Shih
Int. J. Mol. Sci. 2024, 25(10), 5516; https://doi.org/10.3390/ijms25105516 (registering DOI) - 18 May 2024
Abstract
Disordered eating behavior differs between the restricting subtype (AN-R) and the binging and purging subtype (AN-BP) of anorexia nervosa (AN). Yet, little is known about how these differences impact fatty acid (FA) dysregulation in AN. To address this question, we analyzed 26 FAs
[...] Read more.
Disordered eating behavior differs between the restricting subtype (AN-R) and the binging and purging subtype (AN-BP) of anorexia nervosa (AN). Yet, little is known about how these differences impact fatty acid (FA) dysregulation in AN. To address this question, we analyzed 26 FAs and 7 FA lipogenic enzymes (4 desaturases and 3 elongases) in 96 women: 25 AN-R, 25 AN-BP, and 46 healthy control women. Our goal was to assess subtype-specific patterns. Lauric acid was significantly higher in AN-BP than in AN-R at the fasting timepoint (p = 0.038) and displayed significantly different postprandial changes 2 h after eating. AN-R displayed significantly higher levels of n-3 alpha-linolenic acid, stearidonic acid, eicosapentaenoic acid (EPA), docosapentaenoic acid, and n-6 linoleic acid and gamma-linolenic acid compared to controls. AN-BP showed elevated EPA and saturated lauric acid compared to controls. Higher EPA was associated with elevated anxiety in AN-R (p = 0.035) but was linked to lower anxiety in AN-BP (p = 0.043). These findings suggest distinct disordered eating behaviors in AN subtypes contribute to lipid dysregulation and eating disorder comorbidities. A personalized dietary intervention may improve lipid dysregulation and enhance treatment effectiveness for AN.
Full article
(This article belongs to the Special Issue Lipid Metabolism in Human Diseases)
►▼
Show Figures
Figure 1
Open AccessArticle
The Long Non-Coding RNA MALAT1 Modulates NR4A1 Expression through a Downstream Regulatory Element in Specific Cancer Cell Types
by
Sara Wernig-Zorc, Uwe Schwartz, Paulina Martínez-Rodríguez, Josefa Inalef, Francisca Pavicic, Pamela Ehrenfeld, Gernot Längst and Rodrigo Maldonado
Int. J. Mol. Sci. 2024, 25(10), 5515; https://doi.org/10.3390/ijms25105515 (registering DOI) - 18 May 2024
Abstract
Long non-coding RNAs (lncRNAs) have been shown to modulate gene expression and are involved in the initiation and progression of various cancer types. Despite the wealth of studies describing transcriptome changes upon lncRNA knockdown, there is limited information describing lncRNA-mediated effects on regulatory
[...] Read more.
Long non-coding RNAs (lncRNAs) have been shown to modulate gene expression and are involved in the initiation and progression of various cancer types. Despite the wealth of studies describing transcriptome changes upon lncRNA knockdown, there is limited information describing lncRNA-mediated effects on regulatory elements (REs) modulating gene expression. In this study, we investigated how the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) lncRNA regulates primary target genes using time-resolved MALAT1 knockdown followed by parallel RNA-seq and ATAC-seq assays. The results revealed that MALAT1 primarily regulates specific protein-coding genes and a substantial decrease in the accessibility downstream of the NR4A1 gene that was associated with a decreased NR4A1 expression. Moreover, the presence of an NR4A1-downstream RE was demonstrated by CRISPR-i assays to define a functional MALAT1/NR4A1 axis. By analyzing TCGA data, we identified a positive correlation between NR4A1 expression and NR4A1-downstream RE accessibility in breast cancer but not in pancreatic cancer. Accordingly, this regulatory mechanism was experimentally validated in breast cancer cells (MCF7) but not in pancreatic duct epithelial carcinoma (PANC1) cells. Therefore, our results demonstrated that MALAT1 is involved in a molecular mechanism that fine-tunes NR4A1 expression by modulating the accessibility of a downstream RE in a cell type-specific manner.
Full article
(This article belongs to the Special Issue Pathways in Development and Disease: The Role of RNA Regulation in Biological and Pathological Events)
►▼
Show Figures
Graphical abstract
Open AccessArticle
Bifidobacterium longum and Chlorella sorokiniana Combination Modulates IFN-γ, IL-10, and SOCS3 in Rotavirus-Infected Cells
by
Felizardo Velderrain-Armenta, Guadalupe González-Ochoa, Patricia Tamez-Guerra, Ricardo Romero-Arguelles, César I. Romo-Sáenz, Ricardo Gomez-Flores, Lilian Flores-Mendoza, Ramona Icedo-García and José G. Soñanez-Organis
Int. J. Mol. Sci. 2024, 25(10), 5514; https://doi.org/10.3390/ijms25105514 (registering DOI) - 18 May 2024
Abstract
Rotavirus is the main cause of acute diarrhea in children up to five years of age. In this regard, probiotics are commonly used to treat or prevent gastroenteritis including viral infections. The anti-rotavirus effect of Bifidobacterium longum and Chlorella sorokiniana, by reducing
[...] Read more.
Rotavirus is the main cause of acute diarrhea in children up to five years of age. In this regard, probiotics are commonly used to treat or prevent gastroenteritis including viral infections. The anti-rotavirus effect of Bifidobacterium longum and Chlorella sorokiniana, by reducing viral infectivity and improving IFN-type I response, has been previously reported. The present study aimed to study the effect of B. longum and/or C. sorokiniana on modulating the antiviral cellular immune response mediated by IFN-γ, IL-10, SOCS3, STAT1, and STAT2 genes in rotavirus-infected cells. To determine the mRNA relative expression of these genes, HT-29 cells were treated with B. longum and C. sorokiniana alone or in combination, followed by rotavirus infection. In addition, infected cells were treated with B. longum and/or C. sorokiniana. Cellular RNA was purified, used for cDNA synthesis, and amplified by qPCR. Our results demonstrated that the combination of B. longum and C. sorokiniana stimulates the antiviral cellular immune response by upregulating IFN-γ and may block pro-inflammatory cytokines by upregulating IL-10 and SOCS3. The results of our study indicated that B. longum, C. sorokiniana, or their combination improve antiviral cellular immune response and might modulate pro-inflammatory responses.
Full article
(This article belongs to the Special Issue Molecular Mechanisms of Bioactive Nutrients Promoting Health through Gut Microbiota 2.0)
►▼
Show Figures
Figure 1
Open AccessArticle
Genome-Wide Identification and Expression Analysis of ent-kaurene synthase-like Gene Family Associated with Abiotic Stress in Rice
by
Yantong Teng, Yingwei Wang, Yutong Zhang, Qinyu Xie, Qinzong Zeng, Maohong Cai and Tao Chen
Int. J. Mol. Sci. 2024, 25(10), 5513; https://doi.org/10.3390/ijms25105513 (registering DOI) - 18 May 2024
Abstract
Rice (Oryza sativa) is one of the most important crops for humans. The homologs of ent-kaurene synthase (KS) in rice, which are responsible for the biosynthesis of gibberellins and various phytoalexins, are identified by their distinct biochemical functions. However, the
[...] Read more.
Rice (Oryza sativa) is one of the most important crops for humans. The homologs of ent-kaurene synthase (KS) in rice, which are responsible for the biosynthesis of gibberellins and various phytoalexins, are identified by their distinct biochemical functions. However, the KS-Like (KSL) family’s potential functions related to hormone and abiotic stress in rice remain uncertain. Here, we identified the KSL family of 19 species by domain analysis and grouped 97 KSL family proteins into three categories. Collinearity analysis of KSLs among Poaceae indicated that the KSL gene may independently evolve and OsKSL1 and OsKSL4 likely play a significant role in the evolutionary process. Tissue expression analysis showed that two-thirds of OsKSLs were expressed in various tissues, whereas OsKSL3 and OsKSL5 were specifically expressed in the root and OsKSL4 in the leaf. Based on the fact that OsKSL2 participates in the biosynthesis of gibberellins and promoter analysis, we detected the gene expression profiles of OsKSLs under hormone treatments (GA, PAC, and ABA) and abiotic stresses (darkness and submergence). The qRT-PCR results demonstrated that OsKSL1, OsKSL3, and OsKSL4 responded to all of the treatments, meaning that these three genes can be candidate genes for abiotic stress. Our results provide new insights into the function of the KSL family in rice growth and resistance to abiotic stress.
Full article
(This article belongs to the Special Issue Advance in Plant Abiotic Stress)
►▼
Show Figures
Figure 1
Open AccessReview
A Comprehensive Review of Reactive Flame Retardants for Polyurethane Materials: Current Development and Future Opportunities in an Environmentally Friendly Direction
by
Paulina Parcheta-Szwindowska, Julia Habaj, Izabela Krzemińska and Janusz Datta
Int. J. Mol. Sci. 2024, 25(10), 5512; https://doi.org/10.3390/ijms25105512 (registering DOI) - 18 May 2024
Abstract
Polyurethanes are among the most significant types of polymers in development; these materials are used to produce construction products intended for work in various conditions. Nowadays, it is important to develop methods for fire load reduction by using new kinds of additives or
[...] Read more.
Polyurethanes are among the most significant types of polymers in development; these materials are used to produce construction products intended for work in various conditions. Nowadays, it is important to develop methods for fire load reduction by using new kinds of additives or monomers containing elements responsible for materials' fire resistance. Currently, additive antipyrines or reactive flame retardants can be used during polyurethane material processing. The use of additives usually leads to the migration or volatilization of the additive to the surface of the material, which causes the loss of the resistance and aesthetic values of the product. Reactive flame retardants form compounds containing special functional groups that can be chemically bonded with monomers during polymerization, which can prevent volatilization or migration to the surface of the material. In this study, reactive flame retardants are compared. Their impacts on polyurethane flame retardancy, combustion mechanism, and environment are described.
Full article
(This article belongs to the Special Issue Advanced Flame Retardant Polymeric Materials 2.0)
►▼
Show Figures
Graphical abstract
Open AccessArticle
The Impact of the IL-10 Gene Polymorphism on mRNA Expression and IL-10 Serum Concentration in Polish Lupus Patients
by
Agnieszka Żak-Gołąb, Paweł Cieślik, Urszula Siekiera, Dariusz Kuśmierz, Antoni Hrycek and Michał Holecki
Int. J. Mol. Sci. 2024, 25(10), 5511; https://doi.org/10.3390/ijms25105511 (registering DOI) - 18 May 2024
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by the production of autoantibodies against a lot of nuclear components. Despite many studies on the genetic background of this disease, the pathogenesis remains unclear. The aim of the study is to comprehensively
[...] Read more.
Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by the production of autoantibodies against a lot of nuclear components. Despite many studies on the genetic background of this disease, the pathogenesis remains unclear. The aim of the study is to comprehensively evaluate the polymorphism of the IL-10 promoter gene, its mRNA expression, and the serum IL-10 concentration of SLE female patients and females age-matched controls. Analyzing the association between the level of the tested cytokine and the polymorphism genotype-1082; -819; -592, we found statistically higher serum IL-10 levels in SLE patients compared to in healthy controls (11.9 ± 2.2 pg/mL vs. 9.4 ± 1.7 pg/mL, accordingly; p < 0.0001). We did not find statistically significant differences in the gene polymorphism of IL-10 among SLE patients and controls. The most significant observation derived from our study is that IL-10 mRNA transcripts are upregulated in SLE patients compared to in healthy controls (p < 0.0001). According to our results, the presence of the IL-10 genetic polymorphism has no clinical significance for the development of SLE, and subsequent differences in mRNA and IL-10 concentration results from the influence of other factors which should be the subject of further research.
Full article
(This article belongs to the Special Issue Immunopathogenesis and Novel Therapeutics Strategies of Systemic Lupus Erythematosus 2.0)
Open AccessArticle
Determination of Post-Fermentation Waste from Fermented Vegetables as Potential Substitutes for Preservatives in o/w Emulsion
by
Anna Herman, Olga Matulewicz, Eliza Korzeniowska and Andrzej Przemysław Herman
Int. J. Mol. Sci. 2024, 25(10), 5510; https://doi.org/10.3390/ijms25105510 (registering DOI) - 18 May 2024
Abstract
Post-fermentation wastes are rich sources of various biologically active compounds with antimicrobial activity, whose potential is not being fully exploited. One of the possible applications of post-fermentation waste may be its use as a natural preservative that effectively combats pathogens found in formulations.
[...] Read more.
Post-fermentation wastes are rich sources of various biologically active compounds with antimicrobial activity, whose potential is not being fully exploited. One of the possible applications of post-fermentation waste may be its use as a natural preservative that effectively combats pathogens found in formulations. The study aims included the following: (1) compare the antimicrobial and antioxidant activity of fermented vegetable extracts (FVEs), (2) examine the inhibition of cosmetic-borne pathogens by FVEs, and (3) estimate the preservative effectiveness of FVEs in o/w emulsions. It was found that fermented white cabbage, cucumber, celery, and the mixture of fermented white cabbage, cucumber, and celery (1:1:1) showed antibacterial and antifungal activity against all the tested reference microbial strains. The addition of fermented cucumber, celery, and the mixture of fermented white cabbage, cucumber, and celery (1:1:1) to the o/w emulsion fulfilled criterion A of the preservative effectiveness test for S. aureus, E. coli, and A. brasiliensis, but did not fulfill the criterion for P. aeruginosa and C. albicans. The tested FVEs have comparable activity to inhibit pathogens in o/w emulsion as sodium benzoate. The results of our study prove that FVEs can be valuable raw materials supporting the preservative system, which, in turn, can significantly reduce the concentration of preservatives used in o/w emulsion.
Full article
(This article belongs to the Special Issue Investigation of Natural Products as Sources of Bioactive Molecules)
►▼
Show Figures
Figure 1
Open AccessArticle
Profiling of Early Immune Responses to Vaccination Using THP-1-Derived Dendritic Cells
by
Lei Ye, Ping Li, Mingzhe Wang, Feng Wu, Sanyang Han and Lan Ma
Int. J. Mol. Sci. 2024, 25(10), 5509; https://doi.org/10.3390/ijms25105509 (registering DOI) - 18 May 2024
Abstract
The COVID-19 pandemic has made assessing vaccine efficacy more challenging. Besides neutralizing antibody assays, systems vaccinology studies use omics technology to reveal immune response mechanisms and identify gene signatures in human peripheral blood mononuclear cells (PBMCs). However, due to their low proportion in
[...] Read more.
The COVID-19 pandemic has made assessing vaccine efficacy more challenging. Besides neutralizing antibody assays, systems vaccinology studies use omics technology to reveal immune response mechanisms and identify gene signatures in human peripheral blood mononuclear cells (PBMCs). However, due to their low proportion in PBMCs, profiling the immune response signatures of dendritic cells (DCs) is difficult. Here, we develop a predictive model for evaluating early immune responses in dendritic cells. We establish a THP-1-derived dendritic cell (TDDC) model and stimulate their maturation in vitro with an optimal dose of attenuated yellow fever 17D (YF-17D). Transcriptomic analysis reveals that type I interferon (IFN-I)-induced immunity plays a key role in dendritic cells. IFN-I regulatory biomarkers (IRF7, SIGLEC1) and IFN-I-inducible biomarkers (IFI27, IFI44, IFIT1, IFIT3, ISG15, MX1, OAS2, OAS3) are identified and validated in vitro and in vivo. Furthermore, we apply this TDDC approach to various types of vaccines, providing novel insights into their early immune response signatures and their heterogeneity in vaccine recipients. Our findings suggest that a standardizable TDDC model is a promising predictive approach to assessing early immunity in DCs. Further research into vaccine efficacy assessment approaches on various types of immune cells could lead to a systemic regimen for vaccine development in the future.
Full article
(This article belongs to the Special Issue Recent Advances in Molecular Materials and Biomedicine)
►▼
Show Figures
Figure 1
Open AccessArticle
LPA3 Receptor Phosphorylation Sites: Roles in Signaling and Internalization
by
K. Helivier Solís, M. Teresa Romero-Ávila, Ruth Rincón-Heredia and J. Adolfo García-Sáinz
Int. J. Mol. Sci. 2024, 25(10), 5508; https://doi.org/10.3390/ijms25105508 (registering DOI) - 18 May 2024
Abstract
Lysophosphatidic acid (LPA) type 3 (LPA3) receptor mutants were generated in which the sites detected phosphorylated were substituted by non-phosphorylatable amino acids. Substitutions were made in the intracellular loop 3 (IL3 mutant), the carboxyl terminus (Ctail), and both domains (IL3/Ctail). The
[...] Read more.
Lysophosphatidic acid (LPA) type 3 (LPA3) receptor mutants were generated in which the sites detected phosphorylated were substituted by non-phosphorylatable amino acids. Substitutions were made in the intracellular loop 3 (IL3 mutant), the carboxyl terminus (Ctail), and both domains (IL3/Ctail). The wild-type (WT) receptor and the mutants were expressed in T-REx HEK293 cells, and the consequences of the substitutions were analyzed employing different functional parameters. Agonist- and LPA-mediated receptor phosphorylation was diminished in the IL3 and Ctail mutants and essentially abolished in the IL3/Ctail mutant, confirming that the main phosphorylation sites are present in both domains and their role in receptor phosphorylation eliminated by substitution and distributed in both domains. The WT and mutant receptors increased intracellular calcium and ERK 1/2 phosphorylation in response to LPA and PMA. The agonist, Ki16425, diminished baseline intracellular calcium, which suggests some receptor endogenous activity. Similarly, baseline ERK1/2 phosphorylation was diminished by Ki16425. An increase in baseline ERK phosphorylation was detected in the IL3/Ctail mutant. LPA and PMA-induced receptor interaction with β-arrestin 2 and LPA3 internalization were severely diminished in cells expressing the mutants. Mutant-expressing cells also exhibit increased baseline proliferation and response to different stimuli, which were inhibited by the antagonist Ki16425, suggesting a role of LPA receptors in this process. Migration in response to different attractants was markedly increased in the Ctail mutant, which the Ki16425 antagonist also attenuated. Our data experimentally show that receptor phosphorylation in the distinct domains is relevant for LPA3 receptor function
Full article
(This article belongs to the Section Molecular Pharmacology)
►▼
Show Figures
Graphical abstract
Open AccessReview
Long Noncoding RNA MALAT1: Salt-Sensitive Hypertension
by
Mohd Mabood Khan and Annet Kirabo
Int. J. Mol. Sci. 2024, 25(10), 5507; https://doi.org/10.3390/ijms25105507 (registering DOI) - 18 May 2024
Abstract
Hypertension stands as the leading global cause of mortality, affecting one billion individuals and serving as a crucial risk indicator for cardiovascular morbidity and mortality. Elevated salt intake triggers inflammation and hypertension by activating antigen-presenting cells (APCs). We found that one of the
[...] Read more.
Hypertension stands as the leading global cause of mortality, affecting one billion individuals and serving as a crucial risk indicator for cardiovascular morbidity and mortality. Elevated salt intake triggers inflammation and hypertension by activating antigen-presenting cells (APCs). We found that one of the primary reasons behind this pro-inflammatory response is the epithelial sodium channel (ENaC), responsible for transporting sodium ions into APCs and the activation of NADPH oxidase, leading to increased oxidative stress. Oxidative stress increases lipid peroxidation and the formation of pro-inflammatory isolevuglandins (IsoLG). Long noncoding RNAs (lncRNAs) play a crucial role in regulating gene expression, and MALAT1, broadly expressed across cell types, including blood vessels and inflammatory cells, is also associated with inflammation regulation. In hypertension, the decreased transcriptional activity of nuclear factor erythroid 2-related factor 2 (Nrf2 or Nfe2l2) correlates with heightened oxidative stress in APCs and impaired control of various antioxidant genes. Kelch-like ECH-associated protein 1 (Keap1), an intracellular inhibitor of Nrf2, exhibits elevated levels of hypertension. Sodium, through an increase in Sp1 transcription factor binding at its promoter, upregulates MALAT1 expression. Silencing MALAT1 inhibits sodium-induced Keap1 upregulation, facilitating the nuclear translocation of Nrf2 and subsequent antioxidant gene transcription. Thus, MALAT1, acting via the Keap1-Nrf2 pathway, modulates antioxidant defense in hypertension. This review explores the potential role of the lncRNA MALAT1 in controlling the Keap1-Nrf2-antioxidant defense pathway in salt-induced hypertension. The inhibition of MALAT1 holds therapeutic potential for the progression of salt-induced hypertension and cardiovascular disease (CVD).
Full article
(This article belongs to the Special Issue Molecular Pharmacology of Cardiovascular Disease)
►▼
Show Figures
Figure 1
Open AccessArticle
De Novo Antimicrobial Peptide Design with Feedback Generative Adversarial Networks
by
Michaela Areti Zervou, Effrosyni Doutsi, Yannis Pantazis and Panagiotis Tsakalides
Int. J. Mol. Sci. 2024, 25(10), 5506; https://doi.org/10.3390/ijms25105506 (registering DOI) - 18 May 2024
Abstract
Antimicrobial peptides (AMPs) are promising candidates for new antibiotics due to their broad-spectrum activity against pathogens and reduced susceptibility to resistance development. Deep-learning techniques, such as deep generative models, offer a promising avenue to expedite the discovery and optimization of AMPs. A remarkable
[...] Read more.
Antimicrobial peptides (AMPs) are promising candidates for new antibiotics due to their broad-spectrum activity against pathogens and reduced susceptibility to resistance development. Deep-learning techniques, such as deep generative models, offer a promising avenue to expedite the discovery and optimization of AMPs. A remarkable example is the Feedback Generative Adversarial Network (FBGAN), a deep generative model that incorporates a classifier during its training phase. Our study aims to explore the impact of enhanced classifiers on the generative capabilities of FBGAN. To this end, we introduce two alternative classifiers for the FBGAN framework, both surpassing the accuracy of the original classifier. The first classifier utilizes the k-mers technique, while the second applies transfer learning from the large protein language model Evolutionary Scale Modeling 2 (ESM2). Integrating these classifiers into FBGAN not only yields notable performance enhancements compared to the original FBGAN but also enables the proposed generative models to achieve comparable or even superior performance to established methods such as AMPGAN and HydrAMP. This achievement underscores the effectiveness of leveraging advanced classifiers within the FBGAN framework, enhancing its computational robustness for AMP de novo design and making it comparable to existing literature.
Full article
(This article belongs to the Special Issue Molecular Advances in Bioinformatics Analysis of Protein Properties)
►▼
Show Figures
Figure 1
Open AccessArticle
Phenotypic Variability in Novel Doublecortin Gene Variants Associated with Subcortical Band Heterotopia
by
Radha Procopio, Francesco Fortunato, Monica Gagliardi, Mariagrazia Talarico, Ilaria Sammarra, Maria Chiara Sarubbi, Donatella Malanga, Grazia Annesi and Antonio Gambardella
Int. J. Mol. Sci. 2024, 25(10), 5505; https://doi.org/10.3390/ijms25105505 (registering DOI) - 18 May 2024
Abstract
Doublecortin, encoded by the DCX gene, plays a crucial role in the neuronal migration process during brain development. Pathogenic variants of the DCX gene are the major causes of the “lissencephaly (LIS) spectrum”, which comprehends a milder phenotype like Subcortical Band Heterotopia (SBH)
[...] Read more.
Doublecortin, encoded by the DCX gene, plays a crucial role in the neuronal migration process during brain development. Pathogenic variants of the DCX gene are the major causes of the “lissencephaly (LIS) spectrum”, which comprehends a milder phenotype like Subcortical Band Heterotopia (SBH) in heterozygous female subjects. We performed targeted sequencing in three unrelated female cases with SBH. We identified three DCX-related variants: a novel missense (c.601A>G: p.Lys201Glu), a novel nonsense (c.210C>G: p.Tyr70*), and a previously identified nonsense (c.907C>T: p.Arg303*) variant. The novel c.601A>G: p.Lys201Glu variant shows a mother–daughter transmission pattern across four generations. The proband exhibits focal epilepsy and achieved seizure freedom with a combination of oxcarbazepine and levetiracetam. All other affected members have no history of epileptic seizures. Brain MRIs of the affected members shows predominant fronto-central SBH with mixed pachygyria on the overlying cortex. The two nonsense variants were identified in two unrelated probands with SBH, severe drug-resistant epilepsy and intellectual disability. These novel DCX variants further expand the genotypic–phenotypic correlations of lissencephaly spectrum disorders. Our documented phenotypic descriptions of three unrelated families provide valuable insights and stimulate further discussions on DCX-SBH cases.
Full article
(This article belongs to the Special Issue Genetic Variants in Neurological and Psychiatric Diseases)
►▼
Show Figures
Figure 1
Open AccessCommunication
Unlocking New Avenues: Solid-State Synthesis of Molecularly Imprinted Polymers
by
Bogdan-Cezar Iacob, Andreea Elena Bodoki, Diogo Filipe Da Costa Carvalho, Antonio Augusto Serpa Paulino, Lucian Barbu-Tudoran and Ede Bodoki
Int. J. Mol. Sci. 2024, 25(10), 5504; https://doi.org/10.3390/ijms25105504 (registering DOI) - 18 May 2024
Abstract
Molecularly imprinted polymers (MIPs) are established artificial molecular recognition platforms with tailored selectivity towards a target molecule, whose synthesis and functionality are highly influenced by the nature of the solvent employed in their synthesis. Steps towards the “greenification” of molecular imprinting technology (MIT)
[...] Read more.
Molecularly imprinted polymers (MIPs) are established artificial molecular recognition platforms with tailored selectivity towards a target molecule, whose synthesis and functionality are highly influenced by the nature of the solvent employed in their synthesis. Steps towards the “greenification” of molecular imprinting technology (MIT) has already been initiated by the elaboration of green MIT principles; developing MIPs in a solvent-free environment may not only offer an eco-friendly alternative, but could also significantly influence the affinity and expected selectivity of the resulting binding sites. In the current study the first solvent-free mechanochemical synthesis of MIPs via liquid-assisted grinding (LAG) is reported. The successful synthesis of the imprinted polymer was functionally demonstrated by measuring its template rebinding capacity and the selectivity of the molecular recognition process in comparison with the ones obtained by the conventional, non-covalent molecular imprinting process in liquid media. The results demonstrated similar binding capacities towards the template molecule and superior chemoselectivity compared to the solution-based MIP synthesis method. The adoption of green chemistry principles with all their inherent advantages in the synthesis of MIPs may not only be able to alleviate the potential environmental and health concerns associated with their analytical (e.g., selective adsorbents) and biomedical (e.g., drug carriers or reservoirs) applications, but might also offer a conceptual change in molecular imprinting technology.
Full article
(This article belongs to the Special Issue Biomimetic Materials Applied in the Analytical and Biomedical Fields)
►▼
Show Figures
Figure 1
Open AccessReview
Therapeutic Effects of Anti-Inflammatory and Anti-Oxidant Nutritional Supplementation in Retinal Ischemic Diseases
by
Deokho Lee, Zhongjie Fu, Ann Hellstrom and Lois E. H. Smith
Int. J. Mol. Sci. 2024, 25(10), 5503; https://doi.org/10.3390/ijms25105503 (registering DOI) - 18 May 2024
Abstract
Appropriate nutrients are essential for cellular function. Dietary components can alter the risk of systemic metabolic diseases, including cardiovascular diseases, cancer, diabetes, and obesity, and can also affect retinal diseases, including age-related macular degeneration, diabetic retinopathy, and glaucoma. Dietary nutrients have been assessed
[...] Read more.
Appropriate nutrients are essential for cellular function. Dietary components can alter the risk of systemic metabolic diseases, including cardiovascular diseases, cancer, diabetes, and obesity, and can also affect retinal diseases, including age-related macular degeneration, diabetic retinopathy, and glaucoma. Dietary nutrients have been assessed for the prevention or treatment of retinal ischemic diseases and the diseases of aging. In this article, we review clinical and experimental evidence concerning the potential of some nutritional supplements to prevent or treat retinal ischemic diseases and provide further insights into the therapeutic effects of nutritional supplementation on retinopathies. We will review the roles of nutrients in preventing or protecting against retinal ischemic diseases.
Full article
(This article belongs to the Special Issue Emerging Roles of Inflammation in Retinal and Optic Nerve Pathologies)
►▼
Show Figures
Figure 1
Open AccessReview
Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression
by
Ron Mizrahi and Oren Ostersetzer-Biran
Int. J. Mol. Sci. 2024, 25(10), 5502; https://doi.org/10.3390/ijms25105502 - 17 May 2024
Abstract
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U
[...] Read more.
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U deaminations) and both ‘cis’- and ‘trans’-splicing events. These essential processing steps rely on the activities of a large set of nuclear-encoded factors. RNA helicases serve as key players in RNA metabolism, participating in the regulation of transcription, mRNA processing and translation. They unwind RNA secondary structures and facilitate the formation of ribonucleoprotein complexes crucial for various stages of gene expression. Furthermore, RNA helicases are involved in RNA metabolism by modulating pre-mRNA maturation, transport and degradation processes. These enzymes are, therefore, pivotal in RNA quality-control mechanisms, ensuring the fidelity and efficiency of RNA processing and turnover in plant mitochondria. This review summarizes the significant roles played by helicases in regulating the highly dynamic processes of mitochondrial transcription, RNA processing and translation in plants. We further discuss recent advancements in understanding how dysregulation of mitochondrial RNA helicases affects the splicing of organellar genes, leading to respiratory dysfunctions, and consequently, altered growth, development and physiology of land plants.
Full article
(This article belongs to the Special Issue Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression in Plants)
Open AccessArticle
Transcriptome Analysis of Sesame (Sesamum indicum L.) Reveals the LncRNA and mRNA Regulatory Network Responding to Low Nitrogen Stress
by
Pengyu Zhang, Feng Li, Yuan Tian, Dongyong Wang, Jinzhou Fu, Yasi Rong, Yin Wu, Tongmei Gao and Haiyang Zhang
Int. J. Mol. Sci. 2024, 25(10), 5501; https://doi.org/10.3390/ijms25105501 - 17 May 2024
Abstract
Nitrogen is one of the important factors restricting the development of sesame planting and industry in China. Cultivating sesame varieties tolerant to low nitrogen is an effective way to solve the problem of crop nitrogen deficiency. To date, the mechanism of low nitrogen
[...] Read more.
Nitrogen is one of the important factors restricting the development of sesame planting and industry in China. Cultivating sesame varieties tolerant to low nitrogen is an effective way to solve the problem of crop nitrogen deficiency. To date, the mechanism of low nitrogen tolerance in sesame has not been elucidated at the transcriptional level. In this study, two sesame varieties Zhengzhi HL05 (ZZ, nitrogen efficient) and Burmese prolific (MD, nitrogen inefficient) in low nitrogen were used for RNA-sequencing. A total of 3964 DEGs (differentially expressed genes) and 221 DELs (differentially expressed lncRNAs) were identified in two sesame varieties at 3d and 9d after low nitrogen stress. Among them, 1227 genes related to low nitrogen tolerance are mainly located in amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and participate in the process of transporter activity and antioxidant activity. In addition, a total of 209 pairs of lncRNA-mRNA were detected, including 21 pairs of trans and 188 cis. WGCNA (weighted gene co-expression network analysis) analysis divided the obtained genes into 29 modules; phenotypic association analysis identified three low-nitrogen response modules; through lncRNA-mRNA co-expression network, a number of hub genes and cis/trans-regulatory factors were identified in response to low-nitrogen stress including GS1-2 (glutamine synthetase 1–2), PAL (phenylalanine ammonia-lyase), CHS (chalcone synthase, CHS), CAB21 (chlorophyll a-b binding protein 21) and transcription factors MYB54, MYB88 and NAC75 and so on. As a trans regulator, lncRNA MSTRG.13854.1 affects the expression of some genes related to low nitrogen response by regulating the expression of MYB54, thus responding to low nitrogen stress. Our research is the first to provide a more comprehensive understanding of DEGs involved in the low nitrogen stress of sesame at the transcriptome level. These results may reveal insights into the molecular mechanisms of low nitrogen tolerance in sesame and provide diverse genetic resources involved in low nitrogen tolerance research.
Full article
(This article belongs to the Section Molecular Genetics and Genomics)
►▼
Show Figures
Figure 1
Journal Menu
► ▼ Journal Menu-
- IJMS Home
- Aims & Scope
- Editorial Board
- Reviewer Board
- Topical Advisory Panel
- Instructions for Authors
- Special Issues
- Topics
- Sections & Collections
- Article Processing Charge
- Indexing & Archiving
- Most Cited & Viewed
- Journal Statistics
- Journal History
- Journal Awards
- Society Collaborations
- Conferences
- Editorial Office
Journal Browser
► ▼ Journal Browser-
arrow_forward_ios
Forthcoming issue
arrow_forward_ios Current issue - Vol. 25 (2024)
- Vol. 24 (2023)
- Vol. 23 (2022)
- Vol. 22 (2021)
- Vol. 21 (2020)
- Vol. 20 (2019)
- Vol. 19 (2018)
- Vol. 18 (2017)
- Vol. 17 (2016)
- Vol. 16 (2015)
- Vol. 15 (2014)
- Vol. 14 (2013)
- Vol. 13 (2012)
- Vol. 12 (2011)
- Vol. 11 (2010)
- Vol. 10 (2009)
- Vol. 9 (2008)
- Vol. 8 (2007)
- Vol. 7 (2006)
- Vol. 6 (2005)
- Vol. 5 (2004)
- Vol. 4 (2003)
- Vol. 3 (2002)
- Vol. 2 (2001)
- Vol. 1 (2000)
Highly Accessed Articles
Latest Books
E-Mail Alert
News
Topics
Topic in
Biomedicines, Cells, IJMS, Life, Oxygen
Oxidative Stress and Inflammation, 2nd Volume
Topic Editors: Mohamad Allaw, Ines Castangia, Maria Letizia Manca, Matteo Perra, Amparo NacherDeadline: 31 May 2024
Topic in
BioChem, Biomedicines, Biomolecules, IJMS, Metabolites, Molecules
Natural Products in Prevention and Therapy of Metabolic Syndrome
Topic Editors: Jianbo Wan, Ligen LinDeadline: 30 June 2024
Topic in
Cells, Diseases, Healthcare, IJMS, Vaccines
Inflammation: The Cause of all Diseases 2.0
Topic Editors: Vasso Apostolopoulos, Jack Feehan, Vivek P. ChavdaDeadline: 31 July 2024
Topic in
Biomedicines, CIMB, Endocrines, IJMS, JMP, Life, Reprod. Med.
Pathogenesis of Pregnancy-Related Complications 2.0
Topic Editors: Ilona Hromadnikova, Katerina KotlabovaDeadline: 31 August 2024
Conferences
Special Issues
Special Issue in
IJMS
Pharmacogenetics and Personalized Medicine 3.0
Guest Editors: José A. Riancho, Gloria RavegniniDeadline: 20 May 2024
Special Issue in
IJMS
Molecular Mechanisms of Angiogenesis and Cancer
Guest Editor: Vijay AvinDeadline: 30 May 2024
Special Issue in
IJMS
Mitochondrial Dysfunction in Neurodegenerative Diseases
Guest Editors: Ashu Johri, Abhishek ChandraDeadline: 10 June 2024
Special Issue in
IJMS
23rd Anniversary of IJMS: Advances in Biochemistry
Guest Editor: Claudiu T. SupuranDeadline: 30 June 2024
Topical Collections
Topical Collection in
IJMS
Feature Papers in Bioactives and Nutraceuticals
Collection Editor: Maurizio Battino
Topical Collection in
IJMS
State-of-the-Art Molecular Microbiology in Poland
Collection Editors: Alicja Wegrzyn, Satish Raina
Topical Collection in
IJMS
Computational, Structural and Spectroscopic Studies of Enzyme Mechanisms, Inhibition and Dynamics
Collection Editor: Christo Christov