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
Increased H19/miR-675 Expression in Adult T-Cell Leukemia Is Associated with a Unique Notch Signature Pathway
Int. J. Mol. Sci. 2024, 25(10), 5130; https://doi.org/10.3390/ijms25105130 (registering DOI) - 8 May 2024
Abstract
The Notch pathway is a key cancer driver and is important in tumor progression. Early research suggested that Notch activity was highly dependent on the expression of the intracellular cleaved domain of Notch-1 (NICD). However, recent insights into Notch signaling reveal the presence
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The Notch pathway is a key cancer driver and is important in tumor progression. Early research suggested that Notch activity was highly dependent on the expression of the intracellular cleaved domain of Notch-1 (NICD). However, recent insights into Notch signaling reveal the presence of Notch pathway signatures, which may vary depending on different cancer types and tumor microenvironments. Herein, we perform a comprehensive investigation of the Notch signaling pathway in adult T-cell leukemia (ATL) primary patient samples. Using gene arrays, we demonstrate that the Notch pathway is constitutively activated in ATL patient samples. Furthermore, the activation of Notch in ATL cells remains elevated irrespective of the presence of activating mutations in Notch itself or its repressor, FBXW7, and that ATL cells are dependent upon Notch-1 expression for proliferation and survival. We demonstrate that ATL cells exhibit the expression of pivotal Notch-related genes, including notch-1, hes1, c-myc, H19, and hes4, thereby defining a critical Notch signature associated with ATL disease. Finally, we demonstrate that lncRNA H19 is highly expressed in ATL patient samples and ATL cells and contributes to Notch signaling activation. Collectively, our results shed further light on the Notch pathway in ATL leukemia and reveal new therapeutic approaches to inhibit Notch activation in ATL cells.
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(This article belongs to the Special Issue Notch Signaling Pathways)
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Acetate Alleviates Gut Microbiota Depletion-Induced Retardation of Skeletal Muscle Growth and Development in Young Mice
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Guitao Yang, Jinwei Zhang, Yan Liu, Jing Sun, Liangpeng Ge, Lu Lu, Keren Long, Xuewei Li, Dengfeng Xu and Jideng Ma
Int. J. Mol. Sci. 2024, 25(10), 5129; https://doi.org/10.3390/ijms25105129 (registering DOI) - 8 May 2024
Abstract
The normal growth and development of skeletal muscle is essential for the health of the body. The regulation of skeletal muscle by intestinal microorganisms and their metabolites has been continuously demonstrated. Acetate is the predominant short-chain fatty acids synthesized by gut microbiota through
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The normal growth and development of skeletal muscle is essential for the health of the body. The regulation of skeletal muscle by intestinal microorganisms and their metabolites has been continuously demonstrated. Acetate is the predominant short-chain fatty acids synthesized by gut microbiota through the fermentation of dietary fiber; however, the underlying molecular mechanisms governing the interaction between acetate and skeletal muscle during the rapid growth stage remains to be further elucidated. Herein, specific pathogen-free (SPF) mice, germ-free (GF) mice, and germ-free mice supplemented with sodium acetate (GS) were used to evaluate the effects of acetate on the skeletal muscle growth and development of young mice with gut microbiota deficiency. We found that the concentration of serum acetate, body mass gain, succinate dehydrogenase activity, and expression of the myogenesis maker gene of skeletal muscle in the GS group were higher than those in the GF group, following sodium acetate supplementation. Furthermore, the transcriptome analysis revealed that acetate activated the biological processes that regulate skeletal muscle growth and development in the GF group, which are otherwise inhibited due to a gut microbiota deficiency. The in vitro experiment showed that acetate up-regulated Gm16062 to promote skeletal muscle cell differentiation. Overall, our findings proved that acetate promotes skeletal muscle growth and development in young mice via increasing Gm16062 expression.
Full article
(This article belongs to the Section Molecular Microbiology)
Open AccessArticle
The Response of Hormones, Reactive Oxygen Species and Nitric Oxide in the Polyethylene-Glycol-Promoted, Salt–Alkali-Stress-Induced Embryo Germination of Sorbus pohuashanensis
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Xiaodong Wang, Hailong Shen and Ling Yang
Int. J. Mol. Sci. 2024, 25(10), 5128; https://doi.org/10.3390/ijms25105128 (registering DOI) - 8 May 2024
Abstract
Polyethylene glycol can abrogate plant seed dormancy and alleviate salt–alkali stress damage to plants, but its role in embryonic dormancy abrogation and germination in Sorbus pohuashanensis is not yet clear. The mechanism by which polyethylene glycol promotes the release of embryonic dormancy may
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Polyethylene glycol can abrogate plant seed dormancy and alleviate salt–alkali stress damage to plants, but its role in embryonic dormancy abrogation and germination in Sorbus pohuashanensis is not yet clear. The mechanism by which polyethylene glycol promotes the release of embryonic dormancy may be related to the synthesis and metabolism of endogenous hormones, reactive oxygen species and reactive nitrogen. In this article, germination in indoor culture dishes was used, and the most suitable conditions for treating S. pohuashanensis embryos, with polyethylene glycol (PEG) and sodium carbonate (Na2CO3), were selected. Germination was observed and recorded, and related physiological indicators such as endogenous hormones, reactive oxygen species and reactive nitrogen were measured and analyzed to elucidate the mechanism of polyethylene glycol in alleviating salt–alkali stress in S. pohuashanensis embryos. The results showed that soaking seeds in 5% PEG for 5 days is the best condition to promote germination, which can increase the germination rate of embryos under salt–alkali stress by 1–2 times and improve indicators such as germination speed and the germination index. Polyethylene glycol led to an increase in gibberellin (GA), indole-3-acetic acid (IAA), ethylene (ETH), cytokinin (CTK), nitric oxide (NO), soluble protein and soluble sugar in the embryos under salt–alkali stress; increased activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), nitrate reductase (NR) and nitric oxide synthase (NOS) in the embryos; a reduction in the accumulation of abscisic acid (ABA), hydrogen peroxide (H2O2) and malondialdehyde (MDA). Therefore, it is suggested that the inhibitory effect of polyethylene glycol on the salt–alkali-stress-induced germination of S. pohuashanensis embryos is closely related to the response of endogenous hormones, reactive oxygen species and nitric oxide signalling.
Full article
(This article belongs to the Special Issue Nitric Oxide Signalling in Plants)
Open AccessCase Report
New Case of Spinocerebellar Ataxia, Autosomal Recessive 4, Due to VPS13D Variants
by
Denis Kistol, Polina Tsygankova, Fatima Bostanova, Maria Orlova and Ekaterina Zakharova
Int. J. Mol. Sci. 2024, 25(10), 5127; https://doi.org/10.3390/ijms25105127 (registering DOI) - 8 May 2024
Abstract
Movement disorders such as bradykinesia, tremor, dystonia, chorea, and myoclonus most often arise in several neurodegenerative diseases with basal ganglia and white matter involvement. While the pathophysiology of these disorders remains incompletely understood, dysfunction of the basal ganglia and related brain regions is
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Movement disorders such as bradykinesia, tremor, dystonia, chorea, and myoclonus most often arise in several neurodegenerative diseases with basal ganglia and white matter involvement. While the pathophysiology of these disorders remains incompletely understood, dysfunction of the basal ganglia and related brain regions is often implicated. The VPS13D gene, part of the VPS13 family, has emerged as a crucial player in neurological pathology, implicated in diverse phenotypes ranging from movement disorders to Leigh syndrome. We present a clinical case of VPS13D-associated disease with two variants in the VPS13D gene in an adult female. This case contributes to our evolving understanding of VPS13D-related diseases and underscores the importance of genetic screening in diagnosing and managing such conditions.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Prediction of Drug-Target Affinity Using Attention Neural Network
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Xin Tang, Xiujuan Lei and Yuchen Zhang
Int. J. Mol. Sci. 2024, 25(10), 5126; https://doi.org/10.3390/ijms25105126 (registering DOI) - 8 May 2024
Abstract
Studying drug-target interactions (DTIs) is the foundational and crucial phase in drug discovery. Biochemical experiments, while being the most reliable method for determining drug-target affinity (DTA), are time-consuming and costly, making it challenging to meet the current demands for swift and efficient drug
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Studying drug-target interactions (DTIs) is the foundational and crucial phase in drug discovery. Biochemical experiments, while being the most reliable method for determining drug-target affinity (DTA), are time-consuming and costly, making it challenging to meet the current demands for swift and efficient drug development. Consequently, computational DTA prediction methods have emerged as indispensable tools for this research. In this article, we propose a novel deep learning algorithm named GRA-DTA, for DTA prediction. Specifically, we introduce Bidirectional Gated Recurrent Unit (BiGRU) combined with a soft attention mechanism to learn target representations. We employ Graph Sample and Aggregate (GraphSAGE) to learn drug representation, especially to distinguish the different features of drug and target representations and their dimensional contributions. We merge drug and target representations by an attention neural network (ANN) to learn drug-target pair representations, which are fed into fully connected layers to yield predictive DTA. The experimental results showed that GRA-DTA achieved mean squared error of 0.142 and 0.225 and concordance index reached 0.897 and 0.890 on the benchmark datasets KIBA and Davis, respectively, surpassing the most state-of-the-art DTA prediction algorithms.
Full article
(This article belongs to the Special Issue Molecular Computer Science and Artificial Intelligence for Drug Discovery)
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Open AccessArticle
Unravelling the Function of the Sesquiterpene Cyclase STC3 in the Lifecycle of Botrytis cinerea
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Víctor Coca-Ruiz, Ivonne Suárez, Josefina Aleu, Jesús M. Cantoral, Celedonio González, Carlos Garrido, Nélida Brito and Isidro G. Collado
Int. J. Mol. Sci. 2024, 25(10), 5125; https://doi.org/10.3390/ijms25105125 (registering DOI) - 8 May 2024
Abstract
The genome sequencing of Botrytis cinerea supplies a general overview of the map of genes involved in secondary metabolite synthesis. B. cinerea genomic data reveals that this phytopathogenic fungus has seven sesquiterpene cyclase (Bcstc) genes that encode proteins involved in the
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The genome sequencing of Botrytis cinerea supplies a general overview of the map of genes involved in secondary metabolite synthesis. B. cinerea genomic data reveals that this phytopathogenic fungus has seven sesquiterpene cyclase (Bcstc) genes that encode proteins involved in the farnesyl diphosphate cyclization. Three sesquiterpene cyclases (BcStc1, BcStc5 and BcStc7) are characterized, related to the biosynthesis of botrydial, abscisic acid and (+)-4-epi-eremophilenol, respectively. However, the role of the other four sesquiterpene cyclases (BcStc2, BcStc3, BcStc4 and BcStc6) remains unknown. BcStc3 is a well-conserved protein with homologues in many fungal species, and here, we undertake its functional characterization in the lifecycle of the fungus. A null mutant ΔBcstc3 and an overexpressed–Bcstc3 transformant (OvBcstc3) are generated, and both strains show the deregulation of those other sesquiterpene cyclase-encoding genes (Bcstc1, Bcstc5 and Bcstc7). These results suggest a co-regulation of the expression of the sesquiterpene cyclase gene family in B. cinerea. The phenotypic characterization of both transformants reveals that BcStc3 is involved in oxidative stress tolerance, the production of reactive oxygen species and virulence. The metabolomic analysis allows the isolation of characteristic polyketides and eremophilenols from the secondary metabolism of B. cinerea, although no sesquiterpenes different from those already described are identified.
Full article
(This article belongs to the Special Issue Molecular Analysis of Plant–Pathogen Interaction)
Open AccessArticle
Serum Amyloid A3 Promoter-Luciferase Reporter Mice Are Useful for Early Drug-Induced Nephrotoxicity Detection
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Ayane Kudo, Haruka Osedo, Rahmawati Aisyah, Nao Yazawa, Tolulope Peter Saliu, Kenshu Miyata, Thanutchaporn Kumrungsee and Noriyuki Yanaka
Int. J. Mol. Sci. 2024, 25(10), 5124; https://doi.org/10.3390/ijms25105124 (registering DOI) - 8 May 2024
Abstract
Early detection of drug-induced kidney injury is essential for drug development. In this study, multiple low-dose aristolochic acid (AA) and cisplatin (Cis) injections increased renal mRNA levels of inflammation, fibrosis, and renal tubule injury markers. We applied a serum amyloid A3 (Saa3) promoter-driven
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Early detection of drug-induced kidney injury is essential for drug development. In this study, multiple low-dose aristolochic acid (AA) and cisplatin (Cis) injections increased renal mRNA levels of inflammation, fibrosis, and renal tubule injury markers. We applied a serum amyloid A3 (Saa3) promoter-driven luciferase reporter (Saa3 promoter-luc mice) to these two tubulointerstitial nephritis models and performed in vivo bioluminescence imaging to monitor early renal pathologies. The bioluminescent signals from renal tissues with AA or CIS injections were stronger than those from normal kidney tissues obtained from normal mice. To verify whether the visualized bioluminescence signal was specifically generated by the injured kidney, we performed in vivo bioluminescence analysis after opening the stomachs of Saa3 promoter-luc mice, and the Saa3-mediated bioluminescent signal was specifically detected in the injured kidney. This study showed that Saa3 promoter activity is a potent non-invasive indicator for the early detection of drug-induced nephrotoxicity.
Full article
(This article belongs to the Special Issue Advances in Luciferase)
Open AccessArticle
Curcumin Improves Neurogenesis in Alzheimer’s Disease Mice via the Upregulation of Wnt/β-Catenin and BDNF
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Shengchun Lou, Danfeng Gong, Mengting Yang, Qing Qiu, Jialie Luo and Tingting Chen
Int. J. Mol. Sci. 2024, 25(10), 5123; https://doi.org/10.3390/ijms25105123 (registering DOI) - 8 May 2024
Abstract
Adult neurogenesis in the dentate gyrus (DG) is impaired during Alzheimer’s disease (AD) progression. Curcumin has been reported to reduce cell apoptosis and stimulate neurogenesis. This study aimed to investigate the influence of curcumin on adult neurogenesis in AD mice and its potential
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Adult neurogenesis in the dentate gyrus (DG) is impaired during Alzheimer’s disease (AD) progression. Curcumin has been reported to reduce cell apoptosis and stimulate neurogenesis. This study aimed to investigate the influence of curcumin on adult neurogenesis in AD mice and its potential mechanism. Two-month-old male C57BL/6J mice were injected with soluble β-amyloid (Aβ1–42) using lateral ventricle stereolocalization to establish AD models. An immunofluorescence assay, including bromodeoxyuridine (BrdU), doublecortin (DCX), and neuron-specific nuclear antigen (NeuN), was used to detect hippocampal neurogenesis. Western blot and an enzyme-linked immunosorbent assay (ELISA) were used to test the expression of related proteins and the secretion of brain-derived neurotrophic factor (BDNF). A Morris water maze was used to detect the cognitive function of the mice. Our results showed that curcumin administration (100 mg/kg) rescued the impaired neurogenesis of Aβ1–42 mice, shown as enhanced BrdU+/DCX+ and BrdU+/NeuN+ cells in DG. In addition, curcumin regulated the phosphatidylinositol 3 kinase (PI3K)/protein kinase B (Akt) -mediated glycogen synthase kinase-3β (GSK3β) /Wingless/Integrated (Wnt)/β-catenin pathway and cyclic adenosine monophosphate response element-binding protein (CREB)/BDNF in Aβ1–42 mice. Inhibiting Wnt/β-catenin and depriving BDNF could reverse both the upregulated neurogenesis and cognitive function of curcumin-treated Aβ1–42 mice. In conclusion, our study indicates that curcumin, through targeting PI3K/Akt, regulates GSK3β/Wnt/β-catenin and CREB/BDNF pathways, improving the adult neurogenesis of AD mice.
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(This article belongs to the Section Molecular Pharmacology)
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Open AccessReview
The Vital Role of Melatonin and Its Metabolites in the Neuroprotection and Retardation of Brain Aging
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Georgeta Bocheva, Dimitar Bakalov, Petar Iliev and Radka Tafradjiiska-Hadjiolova
Int. J. Mol. Sci. 2024, 25(10), 5122; https://doi.org/10.3390/ijms25105122 (registering DOI) - 8 May 2024
Abstract
While primarily produced in the pineal gland, melatonin’s influence goes beyond its well-known role in regulating sleep, nighttime metabolism, and circadian rhythms, in the field of chronobiology. A plethora of new data demonstrates melatonin to be a very powerful molecule, being a potent
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While primarily produced in the pineal gland, melatonin’s influence goes beyond its well-known role in regulating sleep, nighttime metabolism, and circadian rhythms, in the field of chronobiology. A plethora of new data demonstrates melatonin to be a very powerful molecule, being a potent ROS/RNS scavenger with anti-inflammatory, immunoregulatory, and oncostatic properties. Melatonin and its metabolites exert multiple beneficial effects in cutaneous and systemic aging. This review is focused on the neuroprotective role of melatonin during aging. Melatonin has an anti-aging capacity, retarding the rate of healthy brain aging and the development of age-related neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, multiple sclerosis, amyotrophic lateral sclerosis, etc. Melatonin, as well as its metabolites, N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK) and N1-acetyl-5-methoxykynuramine (AMK), can reduce oxidative brain damage by shielding mitochondria from dysfunction during the aging process. Melatonin could also be implicated in the treatment of neurodegenerative conditions, by modifying their characteristic low-grade neuroinflammation. It can either prevent the initiation of inflammatory responses or attenuate the ongoing inflammation. Drawing on the current knowledge, this review discusses the potential benefits of melatonin supplementation in preventing and managing cognitive impairment and neurodegenerative diseases.
Full article
(This article belongs to the Special Issue Melatonin and Brain Heath)
Open AccessArticle
Characterizing Glomerular Barrier Dysfunction with Patient-Derived Serum in Glomerulus-on-a-Chip Models: Unveiling New Insights into Glomerulonephritis
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Shin Young Kim, Yun Yeong Choi, Eun Jeong Kwon, Seungwan Seo, Wan Young Kim, Sung Hyuk Park, Seokwoo Park, Ho Jun Chin, Ki Young Na and Sejoong Kim
Int. J. Mol. Sci. 2024, 25(10), 5121; https://doi.org/10.3390/ijms25105121 (registering DOI) - 8 May 2024
Abstract
Glomerulonephritis (GN) is characterized by podocyte injury or glomerular filtration dysfunction, which results in proteinuria and eventual loss of kidney function. Progress in studying the mechanism of GN, and developing an effective therapy, has been limited by the absence of suitable in vitro
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Glomerulonephritis (GN) is characterized by podocyte injury or glomerular filtration dysfunction, which results in proteinuria and eventual loss of kidney function. Progress in studying the mechanism of GN, and developing an effective therapy, has been limited by the absence of suitable in vitro models that can closely recapitulate human physiological responses. We developed a microfluidic glomerulus-on-a-chip device that can recapitulate the physiological environment to construct a functional filtration barrier, with which we investigated biological changes in podocytes and dynamic alterations in the permeability of the glomerular filtration barrier (GFB) on a chip. We also evaluated the potential of GN-mimicking devices as a model for predicting responses to human GN. Glomerular endothelial cells and podocytes successfully formed intact monolayers on opposite sides of the membrane in our chip device. Permselectivity analysis confirmed that the chip was constituted by a functional GFB that could accurately perform differential clearance of albumin and dextran. Reduction in cell viability resulting from damage was observed in all serum-induced GN models. The expression of podocyte-specific marker WT1 was also decreased. Albumin permeability was increased in most models of serum-induced IgA nephropathy (IgAN) and membranous nephropathy (MN). However, sera from patients with minimal change disease (MCD) or lupus nephritis (LN) did not induce a loss of permeability. This glomerulus-on-a-chip system may provide a platform of glomerular cell culture for in vitro GFB in formation of a functional three-dimensional glomerular structure. Establishing a disease model of GN on a chip could accelerate our understanding of pathophysiological mechanisms of glomerulopathy.
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(This article belongs to the Special Issue Molecular Study of Renal Diseases)
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Open AccessArticle
Peposertib, a DNA-PK Inhibitor, Enhances the Anti-Tumor Efficacy of Topoisomerase II Inhibitors in Triple-Negative Breast Cancer Models
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Steffie Revia, Felix Neumann, Julia Jabs, Florian Orio, Christian Sirrenberg, Astrid Zimmermann, Christiane Amendt and Joachim Albers
Int. J. Mol. Sci. 2024, 25(10), 5120; https://doi.org/10.3390/ijms25105120 (registering DOI) - 8 May 2024
Abstract
Triple-negative breast cancer (TNBC) remains the most lethal subtype of breast cancer, characterized by poor response rates to current chemotherapies and a lack of additional effective treatment options. While approximately 30% of patients respond well to anthracycline- and taxane-based standard-of-care chemotherapy regimens, the
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Triple-negative breast cancer (TNBC) remains the most lethal subtype of breast cancer, characterized by poor response rates to current chemotherapies and a lack of additional effective treatment options. While approximately 30% of patients respond well to anthracycline- and taxane-based standard-of-care chemotherapy regimens, the majority of patients experience limited improvements in clinical outcomes, highlighting the critical need for strategies to enhance the effectiveness of anthracycline/taxane-based chemotherapy in TNBC. In this study, we report on the potential of a DNA-PK inhibitor, peposertib, to improve the effectiveness of topoisomerase II (TOPO II) inhibitors, particularly anthracyclines, in TNBC. Our in vitro studies demonstrate the synergistic antiproliferative activity of peposertib in combination with doxorubicin, epirubicin and etoposide in multiple TNBC cell lines. Downstream analysis revealed the induction of ATM-dependent compensatory signaling and p53 pathway activation under combination treatment. These in vitro findings were substantiated by pronounced anti-tumor effects observed in mice bearing subcutaneously implanted tumors. We established a well-tolerated preclinical treatment regimen combining peposertib with pegylated liposomal doxorubicin (PLD) and demonstrated strong anti-tumor efficacy in cell-line-derived and patient-derived TNBC xenograft models in vivo. Taken together, our findings provide evidence that co-treatment with peposertib has the potential to enhance the efficacy of anthracycline/TOPO II-based chemotherapies, and it provides a promising strategy to improve treatment outcomes for TNBC patients.
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(This article belongs to the Special Issue DNA Damage and DNA Repair Pathways in Cancer Development)
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Open AccessReview
Additional Sex Combs-like Family Associated with Epigenetic Regulation
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Nackhyoung Kim, Sukyoung Byun and Soo-Jong Um
Int. J. Mol. Sci. 2024, 25(10), 5119; https://doi.org/10.3390/ijms25105119 (registering DOI) - 8 May 2024
Abstract
The additional sex combs-like (ASXL) family, a mammalian homolog of the additional sex combs (Asx) of Drosophila, has been implicated in transcriptional regulation via chromatin modifications. Abnormal expression of ASXL family genes leads to myelodysplastic syndromes and various types of
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The additional sex combs-like (ASXL) family, a mammalian homolog of the additional sex combs (Asx) of Drosophila, has been implicated in transcriptional regulation via chromatin modifications. Abnormal expression of ASXL family genes leads to myelodysplastic syndromes and various types of leukemia. De novo mutation of these genes also causes developmental disorders. Genes in this family and their neighbor genes are evolutionary conserved in humans and mice. This review provides a comprehensive summary of epigenetic regulations associated with ASXL family genes. Their expression is commonly regulated by DNA methylation at CpG islands preceding transcription starting sites. Their proteins primarily engage in histone tail modifications through interactions with chromatin regulators (PRC2, TrxG, PR-DUB, SRC1, HP1α, and BET proteins) and with transcription factors, including nuclear hormone receptors (RAR, PPAR, ER, and LXR). Histone modifications associated with these factors include histone H3K9 acetylation and methylation, H3K4 methylation, H3K27 methylation, and H2AK119 deubiquitination. Recently, non-coding RNAs have been identified following mutations in the ASXL1 or ASXL3 gene, along with circular ASXLs and microRNAs that regulate ASXL1 expression. The diverse epigenetic regulations linked to ASXL family genes collectively contribute to tumor suppression and developmental processes. Our understanding of ASXL-regulated epigenetics may provide insights into the development of therapeutic epigenetic drugs.
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(This article belongs to the Special Issue New Advances in Epigenetics and Epigenomics)
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Open AccessArticle
The Species Effect: Differential Sphingosine-1-Phosphate Responses in the Bone in Human Versus Mouse
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Kathryn Frost, Jonathan W. Lewis, Simon W. Jones, James R. Edwards, Amy J. Naylor and Helen M. McGettrick
Int. J. Mol. Sci. 2024, 25(10), 5118; https://doi.org/10.3390/ijms25105118 (registering DOI) - 8 May 2024
Abstract
The deterioration of osteoblast-led bone formation and the upregulation of osteoclast-regulated bone resorption are the primary causes of bone diseases, including osteoporosis. Numerous circulating factors play a role in bone homeostasis by regulating osteoblast and osteoclast activity, including the sphingolipid—sphingosine-1-phosphate (S1P). However, to
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The deterioration of osteoblast-led bone formation and the upregulation of osteoclast-regulated bone resorption are the primary causes of bone diseases, including osteoporosis. Numerous circulating factors play a role in bone homeostasis by regulating osteoblast and osteoclast activity, including the sphingolipid—sphingosine-1-phosphate (S1P). However, to date no comprehensive studies have investigated the impact of S1P activity on human and murine osteoblasts and osteoclasts. We observed species-specific responses to S1P in both osteoblasts and osteoclasts, where S1P stimulated human osteoblast mineralisation and reduced human pre-osteoclast differentiation and mineral resorption, thereby favouring bone formation. The opposite was true for murine osteoblasts and osteoclasts, resulting in more mineral resorption and less mineral deposition. Species-specific differences in osteoblast responses to S1P were potentially explained by differential expression of S1P receptor 1. By contrast, human and murine osteoclasts expressed comparable levels of S1P receptors but showed differential expression patterns of the two sphingosine kinase enzymes responsible for S1P production. Ultimately, we reveal that murine models may not accurately represent how human bone cells will respond to S1P, and thus are not a suitable model for exploring S1P physiology or potential therapeutic agents.
Full article
(This article belongs to the Special Issue Sphingolipid Metabolism and Signaling: Role in Health and Diseases)
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Skeletal Muscle Injury in Chronic Kidney Disease—From Histologic Changes to Molecular Mechanisms and to Novel Therapies
by
Kylie Heitman, Matthew S. Alexander and Christian Faul
Int. J. Mol. Sci. 2024, 25(10), 5117; https://doi.org/10.3390/ijms25105117 (registering DOI) - 8 May 2024
Abstract
Chronic kidney disease (CKD) is associated with significant reductions in lean body mass and in the mass of various tissues, including skeletal muscle, which causes fatigue and contributes to high mortality rates. In CKD, the cellular protein turnover is imbalanced, with protein degradation
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Chronic kidney disease (CKD) is associated with significant reductions in lean body mass and in the mass of various tissues, including skeletal muscle, which causes fatigue and contributes to high mortality rates. In CKD, the cellular protein turnover is imbalanced, with protein degradation outweighing protein synthesis, leading to a loss of protein and cell mass, which impairs tissue function. As CKD itself, skeletal muscle wasting, or sarcopenia, can have various origins and causes, and both CKD and sarcopenia share common risk factors, such as diabetes, obesity, and age. While these pathologies together with reduced physical performance and malnutrition contribute to muscle loss, they cannot explain all features of CKD-associated sarcopenia. Metabolic acidosis, systemic inflammation, insulin resistance and the accumulation of uremic toxins have been identified as additional factors that occur in CKD and that can contribute to sarcopenia. Here, we discuss the elevation of systemic phosphate levels, also called hyperphosphatemia, and the imbalance in the endocrine regulators of phosphate metabolism as another CKD-associated pathology that can directly and indirectly harm skeletal muscle tissue. To identify causes, affected cell types, and the mechanisms of sarcopenia and thereby novel targets for therapeutic interventions, it is important to first characterize the precise pathologic changes on molecular, cellular, and histologic levels, and to do so in CKD patients as well as in animal models of CKD, which we describe here in detail. We also discuss the currently known pathomechanisms and therapeutic approaches of CKD-associated sarcopenia, as well as the effects of hyperphosphatemia and the novel drug targets it could provide to protect skeletal muscle in CKD.
Full article
(This article belongs to the Special Issue From Molecular Basis to Therapeutic Approaches in Skeletal Muscle Dysfunction)
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Open AccessCommunication
Starch Sodium Octenylsuccinate as a New Type of Stabilizer in the Synthesis of Catalytically Active Gold Nanostructures
by
Beata Tim, Emilia Konował and Anna Modrzejewska-Sikorska
Int. J. Mol. Sci. 2024, 25(10), 5116; https://doi.org/10.3390/ijms25105116 (registering DOI) - 8 May 2024
Abstract
Here, starch derivatives, i.e., sodium starch octenylsuccinate (OSA starch, hereinafter referred to as OSA), were employed as both reducing and stabilizing agents for the unique, inexpensive, and simple synthesis of gold nanoparticles (OSA-AuNPs) in an aqueous solution with gold salt. The obtained OSA-AuNPs
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Here, starch derivatives, i.e., sodium starch octenylsuccinate (OSA starch, hereinafter referred to as OSA), were employed as both reducing and stabilizing agents for the unique, inexpensive, and simple synthesis of gold nanoparticles (OSA-AuNPs) in an aqueous solution with gold salt. The obtained OSA-AuNPs were characterized by UV-vis spectrophotometry, transmission electron microscopy, scanning electron microscopy, and energy-dispersive X-ray spectroscopy. The catalytic activity of the obtained gold colloids was studied in the reduction of organic dyes, including methylene blue (C.I. Basic Blue 9) and rhodamine B (C.I. Basic Violet 10), and food coloring, including tartrazine (E102) and azorubine (E122), by sodium borohydride. Moreover, OSA-AuNPs were utilized as signal amplifiers in surface-enhanced Raman spectroscopy. The obtained results confirmed that gold nanoparticles can be used as effective catalysts in reduction reactions of selected organic dyes, as well as signal enhancers in the SERS technique.
Full article
(This article belongs to the Special Issue Metal Nanoparticles: From Fundamental Studies to New Applications)
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Open AccessArticle
Effect of Garlic Extract on the Erythrocyte as a Simple Model Cell
by
Paulina Furdak, Grzegorz Bartosz, Ireneusz Stefaniuk, Bogumił Cieniek, Edyta Bieszczad-Bedrejczuk, Mirosław Soszyński and Izabela Sadowska-Bartosz
Int. J. Mol. Sci. 2024, 25(10), 5115; https://doi.org/10.3390/ijms25105115 (registering DOI) - 8 May 2024
Abstract
Garlic is known to have diverse effects on mammalian cells, being cytotoxic, especially to cancer cells, but also protect against oxidative stress. Mammalian erythrocyte is a simple cell devoid of intracellular organelles, protein synthesis ability, and most signaling pathways. Therefore, examination of the
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Garlic is known to have diverse effects on mammalian cells, being cytotoxic, especially to cancer cells, but also protect against oxidative stress. Mammalian erythrocyte is a simple cell devoid of intracellular organelles, protein synthesis ability, and most signaling pathways. Therefore, examination of the effects of garlic on erythrocytes allows for revealing primary events in the cellular action of garlic extract. In this study, human erythrocytes or erythrocyte membranes were exposed to garlic extract at various dilutions. Hemoglobin oxidation to methemoglobin, increased binding of hemoglobin to the membrane, and formation of Heinz bodies were observed. Garlic extract depleted acid-soluble thiols, especially glutathione, and induced a prooxidative shift in the cellular glutathione redox potential. The extract increased the osmotic fragility of erythrocytes, induced hemolysis, and inhibited hemolysis in isotonic ammonium chloride, indicative of decreased membrane permeability for Cl− and increased the membrane fluidity. Fluorescent probes indicated an increased level of reactive oxygen species and induction of lipid peroxidation, but these results should be interpreted with care since the extract alone induced oxidation of the probes (dichlorodihydrofluorescein diacetate and BODIPY C11). These results demonstrate that garlic extract induces oxidative changes in the erythrocyte, first of all, thiol and hemoglobin oxidation.
Full article
(This article belongs to the Special Issue Updates on Synthetic and Natural Antioxidants)
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Open AccessArticle
From Jane Doe to Sofia: DNA Extraction Protocol from Bones and Teeth without Liquid Nitrogen for Identifying Skeletal Remains
by
Emanuela Stan, Camelia-Oana Muresan, Raluca Dumache, Veronica Ciocan, Stefania Ungureanu, Alexandra Mihailescu, Ecaterina Daescu, Corina Duda-Seiman, Gheorghita Menghiu, Delia Hutanu and Alexandra Enache
Int. J. Mol. Sci. 2024, 25(10), 5114; https://doi.org/10.3390/ijms25105114 (registering DOI) - 8 May 2024
Abstract
DNA analysis plays a crucial role in forensic investigations, helping in criminal cases, missing persons inquiries, and archaeological research. This study focuses on the DNA concentration in different skeletal elements to improve human identification efforts. Ten cases of unidentified skeletal remains brought to
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DNA analysis plays a crucial role in forensic investigations, helping in criminal cases, missing persons inquiries, and archaeological research. This study focuses on the DNA concentration in different skeletal elements to improve human identification efforts. Ten cases of unidentified skeletal remains brought to the Institute of Forensic Medicine in Timisoara, Romania, underwent DNA analysis between 2019 and 2023. The results showed that teeth are the best source for DNA extraction as they contain the highest concentration of genetic material, at 3.68 ng/µL, compared to the petrous temporal bone (0.936 ng/µL) and femur bone (0.633 ng/µL). These findings highlight the significance of teeth in forensic contexts due to their abundant genetic material. Combining anthropological examination with DNA analysis enhances the understanding and precision of identifying human skeletal remains, thus advancing forensic science. Selecting specific skeletal elements, such as the cochlea or teeth, emerges as crucial for reliable genetic analyses, emphasizing the importance of careful consideration in forensic identification procedures. Our study concludes that automated DNA extraction protocols without liquid nitrogen represent a significant advancement in DNA extraction technology, providing a faster, more efficient, and less labor-intensive method for extracting high-quality DNA from damaged bone and tooth samples.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessEditorial
Special Issue “Cancer Immunotherapy: Tumor Microenvironment, Biomarker Discovery and Immune Resistance”
by
Jason Yongsheng Chan
Int. J. Mol. Sci. 2024, 25(10), 5113; https://doi.org/10.3390/ijms25105113 (registering DOI) - 8 May 2024
Abstract
Since the launch of this Special Issue entitled “Cancer Immunotherapy: Tumor Microenvironment, Biomarker Discovery and Immune Resistance”, the field of cancer immunotherapy has continued to witness rapid growth in the development of novel agents, improvements in our understanding of mechanisms of response and
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Since the launch of this Special Issue entitled “Cancer Immunotherapy: Tumor Microenvironment, Biomarker Discovery and Immune Resistance”, the field of cancer immunotherapy has continued to witness rapid growth in the development of novel agents, improvements in our understanding of mechanisms of response and resistance, and the maturation of emerging technologies such as artificial intelligence, machine learning, single-cell sequencing and spatial profiling [...]
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(This article belongs to the Special Issue Cancer Immunotherapy: Tumor Microenvironment, Biomarker Discovery and Immune Resistance)
Open AccessArticle
ABCB1 C1236T, G2677TA and C3435T Genetic Polymorphisms and Antidepressant Response Phenotypes: Results from a Portuguese Major Depressive Disorder Cohort
by
Marlene Santos, Luis Lima, Serafim Carvalho, Andreia Brandão, Fátima Barroso, Agostinho Cruz and Rui Medeiros
Int. J. Mol. Sci. 2024, 25(10), 5112; https://doi.org/10.3390/ijms25105112 (registering DOI) - 8 May 2024
Abstract
P-glycoprotein (P-GP) is a transporter molecule expressed on the apical surface of capillary endothelial cells of the Blood–Brain Barrier (BBB), whose activity heavily influences drug distribution, including antidepressants. This transporter is encoded by ABCB1 gene, and genetic variations within ABCB1 gene have been
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P-glycoprotein (P-GP) is a transporter molecule expressed on the apical surface of capillary endothelial cells of the Blood–Brain Barrier (BBB), whose activity heavily influences drug distribution, including antidepressants. This transporter is encoded by ABCB1 gene, and genetic variations within ABCB1 gene have been proposed to affect drug efflux and have been previously associated with depression. In this context, we aimed to evaluate the role of C1236T, G2677TA and C3435T ABCB1 genetic polymorphisms in antidepressant treatment phenotypes from a cohort of patients harboring Major Depressive Disorder. Patients enrolled in the study consisted of 80 individuals with Major Depressive Disorder, who took part in a 27-month follow-up study at HML, Portugal. To investigate the correlation between ABCB1 polymorphisms and antidepressant response phenotypes, DNA was extracted from peripheral blood, and C1236T, C3435T and G2677TA polymorphisms were genotyped with TaqMan® SNP Genotyping Assays. Despite the fact that the evaluated polymorphisms (C1236T, C3435T and G2677TA) were not associated with treatment resistant depression, or relapse, we observed that patients carrying TT genotype of the C3435T polymorphism remit earlier than the ones carrying CC or CT genotypes (10.2 weeks vs. 14.9 and 21.3, respectively, p = 0.028, Log-rank test). Since we found an association with C3435T and time to remission, and not to the absence of remission, we suggest that this polymorphism could have an impact on antidepressant drug distribution, and thus influence on the time to remission will occur, without influencing the risk of remission itself.
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(This article belongs to the Special Issue Genetic Variants in Neurological and Psychiatric Diseases)
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Open AccessArticle
Physicochemical Properties and Antioxidant Activity of CRISPR/Cas9-Edited Tomato SGR1 Knockout (KO) Line
by
Jin Young Kim, Dong Hyun Kim, Me-Sun Kim, Yu Jin Jung and Kwon Kyoo Kang
Int. J. Mol. Sci. 2024, 25(10), 5111; https://doi.org/10.3390/ijms25105111 (registering DOI) - 8 May 2024
Abstract
Tomatoes contain many secondary metabolites such as β-carotene, lycopene, phenols, flavonoids, and vitamin C, which are responsible for antioxidant activity. SlSGR1 encodes a STAY-GREEN protein that plays a critical role in the regulation of chlorophyll degradation in tomato leaves and fruits. Therefore,
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Tomatoes contain many secondary metabolites such as β-carotene, lycopene, phenols, flavonoids, and vitamin C, which are responsible for antioxidant activity. SlSGR1 encodes a STAY-GREEN protein that plays a critical role in the regulation of chlorophyll degradation in tomato leaves and fruits. Therefore, the present study was conducted to evaluate the sgr1 null lines based on their physicochemical characteristics, the content of secondary metabolites, and the γ-Aminobutyric acid (GABA) content. The total soluble solids (TSS), titrated acidity (TA), and brix acid ratio (BAR) of the sgr1 null lines were higher than those of the wild type(WT). Additionally, the sgr1 null lines accumulated higher levels of flavor-inducing ascorbic acid and total carotenoids compared to WT. Also, the total phenolic content, total flavonoids, GABA content, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical content of the sgr1 null lines were higher than those of the WT. Therefore, these studies suggest that the knockout of the SGR1 gene by the CRISPR/Cas9 system can improve various functional compounds in tomato fruit, thereby satisfying the antioxidant properties required by consumers.
Full article
(This article belongs to the Special Issue Molecular Breeding of Plants: From CRISPR/Cas9 to Transcriptomics and MABc)
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