International Journal of Molecular Sciences

16 pages, 8325 KiB

Open AccessArticle

Transcriptome-Wide Identification of Dark- and Salt-Induced Senescence-Related NAC Gene Family Members in Alfalfa

by Xiangxue Duan, Daicai Tian, Peiran Gao, Yue Sun, Xiaojing Peng, Jiangqi Wen, Hongli Xie, Zeng-Yu Wang and Maofeng Chai

Int. J. Mol. Sci. 2024, 25(16), 8908; https://doi.org/10.3390/ijms25168908 (registering DOI) - 15 Aug 2024

Abstract

Leaves are a key forage part for livestock, and the aging of leaves affects forage biomass and quality. Preventing or delaying premature leaf senescence leads to an increase in pasture biomass accumulation and an improvement in alfalfa quality. NAC transcription factors have been [...] Read more.

Leaves are a key forage part for livestock, and the aging of leaves affects forage biomass and quality. Preventing or delaying premature leaf senescence leads to an increase in pasture biomass accumulation and an improvement in alfalfa quality. NAC transcription factors have been reported to affect plant growth and abiotic stress responses. In this study, 48 NAC genes potentially associated with leaf senescence were identified in alfalfa under dark or salt stress conditions. A phylogenetic analysis divided MsNACs into six subgroups based on similar gene structure and conserved motif. These MsNACs were unevenly distributed in 26 alfalfa chromosomes. The results of the collinearity analysis show that all of the MsNACs were involved in gene duplication. Some cis-acting elements related to hormones and stress were screened in the 2-kb promoter regions of MsNACs. Nine of the MsNAC genes were subjected to qRT-PCR to quantify their expression and Agrobacterium-mediated transient expression to verify their functions. The results indicate that Ms.gene031485, Ms.gene032313, Ms.gene08494, and Ms.gene77666 might be key NAC genes involved in alfalfa leaf senescence. Our findings extend the understanding of the regulatory function of MsNACs in leaf senescence. Full article

(This article belongs to the Special Issue Plant Response to Abiotic Stress—3rd Edition)

► Show Figures

Figure 1

12 pages, 1828 KiB

Open AccessArticle

Inhibiting CD44-ICD Attenuates LPS-Induced Initiation of Hepatic Inflammation in Septic Mice

by Li-Hsuan Li, Dur-Zong Hsu, Victor Raj Mohan Chandrasekaran and Ming-Yie Liu

Int. J. Mol. Sci. 2024, 25(16), 8907; https://doi.org/10.3390/ijms25168907 (registering DOI) - 15 Aug 2024

Abstract

Sepsis is a severe condition induced by microbial infection. It elicits a systemic inflammatory response, leading to multi-organ failure, and the liver, as a scavenger, plays a significant role in this process. Controlling hepatic inflammation and maintaining liver function is crucial in managing [...] Read more.

Sepsis is a severe condition induced by microbial infection. It elicits a systemic inflammatory response, leading to multi-organ failure, and the liver, as a scavenger, plays a significant role in this process. Controlling hepatic inflammation and maintaining liver function is crucial in managing sepsis. CD44-ICD, as a CD44 signal transductor, is involved in multiple inflammatory responses. However, the role of CD44-ICD in lipopolysaccharide (LPS)-induced hepatic inflammation has not been investigated. Therefore, we aimed to examine whether CD44-ICD initiates hepatic inflammation in septic mice. We induced hepatic inflammation in mice by administering LPS. DAPT, a CD44-ICD inhibitor, was given to mice or Chang cells 30 min or 1 h before LPS administration (10 mg/kg, i.p., or 100 ng/mL, respectively). Inhibition of CD44-ICD decreased the level of aspartate aminotransferase (AST), alanine aminotransferase (ALT), hepatic necrosis, inflammatory cell infiltration, interleukin (IL)-1β, inducible NO synthase (iNOS), nitric oxide (NO) production, nuclear factor (NF)κB signaling pathway proteins, and CD44 expression in mice. CD44-ICD inhibition also decreased IL-1β and CD44 expression levels in Chang cells. CD44-ICD may be a primary regulatory function in CD44-associated LPS-induced initiation of hepatic inflammation in mice. Full article

(This article belongs to the Section Molecular Immunology)

13 pages, 584 KiB

Open AccessArticle

Specific Monoclonal Antibodies against African Swine Fever Virus Protease pS273R Revealed a Novel and Conserved Antigenic Epitope

by Jiajia Zhang, Kaili Zhang, Shaohua Sun, Ping He, Dafu Deng, Pingping Zhang, Wanglong Zheng, Nanhua Chen and Jianzhong Zhu

Int. J. Mol. Sci. 2024, 25(16), 8906; https://doi.org/10.3390/ijms25168906 (registering DOI) - 15 Aug 2024

Abstract

The African swine fever virus (ASFV) is a large enveloped DNA virus that causes a highly pathogenic hemorrhagic disease in both domestic pigs and wild boars. The ASFV genome contains a double-stranded DNA encoding more than 150 proteins. The ASFV possesses only one [...] Read more.

The African swine fever virus (ASFV) is a large enveloped DNA virus that causes a highly pathogenic hemorrhagic disease in both domestic pigs and wild boars. The ASFV genome contains a double-stranded DNA encoding more than 150 proteins. The ASFV possesses only one protease, pS273R, which is important for virion assembly and host immune evasion. Therefore, the specific monoclonal antibody (mAb) against pS273R is useful for ASFV research. Here, we generated two specific anti-pS273R mAbs named 2F3 and 3C2, both of which were successfully applied for ELISA, Western blotting, and immunofluorescence assays. Further, we showed that both 2F3 and 3C2 mAbs recognize a new epitope of N terminal 1–25 amino acids of pS273R protein, which is highly conserved across different ASFV strains including all genotype I and II strains. Based on the recognized epitope, an indirect ELISA was established and was effective in detecting antibodies during ASFV infection. To conclude, the specific pS273R mAbs and corresponding epitope identified will strongly promote ASFV serological diagnosis and vaccine research. Full article

(This article belongs to the Special Issue Novel Insights into Monoclonal Antibodies in Disease)

17 pages, 947 KiB

Open AccessReview

The Effects of Caffeine on Blood Platelets and the Cardiovascular System through Adenosine Receptors

by Kinga Marcinek, Boguslawa Luzak and Marcin Rozalski

Int. J. Mol. Sci. 2024, 25(16), 8905; https://doi.org/10.3390/ijms25168905 (registering DOI) - 15 Aug 2024

Abstract

Caffeine is the most popular and widely consumed behaviourally active substance in the world. This review describes the influence of caffeine on the cardiovascular system, with a special focus on blood platelets. For many years, caffeine was thought to have a negative effect [...] Read more.

Caffeine is the most popular and widely consumed behaviourally active substance in the world. This review describes the influence of caffeine on the cardiovascular system, with a special focus on blood platelets. For many years, caffeine was thought to have a negative effect on the cardiovascular system mainly due to increasing blood pressure. However, more recent data suggest that habitual caffeine consumption may reduce the risk of cardiovascular disease and hypertension. This could be a significant finding as cardiovascular disease is the leading cause of death worldwide. Caffeine is known to inhibit A₁ adenosine receptors, through which it is believed to modulate inter alia coronary blood flow, total peripheral resistance, diuresis, and heart rate. It has been shown that coffee possesses antiplatelet activity, but depending on the dose and the term of its use, caffeine may stimulate or inhibit platelet reactivity. Also, chronic exposure to caffeine may sensitize or upregulate the adenosine receptors in platelets causing increased cAMP accumulation and anti-aggregatory effects and decrease calcium levels elicited by AR agonists. The search for new, selective, and safe AR agonists is one of the new strategies for improving antiplatelet therapy involving targeting multiple pathways of platelet activation. Therefore, this review examines the AR-dependent impact of caffeine on blood platelets in the presence of adenosine receptor agonists. Full article

(This article belongs to the Special Issue New Advances in Platelet Biology and Functions: 2nd Edition)

► Show Figures

Figure 1

14 pages, 1353 KiB

Open AccessArticle

Synthesis and Anti-Cancer Activity of the Novel Selective Glucocorticoid Receptor Agonists of the Phenylethanolamine Series

by Ekaterina M. Zhidkova, Leyla R. Tilova, Timur I. Fetisov, Kirill I. Kirsanov, Evgeny P. Kulikov, Adel D. Enikeev, Irina V. Budunova, Gennadii A. Badun, Maria G. Chernysheva, Valerii Z. Shirinian, Marianna G. Yakubovskaya and Ekaterina A. Lesovaya

Int. J. Mol. Sci. 2024, 25(16), 8904; https://doi.org/10.3390/ijms25168904 (registering DOI) - 15 Aug 2024

Abstract

Glucocorticoids (GCs) are widely used for treating hematological malignancies despite their multiple adverse effects. The biological response to GCs relies on glucocorticoid receptor (GR) transrepression (TR) that mediates the anticancer effects and transactivation (TA) associated with the side effects. Selective GR agonists (SEGRAs) [...] Read more.

Glucocorticoids (GCs) are widely used for treating hematological malignancies despite their multiple adverse effects. The biological response to GCs relies on glucocorticoid receptor (GR) transrepression (TR) that mediates the anticancer effects and transactivation (TA) associated with the side effects. Selective GR agonists (SEGRAs) preferentially activating GR TR could offer greater benefits in cancer treatment. One of the well-characterized SEGRAs, 2-(4-acetoxyphenyl)-2-chloro-N-methylethylammonium-chloride (CpdA), exhibited anticancer activity; however, its translational potential is limited due to chemical instability. To overcome this limitation, we obtained CpdA derivatives, CpdA-01–CpdA-08, employing two synthetic strategies and studied their anti-tumor activity: 4-(1-hydroxy-2-(piperidin-1-yl)ethyl)phenol or CpdA-03 demonstrated superior GR affinity and stability compared to CpdA. In lymphoma Granta and leukemia CEM cell lines, CpdA-03 ligand exhibited typical SEGRA properties, inducing GR TR without triggering GR TA. CpdA-03 effects on cell viability, growth, and apoptosis were similar to the reference GR ligand, dexamethasone (Dex), and the source compound CpdA. In vivo testing of CpdA-03 activity against lymphoma on the transplantable P388 murine lymphoma model showed that CpdA-03 reduced tumor volume threefold, outperforming Dex and CpdA. In conclusion, in this work, we introduce a novel SEGRA CpdA-03 as a promising agent for lymphoma treatment with fewer side effects. Full article

(This article belongs to the Section Molecular Oncology)

► Show Figures

Figure 1

18 pages, 1188 KiB

Open AccessArticle

Dried Blood Spot Metabolome Features of Ischemic–Hypoxic Encephalopathy: A Neonatal Rat Model

by Chupalav Eldarov, Natalia Starodubtseva, Yulia Shevtsova, Kirill Goryunov, Oleg Ionov, Vladimir Frankevich, Egor Plotnikov, Gennady Sukhikh, Dmitry Zorov and Denis Silachev

Int. J. Mol. Sci. 2024, 25(16), 8903; https://doi.org/10.3390/ijms25168903 (registering DOI) - 15 Aug 2024

Abstract

Hypoxic–ischemic encephalopathy (HIE) is a severe neurological disorder caused by perinatal asphyxia with significant consequences. Early recognition and intervention are crucial, with therapeutic hypothermia (TH) being the primary treatment, but its efficacy depends on early initiation of treatment. Accurately assessing the HIE severity [...] Read more.

Hypoxic–ischemic encephalopathy (HIE) is a severe neurological disorder caused by perinatal asphyxia with significant consequences. Early recognition and intervention are crucial, with therapeutic hypothermia (TH) being the primary treatment, but its efficacy depends on early initiation of treatment. Accurately assessing the HIE severity in neonatal care poses challenges, but omics approaches have made significant contribution to understanding its complex pathophysiology. Our study further explores the impact of HIE on the blood metabolome over time and investigated changes associated with hypothermia’s therapeutic effects. Using a rat model of hypoxic–ischemic brain injury, we comprehensively analyzed dried blood spot samples for fat-soluble compounds using HPLC-MS. Our research shows significant changes in the blood metabolome after HIE, with a particularly rapid recovery of lipid metabolism observed. Significant changes in lipid metabolites were observed after 3 h of HIE, including increases in ceramides, carnitines, certain fatty acids, phosphocholines, and phosphoethanolamines, while sphingomyelins and N-acylethanolamines (NAEs) decreased (p < 0.05). Furthermore, NAEs were found to be significant features in the OPLS-DA model for HIE diagnosis, with an area under the curve of 0.812. TH showed a notable association with decreased concentrations of ceramides. Enrichment analysis further corroborated these observations, showing modulation in several key metabolic pathways, including arachidonic acid oxylipin metabolism, eicosanoid metabolism via lipooxygenases, and leukotriene C4 synthesis deficiency. Our study reveals dynamic changes in the blood metabolome after HIE and the therapeutic effects of hypothermia, which improves our understanding of the pathophysiology of HIE and could lead to the development of new rapid diagnostic approaches for neonatal HIE. Full article

(This article belongs to the Special Issue Modeling Neurological Disorders in Experimental Animals: New Insights and Emerging Roles: 4^th Edition)

17 pages, 7328 KiB

Open AccessArticle

R2R3-MYB Gene Family in Coptis teeta Wall.: Genome-Wide Identification, Phylogeny, Evolutionary Expansion, and Expression Analyses during Floral Development

by Jichen Yu, Shaofeng Duan, Zhenyang Shua, Kecheng Li, Guisheng Xiang, Timothy Charles Baldwin, Yingchun Lu and Yanli Liang

Int. J. Mol. Sci. 2024, 25(16), 8902; https://doi.org/10.3390/ijms25168902 (registering DOI) - 15 Aug 2024

Abstract

The R2R3-MYB gene family represents a widely distributed class of plant transcription factors. This gene family plays an important role in many aspects of plant growth and development. However, the characterization of R2R3-MYB genes present in the genome of Coptis teeta has not [...] Read more.

The R2R3-MYB gene family represents a widely distributed class of plant transcription factors. This gene family plays an important role in many aspects of plant growth and development. However, the characterization of R2R3-MYB genes present in the genome of Coptis teeta has not been reported. Here, we describe the bioinformatic identification and characterization of 88 R2R3-MYB genes in this species, and the identification of members of the R2R3-MYB gene family in species within the order Ranales most closely related to Coptis teeta. The CteR2R3-MYB genes were shown to exhibit a higher degree of conservation compared to those of A. thaliana, as evidenced by phylogeny, conserved motifs, gene structure, and replication event analyses. Cis-acting element analysis confirmed the involvement of CteR2R3-MYB genes in a variety of developmental processes, including growth, cell differentiation, and reproduction mediated by hormone synthesis. In addition, through homology comparisons with the equivalent gene family in A. thaliana, protein regulatory network prediction and transcriptome data analysis of floral organs across three time periods of flower development, 17 candidate genes were shown to exhibit biased expression in two floral phenotypes of C. teeta. This suggests their potential involvement in floral development (anther development) in this species. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

► Show Figures

Figure 1

30 pages, 5562 KiB

Open AccessArticle

Transcriptome Profiles Reveal Key Regulatory Networks during Single and Multifactorial Stresses Coupled with Melatonin Treatment in Pitaya (Selenicereus undatus L.)

by Aamir Ali Khokhar, Liu Hui, Darya Khan, Zhang You, Qamar U Zaman, Babar Usman and Hua-Feng Wang

Int. J. Mol. Sci. 2024, 25(16), 8901; https://doi.org/10.3390/ijms25168901 - 15 Aug 2024

Abstract

In response to evolving climatic conditions, plants frequently confront multiple abiotic stresses, necessitating robust adaptive mechanisms. This study focuses on the responses of Selenicereus undatus L. to both individual stresses (cadmium; Cd, salt; S, and drought; D) and their combined applications, with an [...] Read more.

In response to evolving climatic conditions, plants frequently confront multiple abiotic stresses, necessitating robust adaptive mechanisms. This study focuses on the responses of Selenicereus undatus L. to both individual stresses (cadmium; Cd, salt; S, and drought; D) and their combined applications, with an emphasis on evaluating the mitigating effects of (M) melatonin. Through transcriptome analysis, this study identifies significant gene expression changes and regulatory network activations. The results show that stress decreases pitaya growth rates by 30%, reduces stem and cladode development by 40%, and increases Cd uptake under single and combined stresses by 50% and 70%, respectively. Under stress conditions, enhanced activities of H₂O₂, POD, CAT, APX, and SOD and elevated proline content indicate strong antioxidant defenses. We identified 141 common DEGs related to stress tolerance, most of which were related to AtCBP, ALA, and CBP pathways. Interestingly, the production of genes related to signal transduction and hormones, including abscisic acid and auxin, was also significantly induced. Several calcium-dependent protein kinase genes were regulated during M and stress treatments. Functional enrichment analysis showed that most of the DEGs were enriched during metabolism, MAPK signaling, and photosynthesis. In addition, weighted gene co-expression network analysis (WGCNA) identified critical transcription factors (WRKYs, MYBs, bZIPs, bHLHs, and NACs) associated with antioxidant activities, particularly within the salmon module. This study provides morpho-physiological and transcriptome insights into pitaya’s stress responses and suggests molecular breeding techniques with which to enhance plant resistance. Full article

(This article belongs to the Special Issue Recent Research in Plant Abiotic Stress)

► Show Figures

Figure 1

22 pages, 9544 KiB

Open AccessArticle

Role and Regulatory Mechanism of circRNA_14820 in the Proliferation and Differentiation of Goat Skeletal Muscle Satellite Cells

by Pu Yang, Xuelong Li, Chengli Liu, Yanguo Han, Guangxin E and Yongfu Huang

Int. J. Mol. Sci. 2024, 25(16), 8900; https://doi.org/10.3390/ijms25168900 - 15 Aug 2024

Abstract

Skeletal muscle satellite cells (SMSCs), a type of myogenic stem cell, play a pivotal role in postnatal muscle regeneration and repair in animals. Circular RNAs (circRNAs) are a distinct class of non-coding RNA molecules capable of regulating muscle development by modulating gene expression, [...] Read more.

Skeletal muscle satellite cells (SMSCs), a type of myogenic stem cell, play a pivotal role in postnatal muscle regeneration and repair in animals. Circular RNAs (circRNAs) are a distinct class of non-coding RNA molecules capable of regulating muscle development by modulating gene expression, acting as microRNAs, or serving as protein decoys. In this study, we identified circ_14820, an exonic transcript derived from adenosine triphosphatase family protein 2 (ATAD2), through initial RNA-Seq analysis. Importantly, overexpression of circ_14820 markedly enhanced the proliferation of goat SMSCs while concomitantly suppressing their differentiation. Moreover, circ_14820 exhibited predominant localization in the cytoplasm of SMSCs. Subsequent small RNA and mRNA sequencing of circ_14820-overexpressing SMSCs systematically elucidated the molecular regulatory mechanisms associated with circ_14820. Our preliminary findings suggest that the circ_14820-miR-206-CCND2 regulatory axis may govern the development of goat SMSCs. These discoveries contribute to a deeper understanding of circRNA-mediated mechanisms in regulating skeletal muscle development, thereby advancing our knowledge of muscle biology. Full article

(This article belongs to the Section Biochemistry)

23 pages, 1595 KiB

Open AccessReview

Cracking the Codes behind Cancer Cells’ Immune Evasion

by Nikita Mundhara and Pritam Sadhukhan

Int. J. Mol. Sci. 2024, 25(16), 8899; https://doi.org/10.3390/ijms25168899 - 15 Aug 2024

Abstract

Immune evasion is a key phenomenon in understanding tumor recurrence, metastasis, and other critical steps in tumor progression. The tumor microenvironment (TME) is in constant flux due to the tumor’s ability to release signals that affect it, while immune cells within it can [...] Read more.

Immune evasion is a key phenomenon in understanding tumor recurrence, metastasis, and other critical steps in tumor progression. The tumor microenvironment (TME) is in constant flux due to the tumor’s ability to release signals that affect it, while immune cells within it can impact cancer cell behavior. Cancer cells undergo several changes, which can change the enrichment of different immune cells and modulate the activity of existing immune cells in the tumor microenvironment. Cancer cells can evade immune surveillance by downregulating antigen presentation or expressing immune checkpoint molecules. High levels of tumor-infiltrating lymphocytes (TILs) correlate with better outcomes, and robust immune responses can control tumor growth. On the contrary, increased enrichment of Tregs, myeloid-derived suppressor cells, and M2-like anti-inflammatory macrophages can hinder effective immune surveillance and predict poor prognosis. Overall, understanding these immune evasion mechanisms guides therapeutic strategies. Researchers aim to modulate the TME to enhance immune surveillance and improve patient outcomes. In this review article, we strive to summarize the composition of the tumor immune microenvironment, factors affecting the tumor immune microenvironment (TIME), and different therapeutic modalities targeting the immune cells. This review is a first-hand reference to understand the basics of immune surveillance and immune evasion. Full article

(This article belongs to the Special Issue Fifty Years of Targeted Therapy in Cancer: Past, Present and Future)

► Show Figures

Figure 1

19 pages, 4854 KiB

Open AccessArticle

Hematopoietic Growth Factors Regulate the Entry of Monocytes into the Adult Brain via Chemokine Receptor CCR5

by Xuefang Sophie Ren, Junchi He, Songruo Li, Heng Hu, Michele Kyle, Shinichi Kohsaka and Li-Ru Zhao

Int. J. Mol. Sci. 2024, 25(16), 8898; https://doi.org/10.3390/ijms25168898 - 15 Aug 2024

Abstract

Monocytes are circulating macrophage precursors generated from bone marrow hematopoietic stem cells. In adults, monocytes continuously replenish cerebral border-associated macrophages under physiological conditions. Monocytes also rapidly infiltrate the brain in pathological settings. The mechanisms of recruiting monocyte-derived macrophages into the brain under pathological [...] Read more.

Monocytes are circulating macrophage precursors generated from bone marrow hematopoietic stem cells. In adults, monocytes continuously replenish cerebral border-associated macrophages under physiological conditions. Monocytes also rapidly infiltrate the brain in pathological settings. The mechanisms of recruiting monocyte-derived macrophages into the brain under pathological conditions have been extensively studied. However, it remains unclear how monocytes enter the brain to renew border-associated macrophages under physiological conditions. Using both in vitro and in vivo approaches, this study reveals that a combination of two hematopoietic growth factors, stem cell factor (SCF) and granulocyte colony-stimulating factor (G-CSF), complementarily and synergistically enhances the adhesion of monocytes to cerebral endothelial cells in a dose-dependent manner. Cysteine-cysteine chemokine receptor 5 (CCR5) in brain endothelial cells, but not the cell adhesion molecules mediating neuroinflammation-related infiltration of monocyte-derived macrophages, modulates SCF+G-CSF-enhanced monocyte-endothelial cell adhesion. Blocking CCR5 or genetically deleting CCR5 reduces monocyte-endothelial cell adhesion induced by SCF+G-CSF. The SCF+G-CSF-enhanced recruitment of bone marrow-derived monocytes/macrophages into the cerebral perivascular space is also reduced in adult CCR5 knockout mice. This study demonstrates the role of SCF and G-CSF in regulating the entry of monocytes into the adult brain to replenish perivascular macrophages. Full article

(This article belongs to the Special Issue Cellular Responses to Environmental Changes)

► Show Figures

Figure 1

23 pages, 3910 KiB

Open AccessArticle

An Insight into the Mechanism of DNA Cleavage by DNA Endonuclease from the Hyperthermophilic Archaeon Pyrococcus furiosus

by Anastasiia T. Davletgildeeva, Aleksandra A. Kuznetsova, Alexander A. Ishchenko, Murat Saparbaev and Nikita A. Kuznetsov

Int. J. Mol. Sci. 2024, 25(16), 8897; https://doi.org/10.3390/ijms25168897 - 15 Aug 2024

Abstract

Hyperthermophilic archaea such as Pyrococcus furiosus survive under very aggressive environmental conditions by occupying niches inaccessible to representatives of other domains of life. The ability to survive such severe living conditions must be ensured by extraordinarily efficient mechanisms of DNA processing, including repair. [...] Read more.

Hyperthermophilic archaea such as Pyrococcus furiosus survive under very aggressive environmental conditions by occupying niches inaccessible to representatives of other domains of life. The ability to survive such severe living conditions must be ensured by extraordinarily efficient mechanisms of DNA processing, including repair. Therefore, in this study, we compared kinetics of conformational changes of DNA Endonuclease Q from P. furiosus during its interaction with various DNA substrates containing an analog of an apurinic/apyrimidinic site (F-site), hypoxanthine, uracil, 5,6-dihydrouracil, the α-anomer of adenosine, or 1,N⁶-ethenoadenosine. Our examination of DNA cleavage activity and fluorescence time courses characterizing conformational changes of the dye-labeled DNA substrates during the interaction with EndoQ revealed that the enzyme induces multiple conformational changes of DNA in the course of binding. Moreover, the obtained data suggested that the formation of the enzyme–substrate complex can proceed through dissimilar kinetic pathways, resulting in different types of DNA conformational changes, which probably allow the enzyme to perform its biological function at an extreme temperature. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

► Show Figures

Figure 1

11 pages, 3915 KiB

Open AccessArticle

Antibody to Endogenous Cardiotonic Steroid Reverses Vascular Fibrosis and Restores Vasorelaxation in Chronic Kidney Disease

by Natalia I. Agalakova, Elena V. Mikhailova, Ivan A. Ershov, Olga V. Nadei, Arseny A. Pyankov, Michael M. Galagoudza, C. David Adair, Irina V. Romanova and Alexei Y. Bagrov

Int. J. Mol. Sci. 2024, 25(16), 8896; https://doi.org/10.3390/ijms25168896 - 15 Aug 2024

Abstract

Marinobufagenin (MBG) is implicated in chronic kidney disease, where it removes Fli1-induced inhibition of the collagen-1. We hypothesized that (i) in nephrectomized rats, aortic fibrosis develops due to elevated plasma MBG and inhibited Fli1, and (ii) that the antibody to MBG reduces collagen-1 [...] Read more.

Marinobufagenin (MBG) is implicated in chronic kidney disease, where it removes Fli1-induced inhibition of the collagen-1. We hypothesized that (i) in nephrectomized rats, aortic fibrosis develops due to elevated plasma MBG and inhibited Fli1, and (ii) that the antibody to MBG reduces collagen-1 and improves vasodilatation. A partial nephrectomy was performed in male Sprague-Dawley rats. Sham-operated animals comprised the control group. At 5 weeks following nephrectomy, rats were administered the vehicle (n = 8), or the anti-MBG antibody (n = 8). Isolated aortic rings were tested for their responsiveness to sodium nitroprusside following endothelin-1-induced constriction. In nephrectomized rats, there was an increase in the intensity of collagen staining in the aortic wall vs. the controls. In antibody-treated rats, the structure of bundles of collagen fibers had ordered organization. Western blots of the aorta had lower levels of Fli1 (arbitrary units, 1 ± 0.05 vs. 0.2 ± 0.01; p < 0.001) and greater collagen-1 (arbitrary units, 1 ± 0.01 vs. 9 ± 0.4; p < 0.001) vs. the control group. Administration of the MBG antibody to rats reversed the effect of the nephrectomy on Fli1 and collagen-1 proteins. Aortic rings pretreated with endothelin-1 exhibited 50% relaxation following the addition of sodium nitroprusside (EC₅₀ = 0.28 μmol/L). The responsiveness of the aortic rings obtained from nephrectomized rats was markedly reduced (EC₅₀ = 3.5 mol/L) compared to the control rings. Treatment of rats with the antibody restored vasorelaxation. Thus, the anti-MBG antibody counteracts the Fli1-collagen-1 system and reduces aortic fibrosis. Full article

(This article belongs to the Special Issue Cardiotonic Steroids: From Toxins to Hormones—3rd Edition)

► Show Figures

Figure 1

15 pages, 1610 KiB

Open AccessArticle

Levels of Plasma Endothelin-1, Circulating Endothelial Cells, Endothelial Progenitor Cells, and Cytokines after Cardiopulmonary Bypass in Children with Congenital Heart Disease: Role of Endothelin-1 Regulation

by Angélica Rangel-López, Héctor González-Cabello, María Eugenia Paniagua-Medina, Ricardo López-Romero, Lourdes Andrea Arriaga-Pizano, Miguel Lozano-Ramírez, Juan José Pérez-Barragán, Horacio Máquez-González, Dulce López-Sánchez, Minerva Mata-Rocha, Ramon Paniagua-Sierra, Abraham Majluf-Cruz, Dina Villanueva-García, Sergio Zavala-Vega, Juan Carlos Núñez-Enríquez, Juan Manuel Mejía-Aranguré and José Arellano-Galindo

Int. J. Mol. Sci. 2024, 25(16), 8895; https://doi.org/10.3390/ijms25168895 - 15 Aug 2024

Abstract

Congenital heart disease (CHD) can be complicated by pulmonary arterial hypertension (PAH). Cardiopulmonary bypass (CPB) for corrective surgery may cause endothelial dysfunction, involving endothelin-1 (ET-1), circulating endothelial cells (CECs), and endothelial progenitor cells (EPCs). These markers can gauge disease severity, but their levels [...] Read more.

Congenital heart disease (CHD) can be complicated by pulmonary arterial hypertension (PAH). Cardiopulmonary bypass (CPB) for corrective surgery may cause endothelial dysfunction, involving endothelin-1 (ET-1), circulating endothelial cells (CECs), and endothelial progenitor cells (EPCs). These markers can gauge disease severity, but their levels in children’s peripheral blood still lack consensus for prognostic value. The aim of our study was to investigate changes in ET-1, cytokines, and the absolute numbers (Ɲ) of CECs and EPCs in children 24 h before and 48 h after CPB surgery to identify high-risk patients of complications. A cohort of 56 children was included: 41 cases with CHD-PAH (22 with high pulmonary flow and 19 with low pulmonary flow) and 15 control cases. We observed that Ɲ-CECs increased in both CHD groups and that Ɲ-EPCs decreased in the immediate post-surgical period, and there was a strong negative correlation between ET-1 and CEC before surgery, along with significant changes in ET-1, IL8, IL6, and CEC levels. Our findings support the understanding of endothelial cell precursors’ role in endogenous repair and contribute to knowledge about endothelial dysfunction in CHD. Full article

(This article belongs to the Special Issue Cytokines in Inflammation and Health)

► Show Figures

Figure 1

13 pages, 5765 KiB

Open AccessArticle

Agrimonia coreana Extract Exerts Its Therapeutic Effect through CRAC Channel Inhibition for Atopic Dermatitis Treatment

by Jintae Kim, Ji Min Lee, Su Jin Park, Yu Ran Nam, Seong Woo Choi, Joo Hyun Nam, Hyun Jong Kim and Woo Kyung Kim

Int. J. Mol. Sci. 2024, 25(16), 8894; https://doi.org/10.3390/ijms25168894 - 15 Aug 2024

Abstract

Atopic dermatitis (AD) is a common allergic inflammatory skin condition marked by severe itching, skin lichenification, and chronic inflammation. AD results from a complex immune response, primarily driven by T lymphocytes and environmental triggers, leading to a disrupted epidermal barrier function. Traditional treatments, [...] Read more.

Atopic dermatitis (AD) is a common allergic inflammatory skin condition marked by severe itching, skin lichenification, and chronic inflammation. AD results from a complex immune response, primarily driven by T lymphocytes and environmental triggers, leading to a disrupted epidermal barrier function. Traditional treatments, such as topical corticosteroids, have limitations due to long-term side effects, highlighting the need for safer alternatives. Here, we aimed to show that Agrimonia coreana extract (AC_ext) can be used in treating AD-related dermatologic symptoms. AC_ext could inhibit CRAC (Calcium Release-Activated Calcium) channel activity, reducing Orai1/CRAC currents and decreasing intracellular calcium signaling. This inhibition was further confirmed by the reduced IL-2 levels and T cell proliferation upon AC_ext treatment. In a mouse model of AD, AC_ext significantly ameliorates symptoms, improves histological parameters, and enhances skin barrier function, demonstrating its potential for treating AD. Full article

(This article belongs to the Special Issue Drug Discovery Based on Natural Products)

► Show Figures

Figure 1

13 pages, 667 KiB

Open AccessArticle

A One-Month Advanced Glycation End Products—Restricted Diet Improves CML, RAGE, Metabolic and Inflammatory Profile in Patients with End-Stage Renal Disease Undergoing Haemodialysis

by Adamantia Aroni, Paraskevi Detopoulou, Demetrios Presvelos, Eirini Kostopoulou, Anastasios Ioannidis, George I. Panoutsopoulos, Sofia Zyga, Georgios Kosmidis, Bessie E. Spiliotis and Andrea Paola Rojas Gil

Int. J. Mol. Sci. 2024, 25(16), 8893; https://doi.org/10.3390/ijms25168893 - 15 Aug 2024

Abstract

Exogenous and endogenous advanced glycation end products (AGEs) contribute to the pathogenesis and progression of renal disease. This is a one-month controlled dietary counseling trial that restricts nutritional AGEs in patients with end-stage renal disease (ESRD) undergoing haemodialysis (n = 22 participants [...] Read more.

Exogenous and endogenous advanced glycation end products (AGEs) contribute to the pathogenesis and progression of renal disease. This is a one-month controlled dietary counseling trial that restricts nutritional AGEs in patients with end-stage renal disease (ESRD) undergoing haemodialysis (n = 22 participants in the intervention and n = 20 participants in the control group). Haematological, biochemical markers, the soluble form of the receptor for AGEs (sRAGE), and carboxymethyl lysine (CML) were measured at baseline and at follow-up. Mononuclear cells were isolated and the protein expression of RAGE and the inflammatory marker COX-2 was measured using Western immunoblotting. The intervention group presented a lower increase in CML compared to the control group (12.39% median change in the intervention vs. 69.34% in the control group, p = 0.013), while RAGE (% mean change −56.54 in the intervention vs. 46.51 in the control group, p < 0.001) and COX-2 (% mean change −37.76 in the intervention vs. 0.27 in the control group, p < 0.001) were reduced compared to the control group. sRAGE was reduced in both groups. In addition, HbA1c (at two months), total cholesterol, and triglycerides were reduced in the intervention versus the control group. The adoption of healthy cooking methods deserves further research as a possible way of modulating inflammatory markers in patients with CKD. Full article

(This article belongs to the Special Issue Diabetes and Its Complications: From Molecular Mechanisms to Novel Therapeutic Approaches)

► Show Figures

Figure 1

14 pages, 3479 KiB

Open AccessArticle

Study on the Function of SlWRKY80 in Tomato Defense against Meloidogyne incognita

by Yinxia Chen, Zhize Wang, Weidan Nie, Tingjie Zhao, Yule Dang, Chenghao Feng, Lili Liu, Chaonan Wang and Chong Du

Int. J. Mol. Sci. 2024, 25(16), 8892; https://doi.org/10.3390/ijms25168892 - 15 Aug 2024

Abstract

WRKY transcription factors (TFs) can participate in plant biological stress responses and play important roles. SlWRKY80 was found to be differentially expressed in the Mi-1- and Mi-3-resistant tomato lines by RNA-seq and may serve as a key node for disease resistance [...] Read more.

WRKY transcription factors (TFs) can participate in plant biological stress responses and play important roles. SlWRKY80 was found to be differentially expressed in the Mi-1- and Mi-3-resistant tomato lines by RNA-seq and may serve as a key node for disease resistance regulation. This study used RNAi to determine whether SlWRKY80 silencing could influence the sensitivity of ‘M82’ (mi-1/mi-1)-susceptible lines to M. incognita. Further overexpression of this gene revealed a significant increase in tomato disease resistance, ranging from highly susceptible to susceptible, combined with the identification of growth (plant height, stem diameter, and leaf area) and physiological (soluble sugars and proteins; root activity) indicators, clarifying the role of SlWRKY80 as a positive regulatory factor in tomato defense against M. incognita. Based on this phenomenon, a preliminary exploration of its metabolic signals revealed that SlWRKY80 stimulates different degrees of signaling, such as salicylic acid (SA), jasmonic acid (JA), and ethylene (ETH), and may synergistically regulate reactive oxygen species (ROS) accumulation and scavenging enzyme activity, hindering the formation of feeding sites and ultimately leading to the reduction of root gall growth. To our knowledge, SlWRKY80 has an extremely high utilization value for improving tomato resistance to root-knot nematodes and breeding. Full article

(This article belongs to the Special Issue Genetic Regulation of Plant Growth and Protection)

► Show Figures

Figure 1

22 pages, 4975 KiB

Open AccessArticle

Bacterial Production of CDKL5 Catalytic Domain: Insights in Aggregation, Internal Translation and Phosphorylation Patterns

by Andrea Colarusso, Concetta Lauro, Luisa Canè, Flora Cozzolino and Maria Luisa Tutino

Int. J. Mol. Sci. 2024, 25(16), 8891; https://doi.org/10.3390/ijms25168891 - 15 Aug 2024

Abstract

Cyclin-dependent kinase-like 5 (CDKL5) is a serine/threonine protein kinase involved in human brain development and functioning. Mutations in CDKL5, especially in its catalytic domain, cause a severe developmental condition named CDKL5 deficiency disorder. Nevertheless, molecular studies investigating the structural consequences of such mutations [...] Read more.

Cyclin-dependent kinase-like 5 (CDKL5) is a serine/threonine protein kinase involved in human brain development and functioning. Mutations in CDKL5, especially in its catalytic domain, cause a severe developmental condition named CDKL5 deficiency disorder. Nevertheless, molecular studies investigating the structural consequences of such mutations are still missing. The CDKL5 catalytic domain harbors different sites of post-translational modification, such as phosphorylations, but their role in catalytic activity, protein folding, and stability has not been entirely investigated. With this work, we describe the expression pattern of the CDKL5 catalytic domain in Escherichia coli demonstrating that it predominantly aggregates. However, the use of solubility tags, the lowering of the expression temperature, the manual codon optimization to overcome an internal translational start, and the incubation of the protein with K⁺ and MgATP allow the collection of a soluble catalytically active kinase. Interestingly, the resulting protein exhibits hypophosphorylation compared to its eukaryotic counterpart, proving that bacteria are a useful tool to achieve almost unmodified CDKL5. Posing questions about the CDKL5 autoactivation mechanism and the determinants for its stability, this research provides a valuable platform for comparative biophysical studies between bacterial and eukaryotic-expressed proteins, contributing to our understanding of neurodevelopmental disorders associated with CDKL5 dysfunction. Full article

(This article belongs to the Special Issue CDKL5 Deficiency Disorders: From Molecular Mechanisms to Therapeutics)

► Show Figures

Figure 1

12 pages, 1341 KiB

Open AccessArticle

Mining Candidate Genes and Identifying Risk Factors for Leg Disease in Broilers: A Mendelian Randomization Study

by Xinxin Tang, Peihao Liu, Na Luo, Jie Wen, Hegang Li, Guiping Zhao and Bingxing An

Int. J. Mol. Sci. 2024, 25(16), 8890; https://doi.org/10.3390/ijms25168890 - 15 Aug 2024

Abstract

Clinical investigations have highlighted disruptions in bone metabolic processes and abnormal fluctuations in serum indicator levels during the onset of leg disease (LD) in broilers. However, the presence of a genetic causal relationship for this association remains undetermined. Therefore, the aim of this [...] Read more.

Clinical investigations have highlighted disruptions in bone metabolic processes and abnormal fluctuations in serum indicator levels during the onset of leg disease (LD) in broilers. However, the presence of a genetic causal relationship for this association remains undetermined. Therefore, the aim of this study is to discern the risk factors underlying LD development using 1235 sequenced white-feathered broilers. We employed Mendelian randomization (MR) analysis to assess the associations of bone strength (BS), bone mineral density (BMD), tibial bone weight (TBW), tibial bone length (TBL), tibial bone diameter (TBD), bone ash (BA), ash calcium (Ash Ca), ash phosphorus (Ash P), serum calcium (Ca), serum phosphorus (P), serum alkaline phosphatase (ALP), and serum osteoprotegerin (OPG) with the incidence of LD. Compelling evidence underscores a causal link between the risk of developing LD and decreased BMD (odds ratio (OR) = 0.998; 95% CI: 0.983, 0.993; P < 0.001) and narrower TBD (OR = 0.985, 95% CI: 0.975, 0.994, P = 0.002). Additionally, serum OPG concentrations (OR: 0.995, 95% CI: 0.992, 0.999, P = 0.008) were associated with BMD (OR = 0.0078, 95% CI = 0.0043 to 0.0140, P < 0.001), indicating a robust genetic relationship between ALP concentrations (OR: 0.988, 95% CI: 0.984, 0.993, P < 0.001) and TBD (OR = 0.0046, 95% CI = 0.0026, 0.0083, P < 0.001). Moreover, elevated serum Ca (OR: 0.564, 95% CI: 0.487, 0.655, P < 0.001) and P (OR: 0.614, 95% CI: 0.539, 0.699, P < 0.001) levels were associated with a narrower TBD. Elevated serum levels of Ca, P, ALP, and OPG contribute to disturbances in bone metabolism, while decreased BMD and narrower TBD are associated with a greater risk of developing LD in broilers. This discovery elucidates the metabolic risk factors for LD in broilers and could provide information on LDs, such as osteoporosis, in humans. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

► Show Figures

Figure 1

Journal Description

International Journal of Molecular Sciences

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI