International Journal of Molecular Sciences

18 pages, 4948 KiB

Open AccessArticle

Dickkopf-1 Acts as a Profibrotic Mediator in Progressive Chronic Kidney Disease

by Yung-Chien Hsu, Cheng-Chih Chang, Ching-Chuan Hsieh, Yu-Ting Huang, Ya-Hsueh Shih, Hsiu-Ching Chang, Pey-Jium Chang and Chun-Liang Lin

Int. J. Mol. Sci. 2023, 24(8), 7679; https://doi.org/10.3390/ijms24087679 - 21 Apr 2023

Viewed by 1790

Abstract

Chronic kidney disease (CKD) is a serious public health problem. Due to a high variability in the speed of CKD progression to end-stage renal disease (ESRD) and the critical involvement of Wnt/β-catenin signaling in CKD, we investigated the role of the Wnt antagonist [...] Read more.

Chronic kidney disease (CKD) is a serious public health problem. Due to a high variability in the speed of CKD progression to end-stage renal disease (ESRD) and the critical involvement of Wnt/β-catenin signaling in CKD, we investigated the role of the Wnt antagonist Dickkopf-1 (DKK1) in CKD progression. Our data revealed that patients with CKD stages 4–5 had higher DKK1 levels in their serum and renal tissues than the control subjects. In an 8-year follow-up, the serum DKK1-high group in the enrolled CKD patients showed a faster progression to ESRD than the serum DKK1-low group. Using a rat model of 5/6 nephrectomy (Nx)-induced CKD, we consistently detected elevated serum levels and renal production of DKK1 in 5/6 Nx rats compared to sham-operated rats. Importantly, the knockdown of the DKK1 levels in the 5/6 Nx rats markedly attenuated the CKD-associated phenotypes. Mechanistically, we demonstrated that the treatment of mouse mesangial cells with recombinant DKK1 protein induced not only the production of multiple fibrogenic proteins, but also the expression of endogenous DKK1. Collectively, our findings suggest that DKK1 acts as a profibrotic mediator in CKD, and elevated levels of serum DKK1 may be an independent predictor of faster disease progression to ESRD in patients with advanced CKD. Full article

(This article belongs to the Section Molecular Endocrinology and Metabolism)

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11 pages, 663 KiB

Open AccessArticle

The ACE rs1799752 Variant Is Associated with COVID-19 Severity but Is Independent of Serum ACE Activity in Hospitalized and Recovered Patients

by Ingrid Fricke-Galindo, Ivette Buendia-Roldan, Daniel I. Ponce-Aguilar, Gloria Pérez-Rubio, Leslie Chavez-Galan, Jesús Alanis-Ponce, Karina Pérez-Torres, Daniela Valencia-Pérez Rea, Fernanda Téllez-Quijada, Karol J. Nava-Quiroz, Rafael de Jesús Hernández-Zenteno, Angélica Gutiérrez-Nava and Ramcés Falfán-Valencia

Int. J. Mol. Sci. 2023, 24(8), 7678; https://doi.org/10.3390/ijms24087678 - 21 Apr 2023

Cited by 2 | Viewed by 2108

Abstract

This paper assesses the association of the insertion/deletion ACE (angiotensin-converting enzyme) variant (rs1799752 I/D) and the serum ACE activity with the severity of COVID-19 as well as its impact on post-COVID-19, and we compare these associations with those for patients with non-COVID-19 respiratory [...] Read more.

This paper assesses the association of the insertion/deletion ACE (angiotensin-converting enzyme) variant (rs1799752 I/D) and the serum ACE activity with the severity of COVID-19 as well as its impact on post-COVID-19, and we compare these associations with those for patients with non-COVID-19 respiratory disorders. We studied 1252 patients with COVID-19, 104 subjects recovered from COVID-19, and 74 patients hospitalized with a respiratory disease different from COVID-19. The rs1799752 ACE variant was assessed using TaqMan^® Assays. The serum ACE activity was determined using a colorimetric assay. The DD genotype was related to risk for invasive mechanical ventilation (IMV) requirement as an indicator of COVID-19 severity when compared to the frequencies of II + ID genotypes (p = 0.025, OR = 1.428, 95% CI = 1.046–1.949). In addition, this genotype was significantly higher in COVID-19 and post-COVID-19 groups than in the non-COVID-19 subjects. The serum ACE activity levels were lower in the COVID-19 group (22.30 U/L (13.84–32.23 U/L)), which was followed by the non-COVID-19 (27.94 U/L (20.32–53.36 U/L)) and post-COVID-19 subjects (50.00 U/L (42.16–62.25 U/L)). The DD genotype of the rs1799752 ACE variant was associated with the IMV requirement in patients with COVID-19, and low serum ACE activity levels could be related to patients with severe disease. Full article

(This article belongs to the Special Issue Molecular Research on SARS-CoV-2)

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20 pages, 635 KiB

Open AccessReview

Advances in Platelet-Rich Plasma Treatment for Spinal Diseases: A Systematic Review

by Soya Kawabata, Koji Akeda, Junichi Yamada, Norihiko Takegami, Tatsuhiko Fujiwara, Nobuyuki Fujita and Akihiro Sudo

Int. J. Mol. Sci. 2023, 24(8), 7677; https://doi.org/10.3390/ijms24087677 - 21 Apr 2023

Cited by 15 | Viewed by 4795

Abstract

Spinal diseases are commonly associated with pain and neurological symptoms, which negatively impact patients’ quality of life. Platelet-rich plasma (PRP) is an autologous source of multiple growth factors and cytokines, with the potential to promote tissue regeneration. Recently, PRP has been widely used [...] Read more.

Spinal diseases are commonly associated with pain and neurological symptoms, which negatively impact patients’ quality of life. Platelet-rich plasma (PRP) is an autologous source of multiple growth factors and cytokines, with the potential to promote tissue regeneration. Recently, PRP has been widely used for the treatment of musculoskeletal diseases, including spinal diseases, in clinics. Given the increasing popularity of PRP therapy, this article examines the current literature for basic research and emerging clinical applications of this therapy for treating spinal diseases. First, we review in vitro and in vivo studies, evaluating the potential of PRP in repairing intervertebral disc degeneration, promoting bone union in spinal fusion surgeries, and aiding in neurological recovery from spinal cord injury. Second, we address the clinical applications of PRP in treating degenerative spinal disease, including its analgesic effect on low back pain and radicular pain, as well as accelerating bone union during spinal fusion surgery. Basic research demonstrates the promising regenerative potential of PRP, and clinical studies have reported on the safety and efficacy of PRP therapy for treating several spinal diseases. Nevertheless, further high-quality randomized controlled trials would be required to establish clinical evidence of PRP therapy. Full article

(This article belongs to the Special Issue Regeneration for Spinal Diseases 3.0)

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19 pages, 2831 KiB

Open AccessArticle

β-Conglutins’ Unique Mobile Arm Is a Key Structural Domain Involved in Molecular Nutraceutical Properties of Narrow-Leafed Lupin (Lupinus angustifolius L.)

by Elena Lima-Cabello, Julia Escudero-Feliu, Andreina Peralta-Leal, Pedro Garcia-Fernandez, Kadambot H. M. Siddique, Karam B. Singh, Maria I. Núñez, Josefa León and Jose C. Jimenez-Lopez

Int. J. Mol. Sci. 2023, 24(8), 7676; https://doi.org/10.3390/ijms24087676 - 21 Apr 2023

Cited by 1 | Viewed by 2330

Abstract

Narrow-leafed lupin (NLL; Lupinus angustifolius L.) has multiple nutraceutical properties that may result from unique structural features of β-conglutin proteins, such as the mobile arm at the N-terminal, a structural domain rich in α-helices. A similar domain has not been found in other [...] Read more.

Narrow-leafed lupin (NLL; Lupinus angustifolius L.) has multiple nutraceutical properties that may result from unique structural features of β-conglutin proteins, such as the mobile arm at the N-terminal, a structural domain rich in α-helices. A similar domain has not been found in other vicilin proteins of legume species. We used affinity chromatography to purify recombinant complete and truncated (without the mobile arm domain, tβ5 and tβ7) forms of NLL β5 and β7 conglutin proteins. We then used biochemical and molecular biology techniques in ex vivo and in vitro systems to evaluate their anti-inflammatory activity and antioxidant capacity. The complete β5 and β7 conglutin proteins decreased pro-inflammatory mediator levels (e.g., nitric oxide), mRNA expression levels (iNOS, TNFα, IL-1β), and the protein levels of pro-inflammatory cytokine TNF-α, interleukins (IL-1β, IL-2, IL-6, IL-8, IL-12, IL-17, IL-27), and other mediators (INFγ, MOP, S-TNF-R1/-R2, and TWEAK), and exerted a regulatory oxidative balance effect in cells as demonstrated in glutathione, catalase, and superoxide dismutase assays. The truncated tβ5 and tβ7 conglutin proteins did not have these molecular effects. These results suggest that β5 and β7 conglutins have potential as functional food components due to their anti-inflammatory and oxidative cell state regulatory properties, and that the mobile arm of NLL β-conglutin proteins is a key domain in the development of nutraceutical properties, making NLL β5 and β7 excellent innovative candidates as functional foods. Full article

(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins 2.0)

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Figure 1. Purification and identification of tβ5 and tβ7 conglutin proteins. Two purified conglutin tβ5 and tβ7 proteins stained with Coomassie Brilliant Blue had a high level of purity (>95%) (A); Immunoblotting identified the same two purified β-conglutin proteins as the anti-β-conglutin antibody. MW, molecular weight standard (kDa) (B). Full article ">Figure 2
Assessment of mRNA expression levels of TNF-α, IL-1β, and iNOS genes. Culture cells of HepG2 (A), T2D (B), and healthy control subjects (C). Each group of cells was incubated for 24 h in LPS, LPS+tβ5, LPS+β5, LPS+tβ7, or LPS+β7. Bars show TNF-α (black), IL-1β (punted white), and iNOS (gray) color in each cell type described above. * p ˂ 0.05 LPS vs. control; ** p ˂ 0.05 LPS+tβ5 or tβ7 vs. LPS; # p ˂ 0.05 LPS+β5 vs. LPS; ◆ p ˂ 0.05 LPS+β7 vs. LPS. ◊ p ˂ 0.05 LPS+β5 vs. T2D, and ○ p ˂ 0.05 LPS+β7 vs. T2D in T2D cell cultures. Data represent the mean ± SD of three independent experiments. Full article ">Figure 3
β5 and β7 conglutins reduced the protein levels of TNF-α, IL-1β, and iNOS. Culture cells of HepG2 (A), T2D (B), and healthy control subjects (C). Each group of cells was incubated for 24 h in the presence of LPS, LPS+tβ5, LPS+β5, LPS+tβ7, and LPS+β7. Bars show TNF-α (dark gray), IL-1β (gray), and iNOS (light gray) for each cell type described above. * p ˂ 0.05 LPS vs. control; ** p ˂ 0.05 LPS+tβ5 or tβ7 vs. LPS; # p ˂ 0.05 LPS+β5 vs. LPS; ◆ p ˂ 0.05 LPS+β7 vs. LPS. ★ p ˂ 0.05 β5 vs. T2D, and + p ˂ 0.05 β7 vs. T2D in T2D cell cultures. Data represent the mean ± SD of three independent experiments. Full article ">Figure 4
Effect of NLL β5 and β7 conglutins on CAT and SOD enzymatic activities and GSH production in HepG2 culture cells. CAT (A) and SOD (B) activities and GSH production (C). * p ˂ 0.05 LPS vs. control; ** p ˂ 0.05 LPS+tβ5 or LPS+tβ7 vs. LPS; # or ●# p ˂ 0.05 LPS+β5 vs. LPS; ◆ or ◆# p ˂ 0.05 LPS+β7 vs. LPS. Data represent mean ± SD from three independent experiments. Full article ">Figure 5
Effect of NLL β5 and β7 conglutins on CAT and SOD activities and GSH production in Type II diabetes (T2D) culture cells. CAT (A) and SOD (B) activities and GSH production (C). ★ p ˂ 0.05 T2D vs. tβ5 or tβ7; ★★ p ˂ 0.05 β5 vs. T2D; ++ p ˂ 0.05 β7 vs. T2D. Data represent mean ± SD from three independent experiments. Full article ">Figure 6
Effect of NLL β5 and β7 conglutins on CAT and SOD activities and GSH production in healthy subject culture cells. CAT (A) and SOD (B) activities and GSH production (C). * p ˂ 0.05 LPS vs. control; # p ˂ 0.05 LPS+β5 vs. LPS; ◆ p ˂ 0.05 LPS+β7 vs. LPS. Data represent mean ± SD from three independent experiments. Full article ">Figure 7
Effect of β5 and β7 conglutins on nitric oxide production. Culture cells of HepG2 (A), T2D (B), and healthy subjects (C). Each group of cells was incubated for 24 h in the presence of LPS, LPS+tβ5, LPS+β5, LPS+tβ7, or LPS+β7. * p ˂ 0.05 LPS vs. control; ** p ˂ 0.05 LPS+tβ5 or tβ7 vs. LPS; # p ˂ 0.05 LPS+β5 vs. LPS; ◆ p ˂ 0.05 LPS+β7 vs. LPS. ★ p ˂ 0.05 β5 vs. T2D and + p ˂ 0.05 β7 vs. T2D in T2D cell cultures. Data represent the mean ± SD of three independent experiments. Full article ">

18 pages, 4340 KiB

Open AccessArticle

Skin Microbiome in Prurigo Nodularis

by Klaudia Tutka, Magdalena Żychowska, Anna Żaczek, Karolina Maternia-Dudzik, Jakub Pawełczyk, Dominik Strapagiel, Jakub Lach and Adam Reich

Int. J. Mol. Sci. 2023, 24(8), 7675; https://doi.org/10.3390/ijms24087675 - 21 Apr 2023

Cited by 6 | Viewed by 3378

Abstract

Prurigo nodularis (PN) is a chronic condition characterized by the presence of nodular lesions accompanied by intense pruritus. The disease has been linked to several infectious factors, but data on the direct presence of microorganisms in the lesions of PN are scarce. The [...] Read more.

Prurigo nodularis (PN) is a chronic condition characterized by the presence of nodular lesions accompanied by intense pruritus. The disease has been linked to several infectious factors, but data on the direct presence of microorganisms in the lesions of PN are scarce. The aim of this study was to evaluate the diversity and composition of the bacterial microbiome in PN lesions by targeting the region V3-V4 of 16S rRNA. Skin swabs were obtained from active nodules in 24 patients with PN, inflammatory patches of 14 patients with atopic dermatitis (AD) and corresponding skin areas of 9 healthy volunteers (HV). After DNA extraction, the V3-V4 region of the bacterial 16S rRNA gene was amplified. Sequencing was performed using the Illumina platform on the MiSeq instrument. Operational taxonomic units (OTU) were identified. The identification of taxa was carried out using the Silva v.138 database. There was no statistically significant difference in the alpha-diversity (intra-sample diversity) between the PN, AD and HV groups. The beta-diversity (inter-sample diversity) showed statistically significant differences between the three groups on a global level and in paired analyses. Staphylococcus was significantly more abundant in samples from PN and AD patients than in controls. The difference was maintained across all taxonomic levels. The PN microbiome is highly similar to that of AD. It remains unclear whether the disturbed composition of the microbiome and the domination of Staphylococcus in PN lesions may be the trigger factor of pruritus and lead to the development of cutaneous changes or is a secondary phenomenon. Our preliminary results support the theory that the composition of the skin microbiome in PN is altered and justify further research on the role of the microbiome in this debilitating condition. Full article

(This article belongs to the Special Issue Microbial Enzymes and Metabolites)

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14 pages, 985 KiB

Open AccessReview

Molecular and Physiological Determinants of Amyotrophic Lateral Sclerosis: What the DJ-1 Protein Teaches Us

by Federica Sandrelli and Marco Bisaglia

Int. J. Mol. Sci. 2023, 24(8), 7674; https://doi.org/10.3390/ijms24087674 - 21 Apr 2023

Cited by 3 | Viewed by 2149

Abstract

Amyotrophic lateral sclerosis (ALS) is an adult-onset disease which causes the progressive degeneration of cortical and spinal motoneurons, leading to death a few years after the first symptom onset. ALS is mainly a sporadic disorder, and its causative mechanisms are mostly unclear. About [...] Read more.

Amyotrophic lateral sclerosis (ALS) is an adult-onset disease which causes the progressive degeneration of cortical and spinal motoneurons, leading to death a few years after the first symptom onset. ALS is mainly a sporadic disorder, and its causative mechanisms are mostly unclear. About 5–10% of cases have a genetic inheritance, and the study of ALS-associated genes has been fundamental in defining the pathological pathways likely also involved in the sporadic forms of the disease. Mutations affecting the DJ-1 gene appear to explain a subset of familial ALS forms. DJ-1 is involved in multiple molecular mechanisms, acting primarily as a protective agent against oxidative stress. Here, we focus on the involvement of DJ-1 in interconnected cellular functions related to mitochondrial homeostasis, reactive oxygen species (ROS) levels, energy metabolism, and hypoxia response, in both physiological and pathological conditions. We discuss the possibility that impairments in one of these pathways may affect the others, contributing to a pathological background in which additional environmental or genetic factors may act in favor of the onset and/or progression of ALS. These pathways may represent potential therapeutic targets to reduce the likelihood of developing ALS and/or slow disease progression. Full article

(This article belongs to the Special Issue Molecular and Physiological Determinants of Amyotrophic Lateral Sclerosis)

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20 pages, 6380 KiB

Open AccessArticle

Molecular Integrative Analysis of the Inhibitory Effects of Dipeptides on Amyloid β Peptide 1–42 Polymerization

by Nan Yuan, Lianmeng Ye, Yan Sun, Hao Wu, Zhengpan Xiao, Wanmeng Fu, Zuqian Chen, Yechun Pei, Yi Min and Dayong Wang

Int. J. Mol. Sci. 2023, 24(8), 7673; https://doi.org/10.3390/ijms24087673 - 21 Apr 2023

Cited by 1 | Viewed by 1810

Abstract

The major pathological feature of Alzheimer’s disease (AD) is the aggregation of amyloid β peptide (Aβ) in the brain. Inhibition of Aβ₄₂ aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of [...] Read more.

The major pathological feature of Alzheimer’s disease (AD) is the aggregation of amyloid β peptide (Aβ) in the brain. Inhibition of Aβ₄₂ aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of aggregated Aβ with ThT, cell viability, and flow cytometry for the detection of reactive oxygen species (ROS) and apoptosis. Aβ₄₂ polymerizes into fibrils due to hydrophobic interactions to minimize free energy, adopting a β-strand structure and forming three hydrophobic areas. Eight dipeptides were screened by molecular docking from a structural database of 20 L-α-amino acids, and the docking was validated by molecular dynamics (MD) analysis of binding stability and interaction potential energy. Among the dipeptides, arginine dipeptide (RR) inhibited Aβ₄₂ aggregation the most. The ThT assay and EM revealed that RR reduced Aβ₄₂ aggregation, whereas the circular dichroism spectroscopy analysis showed a 62.8% decrease in β-sheet conformation and a 39.3% increase in random coiling of Aβ₄₂ in the presence of RR. RR also significantly reduced the toxicity of Aβ₄₂ secreted by SH-SY5Y cells, including cell death, ROS production, and apoptosis. The formation of three hydrophobic regions and polymerization of Aβ₄₂ reduced the Gibbs free energy, and RR was the most effective dipeptide at interfering with polymerization. Full article

(This article belongs to the Section Molecular Informatics)

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34 pages, 1640 KiB

Open AccessReview

Anti-Glucotoxicity Effect of Phytoconstituents via Inhibiting MGO-AGEs Formation and Breaking MGO-AGEs

by Neera Yadav, Jyoti Dnyaneshwar Palkhede and Sun-Yeou Kim

Int. J. Mol. Sci. 2023, 24(8), 7672; https://doi.org/10.3390/ijms24087672 - 21 Apr 2023

Cited by 6 | Viewed by 3038

Abstract

The therapeutic benefits of phytochemicals in the treatment of various illnesses and disorders are well documented. They show significant promise for the discovery and creation of novel medications for treating a variety of human diseases. Numerous phytoconstituents have shown antibiotic, antioxidant, and wound-healing [...] Read more.

The therapeutic benefits of phytochemicals in the treatment of various illnesses and disorders are well documented. They show significant promise for the discovery and creation of novel medications for treating a variety of human diseases. Numerous phytoconstituents have shown antibiotic, antioxidant, and wound-healing effects in the conventional system. Traditional medicines based on alkaloids, phenolics, tannins, saponins, terpenes, steroids, flavonoids, glycosides, and phytosterols have been in use for a long time and are crucial as alternative treatments. These phytochemical elements are crucial for scavenging free radicals, capturing reactive carbonyl species, changing protein glycation sites, inactivating carbohydrate hydrolases, fighting pathological conditions, and accelerating the healing of wounds. In this review, 221 research papers have been reviewed. This research sought to provide an update on the types and methods of formation of methylglyoxal-advanced glycation end products (MGO-AGEs) and molecular pathways induced by AGEs during the progression of the chronic complications of diabetes and associated diseases as well as to discuss the role of phytoconstituents in MGO scavenging and AGEs breaking. The development and commercialization of functional foods using these natural compounds can provide potential health benefits. Full article

(This article belongs to the Special Issue Novel Natural Compound for Wound and Tissue Repair and Regeneration)

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16 pages, 5112 KiB

Open AccessArticle

Oscillation of Autophagy Induction under Cellular Stress and What Lies behind It, a Systems Biology Study

by Bence Hajdú, Luca Csabai, Margita Márton, Marianna Holczer, Tamás Korcsmáros and Orsolya Kapuy

Int. J. Mol. Sci. 2023, 24(8), 7671; https://doi.org/10.3390/ijms24087671 - 21 Apr 2023

Cited by 4 | Viewed by 1930

Abstract

One of the main inducers of autophagy-dependent self-cannibalism, called ULK1, is tightly regulated by the two sensor molecules of nutrient conditions and energy status, known as mTOR and AMPK kinases, respectively. Recently, we developed a freely available mathematical model to explore the oscillatory [...] Read more.

One of the main inducers of autophagy-dependent self-cannibalism, called ULK1, is tightly regulated by the two sensor molecules of nutrient conditions and energy status, known as mTOR and AMPK kinases, respectively. Recently, we developed a freely available mathematical model to explore the oscillatory characteristic of the AMPK-mTOR-ULK1 regulatory triangle. Here, we introduce a systems biology analysis to explain in detail the dynamical features of the essential negative and double-negative feedback loops and also the periodic repeat of autophagy induction upon cellular stress. We propose an additional regulatory molecule in the autophagy control network that delays some of AMPK’s effect on the system, making the model output more consistent with experimental results. Furthermore, a network analysis on AutophagyNet was carried out to identify which proteins could be the proposed regulatory components in the system. These regulatory proteins should satisfy the following rules: (1) they are induced by AMPK; (2) they promote ULK1; (3) they down-regulate mTOR upon cellular stress. We have found 16 such regulatory components that have been experimentally proven to satisfy at least two of the given rules. Identifying such critical regulators of autophagy induction could support anti-cancer- and ageing-related therapeutic efforts. Full article

(This article belongs to the Special Issue Complexity and Networking in Molecular Systems)

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The characteristic of the time-delayed ULK1-mTORC1-AMPK regulatory triangle. The simple wiring diagram of autophagy induction controlled by an extra regulatory protein (REG). Dashed lines show how the molecules can influence each other. Blocked end lines denote inhibition. Full article ">Figure 2
The characteristic of the time-delayed ULK1-mTOR-AMPK regulatory triangle upon cellular stress. (A) The simple wiring diagram of autophagy induction controlled by an extra protein upon (upper panel) cellular stress (stress = 0.5) or (lower panel) rapamycin treatment (mTORT = 0.5). Dashed lines show how the molecules can influence each other. Blocked end lines denote inhibition. (B) Phase plane diagrams are plotted upon (upper panel) cellular stress (stress = 0.5) or (lower panel) rapamycin treatment (mTORT = 0.5). The balance curves of ULK1 (green) and AMPK (blue) are plotted. Intersections of nullclines represent unstable (unfilled circle) steady states. Trajectories are depicted with dotted grey lines. (C) The temporal dynamics is simulated under (upper panel) cellular stress (stress = 0.5) or (lower panel) rapamycin treatment (mTORT = 0.5). The relative activity of mTOR, AMPK, ULK1 and REG is shown. Full article ">Figure 3
The characteristic of double-negative feedback between ULK1 and mTOR. (A) Wiring diagram of the ULK1-mTOR double-negative feedback loop. Dashed lines show how the molecules can influence each other. Blocked end lines denote inhibition. Grey colour means that the connection and component are removed from the network. (B) Phase plane diagrams are plotted upon various levels of stress. The balance curves of ULK1 (green) and mTOR (red) are plotted. The phase plane is shown for stress = 0.1, 0.5, 1 and mTORT = 0.1, 1. Intersections of nullclines represent the stable (filled circle) and unstable (unfilled circle) steady states. Signal response curves of (C) ULK1 and (D) mTOR are shown. The solid lines in the signal response curve denote stable states, while dashed lines depict the unstable state. Full article ">Figure 4
The introduction of the negative feedback loop between ULK1 and AMPK. (A) The wiring diagram of the ULK1-AMPK-mTOR regulatory network upon (upper panel) cellular stress (stress = 5) or (lower panel) rapamycin treatment (mTORT = 0.01). Dashed lines show how the molecules can influence each other. Blocked end lines denote inhibition. Grey colour means the connection and component are removed from the network. (B) Phase plane diagrams are plotted upon (upper panel) starvation (stress = 5) or (lower panel) rapamycin treatment (mTORT = 0.01). The balance curves of ULK1 (green) and AMPK (blue) are plotted. Intersections of nullclines represent the stable (filled circle) and unstable (unfilled circle) steady states. Trajectories are depicted with dotted grey lines. Full article ">Figure 5
The characteristic of the ULK1-mTOR-AMPK regulatory triangle. (A) The wiring diagram of ULK1-AMPK-mTOR regulatory network upon (upper panel) cellular stress (stress = 3) or (lower panel) rapamycin treatment (mTORT = 0.01). Dashed lines show how the molecules can influence each other. Blocked end lines denote inhibition. Grey colour means that the connection and component are removed from the network. (B) Phase plane diagrams are plotted upon (upper panel) cellular stress (stress = 3) or (lower panel) rapamycin treatment (mTORT = 0.01). The balance curves of ULK1 (green) and mTORC1 (red) are plotted. Intersections of nullclines represent the stable (filled circle) and unstable (unfilled circle) steady states. Trajectories are depicted with dotted grey lines. Full article ">Figure 6
Results of network analysis. (A) Network image of filtered dataset from AutophagyNet. The AMPK-mTOR-ULK1 triangle is shown at the bottom, with proteins meeting all (CDC37) or two of the defined criteria. Above, the network of indirect regulators is shown. (B) Top 10 significantly enriched biological functions of the upstream network of CDC37. (C) Top 10 significantly enriched biological functions of the upstream network of CFTR. (D) Top 10 significantly enriched biological functions of the upstream network of PDPK1. (E) Top 10 significantly enriched biological functions of the upstream network of TRAF6. Full article ">Figure 7
The extra protein acts like a key “regulator” of autophagy induction upon cellular stress. (A) The simple wiring diagram of autophagy induction controlled by an extra protein upon cellular stress when (upper panel) REG -> ULK1 (kaulk’ = 0) or (lower panel) REG -| mTOR (kimtor”’ = 0) regulatory connections are missing (see grey lines). Dashed lines show how the molecules can influence each other. Blocked end lines denote inhibition. (B) Phase plane diagrams are plotted upon cellular stress when (upper panel) REG -> ULK1 (kaulk’ = 0) or (lower panel) REG -| mTOR (kimtor”’ = 0) regulatory connections are missing. The balance curves of ULK1 (green) and mTOR (red) are plotted. Intersections of nullclines represent the stable (filled circle) and unstable (unfilled circle) steady states. Trajectories are depicted with dotted grey lines. (C) The temporal dynamics is simulated under cellular stress when (upper panel) REG -> ULK1 (kaulk’ = 0) or (lower panel) REG -| mTOR (kimtor”’ = 0) regulatory connections are missing. The relative activity of mTOR, AMPK, ULK1 and REG is shown. Full article ">

18 pages, 2728 KiB

Open AccessArticle

Kinetic and Regulatory Properties of Yarrowia lipolytica Aconitate Hydratase as a Model-Indicator of Cell Redox State under pH Stress

by Tatyana I. Rakhmanova, Varvara Yu. Sekova, Natalya N. Gessler, Elena P. Isakova, Yulia I. Deryabina, Tatyana N. Popova, Yevgeniya I. Shurubor and Boris F. Krasnikov

Int. J. Mol. Sci. 2023, 24(8), 7670; https://doi.org/10.3390/ijms24087670 - 21 Apr 2023

Viewed by 1639

Abstract

This paper presents an analysis of the regulation activity of the partially purified preparations of cellular aconitate hydratase (AH) on the yeast Yarrowia lipolytica cultivated at extreme pH. As a result of purification, enzyme preparations were obtained from cells grown on media at [...] Read more.

This paper presents an analysis of the regulation activity of the partially purified preparations of cellular aconitate hydratase (AH) on the yeast Yarrowia lipolytica cultivated at extreme pH. As a result of purification, enzyme preparations were obtained from cells grown on media at pH 4.0, 5.5, and 9.0, purified by 48-, 46-, and 51-fold and having a specific activity of 0.43, 0.55 and 0.36 E/mg protein, respectively. The kinetic parameters of preparations from cells cultured at extreme pH demonstrated: (1) an increase in the affinity for citrate and isocitrate; and (2) a shift in the pH optima to the acidic and alkaline side in accordance with the modulation of the medium pH. The regulatory properties of the enzyme from cells subjected to alkaline stress showed increased sensitivity to Fe²⁺ ions and high peroxide resistance. Reduced glutathione (GSH) stimulated AH, while oxidized glutathione (GSSG) inhibited AH. A more pronounced effect of both GSH and GSSG was noted for the enzyme obtained from cells grown at pH 5.5. The data obtained provide new approaches to the use of Y. lipolytica as a model of eukaryotic cells demonstrating the development of a stress-induced pathology and to conducting a detailed analysis of enzymatic activity for its correction. Full article

(This article belongs to the Special Issue 21st Century Enzymology: Further Advances in Identification and Characterization of Enzymes)

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22 pages, 2399 KiB

Open AccessReview

Biochemical Screening for Fetal Trisomy 21: Pathophysiology of Maternal Serum Markers and Involvement of the Placenta

by Jean Guibourdenche, Marie-Clémence Leguy, Guillaume Pidoux, Marylise Hebert-Schuster, Christelle Laguillier, Olivia Anselem, Gilles Grangé, Fidéline Bonnet and Vassilis Tsatsaris

Int. J. Mol. Sci. 2023, 24(8), 7669; https://doi.org/10.3390/ijms24087669 - 21 Apr 2023

Cited by 5 | Viewed by 5486

Abstract

It is now well established that maternal serum markers are often abnormal in fetal trisomy 21. Their determination is recommended for prenatal screening and pregnancy follow-up. However, mechanisms leading to abnormal maternal serum levels of such markers are still debated. Our objective was [...] Read more.

It is now well established that maternal serum markers are often abnormal in fetal trisomy 21. Their determination is recommended for prenatal screening and pregnancy follow-up. However, mechanisms leading to abnormal maternal serum levels of such markers are still debated. Our objective was to help clinicians and scientists unravel the pathophysiology of these markers via a review of the main studies published in this field, both in vivo and in vitro, focusing on the six most widely used markers (hCG, its free subunit hCGβ, PAPP-A, AFP, uE3, and inhibin A) as well as cell-free feto–placental DNA. Analysis of the literature shows that mechanisms underlying each marker’s regulation are multiple and not necessarily directly linked with the supernumerary chromosome 21. The crucial involvement of the placenta is also highlighted, which could be defective in one or several of its functions (turnover and apoptosis, endocrine production, and feto–maternal exchanges and transfer). These defects were neither constant nor specific for trisomy 21, and might be more or less pronounced, reflecting a high variability in placental immaturity and alteration. This explains why maternal serum markers can lack both specificity and sensitivity, and are thus restricted to screening. Full article

(This article belongs to the Special Issue Placental Related Disorders of Pregnancy 2.0.)

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Structure and secretion of hCG in vivo (A) and in vitro (B). hCG is a dimeric glycoprotein composed of a common α subunit (hCGα), and a specific ß subunit (hCGβ). The secretion of hCG and its free ß subunit in maternal blood increase during the first trimester of gestation, and decrease thereafter; the secretion of its free α subunit increases all through pregnancy in line with placental mass (A). In vitro and vivo, the morphological differentiation of the villous cytotrophoblasts (VCT) into a syncytiotrophoblast (ST) is mainly associated with functional differentiation, as assessed by the increasing production of hCG and its subunits (B). Full article ">Figure 2
Human placental definitive villi and trophoblastic tissue. From the end of the first trimester of gestation, the human placenta is composed of two types of villi: the anchoring villi with extravillous cytotrophoblasts (EVCT) that proliferate, migrate, and invade the maternal uterine wall to reach the spiral artery; the floating villi composed of villous cytotrophoblasts (VCT), aggregating and fusing to form the syncytiotrophoblast (ST) on the borders of floating villi in contact with maternal blood as from 10 to 12 WG. EVCT is likely to be the major source of maternal serum markers in early pregnancy, whereas ST becomes the major source at the end of the first trimester of gestation. Full article ">Figure 3
Structure and main functions of pregnancy-associated plasmatic protein A (PAPP-A). Full article ">Figure 4
Synthesis and secretion of alpha feto protein (AFP) during pregnancy. AFP is mainly synthetized by the fetal liver and secreted in fetal blood. It is then excreted by the immature fetal kidneys via urine in amniotic fluid, peaking at around 14 WG. Thereafter, renal AFP filtration decreases with kidney maturation and therefore its amniotic levels fall until the end of pregnancy. AFP reaches the maternal circulation through the membranes and placenta. This transfer, which may involve lectins, is very low and reaches a plateau at about 32 WG. Full article ">Figure 5
Synthesis and secretion of estriol during pregnancy. The human placenta lacks cytochrome P450 17alpha-hydroxylase-17:20 lyase, which is required to convert progestins into androgens (a). Thus, the placenta participates in the enzymatic conversion of fetal 16α-OH-DHEA-S, DHEA-S (b), and the maternal DHEA-S (b’) into E3, by sulfatase (STS), and aromatase activities (c). Estrogens diffuse into both the fetal and maternal compartments (d). estriol (E3), estradiol (E2), estrone (E1), dehydroepiandrostenedione (DHEA), sulfate of dehydroepiandrostenedione (SDHEA), delta 4 androstenedione (Δ4A). Full article ">Figure 6
Physiopathology of maternal serum markers in trisomy 21-affected pregnancies. The human placenta releases soluble markers into the maternal blood as well as cells and cell-free DNA. Soluble markers can be of fetal origin, such as the alpha feto protein (AFP), of feto–placental origin, such as the unconjugated estriol (uE3), or of placental origin, such as the human chorionic gonadotropin (hCG) and its free beta subunit (hCGβ), the pregnancy-associated plasmatic protein A (PAPP-A), and the inhibin A (inhibin A). In trisomy 21-affected pregnancies, both placental and fetal functions are disrupted, leading to the decrease (↓) or the increase (↑) of their concentrations in maternal blood. Full article ">

25 pages, 1560 KiB

Open AccessArticle

Sow-Offspring Diets Supplemented with Probiotics and Synbiotics Are Associated with Offspring’s Growth Performance and Meat Quality

by Qian Zhu, Md. Abul Kalam Azad, Haibo Dong, Chenjian Li, Ruixuan Li, Yating Cheng, Yang Liu, Yulong Yin and Xiangfeng Kong

Int. J. Mol. Sci. 2023, 24(8), 7668; https://doi.org/10.3390/ijms24087668 - 21 Apr 2023

Cited by 5 | Viewed by 2379

Abstract

Probiotics and synbiotics supplementation have been shown to play potential roles in animal production. The present study aimed to evaluate the effects of dietary probiotics and synbiotics supplementation to sows during gestation and lactation and to offspring pigs (sow-offspring) on offspring pigs’ growth [...] Read more.

Probiotics and synbiotics supplementation have been shown to play potential roles in animal production. The present study aimed to evaluate the effects of dietary probiotics and synbiotics supplementation to sows during gestation and lactation and to offspring pigs (sow-offspring) on offspring pigs’ growth performance and meat quality. Sixty-four healthy Bama mini-pigs were selected and randomly allocated into four groups after mating: the control, antibiotics, probiotics, and synbiotics groups. After weaning, two offspring pigs per litter were selected, and four offspring pigs from two litters were merged into one pen. The offspring pigs were fed a basal diet and the same feed additive according to their corresponding sows, representing the control group (Con group), sow-offspring antibiotics group (S-OA group), sow-offspring probiotics group (S-OP group), and sow-offspring synbiotics group (S-OS group). Eight pigs per group were euthanized and sampled at 65, 95, and 125 d old for further analyses. Our findings showed that probiotics supplementation in sow-offspring diets promoted growth and feed intake of offspring pigs during 95–125 d old. Moreover, sow-offspring diets supplemented with probiotics and synbiotics altered meat quality (meat color, pH_45min, pH_24h, drip loss, cooking yield, and shear force), plasma UN and AMM levels, and gene expressions associated with muscle-fiber types (MyHCI, MyHCIIa, MyHCIIx, and MyHCIIb) and muscle growth and development (Myf5, Myf6, MyoD, and MyoG). This study provides a theoretical basis for the maternal-offspring integration regulation of meat quality by dietary probiotics and synbiotics supplementation. Full article

(This article belongs to the Topic Application of Probiotics and Their Potential Health Benefits)

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Effects of probiotics and synbiotics supplementation in sow-offspring diets on mRNA expressions of myosin heavy chain (MyHC) isoforms and myogenic regulatory factors (MRFs) in the skeletal muscle of offspring pigs at 65, 95, and 125 d old. (A) and (E) are mRNA expressions of MyHC isoforms in the longissimus doris muscle (LDM) and psoas major muscle (PMM), respectively. (B–D) and (F−H) are mRNA expressions of MRFs in the LDM and PMM, respectively. a–c Different letters mean significant differences (p < 0.05). MyHCI, myosin heavy chain I; MyHCIIa, myosin heavy chain IIa; MyHCIIb, myosin heavy chain IIb; MyHCIIx, myosin heavy chain IIx; MyoD, myogenic differentiation factor; MyoG, myogenin; Myf5, myogenic factor 5; Myf6, myogenic factor 6; IGF1, insulin-like growth factor 1; MAFbx, muscle atrophy Fbox-1 protein; MSTN, myostatin. Con group: sow and offspring pigs fed with a basal diet; S-OA group: sow and offspring pigs fed with antibiotics; S-OP group: sow and offspring pigs fed with probiotics; S-OS group: sow and offspring pigs fed with synbiotics. The replicates per group at 65 d old were 8. The replicates of the Con, S-OA, S-OP, and S-OS groups at 95 d old were 8, 8, 8, and 7, respectively. The replicates of the Con, S-OA, S-OP, and S-OS groups at 125 d old were 8, 5, 6, and 6, respectively. Full article ">Figure 2
Schematic presentation of the experimental design. Full article ">

24 pages, 9827 KiB

Open AccessArticle

Hybrid Silver-Containing Materials Based on Various Forms of Bacterial Cellulose: Synthesis, Structure, and Biological Activity

by Alexander Vasil’kov, Ivan Butenko, Alexander Naumkin, Anastasiia Voronova, Alexandre Golub, Mikhail Buzin, Eleonora Shtykova, Vladimir Volkov and Vera Sadykova

Int. J. Mol. Sci. 2023, 24(8), 7667; https://doi.org/10.3390/ijms24087667 - 21 Apr 2023

Cited by 5 | Viewed by 2436

Abstract

Sustained interest in the use of renewable resources for the production of medical materials has stimulated research on bacterial cellulose (BC) and nanocomposites based on it. New Ag-containing nanocomposites were obtained by modifying various forms of BC with Ag nanoparticles prepared by metal–vapor [...] Read more.

Sustained interest in the use of renewable resources for the production of medical materials has stimulated research on bacterial cellulose (BC) and nanocomposites based on it. New Ag-containing nanocomposites were obtained by modifying various forms of BC with Ag nanoparticles prepared by metal–vapor synthesis (MVS). Bacterial cellulose was obtained in the form of films (BCF) and spherical BC beads (SBCB) by the Gluconacetobacter hansenii GH-1/2008 strain under static and dynamic conditions. The Ag nanoparticles synthesized in 2-propanol were incorporated into the polymer matrix using metal-containing organosol. MVS is based on the interaction of extremely reactive atomic metals formed by evaporation in vacuum at a pressure of 10⁻² Pa with organic substances during their co-condensation on the cooled walls of a reaction vessel. The composition, structure, and electronic state of the metal in the materials were characterized by transmission and scanning electron microscopy (TEM, SEM), powder X-ray diffraction (XRD), small-angle X-ray scattering (SAXS) and X-ray photoelectron spectroscopy (XPS). Since antimicrobial activity is largely determined by the surface composition, much attention was paid to studying its properties by XPS, a surface-sensitive method, at a sampling depth about 10 nm. C 1s and O 1s spectra were analyzed self-consistently. XPS C 1s spectra of the original and Ag-containing celluloses showed an increase in the intensity of the C-C/C-H groups in the latter, which are associated with carbon shell surrounding metal in Ag nanoparticles (Ag NPs). The size effect observed in Ag 3d spectra evidenced on a large proportion of silver nanoparticles with a size of less than 3 nm in the near-surface region. Ag NPs in the BC films and spherical beads were mainly in the zerovalent state. BC-based nanocomposites with Ag nanoparticles exhibited antimicrobial activity against Bacillus subtilis, Staphylococcus aureus, Escherichia coli bacteria and Candida albicans and Aspergillus niger fungi. It was found that AgNPs/SBCB nanocomposites are more active than Ag NPs/BCF samples, especially against Candida albicans and Aspergillus niger fungi. These results increase the possibility of their medical application. Full article

(This article belongs to the Special Issue Recent Advances in Cellulose Chemistry)

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13 pages, 7521 KiB

Open AccessCase Report

Coexisting Nodular Sclerosis Hodgkin Lymphoma and Kimura’s Disease: A Case Report and Literature Review

by Chih-Chun Lee, Sing-Ya Chang, Wen-Chieh Teng, Chih-Ju Wu, Chi-Hung Liu, Szu-Wei Huang, Chiao-En Wu, Kuang-Hui Yu and Tien-Ming Chan

Int. J. Mol. Sci. 2023, 24(8), 7666; https://doi.org/10.3390/ijms24087666 - 21 Apr 2023

Viewed by 2077

Abstract

Kimura’s disease (KD) is a rare lymphoproliferative fibroinflammatory disorder that commonly affects the subcutaneous tissue and lymph nodes of the head and neck. The condition is a reactive process involving T helper type 2 cytokines. Concurrent malignancies have not been described. Differential diagnosis [...] Read more.

Kimura’s disease (KD) is a rare lymphoproliferative fibroinflammatory disorder that commonly affects the subcutaneous tissue and lymph nodes of the head and neck. The condition is a reactive process involving T helper type 2 cytokines. Concurrent malignancies have not been described. Differential diagnosis with lymphoma can be challenging without tissue biopsy. Here, we present the first reported case of coexisting KD and eosinophilic nodular sclerosis Hodgkin lymphoma of the right cervical lymphatics in a 72-year-old Taiwanese man. Full article

(This article belongs to the Section Molecular Immunology)

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Histopathological examination of an enlarged right cervical lymph node; collected via complete surgical resection at our institution. (a–c): Hematoxylin–eosin staining showed the follicular hyperplasia of the lymphoid tissue with well-formed germinal centers, interfollicular dense eosinophilic infiltrates, eosinophilic microabscesses, vascular proliferation, and prominent interstitial fibrosis. Full article ">Figure 1 Cont.
Histopathological examination of an enlarged right cervical lymph node; collected via complete surgical resection at our institution. (a–c): Hematoxylin–eosin staining showed the follicular hyperplasia of the lymphoid tissue with well-formed germinal centers, interfollicular dense eosinophilic infiltrates, eosinophilic microabscesses, vascular proliferation, and prominent interstitial fibrosis. Full article ">Figure 2
Histopathological examination of enlarged right cervical lymph node; obtained from his previous healthcare provider. (a–c): Hematoxylin–eosin staining demonstrated a thick fibrous capsule, focal nodular sclerosis, near-total nodal structure effacement, and increased vascularity. Scattered Hodgkin-like and Reed–Sternberg-like cells were seen in the background of small lymphocytes, plasma cells, neutrophils, histiocytes, and an excess of eosinophils. Full article ">Figure 2 Cont.
Histopathological examination of enlarged right cervical lymph node; obtained from his previous healthcare provider. (a–c): Hematoxylin–eosin staining demonstrated a thick fibrous capsule, focal nodular sclerosis, near-total nodal structure effacement, and increased vascularity. Scattered Hodgkin-like and Reed–Sternberg-like cells were seen in the background of small lymphocytes, plasma cells, neutrophils, histiocytes, and an excess of eosinophils. Full article ">Figure 3
Immunohistochemical studies of an enlarged right cervical lymph node; obtained from his previous healthcare provider. (a–c): The Reed–Sternberg-like cells were positive for CD20, CD30, and PAX5, respectively. Full article ">Figure 3 Cont.
Immunohistochemical studies of an enlarged right cervical lymph node; obtained from his previous healthcare provider. (a–c): The Reed–Sternberg-like cells were positive for CD20, CD30, and PAX5, respectively. Full article ">Figure 4
(a,b): Whole-body positron emission tomography-computed tomography revealed malignant involvement of the right cervical level III and V and supraclavicular lymph nodes. The uptake of radiation was elevated to standardized uptake value (SUV) 9.19, 3.79, and 10.15, respectively, corresponding to a score of 4 (high probability of malignancy). Full article ">Figure 4 Cont.
(a,b): Whole-body positron emission tomography-computed tomography revealed malignant involvement of the right cervical level III and V and supraclavicular lymph nodes. The uptake of radiation was elevated to standardized uptake value (SUV) 9.19, 3.79, and 10.15, respectively, corresponding to a score of 4 (high probability of malignancy). Full article ">

3 pages, 458 KiB

Open AccessEditorial

For Special Issue “Molecular Mechanisms of Responses to Low-Intensity Exposures 2.0” of International Journal of Molecular Sciences

by Nadezhda S. Kudryasheva

Int. J. Mol. Sci. 2023, 24(8), 7665; https://doi.org/10.3390/ijms24087665 - 21 Apr 2023

Viewed by 1169

Abstract

The intention of this Special Issue is to highlight the peculiarities of low-intensity/low-concentration exposures for organisms and to examine the molecular mechanisms of the organismal responses [...] Full article

(This article belongs to the Special Issue Molecular Mechanisms of Responses to Low-Intensity Exposures 2.0)

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15 pages, 8949 KiB

Open AccessArticle

Human Embryonic Stem-Cell-Derived Exosomes Repress NLRP3 Inflammasome to Alleviate Pyroptosis in Nucleus Pulposus Cells by Transmitting miR-302c

by Yawen Yu, Wenting Li, Tinghui Xian, Mei Tu, Hao Wu and Jiaqing Zhang

Int. J. Mol. Sci. 2023, 24(8), 7664; https://doi.org/10.3390/ijms24087664 - 21 Apr 2023

Cited by 9 | Viewed by 2175

Abstract

Recent studies have shown that the NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome is extensively activated in the process of intervertebral disc degeneration (IVDD), leading to the pyroptosis of nucleus pulposus cells (NPCs) and the exacerbation of the pathological development of [...] Read more.

Recent studies have shown that the NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome is extensively activated in the process of intervertebral disc degeneration (IVDD), leading to the pyroptosis of nucleus pulposus cells (NPCs) and the exacerbation of the pathological development of the intervertebral disc (IVD). Exosomes derived from human embryonic stem cells (hESCs-exo) have shown great therapeutic potential in degenerative diseases. We hypothesized that hESCs-exo could alleviate IVDD by downregulating NLRP3. We measured the NLRP3 protein levels in different grades of IVDD and the effect of hESCs-exo on the H₂O₂-induced pyroptosis of NPCs. Our results indicate that the expression of NLRP3 was upregulated with the increase in IVD degeneration. hESCs-exo were able to reduce the H₂O₂-mediated pyroptosis of NPCs by downregulating the expression levels of NLRP3 inflammasome-related genes. Bioinformatics software predicted that miR-302c, an embryonic stem-cell-specific RNA, can inhibit NLRP3, thereby alleviating the pyroptosis of NPCs, and this was further verified by the overexpression of miR-302c in NPCs. In vivo experiments confirmed the above results in a rat caudal IVDD model. Our study demonstrates that hESCs-exo could inhibit excessive NPC pyroptosis by downregulating the NLRP3 inflammasome during IVDD, and miR-302c may play a key role in this process. Full article

(This article belongs to the Special Issue Regeneration for Spinal Diseases 3.0)

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17 pages, 5589 KiB

Open AccessArticle

Plasma Surface Modification of 3Y-TZP at Low and Atmospheric Pressures with Different Treatment Times

by Sung Un Kang, Chul-Ho Kim, Sanghyun You, Da-Young Lee, Yu-Kwon Kim, Seung-Joo Kim, Chang-Koo Kim and Hee-Kyung Kim

Int. J. Mol. Sci. 2023, 24(8), 7663; https://doi.org/10.3390/ijms24087663 - 21 Apr 2023

Viewed by 2084

Abstract

The efficiency of plasma surface modifications depends on the operating conditions. This study investigated the effect of chamber pressure and plasma exposure time on the surface properties of 3Y-TZP with N₂/Ar gas. Plate-shaped zirconia specimens were randomly divided into two categories: [...] Read more.

The efficiency of plasma surface modifications depends on the operating conditions. This study investigated the effect of chamber pressure and plasma exposure time on the surface properties of 3Y-TZP with N₂/Ar gas. Plate-shaped zirconia specimens were randomly divided into two categories: vacuum plasma and atmospheric plasma. Each group was subdivided into five subgroups according to the treatment time: 1, 5, 10, 15, and 20 min. Following the plasma treatments, we characterized the surface properties, including wettability, chemical composition, crystal structure, surface morphology, and zeta potential. These were analyzed through various techniques, such as contact angle measurement, XPS, XRD, SEM, FIB, CLSM, and electrokinetic measurements. The atmospheric plasma treatments increased zirconia’s electron donation (

γ^{-}

) capacity, while the vacuum plasma treatments decreased

γ^{-}

parameter with increasing times. The highest concentration of the basic hydroxyl OH(b) groups was identified after a 5 min exposure to atmospheric plasmas. With longer exposure times, the vacuum plasmas induce electrical damage. Both plasma systems increased the zeta potential of 3Y-TZP, showing positive values in a vacuum. In the atmosphere, the zeta potential rapidly increased after 1 min. Atmospheric plasma treatments would be beneficial for the adsorption of oxygen and nitrogen from ambient air and the generation of various active species on the zirconia surface. Full article

(This article belongs to the Special Issue Advances and Challenges in Dental Materials)

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Changes in water contact angles as a function of plasma treatment time with atmospheric plasma and with vacuum plasma. The contact angle decreased with increasing treatment time for both plasma systems. The means within each plasma system that share identical letters are not significantly different from each other (p > 0.05). Full article ">Figure 2
XPS spectra correspond to the C1s (A), N 1s (B), and O 1s (C) regions of all experimental groups. (D) Chemical composition obtained from SEM-EDS analysis. (E) Atomic percentages of C, N, and O on the zirconia surfaces were obtained from XPS spectra. (F) The relative ratios of lattice oxygen (OL), OH(a), and OH(b) in the O 1s core level XPS spectra. (G) N atomic percentage as a function of plasma treatment time obtained by XPS analysis. Full article ">Figure 3
The surface texture parameters (Sa, Sq, and Sv) of all test groups. No significant differences in Sa, Sq, and Sv were observed among all plasma-treated groups. Means with identical letters are not significantly different from each other (p > 0.05). Full article ">Figure 4
SEM images at 40,000× magnification (left) and FIB cross-sectional images of cross-sections at 6000× magnification (right) of each group. The vacuum plasma caused surface erosion due to electrical discharges, although it did not alter the subsurface microstructures. Full article ">Figure 5
(A) X-ray diffraction patterns of all experimental groups; Rietveld quantitative analyses as a function of the plasma exposure time for vacuum plasma groups (B) and atmospheric plasma groups (C); (D) The unit cell parameter (Å) of cubic phase as a function of the plasma exposure time. Full article ">Figure 6
Changes in zeta potential as a function of the plasma treatment time with atmospheric plasma and with vacuum plasma. The zeta potentials of control, atmospheric plasma groups, and V1 are negative, while those of the vacuum plasma groups except V1 are positive. Full article ">Figure 7
Schematic diagrams of experimental setups for plasma surface modifications: (A) ICP vacuum plasma system, (B) DBD atmospheric plasma system, and (C) mechanism of the plasma surface modification of 3Y-TZP. Full article ">

20 pages, 3320 KiB

Open AccessArticle

A Pseudomonas Lysogenic Bacteriophage Crossing the Antarctic and Arctic, Representing a New Genus of Autographiviridae

by Zhenyu Liu, Wenhui Jiang, Cholsong Kim, Xiaoya Peng, Cong Fan, Yingliang Wu, Zhixiong Xie and Fang Peng

Int. J. Mol. Sci. 2023, 24(8), 7662; https://doi.org/10.3390/ijms24087662 - 21 Apr 2023

Cited by 2 | Viewed by 3043

Abstract

Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a [...] Read more.

Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a lysogenic phage, vB_PaeM-G11, from Pseudomonas sp. D3 isolated from the Antarctic, which formed clear phage plaques on the lawn of Pseudomonas sp. G11 isolated from the Arctic. From permafrost metagenomic data of the Arctic tundra, we found the genome with high-similarity to that of vB_PaeM-G11, demonstrating that vB_PaeM-G11 may have a distribution in both the Antarctic and Arctic. Phylogenetic analysis indicated that vB_PaeM-G11 is homologous to five uncultured viruses, and that they may represent a new genus in the Autographiviridae family, named Fildesvirus here. vB_PaeM-G11 was stable in a temperature range (4–40 °C) and pH (4–11), with latent and rise periods of about 40 and 10 min, respectively. This study is the first isolation and characterization study of a Pseudomonas phage distributed in both the Antarctic and Arctic, identifying its lysogenic host and lysis host, and thus provides essential information for further understanding the interaction between polar phages and their hosts and the ecological functions of phages in polar regions. Full article

(This article belongs to the Section Molecular Microbiology)

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(A) Phage plaques formed by vB_PaeM-G11 on the lawn of its sensitive strain, Pseudomonas sp. G11. (B) Transmission electron micrograph (TEM) of phage vB_PaeM-G11. (C) Adsorption curves of phage vB_PaeM-G11 on Pseudomonas sp. G11. (D) One-step growth curve of vB_PaeM-G11. (E) Temperature adaptation range of vB_PaeM-G11. (F) pH adaptation range of vB_PaeM-G11. Full article ">Figure 2
Circular diagram of functional assignments of the Pseudomonas phage vB_PaeM-G11 genome. The outermost circle represents the 50 ORFs contained by phage vB-PaeM-G11. Arrows represent the direction of gene transcription, and different colors indicate genes with different functions: integrase (dark blue); auxiliary metabolic genes (green); transcription- and translation-related genes (purple); DNA replication and metabolism genes (light blue); transcriptional regulatory genes (brown); packaging and structural protein genes (orange); host cleavage genes (red); and hypothetical protein (gray). The GC skew of the genome sequence is indicated by the internal purple or green histograms. Full article ">Figure 3
Analysis of 12% SDS-PAGE for phage vB_PaeM-G11 structural proteins. M represents the protein molecular weight marker. P represents the structure protein solution of vB_PaeM-G11. On the right are the descriptions of the molecular sizes based on the protein sequences and their possible functions. Full article ">Figure 4
Phylogenetic and comparative genomic analysis of vB_PaeM-G11. (A) Proteomic tree of viral genome sequences based on the whole genome represented in the circular view, and a red pentagram marks vB_PaeM-G11. (B) Regenerated proteomic tree of vB_PaeM-G11 and 30 closely related phage genome sequences. (C) Intergenomic similarity between vB_PaeM-G11 and the most similar phage calculated using VIRIDIC. The heat map indicates the similarity between genomes; for display purposes, only the top 20 high-similarity species are shown. (D) Genome alignment between vB_PaeM-G11 and the high-similarity phage from NCBI RefSeq. High-similarity regions detected by tBLASTx are color-coded in the alignment based on the reported identity %. Dot plots summarizing these high-similarity regions are shown beside the alignment. Full article ">Figure 5
Proteome-based similarity network showing all vB_PaeM-G11 Autographiviridae phages from the NCBI RefSeq, and five related UViGs from the IMG/VR database. Each node represents a single phage genome, and the edge represents similarity scores between proteomes of related phages. Different colors indicate the clustered viruses. Circles represent phages from the NCBI RefSeq database, the hexagon represents vB_PaeM-G11, and triangles indicate UViGs from the IMG/VR database. Gray squares represent singleton nodes. The network was visualized using Cytoscape 3.9.1. Full article ">Figure 6
Genome-wide phylogenetic tree constructed by VICTOR with the formula d0. The phylogenic tree consists of 100 phage genomes (vB_PaeM-G11, 94 Autographiviridae phages from NCBI RefSeq and five related UViGs from IMG/VR). Each unique color indicates each ICTV genus. The vB_PaeM-G11 genus is shown in red, and a red hexagon marks vB_PaeM-G11. Bootstrap values of ≥50 are shown. Full article ">Figure 7
Biogeography of the Fildesvirus. A blue hexagon represents Pseudomonas sp. G11. A red hexagon represents Pseudomonas sp. D3. Two UViGs (no. IMGVR_UViG_3300005980_000007 and IMGVR_UViG_3300026272_000008) that have over 95% similarity to vB_PaeM-G11 are represented by red triangles. The other three UViGs (no. IMGVR_UViG_3300048920_000060, IMGVR_UViG_3300048921_000055, and IMGVR_UViG_3300048921_000616) are represented by green triangles. The labels show the ecosystem type, sample collection date, and geographic location of the microbiome. Full article ">

24 pages, 1780 KiB

Open AccessReview

Ferroptosis in Haematological Malignancies and Associated Therapeutic Nanotechnologies

by Rachel L. Mynott, Ali Habib, Oliver G. Best and Craig T. Wallington-Gates

Int. J. Mol. Sci. 2023, 24(8), 7661; https://doi.org/10.3390/ijms24087661 - 21 Apr 2023

Cited by 6 | Viewed by 4577

Abstract

Haematological malignancies are heterogeneous groups of cancers of the bone marrow, blood or lymph nodes, and while therapeutic advances have greatly improved the lifespan and quality of life of those afflicted, many of these cancers remain incurable. The iron-dependent, lipid oxidation-mediated form of [...] Read more.

Haematological malignancies are heterogeneous groups of cancers of the bone marrow, blood or lymph nodes, and while therapeutic advances have greatly improved the lifespan and quality of life of those afflicted, many of these cancers remain incurable. The iron-dependent, lipid oxidation-mediated form of cell death, ferroptosis, has emerged as a promising pathway to induce cancer cell death, particularly in those malignancies that are resistant to traditional apoptosis-inducing therapies. Although promising findings have been published in several solid and haematological malignancies, the major drawbacks of ferroptosis-inducing therapies are efficient drug delivery and toxicities to healthy tissue. The development of tumour-targeting and precision medicines, particularly when combined with nanotechnologies, holds potential as a way in which to overcome these obstacles and progress ferroptosis-inducing therapies into the clinic. Here, we review the current state-of-play of ferroptosis in haematological malignancies as well as encouraging discoveries in the field of ferroptosis nanotechnologies. While the research into ferroptosis nanotechnologies in haematological malignancies is limited, its pre-clinical success in solid tumours suggests this is a very feasible therapeutic approach to treat blood cancers such as multiple myeloma, lymphoma and leukaemia. Full article

(This article belongs to the Special Issue Emerging Topics in Ferroptosis)

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Biochemical pathways involved in the regulation of ferroptosis. ACSL4, acyl-CoA synthetase long-chain family member 4; CO, carbon monoxide; Fe2+, ferrous iron; GPX4, glutathione peroxidase 4; HO-1, heme oxygenase 1; LOXs, lipoxygenases; LPCAT3, lysophosphatidylcholine acyltransferase 3; NCOA4, nuclear receptor coactivator 4; PL, phospholipid; PUFA, polyunsaturated fatty acid; ROS, reactive oxygen species; TfR, transferrin receptor. Full article ">Figure 2
Schematic representation of the mevalonate pathway and its role in inhibition of ferroptosis. CoQ10, ubiquinone; CoQ10-H2, ubiquinol; FDPS, farnesyl diphosphate synthase; FPP, farnesyl phosphate; FSP1, ferroptosis suppressor protein 1; GPX4, glutathione peroxidase 4; IPP, isopentenyl phosphate; MDD, mevalonate diphosphate decarboxylase; PLOO−, lipid peroxyl radicals; Sec, selenocysteine. Dotted arrows represent multiple steps within a pathway. Full article ">Figure 3
Basic structure of common nanotechnologies used to induce ferroptosis. Sizes: dendrimers 1–10 nm [<a href="#B141-ijms-24-07661" class="html-bibr">141</a>], iron oxide nanoparticles 10–20 nm [<a href="#B142-ijms-24-07661" class="html-bibr">142</a>], micelles 10–100 nm [<a href="#B143-ijms-24-07661" class="html-bibr">143</a>], liposomes 30 nm to several microns [<a href="#B143-ijms-24-07661" class="html-bibr">143</a>]. Created with BioRender.com (accessed on 22 March 2023). Full article ">Figure 4
Example of a tumour-targeting, ferroptosis-inducing liposome. Created with BioRender.com (accessed on 27 March 2023). Full article ">

15 pages, 2999 KiB

Open AccessArticle

Inflammatory Response and Exosome Biogenesis of Choroid Plexus Organoids Derived from Human Pluripotent Stem Cells

by Laureana Muok, Chang Liu, Xingchi Chen, Colin Esmonde, Peggy Arthur, Xueju Wang, Mandip Singh, Tristan Driscoll and Yan Li

Int. J. Mol. Sci. 2023, 24(8), 7660; https://doi.org/10.3390/ijms24087660 - 21 Apr 2023

Cited by 2 | Viewed by 3301

Abstract

The choroid plexus (ChP) is a complex structure in the human brain that is responsible for the secretion of cerebrospinal fluid (CSF) and forming the blood–CSF barrier (B-CSF-B). Human-induced pluripotent stem cells (hiPSCs) have shown promising results in the formation of brain organoids [...] Read more.

The choroid plexus (ChP) is a complex structure in the human brain that is responsible for the secretion of cerebrospinal fluid (CSF) and forming the blood–CSF barrier (B-CSF-B). Human-induced pluripotent stem cells (hiPSCs) have shown promising results in the formation of brain organoids in vitro; however, very few studies to date have generated ChP organoids. In particular, no study has assessed the inflammatory response and the extracellular vesicle (EV) biogenesis of hiPSC-derived ChP organoids. In this study, the impacts of Wnt signaling on the inflammatory response and EV biogenesis of ChP organoids derived from hiPSCs was investigated. During days 10–15, bone morphogenetic protein 4 was added along with (+/−) CHIR99021 (CHIR, a small molecule GSK-3β inhibitor that acts as a Wnt agonist). At day 30, the ChP organoids were characterized by immunocytochemistry and flow cytometry for TTR (~72%) and CLIC6 (~20%) expression. Compared to the −CHIR group, the +CHIR group showed an upregulation of 6 out of 10 tested ChP genes, including CLIC6 (2-fold), PLEC (4-fold), PLTP (2–4-fold), DCN (~7-fold), DLK1 (2–4-fold), and AQP1 (1.4-fold), and a downregulation of TTR (0.1-fold), IGFBP7 (0.8-fold), MSX1 (0.4-fold), and LUM (0.2–0.4-fold). When exposed to amyloid beta 42 oligomers, the +CHIR group had a more sensitive response as evidenced by the upregulation of inflammation-related genes such as TNFα, IL-6, and MMP2/9 when compared to the −CHIR group. Developmentally, the EV biogenesis markers of ChP organoids showed an increase over time from day 19 to day 38. This study is significant in that it provides a model of the human B-CSF-B and ChP tissue for the purpose of drug screening and designing drug delivery systems to treat neurological disorders such as Alzheimer’s disease and ischemic stroke. Full article

(This article belongs to the Special Issue The Link between Stem Cells and Nervous System)

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Graphical abstract
Full article ">Figure 1
ChP organoid differentiation from hiPSCs. (A) Illustration of ChP differentiation; (B) the ChP organoid morphology for CHIR+/− conditions during the differentiation. Scale bar: 200 µm. BMP: bone morphogenetic protein; EBs: embryoid bodies. EV: extracellular vesicles. Full article ">Figure 2
Expression of ChP markers for CHIR+/− conditions. (A) Immunostaining of ChP markers at day 32. Scale bar: 50 µm. (B) Flow cytometry histograms of ChP markers for CHIR+/− conditions. The assays were performed at day 30. Black line: negative control. Red line: marker of interest. TTR (transthyretin) and CLIC6 (chloride intracellular channel 6) are ChP markers. CHIR(+/−) indicates treatment with CHIR99021. Full article ">Figure 3
mRNA expression of ChP markers at days 18 and 30 for CHIR+/− conditions. mRNA expression was determined by RT-qPCR. (A) Day 18; (B) day 30 of differentiation. N = 3. * indicates p < 0.05. CHIR(+/−) indicates treatment with CHIR99021. Full article ">Figure 4
Inflammatory response to Aβ42 oligomer stimulation for ChP organoids of CHIR+/− conditions. mRNA expression determined by RT-qPCR for (A) proinflammatory markers (day 33); (B) anti-inflammatory markers (day 33); these markers were relative to the CHIR+ condition. (C) MMP2, MMP3, and MMP9 expression affected by Aβ42 oligomers (day 33); (D) MMP2, MMP3, and MMP9 expression affected by CHIR at days 19 and 38. N = 3. * indicates p < 0.05. The MMP2, MMP3, and MMP9 expression was relative to the CHIR−D19 condition. CHIR(+/−) indicates treatment with CHIR99021, D19 and D38 indicates days 19 and 38, AB(+/−) indicates treatment with amyloid β 42 oligomers. The CHIR+ group is more responsive than the CHIR− group. Full article ">Figure 5
Extracellular vesicle biogenesis of ChP organoids with CHIR+/− conditions. (A) mRNA expression determined by RT-qPCR for (i) ESCRT-dependent EV biogenesis markers; (ii) ESCRT-independent EV biogenesis markers; N = 3. * indicates p < 0.05 for the compared conditions, and # indicates p < 0.05 compared to the CHIR− condition at the same time point. CHIR(+/−) indicates treatment with CHIR99021 (3 µM), D19 and D38 indicates days 19 and 38 during differentiation. (B) Nanoparticle tracking analysis (NTA) for the isolated ChP organoid-EVs; (i) particle size distribution and zeta potential by ZetaView; (ii) particle size distribution by NanoSight. (C) Transmission electron microscopy images showing exosome morphology; scale bar: 100 nm. Full article ">

4 pages, 219 KiB

Open AccessEditorial

Cardiovascular Disease, Atherosclerosis and Familial Hypercholesterolemia: From Molecular Mechanisms Causing Pathogenicity to New Therapeutic Approaches

by Shifa Jebari-Benslaiman, Asier Larrea-Sebal, Asier Benito-Vicente and César Martín

Int. J. Mol. Sci. 2023, 24(8), 7659; https://doi.org/10.3390/ijms24087659 - 21 Apr 2023

Cited by 1 | Viewed by 1472

Abstract

This Special Issue, “Cardiovascular Disease, Atherosclerosis and Familial Hypercholesterolemia: From Molecular Mechanisms Causing Pathogenicity to New Therapeutic Approaches”, contributes to advancing our knowledge of the molecular mechanisms that drive cardiovascular disease, atherosclerosis and familial hypercholesterolemia and the development of state-of-the-art research in the [...] Read more.

This Special Issue, “Cardiovascular Disease, Atherosclerosis and Familial Hypercholesterolemia: From Molecular Mechanisms Causing Pathogenicity to New Therapeutic Approaches”, contributes to advancing our knowledge of the molecular mechanisms that drive cardiovascular disease, atherosclerosis and familial hypercholesterolemia and the development of state-of-the-art research in the field [...] Full article

(This article belongs to the Special Issue Cardiovascular Disease, Atherosclerosis and Familial Hypercholesterolemia: From Molecular Mechanisms Causing Pathogenicity till New Therapeutic Approaches 2.0)

22 pages, 5262 KiB

Open AccessArticle

TDP-43 Controls HIV-1 Viral Production and Virus Infectiveness

by Romina Cabrera-Rodríguez, Silvia Pérez-Yanes, Iria Lorenzo-Sánchez, Judith Estévez-Herrera, Jonay García-Luis, Rodrigo Trujillo-González and Agustín Valenzuela-Fernández

Int. J. Mol. Sci. 2023, 24(8), 7658; https://doi.org/10.3390/ijms24087658 - 21 Apr 2023

Cited by 4 | Viewed by 2137

Abstract

The transactive response DNA-binding protein (TARDBP/TDP-43) is known to stabilize the anti-HIV-1 factor, histone deacetylase 6 (HDAC6). TDP-43 has been reported to determine cell permissivity to HIV-1 fusion and infection acting on tubulin-deacetylase HDAC6. Here, we studied the functional involvement of TDP-43 in [...] Read more.

The transactive response DNA-binding protein (TARDBP/TDP-43) is known to stabilize the anti-HIV-1 factor, histone deacetylase 6 (HDAC6). TDP-43 has been reported to determine cell permissivity to HIV-1 fusion and infection acting on tubulin-deacetylase HDAC6. Here, we studied the functional involvement of TDP-43 in the late stages of the HIV-1 viral cycle. The overexpression of TDP-43, in virus-producing cells, stabilized HDAC6 (i.e., mRNA and protein) and triggered the autophagic clearance of HIV-1 Pr55^Gag and Vif proteins. These events inhibited viral particle production and impaired virion infectiveness, observing a reduction in the amount of Pr55^Gag and Vif proteins incorporated into virions. A nuclear localization signal (NLS)-TDP-43 mutant was not able to control HIV-1 viral production and infection. Likewise, specific TDP-43-knockdown reduced HDAC6 expression (i.e., mRNA and protein) and increased the expression level of HIV-1 Vif and Pr55^Gag proteins and α-tubulin acetylation. Thus, TDP-43 silencing favored virion production and enhanced virus infectious capacity, thereby increasing the amount of Vif and Pr55^Gag proteins incorporated into virions. Noteworthy, there was a direct relationship between the content of Vif and Pr55^Gag proteins in virions and their infection capacity. Therefore, for TDP-43, the TDP-43/HDAC6 axis could be considered a key factor to control HIV-1 viral production and virus infectiveness. Full article

(This article belongs to the Special Issue Molecular Advances in Infectious Disease)

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22 pages, 2558 KiB

Open AccessArticle

Carrageenans and Their Oligosaccharides from Red Seaweeds Ahnfeltiopsis flabelliformis and Mastocarpus pacificus (Phyllophoraceae) and Their Antiproliferative Activity

by Anna O. Kravchenko, Ekaterina S. Menchinskaya, Vladimir V. Isakov, Valery P. Glazunov and Irina M. Yermak

Int. J. Mol. Sci. 2023, 24(8), 7657; https://doi.org/10.3390/ijms24087657 - 21 Apr 2023

Cited by 5 | Viewed by 2087

Abstract

Comparative structural analysis of gelling polysaccharides from A. flabelliformis and M. pacificus belonging to Phyllophoraceae and the effect of their structural features and molecular weight on human colon cancer cell lines (HT-29, DLD-1, HCT-116) was carried out. According to chemical analysis, IR and [...] Read more.

Comparative structural analysis of gelling polysaccharides from A. flabelliformis and M. pacificus belonging to Phyllophoraceae and the effect of their structural features and molecular weight on human colon cancer cell lines (HT-29, DLD-1, HCT-116) was carried out. According to chemical analysis, IR and NMR spectroscopies, M. pacificus produces kappa/iota-carrageenan with a predominance of kappa units and minor amounts of mu and/or nu units, while the polysaccharide from A. flabelliformis is iota/kappa-carrageenan (predominance of iota units) and contains negligible amounts of beta- and nu-carrageenans. Iota/kappa- (Afg-OS) and kappa/iota-oligosaccharides (Mp-OS) were obtained from the original polysaccharides through mild acid hydrolysis. The content of more sulfated iota units in Afg-OS (iota/kappa 7:1) was higher than in Mp-OS (1.0:1.8). The poly- and oligosaccharides up to 1 mg/mL did not show a cytotoxic effect on all tested cell lines. Polysaccharides showed an antiproliferative effect only at 1 mg/mL. Oligosaccharides had a more pronounced effect on HT-29 and HCT-116 cells than the original polymers, while HCT-116 cells were slightly more sensitive to their action. Kappa/iota-oligosaccharides exhibit a greater antiproliferative effect and more strongly decrease the number of colonies forming in HCT-116 cells. At the same time, iota/kappa-oligosaccharides inhibit cell migration more strongly. Kappa/iota-oligosaccharides induce apoptosis in the SubG0 and G2/M phases, while iota/kappa-oligosaccharides in the SubG0 phase. Full article

(This article belongs to the Special Issue Advances and Applications of Polysaccharides)

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Figure 1
13C-1H HSQC NMR spectra of Afg-OS (A) and Mp-OS (B). Full article ">Figure 2
Antiproliferative effect of oligosaccharides Mp-OS (A) and Afg-OS (B) against three types of tumor cells (HCT-116, DLD-1, HT-29). Incubation time with cells—2 h. Full article ">Figure 3
Cell migration into wound areas was observed under EVOS XL Core microscope at 0, 6, 24 and 48 h. ImageJ 1.52 software was used to analyze cell migration into wound areas. Data are presented as means ± SEM. * p value < 0.05 considered significant. Full article ">Figure 4
Colony images under different treatments. Oligosaccharides Mp-OS and Afg-OS reduced number of HCT-116 cell colonies in a dose-dependent manner. ImageJ 1.52 software was used to count the cell colonies. Data are presented as means ± SEM. * p value < 0.05 considered significant. Full article ">Figure 5
Hoechst 33342 staining showing chromatin condensation and DNA fragmentation in apoptotic cells under treatment of control, Mp-OS 300 and 200 mg/mL and Afg-OS 300 and 200 mg/mL. Arrows indicate nuclei with condensed chromatin. Apoptotic profile (Muse™ Annexin V and Dead Cell Assay) for HCT-116 cells, control, Mp-OS and Afg-OS. In all cases, the profiles were determined 72 h after incubation with substances. Each graph has 4 quadrant markers representing different cellular conditions: upper-left quadrant contains dead cells (dead cells/necrosis), upper-right quadrant contains late apoptotic/dead cells (cells positive for both annexin V and cell death marker 7-AAD), lower left contains live cells and lower right contains early apoptotic cells (cells positive for annexin V only). Data are presented as means ± SEM. * p value < 0.05 considered significant. Full article ">Figure 6
Histograms of the distribution of HCT-116 cells by phases in the control (A). Effect of Mp-OS ((B)-300 μg/mL, (C)-200 μg/mL) and Afg-OS (D)-300 μg/mL, (E)-200 μg/mL) on the distribution of HCT-116 cells by cell cycle phases. Graph of cell distribution by cell cycle phases (F). The time of incubation of oligosaccharides with cells is 72 h. Data are presented as means ± SEM. * p value < 0.05 considered significant. Full article ">

24 pages, 1538 KiB

Open AccessReview

Drug Discovery Targeting Post-Translational Modifications in Response to DNA Damages Induced by Space Radiation

by Dafei Xie, Qi Huang and Pingkun Zhou

Int. J. Mol. Sci. 2023, 24(8), 7656; https://doi.org/10.3390/ijms24087656 - 21 Apr 2023

Cited by 1 | Viewed by 3678

Abstract

DNA damage in astronauts induced by cosmic radiation poses a major barrier to human space exploration. Cellular responses and repair of the most lethal DNA double-strand breaks (DSBs) are crucial for genomic integrity and cell survival. Post-translational modifications (PTMs), including phosphorylation, ubiquitylation, and [...] Read more.

DNA damage in astronauts induced by cosmic radiation poses a major barrier to human space exploration. Cellular responses and repair of the most lethal DNA double-strand breaks (DSBs) are crucial for genomic integrity and cell survival. Post-translational modifications (PTMs), including phosphorylation, ubiquitylation, and SUMOylation, are among the regulatory factors modulating a delicate balance and choice between predominant DSB repair pathways, such as non-homologous end joining (NHEJ) and homologous recombination (HR). In this review, we focused on the engagement of proteins in the DNA damage response (DDR) modulated by phosphorylation and ubiquitylation, including ATM, DNA-PKcs, CtIP, MDM2, and ubiquitin ligases. The involvement and function of acetylation, methylation, PARylation, and their essential proteins were also investigated, providing a repository of candidate targets for DDR regulators. However, there is a lack of radioprotectors in spite of their consideration in the discovery of radiosensitizers. We proposed new perspectives for the research and development of future agents against space radiation by the systematic integration and utilization of evolutionary strategies, including multi-omics analyses, rational computing methods, drug repositioning, and combinations of drugs and targets, which may facilitate the use of radioprotectors in practical applications in human space exploration to combat fatal radiation hazards. Full article

(This article belongs to the Special Issue Cellular and Molecular Signaling Meet the Space Environment 2.0)

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19 pages, 4932 KiB

Open AccessArticle

HD-ZIP Transcription Factors and Brassinosteroid Signaling Play a Role in Capitulum Patterning in Chrysanthemum

by Annemarie Castricum, Erin H. Bakker, Nick C. M. H. de Vetten, Mieke Weemen, Gerco C. Angenent, Richard G. H. Immink and Marian Bemer

Int. J. Mol. Sci. 2023, 24(8), 7655; https://doi.org/10.3390/ijms24087655 - 21 Apr 2023

Cited by 3 | Viewed by 2203

Abstract

Chrysanthemum is a genus in the Asteraceae family containing numerous cut flower varieties with high ornamental value. It owes its beauty to the composite flower head, which resembles a compact inflorescence. This structure is also known as a capitulum, in which many ray [...] Read more.

Chrysanthemum is a genus in the Asteraceae family containing numerous cut flower varieties with high ornamental value. It owes its beauty to the composite flower head, which resembles a compact inflorescence. This structure is also known as a capitulum, in which many ray and disc florets are densely packed. The ray florets are localized at the rim, are male sterile, and have large colorful petals. The centrally localized disc florets develop only a small petal tube but produce fertile stamens and a functional pistil. Nowadays, varieties with more ray florets are bred because of their high ornamental value, but, unfortunately, this is at the expense of their seed setting. In this study, we confirmed that the disc:ray floret ratio is highly correlated to seed set efficiency, and therefore, we further investigated the mechanisms that underlie the regulation of the disc:ray floret ratio. To this end, a comprehensive transcriptomics analysis was performed in two acquired mutants with a higher disc:ray floret ratio. Among the differentially regulated genes, various potential brassinosteroid (BR) signaling genes and HD-ZIP class IV homeodomain transcription factors stood out. Detailed follow-up functional studies confirmed that reduced BR levels and downregulation of HD-ZIP IV gene Chrysanthemum morifolium PROTODERMAL FACTOR 2 (CmPDF2) result in an increased disc:ray floret ratio, thereby providing ways to improve seed set in decorative chrysanthemum varieties in the future. Full article

(This article belongs to the Special Issue Advances in Research for Ornamental Plants Breeding)

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Figure 1
Chrysanthemum capitulum development and the correlation between seed set efficiency and the relative number of disc florets in the capitulum. (A) Morphology differences between a full-grown mature disc floret (left) and ray floret (right). The corolla tube of the disc floret was partially removed to display the anthers (arrow); the ray floret ligule was cut at the top. (B) Representative examples of a Daisy-type (DAI), Half-Decorative-type (HDEC), and a Decorative-type (DEC) capitulum, going from mainly disc florets to mainly ray florets, respectively. Per type, the average seed set on a single capitulum is shown upon hand pollination with the same amount of pollen. (C) Six subsequent developmental stages (S0–S5) of a chrysanthemum capitulum. For each stage, the closed capitulum bud is shown on the left. Next to it on the right, dissected capitulum buds are shown in which the initial stages of floret development are visible. For S2 and S3, part of the capitulum (boxed region) is enlarged. In this zoom-in representation, the radially symmetrical disc florets (marked with an asterisk) can be distinguished from zygomorphically symmetrical ray florets. (D) Expression of LFY, AG, and CYC2c in the six capitulum developmental stages as determined by qRT-PCR. Significance in (B) determined by ANOVA, p < 0.05. Error bars represent standard error. Number of measurements: DAI, 7486; HDE, 3086; DEC, 17,987. Size bar in (C) = 1 mm. Full article ">Figure 2
Phenotypic characterization of a spontaneous chrysanthemum mutant with decreased disc:ray floret ratio. (A) Top view of a mature capitulum from variety 1 (V1; left) and its spontaneous mutant (M1; right) that showed a strong increase in the number of disc florets and yellow instead of white ligules. (B) Boxplot showing the number of disc and ray florets and the total number of florets in V1 and M1 capitula (n = 7). (C) GO-term enrichment analysis with the DEGs of M1 vs. V1 at stages 0 and 1. The legend for the category numbers is displayed on the right. The y-axis displays the fold enrichment of the number of genes in the category compared to the Arabidopsis genome; the x-axis displays the different significantly enriched categories (FDR < 0.05). The categories discussed in the text are displayed in yellow and green. (D) Expression plots for five selected genes from the RNA-seq experiment (RPKM read count values are displayed). The transcript identifiers are as follows: CmDWF1, DN96938; CmBEN1, DN45086; CmPDF2, DN65126; CmGIR1, DN43323; and CmFWA, DN60377. The numbers at the x-axis indicate the stages. Error bars indicate the SE of the three biological replicates; asterisks indicate significance at Padj < 0.01. Full article ">Figure 3
DEG analysis in a second genetic background. (A) Pictures of variety 2 (left panels) and mutant 2 (right panels) of a complete inflorescence (top) and transversely sectioned inflorescence (bottom). (B) Overlap of DEGs between V1/M1 and V2/M2 in stages 0 and 1. (C) Read count data from the second RNA-seq experiment (V2/M2) for CmDWF5 (DN57668), CmHERK1 (DN68032), and CmPDL2 (DN38497). (D) qPCR data for CYC2c and read count data for CYC2d from both RNA-seq experiments (V1/M1 left; M2/V2 right). Error bars indicate SE; asterisks indicate significance (qPCR: p < 0.05; RNA-seq: Padj < 0.01). Full article ">Figure 4
Functional characterization of CmPDF2, CmGIR1, and CmDWF1. (A) qPCR analysis of CmPDF2, CmGIR1, and CmDWF1 expression in different tissues. B1, bud stage 1; DF, mature disc florets; RF, mature ray florets; L, leaf; St, stem. (B) Downregulation of CmDWF1 transcripts in different RNAi lines (top panel) and the quantification of the corresponding capitulum phenotypes (bottom panel) (C) Transverse sections of the capitula of two lines with CmDWF1 downregulation compared to the WT (top). A higher number of disc florets is visible in the center of the transgenic capitula. (D) Downregulation of CmPDF2 transcripts in different RNAi lines (top panel) and the quantification of the corresponding capitulum phenotypes (bottom panel). (E) Transverse sections of the capitula of two lines with CmPDF2 downregulation compared to the WT (top). A higher number of disc florets is visible in the center of the transgenic capitula. (F) Brassinozole treatment of WT inflorescence buds results in a higher number of disc florets. Error bars indicate SE; asterisks indicate significance (qPCR: p < 0.05; RNA-seq: Padj < 0.01). Full article ">

28 pages, 7434 KiB

Open AccessArticle

Integrative Proteomics and Metabolomics Analysis Reveals the Role of Small Signaling Peptide Rapid Alkalinization Factor 34 (RALF34) in Cucumber Roots

by Julia Shumilina, Alexey S. Kiryushkin, Nadezhda Frolova, Valeria Mashkina, Elena L. Ilina, Vera A. Puchkova, Katerina Danko, Svetlana Silinskaya, Evgeny B. Serebryakov, Alena Soboleva, Tatiana Bilova, Anastasia Orlova, Elizaveta D. Guseva, Egor Repkin, Katharina Pawlowski, Andrej Frolov and Kirill N. Demchenko

Int. J. Mol. Sci. 2023, 24(8), 7654; https://doi.org/10.3390/ijms24087654 - 21 Apr 2023

Cited by 4 | Viewed by 3311

Abstract

The main role of RALF small signaling peptides was reported to be the alkalization control of the apoplast for improvement of nutrient absorption; however, the exact function of individual RALF peptides such as RALF34 remains unknown. The Arabidopsis RALF34 (AtRALF34) peptide [...] Read more.

The main role of RALF small signaling peptides was reported to be the alkalization control of the apoplast for improvement of nutrient absorption; however, the exact function of individual RALF peptides such as RALF34 remains unknown. The Arabidopsis RALF34 (AtRALF34) peptide was proposed to be part of the gene regulatory network of lateral root initiation. Cucumber is an excellent model for studying a special form of lateral root initiation taking place in the meristem of the parental root. We attempted to elucidate the role of the regulatory pathway in which RALF34 is a participant using cucumber transgenic hairy roots overexpressing CsRALF34 for comprehensive, integrated metabolomics and proteomics studies, focusing on the analysis of stress response markers. CsRALF34 overexpression resulted in the inhibition of root growth and regulation of cell proliferation, specifically in blocking the G2/M transition in cucumber roots. Based on these results, we propose that CsRALF34 is not part of the gene regulatory networks involved in the early steps of lateral root initiation. Instead, we suggest that CsRALF34 modulates ROS homeostasis and triggers the controlled production of hydroxyl radicals in root cells, possibly associated with intracellular signal transduction. Altogether, our results support the role of RALF peptides as ROS regulators. Full article

(This article belongs to the Special Issue Meristem and Stem Cells and Stem Cell Regulation in Plants)

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29 pages, 3288 KiB

Open AccessReview

Methods to Identify Cognitive Alterations from Animals to Humans: A Translational Approach

by Daniela Navarro, Ani Gasparyan, Silvia Martí Martínez, Carmen Díaz Marín, Francisco Navarrete, María Salud García Gutiérrez and Jorge Manzanares

Int. J. Mol. Sci. 2023, 24(8), 7653; https://doi.org/10.3390/ijms24087653 - 21 Apr 2023

Cited by 7 | Viewed by 2533

Abstract

The increasing prevalence of cognitive dysfunction and dementia in developed countries, associated with population aging, has generated great interest in characterizing and quantifying cognitive deficits in these patients. An essential tool for accurate diagnosis is cognitive assessment, a lengthy process that depends on [...] Read more.

The increasing prevalence of cognitive dysfunction and dementia in developed countries, associated with population aging, has generated great interest in characterizing and quantifying cognitive deficits in these patients. An essential tool for accurate diagnosis is cognitive assessment, a lengthy process that depends on the cognitive domains analyzed. Cognitive tests, functional capacity scales, and advanced neuroimaging studies explore the different mental functions in clinical practice. On the other hand, animal models of human diseases with cognitive impairment are essential for understanding disease pathophysiology. The study of cognitive function using animal models encompasses multiple dimensions, and deciding which ones to investigate is necessary to select the most appropriate and specific tests. Therefore, this review studies the main cognitive tests for assessing cognitive deficits in patients with neurodegenerative diseases. Cognitive tests, the most commonly used functional capacity scales, and those resulting from previous evidence are considered. In addition, the leading behavioral tests that assess cognitive functions in animal models of disorders with cognitive impairment are highlighted. Full article

(This article belongs to the Special Issue Cognitive Impairment in Neurological Diseases)

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15 pages, 957 KiB

Open AccessReview

Improving the Treatment Effect of Carotenoids on Alzheimer’s Disease through Various Nano-Delivery Systems

by Wenjing Su, Wenhao Xu, Enshuo Liu, Weike Su and Nikolay E. Polyakov

Int. J. Mol. Sci. 2023, 24(8), 7652; https://doi.org/10.3390/ijms24087652 - 21 Apr 2023

Cited by 7 | Viewed by 3345

Abstract

Natural bioactive compounds have recently emerged as a current strategy for Alzheimer’s disease treatment. Carotenoids, including astaxanthin, lycopene, lutein, fucoxanthin, crocin and others are natural pigments and antioxidants, and can be used to treat a variety of diseases, including Alzheimer’s disease. However, carotenoids, [...] Read more.

Natural bioactive compounds have recently emerged as a current strategy for Alzheimer’s disease treatment. Carotenoids, including astaxanthin, lycopene, lutein, fucoxanthin, crocin and others are natural pigments and antioxidants, and can be used to treat a variety of diseases, including Alzheimer’s disease. However, carotenoids, as oil-soluble substances with additional unsaturated groups, suffer from low solubility, poor stability and poor bioavailability. Therefore, the preparation of various nano-drug delivery systems from carotenoids is a current measure to achieve efficient application of carotenoids. Different carotenoid delivery systems can improve the solubility, stability, permeability and bioavailability of carotenoids to a certain extent to achieve Alzheimer’s disease efficacy. This review summarizes recent data on different carotenoid nano-drug delivery systems for the treatment of Alzheimer’s disease, including polymer, lipid, inorganic and hybrid nano-drug delivery systems. These drug delivery systems have been shown to have a beneficial therapeutic effect on Alzheimer’s disease to a certain extent. Full article

(This article belongs to the Special Issue The Role of Carotenoids in Health and Disease)

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21 pages, 1108 KiB

Open AccessReview

HBV Infection and Host Interactions: The Role in Viral Persistence and Oncogenesis

by Riccardo Nevola, Domenico Beccia, Valerio Rosato, Rachele Ruocco, Davide Mastrocinque, Angela Villani, Pasquale Perillo, Simona Imbriani, Augusto Delle Femine, Livio Criscuolo, Maria Alfano, Marco La Montagna, Antonio Russo, Raffaele Marfella, Domenico Cozzolino, Ferdinando Carlo Sasso, Luca Rinaldi, Aldo Marrone, Luigi Elio Adinolfi and Ernesto Claar

Int. J. Mol. Sci. 2023, 24(8), 7651; https://doi.org/10.3390/ijms24087651 - 21 Apr 2023

Cited by 8 | Viewed by 3384

Abstract

Hepatitis B virus (HBV) is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Despite the advent of vaccines and potent antiviral agents able to suppress viral replication, recovery from chronic HBV infection is still an extremely difficult goal to achieve. [...] Read more.

Hepatitis B virus (HBV) is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Despite the advent of vaccines and potent antiviral agents able to suppress viral replication, recovery from chronic HBV infection is still an extremely difficult goal to achieve. Complex interactions between virus and host are responsible for HBV persistence and the risk of oncogenesis. Through multiple pathways, HBV is able to silence both innate and adaptive immunological responses and become out of control. Furthermore, the integration of the viral genome into that of the host and the production of covalently closed circular DNA (cccDNA) represent reservoirs of viral persistence and account for the difficult eradication of the infection. An adequate knowledge of the virus–host interaction mechanisms responsible for viral persistence and the risk of hepatocarcinogenesis is necessary for the development of functional cures for chronic HBV infection. The purpose of this review is, therefore, to analyze how interactions between HBV and host concur in the mechanisms of infection, persistence, and oncogenesis and what are the implications and the therapeutic perspectives that follow. Full article

(This article belongs to the Special Issue Host and Human Oncovirus Interaction)

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Open AccessReview

The Novel Role of Noncoding RNAs in Modulating Platelet Function: Implications in Activation and Aggregation

by Giovanni Cimmino, Stefano Conte, Domenico Palumbo, Simona Sperlongano, Michele Torella, Alessandro Della Corte and Paolo Golino

Int. J. Mol. Sci. 2023, 24(8), 7650; https://doi.org/10.3390/ijms24087650 - 21 Apr 2023

Cited by 1 | Viewed by 3256

Abstract

It is currently believed that plaque complication, with the consequent superimposed thrombosis, is a key factor in the clinical occurrence of acute coronary syndromes (ACSs). Platelets are major players in this process. Despite the considerable progress made by the new antithrombotic strategies (P2Y12 [...] Read more.

It is currently believed that plaque complication, with the consequent superimposed thrombosis, is a key factor in the clinical occurrence of acute coronary syndromes (ACSs). Platelets are major players in this process. Despite the considerable progress made by the new antithrombotic strategies (P2Y12 receptor inhibitors, new oral anticoagulants, thrombin direct inhibitors, etc.) in terms of a reduction in major cardiovascular events, a significant number of patients with previous ACSs treated with these drugs continue to experience events, indicating that the mechanisms of platelet remain largely unknown. In the last decade, our knowledge of platelet pathophysiology has improved. It has been reported that, in response to physiological and pathological stimuli, platelet activation is accompanied by de novo protein synthesis, through a rapid and particularly well-regulated translation of resident mRNAs of megakaryocytic derivation. Although the platelets are anucleate, they indeed contain an important fraction of mRNAs that can be quickly used for protein synthesis following their activation. A better understanding of the pathophysiology of platelet activation and the interaction with the main cellular components of the vascular wall will open up new perspectives in the treatment of the majority of thrombotic disorders, such as ACSs, stroke, and peripheral artery diseases before and after the acute event. In the present review, we will discuss the novel role of noncoding RNAs in modulating platelet function, highlighting the possible implications in activation and aggregation. Full article

(This article belongs to the Special Issue Drug Discovery and Novel Platelet Signaling in Thrombogenesis)

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Int. J. Mol. Sci., Volume 24, Issue 8 (April-2 2023) – 807 articles

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