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Volume 22
Issue 16
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Int. J. Mol. Sci., Volume 22, Issue 16 (August-2 2021) – 748 articles

Cover Story (view full-size image): Platelet-derived extracellular vesicles (pEVs) are nanosized membranous subcellular structures released by platelets, which comprise different subpopulations that differ on morphology, size and composition. They work as intercellular communicators, exerting their function by transporting their cargo, including nucleic acids, proteins and lipids. pEVs mediate the same functions as platelets, presenting great potential for the development of new biomedical treatments. In fact, some studies have shown pEVs regenerative capability in wound healing and haemorrhagic shock, in addition to their capacity to induce cellular differentiation, enhancing musculoskeletal or neural regeneration. However, further characterization report and standardization of requirements should be performed to facilitate its clinical use. View this paper
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16 pages, 3166 KiB  
Article
RNA Binding Properties of the Ty1 LTR-Retrotransposon Gag Protein
by Julita Gumna, Angelika Andrzejewska-Romanowska, David J. Garfinkel and Katarzyna Pachulska-Wieczorek
Int. J. Mol. Sci. 2021, 22(16), 9103; https://doi.org/10.3390/ijms22169103 - 23 Aug 2021
Cited by 3 | Viewed by 3558
Abstract
A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. The Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. In addition to capsid assembly functions, [...] Read more.
A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. The Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. In addition to capsid assembly functions, Ty1 Gag promotes Ty1 RNA dimerization and cyclization and initiation of reverse transcription. Direct interactions between Gag and retrotransposon genomic RNA (gRNA) are needed for Ty1 replication, and mutations in the RNA-binding domain disrupt nucleation of retrosomes and assembly of functional virus-like particles (VLPs). Unlike retroviral Gag, the specificity of Ty1 Gag-RNA interactions remain poorly understood. Here we use microscale thermophoresis (MST) and electrophoretic mobility shift assays (EMSA) to analyze interactions of immature and mature Ty1 Gag with RNAs. The salt-dependent experiments showed that Ty1 Gag binds with high and similar affinity to different RNAs. However, we observed a preferential interaction between Ty1 Gag and Ty1 RNA containing a packaging signal (Psi) in RNA competition analyses. We also uncover a relationship between Ty1 RNA structure and Gag binding involving the pseudoknot present on Ty1 gRNA. In all likelihood, the differences in Gag binding affinity detected in vitro only partially explain selective Ty1 RNA packaging into VLPs in vivo. Full article
(This article belongs to the Special Issue Proteins and Protein-Ligand Interactions)
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18 pages, 1161 KiB  
Review
Cross-Talks between the Cardiovascular Disease-Sarcopenia-Osteoporosis Triad and Magnesium in Humans
by Marie-Eva Pickering
Int. J. Mol. Sci. 2021, 22(16), 9102; https://doi.org/10.3390/ijms22169102 - 23 Aug 2021
Cited by 9 | Viewed by 4569
Abstract
Magnesium (Mg) is a pivotal and very complex component of healthy aging in the cardiovascular-muscle-bone triad. Low Mg levels and low Mg intake are common in the general aging population and are associated with poorer outcomes than higher levels, including vascular calcification, endothelial [...] Read more.
Magnesium (Mg) is a pivotal and very complex component of healthy aging in the cardiovascular-muscle-bone triad. Low Mg levels and low Mg intake are common in the general aging population and are associated with poorer outcomes than higher levels, including vascular calcification, endothelial dysfunction, osteoporosis, or muscle dysfunction/sarcopenia. While Mg supplementation appears to reverse these processes and benefit the triad, more randomized clinical trials are needed. These will allow improvement of preventive and curative strategies and propose guidelines regarding the pharmaceutical forms and the dosages and durations of treatment in order to optimize and adapt Mg prescription for healthy aging and for older vulnerable persons with comorbidities. Full article
(This article belongs to the Special Issue Magnesium in Development and Aging)
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13 pages, 869 KiB  
Review
Neuroblastoma GD2 Expression and Computational Analysis of Aptamer-Based Bioaffinity Targeting
by Godfred O. Sabbih and Michael K. Danquah
Int. J. Mol. Sci. 2021, 22(16), 9101; https://doi.org/10.3390/ijms22169101 - 23 Aug 2021
Cited by 9 | Viewed by 3732
Abstract
Neuroblastoma (NB) is a neuroectodermal embryonic cancer that originates from primordial neural crest cells, and amongst pediatric cancers with high mortality rates. NB is categorized into high-, intermediate-, and low-risk cases. A significant proportion of high-risk patients who achieve remission have a minimal [...] Read more.
Neuroblastoma (NB) is a neuroectodermal embryonic cancer that originates from primordial neural crest cells, and amongst pediatric cancers with high mortality rates. NB is categorized into high-, intermediate-, and low-risk cases. A significant proportion of high-risk patients who achieve remission have a minimal residual disease (MRD) that causes relapse. Whilst there exists a myriad of advanced treatment options for NB, it is still characterized by a high relapse rate, resulting in a reduced chance of survival. Disialoganglioside (GD2) is a lipo-ganglioside containing a fatty acid derivative of sphingosine that is coupled to a monosaccharide and a sialic acid. Amongst pediatric solid tumors, NB tumor cells are known to express GD2; hence, it represents a unique antigen for subclinical NB MRD detection and analysis with implications in determining a response for treatment. This article discusses NB MRD expression and analytical assays for GD2 detection and quantification as well as computational approaches for GD2 characterization based on high-throughput image processing and genomic data analysis. Full article
(This article belongs to the Special Issue Aptamer-Mediated Cancer Theranostics)
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21 pages, 1676 KiB  
Review
Extracellular DNA (eDNA). A Major Ubiquitous Element of the Bacterial Biofilm Architecture
by Davide Campoccia, Lucio Montanaro and Carla Renata Arciola
Int. J. Mol. Sci. 2021, 22(16), 9100; https://doi.org/10.3390/ijms22169100 - 23 Aug 2021
Cited by 80 | Viewed by 5691
Abstract
After the first ancient studies on microbial slime (the name by which the biofilm matrix was initially indicated), multitudes of studies on the morphology, composition and physiology of biofilms have arisen. The emergence of the role that biofilms play in the pathogenesis of [...] Read more.
After the first ancient studies on microbial slime (the name by which the biofilm matrix was initially indicated), multitudes of studies on the morphology, composition and physiology of biofilms have arisen. The emergence of the role that biofilms play in the pathogenesis of recalcitrant and persistent clinical infections, such as periprosthetic orthopedic infections, has reinforced scientific interest. Extracellular DNA (eDNA) is a recently uncovered component that is proving to be almost omnipresent in the extracellular polymeric substance (EPS) of biofilm. This macromolecule is eliciting unprecedented consideration for the critical impact on the pathogenesis of chronic clinical infections. After a systematic review of the literature, an updated description of eDNA in biofilms is presented, with a special focus on the latest findings regarding its fundamental structural role and the contribution it makes to the complex architecture of bacterial biofilms through interactions with a variety of other molecular components of the biofilm matrix. Full article
(This article belongs to the Section Molecular Microbiology)
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16 pages, 3050 KiB  
Article
Molecular Conditional Generation and Property Analysis of Non-Fullerene Acceptors with Deep Learning
by Shi-Ping Peng, Xin-Yu Yang and Yi Zhao
Int. J. Mol. Sci. 2021, 22(16), 9099; https://doi.org/10.3390/ijms22169099 - 23 Aug 2021
Cited by 2 | Viewed by 3176
Abstract
The proposition of non-fullerene acceptors (NFAs) in organic solar cells has made great progress in the raise of power conversion efficiency, and it also broadens the ways for searching and designing new acceptor molecules. In this work, the design of novel NFAs with [...] Read more.
The proposition of non-fullerene acceptors (NFAs) in organic solar cells has made great progress in the raise of power conversion efficiency, and it also broadens the ways for searching and designing new acceptor molecules. In this work, the design of novel NFAs with required properties is performed with the conditional generative model constructed from a convolutional neural network (CNN). The temporal CNN is firstly trained to be a good string-based molecular conditional generative model to directly generate the desired molecules. The reliability of generated molecular properties is then demonstrated by a graph-based prediction model and evaluated with quantum chemical calculations. Specifically, the global attention mechanism is incorporated in the prediction model to pool the extracted information of molecular structures and provide interpretability. By combining the generative and prediction models, thousands of NFAs with required frontier molecular orbital energies are generated. The generated new molecules essentially explore the chemical space and enrich the database of transformation rules for molecular design. The conditional generation model can also be trained to generate the molecules from molecular fragments, and the contribution of molecular fragments to the properties is subsequently predicted by the prediction model. Full article
(This article belongs to the Special Issue In Silico Molecular Design)
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37 pages, 10058 KiB  
Review
GSK-3β, FYN, and DYRK1A: Master Regulators in Neurodegenerative Pathways
by Stefania Demuro, Rita M. C. Di Martino, Jose A. Ortega and Andrea Cavalli
Int. J. Mol. Sci. 2021, 22(16), 9098; https://doi.org/10.3390/ijms22169098 - 23 Aug 2021
Cited by 49 | Viewed by 5647
Abstract
Protein kinases (PKs) have been recognized as central nervous system (CNS)-disease-relevant targets due to their master regulatory role in different signal transduction cascades in the neuroscience space. Among them, GSK-3β, FYN, and DYRK1A play a crucial role in the neurodegeneration context, and the [...] Read more.
Protein kinases (PKs) have been recognized as central nervous system (CNS)-disease-relevant targets due to their master regulatory role in different signal transduction cascades in the neuroscience space. Among them, GSK-3β, FYN, and DYRK1A play a crucial role in the neurodegeneration context, and the deregulation of all three PKs has been linked to different CNS disorders with unmet medical needs, including Alzheimer’s disease (AD), Parkinson’s disease (PD), frontotemporal lobar degeneration (FTLD), and several neuromuscular disorders. The multifactorial nature of these diseases, along with the failure of many advanced CNS clinical trials, and the lengthy approval process of a novel CNS drug have strongly limited the CNS drug discovery. However, in the near-decade from 2010 to 2020, several computer-assisted drug design strategies have been combined with synthetic efforts to develop potent and selective GSK-3β, FYN, and DYRK1A inhibitors as disease-modifying agents. In this review, we described both structural and functional aspects of GSK-3β, FYN, and DYRK1A and their involvement and crosstalk in different CNS pathological signaling pathways. Moreover, we outlined attractive medicinal chemistry approaches including multi-target drug design strategies applied to overcome some limitations of known PKs inhibitors and discover improved modulators with suitable blood–brain barrier (BBB) permeability and drug-like properties. Full article
(This article belongs to the Special Issue Protein Kinases and Their Inhibitors in CNS Diseases)
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18 pages, 1163 KiB  
Review
The Impact of Vitamin D on Skin Aging
by Georgeta Bocheva, Radomir M. Slominski and Andrzej T. Slominski
Int. J. Mol. Sci. 2021, 22(16), 9097; https://doi.org/10.3390/ijms22169097 - 23 Aug 2021
Cited by 63 | Viewed by 14061
Abstract
The active metabolites of vitamin D3 (D3) and lumisterol (L3) exert a variety of antiaging and photoprotective effects on the skin. These are achieved through immunomodulation and include anti-inflammatory actions, regulation of keratinocytes proliferation, and differentiation programs to [...] Read more.
The active metabolites of vitamin D3 (D3) and lumisterol (L3) exert a variety of antiaging and photoprotective effects on the skin. These are achieved through immunomodulation and include anti-inflammatory actions, regulation of keratinocytes proliferation, and differentiation programs to build the epidermal barrier necessary for maintaining skin homeostasis. In addition, they induce antioxidative responses, inhibit DNA damage and induce DNA repair mechanisms to attenuate premature skin aging and cancerogenesis. The mechanism of action would involve interaction with multiple nuclear receptors including VDR, AhR, LXR, reverse agonism on RORα and -γ, and nongenomic actions through 1,25D3-MARRS receptor and interaction with the nongenomic binding site of the VDR. Therefore, active forms of vitamin D3 including its canonical (1,25(OH)2D3) and noncanonical (CYP11A1-intitated) D3 derivatives as well as L3 derivatives are promising agents for the prevention, attenuation, or treatment of premature skin aging. They could be administrated orally and/or topically. Other forms of parenteral application of vitamin D3 precursor should be considered to avoid its predominant metabolism to 25(OH)D3 that is not recognized by CYP11A1 enzyme. The efficacy of topically applied vitamin D3 and L3 derivatives needs further clinical evaluation in future trials. Full article
(This article belongs to the Special Issue Recent Advances in Biology of Ultraviolet Radiation (UVR) and Vitamin D)
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14 pages, 4437 KiB  
Review
Bile Acid Signaling in Inflammatory Bowel Disease
by Mariusz A. Bromke and Małgorzata Krzystek-Korpacka
Int. J. Mol. Sci. 2021, 22(16), 9096; https://doi.org/10.3390/ijms22169096 - 23 Aug 2021
Cited by 27 | Viewed by 4979
Abstract
Inflammatory bowel disease is a chronic, idiopathic and complex condition, which most often manifests itself in the form of ulcerative colitis or Crohn’s disease. Both forms are associated with dysregulation of the mucosal immune system, compromised intestinal epithelial barrier, and dysbiosis of the [...] Read more.
Inflammatory bowel disease is a chronic, idiopathic and complex condition, which most often manifests itself in the form of ulcerative colitis or Crohn’s disease. Both forms are associated with dysregulation of the mucosal immune system, compromised intestinal epithelial barrier, and dysbiosis of the gut microbiome. It has been observed for a long time that bile acids are involved in inflammatory disorders, and recent studies show their significant physiological role, reaching far beyond being emulsifiers helping in digestion of lipids. Bile acids are also signaling molecules, which act, among other things, on lipid metabolism and immune responses, through several nuclear and membrane receptors in hepatocytes, enterocytes and cells of the immune system. Gut microbiota homeostasis also seems to be affected, directly and indirectly, by bile acid metabolism and signaling. This review summarizes recent advances in the field of bile acid signaling, studies of inflamed gut microbiome, and the therapeutic potential of bile acids in the context of inflammatory bowel disease. Full article
(This article belongs to the Special Issue Lipid Molecules in Inflammation and Chronic Diseases)
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21 pages, 23959 KiB  
Article
Photodynamic Inactivation of Legionella pneumophila Biofilm Formation by Cationic Tetra- and Tripyridylporphyrins in Waters of Different Hardness
by Martina Mušković, Iva Ćavar, Andrija Lesar, Martin Lončarić, Nela Malatesti and Ivana Gobin
Int. J. Mol. Sci. 2021, 22(16), 9095; https://doi.org/10.3390/ijms22169095 - 23 Aug 2021
Cited by 5 | Viewed by 2788
Abstract
The bacterium Legionella pneumophila is still one of the probable causes of waterborne diseases, causing serious respiratory illnesses. In the aquatic systems, L. pneumophila exists inside free-living amoebae or can form biofilms. Currently developed disinfection methods are not sufficient for complete eradication of [...] Read more.
The bacterium Legionella pneumophila is still one of the probable causes of waterborne diseases, causing serious respiratory illnesses. In the aquatic systems, L. pneumophila exists inside free-living amoebae or can form biofilms. Currently developed disinfection methods are not sufficient for complete eradication of L. pneumophila biofilms in water systems of interest. Photodynamic inactivation (PDI) is a method that results in an antimicrobial effect by using a combination of light and a photosensitizer (PS). In this work, the effect of PDI in waters of natural origin and of different hardness, as a treatment against L. pneumophila biofilm, was investigated. Three cationic tripyridylporphyrins, which were previously described as efficient agents against L. pneumophila alone, were used as PSs. We studied how differences in water hardness affect the PSs’ stability, the production of singlet oxygen, and the PDI activity on L. pneumophila adhesion and biofilm formation and in biofilm destruction. Amphiphilic porphyrin showed a stronger tendency for aggregation in hard and soft water, but its production of singlet oxygen was higher in comparison to tri- and tetracationic hydrophilic porphyrins that were stable in all water samples. All three studied porphyrins were shown to be effective as PDI agents against the adhesion of the L. pneumophila to polystyrene, against biofilm formation, and in the destruction of the formed biofilm, in their micromolar concentrations. However, a higher number of dissolved ions, i.e., water hardness, generally reduced somewhat the PDI activity of all the porphyrins at all tested biofilm growth stages. Full article
(This article belongs to the Section Molecular Microbiology)
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20 pages, 9920 KiB  
Article
TRIM25 and DEAD-Box RNA Helicase DDX3X Cooperate to Regulate RIG-I-Mediated Antiviral Immunity
by Sarah C. Atkinson, Steven M. Heaton, Michelle D. Audsley, Oded Kleifeld and Natalie A. Borg
Int. J. Mol. Sci. 2021, 22(16), 9094; https://doi.org/10.3390/ijms22169094 - 23 Aug 2021
Cited by 11 | Viewed by 4033
Abstract
The cytoplasmic retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) initiate interferon (IFN) production and antiviral gene expression in response to RNA virus infection. Consequently, RLR signalling is tightly regulated by both host and viral factors. Tripartite motif protein 25 (TRIM25) is an E3 ligase [...] Read more.
The cytoplasmic retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) initiate interferon (IFN) production and antiviral gene expression in response to RNA virus infection. Consequently, RLR signalling is tightly regulated by both host and viral factors. Tripartite motif protein 25 (TRIM25) is an E3 ligase that ubiquitinates multiple substrates within the RLR signalling cascade, playing both ubiquitination-dependent and -independent roles in RIG-I-mediated IFN induction. However, additional regulatory roles are emerging. Here, we show a novel interaction between TRIM25 and another protein in the RLR pathway that is essential for type I IFN induction, DEAD-box helicase 3X (DDX3X). In vitro assays and knockdown studies reveal that TRIM25 ubiquitinates DDX3X at lysine 55 (K55) and that TRIM25 and DDX3X cooperatively enhance IFNB1 induction following RIG-I activation, but the latter is independent of TRIM25’s catalytic activity. Furthermore, we found that the influenza A virus non-structural protein 1 (NS1) disrupts the TRIM25:DDX3X interaction, abrogating both TRIM25-mediated ubiquitination of DDX3X and cooperative activation of the IFNB1 promoter. Thus, our results reveal a new interplay between two RLR-host proteins that cooperatively enhance IFN-β production. We also uncover a new and further mechanism by which influenza A virus NS1 suppresses host antiviral defence. Full article
(This article belongs to the Special Issue Ubiquitination and Deubiquitination in Cellular Homeostasis)
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18 pages, 3520 KiB  
Article
Palmitic Acid Lipotoxicity in Microglia Cells Is Ameliorated by Unsaturated Fatty Acids
by C.J. Urso and Heping Zhou
Int. J. Mol. Sci. 2021, 22(16), 9093; https://doi.org/10.3390/ijms22169093 - 23 Aug 2021
Cited by 26 | Viewed by 6231
Abstract
Obesity and metabolic syndrome are associated with cognitive decline and dementia. Palmitic acid (PA) is increased in the cerebrospinal fluid of obese patients with cognitive impairment. This study was therefore designed to examine fatty acid (FA) lipotoxicity in BV2 microglia cells. We found [...] Read more.
Obesity and metabolic syndrome are associated with cognitive decline and dementia. Palmitic acid (PA) is increased in the cerebrospinal fluid of obese patients with cognitive impairment. This study was therefore designed to examine fatty acid (FA) lipotoxicity in BV2 microglia cells. We found that PA induced time- and dose-dependent decrease in cell viability and increase in cell death without affecting the cell cycle profile and that PA lipotoxicity did not depend on cell surface free fatty acid receptors but rather on FA uptake. Treatment with sulfosuccinimidyl oleate (SSO), an irreversible inhibitor of fatty acid translocase CD36, significantly inhibited FA uptake in BSA- and PA-treated cells and blocked PA-induced decrease in cell viability. Inhibition of ER stress or treatment with N-acetylcysteine was not able to rescue PA lipotoxicity. Our study also showed that unsaturated fatty acids (UFAs), such as linoleic acid (LA), oleic acid (OA), α-linolenic acid (ALA), and docosahexaenoic acid (DHA), were not lipotoxic but instead protected microglia against PA-induced decrease in cell viability. Co-treatment of PA with LA, OA, and DHA significantly inhibited FA uptake in PA-treated cells. All UFAs tested induced the incorporation of FAs into and the amount of neutral lipids, while PA did not significantly affect the amount of neutral lipids compared with BSA control. Full article
(This article belongs to the Section Molecular Neurobiology)
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31 pages, 7085 KiB  
Review
Peptide-Assisted Nucleic Acid Delivery Systems on the Rise
by Shabnam Tarvirdipour, Michal Skowicki, Cora-Ann Schoenenberger and Cornelia G. Palivan
Int. J. Mol. Sci. 2021, 22(16), 9092; https://doi.org/10.3390/ijms22169092 - 23 Aug 2021
Cited by 12 | Viewed by 5711
Abstract
Concerns associated with nanocarriers’ therapeutic efficacy and side effects have led to the development of strategies to advance them into targeted and responsive delivery systems. Owing to their bioactivity and biocompatibility, peptides play a key role in these strategies and, thus, have been [...] Read more.
Concerns associated with nanocarriers’ therapeutic efficacy and side effects have led to the development of strategies to advance them into targeted and responsive delivery systems. Owing to their bioactivity and biocompatibility, peptides play a key role in these strategies and, thus, have been extensively studied in nanomedicine. Peptide-based nanocarriers, in particular, have burgeoned with advances in purely peptidic structures and in combinations of peptides, both native and modified, with polymers, lipids, and inorganic nanoparticles. In this review, we summarize advances on peptides promoting gene delivery systems. The efficacy of nucleic acid therapies largely depends on cell internalization and the delivery to subcellular organelles. Hence, the review focuses on nanocarriers where peptides are pivotal in ferrying nucleic acids to their site of action, with a special emphasis on peptides that assist anionic, water-soluble nucleic acids in crossing the membrane barriers they encounter on their way to efficient function. In a second part, we address how peptides advance nanoassembly delivery tools, such that they navigate delivery barriers and release their nucleic acid cargo at specific sites in a controlled fashion. Full article
(This article belongs to the Special Issue Synthetic Peptides and Peptidomimetics: From Basic Science to Biomedical Applications)
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17 pages, 1172 KiB  
Review
Experimental Evidence of 2,3,7,8-Tetrachlordibenzo-p-Dioxin (TCDD) Transgenerational Effects on Reproductive Health
by Laura Gaspari, Françoise Paris, Nicolas Kalfa, Marie-Odile Soyer-Gobillard, Charles Sultan and Samir Hamamah
Int. J. Mol. Sci. 2021, 22(16), 9091; https://doi.org/10.3390/ijms22169091 - 23 Aug 2021
Cited by 22 | Viewed by 3759
Abstract
Previous studies have demonstrated that endocrine disruptors (EDs) can promote the transgenerational inheritance of disease susceptibility. Among the many existing EDs, 2,3,7,8-tetrachlordibenzo-p-dioxin (TCDD) affects reproductive health, including in humans, following direct occupational exposure or environmental disasters, for instance the Agent Orange sprayed during [...] Read more.
Previous studies have demonstrated that endocrine disruptors (EDs) can promote the transgenerational inheritance of disease susceptibility. Among the many existing EDs, 2,3,7,8-tetrachlordibenzo-p-dioxin (TCDD) affects reproductive health, including in humans, following direct occupational exposure or environmental disasters, for instance the Agent Orange sprayed during the Vietnam War. Conversely, few studies have focused on TCDD multigenerational and transgenerational effects on human reproductive health, despite the high amount of evidence in animal models of such effects on male and female reproductive health that mimic human reproductive system disorders. Importantly, these studies show that paternal ancestral TCDD exposure substantially contributes to pregnancy outcome and fetal health, although pregnancy outcome is considered tightly related to the woman’s health. In this work, we conducted a systematic review of the literature and a knowledge synthesis in order (i) to describe the findings obtained in rodent models concerning TCDD transgenerational effects on reproductive health and (ii) to discuss the epigenetic molecular alterations that might be involved in this process. As ancestral toxicant exposure cannot be changed in humans, identifying the crucial reproductive functions that are negatively affected by such exposure may help clinicians to preserve male and female fertility and to avoid adverse pregnancy outcomes. Full article
(This article belongs to the Section Biochemistry)
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21 pages, 1073 KiB  
Review
Stress Adaptation and the Brainstem with Focus on Corticotropin-Releasing Hormone
by Tiago Chaves, Csilla Lea Fazekas, Krisztina Horváth, Pedro Correia, Adrienn Szabó, Bibiána Török, Krisztina Bánrévi and Dóra Zelena
Int. J. Mol. Sci. 2021, 22(16), 9090; https://doi.org/10.3390/ijms22169090 - 23 Aug 2021
Cited by 16 | Viewed by 8569
Abstract
Stress adaptation is of utmost importance for the maintenance of homeostasis and, therefore, of life itself. The prevalence of stress-related disorders is increasing, emphasizing the importance of exploratory research on stress adaptation. Two major regulatory pathways exist: the hypothalamic–pituitary–adrenocortical axis and the sympathetic [...] Read more.
Stress adaptation is of utmost importance for the maintenance of homeostasis and, therefore, of life itself. The prevalence of stress-related disorders is increasing, emphasizing the importance of exploratory research on stress adaptation. Two major regulatory pathways exist: the hypothalamic–pituitary–adrenocortical axis and the sympathetic adrenomedullary axis. They act in unison, ensured by the enormous bidirectional connection between their centers, the paraventricular nucleus of the hypothalamus (PVN), and the brainstem monoaminergic cell groups, respectively. PVN and especially their corticotropin-releasing hormone (CRH) producing neurons are considered to be the centrum of stress regulation. However, the brainstem seems to be equally important. Therefore, we aimed to summarize the present knowledge on the role of classical neurotransmitters of the brainstem (GABA, glutamate as well as serotonin, noradrenaline, adrenaline, and dopamine) in stress adaptation. Neuropeptides, including CRH, might be co-localized in the brainstem nuclei. Here we focused on CRH as its role in stress regulation is well-known and widely accepted and other CRH neurons scattered along the brain may also complement the function of the PVN. Although CRH-positive cells are present on some parts of the brainstem, sometimes even in comparable amounts as in the PVN, not much is known about their contribution to stress adaptation. Based on the role of the Barrington’s nucleus in micturition and the inferior olivary complex in the regulation of fine motoric—as the main CRH-containing brainstem areas—we might assume that these areas regulate stress-induced urination and locomotion, respectively. Further studies are necessary for the field. Full article
(This article belongs to the Special Issue Neuroendocrine Factors in Health and Disease)
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18 pages, 3449 KiB  
Article
CSBD Healing in Rats after Application of Bovine Xenogeneic Biomaterial Enriched with Magnesium Alloy
by Ana Terezija Jerbić Radetić, Sanja Zoričić Cvek, Matej Tomas, Igor Erjavec, Matko Oguić, Željka Perić Kačarević and Olga Cvijanović Peloza
Int. J. Mol. Sci. 2021, 22(16), 9089; https://doi.org/10.3390/ijms22169089 - 23 Aug 2021
Cited by 8 | Viewed by 3180
Abstract
Xenogeneic biomaterials Cerbone® and OsteoBiol® are widely used in oral implantology. In dental practice, xenogeneic biomaterial is usually combined with autologous bone to provide bone volume stability needed for long-term dental implants. Magnesium alloy implants dissolve and form mineral corrosion layer [...] Read more.
Xenogeneic biomaterials Cerbone® and OsteoBiol® are widely used in oral implantology. In dental practice, xenogeneic biomaterial is usually combined with autologous bone to provide bone volume stability needed for long-term dental implants. Magnesium alloy implants dissolve and form mineral corrosion layer that is directly in contact with bone tissue, allowing deposition of the newly formed bone. CSBD heals by intramembranous ossification and therefore is a convenient model for analyses of ostoconductive and osteoinductive properties of different type of biomaterials. Magnesium alloy-enriched biomaterials have not yet been applied in oral implantology. Therefore, the aim of the current study was to investigate biological properties of potentially new bovine xenogeneic biomaterial enriched with magnesium alloy in a 5 mm CSBD model. Osteoconductive properties of Cerabone®, Cerabone® + Al. bone, and OsteoBiol® were also analyzed. Dynamics of bone healing was followed up on the days 3, 7, 15, 21, and 30. Calvary bone samples were analyzed by micro-CT, and values of the bone morphometric parameters were assessed. Bone samples were further processed for histological and immunohistochemical analyses. Histological observation revealed CSBD closure at day 30 of the given xenogeneic biomaterial groups, with the exception of the control group. TNF-α showed high intensity of expression at the sites of MSC clusters that underwent ossification. Osx was expressed in pre-osteoblasts, which were differentiated into mature osteoblasts and osteocytes. Results of the micro-CT analyses showed linear increase in bone volume of all xenogeneic biomaterial groups and also in the control. The highest average values of bone volume were found for the Cerabone® + Mg group. In addition, less residual biomaterial was estimated in the Cerabone® + Mg group than in the Cerabone® group, indicating its better biodegradation during CSBD healing. Overall, the magnesium alloy xenogeneic biomaterial demonstrated key properties of osteoinduction and biodegradidibility during CSBD healing, which is the reason why it should be recommended for application in clinical practice of oral implantology. Full article
(This article belongs to the Special Issue Biomaterials for Bone Tissue Engineering 2.0)
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17 pages, 1021 KiB  
Article
Spaceflight Modulates the Expression of Key Oxidative Stress and Cell Cycle Related Genes in Heart
by Akhilesh Kumar, Candice G. T. Tahimic, Eduardo A. C. Almeida and Ruth K. Globus
Int. J. Mol. Sci. 2021, 22(16), 9088; https://doi.org/10.3390/ijms22169088 - 23 Aug 2021
Cited by 18 | Viewed by 3543
Abstract
Spaceflight causes cardiovascular changes due to microgravity-induced redistribution of body fluids and musculoskeletal unloading. Cardiac deconditioning and atrophy on Earth are associated with altered Trp53 and oxidative stress-related pathways, but the effects of spaceflight on cardiac changes at the molecular level are less [...] Read more.
Spaceflight causes cardiovascular changes due to microgravity-induced redistribution of body fluids and musculoskeletal unloading. Cardiac deconditioning and atrophy on Earth are associated with altered Trp53 and oxidative stress-related pathways, but the effects of spaceflight on cardiac changes at the molecular level are less understood. We tested the hypothesis that spaceflight alters the expression of key genes related to stress response pathways, which may contribute to cardiovascular deconditioning during extended spaceflight. Mice were exposed to spaceflight for 15 days or maintained on Earth (ground control). Ventricle tissue was harvested starting ~3 h post-landing. We measured expression of select genes implicated in oxidative stress pathways and Trp53 signaling by quantitative PCR. Cardiac expression levels of 37 of 168 genes tested were altered after spaceflight. Spaceflight downregulated transcription factor, Nfe2l2 (Nrf2), upregulated Nox1 and downregulated Ptgs2, suggesting a persistent increase in oxidative stress-related target genes. Spaceflight also substantially upregulated Cdkn1a (p21) and cell cycle/apoptosis-related gene Myc, and downregulated the inflammatory response gene Tnf. There were no changes in apoptosis-related genes such as Trp53. Spaceflight altered the expression of genes regulating redox balance, cell cycle and senescence in cardiac tissue of mice. Thus, spaceflight may contribute to cardiac dysfunction due to oxidative stress. Full article
(This article belongs to the Special Issue Dysregulation of Human Molecular and Metabolic Mechanisms Resulting in Oxidative Stress and Damage Generation in the Space Environment)
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13 pages, 3375 KiB  
Article
Small Structural Proteins E and M Render the SARS-CoV-2 Pseudovirus More Infectious and Reveal the Phenotype of Natural Viral Variants
by Hsin-I Wang, Zih-Shiuan Chuang, Yu-Ting Kao, Yi-Ling Lin, Jian-Jong Liang, Chun-Che Liao, Ching-Len Liao, Michael M. C. Lai and Chia-Yi Yu
Int. J. Mol. Sci. 2021, 22(16), 9087; https://doi.org/10.3390/ijms22169087 - 23 Aug 2021
Cited by 14 | Viewed by 3905
Abstract
The SARS-CoV-2 pseudovirus is a commonly used strategy that mimics certain biological functions of the authentic virus by relying on biological legitimacy at the molecular level. Despite the fact that spike (S), envelope (E), and membrane (M) proteins together wrap up the SARS-CoV-2 [...] Read more.
The SARS-CoV-2 pseudovirus is a commonly used strategy that mimics certain biological functions of the authentic virus by relying on biological legitimacy at the molecular level. Despite the fact that spike (S), envelope (E), and membrane (M) proteins together wrap up the SARS-CoV-2 virion, most of the reported pseudotype viruses consist of only the S protein. Here, we report that the presence of E and M increased the virion infectivity by promoting the S protein priming. The S, E, and M (SEM)-coated pseudovirion is spherical, containing crown-like spikes on the surface. Both S and SEM pseudoviruses packaged the same amounts of viral RNA, but the SEM virus bound more efficiently to cells stably expressing the viral receptor human angiotensin-converting enzyme II (hACE2) and became more infectious. Using this SEM pseudovirus, we examined the infectivity and antigenic properties of the natural SARS-CoV-2 variants. We showed that some variants have higher infectivity than the original virus and that some render the neutralizing plasma with lower potency. These studies thus revealed possible mechanisms of the dissemination advantage of these variants. Hence, the SEM pseudovirion provides a useful tool to evaluate the viral infectivity and capability of convalescent sera in neutralizing specific SARS-CoV-2 S dominant variants. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants, Antibodies and Vaccines)
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24 pages, 12300 KiB  
Article
Programmed Cell Death in Developing Brachypodium distachyon Grain
by Safia Saada, Charles Ugochukwu Solomon and Sinéad Drea
Int. J. Mol. Sci. 2021, 22(16), 9086; https://doi.org/10.3390/ijms22169086 - 23 Aug 2021
Cited by 4 | Viewed by 2320
Abstract
The normal developmental sequence in a grass grain entails the death of several maternal and filial tissues in a genetically regulated process termed programmed cell death (PCD). The progression and molecular aspects of PCD in developing grains have been reported for domesticated species [...] Read more.
The normal developmental sequence in a grass grain entails the death of several maternal and filial tissues in a genetically regulated process termed programmed cell death (PCD). The progression and molecular aspects of PCD in developing grains have been reported for domesticated species such as barley, rice, maize and wheat. Here, we report a detailed investigation of PCD in the developing grain of the wild model species Brachypodium distachyon. We detected PCD in developing Brachypodium grains using molecular and histological approaches. We also identified in Brachypodium the orthologs of protease genes known to contribute to grain PCD and surveyed their expression. We found that, similar to cereals, PCD in the Brachypodium nucellus occurs in a centrifugal pattern following anthesis. However, compared to cereals, the rate of post-mortem clearance in the Brachypodium nucellus is slower. However, compared to wheat and barley, mesocarp PCD in Brachypodium proceeds more rapidly in lateral cells. Remarkably, Brachypodium mesocarp PCD is not coordinated with endosperm development. Phylogenetic analysis suggests that barley and wheat possess more vacuolar processing enzymes that drive nucellar PCD compared to Brachypodium and rice. Our expression analysis highlighted putative grain-specific PCD proteases in Brachypodium. Combined with existing knowledge on grain PCD, our study suggests that the rate of nucellar PCD moderates grain size and that the pattern of mesocarp PCD influences grain shape. Full article
(This article belongs to the Special Issue Fruit and Seed Development)
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18 pages, 13124 KiB  
Article
Natural Mutations Affect Structure and Function of gC1q Domain of Otolin-1
by Rafał Hołubowicz, Andrzej Ożyhar and Piotr Dobryszycki
Int. J. Mol. Sci. 2021, 22(16), 9085; https://doi.org/10.3390/ijms22169085 - 23 Aug 2021
Cited by 6 | Viewed by 2509
Abstract
Otolin-1 is a scaffold protein of otoliths and otoconia, calcium carbonate biominerals from the inner ear. It contains a gC1q domain responsible for trimerization and binding of Ca2+. Knowledge of a structure–function relationship of gC1q domain of otolin-1 is crucial for [...] Read more.
Otolin-1 is a scaffold protein of otoliths and otoconia, calcium carbonate biominerals from the inner ear. It contains a gC1q domain responsible for trimerization and binding of Ca2+. Knowledge of a structure–function relationship of gC1q domain of otolin-1 is crucial for understanding the biology of balance sensing. Here, we show how natural variants alter the structure of gC1q otolin-1 and how Ca2+ are able to revert some effects of the mutations. We discovered that natural substitutions: R339S, R342W and R402P negatively affect the stability of apo-gC1q otolin-1, and that Q426R has a stabilizing effect. In the presence of Ca2+, R342W and Q426R were stabilized at higher Ca2+ concentrations than the wild-type form, and R402P was completely insensitive to Ca2+. The mutations affected the self-association of gC1q otolin-1 by inducing detrimental aggregation (R342W) or disabling the trimerization (R402P) of the protein. Our results indicate that the natural variants of gC1q otolin-1 may have a potential to cause pathological changes in otoconia and otoconial membrane, which could affect sensing of balance and increase the probability of occurrence of benign paroxysmal positional vertigo (BPPV). Full article
(This article belongs to the Special Issue Frontiers in Protein Structure Research)
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10 pages, 1894 KiB  
Article
Bone Fracture-Treatment Method: Fixing 3D-Printed Polycaprolactone Scaffolds with Hydrogel Type Bone-Derived Extracellular Matrix and β-Tricalcium Phosphate as an Osteogenic Promoter
by Seokhwan Yun, Dami Choi, Dong-Jin Choi, Songwan Jin, Won-Soo Yun, Jung-Bo Huh and Jin-Hyung Shim
Int. J. Mol. Sci. 2021, 22(16), 9084; https://doi.org/10.3390/ijms22169084 - 23 Aug 2021
Cited by 14 | Viewed by 2873
Abstract
Bone formation and growth are crucial for treating bone fractures. Improving bone-reconstruction methods using autologous bone and synthetic implants can reduce the recovery time. Here, we investigated three treatments using two different materials, a bone-derived decellularized extracellular matrix (bdECM) and β-tricalcium phosphate (β-TCP), [...] Read more.
Bone formation and growth are crucial for treating bone fractures. Improving bone-reconstruction methods using autologous bone and synthetic implants can reduce the recovery time. Here, we investigated three treatments using two different materials, a bone-derived decellularized extracellular matrix (bdECM) and β-tricalcium phosphate (β-TCP), individually and in combination, as osteogenic promoter between bone and 3D-printed polycaprolactone scaffold (6-mm diameter) in rat calvarial defects (8-mm critical diameter). The materials were tested with a human pre-osteoblast cell line (MG63) to determine the effects of the osteogenic promoter on bone formation in vitro. A polycaprolactone (PCL) scaffold with a porous structure was placed at the center of the in vivo rat calvarial defects. The gap between the defective bone and PCL scaffold was filled with each material. Animals were sacrificed four weeks post-implantation, and skull samples were preserved for analysis. The preserved samples were scanned by micro-computed tomography and analyzed histologically to examine the clinical benefits of the materials. The bdECM–β-TCP mixture showed faster bone formation and a lower inflammatory response in the rats. Therefore, our results imply that a bdECM–β-TCP mixture is an ideal osteogenic promoter for treating fractures. Full article
(This article belongs to the Special Issue 3D Printing and Biomaterials for Biological and Medical Application)
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54 pages, 17225 KiB  
Review
Diabetic Kinome Inhibitors—A New Opportunity for β-Cells Restoration
by Barbara Pucelik, Agata Barzowska, Janusz M. Dąbrowski and Anna Czarna
Int. J. Mol. Sci. 2021, 22(16), 9083; https://doi.org/10.3390/ijms22169083 - 23 Aug 2021
Cited by 13 | Viewed by 4695
Abstract
Diabetes, and several diseases related to diabetes, including cancer, cardiovascular diseases and neurological disorders, represent one of the major ongoing threats to human life, becoming a true pandemic of the 21st century. Current treatment strategies for diabetes mainly involve promoting β-cell differentiation, and [...] Read more.
Diabetes, and several diseases related to diabetes, including cancer, cardiovascular diseases and neurological disorders, represent one of the major ongoing threats to human life, becoming a true pandemic of the 21st century. Current treatment strategies for diabetes mainly involve promoting β-cell differentiation, and one of the most widely studied targets for β-cell regeneration is DYRK1A kinase, a member of the DYRK family. DYRK1A has been characterized as a key regulator of cell growth, differentiation, and signal transduction in various organisms, while further roles and substrates are the subjects of extensive investigation. The targets of interest in this review are implicated in the regulation of β-cells through DYRK1A inhibition—through driving their transition from highly inefficient and death-prone populations into efficient and sufficient precursors of islet regeneration. Increasing evidence for the role of DYRK1A in diabetes progression and β-cell proliferation expands the potential for pharmaceutical applications of DYRK1A inhibitors. The variety of new compounds and binding modes, determined by crystal structure and in vitro studies, may lead to new strategies for diabetes treatment. This review provides recent insights into the initial self-activation of DYRK1A by tyrosine autophosphorylation. Moreover, the importance of developing novel DYRK1A inhibitors and their implications for the treatment of diabetes are thoroughly discussed. The evolving understanding of DYRK kinase structure and function and emerging high-throughput screening technologies have been described. As a final point of this work, we intend to promote the term “diabetic kinome” as part of scientific terminology to emphasize the role of the synergistic action of multiple kinases in governing the molecular processes that underlie this particular group of diseases. Full article
(This article belongs to the Special Issue Protein Kinases in Metabolic Disorders)
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19 pages, 2744 KiB  
Review
Nanomedicine for Neurodegenerative Disorders: Focus on Alzheimer’s and Parkinson’s Diseases
by Keelan Jagaran and Moganavelli Singh
Int. J. Mol. Sci. 2021, 22(16), 9082; https://doi.org/10.3390/ijms22169082 - 23 Aug 2021
Cited by 50 | Viewed by 6514
Abstract
Neurodegenerative disorders involve the slow and gradual degeneration of axons and neurons in the central nervous system (CNS), resulting in abnormalities in cellular function and eventual cellular demise. Patients with these disorders succumb to the high medical costs and the disruption of their [...] Read more.
Neurodegenerative disorders involve the slow and gradual degeneration of axons and neurons in the central nervous system (CNS), resulting in abnormalities in cellular function and eventual cellular demise. Patients with these disorders succumb to the high medical costs and the disruption of their normal lives. Current therapeutics employed for treating these diseases are deemed palliative. Hence, a treatment strategy that targets the disease’s cause, not just the symptoms exhibited, is desired. The synergistic use of nanomedicine and gene therapy to effectively target the causative mutated gene/s in the CNS disease progression could provide the much-needed impetus in this battle against these diseases. This review focuses on Parkinson’s and Alzheimer’s diseases, the gene/s and proteins responsible for the damage and death of neurons, and the importance of nanomedicine as a potential treatment strategy. Multiple genes were identified in this regard, each presenting with various mutations. Hence, genome-wide sequencing is essential for specific treatment in patients. While a cure is yet to be achieved, genomic studies form the basis for creating a highly efficacious nanotherapeutic that can eradicate these dreaded diseases. Thus, nanomedicine can lead the way in helping millions of people worldwide to eventually lead a better life. Full article
(This article belongs to the Special Issue Nanoparticles in CNS Diseases)
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20 pages, 1349 KiB  
Review
Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
by Aljaž Gaber and Miha Pavšič
Int. J. Mol. Sci. 2021, 22(16), 9081; https://doi.org/10.3390/ijms22169081 - 23 Aug 2021
Cited by 14 | Viewed by 6878
Abstract
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects [...] Read more.
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability. Full article
(This article belongs to the Special Issue Protein Oligomerization)
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14 pages, 2239 KiB  
Article
Combined Transcriptomic Analysis and RNA Interference Reveal the Effects of Methoxyfenozide on Ecdysone Signaling Pathway of Spodoptera exigua
by Zhixian Zhang, Yajie Ma, Xiaoyan Ma, Hongyan Hu, Dan Wang, Xianpeng Song, Xiangliang Ren and Yan Ma
Int. J. Mol. Sci. 2021, 22(16), 9080; https://doi.org/10.3390/ijms22169080 - 23 Aug 2021
Cited by 6 | Viewed by 2172
Abstract
Spodoptera exigua is a worldwide pest afflicting edible vegetables and has developed varying levels of resistance to insecticides. Methoxyfenozide (MET), an ecdysteroid agonist, is effective against lepidopteran pests such as S. exigua. However, the mechanism of MET to S. exigua remains unclear. [...] Read more.
Spodoptera exigua is a worldwide pest afflicting edible vegetables and has developed varying levels of resistance to insecticides. Methoxyfenozide (MET), an ecdysteroid agonist, is effective against lepidopteran pests such as S. exigua. However, the mechanism of MET to S. exigua remains unclear. In this study, we analyzed the expression patterns of genes related to the ecdysone signaling pathway in transcriptome data treated with sublethal doses of MET and analyzed how expression levels of key genes affect the toxicity of MET on S. exigua. Our results demonstrated that 2639 genes were up-regulated and 2512 genes were down-regulated in S. exigua treated with LC30 of MET. Of these, 15 genes were involved in the ecdysone signaling pathway. qPCR results demonstrated that ecdysone receptor A (EcRA) expression levels significantly increased in S. exigua when treated with different doses of MET, and that the RNAi-mediated silencing of EcRA significantly increased mortality to 55.43% at 72 h when L3 S. exigua larvae were exposed to MET at the LC30 dose. Additionally, knocking down EcRA suppressed the most genes expressed in the ecdysone signaling pathway. The combination of MET and dsEcRA affected the expression of E74 and enhanced the expression of TREA. These results demonstrate that the adverse effects of sublethal MET disturb the ecdysone signaling pathway in S. exigua, and EcRA is closely related to MET toxic effect. This study increases our collective understanding of the mechanisms of MET in insect pests. Full article
(This article belongs to the Section Molecular Plant Sciences)
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21 pages, 1707 KiB  
Review
A Brief Review on the High-Energy Electromagnetic Radiation-Shielding Materials Based on Polymer Nanocomposites
by Angel Acevedo-Del-Castillo, Ernesto Águila-Toledo, Santiago Maldonado-Magnere and Héctor Aguilar-Bolados
Int. J. Mol. Sci. 2021, 22(16), 9079; https://doi.org/10.3390/ijms22169079 - 23 Aug 2021
Cited by 18 | Viewed by 5472
Abstract
This paper revises the use of polymer nanocomposites to attenuate high-energy electromagnetic radiation (HE-EMR), such as gamma radiation. As known, high-energy radiation produces drastic damage not only in facilities or electronic devices but also to life and the environment. Among the different approaches [...] Read more.
This paper revises the use of polymer nanocomposites to attenuate high-energy electromagnetic radiation (HE-EMR), such as gamma radiation. As known, high-energy radiation produces drastic damage not only in facilities or electronic devices but also to life and the environment. Among the different approaches to attenuate the HE-EMR, we consider the use of compounds with a high atomic number (Z), such as lead, but as known, lead is toxic. Therefore, different works have considered low-toxicity post-transitional metal-based compounds, such as bismuth. Additionally, nanosized particles have shown higher performance to attenuate HE-EMR than those that are micro-sized. On the other hand, materials with π-conjugated systems can also play a role in spreading the energy of electrons ejected as a consequence of the interaction of HE-EMR with matter, preventing the ionization and bond scission of polymers. The different effects produced by the interactions of the matter with HE-EMR are revised. The increase of the shielding properties of lightweight, flexible, and versatile materials such as polymer-based materials can be a contribution for developing technologies to obtain more efficient materials for preventing the damage produced for the HE-EMR in different industries where it is found. Full article
(This article belongs to the Section Materials Science)
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16 pages, 1610 KiB  
Review
Protective Effects of Black Cumin (Nigella sativa) and Its Bioactive Constituent, Thymoquinone against Kidney Injury: An Aspect on Pharmacological Insights
by Md. Abdul Hannan, Md. Sarwar Zahan, Partha Protim Sarker, Akhi Moni, Hunjoo Ha and Md Jamal Uddin
Int. J. Mol. Sci. 2021, 22(16), 9078; https://doi.org/10.3390/ijms22169078 - 23 Aug 2021
Cited by 31 | Viewed by 13965
Abstract
The prevalence of chronic kidney disease (CKD) is increasing worldwide, and a close association between acute kidney injury (AKI) and CKD has recently been identified. Black cumin (Nigella sativa) has been shown to be effective in treating various kidney diseases. Accumulating [...] Read more.
The prevalence of chronic kidney disease (CKD) is increasing worldwide, and a close association between acute kidney injury (AKI) and CKD has recently been identified. Black cumin (Nigella sativa) has been shown to be effective in treating various kidney diseases. Accumulating evidence shows that black cumin and its vital compound, thymoquinone (TQ), can protect against kidney injury caused by various xenobiotics, namely chemotherapeutic agents, heavy metals, pesticides, and other environmental chemicals. Black cumin can also protect the kidneys from ischemic shock. The mechanisms underlying the kidney protective potential of black cumin and TQ include antioxidation, anti-inflammation, anti-apoptosis, and antifibrosis which are manifested in their regulatory role in the antioxidant defense system, NF-κB signaling, caspase pathways, and TGF-β signaling. In clinical trials, black seed oil was shown to normalize blood and urine parameters and improve disease outcomes in advanced CKD patients. While black cumin and its products have shown promising kidney protective effects, information on nanoparticle-guided targeted delivery into kidney is still lacking. Moreover, the clinical evidence on this natural product is not sufficient to recommend it to CKD patients. This review provides insightful information on the pharmacological benefits of black cumin and TQ against kidney damage. Full article
(This article belongs to the Special Issue Biological Properties of Medicinal Plants)
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18 pages, 2776 KiB  
Article
Cappable-Seq Reveals Specific Patterns of Metabolism and Virulence for Salmonella Typhimurium Intracellular Survival within Acanthamoeba castellanii
by Alexander S. Balkin, Andrey O. Plotnikov, Natalia E. Gogoleva, Yuri V. Gogolev, Kirill N. Demchenko and Sergey V. Cherkasov
Int. J. Mol. Sci. 2021, 22(16), 9077; https://doi.org/10.3390/ijms22169077 - 23 Aug 2021
Cited by 1 | Viewed by 2991
Abstract
The bacterial pathogen Salmonella enterica, which causes enteritis, has a broad host range and extensive environmental longevity. In water and soil, Salmonella interacts with protozoa and multiplies inside their phagosomes. Although this relationship resembles that between Salmonella and mammalian phagocytes, the interaction [...] Read more.
The bacterial pathogen Salmonella enterica, which causes enteritis, has a broad host range and extensive environmental longevity. In water and soil, Salmonella interacts with protozoa and multiplies inside their phagosomes. Although this relationship resembles that between Salmonella and mammalian phagocytes, the interaction mechanisms and bacterial genes involved are unclear. Here, we characterized global gene expression patterns of S. enterica serovar Typhimurium within Acanthamoeba castellanii at the early stage of infection by Cappable-Seq. Gene expression features of S. Typhimurium within A. castellanii were presented with downregulation of glycolysis-related, and upregulation of glyoxylate cycle-related genes. Expression of Salmonella Pathogenicity Island-1 (SPI-1), chemotaxis system, and flagellar apparatus genes was upregulated. Furthermore, expression of genes mediating oxidative stress response and iron uptake was upregulated within A. castellanii as well as within mammalian phagocytes. Hence, global S. Typhimurium gene expression patterns within A. castellanii help better understand the molecular mechanisms of Salmonella adaptation to an amoeba cell and intracellular persistence in protozoa inhabiting water and soil ecosystems. Full article
(This article belongs to the Special Issue Host-Pathogen Interaction 3.0)
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29 pages, 12896 KiB  
Article
The Effect of Modifiers on the Performance of Ni/CeO2 and Ni/La2O3 Catalysts in the Oxy–Steam Reforming of LNG
by Magdalena Mosinska, Waldemar Maniukiewicz, Malgorzata I. Szynkowska-Jozwik and Pawel Mierczynski
Int. J. Mol. Sci. 2021, 22(16), 9076; https://doi.org/10.3390/ijms22169076 - 23 Aug 2021
Cited by 3 | Viewed by 2203
Abstract
This work interrogates for the first time the catalytic properties of various monometallic Ni catalysts in the oxy-steam reforming of LNG. Various research techniques, including X-ray diffraction (XRD), specific surface area and porosity analysis (BET method), scanning electron microscopy with X-ray microanalysis (SEM-EDS), [...] Read more.
This work interrogates for the first time the catalytic properties of various monometallic Ni catalysts in the oxy-steam reforming of LNG. Various research techniques, including X-ray diffraction (XRD), specific surface area and porosity analysis (BET method), scanning electron microscopy with X-ray microanalysis (SEM-EDS), temperature-programmed desorption of ammonia (TPD-NH3), temperature-programmed reduction (TPR-H2) and the FTIR method, were used to study their physicochemical properties. The mechanism of the oxy-steam reforming of LNG is also discussed in this paper. The high activity of monometallic catalysts supported on 5% La2O3–CeO2 and 5% ZrO2–CeO2 oxides in the studied process have been proven and explained on the basis of their acidity, specific surface area, sorption properties in relation to the reaction products, the crystallite size of the metallic nickel and their phase composition. Full article
(This article belongs to the Section Physical Chemistry and Chemical Physics)
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3 pages, 224 KiB  
Comment
Comment on Siracusa et al. Fibromyalgia: Pathogenesis, Mechanisms, Diagnosis and Treatment Options Update. Int. J. Mol. Sci. 2021, 22, 3891
by Iván Cuyul-Vásquez, Felipe Araya-Quintanilla and Héctor Gutiérrez-Espinoza
Int. J. Mol. Sci. 2021, 22(16), 9075; https://doi.org/10.3390/ijms22169075 - 23 Aug 2021
Cited by 2 | Viewed by 2607
Abstract
We have read the study by Siracusa et al. [...] Full article
(This article belongs to the Special Issue Environmental Sensitivity Illnesses: Mechanisms and Molecular Signatures 2.0)
12 pages, 13888 KiB  
Article
Molecular Mechanisms of Skewed X-Chromosome Inactivation in Female Hemophilia Patients—Lessons from Wide Genome Analyses
by Rima Dardik, Einat Avishai, Shadan Lalezari, Assaf A. Barg, Sarina Levy-Mendelovich, Ivan Budnik, Ortal Barel, Yulia Khavkin, Gili Kenet and Tami Livnat
Int. J. Mol. Sci. 2021, 22(16), 9074; https://doi.org/10.3390/ijms22169074 - 23 Aug 2021
Cited by 12 | Viewed by 3560
Abstract
Introduction: Hemophilia A (HA) is an X-linked bleeding disorder caused by factor VIII (FVIII) deficiency or dysfunction due to F8 gene mutations. HA carriers are usually asymptomatic because their FVIII levels correspond to approximately half of the concentration found in healthy individuals. However, [...] Read more.
Introduction: Hemophilia A (HA) is an X-linked bleeding disorder caused by factor VIII (FVIII) deficiency or dysfunction due to F8 gene mutations. HA carriers are usually asymptomatic because their FVIII levels correspond to approximately half of the concentration found in healthy individuals. However, in rare cases, a carrier may exhibit symptoms of moderate to severe HA primarily due to skewed inactivation of her non-hemophilic X chromosome. Aim: The aim of the study was to investigate X-chromosome inactivation (XCI) patterns in HA carriers, with special emphasis on three karyotypically normal HA carriers presenting with moderate to severe HA phenotype due to skewed XCI, in an attempt to elucidate the molecular mechanism underlying skewed XCI in these symptomatic HA carriers. The study was based on the hypothesis that the presence of a pathogenic mutation on the non-hemophilic X chromosome is the cause of extreme inactivation of that X chromosome. Methods: XCI patterns were studied by PCR analysis of the CAG repeat region in the HUMARA gene. HA carriers that demonstrated skewed XCI were further studied by whole-exome sequencing (WES) followed by X chromosome-targeted bioinformatic analysis. Results: All three HA carriers presenting with the moderate to severe HA phenotype due to skewed XCI were found to carry pathogenic mutations on their non-hemophilic X chromosomes. Patient 1 was diagnosed with a frameshift mutation in the PGK1 gene that was associated with familial XCI skewing in three generations. Patient 2 was diagnosed with a missense mutation in the SYTL4 gene that was associated with familial XCI skewing in two generations. Patient 3 was diagnosed with a nonsense mutation in the NKAP gene that was associated with familial XCI skewing in two generations. Conclusion: Our results indicate that the main reason for skewed XCI in our female HA patients was negative selection against cells with a disadvantage caused by an additional deleterious mutation on the silenced X chromosome, thus complicating the phenotype of a monogenic X-linked disease. Based on our study, we are currently offering the X inactivation test to symptomatic hemophilia carriers and plan to expand this approach to symptomatic carriers of other X-linked diseases, which can be further used in pregnancy planning. Full article
(This article belongs to the Special Issue Complex Molecular Mechanisms of Monogenic Diseases)
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