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17 pages, 2717 KiB  
Review
Enzymatic Regulation of the Gut Microbiota: Mechanisms and Implications for Host Health
by Zipeng Jiang, Liang Mei, Yuqi Li, Yuguang Guo, Bo Yang, Zhiyi Huang and Yangyuan Li
Biomolecules 2024, 14(12), 1638; https://doi.org/10.3390/biom14121638 - 20 Dec 2024
Viewed by 449
Abstract
The gut microbiota, a complex ecosystem, is vital to host health as it aids digestion, modulates the immune system, influences metabolism, and interacts with the brain-gut axis. Various factors influence the composition of this microbiota. Enzymes, as essential catalysts, actively participate in biochemical [...] Read more.
The gut microbiota, a complex ecosystem, is vital to host health as it aids digestion, modulates the immune system, influences metabolism, and interacts with the brain-gut axis. Various factors influence the composition of this microbiota. Enzymes, as essential catalysts, actively participate in biochemical reactions that have an impact on the gut microbial community, affecting both the microorganisms and the gut environment. Enzymes play an important role in the regulation of the intestinal microbiota, but the interactions between enzymes and microbial communities, as well as the precise mechanisms of enzymes, remain a challenge in scientific research. Enzymes serve both traditional nutritional functions, such as the breakdown of complex substrates into absorbable small molecules, and non-nutritional roles, which encompass antibacterial function, immunomodulation, intestinal health maintenance, and stress reduction, among others. This study categorizes enzymes according to their source and explores the mechanistic principles by which enzymes drive gut microbial activity, including the promotion of microbial proliferation, the direct elimination of harmful microbes, the modulation of bacterial interaction networks, and the reduction in immune stress. A systematic understanding of enzymes in regulating the gut microbiota and the study of their associated molecular mechanisms will facilitate the application of enzymes to precisely regulate the gut microbiota in the future and suggest new therapeutic strategies and dietary recommendations. In conclusion, this review provides a comprehensive overview of the role of enzymes in modulating the gut microbiota. It explores the underlying molecular and cellular mechanisms and discusses the potential applications of enzyme-mediated microbiota regulation for host gut health. Full article
(This article belongs to the Special Issue Novel Antimicrobial Strategies for Animal Health)
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<p>Classification of enzymes and their functions.</p>
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<p>Mechanisms of enzyme regulation of gut microbes. The main ways in which enzymes regulate the intestinal microbiota include (1) stimulation of microbial growth: enzymes can stimulate the growth of beneficial gut microbes; (2) direct microbial killing: certain enzymes can kill gut microbes directly; (3) interference with microbial networks: enzymes can disrupt microbial networks, such as quorum sensing (QS), which is a communication system used by microbes to coordinate their behavior; and (4) alleviating the immune stress: the use of enzymes to reduce the occurrence of immune stress is through the degradation of resemble immunogenic substances.</p>
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35 pages, 1745 KiB  
Review
Endothelial Dysfunction and Cardiovascular Disease: Hyperbaric Oxygen Therapy as an Emerging Therapeutic Modality?
by Tanja Batinac, Lara Batičić, Antea Kršek, Danijel Knežević, Emanuela Marcucci, Vlatka Sotošek and Božena Ćurko-Cofek
J. Cardiovasc. Dev. Dis. 2024, 11(12), 408; https://doi.org/10.3390/jcdd11120408 - 19 Dec 2024
Viewed by 338
Abstract
Maintaining the physiological function of the vascular endothelium and endothelial glycocalyx is crucial for the prevention of cardiovascular disease, which is one of the leading causes of morbidity and mortality worldwide. Damage to these structures can lead to atherosclerosis, hypertension, and other cardiovascular [...] Read more.
Maintaining the physiological function of the vascular endothelium and endothelial glycocalyx is crucial for the prevention of cardiovascular disease, which is one of the leading causes of morbidity and mortality worldwide. Damage to these structures can lead to atherosclerosis, hypertension, and other cardiovascular problems, especially in individuals with risk factors such as diabetes and obesity. Endothelial dysfunction is associated with ischemic disease and has a negative impact on overall cardiovascular health. The aim of this review was to comprehensively summarize the crucial role of the vascular endothelium and glycocalyx in cardiovascular health and associated thrombo-inflammatory conditions. It highlights how endothelial dysfunction, influenced by factors such as diabetes, chronic kidney disease, and obesity, leads to adverse cardiovascular outcomes, including heart failure. Recent evidence suggests that hyperbaric oxygen therapy (HBOT) may offer therapeutic benefits in the treatment of cardiovascular risk factors and disease. This review presents the current evidence on the mechanisms by which HBOT promotes angiogenesis, shows antimicrobial and immunomodulatory effects, enhances antioxidant defenses, and stimulates stem cell activity. The latest findings on important topics will be presented, including the effects of HBOT on endothelial dysfunction, cardiac function, atherosclerosis, plaque stability, and endothelial integrity. In addition, the role of HBOT in alleviating cardiovascular risk factors such as hypertension, aging, obesity, and glucose metabolism regulation is discussed, along with its impact on inflammation in cardiovascular disease and its potential benefit in ischemia–reperfusion injury. While HBOT demonstrates significant therapeutic potential, the review also addresses potential risks associated with excessive oxidative stress and oxygen toxicity. By combining information on the molecular mechanisms of HBOT and its effects on the maintenance of vascular homeostasis, this review provides valuable insights into the development of innovative therapeutic strategies aimed at protecting and restoring endothelial function to prevent and treat cardiovascular diseases. Full article
(This article belongs to the Section Acquired Cardiovascular Disease)
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<p>Schematic representation of endothelial glycocalyx structure. MMP–matrix metalloproteinases.</p>
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<p>Key effects of a therapeutic intervention across six biological pathways: Angiogenesis stimulation encourages new blood vessel growth through molecules like nitric oxide (NO), vascular endothelial growth factor (VEGF), and growth factors (GFs) such as platelet-derived growth factor (PDGF-2) and fibroblast growth factor (FGF-2), which help repair and regenerate tissues. Inflammation alleviation reduces inflammation by increasing anti-inflammatory cytokines [e.g., interleukins (IL-4, IL-10)] and lowering pro-inflammatory molecules [e.g., cyclooxygenase-2 (COX-2) and tumor necrosis factor alpha (TNF-α)], aiding immune regulation and reducing tissue damage. Antimicrobial activity boosts the body’s ability to kill anaerobic bacteria and reduces biofilm formation, enhancing resistance to infections. Cellular senescence suppression slows down the aging process by downregulating markers of cellular senescence (e.g., senescence-associated β-galactosidase (SA-β-gal) and cellular senescence markers (p16/p21/p53)) and promoting telomere elongation, which helps cells avoid age-related dysfunction and re-enter the cell cycle. Stem cell stimulation increases the number of circulating stem cells, promoting their differentiation into various tissue types like adipose cells and osteocytes, thus supporting tissue regeneration and healing. Elevation of antioxidant activity enhances antioxidant defenses by modulating the balance between free radicals and scavengers, protecting cells from oxidative stress and damage, which is crucial for maintaining cellular health.</p>
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<p>The tissue response to hypoxia and repeated intermittent hyperoxia during hyperbaric oxygen therapy (HBOT) results in a biphasic response and involves an accumulation of reactive oxygen species (ROS) alongside an enhanced cytoprotective antioxidant response. Hypoxia and intermittent HBOT promote the activation of hypoxia-inducible factor-1 (HIF-1), either by directly inhibiting prolyl hydroxylase domains (PHDs) or by increasing antioxidants that suppress PHD activity. During hyperoxia, ROS production increases, leading to the activation of HIF-1α, which conjugates with HIF-1β to stabilize HIF-1 in its active form. HIF-1, in turn, inhibits mitochondrial biogenesis. Increased mitochondrial consumption of NADH raises NAD+ levels, which activates SIRT1, improving mitochondrial biogenesis and inducing antioxidant defenses. As part of an adaptive mechanism, elevated ROS levels stimulate the production of endogenous scavengers, whose elimination half-life is significantly longer than that of ROS. Additionally, HBOT enhances antioxidant enzyme levels by activating transcription factors and gene expression via the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway and its downstream targets, including heme oxygenase-1 (HO-1), NAD(P)H quinone dehydrogenase 1 (NQO-1), catalase (CAT), glutathione peroxidase (GPx), superoxide dismutase (SOD), and glutamate–cysteine ligase catalytic subunit (GCLC), while reducing pro-oxidant enzymes such as inducible nitric oxide synthase (iNOS) and gp91-phox.</p>
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<p>The effect of hyperbaric oxygen therapy (HBOT) on oxidative stress balance at the level of the mitochondrial membrane. In HBOT, oxygen from the lungs increases the content of oxygen dissolved in the plasma, resulting in tissue hyperoxia that boosts the citric acid cycle in mitochondria, increasing nicotinamide adenine dinucleotide (NADH) production, which can react directly with oxygen to produce reactive oxygen species (ROS). Increased ROS levels can produce more endogenous scavengers, with the elimination half-life being much longer than that of ROS. HBOT stimulates antioxidant defenses via activation of nuclear factor erythroid 2-related factor 2 (Nrf2) and its downstream targets such as heme oxygenase-1 (HO-1), NAD(P)H quinone dehydrogenase 1 (NQO-1), catalase (CAT), glutathione peroxidase (GPx), superoxide dismutase (SOD), and glutamate–cysteine ligase catalytic subunit (GCLC), while decreasing expression of pro-oxidant enzymes such as inducible nitric oxide synthase (iNOS) and gp91-phox.</p>
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27 pages, 3990 KiB  
Article
A Randomized, Blinded, Vehicle-Controlled Dose-Ranging Study to Evaluate and Characterize Remdesivir Efficacy Against Ebola Virus in Rhesus Macaques
by Elizabeth E. Zumbrun, Carly B. Garvey, Jay B. Wells, Ginger C. Lynn, Sean A. Van Tongeren, Jesse T. Steffens, Kelly S. Wetzel, Darrell L. Wetzel, Heather L. Esham, Nicole L. Garza, Eric D. Lee, Jennifer L. Scruggs, Franco D. Rossi, Elizabeth S. Brown, Jessica M. Weidner, Laura M. Gomba, Kristan A. O’Brien, Alexandra N. Jay, Xiankun Zeng, Kristen S. Akers, Paul A. Kallgren, Ethan Englund, J. Matthew Meinig, Jeffrey R. Kugelman, Joshua L. Moore, Holly A. Bloomfield, Sarah L. Norris, Tameka Bryan, Christie H. Scheuerell, Jesse Walters, Nevena Mollova, Christiana Blair, Darius Babusis, Tomas Cihlar, Danielle P. Porter, Bali Singh, Charlotte Hedskog, Sina Bavari, Travis K. Warren and Roy Bannisteradd Show full author list remove Hide full author list
Viruses 2024, 16(12), 1934; https://doi.org/10.3390/v16121934 - 18 Dec 2024
Viewed by 285
Abstract
Ebola virus (EBOV) causes severe disease in humans, with mortality as high as 90%. The small-molecule antiviral drug remdesivir (RDV) has demonstrated a survival benefit in EBOV-exposed rhesus macaques. Here, we characterize the efficacy of multiple intravenous RDV dosing regimens on survival of [...] Read more.
Ebola virus (EBOV) causes severe disease in humans, with mortality as high as 90%. The small-molecule antiviral drug remdesivir (RDV) has demonstrated a survival benefit in EBOV-exposed rhesus macaques. Here, we characterize the efficacy of multiple intravenous RDV dosing regimens on survival of rhesus macaques 42 days after intramuscular EBOV exposure. Thirty rhesus macaques underwent surgical implantation of telemetry devices for the fine-scale monitoring of body temperature and activity, as well as central venous catheters, to enable treatment administration and blood collection. Treatment, consisting of a loading dose of RDV followed by once-daily maintenance doses for 11 days, was initiated 4 days after virus exposure when all animals were exhibiting disease signs consistent with incipient EBOV disease as well as quantifiable levels of EBOV RNA in plasma. In the RDV treatment groups receiving loading/maintenance doses of 5/2.5 mg/kg, 10/5 mg/kg, and 20/10 mg/kg, a total of 6 of 8 (75%), 7 of 8 (87.5%), and 5 of 7 (71.4%) animals survived, respectively. In the vehicle control group, one of seven animals (14.3%) survived. The improved survival rate compared to the control group was statistically significant only for the 10/5 mg/kg RDV treatment group. This treatment regimen also resulted in a significantly lower systemic viral load compared to the vehicle control after a single RDV treatment. All three RDV regimens produced a significantly lower systemic viral load after two treatments. For most animals, RDV treatment, regardless of dose, resulted in the amelioration of many of the clinical–pathological changes associated with EBOV disease in this model. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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<p>Kaplan–Meier plot of animal survival in each treatment group.</p>
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<p>Schematic of daily maximum responsiveness scores by individual animal. All animals were assessed daily and assigned a score of physical signs and responses based on the following criteria: 0 = alert, responsive, normal species-specific behavior; 1 = slightly diminished general activity, subdued, but responds normally to external stimuli; 2 = withdrawn, may have head down, upright fetal posture, hunched, reduced response to external stimuli; 3 = prostrate but able to rise if stimulated or dramatically reduced response to external stimuli; 4 = persistently prostrate, severely or completely unresponsive. The scores shown are the highest for each day. Animals were considered moribund and were euthanized upon assignment of a responsiveness score of 4. One animal in Group 4 was euthanized due to serum chemistry findings, consistent with kidney failure despite a responsiveness score of 3. One animal in Group 1 was found deceased (FD).</p>
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<p>Group mean plasma viral RNA over time. Vertical bars show the standard deviation. Dotted lines show the limit of detection (LOD = 3 log<sub>10</sub> ge/mL) and the lower limit of quantitation (LLOQ = 4.903 log<sub>10</sub> ge/mL). For display and analyses, EBOV RNA values below the LOD were imputed as 3 log<sub>10</sub> ge/mL; values above the LOD but below the LLOQ (“&gt;LOD, &lt;LLOQ”) were imputed as 4.903 log<sub>10</sub> ge/mL. The X-axis has been truncated to highlight responses during the acute phase of disease. Data for days on which only terminal samples were obtained from animals that succumbed are not included.</p>
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<p>Group mean GS-5734, GS-704277, and GS-441524 concentrations in rhesus monkey plasma samples, as measured using liquid chromatography coupled with tandem mass spectrometry. Vertical bars show the standard deviation.</p>
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<p>Body temperature and activity measured by telemetry. Days post-inoculation are calendar days. Vertical bars in all figures represent the standard error of the mean. Max ∆T, or maximum daily temperature elevation, is the largest change in temperature value for the 24 h daily time period. % TE<sub>Sig</sub> duration is the percentage of the 24 h daily time period during which body temperatures were significantly elevated.</p>
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<p>Timing of statistically significant clinicopathologic changes. The <span class="html-italic">p</span>-values shown represent the comparison to baseline within each group. Alb, albumin; Creat, creatinine; Fbg, fibrinogen; Hct, hematocrit; Hgb, hemoglobin; Lymph, lymphocytes; Neut, neutrophils; Plt, platelets; RBC, red blood cells; TP, total protein. White cells denote a lack of significance; pink shading is a heatmap, with deeper pink denoting greater significance. <span class="html-italic">p</span>-values of 0.999 are &gt;0.999.</p>
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<p>Hematological and inflammatory parameters. Figures show group means by day; vertical bars represent standard deviation. RBC, red blood cells; #, absolute numbers.</p>
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<p>Coagulation parameters. Figures show group means by day; vertical bars represent standard deviation. APTT, activated partial thromboplastin time; PT, prothrombin time.</p>
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<p>Hepatocellular parameters. Figures show group means by day; vertical bars represent standard deviation. ALT, alanine aminotransferase; AST, aspartate aminotransferase.</p>
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<p>Renal parameters. Figures show group means by day; vertical bars represent standard deviation.</p>
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11 pages, 2678 KiB  
Article
The Placenta as the Main Source of Serotonin in Ontogenetic Dynamics: Inflammation-Induced Modulation of Placental Serotonin Can Be Prevented by Immunoglobulin Administration
by Nadezhda Bondarenko, Nadezhda Lifantseva, Svetlana Voronova and Victoria Melnikova
Int. J. Mol. Sci. 2024, 25(24), 13532; https://doi.org/10.3390/ijms252413532 - 18 Dec 2024
Viewed by 258
Abstract
Placental serotonin is recognized as a key component of feto-placental physiology and can be influenced by environmental factors such as maternal diet, drugs, stress, and immune activation. In this study, we compared the contribution of placental and fetal sources to the maintenance of [...] Read more.
Placental serotonin is recognized as a key component of feto-placental physiology and can be influenced by environmental factors such as maternal diet, drugs, stress, and immune activation. In this study, we compared the contribution of placental and fetal sources to the maintenance of serotonin levels required for normal fetal development during ontogenetic dynamics. Our results demonstrated the leading role of the placenta at almost all stages of development. We investigated the modulatory effect of inflammation on placental serotonin levels. The data obtained showed that the susceptibility to prenatal inflammation depends on its severity and varies considerably at different stages of development. According to our results, inflammation-induced modulation of placental serotonin levels can be prevented by immunoglobulin administration at both early and late stages of development. Disturbances in placental serotonin signaling during critical developmental periods may have long-lasting consequences for the health and behavior of the offspring. Therefore, the ability to prevent environmental modulation of placental serotonin, and hence negative effects on the developing fetus, is of great importance. Full article
(This article belongs to the Special Issue Serotonin in Health and Diseases)
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<p>The expression of tryptophan hydroxylase (TPH) in placenta at different developmental stages revealed by immunohistochemistry. Nuclei were stained with DAPI, “f”—fetal and “m”—maternal compartments of the placenta, bar—100 μm.</p>
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<p>Comparative analysis of different serotonin sources in feto-placental unit during ontogenetic dynamics, (<b>a</b>) serotonin contents in the placenta and in the head and trunk of the fetus during the ontogenetic dynamics (n = 9, * <span class="html-italic">p</span> &lt; 0.05 placenta vs. head, # <span class="html-italic">p</span> &lt; 0.05 placenta vs. trunk at each developmental stage), (<b>b</b>) the ontogenetic dynamics of the placental weight between stages E12 and E21 (n = 12, * <span class="html-italic">p</span> &lt; 0.05 vs. previous stage), (<b>c</b>), serotonin concentrations in the placenta and in the fetal head during the ontogenetic dynamics (n = 9, * <span class="html-italic">p</span> &lt; 0.05 placenta vs. head at each developmental stage).</p>
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<p>The effect of LPS administration on the placental serotonin content during ontogenetic dynamics. Pregnant rats received LPS at doses 25 or 250 μg/kg b.w., and the placental serotonin content was measured 24 h after injection. n = 8 for each experimental group, * <span class="html-italic">p</span> &lt; 0.05 vs. control.</p>
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<p>The preventive effect of immunoglobulin administration on the placental serotonin level in LPS-treated rats at E14 (<b>a</b>–<b>c</b>) and E20 (<b>d</b>–<b>f</b>). (<b>a</b>,<b>d</b>)—serotonin content per placenta, (<b>b</b>,<b>e</b>)—serotonin concentration per mg tissue, (<b>c</b>,<b>f</b>)—the weight of placenta. n = 8 for each experimental group, * <span class="html-italic">p</span> &lt; 0.05 vs. control, # <span class="html-italic">p</span> &lt; 0.05 between “LPS” and “LPS + Igs” groups.</p>
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11 pages, 1357 KiB  
Article
Lifestyle, Cognition, and Disability Outcomes in Multiple Sclerosis: A Comprehensive Cohort Study
by Kenia R. Campanholo, Graziella A. S. Faria, Milena S. Pitombeira, Samira L. Apóstolos-Pereira, Dagoberto Callegaro, Carlos Alberto Buchpiguel and Daniele de Paula Faria
Sclerosis 2024, 2(4), 394-404; https://doi.org/10.3390/sclerosis2040026 - 18 Dec 2024
Viewed by 685
Abstract
Background/Objectives: People with multiple sclerosis (MS) often experience sensory, psychomotor, and cognitive impairment, sphincter disturbances, and fatigue, which can affect their ability to perform work-related tasks, self-care, and daily activities. This study aimed to analyze the lifestyle changes, cognitive function, and disability outcomes [...] Read more.
Background/Objectives: People with multiple sclerosis (MS) often experience sensory, psychomotor, and cognitive impairment, sphincter disturbances, and fatigue, which can affect their ability to perform work-related tasks, self-care, and daily activities. This study aimed to analyze the lifestyle changes, cognitive function, and disability outcomes over a seven-year follow-up period, exploring potential associations with predictive markers. Methods: At the end of the seven-year follow-up period, 32 participants returned for cognitive and clinical reassessment with the Twenty-Five-Foot Walk Test, Nine-Hole Peg Test, and Brief Repeatable Neuropsychological Battery. Lifestyle data were acquired via interviews regarding sleep quality, reading habits, technology use, physical activity levels, household responsibilities, and participation in leisure and cultural activities. Results: The occupational profile did not demonstrate significant changes, but 11 (34%) participants showed disability accumulation, and the number of relapses increased (p = 0.001). Over time, improvement was observed in verbal episodic memory and worsening in psychomotor speed. Better cognitive performance in mental agility was associated with higher levels of physical activity (p = 0.021) and technology use (p = 0.039). In addition, better cognition (verbal memory p = 0.038 and processing speed 0.015) and psychomotor speed (upper limbs p = 0.017 and lower limbs p = 0.003) and lower functional disability (p = 0.022) were associated with maintenance of household activities. Conclusions: The changes in verbal memory and psychomotor speed were more prominent over time, and verbal memory, psychomotor and processing speed, and mental agility were associated with good lifestyle habits, mainly household activities. The treatment strategies should include lifestyle changes and pharmacological interventions. Full article
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<p>Longitudinal comparisons for cognitive test and psychomotor speed tasks. Legend: the graphs show crude scores. (*) Generalized Equation Estimation time effect. (**) Generalized Equation Estimation time effect adjusted for age and years of education. Acronyms: PASAT—Paced Auditory Serial Addition Test; SDMT—Symbol Digit Modalities Test; SpRT—Spatial Recall Test; SRT—Selective Reminding Test; WLG—Word List Generation; 9HPT—Nine-Hole Peg Test; 25FWT—Twenty-Five-Foot Walk Test.</p>
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<p>Lifestyle activities at follow-up: frequency and proportion.</p>
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12 pages, 3468 KiB  
Article
Investigating the Potential of Extracellular Vesicles as Delivery Systems for Chemotherapeutics
by Alessia Brancolini and Riccardo Vago
Biomedicines 2024, 12(12), 2863; https://doi.org/10.3390/biomedicines12122863 - 17 Dec 2024
Viewed by 345
Abstract
Background/Objectives: Standard chemotherapy is generally considered the best approach to treat many solid cancers, even accounting for severe side effects. Therefore, the development of a drug delivery system for chemotherapeutic administration could significantly improve standard chemotherapy by maintaining the cytotoxic effects of the [...] Read more.
Background/Objectives: Standard chemotherapy is generally considered the best approach to treat many solid cancers, even accounting for severe side effects. Therefore, the development of a drug delivery system for chemotherapeutic administration could significantly improve standard chemotherapy by maintaining the cytotoxic effects of the drugs while decreasing the inherent side effects of the treatment. The aim of our study is the optimization of a loading strategy that conjugates the use of extracellular vesicles (EVs) as drug delivery carriers, by preserving their integrity, with the loading efficiency and activity maintenance of chemotherapeutics. Methods: We compared the EV loading of the chemotherapeutics epirubicin, mitomycin, methotrexate and mitoxantrone by co-incubation. Once loaded, the activity of drug-carrying EVs was tested on cancer cells and compared to that of free chemotherapeutics. Results: We defined a linear correlation between chemotherapeutics’ concentration and their absorbance at the drug-specific wavelength, which allowed the definition of a highly sensitive absorbance-based spectrophotometric quantification system, enabling the assessment of drug loading efficiency. Co-incubation of EVs and chemotherapeutics was sufficient to obtain quantifiable drug loading, and the efficacy of EV loading was drug-dependent. Epirubicin-loaded vesicles showed increased toxicity to bladder cancer cells with respect to the free chemotherapeutic. The cytotoxicity was maintained even upon 6-month storage at −80 °C of loaded EVs. Conclusion: We established an absorbance-based spectrophotometric quantification system that enables a straightforward measure of drug loading efficiency into EVs, and we demonstrated that chemotherapeutic-carrying EVs can be obtained by co-incubation, preserving and increasing drug cytotoxicity. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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<p>Molecular and chemical properties of chemotherapeutics used as EV payloads.</p>
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<p>Definition of a chemotherapeutic spectrophotometric quantification system. Absorption curves of the chemotherapeutic drugs epirubicin (<b>A</b>), mitomycin (<b>B</b>), methotrexate (<b>C</b>) and mitoxantrone (<b>D</b>), measured alone (N.T.) or in the presence of EVs, expressed as absorbance versus wavelength (upper panels) or versus concentration (lower panels) at those particular chemotherapeutics’ specific absorption wavelengths, as reported in (<b>E</b>). The peak of the absorption curve is used for the definition of chemotherapeutics’ specific absorption wavelengths. Data are expressed as the mean ± SD. D.limit: detection limit.</p>
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<p>Dose–response curves of free drugs in the RT112 human bladder cancer cell line. Cell viability upon incubation with epirubicin (<b>A</b>), mitomycin (<b>B</b>), methotrexate (<b>C</b>) and mitoxantrone (<b>D</b>) was measured through an MTT assay and expressed as percentages normalized to untreated cells. Data are expressed as the mean ± SD. (<b>E</b>) Table summarizing IC<sub>50</sub> values of chemotherapeutics; values are expressed as the mean ± SE.</p>
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<p>Quantification of chemotherapeutic drug loading into EVs. Chemotherapeutic loading into EVs was measured by exploiting the drug-specific spectrophotometric system described above. The percentage of loading is shown; values are expressed as the mean ± SE.</p>
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<p>Comparison of chemotherapeutic-loaded EVs and free administered drugs toxicity on RT112 bladder cancer cells. Representative dose–response curves of epirubicin-loaded (<b>A</b>), mitoxantrone-loaded (<b>B</b>) and methotrexate-loaded (<b>C</b>) EVs (solid line) and free administered drugs (dotted line) in RT112 cells. For each drug concentration value, viability is expressed as the mean ± SD. (<b>D</b>) Comparison of IC<sub>50</sub> values between chemotherapeutic-loaded EVs and free administered drugs. *: <span class="html-italic">p</span> &lt; 0.05, ns: non-significant. (<b>E</b>) Table of IC<sub>50</sub> values: concentrations are expressed as the mean ± SE and for each chemotherapeutic.</p>
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<p>Comparison of chemotherapeutic-loaded EVs and free administered drugs toxicity on UM-UC3 bladder cancer cells. Representative dose-response curves of epirubicin (<b>A</b>), mitoxantrone (<b>B</b>) and methotrexate (<b>C</b>) loaded EVs (solid line) and free administered drugs (dotted line) on UM-UC3 cells. For each drug concentration value, viability is expressed as Mean ± SD. (<b>D</b>) Comparison of IC<sub>50</sub> values between chemotherapeutic loaded EVs and free administered drugs, expressed as Mean ± SE. *: <span class="html-italic">p</span> &lt; 0.05.</p>
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<p>Evaluation of chemotherapeutic loaded EVs integrity upon storage. Transmission electron microscopy representative images of methotrexate and mitoxantrone-loaded EVs after 6-month storage at −80 °C. Frozen or freshly isolated, unloaded EVs are shown as controls.</p>
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<p>Evaluation of chemotherapeutic-loaded EVs’ cytotoxicity after storage. Cell viability curves upon administration of methotrexate-loaded (<b>A</b>) and mitoxantrone-loaded (<b>B</b>) EVs stored at −80 °C for 1 (red line) or 6 (green line) months. Freshly prepared drug-carrying EVs were used as a control (blue line). For each EV protein concentration, viability is expressed as the mean ± SD.</p>
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18 pages, 9492 KiB  
Article
Noise Reduction in CWRU Data Using DAE and Classification with ViT
by Jun-gyo Jang, Soon-sup Lee, Se-yun Hwang and Jae-chul Lee
Appl. Sci. 2024, 14(24), 11771; https://doi.org/10.3390/app142411771 - 17 Dec 2024
Viewed by 283
Abstract
With the Fourth Industrial Revolution unfolding worldwide, technologies including the Internet of Things, sensors, and artificial intelligence are undergoing rapid development. These technological advancements have played a significant role in the dramatic growth of the predictive maintenance market for mechanical equipment, prompting active [...] Read more.
With the Fourth Industrial Revolution unfolding worldwide, technologies including the Internet of Things, sensors, and artificial intelligence are undergoing rapid development. These technological advancements have played a significant role in the dramatic growth of the predictive maintenance market for mechanical equipment, prompting active research on noise removal techniques and classification algorithms for the accurate determination of the causes of equipment failure. In this study, time series data were preprocessed using the denoising autoencoder technique, a deep learning-based noise removal method, to improve the accuracy of failure classification from mechanical equipment data. To convert the preprocessed time series data into frequency components, the short-time Fourier transform technique was employed. The fault types of mechanical equipment were classified using the vision transformer (ViT) technique, a deep learning technique that has been actively used in recent image analysis research. Additionally, the classification performance of the ViT-based technique for vibration time series data was comparatively validated against existing classification algorithms. The accuracy of failure classification was the highest when the data, preprocessed using a Denoising Autoencoder (DAE), were classified by a Vision Transformer (ViT). Full article
(This article belongs to the Section Applied Industrial Technologies)
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<p>The importance of data preprocessing.</p>
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<p>Research flowchart.</p>
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<p>Short−time Fourier transform theory.</p>
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<p>Result of STFT ((<b>a</b>) normal; (<b>b</b>) ball; (<b>c</b>) inner; (<b>d</b>) outer).</p>
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<p>Learning method of the Denoising Autoencoder.</p>
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<p>Image division for ViT learning.</p>
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<p>Structure of the vision transformer (* New learnable parameters) [<a href="#B31-applsci-14-11771" class="html-bibr">31</a>].</p>
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<p>Experiment device [<a href="#B34-applsci-14-11771" class="html-bibr">34</a>].</p>
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<p>DAE model structure.</p>
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<p>Result of normal data ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>Result of ball fault data ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>Result of inner-race data ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>Result of outer-race data ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>Result of normal-data STFT ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>Result of ball-fault-data STFT ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>Result of inner-race-data STFT ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>Result of outer-race-data STFT ((<b>a</b>) raw data; (<b>b</b>) DAE data).</p>
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<p>The result of classifying raw data by applying it to ViT.</p>
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<p>The result of classification by applying DAE data to ViT.</p>
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<p>Configuring data for K-fold cross-validation.</p>
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<p>Classification result based on CNN—1.</p>
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<p>Classification result based on CNN—2 ((<b>a</b>) CNN channel-wise accuracy; (<b>b</b>) confusion matrix of 3 Channel CNN).</p>
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24 pages, 19392 KiB  
Article
Platinum Compound on Gold–Magnesia Hybrid Structure: A Theoretical Investigation on Adsorption, Hydrolysis, and Interaction with DNA Purine Bases
by Zhenjun Song, Mingyue Liu, Aiguo Zhong, Meiding Yang, Zhicai He, Wenmin Wang and Hongdao Li
Nanomaterials 2024, 14(24), 2027; https://doi.org/10.3390/nano14242027 - 17 Dec 2024
Viewed by 301
Abstract
Cisplatin-based platinum compounds are important clinical chemotherapeutic agents that participate in most tumor chemotherapy regimens. Through density-functional theory calculations, the formation and stability of the inorganic oxide carrier, the mechanisms of the hydrolysis reaction of the activated platinum compound, and its binding mechanism [...] Read more.
Cisplatin-based platinum compounds are important clinical chemotherapeutic agents that participate in most tumor chemotherapy regimens. Through density-functional theory calculations, the formation and stability of the inorganic oxide carrier, the mechanisms of the hydrolysis reaction of the activated platinum compound, and its binding mechanism with DNA bases can be studied. The higher the oxidation state of Pt (II to IV), the more electrons transfer from the magnesia–gold composite material to the platinum compound. After adsorption on the composite carrier, 5d←2p coordination bonds of Pt-N are strengthened. For flat and oblique adsorption modes of cisplatin, there is no significant difference in the density of states of the gold and magnesium oxide film, indicating the maintenance of the heterojunction structural framework. However, there are significant changes in the electronic states of cisplatin itself with different adsorption configurations. In the flat configuration, the band gap width of cisplatin is larger than that of the oblique configuration. The Cl-Pt bond range in the Pt(III) compound shows a clear charge reduction on the magnesia film, indicating the Cl-Pt bond is an active site with the potential for decomposition and hydrolysis. The substitution of chloride ions by water can lead to hydrolysis products, enhancing the polarization of the composite and showing strong charge separation. The hydrolysis of the free platinum compound is endothermic by 0.309 eV, exceeding the small activation energy barrier of 0.399 eV, indicating that hydrolysis of this platinum compound is easily achievable. ADME (absorption, distribution, metabolism, and excretion) prediction parameters indicate that hydrolysis products have good ESOL (Estimated SOLubility) solubility and high gastrointestinal absorption, consistent with Lipinski’s rule. During the coordination reaction process, there are significant changes in the distribution of frontier molecular orbitals, with the HOMO (highest occupied molecular orbital) of the initial state primarily located on the purine base, providing the possibility for electron transfer to the empty orbitals of the platinum compound in the LUMO (lowest unoccupied molecular orbital). The HOMO and HOMO-1 of the transition state and product are mainly distributed on the platinum compound, indicating clear electron transfer and orbital rearrangement. The activation energy barrier for the purine coordination reaction with the hydrolysis products is reduced to 0.61 eV, and the dipole moment gradually decreases to 6.77 Debye during the reaction, indicating a reduction in the system’s charge separation and polarization. This contribution is anticipated to provide a new theoretical clue for developing inorganic oxide carriers of platinum compounds. Full article
(This article belongs to the Section Biology and Medicines)
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<p>The structure and charge population of gold (111) film fully optimized with gamma point and (2 × 2 × 1) k-point meshing. The Au-Au distances and charges in parentheses correspond to the values obtained at denser (2 × 2 × 1) k-point meshing.</p>
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<p>The structure and charge population of gold (111)-supported magnesia (111) film. (<b>a</b>,<b>b</b>) correspond to the stable equilibrium structure, while (<b>c</b>,<b>d</b>) correspond to the unstable structure with perpendicular gold-oxygen bonds. Green and red balls represent magnesium and oxygen atoms, and the pink, cyan, and brown balls represent top-layer, second-layer, and bottom-two-layer gold atoms.</p>
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<p>The differential charge density contour with charge density isosurface value of 0.001 e Bohr<sup>−3</sup> (<b>a</b>,<b>b</b>) and localized density of states for gold (111)-supported magnesia (111) film (<b>c</b>). The yellow and cyan slices represent electron accumulation and electron depletion areas, respectively.</p>
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<p>Adsorption and transformation of cisplatin compound on gold-supported 1 ML ultrathin magnesia (111). The Gibbs free energies are shown relative to the ground-state molecular adsorption state with flat adsorption configuration and Gibbs free energy of −380.373 eV. The white, blue, red, purple-, green-, cyan-, and yellow-colored balls stand for H, N, O, Cl, Mg, Pt, and Au, respectively.</p>
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<p>Charge density contours with isosurface value 0.05 e Bohr<sup>−3</sup> (<b>a</b>), highest occupied molecular orbital and lowest unoccupied molecular orbital of cisplatin molecule (<b>b</b>), and differential charge density contours (<b>c</b>) with isosurface value 0.001 e Bohr<sup>−3</sup>. For differential charge density, the isosurfaces colored in turquoise and dark yellow represent charge accumulation and depletion, respectively.</p>
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<p>Localized density of states of platinum central ion, coordinated ammonia nitrogen, chloride ions, magnesium, oxygen, and gold slab for flat adsorption configuration (<b>a</b>,<b>b</b>) and oblique adsorption configuration (<b>c</b>,<b>d</b>).</p>
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<p>Charge density contours with isosurface value 0.15 e Bohr<sup>−3</sup> (<b>a</b>) and differential charge density contours with isosurface value 0.003 e Bohr<sup>−3</sup> (<b>b</b>) for Pt(III) compound adsorption on gold-supported magnesia (111) film. The isosurfaces colored in dark yellow and turquoise represent charge accumulation and charge depletion, respectively.</p>
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<p>The hydrolysis of adsorbed cisplatin occurs gradually by water substitution. The assumed structure for water adsorption with oxygen linked with platinum (<b>a</b>), the optimized structure for water adsorption with hydrogen linked with platinum (<b>b</b>), water adsorption on ammonia (<b>c</b>), the water substitution structure (<b>d</b>), the water adsorption energy (<b>e</b>) and Bader charge for structural sites of water adsorption on platinum (<b>f</b>) and hydrolysis product (<b>g</b>).</p>
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<p>Potential energy diagram for hydrolysis reaction for Pt(III) compound on magnesia film. Structural models show relaxed structures for water adsorption on ammonia ligand (initial state), transition state, and water substitution product. The star * represents adsorption site.</p>
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<p>Potential energy diagram for the hydrolysis reaction in the first step for a free Pt(III) compound. Structural models show relaxed structures for water adsorption on ammonia ligands (initial state), transition state (TS), and water-substituted product.</p>
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<p>Potential energy diagram for second step hydrolysis reaction for free Pt(III) compound. Structural models show relaxed structures for water adsorption on ammonia ligand (initial state), transition state (TS), and water-substituted product.</p>
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<p>Potential energy diagram for guanine interaction with the Pt(III) compound. Relaxed structures for physical adduct with hydrogen bonding (initial state), transition state (TS), and the formation of coordination bond (final state).</p>
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<p>The optimized structures with dipole moment vectors (shown in red arrows), LUMO and HOMO frontier orbitals for reactant (IS), transition state (TS), and final product (FS, (<b>a</b>)); the electron spin density for reactant (<b>b</b>) and final product (<b>c</b>); the platinum NBO charge population (<b>d</b>), enthalpy diagram (<b>e</b>), N(Guanine)-Pt distance (<b>f</b>) and dipole moment analysis (<b>g</b>). The isosurface values for molecular orbital and electronic density are 0.02 and 0.0004, respectively.</p>
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<p>Temperature influence on the energetics (<span class="html-italic">U, H, G</span>) of primary platinum hydrolysis species (<b>a</b>), the initial reactant adduct (<b>b</b>), the coordination product (<b>c</b>), and the coordination reaction energy of primary platinum hydrolysis species interacting with guanine (<b>d</b>).</p>
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<p>The energetics, dipole moment, Cl-Pt distance, Wiberg bond index, and N(5′-guanylic acid) Mulliken charge during coordination reaction between 5′-guanylic acid and platinum compound.</p>
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18 pages, 1780 KiB  
Review
The Wilms’ Tumor Suppressor WT1 in Cardiomyocytes: Implications for Cardiac Homeostasis and Repair
by Sandra Díaz del Moral, Nicole Wagner and Kay-Dietrich Wagner
Cells 2024, 13(24), 2078; https://doi.org/10.3390/cells13242078 - 17 Dec 2024
Viewed by 455
Abstract
The Wilms’ tumor suppressor WT1 is essential for the development of the heart, among other organs such as the kidneys and gonads. The Wt1 gene encodes a zinc finger transcription factor that regulates proliferation, cellular differentiation processes, and apoptosis. WT1 is also involved [...] Read more.
The Wilms’ tumor suppressor WT1 is essential for the development of the heart, among other organs such as the kidneys and gonads. The Wt1 gene encodes a zinc finger transcription factor that regulates proliferation, cellular differentiation processes, and apoptosis. WT1 is also involved in cardiac homeostasis and repair. In adulthood, WT1-expression levels are lower compared to those observed through development, and WT1 expression is restricted to a few cell types. However, its systemic deletion in adult mice is lethal, demonstrating that its presence is also key for organ maintenance. In response to injury, the epicardium re-activates the expression of WT1, but little is known about the roles it plays in cardiomyocytes, which are the main cell type affected after myocardial infarction. The fact that cardiomyocytes exhibit a low proliferation rate in the adult heart in mammals highlights the need to explore new approaches for cardiac regeneration. The aim of this review is to emphasize the functions carried out by WT1 in cardiomyocytes in cardiac homeostasis and heart regeneration. Full article
(This article belongs to the Section Cells of the Cardiovascular System)
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<p>Illustration of WT1 expression in different cardiac cell types in the embryonic, adult, and injured heart. Through cardiac development (<b>left</b>), high levels of WT1 are detected in the epicardium, endothelial cells, fibroblasts, and cardiomyocytes. In the adult heart (<b>central</b>), its expression is reduced and limited to a subset of epicardial cells, cardiomyocytes, and endothelial cells. After ischemia (<b>right</b>), high re-expression of WT1 is observed in the cardiomyocytes, endothelial, epicardial, and smooth muscle cells, mainly located in the border zone of infarction. Cells that express WT1 are colored in green. The infarcted area is represented by the red and black halo. MI: myocardial infarction. Created with BioRender.com.</p>
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<p>Consequences of in vitro Wt1-silencing in neonatal cardiomyocytes. Cultured neonatal cardiomyocytes were transduced with lentiviral particles expressing NC-RNA (non-coding RNA) as the control, or Wt1 shRNA (short hairpin RNA). Wt1 silencing causes a reduction in STIM1 expression levels, a gene directly regulated by WT1 [<a href="#B60-cells-13-02078" class="html-bibr">60</a>], and CaMKIIδ. This, in combination with the possible additional alteration of other genes that may participate in calcium homeostasis (represented by a question mark), triggers an increase in the intracellular levels of this ion. The lack of WT1 expression in neonatal cardiomyocytes also lowers the mitochondrial content and alters their polarization state. Ca<sup>2+</sup>: calcium. Schematic representation from the Wt1 silencing performed in [<a href="#B53-cells-13-02078" class="html-bibr">53</a>]. Created with BioRender.com.</p>
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<p>Direct effects of cardiomyocyte specific <span class="html-italic">Wt1</span> deletion in adult mice under homeostatic conditions. The transgenic mouse model αMHC<sup>merCremer/+</sup>;Wt1<sup>Flox/Flox</sup> was used to perform the conditional <span class="html-italic">Wt1</span> deletion in adult cardiomyocytes. Compared with the controls, hearts with cardiomyocytic <span class="html-italic">Wt1</span> deletion were highly fibrotic. Cardiomyocytes with loss of WT1 function were hypertrophic and showed an abnormal metabolic profile, with a reduction in the proteins involved in fatty acid metabolism as well as in the electron transport chain and oxidative phosphorylation pathways. ETC: electron transport chain. Schematic representation from the <span class="html-italic">Wt1</span> ablation assessed in [<a href="#B53-cells-13-02078" class="html-bibr">53</a>]. Created with BioRender.com.</p>
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<p>Differential expression pattern of HIF-1, WT1, STIM1, and CaMKIIδ in the heart through development, homeostasis, and injury. The hypoxic environment established in the embryonic heart (<b>left</b>), drives high levels of HIF-1, which triggers WT1 expression. At early developmental stages, calcium regulation in the heart is mainly orchestrated by the SOCE pathway, which explains the high levels of STIM1 and low CaMKIIδ expression. In homeostasis (<b>central</b>), CaMKIIδ expression starts to increase as its role is more essential, and the STIM1 levels drop in cardiomyocytes after birth. The augmented oxygen availability causes the downregulation of HIF-1, and WT1 expression becomes restricted to a low number of cardiac cells. After ischemia (<b>right</b>), not only does HIF-1 expression increase, but the CaMKIIδ levels are also higher compared to homeostasis. Genes highly expressed during embryonic development, such as STIM1 and WT1, are reactivated in the injured heart. MI: myocardial infarction. Created with BioRender.com.</p>
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<p>Changes in the methylation levels of WT1 promoter. In the developing heart (<b>left</b>), WT1 is highly expressed in embryonic cardiomyocytes, and the WT1 promoter is active. Under homeostatic conditions (<b>central</b>), the levels of WT1 are reduced in adult cardiomyocytes, likely due to hypermethylation of its promoter. An interesting approach to enhance the WT1 expression in cardiomyocytes following myocardial infarction (<b>right</b>) could be based on the use of “epidrugs”, chemical compounds that can specifically target transcriptional modifications. Therefore, inhibition of DNA methylation in the WT1 promoter would reverse its repression in the adult injured heart. MI: myocardial infarction. Created with BioRender.com.</p>
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16 pages, 3001 KiB  
Brief Report
Epstein–Barr Virus BRRF1 Induces Butyrophilin 2A1 in Nasopharyngeal Carcinoma NPC43 Cells via the IL-22/JAK3-STAT3 Pathway
by Yue Liu, Ka Sin Lui, Zuodong Ye, Luo Chen and Allen Ka Loon Cheung
Int. J. Mol. Sci. 2024, 25(24), 13452; https://doi.org/10.3390/ijms252413452 - 15 Dec 2024
Viewed by 657
Abstract
Epstein–Barr virus is highly associated with nasopharyngeal carcinoma (NPC) with genes expressed for tumor transformation or maintenance of viral latency, but there are certain genes that can modulate immune molecules. Butyrophilin 2A1 (BTN2A1) is an important activating protein for presenting phosphoantigens for recognition [...] Read more.
Epstein–Barr virus is highly associated with nasopharyngeal carcinoma (NPC) with genes expressed for tumor transformation or maintenance of viral latency, but there are certain genes that can modulate immune molecules. Butyrophilin 2A1 (BTN2A1) is an important activating protein for presenting phosphoantigens for recognition by Vγ9Vδ2 T cells to achieve antitumor activities. We have previously shown that Vγ9Vδ2 T cells achieve efficacy against NPC when BTN2A1 and BTN3A1 are upregulated by stimulating EBV gene expression, particularly LMP1. While BTN3A1 can be induced by the LMP1-mediated IFN-γ/JNK/NLRC5 pathway, the viral gene that can regulate BTN2A1 remains elusive. We showed that BTN2A1 expression is directly mediated by EBV BRRF1, which can trigger the BTN2A1 promoter and downstream JAK3-STAT3 pathway in NPC43 cells, as shown by RNA-seq data and verified via inhibitor experiments. Furthermore, BRRF1 downregulated IL-22 binding protein (IL-22RA2) to complement the EBNA1-targeting probe (P4)-induced IL-22 expression. Therefore, this study elucidated a new mechanism of stimulating BTN2A1 expression in NPC cells via the EBV gene BRRF1. The JAK3-STAT3 pathway could act in concordance with IL-22 to enhance the expression of BTN2A1, which likely leads to increased tumor cell killing by Vγ9Vδ2 T cells for enhanced potential as immunotherapy against the cancer. Full article
(This article belongs to the Special Issue New Insights in Tumor Immunity)
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Graphical abstract
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<p>BRRF1 overexpression induced the expression of BTN2A1 and BTN3A1 in certain tumor cell lines. Cells were transfected with BRRF1 and assessed for <span class="html-italic">BTN2A1</span> and <span class="html-italic">BTN3A1</span> gene expression for 6 h (<b>A</b>,<b>B</b>) and 24 h (<b>C</b>,<b>D</b>), respectively, via RT–qPCR. (<b>E</b>) Western blot analysis of BTN2A1, BTN3A1, and β-actin protein levels of BRRF1 overexpression in different cell lines for 24 h compared to vehicle control. Representative immunoblots are shown. (<b>F</b>,<b>G</b>) Band intensities for BTN2A1 and BTN3A1 normalized to the β-actin for the different cell lines as column graphs are shown. (<b>H</b>) Luciferase activities from promoters for <span class="html-italic">BTN2A1</span> and <span class="html-italic">BTN3A1</span> in 293T cells cotransfected with plasmids encoding BRRF1 or vector control for 1 day. Data shown as the mean ± SEM from 3 independent experiments. Student’s <span class="html-italic">t</span>-test was performed for statistical analysis. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>RNA sequencing analysis of genes altered by BRRF1 overexpression in NPC43 cells. (<b>A</b>) Heatmap of the RNA sequencing data in the control and BRRF1 overexpression groups. Three samples from each group were used for clustering. The degree of gene expression of BRRF1 compared to the control ranged from blue (downregulated) to red (upregulated) on a log<sub>2</sub> scale. (<b>B</b>) KEGG and (<b>C</b>) GO analysis of the differentially expressed genes in BRRF1 versus control.</p>
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<p>BRRF1 induces BTN2A1 expression through the IL22 and JAK3 pathways. (<b>A</b>) NPC43 cells were transfected with BRRF1 for 3 h and assessed for <span class="html-italic">JAK3</span>, <span class="html-italic">RhoB</span>, and <span class="html-italic">IL22RA2</span> gene expression via RT–qPCR. (<b>B</b>) Representative immunoblots from Western blot analysis of BRRF1 (Myc), RhoB, IL22RA2, and JAK3 expression following transfection of NPC43 cells by BRRF1 for 24 h. Band intensities are calculated and normalized to GAPDH. (<b>C</b>) NPC43 cells were transfected with BRRF1 or treated with 10 mM P<sub>4</sub> and assessed for <span class="html-italic">IL22</span> gene expression via RT–qPCR. <span class="html-italic">BTN2A1</span> expression was assessed following BRRF1 overexpression with or without IL-22 treatment on (<b>D</b>) NPC43, and (<b>E</b>) HK1-EBV cells. (<b>F</b>) RT–qPCR of <span class="html-italic">BTN2A1</span> gene expression in NPC43 cells treated with the JAK3 inhibitor ritlecitinib (0.5 and 5 μM) or DMSO control. (<b>G</b>) Luciferase reporter assays using the <span class="html-italic">BTN2A1</span> promoter in NPC43 cells following BRRF1 overexpression with or without IL-22 (10 ng/mL) treatment. Column graphs represent data as the mean ± SEM from ≥3 independent experiments. Student’s <span class="html-italic">t</span> test was performed for statistical analysis. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>BRRF1 induces the BTN2A1 protein expression level through the JAK3-STAT3 pathway. (<b>A</b>) Western blot analysis of TYK2, p-TYK2, JAK1, p-JAK1, JAK2, p-JAK2, JAK3, p-JAK3, BTN2A1, and BTN3A1, as well as (<b>B</b>) STAT3, p-STAT3, STAT1, p-STAT1, STAT5, p-STAT5, JNK, and p-JNK protein expression of NPC43 cells by BRRF1 overexpression with or without ritlecitinib (5 μM) treatment. Representative immunoblots are shown.</p>
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<p>BTN2A1 expression is reduced when JAK3/STAT3 is suppressed. Expression of <span class="html-italic">JAK3</span> and <span class="html-italic">STAT3</span> was assessed following transfection with siRNA against JAK3 or STAT3, or scrambled control (si-Ctrl) in NPC43 (<b>A</b>) and HK1-EBV (<b>B</b>) cells. RT-qPCR analysis of <span class="html-italic">BTN2A1</span> expression under BRRF1 overexpression and/or IL-22 treatment in (<b>C</b>) NPC43 or (<b>D</b>) HK1-EBV cells following siRNA transfection for 48 h. Under these treatments, protein expression of BTN2A1 in NPC43 and HK1-EBV was assessed via Western blot analysis. (<b>E</b>) The representative immunoblots for HK1-EBV are shown, or as band intensities for (<b>F</b>) NPC43 and (<b>G</b>) HK1-EBV under different treatments. Data represents mean ± SEM from at least 3 independent experiments. ANOVA was performed for statistical analysis. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001.</p>
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20 pages, 21952 KiB  
Article
Evolution and Predictive Analysis of Spatiotemporal Patterns of Habitat Quality in the Turpan–Hami Basin
by Yaqian Li, Yongqiang Liu, Yan Qin, Kun Zhang, Reifat Enwer, Weiping Wang and Shuai Yuan
Land 2024, 13(12), 2186; https://doi.org/10.3390/land13122186 - 14 Dec 2024
Viewed by 532
Abstract
The expansion of urban areas and unsustainable land use associated with human activities have brought about a decline in habitat quality (HQ), especially in arid regions with fragile ecosystems. A precise prediction of land use and habitat quality changes across different scenarios is [...] Read more.
The expansion of urban areas and unsustainable land use associated with human activities have brought about a decline in habitat quality (HQ), especially in arid regions with fragile ecosystems. A precise prediction of land use and habitat quality changes across different scenarios is crucial for the sustainable maintenance of ecological diversity. In this article, the InVEST model was employed to assess both the quality and degradation levels of habitats in the Turpan–Hami Basin (THB) spanning 1990~2020. Additionally, the InVEST-PLUS coupling model was employed to forecast habitat conditions under three different scenarios in 2050. Specifically, it involved the comparison of land use changes and spatial distribution of HQ across natural development (ND) scenarios, town development (UD) scenarios, and ecological protection (EP) scenarios, along with the analysis of hot spots of HQ spanning 1990~2050. The outcomes revealed the following: (1) The primary land use in the THB was categorized as unused land, alongside notable expansions in cultivated land, grassland, and built-up land. Conversely, there was a considerable decline observed in forests, water bodies, and unused land spanning 1990~2020. (2) The HQ within the THB exhibited evident spatial clustering characteristics. Between 1990 and 2020, areas with low HQ accounted for over 85%, areas with unchanged HQ constituted 88.19%, areas experiencing deteriorated HQ comprised approximately 5.02%, and areas displaying improved HQ encompassed around 6.79%. (3) Through the comparison of HQ for the ND, UD, and EP scenarios in 2050, it was observed that the average HQ under the EP scenario ranked highest, exhibiting the lowest degree of degradation on average. This indicates that the EP scenario is most advantageous for preserving HQ. Conclusively, this research provides valuable viewpoints for making decisions aimed at enhancing HQ in ecologically fragile arid regions. Full article
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<p>(<b>a</b>) Location of the study area in China and (<b>b</b>) elevation of the study area.</p>
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<p>Land use types in different times: (<b>a</b>) 1990, (<b>b</b>) 2000, (<b>c</b>) 2010, and (<b>d</b>) 2020.</p>
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<p>Sankey map of land use changes in THB spanning 1990~2020.</p>
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<p>(<b>a</b>) Area decrease and (<b>b</b>) area increase of land use types in THK spanning 1990~2020.</p>
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<p>Habitat degradation maps in THB at different times: (<b>a</b>) 1990, (<b>b</b>) 2000, (<b>c</b>) 2010 and (<b>d</b>) 2020; Bold 1, 2 represent two sample areas.</p>
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<p>Extent of habitat degradation in THB at different times: (<b>a</b>) 1990, (<b>b</b>) 2000, (<b>c</b>) 2010, and (<b>d</b>) 2020. (<b>e</b>) Changes in habitat degradation during 1990–2020.</p>
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<p>HQ levels in THB at different times: (<b>a</b>) 1990, (<b>b</b>) 2000, (<b>c</b>) 2010 and (<b>d</b>) 2020; Bold 1, 2 represent two sample areas.</p>
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<p>HQ levels in THB at different times: (<b>a</b>) 1990, (<b>b</b>) 2000, (<b>c</b>) 2010, and (<b>d</b>) 2020; (<b>e</b>) HQ variations spanning 1990~2020.</p>
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<p>Land use type distribution for the (<b>a</b>) ND, (<b>b</b>) UD, (<b>c</b>) EP scenarios in 2050.</p>
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<p>Habitat degradation levels and proportions under three scenarios in 2050: (<b>a</b>) ND, (<b>b</b>) UD, (<b>c</b>) EP.</p>
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<p>HQ classification chart for three scenarios in 2050: (<b>a</b>) ND; (<b>b</b>) UD; (<b>c</b>) EP. (<b>d</b>) Comparison of HQ between ND scenario and UD scenario; (<b>e</b>) comparison of HQ between ND scenario and EP scenario.</p>
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<p>Contribution map of driving factors of environmental quality in 2020. A: DEM; B: GDP; C: night lights; D: NDVI; E: NPP; F: potential evapotranspiration; G: population; H: rainfall; I: slope; J: soil type; K: temperature; L: distance from the 1st-class road; M: distance from the 2nd-class road; N: distance from the 3rd-class road; O: distance from highway; P: distance from railway; Q: distance from water; R: distance from county seat.</p>
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<p>Distribution of hot spots of HQ in the THB at different times: (<b>a</b>) 1990, (<b>b</b>) 2000, (<b>c</b>) 2010, (<b>d</b>) 2020. Distribution of hot spots of HQ for the three scenarios in 2050: (<b>e</b>) ND; (<b>f</b>) UD; (<b>g</b>) EP.</p>
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12 pages, 1309 KiB  
Review
Life History Differences Between Lepidoptera Larvae and Blattodea Nymphs Lead to Different Energy Allocation Strategies and Cellular Qualities
by Fahimeh Taheri and Chen Hou
Insects 2024, 15(12), 991; https://doi.org/10.3390/insects15120991 - 13 Dec 2024
Viewed by 514
Abstract
Different life histories result in different strategies to allocate energy in biosynthesis, including growth and reproduction, and somatic maintenance. One of the most notable life history differences between Lepidoptera and Blattodea species is that the former grow much faster than the latter, and [...] Read more.
Different life histories result in different strategies to allocate energy in biosynthesis, including growth and reproduction, and somatic maintenance. One of the most notable life history differences between Lepidoptera and Blattodea species is that the former grow much faster than the latter, and during metamorphosis, a large amount of tissue in Lepidoptera species disintegrates. In this review, using Lepidoptera caterpillars and cockroach nymphs as examples, we show that, due to these differences in growth processes, cockroach nymphs spend 20 times more energy on synthesizing one unit of biomass (indirect cost of growth) than butterfly caterpillars. Because of the low indirect cost of growth in caterpillars, the fraction of metabolic energy allocated to growth is six times lower, and that for maintenance is seven times higher in caterpillars, compared to cockroach nymphs, despite caterpillar’s higher growth rates. Moreover, due to the higher biosynthetic energy cost in cockroach nymphs, they have better cellular qualities, including higher proteasomal activity for protein quality control and higher resistance to oxidative stress. We also show that under food restriction conditions, the fraction of assimilated energy allocated to growth was reduced by 120% in cockroach nymphs, as they lost body weight under food restriction, while this reduction was only 14% in hornworms, and the body mass increased at a lower rate. Finaly, we discuss future research, especially the difference in adult lifespans associated with the energetic differences. Full article
(This article belongs to the Section Insect Physiology, Reproduction and Development)
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<p>Energy budget of total metabolic energy of hornworms and cockroach nymphs.</p>
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<p>Energy budget of total assimilated energy of hornworms and cockroach nymphs.</p>
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<p>Values of <span class="html-italic">E<sub>m</sub></span> of a few ectothermic species. The red bars represent the species discussed in this paper. (Data from [<a href="#B11-insects-15-00991" class="html-bibr">11</a>,<a href="#B13-insects-15-00991" class="html-bibr">13</a>,<a href="#B43-insects-15-00991" class="html-bibr">43</a>,<a href="#B45-insects-15-00991" class="html-bibr">45</a>,<a href="#B48-insects-15-00991" class="html-bibr">48</a>,<a href="#B49-insects-15-00991" class="html-bibr">49</a>,<a href="#B50-insects-15-00991" class="html-bibr">50</a>,<a href="#B51-insects-15-00991" class="html-bibr">51</a>,<a href="#B52-insects-15-00991" class="html-bibr">52</a>,<a href="#B53-insects-15-00991" class="html-bibr">53</a>].)</p>
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14 pages, 7286 KiB  
Article
Activity-Based Prospective Memory and Motor Sleep Inertia in Insomnia
by Lorenzo Tonetti, Miranda Occhionero, Sara Giovagnoli, Federica Giudetti, Elena Briganti and Vincenzo Natale
Brain Sci. 2024, 14(12), 1248; https://doi.org/10.3390/brainsci14121248 - 12 Dec 2024
Viewed by 518
Abstract
Background/Objectives: The aim of this study is to shed light on activity-based prospective memory upon the awakening and its association with motor sleep inertia in different phenotypes of insomnia disorder. Methods: To this end, 67 patients with insomnia and 51 healthy controls took [...] Read more.
Background/Objectives: The aim of this study is to shed light on activity-based prospective memory upon the awakening and its association with motor sleep inertia in different phenotypes of insomnia disorder. Methods: To this end, 67 patients with insomnia and 51 healthy controls took part in the study. After enrollment, previously proposed actigraphic quantitative criteria were adopted, and the following phenotypes of insomnia disorder were observed in the patient sample: sleep onset (n = 12), maintenance (n = 19), mixed (n = 17), and negative misperception (n = 19). Each participant had used the Micro Motionlogger Watch (Ambulatory Monitoring, Inc., Ardsley, NY, USA) actigraph for one week. Actigraphic recording allowed for a description of both the activity-based prospective memory performance upon the awakening—by computing the time interval between sleep end and the time participants actually remembered to push the event-marker button of the actigraph—and the motor sleep inertia, i.e., the mean motor activity, minute-by-minute, in the first 60 min after sleep end in the morning. Results: Compared to healthy controls, a longer time interval was observed between sleep end and activity-based prospective memory performance in patients with mixed and maintenance insomnia. Moreover, a significant association was highlighted between motor sleep inertia and the activity-based prospective memory performance: higher levels of motor activity in those who remembered to perform the memory task early after sleep end, that spread over a longer time interval in maintenance and mixed insomnia. Conclusions: Overall, the present results seem to highlight a more marked cognitive inertia in patients with mixed and maintenance insomnia as well as a significant association between motor and cognitive inertia that spreads over a different time interval according to the phenotype of insomnia. Full article
(This article belongs to the Section Sleep and Circadian Neuroscience)
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<p>Example of an actigraphic record spanning two days, with one line representing each day. The x-axis indicates the time of day, while the y-axis represents motor activity. The dates 15/02/92 (first line) and 16/09/92 (second line) refer to the recordings’ day/month/year. The actigraphic software assigns a number to each day of the week: 1 for Sunday, 2 for Monday, 3 for Tuesday, 4 for Wednesday, 5 for Thursday, 6 for Friday, and 7 for Saturday. Therefore, the number 7 next to the date 15/09/92 indicates that it was a Saturday, while the number 1 next to 16/02/92 shows that it was a Sunday. In this figure, the black histograms represent motor activity counts recorded minute-by-minute, while the colored area indicates the time spent in bed. The red indicates that the algorithm scored the corresponding epoch as sleep. The triangle marks the moment the participant pressed the event-marker button on the actigraph. As observed in the figure, the ecological activity-based prospective memory task was performed upon waking after the second night (labeled (<b>B</b>)). In contrast, it was not performed after the awakening from the first night (labeled (<b>A</b>)).</p>
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<p>Boxplots of the time interval (in minutes) between sleep end and the time at which participants remembered to perform the activity-based prospective memory task, in the healthy controls (HC), the patients with maintenance (MA-I), mixed (MIX-I), negative misperception (NM-I), and SO-I (sleep onset) insomnia. The boxes represent the interquartile ranges (IQR), that is, the range between the first quartile (Q1) and third quartile (Q3); the central line is the median (Q2). Whiskers indicate the dispersion of values below the first and above the third quartile that were not classified as outliers (1.5 × IQR from the edge of the box). The circles represent the mild outliers (Q3 + 1.5 × IQR), and the stars represent the extreme outliers (Q3 + 3 × IQR).</p>
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<p>An FLM plot showing—in the upper panel—the functional forms of motor activity, minute-by-minute, over the first 60 min after sleep end in the patients with insomnia (I, red line) and in the healthy controls (HC, black line). The lower panel shows the results of the non-parametric permutation F test, with significant results when the observed statistic (red solid line) is above the global (blue dashed line) and point-wise (blue dotted line) tests of significance. The rectangle highlights the time window with significant differences between I and HC.</p>
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<p>In the upper panel of the FLM plot, the functional forms of motor activity are depicted, minute-by-minute, over the first 60 min after sleep end in patients with sleep onset insomnia (SO-I, black line), negative misperception insomnia (NM-I, red line), maintenance insomnia (MA-I, green line), and mixed insomnia (MIX-I, blue line). The lower panel shows the results of the non-parametric permutation F test. The rectangle highlights the time window with significant differences among different insomnia phenotypes.</p>
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<p>The upper panel of the FLM plot shows the functional forms of motor activity, minute-by-minute, over the first 60 min after sleep end, plotted against the time interval, in minutes, between sleep end and the time at which HC remembered to perform the activity-based prospective memory task, reported in the plot’s color spectrum legend. In addition, each line of the upper panel corresponds to the motor activity profile of a single participant marked with a color that indicates the time interval in minutes taken to perform the prospective memory task after morning awakening, with the dark colors pointing to a lower time interval while the light colors show a longer time interval. The lower panel shows the results of the non-parametric permutation F test. The rectangle highlights the time window with significant differences in motor activity according to the time interval between sleep end and the activity-based prospective memory performance.</p>
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<p>FLM plot showing—in the upper panel—the functional forms of motor activity, minute-by-minute, over the first 60 min after sleep end, plotted against the time interval, in minutes, between sleep end and the time at which patients with SO-I remembered to perform the activity-based prospective memory task, with the dark colors pointing to a lower time interval while the light colors show a longer time interval as reported in the plot’s color spectrum legend. The lower panel shows the results of the non-parametric permutation F test. The rectangle highlights the time window with significant differences in motor activity according to the time interval between sleep end and the activity-based prospective memory performance.</p>
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<p>FLM plot showing—in the upper panel—the functional forms of motor activity, minute-by-minute, over the first 60 min after sleep end plotted against the time interval, in minutes, between sleep end and the time at which patients with NM-I remembered to perform the activity-based prospective memory task, with the dark colors pointing to a lower time interval while the light colors show a longer time interval as reported in the plot’s color spectrum legend. The lower panel shows the results of the non-parametric permutation F test. The rectangle highlights the time window with significant differences in motor activity according to the time interval between sleep end and the activity-based prospective memory performance.</p>
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<p>The upper panel of the FLM plot shows the functional forms of motor activity, minute-by-minute, over the first 60 min after sleep end plotted against the time interval, in minutes, between the sleep end and the time at which patients with MA-I remembered to perform the activity-based prospective memory task, with the dark colors pointing to a lower time interval while light colors show a longer time interval as reported in the plot’s color spectrum legend. The lower panel shows the results of the non-parametric permutation F test. The rectangle highlights the time window with significant differences in motor activity according to the time interval between sleep end and the activity-based prospective memory performance.</p>
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<p>The upper panel of the FLM plot shows the functional forms of motor activity, minute-by-minute, over the first 60 min after sleep end plotted against the time interval, in minutes, between sleep end and the time at which patients with MIX-I remembered to perform the activity-based prospective memory task, with the dark colors pointing to a lower time interval while light colors show a longer time interval as reported in the plot’s color spectrum legend. The lower panel shows the results of the non-parametric permutation F test. The rectangle highlights the time window with significant differences in motor activity according to the time interval between sleep end and the activity-based prospective memory performance.</p>
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30 pages, 5352 KiB  
Article
Addressing the Unmet Need in Acne Management: A Novel Dermocosmetics Guideline Tailored to Asian Patient Subgroups
by Hei Sung Kim, Joo Yeon Ko, Dong Hye Suh, Hwa Jung Ryu, Eunsun Baek and Soyun Cho
Cosmetics 2024, 11(6), 220; https://doi.org/10.3390/cosmetics11060220 - 12 Dec 2024
Viewed by 685
Abstract
Acne, a commonly treated skin disease, requires control of one’s daily routine for an optimal outcome. As skincare products continue to advance, and with the introduction of dermocosmetics (active cosmetics, functional cosmetics, cosmeceuticals), it is necessary for clinicians to stay updated and give [...] Read more.
Acne, a commonly treated skin disease, requires control of one’s daily routine for an optimal outcome. As skincare products continue to advance, and with the introduction of dermocosmetics (active cosmetics, functional cosmetics, cosmeceuticals), it is necessary for clinicians to stay updated and give professional guidance. Following a literature review, a panel discussed and, using an online review process, explored the available acne dermocosmetics and convened to develop consensus statements on acne skincare incorporating patient- and treatment-related factors. Recommendations tailored to several distinct patient subgroups, namely, preadolescent acne, adolescent/adult acne, acne with comorbid atopic dermatitis, acne in pregnancy, drug-induced acne, and acne cosmetica, were generated to maximize the use of dermocosmetics in acne management. In adolescent and adult acne, products with active ingredients that mark key aspects of acne pathophysiology are called for; in atopics, agents which protect and restore the skin barrier are primarily considered; and in the preadolescent age group and pregnant and lactating women, the use of acne dermocosmetics should be prioritized as there are limited treatment options. While skincare alone is often sufficient for mild acne and for maintenance, adjunctive skincare can enhance treatment efficacy as well as patient adherence in various settings. This guideline seeks to offer insights into acne dermocosmetics and provide skincare recommendation tailored to Asian patient subgroups. Full article
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<p>Acne pathomechanism is complex involving C. acnes, hyperseborrhea, hyperkeratosis, and inflammation (reprinted with permission from Lee et al. [<a href="#B14-cosmetics-11-00220" class="html-bibr">14</a>]).</p>
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<p>The six pillars of acne dermocosmetics with active ingredients categorized according to their mode of action. APF: also known as <span class="html-italic">Vitreoscilla filiformis</span>, this postbiotic is an exclusive, patented ingredient cultivated in the La Roche-Posay Thermal Spring Water. Procerad<sup>TM</sup>: exclusive, patented anti-mark ceramide that acts upstream to prevent the button from leaving a red or brown mark. Melasyl<sup>TM</sup>: The multi-patented La Roche-Posay ingredient is designed to attenuate dark spots and discoloration. AHA, Alpha Hydroxy Acid; LHA, Lipo Hydroxy Acid; HEPES, Hydroxyethylpiperazine Ethane Sulfonic Acid; EGCG, Epigallocatechin Gallate; APF, Aqua Posae Filiformis; BPO, Benzoyl Peroxide; EGF, Epidermal Growth Factor.</p>
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<p>Acne dermocosmetics best for the patient’s skin type and acne status.</p>
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<p>Treatment algorithm for preadolescent acne.</p>
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<p>Clinical treatment algorithm for adolescent and adult acne.</p>
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<p>Clinical treatment algorithm for acne in AD.</p>
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<p>Acne treatment algorithm for pregnant and lactating women.</p>
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<p>Treatment algorithm for drug-induced acne.</p>
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<p>Treatment algorithm for acne cosmetica.</p>
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27 pages, 3670 KiB  
Article
Helichrysum populifolium Compounds Inhibit MtrCDE Efflux Pump Transport Protein for the Potential Management of Gonorrhoea Infection
by Vhangani E. Mulaudzi, Idowu J. Adeosun, Adeniyi T. Adewumi, Mahmoud E. S. Soliman and Sekelwa Cosa
Int. J. Mol. Sci. 2024, 25(24), 13310; https://doi.org/10.3390/ijms252413310 - 11 Dec 2024
Viewed by 518
Abstract
The progressive development of resistance in Neisseria gonorrhoeae to almost all available antibiotics has made it crucial to develop novel approaches to tackling multi-drug resistance (MDR). One of the primary causes of antibiotic resistance is the over-expression of the MtrCDE efflux pump protein, [...] Read more.
The progressive development of resistance in Neisseria gonorrhoeae to almost all available antibiotics has made it crucial to develop novel approaches to tackling multi-drug resistance (MDR). One of the primary causes of antibiotic resistance is the over-expression of the MtrCDE efflux pump protein, making this protein a vital target for fighting against antimicrobial resistance (AMR) in N. gonorrhoeae. This study was aimed at evaluating the potential MtrCDE efflux pump inhibitors (EPIs) and their stability in treating gonorrhoea infection. This is significant because finding novel EPIs would allow for the longer maintenance of antibiotics at therapeutic levels, thereby prolonging the susceptibility of currently available antibiotics. A virtual screening of the selected Helichrysum populifolium compounds (4,5-dicaffeoylquinic acid, apigeninin-7-glucoside, and carvacrol) was conducted to evaluate their potential EPI activity. An integrated computational framework consisting of molecular docking (MD), molecular mechanics generalized born, and surface area solvation (MMGBSA) analysis, molecular dynamics simulations (MDS), and absorption, distribution, metabolism, and excretion (ADME) properties calculations were conducted. Of the tested compounds, 4,5-dicaffeoylquinic acid revealed the highest molecular docking binding energies (−8.8 kcal/mol), equivalent MMGBSA binding free energy (−54.82 kcal/mol), indicative of consistent binding affinity with the MtrD protein, reduced deviations and flexibility (root mean square deviation (RMSD) of 5.65 Å) and, given by root mean square fluctuation (RMSF) of 1.877 Å. Carvacrol revealed a docking score of −6.0 kcal/mol and a MMGBSA computed BFE of −16.69 kcal/mol, demonstrating the lowest binding affinity to the MtrD efflux pump compared to the remaining test compounds. However, the average RMSD (4.45 Å) and RMSF (1.638 Å) of carvacrol-bound MtrD protein showed no significant difference from the unbound MtrD protein, except for the reference compounds, implying consistent MtrD conformation throughout simulations and indicates a desirable feature during drug design. Additionally, carvacrol obeyed the Lipinski rule of five which confirmed the compound’s drug-likeness properties making it the most promising EPI candidate based on its combined attributes of a reasonable binding affinity, sustained stability during MDS, its obedience to the Lipinski rule of five and compliance with drug-likeness criteria. An in vitro validation of the potential EPI activities of H. populifolium compounds confirmed that 4,5-dicaffeoylquinic acid reduced the expulsion of the bis-benzimide dye by MtrCDE pump, while carvacrol showed low accumulation compared to other compounds. While 4,5-dicaffeoylquinic acid demonstrated the highest binding affinity in computational analysis and an EPI activity in vitro, it showed lower stability compared to the other compounds, as indicated in MDS. This leaves carvacrol, as a better EPI candidate for the management of gonorrhoea infection. Full article
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<p>(<b>A</b>) Crystal structure of MtrCDE efflux pump protein from <span class="html-italic">Neisseria gonorrhoea</span> with its distinguished chains. (<b>B</b>) The crystal structure of the MtrD chain of the MtrCDE efflux pump used in this study for molecular docking and molecular dynamic simulations assays, which consists of the proximal and distal multi-drug-binding sites.</p>
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<p>Two-dimensional and three-dimensional interaction network between the MtrD (PDB ID: 6VKS) EP protein in <span class="html-italic">N. gonorrhoeae</span> and test compounds from <span class="html-italic">H. populifolium</span> generated after molecular docking. As the binding of these compounds within the MtrD efflux pump multi-drug-binding site was within the −5 to −15 kcal/mol an indication that these compounds can fit perfectly within the binding pockets of the MtrD multi-drug-binding site. Hydrogen bonds are noted by the green lines, pi–alkyl interactions by light-pink color, pi–pi T-shaped interaction with the dark pink color, pi–sulfur interaction with the orange color, and unfavorable donor-to-donor interactions with the red color. (<b>A</b>) 4,5-dicaffeoylquinic acid. (<b>B</b>) Apigenin-7-glucoside. (<b>C</b>) Carvacrol. (<b>D</b>) Phenylalanine-arginine-β-naphylamide (PaβN). (<b>E</b>) Quercetin.</p>
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<p>Two-dimensional and three-dimensional interaction network between the MtrD (PDB ID: 6VKS) EP protein in <span class="html-italic">N. gonorrhoeae</span> and test compounds from <span class="html-italic">H. populifolium</span> generated after molecular docking. As the binding of these compounds within the MtrD efflux pump multi-drug-binding site was within the −5 to −15 kcal/mol an indication that these compounds can fit perfectly within the binding pockets of the MtrD multi-drug-binding site. Hydrogen bonds are noted by the green lines, pi–alkyl interactions by light-pink color, pi–pi T-shaped interaction with the dark pink color, pi–sulfur interaction with the orange color, and unfavorable donor-to-donor interactions with the red color. (<b>A</b>) 4,5-dicaffeoylquinic acid. (<b>B</b>) Apigenin-7-glucoside. (<b>C</b>) Carvacrol. (<b>D</b>) Phenylalanine-arginine-β-naphylamide (PaβN). (<b>E</b>) Quercetin.</p>
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<p>Two-dimensional and three-dimensional interaction network between the MtrD (PDB ID: 6VKS) EP protein in <span class="html-italic">N. gonorrhoeae</span> and test compounds from <span class="html-italic">H. populifolium</span> generated after molecular docking. As the binding of these compounds within the MtrD efflux pump multi-drug-binding site was within the −5 to −15 kcal/mol an indication that these compounds can fit perfectly within the binding pockets of the MtrD multi-drug-binding site. Hydrogen bonds are noted by the green lines, pi–alkyl interactions by light-pink color, pi–pi T-shaped interaction with the dark pink color, pi–sulfur interaction with the orange color, and unfavorable donor-to-donor interactions with the red color. (<b>A</b>) 4,5-dicaffeoylquinic acid. (<b>B</b>) Apigenin-7-glucoside. (<b>C</b>) Carvacrol. (<b>D</b>) Phenylalanine-arginine-β-naphylamide (PaβN). (<b>E</b>) Quercetin.</p>
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<p>Per-residue energy contributions of the interacting residues of the MtrD protein (PDB ID: 6VKS) with the <span class="html-italic">H. populifolium</span> test compounds and standards. (<b>A</b>) 4,5-dicaffeoylquinic acid. (<b>B</b>) Apigenin-7-glucoside. (<b>C</b>) Carvacrol. (<b>D</b>) Phenylalanine-arginine-β-naphylamide (PaβN). (<b>E</b>) Quercetin.</p>
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<p>(<b>A</b>) Protein–ligand complex of the MtrD efflux pump bound by 4,5-dicaffeoylquinic acid in magenta. The yellow color on the MtrCDE efflux pump protein structure represents the proximal and distal multi-drug efflux pump residues interacting with 4,5-dicaffeoylquinic acid. (<b>B</b>) Comparative C-α RMSD plots displaying the degree of stability and convergence of the studied compounds when bound to the MtrD protein for a period of 175 ns. (<b>C</b>) Comparative C-α RMSF plot shows the degree of flexibility of the studied compounds when bound to the MtrD protein for a period of 175 ns. (<b>D</b>) Comparative C-α RMSF plot, showing the degree of flexibility of the studied compounds when bound to the drug-binding site for a period of 175 ns. For both RMSD and RMSF plots, the black line graph represents data for the Apo protein (Unbound MtrD protein), the red line graph shows Apo-INH1, the green line graph shows Apo-INH2, the dark blue line graph shows Apo-INH3, the light blue line graph shows Apo-STD1, and the pink line graph shows Apo-STD2.</p>
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<p>Hoechest (bis-benzimide) accumulation assay in <span class="html-italic">Neisseria gonorrhoea</span> ATCC 49981 after treatment with <span class="html-italic">H. populifolium</span> compounds: 4,5-dicaffeoylquinic acid (orange line graph), apigenin-7-glucoside (gray line graph), and carvacrol (yellow line graph). PaβN was used as the positive control, while untreated <span class="html-italic">N. gonorrhoeae</span> was used as the negative control. The heat-inactivated <span class="html-italic">N. gonorrhoeae</span> ATCC 49981 cells serve as a point of reference for maximal dye accumulation due to the loss of membrane integrity, leading to a high influx and retention of the dye.</p>
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