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Int. J. Mol. Sci., Volume 25, Issue 2 (January-2 2024) – 678 articles

Cover Story (view full-size image): The dopamine D4 receptor (D4R) is a promising therapeutic target for widespread diseases, driving the search for novel agonists and antagonists. Using dynamic network analysis and a fragment molecular orbital with pair interaction energy decomposition analysis scheme, the binding behaviors, dynamics, and energies for D4R agonists and antagonists were explored. We identified a strong salt bridge with the D3.32 initiating inhibition of the D4 receptor; this mechanism is shared with the agonists. However, the agonists induce receptor conformational changes through interaction with cysteine C3.36, suggesting an alternative activation pathway. The energy calculations reveal that the antagonists exhibit repulsive interactions with S5.46, distinguishing them from the agonists. View this paper
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3 pages, 186 KiB  
Editorial
Molecular Advances in Microbial Metabolism 2.0
by Rosa María Martínez-Espinosa
Int. J. Mol. Sci. 2024, 25(2), 1361; https://doi.org/10.3390/ijms25021361 - 22 Jan 2024
Viewed by 932
Abstract
The advances in molecular biology techniques and omics approaches have made it possible to take giant steps in applied research in life sciences [...] Full article
(This article belongs to the Special Issue Molecular Advances in Microbial Metabolism 2.0)
22 pages, 2694 KiB  
Article
Genetic Analysis of Partially Resistant and Susceptible Chickpea Cultivars in Response to Ascochyta rabiei Infection
by Amit A. Deokar, Mandeep Sagi and Bunyamin Tar’an
Int. J. Mol. Sci. 2024, 25(2), 1360; https://doi.org/10.3390/ijms25021360 - 22 Jan 2024
Cited by 1 | Viewed by 1076
Abstract
The molecular mechanism involved in chickpea (Cicer arietinum L.) resistance to the necrotrophic fungal pathogen Ascochyta rabiei is not well documented. A. rabiei infection can cause severe damage in chickpea, resulting in significant economic losses. Understanding the resistance mechanism against ascochyta blight [...] Read more.
The molecular mechanism involved in chickpea (Cicer arietinum L.) resistance to the necrotrophic fungal pathogen Ascochyta rabiei is not well documented. A. rabiei infection can cause severe damage in chickpea, resulting in significant economic losses. Understanding the resistance mechanism against ascochyta blight can help to define strategies to develop resistant cultivars. In this study, differentially expressed genes from two partially resistant cultivars (CDC Corinne and CDC Luna) and a susceptible cultivar (ICCV 96029) to ascochyta blight were identified in the early stages (24, 48 and 72 h) of A. rabiei infection using RNA-seq. Altogether, 3073 genes were differentially expressed in response to A. rabiei infection across different time points and cultivars. A larger number of differentially expressed genes (DEGs) were found in CDC Corinne and CDC Luna than in ICCV 96029. Various transcription factors including ERF, WRKY, bHLH and MYB were differentially expressed in response to A. rabiei infection. Genes involved in pathogen detection and immune signalings such as receptor-like kinases (RLKs), Leucine-Rich Repeat (LRR)-RLKs, and genes associated with the post-infection defence response were differentially expressed among the cultivars. GO functional enrichment and pathway analysis of the DEGs suggested that the biological processes such as metabolic process, response to stimulus and catalytic activity were overrepresented in both resistant and susceptible chickpea cultivars. The expression patterns of eight randomly selected genes revealed by RNA-seq were confirmed by quantitative PCR (qPCR) analysis. The results provide insights into the complex molecular mechanism of the chickpea defence in response to the A. rabiei infection. Full article
(This article belongs to the Section Molecular Plant Sciences)
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31 pages, 8076 KiB  
Review
Development of Liquid Organic Hydrogen Carriers for Hydrogen Storage and Transport
by Thi-Hoa Le, Ngo Tran and Hyun-Jong Lee
Int. J. Mol. Sci. 2024, 25(2), 1359; https://doi.org/10.3390/ijms25021359 - 22 Jan 2024
Cited by 1 | Viewed by 2386
Abstract
The storage and transfer of energy require a safe technology to mitigate the global environmental issues resulting from the massive application of fossil fuels. Fuel cells have used hydrogen as a clean and efficient energy source. Nevertheless, the storage and transport of hydrogen [...] Read more.
The storage and transfer of energy require a safe technology to mitigate the global environmental issues resulting from the massive application of fossil fuels. Fuel cells have used hydrogen as a clean and efficient energy source. Nevertheless, the storage and transport of hydrogen have presented longstanding problems. Recently, liquid organic hydrogen carriers (LOHCs) have emerged as a solution to these issues. The hydrogen storage technique in LOHCs is more attractive than those of conventional energy storage systems like liquefaction, compression at high pressure, and methods of adsorption and absorption. The release and acceptance of hydrogen should be reversible by LOHC molecules following favourable reaction kinetics. LOHCs comprise liquid and semi-liquid organic compounds that are hydrogenated to store hydrogen. These hydrogenated molecules are stored and transported and finally dehydrogenated to release the required hydrogen for supplying energy. Hydrogenation and dehydrogenation are conducted catalytically for multiple cycles. This review elaborates on the characteristics of different LOHC molecules, based on their efficacy as energy generators. Additionally, different catalysts used for both hydrogenation and dehydrogenation are discussed. Full article
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30 pages, 8716 KiB  
Article
Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor
by Fady Baselious, Sebastian Hilscher, Dina Robaa, Cyril Barinka, Mike Schutkowski and Wolfgang Sippl
Int. J. Mol. Sci. 2024, 25(2), 1358; https://doi.org/10.3390/ijms25021358 - 22 Jan 2024
Cited by 3 | Viewed by 1665
Abstract
HDAC11 is a class IV histone deacylase with no crystal structure reported so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms, which makes conventional homology modeling less reliable. AlphaFold is a machine learning approach that can predict [...] Read more.
HDAC11 is a class IV histone deacylase with no crystal structure reported so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms, which makes conventional homology modeling less reliable. AlphaFold is a machine learning approach that can predict the 3D structure of proteins with high accuracy even in absence of similar structures. However, the fact that AlphaFold models are predicted in the absence of small molecules and ions/cofactors complicates their utilization for drug design. Previously, we optimized an HDAC11 AlphaFold model by adding the catalytic zinc ion and minimization in the presence of reported HDAC11 inhibitors. In the current study, we implement a comparative structure-based virtual screening approach utilizing the previously optimized HDAC11 AlphaFold model to identify novel and selective HDAC11 inhibitors. The stepwise virtual screening approach was successful in identifying a hit that was subsequently tested using an in vitro enzymatic assay. The hit compound showed an IC50 value of 3.5 µM for HDAC11 and could selectively inhibit HDAC11 over other HDAC subtypes at 10 µM concentration. In addition, we carried out molecular dynamics simulations to further confirm the binding hypothesis obtained by the docking study. These results reinforce the previously presented AlphaFold optimization approach and confirm the applicability of AlphaFold models in the search for novel inhibitors for drug discovery. Full article
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0 pages, 603 KiB  
Review
Systemic Antibiotic Use in Acute Irreversible Pulpitis: Evaluating Clinical Practices and Molecular Insights
by Shahnawaz Khijmatgar, Gionata Bellucci, Luca Creminelli, Giulia Margherita Tartaglia, Jr. and Margherita Tumedei
Int. J. Mol. Sci. 2024, 25(2), 1357; https://doi.org/10.3390/ijms25021357 - 22 Jan 2024
Viewed by 1668
Abstract
This scoping review systematically evaluates the use of systemic antibiotics in treating acute irreversible pulpitis, integrating clinical practice patterns with recent molecular insights. We analyzed clinical evidence on antibiotic prescription trends among dental professionals and examined molecular research advancements in relation to pulpitis. [...] Read more.
This scoping review systematically evaluates the use of systemic antibiotics in treating acute irreversible pulpitis, integrating clinical practice patterns with recent molecular insights. We analyzed clinical evidence on antibiotic prescription trends among dental professionals and examined molecular research advancements in relation to pulpitis. This review is intended to bridge the gap between clinical practice and molecular research, guiding more evidence-based approaches to treating acute irreversible pulpitis. Electronic databases were searched for relevant articles published in English based on the objective of the review. A second search using all identified keywords and index terms was undertaken across all the included databases. In addition, a reference list of identified articles was searched. Studies including original research, systematic reviews, meta-analyses, clinical trials, and observational and retrospective studies, all written in English and published from 2010 onwards, were included, and an analysis of the text words contained in the titles and abstracts of the retrieved papers and of the index terms used to describe the articles was performed. A total of N = 53 articles were selected. Altogether, N = 43 (76.79%) articles were cross-sectional studies, N = 4 (11.11%) were systematic reviews, and N = 3 (5.36%) were guidelines. The most frequent level of evidence was level VI (N = 43 (76.79%). The mean percentage of dentists who prescribed antibiotics to treat acute irreversible pulpitis was 23.89 ± 23.74% (range: 0.05–75.7). Similarly, for specialists, it was 22.41 ± 15.64 (range 2.2–50.4), and the percentage for undergraduates was 17.52 ± 20.59 (range 0–62.6). The significant developments in research models for pulpitis research and the characterisation of biomarkers have led to better management strategies. Concurrently, significant advancements in molecular research provide new understandings of pulpitis, suggesting alternative therapeutic approaches. Although there are guidelines available, increased rates of antibiotic prescription are still prevalent around the globe. Full article
(This article belongs to the Special Issue Molecular Advances in Oral Microbiome and Diseases)
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20 pages, 3058 KiB  
Article
MicroRNA Profiling of the Inflammatory Response after Early and Late Asthmatic Reaction
by Ruth P. Duecker, Oguzhan Alemdar, Andreas Wimmers, Lucia Gronau, Andreas G. Chiocchetti, Eva M. Valesky, Helena Donath, Jordis Trischler, Katharina Blumchen, Stefan Zielen and Ralf Schubert
Int. J. Mol. Sci. 2024, 25(2), 1356; https://doi.org/10.3390/ijms25021356 - 22 Jan 2024
Viewed by 940
Abstract
A high proportion of house dust mite (HDM)-allergic asthmatics suffer from both an early asthmatic reaction (EAR) and a late asthmatic reaction (LAR) which follows it. In these patients, allergic inflammation is more relevant. MiRNAs have been shown to play an important role [...] Read more.
A high proportion of house dust mite (HDM)-allergic asthmatics suffer from both an early asthmatic reaction (EAR) and a late asthmatic reaction (LAR) which follows it. In these patients, allergic inflammation is more relevant. MiRNAs have been shown to play an important role in the regulation of asthma’s pathology. The aim of this study was to analyze the miRNA profile in patients with mild asthma and an HDM allergy after bronchial allergen provocation (BAP). Seventeen patients with EAR/no LAR and 17 patients with EAR plus LAR, determined by a significant fall in FEV1 after BAP, were differentially analyzed. As expected, patients with EAR plus LAR showed a more pronounced allergic inflammation and FEV1 delta drop after 24 h. NGS-miRNA analysis identified the down-regulation of miR-15a-5p, miR-15b-5p, and miR-374a-5p after BAP with the highest significance in patients with EAR plus LAR, which were negatively correlated with eNO and the maximum decrease in FEV1. These miRNAs have shared targets like CCND1, VEGFA, and GSK3B, which are known to be involved in airway remodeling, basement membrane thickening, and Extracellular Matrix deposition. NGS-profiling identified miRNAs involved in the inflammatory response after BAP with HDM extract, which might be useful to predict a LAR. Full article
(This article belongs to the Section Molecular Immunology)
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17 pages, 2664 KiB  
Article
Comprehensive Analysis of 1-Year-Old Female Apolipoprotein E-Deficient Mice Reveals Advanced Atherosclerosis with Vulnerable Plaque Characteristics
by Sotirios Kotsovilis, Maria Salagianni, Aimilia Varela, Constantinos H. Davos, Ioanna E. Galani and Evangelos Andreakos
Int. J. Mol. Sci. 2024, 25(2), 1355; https://doi.org/10.3390/ijms25021355 - 22 Jan 2024
Viewed by 1137
Abstract
Apolipoprotein E-knockout (Apoe-/-) mice constitute the most widely employed animal model of atherosclerosis. Deletion of Apoe induces profound hypercholesterolemia and promotes the development of atherosclerosis. However, despite its widespread use, the Apoe-/- mouse model remains incompletely characterized, especially at late [...] Read more.
Apolipoprotein E-knockout (Apoe-/-) mice constitute the most widely employed animal model of atherosclerosis. Deletion of Apoe induces profound hypercholesterolemia and promotes the development of atherosclerosis. However, despite its widespread use, the Apoe-/- mouse model remains incompletely characterized, especially at late time points and advanced disease stages. Thus, it is unclear how late atherosclerotic plaques compare to earlier ones in terms of lipid deposition, calcification, macrophage accumulation, smooth muscle cell presence, or plaque necrosis. Additionally, it is unknown how cardiac function and hemodynamic parameters are affected at late disease stages. Here, we used a comprehensive analysis based on histology, fluorescence microscopy, and Doppler ultrasonography to show that in normal chow diet-fed Apoe-/- mice, atherosclerotic lesions at the level of the aortic valve evolve from a more cellular macrophage-rich phenotype at 26 weeks to an acellular, lipid-rich, and more necrotic phenotype at 52 weeks of age, also marked by enhanced lipid deposition and calcification. Coronary artery atherosclerotic lesions are sparse at 26 weeks but ubiquitous and extensive at 52 weeks; yet, left ventricular function was not significantly affected. These findings demonstrate that atherosclerosis in Apoe-/- mice is a highly dynamic process, with atherosclerotic plaques evolving over time. At late disease stages, histopathological characteristics of increased plaque vulnerability predominate in combination with frequent and extensive coronary artery lesions, which nevertheless may not necessarily result in impaired cardiac function. Full article
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28 pages, 5439 KiB  
Article
Initial Molecular Mechanisms of the Pathogenesis of Parkinson’s Disease in a Mouse Neurotoxic Model of the Earliest Preclinical Stage of This Disease
by Anna Kolacheva, Ekaterina Pavlova, Alyona Bannikova, Vsevolod Bogdanov and Michael Ugrumov
Int. J. Mol. Sci. 2024, 25(2), 1354; https://doi.org/10.3390/ijms25021354 - 22 Jan 2024
Cited by 1 | Viewed by 960
Abstract
Studying the initial molecular mechanisms of the pathogenesis of Parkinson’s disease (PD), primarily in the nigrostriatal dopaminergic system, is one of the priorities in neurology. Of particular interest is elucidating these mechanisms in the preclinical stage of PD, which lasts decades before diagnosis [...] Read more.
Studying the initial molecular mechanisms of the pathogenesis of Parkinson’s disease (PD), primarily in the nigrostriatal dopaminergic system, is one of the priorities in neurology. Of particular interest is elucidating these mechanisms in the preclinical stage of PD, which lasts decades before diagnosis and is therefore not available for study in patients. Therefore, our main goal was to study the initial molecular mechanisms of the pathogenesis of PD in the striatum, the key center for dopamine regulation in motor function, in a mouse model of the earliest preclinical stage of PD, from 1 to 24 h after the administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). It was shown that the content of tyrosine hydroxylase (TH), the first enzyme in dopamine synthesis, does not change within 6 h after the administration of MPTP, but decreases after 24 h. In turn, TH activity increases after 1 h, decreases after 3 h, remains at the control level after 6 h, and decreases 24 h after the administration of MPTP. The concentration of dopamine in the striatum gradually decreases after MPTP administration, despite a decrease in its degradation. The identified initial molecular mechanisms of PD pathogenesis are considered as potential targets for the development of preventive neuroprotective treatment. Full article
(This article belongs to the Special Issue Role of Dopamine in Health and Disease: Biological Aspect 2.0)
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18 pages, 2537 KiB  
Article
Differential Ability of Spike Protein of SARS-CoV-2 Variants to Downregulate ACE2
by Yosuke Maeda, Mako Toyoda, Takeo Kuwata, Hiromi Terasawa, Umiru Tokugawa, Kazuaki Monde, Tomohiro Sawa, Takamasa Ueno and Shuzo Matsushita
Int. J. Mol. Sci. 2024, 25(2), 1353; https://doi.org/10.3390/ijms25021353 - 22 Jan 2024
Viewed by 1195
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 19 (COVID-19) and employs angiotensin-converting enzyme 2 (ACE2) as the receptor. Although the expression of ACE2 is crucial for cellular entry, we found that the interaction between ACE2 and [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 19 (COVID-19) and employs angiotensin-converting enzyme 2 (ACE2) as the receptor. Although the expression of ACE2 is crucial for cellular entry, we found that the interaction between ACE2 and the Spike (S) protein in the same cells led to its downregulation through degradation in the lysosomal compartment via the endocytic pathway. Interestingly, the ability of the S protein from previous variants of concern (VOCs) to downregulate ACE2 was variant-dependent and correlated with disease severity. The S protein from the Omicron variant, associated with milder disease, exhibited a lower capacity to downregulate ACE2 than that of the Delta variant, which is linked to a higher risk of hospitalization. Chimeric studies between the S proteins from the Delta and Omicron variants revealed that both the receptor-binding domain (RBD) and the S2 subunit played crucial roles in the reduced ACE2 downregulation activity observed in the Omicron variant. In contrast, three mutations (L452R/P681R/D950N) located in the RBD, S1/S2 cleavage site, and HR1 domain were identified as essential for the higher ACE2 downregulation activity observed in the Delta variant compared to that in the other VOCs. Our results suggested that dysregulation of the renin–angiotensin system due to the ACE2 downregulation activity of the S protein of SARS-CoV-2 may play a key role in the pathogenesis of COVID-19. Full article
(This article belongs to the Special Issue Molecular Mechanisms and Treatment of Infectious Diseases)
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12 pages, 1267 KiB  
Article
The Risk Function of Breast and Ovarian Cancers in the Avrami–Dobrzyński Cellular Phase-Transition Model
by Anna Zawadzka, Beata Brzozowska, Anna Matyjanka, Michał Mikula, Joanna Reszczyńska, Adrianna Tartas and Krzysztof W. Fornalski
Int. J. Mol. Sci. 2024, 25(2), 1352; https://doi.org/10.3390/ijms25021352 - 22 Jan 2024
Viewed by 1135
Abstract
Specifying the role of genetic mutations in cancer development is crucial for effective screening or targeted treatments for people with hereditary cancer predispositions. Our goal here is to find the relationship between a number of cancerogenic mutations and the probability of cancer induction [...] Read more.
Specifying the role of genetic mutations in cancer development is crucial for effective screening or targeted treatments for people with hereditary cancer predispositions. Our goal here is to find the relationship between a number of cancerogenic mutations and the probability of cancer induction over the lifetime of cancer patients. We believe that the Avrami–Dobrzyński biophysical model can be used to describe this mechanism. Therefore, clinical data from breast and ovarian cancer patients were used to validate this model of cancer induction, which is based on a purely physical concept of the phase-transition process with an analogy to the neoplastic transformation. The obtained values of model parameters established using clinical data confirm the hypothesis that the carcinogenic process strongly follows fractal dynamics. We found that the model’s theoretical prediction and population clinical data slightly differed for patients with the age below 30 years old, and that might point to the existence of an ancillary protection mechanism against cancer development. Additionally, we reveal that the existing clinical data predict breast or ovarian cancers onset two years earlier for patients with BRCA1/2 mutations. Full article
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14 pages, 4531 KiB  
Article
Effects of TiO2 Nanotubes and Reduced Graphene Oxide on Streptococcus mutans and Preosteoblastic Cells at an Early Stage
by Min-Kyung Ji, Hyeonji Kim, Geonwoo Jeong, Won-Jae Kim, Je-Hwang Ryu, Hoonsung Cho and Hyun-Pil Lim
Int. J. Mol. Sci. 2024, 25(2), 1351; https://doi.org/10.3390/ijms25021351 - 22 Jan 2024
Viewed by 877
Abstract
The effects of TiO2 nanotube (TNT) and reduced graphene oxide (rGO) deposition onto titanium, which is widely used in dental implants, on Streptococcus mutans (S. mutans) and preosteoblastic cells were evaluated. TNTs were formed through anodic oxidation on pure titanium, [...] Read more.
The effects of TiO2 nanotube (TNT) and reduced graphene oxide (rGO) deposition onto titanium, which is widely used in dental implants, on Streptococcus mutans (S. mutans) and preosteoblastic cells were evaluated. TNTs were formed through anodic oxidation on pure titanium, and rGO was deposited using an atmospheric plasma generator. The specimens used were divided into a control group of titanium specimens and three experimental groups: Group N (specimens with TNT formation), Group G (rGO-deposited specimens), and Group NG (specimens under rGO deposition after TNT formation). Adhesion of S. mutans to the surface was assessed after 24 h of culture using a crystal violet assay, while adhesion and proliferation of MC3T3-E1 cells, a mouse preosteoblastic cell line, were evaluated after 24 and 72 h through a water-soluble tetrazolium salt assay. TNT formation and rGO deposition on titanium decreased S. mutans adhesion (p < 0.05) and increased MC3T3-E1 cell adhesion and proliferation (p < 0.0083). In Group NG, S. mutans adhesion was the lowest (p < 0.05), while MC3T3-E1 cell proliferation was the highest (p < 0.0083). In this study, TNT formation and rGO deposition on a pure titanium surface inhibited the adhesion of S. mutans at an early stage and increased the initial adhesion and proliferation of preosteoblastic cells. Full article
(This article belongs to the Special Issue Recent Process Design and Development Strategies for Dental Materials)
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17 pages, 4648 KiB  
Article
Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick Assay for the Rapid and Sensitive Detection of Pseudo-nitzschia multiseries
by Yuqing Yao, Ningjian Luo, Yujie Zong, Meng Jia, Yichen Rao, Hailong Huang and Haibo Jiang
Int. J. Mol. Sci. 2024, 25(2), 1350; https://doi.org/10.3390/ijms25021350 - 22 Jan 2024
Viewed by 1140
Abstract
The harmful algal bloom (HAB) species Pseudo-nitzschia multiseries is widely distributed worldwide and is known to produce the neurotoxin domoic acid, which harms marine wildlife and humans. Early detection and preventative measures are more critical than late management. However, the major challenge related [...] Read more.
The harmful algal bloom (HAB) species Pseudo-nitzschia multiseries is widely distributed worldwide and is known to produce the neurotoxin domoic acid, which harms marine wildlife and humans. Early detection and preventative measures are more critical than late management. However, the major challenge related to early detection is the accurate and sensitive detection of microalgae present in low abundance. Therefore, developing a sensitive and specific method that can rapidly detect P. multiseries is critical for expediting the monitoring and prediction of HABs. In this study, a novel assay method, recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD), is first developed for the detection of P. multiseries. To obtain the best test results, several important factors that affected the amplification effect were optimized. The internal transcribed spacer sequence of the nuclear ribosomal DNA from P. multiseries was selected as the target region. The results showed that the optimal amplification temperature and time for the recombinase polymerase amplification (RPA) of P. multiseries were 37 °C and 15 min. The RPA products could be visualized directly using the lateral flow dipstick after only 3 min. The RPA-LFD assay sensitivity for detection of recombinant plasmid DNA (1.9 × 100 pg/μL) was 100 times more sensitive than that of RPA, and the RPA-LFD assay sensitivity for detection of genomic DNA (2.0 × 102 pg/μL) was 10 times more sensitive than that of RPA. Its feasibility in the detection of environmental samples was also verified. In conclusion, these results indicated that the RPA-LFD detection of P. multiseries that was established in this study has high efficiency, sensitivity, specificity, and practicability. Management measures made based on information gained from early detection methods may be able to prevent certain blooms. The use of a highly sensitive approach for early warning detection of P. multiseries is essential to alleviate the harmful impacts of HABs on the environment, aquaculture, and human health. Full article
(This article belongs to the Section Biochemistry)
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13 pages, 2019 KiB  
Article
The Effect of S-Allyl L-Cysteine on Retinal Ischemia: The Contributions of MCP-1 and PKM2 in the Underlying Medicinal Properties
by Windsor Wen-Jin Chao, Howard Wen-Haur Chao, Hung-Fu Lee and Hsiao-Ming Chao
Int. J. Mol. Sci. 2024, 25(2), 1349; https://doi.org/10.3390/ijms25021349 - 22 Jan 2024
Viewed by 945
Abstract
Retinal ischemia plays a vital role in vision-threatening retinal ischemic disorders, such as diabetic retinopathy, age-related macular degeneration, glaucoma, etc. The aim of this study was to investigate the effects of S-allyl L-cysteine (SAC) and its associated therapeutic mechanism. Oxidative stress was induced [...] Read more.
Retinal ischemia plays a vital role in vision-threatening retinal ischemic disorders, such as diabetic retinopathy, age-related macular degeneration, glaucoma, etc. The aim of this study was to investigate the effects of S-allyl L-cysteine (SAC) and its associated therapeutic mechanism. Oxidative stress was induced by administration of 500 μM H2O2 for 24 h; SAC demonstrated a dose-dependent neuroprotective effect with significant cell viability effects at 100 μM, and it concurrently downregulated angiogenesis factor PKM2 and inflammatory biomarker MCP-1. In a Wistar rat model of high intraocular pressure (HIOP)-induced retinal ischemia and reperfusion (I/R), post-administration of 100 μM SAC counteracted the ischemic-associated reduction of ERG b-wave amplitude and fluorogold-labeled RGC reduction. This study supports that SAC could protect against retinal ischemia through its anti-oxidative, anti-angiogenic, anti-inflammatory, and neuroprotective properties. Full article
(This article belongs to the Special Issue Molecular Insight into Retinal Diseases)
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19 pages, 4470 KiB  
Review
Recent Advances in Synthesis of Non-Alternating Polyketone Generated by Copolymerization of Carbon Monoxide and Ethylene
by Xieyi Xiao, Handou Zheng, Heng Gao, Zhaocong Cheng, Chunyu Feng, Jiahao Yang and Haiyang Gao
Int. J. Mol. Sci. 2024, 25(2), 1348; https://doi.org/10.3390/ijms25021348 - 22 Jan 2024
Cited by 1 | Viewed by 1039
Abstract
The copolymers of carbon monoxide (CO) and ethylene, namely aliphatic polyketones (PKs), have attracted considerable attention due to their unique property and degradation. Based on the arrangement of the ethylene and carbonyl groups in the polymer chain, PKs can be divided into perfect [...] Read more.
The copolymers of carbon monoxide (CO) and ethylene, namely aliphatic polyketones (PKs), have attracted considerable attention due to their unique property and degradation. Based on the arrangement of the ethylene and carbonyl groups in the polymer chain, PKs can be divided into perfect alternating and non-perfect alternating copolymers. Perfect alternating PKs have been previously reviewed, we herein focus on recent advances in the synthesis of PKs without a perfect alternating structure including non-perfect alternating PKs and PE with in-chain ketones. The chain structure of PKs, catalytic copolymerization mechanism, and non-alternating polymerization catalysts including phosphine–sulfonate Pd, diphosphazane monoxide (PNPO) Pd/Ni, and phosphinophenolate Ni catalysts are comprehensively summarized. This review aims to enlighten the design of ethylene/CO non-alternating polymerization catalysts for the development of new polyketone materials. Full article
(This article belongs to the Special Issue Synthesis of Advanced Polymer Materials 2.0)
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20 pages, 1852 KiB  
Article
SumVg: Total Heritability Explained by All Variants in Genome-Wide Association Studies Based on Summary Statistics with Standard Error Estimates
by Hon-Cheong So, Xiao Xue, Zhijie Ma and Pak-Chung Sham
Int. J. Mol. Sci. 2024, 25(2), 1347; https://doi.org/10.3390/ijms25021347 - 22 Jan 2024
Cited by 1 | Viewed by 884
Abstract
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits/diseases, and a key question is how much heritability could be explained by all single nucleotide polymorphisms (SNPs) in GWAS. One widely used approach that relies on summary statistics [...] Read more.
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits/diseases, and a key question is how much heritability could be explained by all single nucleotide polymorphisms (SNPs) in GWAS. One widely used approach that relies on summary statistics only is linkage disequilibrium score regression (LDSC); however, this approach requires certain assumptions about the effects of SNPs (e.g., all SNPs contribute to heritability and each SNP contributes equal variance). More flexible modeling methods may be useful. We previously developed an approach recovering the “true” effect sizes from a set of observed z-statistics with an empirical Bayes approach, using only summary statistics. However, methods for standard error (SE) estimation are not available yet, limiting the interpretation of our results and the applicability of the approach. In this study, we developed several resampling-based approaches to estimate the SE of SNP-based heritability, including two jackknife and three parametric bootstrap methods. The resampling procedures are performed at the SNP level as it is most common to estimate heritability from GWAS summary statistics alone. Simulations showed that the delete-d-jackknife and parametric bootstrap approaches provide good estimates of the SE. In particular, the parametric bootstrap approaches yield the lowest root-mean-squared-error (RMSE) of the true SE. We also explored various methods for constructing confidence intervals (CIs). In addition, we applied our method to estimate the SNP-based heritability of 12 immune-related traits (levels of cytokines and growth factors) to shed light on their genetic architecture. We also implemented the methods to compute the sum of heritability explained and the corresponding SE in an R package SumVg. In conclusion, SumVg may provide a useful alternative tool for calculating SNP heritability and estimating SE/CI, which does not rely on distributional assumptions of SNP effects. Full article
(This article belongs to the Collection Feature Papers in “Molecular Biology”)
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24 pages, 5040 KiB  
Article
Genome-Wide and Expression Pattern Analysis of the DVL Gene Family Reveals GhM_A05G1032 Is Involved in Fuzz Development in G. hirsutum
by Yang Jiao, Fuxiang Zhao, Shiwei Geng, Shengmei Li, Zhanlian Su, Quanjia Chen, Yu Yu and Yanying Qu
Int. J. Mol. Sci. 2024, 25(2), 1346; https://doi.org/10.3390/ijms25021346 - 22 Jan 2024
Viewed by 910
Abstract
DVL is one of the small polypeptides which plays an important role in regulating plant growth and development, tissue differentiation, and organ formation in the process of coping with stress conditions. So far, there has been no comprehensive analysis of the expression profile [...] Read more.
DVL is one of the small polypeptides which plays an important role in regulating plant growth and development, tissue differentiation, and organ formation in the process of coping with stress conditions. So far, there has been no comprehensive analysis of the expression profile and function of the cotton DVL gene. According to previous studies, a candidate gene related to the development of fuzz was screened, belonging to the DVL family, and was related to the development of trichomes in Arabidopsis thaliana. However, the comprehensive identification and systematic analysis of DVL in cotton have not been conducted. In this study, we employed bioinformatics approaches to conduct a novel analysis of the structural characteristics, phylogenetic tree, gene structure, expression pattern, evolutionary relationship, and selective pressure of the DVL gene family members in four cotton species. A total of 117 DVL genes were identified, including 39 members in G. hirsutum. Based on the phylogenetic analysis, the DVL protein sequences were categorized into five distinct subfamilies. Additionally, we successfully mapped these genes onto chromosomes and visually represented their gene structure information. Furthermore, we predicted the presence of cis-acting elements in DVL genes in G. hirsutum and characterized the repeat types of DVL genes in the four cotton species. Moreover, we computed the Ka/Ks ratio of homologous genes across the four cotton species and elucidated the selective pressure acting on these homologous genes. In addition, we described the expression patterns of the DVL gene family using RNA-seq data, verified the correlation between GhMDVL3 and fuzz development through VIGS technology, and found that some DVL genes may be involved in resistance to biotic and abiotic stress conditions through qRT-PCR technology. Furthermore, a potential interaction network was constructed by WGCNA, and our findings demonstrated the potential of GhM_A05G1032 to interact with numerous genes, thereby playing a crucial role in regulating fuzz development. This research significantly contributed to the comprehension of DVL genes in upland cotton, thereby establishing a solid basis for future investigations into the functional aspects of DVL genes in cotton. Full article
(This article belongs to the Section Molecular Plant Sciences)
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20 pages, 7372 KiB  
Article
Inhibition of Autophagy Aggravates Arachis hypogaea L. Skin Extracts-Induced Apoptosis in Cancer Cells
by Chia-Hung Tsai, Hui-Chi Huang, Kuan-Jung Lin, Jui-Ming Liu, Guan-Lin Chen, Yi-Hsien Yeh, Te-Ling Lu, Hsiang-Wen Lin, Meng-Tien Lu and Po-Chen Chu
Int. J. Mol. Sci. 2024, 25(2), 1345; https://doi.org/10.3390/ijms25021345 - 22 Jan 2024
Viewed by 1141
Abstract
The skin of Arachis hypogaea L. (peanut or groundnut) is a rich source of polyphenols, which have been shown to exhibit a wider spectrum of noteworthy biological activities, including anticancer effects. However, the anticancer activity of peanut skin extracts against melanoma and colorectal [...] Read more.
The skin of Arachis hypogaea L. (peanut or groundnut) is a rich source of polyphenols, which have been shown to exhibit a wider spectrum of noteworthy biological activities, including anticancer effects. However, the anticancer activity of peanut skin extracts against melanoma and colorectal cancer (CRC) cells remains elusive. In this study, we systematically investigated the cytotoxic, antiproliferative, pro-apoptotic, and anti-migration effects of peanut skin ethanolic extract and its fractions on melanoma and CRC cells. Cell viability results showed that the ethyl acetate fraction (AHE) of peanut skin ethanolic crude extract and one of the methanolic fractions (AHE-2) from ethyl acetate extraction exhibited the highest cytotoxicity against melanoma and CRC cells but not in nonmalignant human skin fibroblasts. AHE and AHE-2 effectively modulated the cell cycle-related proteins, including the suppression of cyclin-dependent kinase 4 (CDK4), cyclin-dependent kinase 6 (CDK6), phosphorylation of Retinoblastoma (p-Rb), E2F1, Cyclin A, and activation of tumor suppressor p53, which was associated with cell cycle arrest and paralleled their antiproliferative efficacies. AHE and AHE-2 could also induce caspase-dependent apoptosis and inhibit migration activities in melanoma and CRC cells. Moreover, it is noteworthy that autophagy, manifested by microtubule-associated protein light chain 3B (LC3B) conversion and the aggregation of GFP-LC3, was detected after AHE and AHE-2 treatment and provided protective responses in cancer cells. Significantly, inhibition of autophagy enhanced AHE- and AHE-2-induced cytotoxicity and apoptosis. Together, these findings not only elucidate the anticancer potential of peanut skin extracts against melanoma and CRC cells but also provide a new insight into autophagy implicated in peanut skin extracts-induced cancer cell death. Full article
(This article belongs to the Collection Feature Papers in Molecular Oncology)
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29 pages, 1205 KiB  
Review
Phospholipase C Zeta in Human Spermatozoa: A Systematic Review on Current Development and Clinical Application
by Alessandra Parrella, Llanos Medrano, Jon Aizpurua and María José Gómez-Torres
Int. J. Mol. Sci. 2024, 25(2), 1344; https://doi.org/10.3390/ijms25021344 - 22 Jan 2024
Viewed by 1148
Abstract
During fertilization, the fusion of the spermatozoa with the oocytes causes the release of calcium from the oocyte endoplasmatic reticulum. This, in turn, triggers a series of calcium ion (Ca2+) oscillations, a process known as oocyte activation. The sperm-specific factor responsible [...] Read more.
During fertilization, the fusion of the spermatozoa with the oocytes causes the release of calcium from the oocyte endoplasmatic reticulum. This, in turn, triggers a series of calcium ion (Ca2+) oscillations, a process known as oocyte activation. The sperm-specific factor responsible for oocyte activation is phospholipase C zeta (PLCζ). Men undergoing intracytoplasmic sperm injection (ICSI) with their spermatozoa lacking PLCζ are incapable of generating Ca2+ oscillation, leading to fertilization failure. The immunofluorescence assay is the most used technique to assess the expression and localization of PLCζ and to diagnose patients with reduced/absent ability to activate the oocytes. In these patients, the use of assisted oocyte activation (AOA) technique can help to yield successful ICSI results and shorten the time of pregnancy. However, the production of a stable PLCζ recombinant protein represents a new powerful therapeutic approach to treating individuals with this condition. We aim to conduct a systematic review focusing on the expression, level, and localization of PLCζ, discussing the novel genetic mutation associated with its impairment. In addition, we highlight the benefits of AOA, looking at new and less invasive methods to diagnose and treat cases with PLCζ dysfunction. Full article
(This article belongs to the Special Issue A Molecular Perspective on Reproductive Health)
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19 pages, 5467 KiB  
Article
Insights into the Hormone-Regulating Mechanism of Adventitious Root Formation in Softwood Cuttings of Cyclocarya paliurus and Optimization of the Hormone-Based Formula for Promoting Rooting
by Yuan Tian, Wanxia Yang, Shiying Wan and Shengzuo Fang
Int. J. Mol. Sci. 2024, 25(2), 1343; https://doi.org/10.3390/ijms25021343 - 22 Jan 2024
Viewed by 820
Abstract
Adventitious root (AR) formation is vital for successful cutting propagation in plants, while the dynamic regulation of phytohormones is viewed as one of the most important factors affecting AR formation. Cyclocarya paliurus, a hard-to-root plant, is faced with the bottleneck of cloning [...] Read more.
Adventitious root (AR) formation is vital for successful cutting propagation in plants, while the dynamic regulation of phytohormones is viewed as one of the most important factors affecting AR formation. Cyclocarya paliurus, a hard-to-root plant, is faced with the bottleneck of cloning its superior varieties in practice. In this study, ten treatments were designed to figure out the best hormone-based formula for promoting AR formation in softwood cuttings and explore their hormone-regulating mechanisms. Both the rooting process and the rooting parameters of the softwood cuttings were significantly affected by different hormone-based formulas (p < 0.05), while the greatest rooting rate (93%) and root quality index were achieved in the H3 formula (SR3:IR3 = 1:1). Significant differences in the measured phytohormone concentrations, as well as in their ratios, were detected among the cuttings sampled at various AR formation stages (p < 0.05), whereas the dynamics for each phytohormone varied greatly during AR formation. The transcriptome analysis showed 12,028 differentially expressed genes (DEGs) identified during the rooting process of C. paliurus cuttings, while the KEGG enrichment analysis indicated that a total of 20 KEGG terms were significantly enriched in all the comparison samples, with 253 DEGs detected in signal transduction. Furthermore, 19 genes with vital functions in regulating the hormone signaling pathway were identified by means of a WGCNA analysis. Our results not only optimize a hormone-based formula for improving the rooting of C. paliurus cuttings but also provide an insight into the hormonal regulatory network during AR formation in softwood C. paliurus cuttings. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics)
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24 pages, 4717 KiB  
Review
8-Oxoadenine: A «New» Player of the Oxidative Stress in Mammals?
by Alexander A. Kruchinin, Polina N. Kamzeeva, Dmitry O. Zharkov, Andrey V. Aralov and Alena V. Makarova
Int. J. Mol. Sci. 2024, 25(2), 1342; https://doi.org/10.3390/ijms25021342 - 22 Jan 2024
Viewed by 1211
Abstract
Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic [...] Read more.
Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic studies have demonstrated the mutagenic potential of 8-oxoA in eukaryotic cells, very little biochemical and bioinformatics data about the mechanism of 8-oxoA-induced mutagenesis are available. In this review, we discuss dual coding properties of 8-oxoA, summarize historical and recent genotoxicity and biochemical studies, and address the main protective cellular mechanisms of response to 8-oxoA. We also discuss the available structural data for 8-oxoA bypass by different DNA polymerases as well as the mechanisms of 8-oxoA recognition by DNA repair enzymes. Full article
(This article belongs to the Special Issue Molecular Mechanism of DNA Replication and Repair, 2nd Edition )
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24 pages, 11403 KiB  
Article
Genome-Wide Identification and Expression Profiling of Potato (Solanum tuberosum L.) Universal Stress Proteins Reveal Essential Roles in Mechanical Damage and Deoxynivalenol Stress
by Tianshuai Qi, Fumeng He, Xinqi Zhang, Jiaqi Wang, Zengli Zhang, Heran Jiang, Biao Zhao, Chong Du, Yunzhu Che, Xu Feng, Yingnan Wang and Fenglan Li
Int. J. Mol. Sci. 2024, 25(2), 1341; https://doi.org/10.3390/ijms25021341 - 22 Jan 2024
Viewed by 1330
Abstract
Universal stress proteins (USPs) play an important regulatory role in responses to abiotic stress. Most of the research related to USPs so far has been conducted on plant models such as Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa L.), and cotton [...] Read more.
Universal stress proteins (USPs) play an important regulatory role in responses to abiotic stress. Most of the research related to USPs so far has been conducted on plant models such as Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa L.), and cotton (Gossypium hirsutum L.). The potato (Solanum tuberosum L.) is one of the four major food crops in the world. The potato is susceptible to mechanical damage and infection by pathogenic fungi during transport and storage. Deoxynivalenol (DON) released by Fusarium can seriously degrade the quality of potatoes. As a result, it is of great significance to study the expression pattern of the potato StUSP gene family under abiotic stress conditions. In this study, a total of 108 USP genes were identified from the genome of the Atlantic potato, divided into four subgroups. Based on their genetic structure, the physical and chemical properties of their proteins and other aspects of their biological characteristics are comprehensively analyzed. Collinear analysis showed that the homologous genes of StUSPs and four other representative species (Solanum lycopersicum, Arabidopsis, Oryza sativa L., and Nicotiana attenuata) were highly conserved. The cis-regulatory elements of the StUSPs promoter are involved in plant hormones, environmental stress, mechanical damage, and light response. RNA-seq analysis showed that there are differences in the expression patterns of members of each subgroup under different abiotic stresses. A Weighted Gene Coexpression Network Analysis (WGCNA) of the central gene showed that the differential coexpression gene is mainly involved in the plant–pathogen response process, plant hormone signal transduction, and the biosynthesis process of secondary metabolites. Through qRT-PCR analysis, it was confirmed that StUSP13, StUSP14, StUSP15, and StUSP41 may be important candidate genes involved in the response to adversity stress in potatoes. The results of this study provide a basis for further research on the functional analysis of StUSPs in the response of potatoes to adversity stress. Full article
(This article belongs to the Special Issue Advances in Research for Solanaceae Breeding and Genetics)
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12 pages, 765 KiB  
Review
Disinhibition Is an Essential Network Motif Coordinated by GABA Levels and GABA B Receptors
by Nelson Villalobos
Int. J. Mol. Sci. 2024, 25(2), 1340; https://doi.org/10.3390/ijms25021340 - 22 Jan 2024
Viewed by 1055
Abstract
Network dynamics are crucial for action and sensation. Changes in synaptic physiology lead to the reorganization of local microcircuits. Consequently, the functional state of the network impacts the output signal depending on the firing patterns of its units. Networks exhibit steady states in [...] Read more.
Network dynamics are crucial for action and sensation. Changes in synaptic physiology lead to the reorganization of local microcircuits. Consequently, the functional state of the network impacts the output signal depending on the firing patterns of its units. Networks exhibit steady states in which neurons show various activities, producing many networks with diverse properties. Transitions between network states determine the output signal generated and its functional results. The temporal dynamics of excitation/inhibition allow a shift between states in an operational network. Therefore, a process capable of modulating the dynamics of excitation/inhibition may be functionally important. This process is known as disinhibition. In this review, we describe the effect of GABA levels and GABAB receptors on tonic inhibition, which causes changes (due to disinhibition) in network dynamics, leading to synchronous functional oscillations. Full article
(This article belongs to the Collection Feature Papers in Molecular Neurobiology)
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22 pages, 2834 KiB  
Article
Cyclobutanone Inhibitors of Diaminopimelate Desuccinylase (DapE) as Potential New Antibiotics
by Thahani S. Habeeb Mohammad, Emma H. Kelley, Cory T. Reidl, Katherine Konczak, Megan Beulke, Janielle Javier, Kenneth W. Olsen and Daniel P. Becker
Int. J. Mol. Sci. 2024, 25(2), 1339; https://doi.org/10.3390/ijms25021339 - 22 Jan 2024
Viewed by 871
Abstract
Based on our previous success in using cyclobutanone derivatives as enzyme inhibitors, we have designed and prepared a 37-member library of α-aminocyclobutanone amides and sulfonamides, screened for inhibition of the bacterial enzyme diaminopimelate desuccinylase (DapE), which is a promising antibiotic target, and identified [...] Read more.
Based on our previous success in using cyclobutanone derivatives as enzyme inhibitors, we have designed and prepared a 37-member library of α-aminocyclobutanone amides and sulfonamides, screened for inhibition of the bacterial enzyme diaminopimelate desuccinylase (DapE), which is a promising antibiotic target, and identified several inhibitors with micromolar inhibitory potency. Molecular docking suggests binding of the deprotonated hydrate of the strained cyclobutanone, and thermal shift analysis with the most potent inhibitor (3y, IC50 = 23.1 µM) enabled determination of a Ki value of 10.2 +/− 0.26 µM and observed two separate Tm values for H. influenzae DapE (HiDapE). Full article
(This article belongs to the Special Issue Rational Design and Synthesis of Bioactive Molecules)
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16 pages, 868 KiB  
Article
The Impact of the Mediterranean Diet and Lifestyle Intervention on Lipoprotein Subclass Profiles among Metabolic Syndrome Patients: Findings of a Randomized Controlled Trial
by Beatriz Candás-Estébanez, Bárbara Fernández-Cidón, Emili Corbella, Cristian Tebé, Marta Fanlo-Maresma, Virginia Esteve-Luque, Jordi Salas-Salvadó, Montserrat Fitó, Antoni Riera-Mestre, Emilio Ros and Xavier Pintó
Int. J. Mol. Sci. 2024, 25(2), 1338; https://doi.org/10.3390/ijms25021338 - 22 Jan 2024
Cited by 1 | Viewed by 1865
Abstract
Metabolic syndrome (MetS) is associated with alterations of lipoprotein structure and function that can be characterized with advanced lipoprotein testing (ADLT). The effect of the Mediterranean diet (MedDiet) and weight loss on the lipoprotein subclass profile has been scarcely studied. Within the PREDIMED-Plus [...] Read more.
Metabolic syndrome (MetS) is associated with alterations of lipoprotein structure and function that can be characterized with advanced lipoprotein testing (ADLT). The effect of the Mediterranean diet (MedDiet) and weight loss on the lipoprotein subclass profile has been scarcely studied. Within the PREDIMED-Plus randomized controlled trial, a sub-study conducted at Bellvitge Hospital recruiting center evaluated the effects of a weight loss program based on an energy-reduced MedDiet (er-MedDiet) and physical activity (PA) promotion (intervention group) compared with energy-unrestricted MedDiet recommendations (control group) on ADLT-assessed lipoprotein subclasses. 202 patients with MetS (n = 107, intervention; n = 95, control) were included. Lipid profiles were determined, and ADLT was performed at baseline, 6, and 12 months. Linear mixed models were used to assess the effects of intervention on lipoprotein profiles. Compared to the control diet, at 12 months, the er-MedDiet+PA resulted in a significant additional 4.2 kg of body weight loss, a decrease in body mass index by 1.4 kg/m2, reduction in waist circumference by 2.2 cm, decreased triglycerides, LDL-cholesterol and non-HDL-cholesterol, and increased HDL-cholesterol. In er-MedDiet+PA participants, ADLT revealed a decrease in small dense-LDL-cholesterol (sd-LDL-C), intermediate-density lipoproteins, VLDL-triglyceride, and HDL-Triglyceride, and an increase in large LDL and large VLDL particles. In conclusion, compared to an ad libitum MedDiet (control group), er-MedDiet+PA decreased plasma triglycerides and the triglyceride content in HDL and VLDL particles, decreased sd-LDL-C, and increased large LDL particles, indicating beneficial changes against cardiovascular disease. Full article
(This article belongs to the Special Issue Apolipoproteins and Lipoproteins in Health and Disease 2.0)
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15 pages, 688 KiB  
Review
The Efficacy and Safety of Transvaginal Ethanol Sclerotherapy in the Treatment of Endometrial Cysts—A Systematic Review
by Karolina Frankowska, Izabela Dymanowska-Dyjak, Monika Abramiuk and Grzegorz Polak
Int. J. Mol. Sci. 2024, 25(2), 1337; https://doi.org/10.3390/ijms25021337 - 22 Jan 2024
Cited by 2 | Viewed by 1494
Abstract
Endometriosis, as a chronic disorder that is a source of severe pain ailments and infertility, requires a comprehensive therapeutic approach. Sclerotherapy, consisting of the administration of sclerosing agents into the cyst, is a constantly evolving minimally invasive treatment method for this disease. Hence, [...] Read more.
Endometriosis, as a chronic disorder that is a source of severe pain ailments and infertility, requires a comprehensive therapeutic approach. Sclerotherapy, consisting of the administration of sclerosing agents into the cyst, is a constantly evolving minimally invasive treatment method for this disease. Hence, the main objective of this systematic review was to evaluate the impact of its most often used variant, transvaginal ethanol sclerotherapy, on endometriosis-related symptoms, endometrial cyst recurrence rate, ovarian reserve, assisted reproductive technology (ART) outcomes, and pregnancy outcomes, as well as to assess potential complications resulting from this treatment. This systematic review was undertaken using PubMed, Scopus, Web of Science, and Cochrane Library databases on 24 November 2023. The risk of bias in included studies was assessed with the use of the Newcastle–Ottawa scale (NOS) and the revised Cochrane risk of bias 2.0 tool for randomized controlled trials. From the 1141 records obtained from all databases, 16 studies have been included in this review. The use of ethanol sclerotherapy was characterized by a low rate of post-procedural complications. The recurrence rate of endometrial cysts after the procedure depended on the ethanol instillation time within the cyst. Although ethanol sclerotherapy had negligible influence on ovarian reserves when compared to laparoscopic cystectomy, the effects of both these methods on pregnancy outcomes were comparable. This review identifies that sclerotherapy is safe, provides significant relief of symptoms, and does not impair the reproductive potential of the patients. Full article
(This article belongs to the Special Issue Endometriosis: From Molecular Basis to Therapy)
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15 pages, 2114 KiB  
Article
SlSERK3B Promotes Tomato Seedling Growth and Development by Regulating Photosynthetic Capacity
by Zhiqi Ding, Yandong Yao, Kangding Yao, Xuemei Hou, Zhuohui Zhang, Yi Huang, Chunlei Wang and Weibiao Liao
Int. J. Mol. Sci. 2024, 25(2), 1336; https://doi.org/10.3390/ijms25021336 - 22 Jan 2024
Viewed by 854
Abstract
Brassinosteroids (BRs) are a group of polyhydroxylated steroids for plant growth and development, regulating numerous physiological and biochemical processes and participating in multi-pathway signaling in plants. 24-Epibrassinolide (EBR) is the most commonly used BR for the investigation of the effects of exogenous steroidal [...] Read more.
Brassinosteroids (BRs) are a group of polyhydroxylated steroids for plant growth and development, regulating numerous physiological and biochemical processes and participating in multi-pathway signaling in plants. 24-Epibrassinolide (EBR) is the most commonly used BR for the investigation of the effects of exogenous steroidal phytohormones on plant physiology. Although SlSERK3B is considered a gene involved in the brassinosteroid (BR) signaling pathway, its specific role in plant growth and development has not been reported in detail. In this study, tomato (Solanum lycopersicum L.) seedlings treated with 0.05 μmol L−1 EBR showed a significant increase in plant height, stem diameter, and fresh weight, demonstrating that BR promotes the growth of tomato seedlings. EBR treatment increased the expression of the BR receptor gene SlBRI1, the co-receptor gene SlSERK3A and its homologs SlSERK3B, and SlBZR1. The SlSERK3B gene was silenced by TRV-mediated virus-induced gene silencing (VIGS) technology. The results showed that both brassinolide (BL) content and BR synthesis genes were significantly up-regulated in TRV-SlSERK3B-infected seedlings compared to the control seedlings. In contrast, plant height, stem diameter, fresh weight, leaf area and total root length were significantly reduced in silenced plants. These results suggest that silencing SlSERK3B may affect BR synthesis and signaling, thereby affecting the growth of tomato seedlings. Furthermore, the photosynthetic capacity of TRV-SlSERK3B-infected tomato seedlings was reduced, accompanied by decreased photosynthetic pigment content chlorophyll fluorescence, and photosynthesis parameters. The expression levels of chlorophyll-degrading genes were significantly up-regulated, and carotenoid-synthesising genes were significantly down-regulated in TRV-SlSERK3B-infected seedlings. In conclusion, silencing of SlSERK3B inhibited BR signaling and reduced photosynthesis in tomato seedlings, and this correlation suggests that SlSERK3B may be related to BR signaling and photosynthesis enhancement. Full article
(This article belongs to the Special Issue Brassinosteroid (BR) Signal Transduction in Plants)
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34 pages, 4213 KiB  
Review
Advances in Mass Spectrometry of Gangliosides Expressed in Brain Cancers
by Maria Roxana Biricioiu, Mirela Sarbu, Raluca Ica, Željka Vukelić, Svjetlana Kalanj-Bognar and Alina D. Zamfir
Int. J. Mol. Sci. 2024, 25(2), 1335; https://doi.org/10.3390/ijms25021335 - 22 Jan 2024
Cited by 1 | Viewed by 1296
Abstract
Gangliosides are highly abundant in the human brain where they are involved in major biological events. In brain cancers, alterations of ganglioside pattern occur, some of which being correlated with neoplastic transformation, while others with tumor proliferation. Of all techniques, mass spectrometry (MS) [...] Read more.
Gangliosides are highly abundant in the human brain where they are involved in major biological events. In brain cancers, alterations of ganglioside pattern occur, some of which being correlated with neoplastic transformation, while others with tumor proliferation. Of all techniques, mass spectrometry (MS) has proven to be one of the most effective in gangliosidomics, due to its ability to characterize heterogeneous mixtures and discover species with biomarker value. This review highlights the most significant achievements of MS in the analysis of gangliosides in human brain cancers. The first part presents the latest state of MS development in the discovery of ganglioside markers in primary brain tumors, with a particular emphasis on the ion mobility separation (IMS) MS and its contribution to the elucidation of the gangliosidome associated with aggressive tumors. The second part is focused on MS of gangliosides in brain metastases, highlighting the ability of matrix-assisted laser desorption/ionization (MALDI)-MS, microfluidics-MS and tandem MS to decipher and structurally characterize species involved in the metastatic process. In the end, several conclusions and perspectives are presented, among which the need for development of reliable software and a user-friendly structural database as a search platform in brain tumor diagnostics. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Biology in Romania)
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13 pages, 871 KiB  
Review
The Potential of Korean Bioactive Substances and Functional Foods for Immune Enhancement
by Mi Eun Kim and Jun Sik Lee
Int. J. Mol. Sci. 2024, 25(2), 1334; https://doi.org/10.3390/ijms25021334 - 22 Jan 2024
Cited by 1 | Viewed by 1094
Abstract
In this review, we explore the immunomodulatory properties of Korean foods, focusing on ginseng and fermented foods. One notable example is Korean red ginseng, known for its immune system-regulating effects attributed to the active ingredient, ginsenoside. Ginsenoside stimulates immune cells, enhancing immune function [...] Read more.
In this review, we explore the immunomodulatory properties of Korean foods, focusing on ginseng and fermented foods. One notable example is Korean red ginseng, known for its immune system-regulating effects attributed to the active ingredient, ginsenoside. Ginsenoside stimulates immune cells, enhancing immune function and suppressing inflammatory responses. With a long history, Korean red ginseng has demonstrated therapeutic effects against various diseases. Additionally, Korean fermented foods like kimchi, doenjang, chongkukjang, gochujang, vinegar, and jangajji provide diverse nutrients and bioactive substances, contributing to immune system enhancement. Moreover, traditional Korean natural herbs such as Cirsium setidens Nakai, Gomchwi, Beak-Jak-Yak, etc. possess immune-boosting properties and are used in various Korean foods. By incorporating these foods into one’s diet, one can strengthen their immune system, positively impacting their overall health and well-being. Full article
(This article belongs to the Special Issue Latest Review Papers in Bioactives and Nutraceuticals 2023)
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16 pages, 3110 KiB  
Article
Circulating Monocyte Chemoattractant Protein-1 (MCP-1) in Patients with Primary Biliary Cholangitis
by Alicja Bauer and Tomasz Rawa
Int. J. Mol. Sci. 2024, 25(2), 1333; https://doi.org/10.3390/ijms25021333 - 22 Jan 2024
Viewed by 1154
Abstract
Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease that leads to the destruction of the intrahepatic bile ducts. While the inflammatory process can be mediated by monocyte chemotactic protein-1 (MCP-1), the importance of circulating MCP-1 as a biomarker is unclear. Our [...] Read more.
Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease that leads to the destruction of the intrahepatic bile ducts. While the inflammatory process can be mediated by monocyte chemotactic protein-1 (MCP-1), the importance of circulating MCP-1 as a biomarker is unclear. Our aim was to assess the diagnostic significance of the serum concentrations of MCP-1 in PBC patients. We compared circulating MCP-1 with biochemical, immunological and histological parameters. Serum samples were collected from 120 PBC patients, 60 pathologic controls and 30 healthy donors. MCP-1 levels were determined by using commercial enzyme-linked immunosorbent assay (ELISA). Elevated serum MCP-1 levels were detected in 66% of PBC patients with a specificity of 97%. Significantly higher levels of MCP-1 protein were found in the sera of patients with PBC than in the group of healthy individuals—410.2 pg/mL vs. 176.0 pg/mL, p < 0.01). Patients with higher concentrations of alkaline phosphatase also had higher levels of MCP-1 (r = 0.4, p < 0.01). In accordance with Ludwig’s classification, a positive correlation of serum MCP-1 concentration with the degree of fibrosis was observed, OR = 6.1, p = 0.0003. We compared the MCP-1 with procollagen type III, hyaluronic acid (HA), FIB-4 index, APRI and collagen type IV when predicting the advance of liver fibrosis. Circulating MCP-1 is better correlated with liver fibrosis and is also associated with the occurrence of specific antimitochondrial autoantibodies and specific anti-nuclear autoantibodies—anti-gp210. MPC-1 can be considered to be a tool for diagnosing the degree of fibrosis in PBC, and combinations of MCP-1 and other specific biomarkers could support the diagnosis of PBC. Full article
(This article belongs to the Special Issue Advances in Molecular Research on Autoimmune Diseases)
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19 pages, 6709 KiB  
Article
Functional Characterization of CsSWEET5a, a Cucumber Hexose Transporter That Mediates the Hexose Supply for Pollen Development and Rescues Male Fertility in Arabidopsis
by Liping Hu, Jiaxing Tian, Feng Zhang, Shuhui Song, Bing Cheng, Guangmin Liu, Huan Liu, Xuezhi Zhao, Yaqin Wang and Hongju He
Int. J. Mol. Sci. 2024, 25(2), 1332; https://doi.org/10.3390/ijms25021332 - 22 Jan 2024
Viewed by 969
Abstract
Pollen cells require large amounts of sugars from the anther to support their development, which is critical for plant sexual reproduction and crop yield. Sugars Will Eventually be Exported Transporters (SWEETs) have been shown to play an important role in the apoplasmic unloading [...] Read more.
Pollen cells require large amounts of sugars from the anther to support their development, which is critical for plant sexual reproduction and crop yield. Sugars Will Eventually be Exported Transporters (SWEETs) have been shown to play an important role in the apoplasmic unloading of sugars from anther tissues into symplasmically isolated developing pollen cells and thereby affect the sugar supply for pollen development. However, among the 17 CsSWEET genes identified in the cucumber (Cucumis sativus L.) genome, the CsSWEET gene involved in this process has not been identified. Here, a member of the SWEET gene family, CsSWEET5a, was identified and characterized. The quantitative real-time PCR and β-glucuronidase expression analysis revealed that CsSWEET5a is highly expressed in the anthers and pollen cells of male cucumber flowers from the microsporocyte stage (stage 9) to the mature pollen stage (stage 12). Its subcellular localization indicated that the CsSWEET5a protein is localized to the plasma membrane. The heterologous expression assays in yeast demonstrated that CsSWEET5a encodes a hexose transporter that can complement both glucose and fructose transport deficiencies. CsSWEET5a can significantly rescue the pollen viability and fertility of atsweet8 mutant Arabidopsis plants. The possible role of CsSWEET5a in supplying hexose to developing pollen cells via the apoplast is also discussed. Full article
(This article belongs to the Section Molecular Plant Sciences)
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