International Journal of Molecular Sciences

16 pages, 13546 KiB

Open AccessArticle

Secretome Analyses Identify FKBP4 as a GBA1-Associated Protein in CSF and iPS Cells from Parkinson’s Disease Patients with GBA1 Mutations

by Rika Kojima, Wojciech Paslawski, Guochang Lyu, Ernest Arenas, Xiaoqun Zhang and Per Svenningsson

Int. J. Mol. Sci. 2024, 25(1), 683; https://doi.org/10.3390/ijms25010683 - 4 Jan 2024

Cited by 1 | Viewed by 4146

Abstract

Mutations in the GBA1 gene increase the risk of developing Parkinson’s disease (PD). However, most carriers of GBA1 mutations do not develop PD throughout their lives. The mechanisms of how GBA1 mutations contribute to PD pathogenesis remain unclear. Cerebrospinal fluid (CSF) is used [...] Read more.

Mutations in the GBA1 gene increase the risk of developing Parkinson’s disease (PD). However, most carriers of GBA1 mutations do not develop PD throughout their lives. The mechanisms of how GBA1 mutations contribute to PD pathogenesis remain unclear. Cerebrospinal fluid (CSF) is used for detecting pathological conditions of diseases, providing insights into the molecular mechanisms underlying neurodegenerative disorders. In this study, we utilized the proximity extension assay to examine the levels of metabolism-linked protein in the CSF from 17 PD patients carrying GBA1 mutations (GBA1-PD) and 17 idiopathic PD (iPD). The analysis of CSF secretome in GBA1-PD identified 11 significantly altered proteins, namely FKBP4, THOP1, GLRX, TXNDC5, GAL, SEMA3F, CRKL, APLP1, LRP11, CD164, and NPTXR. To investigate GBA1-associated CSF changes attributed to specific neuronal subtypes responsible for PD, we analyzed the cell culture supernatant from GBA1-PD-induced pluripotent stem cell (iPSC)-derived midbrain dopaminergic (mDA) neurons. The secretome analysis of GBA1-PD iPSC-derived mDA neurons revealed that five differently regulated proteins overlapped with those identified in the CSF analysis: FKBP4, THOP1, GLRX, GAL, and CRKL. Reduced intracellular level of the top hit, FKPB4, was confirmed via Western Blot. In conclusion, our findings identify significantly altered CSF GBA1-PD-associated proteins with FKPB4 being firmly attributed to mDA neurons. Full article

(This article belongs to the Special Issue Translational and Molecular Research of Neurological Disorders)

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17 pages, 8974 KiB

Open AccessArticle

Porcine Kidney Organoids Derived from Naïve-like Embryonic Stem Cells

by Meishuang Li, Xiyun Guo, Linxin Cheng, Hong Zhang, Meng Zhou, Manling Zhang, Zhibao Yin, Tianxu Guo, Lihua Zhao, Han Liu, Xiubin Liang and Rongfeng Li

Int. J. Mol. Sci. 2024, 25(1), 682; https://doi.org/10.3390/ijms25010682 - 4 Jan 2024

Cited by 2 | Viewed by 2669

Abstract

The scarcity of donor kidneys greatly impacts the survival of patients with end-stage renal failure. Pigs are increasingly becoming potential organ donors but are limited by immunological rejection. Based on the human kidney organoid already established with the CHIR99021 and FGF9 induction strategy, [...] Read more.

The scarcity of donor kidneys greatly impacts the survival of patients with end-stage renal failure. Pigs are increasingly becoming potential organ donors but are limited by immunological rejection. Based on the human kidney organoid already established with the CHIR99021 and FGF9 induction strategy, we generated porcine kidney organoids from porcine naïve-like ESCs (nESCs). The derived porcine organoids had a tubule-like constructure and matrix components. The porcine organoids expressed renal markers including AQP1 (proximal tubule), WT1 and PODO (podocyte), and CD31 (vascular endothelial cells). These results imply that the organoids had developed the majority of the renal cell types and structures, including glomeruli and proximal tubules. The porcine organoids were also identified to have a dextran absorptive function. Importantly, porcine organoids have a certain abundance of vascular endothelial cells, which are the basis for investigating immune rejection. The derived porcine organoids might serve as materials for immunosuppressor screening for xenotransplantation. Full article

(This article belongs to the Special Issue Embryonic Development and Differentiation)

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20 pages, 6063 KiB

Open AccessArticle

Tailoring the Structural and Optical Properties of Cerium Oxide Nanoparticles Prepared by an Ecofriendly Green Route Using Plant Extracts

by Nicusor Fifere, Rodinel Ardeleanu, Florica Doroftei, Marius Dobromir and Anton Airinei

Int. J. Mol. Sci. 2024, 25(1), 681; https://doi.org/10.3390/ijms25010681 - 4 Jan 2024

Cited by 6 | Viewed by 2125

Abstract

The present study explores an environmentally friendly green approach to obtain cerium oxide nanoparticles via a biomediated route using Mellisa officinalis and Hypericum perforatum plant extracts as reducing agents. The as-prepared nanoparticles were studied for their structural and morphological characteristics using XRD diffractometry, [...] Read more.

The present study explores an environmentally friendly green approach to obtain cerium oxide nanoparticles via a biomediated route using Mellisa officinalis and Hypericum perforatum plant extracts as reducing agents. The as-prepared nanoparticles were studied for their structural and morphological characteristics using XRD diffractometry, scanning electron microscopy, Raman, fluorescence and electronic absorption spectra, and X-ray photoelectron spectroscopy (XPS). The XRD pattern has shown the centered fluorite crystal structure of cerium oxide nanoparticles with average crystallite size below 10 nm. These observations were in agreement with the STEM data. The cubic fluorite structure of the cerium oxide nanoparticles was confirmed by the vibrational mode around 462 cm⁻¹ due to the Ce-08 unit. The optical band gap was estimated from UV-Vis reflectance spectra, which was found to decrease from 3.24 eV to 2.98 eV. A higher specific area was determined for the sample using M. officinalis aqueous extract. The EDX data indicated that only cerium and oxygen are present in the green synthesized nanoparticles. Full article

(This article belongs to the Special Issue Nanostructures: Preparation, Structural Characteristics and Properties)

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26 pages, 3694 KiB

Open AccessArticle

Specific Circular RNA Signature of Endothelial Cells: Potential Implications in Vascular Pathophysiology

by Leïla Halidou Diallo, Jérôme Mariette, Nathalie Laugero, Christian Touriol, Florent Morfoisse, Anne-Catherine Prats, Barbara Garmy-Susini and Eric Lacazette

Int. J. Mol. Sci. 2024, 25(1), 680; https://doi.org/10.3390/ijms25010680 - 4 Jan 2024

Cited by 2 | Viewed by 1864

Abstract

Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within [...] Read more.

Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within vascular endothelial cells and cancer cells independently. However, to date, no comparative study of circular RNA expression in different types of endothelial cells has been performed and analysed through the lens of their central role in vascular physiology and pathology. In this work, we analysed publicly available and original RNA sequencing datasets from arterial, veinous, and lymphatic endothelial cells to identify common and distinct circRNA expression profiles. We identified 4713 distinct circRNAs in the compared endothelial cell types, 95% of which originated from exons. Interestingly, the results show that the expression profile of circular RNAs is much more specific to each cell type than linear RNAs, and therefore appears to be more suitable for distinguishing between them. As a result, we have discovered a specific circRNA signature for each given endothelial cell type. Furthermore, we identified a specific endothelial cell circRNA signature that is composed four circRNAs: circCARD6, circPLXNA2, circCASC15 and circEPHB4. These circular RNAs are produced by genes that are related to endothelial cell migration pathways and cancer progression. More detailed studies of their functions could lead to a better understanding of the mechanisms involved in physiological and pathological (lymph)angiogenesis and might open new ways to tackle tumour spread through the vascular system. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Biology in France)

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12 pages, 2921 KiB

Open AccessArticle

Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2)

by Iga Biskupek and Artur Gieldon

Int. J. Mol. Sci. 2024, 25(1), 679; https://doi.org/10.3390/ijms25010679 - 4 Jan 2024

Cited by 1 | Viewed by 1760

Abstract

The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly contagious illness with effects ranging from mild symptoms to severe illness. It is also one of the best-known pathogens since more than 200,000 scientific papers occurred in the last [...] Read more.

The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly contagious illness with effects ranging from mild symptoms to severe illness. It is also one of the best-known pathogens since more than 200,000 scientific papers occurred in the last few years. With the publication of the SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in a complex with human ACE2 (hACE2) (PDB (6LZG)), the molecular analysis of one of the most crucial steps on the infection pathway was possible. The aim of this manuscript is to simulate the most widely spread mutants of SARS-CoV-2, namely Alpha, Beta, Gamma, Delta, Omicron, and the first recognized variant (natural wild type). With the wide search of the hypersurface of the potential energy performed using the UNRES force field, the intermediate state of the ACE2–RBD complex was found. R403, K/N/T417, L455, F486, Y489, F495, Y501, and Y505 played a crucial role in the protein recognition mechanism. The intermediate state cannot be very stable since it will prevent the infection cascade. Full article

(This article belongs to the Special Issue Novel Approaches to Potential COVID-19 Molecular Therapeutics)

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12 pages, 1323 KiB

Open AccessArticle

Effect of Solute on Interfacial Properties and Micelle Structure of Dodecylbenzenesulfonate (DBS): Experimental and Molecular Dynamics Studies

by Huang-Chin Hung and Gina S. Shreve

Int. J. Mol. Sci. 2024, 25(1), 678; https://doi.org/10.3390/ijms25010678 - 4 Jan 2024

Viewed by 1322

Abstract

A combined experimental and molecular dynamic simulation approach was used to examine the structure and interfacial properties of solute-saturated micelles. The properties of dodecylbenzenesulfonate (DBS) micelles were examined in dodecane and benzene hydrocarbon systems. Pyrene fluorescence was used to determine the aggregation number [...] Read more.

A combined experimental and molecular dynamic simulation approach was used to examine the structure and interfacial properties of solute-saturated micelles. The properties of dodecylbenzenesulfonate (DBS) micelles were examined in dodecane and benzene hydrocarbon systems. Pyrene fluorescence was used to determine the aggregation number of surfactant monomers in the micelle systems. Molecular dynamic (MD) simulations using energy minimization applying the CHARMm force field with the TIP3P model for water. Comparison of the DBS/benzene and DBS/Dodecane micelles equilibrium structures via radial distribution function (RDF) and probability distribution function (PDF) analysis indicates that the area per head group for the DBS/Benzene micelle interface is significantly larger than that of the DBS/Dodecane at the interface. It was also determined that benzene molecules can move freely within the micelle while dodecane is strictly confined in the core of the micelle. The increased interfacial area per monomer caused by the insertion of benzene also reduces the effectiveness of the surfactant, which has implications for use in various environmental applications. However, the DBS/benzene micelle can solubilize many more hydrocarbon molecules in one micelle with less surfactant monomer (i.e., lower aggregation number) per micelle due to the increased available packing positions within the micelle. This, in turn, increases the efficiency of the surfactant in real-world applications which is consistent with previous laboratory results. Understanding the differing solubilization characteristics of surfactants against various classes of hydrocarbons in single solute systems is a necessary step to beginning to understand their solubilization properties in the mixed waste systems prevalent in most surfactant enhanced remediation (SEAR) strategies. Full article

(This article belongs to the Collection Feature Papers in Materials Science)

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29 pages, 5786 KiB

Open AccessArticle

Block Synthesis and Step-Growth Polymerization of C-6-Sulfonatomethyl-Containing Sulfated Malto-Oligosaccharides and Their Biological Profiling

by Mihály Herczeg, Fruzsina Demeter, Tibor Nagy, Ágnes Rusznyák, Jan Hodek, Éva Sipos, István Lekli, Ferenc Fenyvesi, Jan Weber, Sándor Kéki and Anikó Borbás

Int. J. Mol. Sci. 2024, 25(1), 677; https://doi.org/10.3390/ijms25010677 - 4 Jan 2024

Viewed by 1637

Abstract

Highly sulfated malto-oligomers, similar to heparin and heparan-sulfate, have good antiviral, antimetastatic, anti-inflammatory and cell growth inhibitory effects. Due to their broad biological activities and simple structure, sulfated malto-oligomer derivatives have a great therapeutic potential, therefore, the development of efficient synthesis methods for [...] Read more.

Highly sulfated malto-oligomers, similar to heparin and heparan-sulfate, have good antiviral, antimetastatic, anti-inflammatory and cell growth inhibitory effects. Due to their broad biological activities and simple structure, sulfated malto-oligomer derivatives have a great therapeutic potential, therefore, the development of efficient synthesis methods for their production is of utmost importance. In this work, preparation of α-(1→4)-linked oligoglucosides containing a sulfonatomethyl moiety at position C-6 of each glucose unit was studied by different approaches. Malto-oligomeric sulfonic acid derivatives up to dodecasaccharides were prepared by polymerization using different protecting groups, and the composition of the product mixtures was analyzed by MALDI-MS methods and size-exclusion chromatography. Synthesis of lower oligomers was also accomplished by stepwise and block synthetic methods, and then the oligosaccharide products were persulfated. The antiviral, anti-inflammatory and cell growth inhibitory activity of the fully sulfated malto-oligosaccharide sulfonic acids were determined by in vitro tests. Four tested di- and trisaccharide sulfonic acids effectively inhibited the activation of the TNF-α-mediated inflammatory pathway without showing cytotoxicity. Full article

(This article belongs to the Special Issue Heparin, Heparan Sulfate and Heparanase in Health and Disease)

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Graphical abstract

13 pages, 879 KiB

Open AccessReview

Programmed Cell Death Ligand 1 Immunohistochemical Expression and Cutaneous Melanoma: A Controversial Relationship

by Vincenzo Fiorentino, Cristina Pizzimenti, Mariausilia Franchina, Ludovica Pepe, Fernanda Russotto, Pietro Tralongo, Marina Gloria Micali, Gaetano Basilio Militi and Maria Lentini

Int. J. Mol. Sci. 2024, 25(1), 676; https://doi.org/10.3390/ijms25010676 - 4 Jan 2024

Cited by 2 | Viewed by 2730

Abstract

Cutaneous melanoma (CM) is traditionally considered one of the most “immunogenic” tumors, eliciting a high immune response. However, despite the presence of tumor-infiltrating lymphocytes (TILs), melanoma cells use strategies to suppress antitumor immunity and avoid being eliminated by immune surveillance. The PD-1 (programmed [...] Read more.

Cutaneous melanoma (CM) is traditionally considered one of the most “immunogenic” tumors, eliciting a high immune response. However, despite the presence of tumor-infiltrating lymphocytes (TILs), melanoma cells use strategies to suppress antitumor immunity and avoid being eliminated by immune surveillance. The PD-1 (programmed death-1)/PD-L1 (programmed death-ligand 1) axis is a well-known immune escape system adopted by neoplastic cells. Therefore, immunotherapy with PD-1 and PD-L1 inhibitors is quickly becoming the main treatment approach for metastatic melanoma patients. However, the clinical utility of PD-L1 expression assessment in CM is controversial, and the interpretation of PD-L1 scores in clinical practice is still a matter of debate. Nonetheless, the recent literature data show that by adopting specific PD-L1 assessment methods in melanoma samples, a correlation between the expression of such a biomarker and a positive response to PD-1-based immunotherapy can be seen. Our review aims to describe the state-of-the-art knowledge regarding the prognostic and predictive role of PD-L1 expression in CM while also referring to possible biological explanations for the variability in its expressions and related treatment responses. Full article

(This article belongs to the Special Issue Advances in Melanoma and Skin Cancers)

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37 pages, 2322 KiB

Open AccessReview

The Role of Endocrine Disruptors Bisphenols and Phthalates in Obesity: Current Evidence, Perspectives and Controversies

by Maria Dalamaga, Dimitrios Kounatidis, Dimitrios Tsilingiris, Natalia G. Vallianou, Irene Karampela, Sotiria Psallida and Athanasios G. Papavassiliou

Int. J. Mol. Sci. 2024, 25(1), 675; https://doi.org/10.3390/ijms25010675 - 4 Jan 2024

Cited by 11 | Viewed by 6979

Abstract

Excess body weight constitutes one of the major health challenges for societies and healthcare systems worldwide. Besides the type of diet, calorie intake and the lack of physical exercise, recent data have highlighted a possible association between endocrine-disrupting chemicals (EDCs), such as bisphenol [...] Read more.

Excess body weight constitutes one of the major health challenges for societies and healthcare systems worldwide. Besides the type of diet, calorie intake and the lack of physical exercise, recent data have highlighted a possible association between endocrine-disrupting chemicals (EDCs), such as bisphenol A, phthalates and their analogs, and obesity. EDCs represent a heterogeneous group of chemicals that may influence the hormonal regulation of body mass and adipose tissue morphology. Based on the available data from mechanistic, animal and epidemiological studies including meta-analyses, the weight of evidence points towards the contribution of EDCs to the development of obesity, associated disorders and obesity-related adipose tissue dysfunction by (1) impacting adipogenesis; (2) modulating epigenetic pathways during development, enhancing susceptibility to obesity; (3) influencing neuroendocrine signals responsible for appetite and satiety; (4) promoting a proinflammatory milieu in adipose tissue and inducing a state of chronic subclinical inflammation; (5) dysregulating gut microbiome and immune homeostasis; and (6) inducing dysfunction in thermogenic adipose tissue. Critical periods of exposure to obesogenic EDCs are the prenatal, neonatal, pubertal and reproductive periods. Interestingly, EDCs even at low doses may promote epigenetic transgenerational inheritance of adult obesity in subsequent generations. The aim of this review is to summarize the available evidence on the role of obesogenic EDCs, specifically BPA and phthalate plasticizers, in the development of obesity, taking into account in vitro, animal and epidemiologic studies; discuss mechanisms linking EDCs to obesity; analyze the effects of EDCs on obesity in critical chronic periods of exposure; and present interesting perspectives, challenges and preventive measures in this research area. Full article

(This article belongs to the Special Issue Hormone Receptors: A 2023 Update)

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18 pages, 3171 KiB

Open AccessArticle

A Million-Cow Validation of a Chromosome 14 Region Interacting with All Chromosomes for Fat Percentage in U.S. Holstein Cows

by Dzianis Prakapenka, Zuoxiang Liang, Hafedh B. Zaabza, Paul M. VanRaden, Curtis P. Van Tassell and Yang Da

Int. J. Mol. Sci. 2024, 25(1), 674; https://doi.org/10.3390/ijms25010674 - 4 Jan 2024

Cited by 4 | Viewed by 2142

Abstract

A genome-wide association study (GWAS) of fat percentage (FPC) using 1,231,898 first lactation cows and 75,198 SNPs confirmed a previous result that a Chr14 region about 9.38 Mb in size (0.14–9.52 Mb) had significant inter-chromosome additive × additive (A×A) effects with all chromosomes [...] Read more.

A genome-wide association study (GWAS) of fat percentage (FPC) using 1,231,898 first lactation cows and 75,198 SNPs confirmed a previous result that a Chr14 region about 9.38 Mb in size (0.14–9.52 Mb) had significant inter-chromosome additive × additive (A×A) effects with all chromosomes and revealed many new such effects. This study divides this 9.38 Mb region into two sub-regions, Chr14a at 0.14–0.88 Mb (0.74 Mb in size) with 78% and Chr14b at 2.21–9.52 Mb (7.31 Mb in size) with 22% of the 2761 significant A×A effects. These two sub-regions were separated by a 1.3 Mb gap at 0.9–2.2 Mb without significant inter-chromosome A×A effects. The PPP1R16A-FOXH1-CYHR1-TONSL (PFCT) region of Chr14a (29 Kb in size) with four SNPs had the largest number of inter-chromosome A×A effects (1141 pairs) with all chromosomes, including the most significant inter-chromosome A×A effects. The SLC4A4-GC-NPFFR2 (SGN) region of Chr06, known to have highly significant additive effects for some production, fertility and health traits, specifically interacted with the PFCT region and a Chr14a region with CPSF1, ADCK5, SLC52A2, DGAT1, SMPD5 and PARP10 (CASDSP) known to have highly significant additive effects for milk production traits. The most significant effects were between an SNP in SGN and four SNPs in PFCT. The CASDSP region mostly interacted with the SGN region. In the Chr14b region, the 2.28–2.42 Mb region (138.46 Kb in size) lacking coding genes had the largest cluster of A×A effects, interacting with seventeen chromosomes. The results from this study provide high-confidence evidence towards the understanding of the genetic mechanism of FPC in Holstein cows. Full article

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

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14 pages, 2489 KiB

Open AccessArticle

Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity

by Agata Anna Cisek, Edyta Szymańska, Aldona Wierzbicka-Rucińska, Tamara Aleksandrzak-Piekarczyk and Bożena Cukrowska

Int. J. Mol. Sci. 2024, 25(1), 673; https://doi.org/10.3390/ijms25010673 - 4 Jan 2024

Cited by 3 | Viewed by 1779

Abstract

The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens—especially those focused on children—are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) [...] Read more.

The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens—especially those focused on children—are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn’s disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn’s Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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12 pages, 1333 KiB

Open AccessArticle

A Nested PCR Telomere Fusion Assay Highlights the Widespread End-Capping Protection of Arabidopsis CTC1

by María I. Vaquero-Sedas and Miguel A. Vega-Palas

Int. J. Mol. Sci. 2024, 25(1), 672; https://doi.org/10.3390/ijms25010672 - 4 Jan 2024

Viewed by 1499

Abstract

Telomeres protect the ends of linear eukaryotic chromosomes from being recognized as DNA double-strand breaks. Two major protein complexes are involved in the protection of telomeres: shelterin and CST. The dysfunction of these complexes can challenge the function of telomeres and lead to [...] Read more.

Telomeres protect the ends of linear eukaryotic chromosomes from being recognized as DNA double-strand breaks. Two major protein complexes are involved in the protection of telomeres: shelterin and CST. The dysfunction of these complexes can challenge the function of telomeres and lead to telomere fusions, breakage–fusion–bridge cycles, and cell death. Therefore, monitoring telomere fusions helps to understand telomeres biology. Telomere fusions are often analyzed by Fluorescent In Situ Hybridization (FISH) or PCR. Usually, both methods involve hybridization with a telomeric probe, which allows the detection of fusions containing telomeric sequences, but not of those lacking them. With the aim of detecting both types of fusion events, we have developed a nested PCR method to analyze telomere fusions in Arabidopsis thaliana. This method is simple, accurate, and does not require hybridization. We have used it to analyze telomere fusions in wild-type and mutant plants altered in CTC1, one of the three components of the Arabidopsis CST telomere capping complex. Our results show that null ctc1-2 mutant plants display fusions between all telomeric regions present in Arabidopsis chromosomes 1, 3 and 5, thus highlighting the widespread end-capping protection achieved by CTC1. Full article

(This article belongs to the Special Issue Telomeres in Development, Senescence and Genome Instability)

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24 pages, 8950 KiB

Open AccessArticle

Binding Free Energy Calculation Based on the Fragment Molecular Orbital Method and Its Application in Designing Novel SHP-2 Allosteric Inhibitors

by Zhen Yuan, Xingyu Chen, Sisi Fan, Longfeng Chang, Linna Chu, Ying Zhang, Jie Wang, Shuang Li, Jinxin Xie, Jianguo Hu, Runyu Miao, Lili Zhu, Zhenjiang Zhao, Honglin Li and Shiliang Li

Int. J. Mol. Sci. 2024, 25(1), 671; https://doi.org/10.3390/ijms25010671 - 4 Jan 2024

Cited by 9 | Viewed by 2823

Abstract

The accurate prediction of binding free energy is a major challenge in structure-based drug design. Quantum mechanics (QM)-based approaches show promising potential in predicting ligand–protein binding affinity by accurately describing the behavior and structure of electrons. However, traditional QM calculations face computational limitations, [...] Read more.

The accurate prediction of binding free energy is a major challenge in structure-based drug design. Quantum mechanics (QM)-based approaches show promising potential in predicting ligand–protein binding affinity by accurately describing the behavior and structure of electrons. However, traditional QM calculations face computational limitations, hindering their practical application in drug design. Nevertheless, the fragment molecular orbital (FMO) method has gained widespread application in drug design due to its ability to reduce computational costs and achieve efficient ab initio QM calculations. Although the FMO method has demonstrated its reliability in calculating the gas phase potential energy, the binding of proteins and ligands also involves other contributing energy terms, such as solvent effects, the ‘deformation energy’ of a ligand’s bioactive conformations, and entropy. Particularly in cases involving ionized fragments, the calculation of solvation free energy becomes particularly crucial. We conducted an evaluation of some previously reported implicit solvent methods on the same data set to assess their potential for improving the performance of the FMO method. Herein, we develop a new QM-based binding free energy calculation method called FMOScore, which enhances the performance of the FMO method. The FMOScore method incorporates linear fitting of various terms, including gas-phase potential energy, deformation energy, and solvation free energy. Compared to other widely used traditional prediction methods such as FEP+, MM/PBSA, MM/GBSA, and Autodock vina, FMOScore showed good performance in prediction accuracies. By constructing a retrospective case study, it was observed that incorporating calculations for solvation free energy and deformation energy can further enhance the precision of FMO predictions for binding affinity. Furthermore, using FMOScore-guided lead optimization against Src homology-2-containing protein tyrosine phosphatase 2 (SHP-2), we discovered a novel and potent allosteric SHP-2 inhibitor (compound 8). Full article

(This article belongs to the Section Biochemistry)

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18 pages, 6730 KiB

Open AccessArticle

Isorhamnetin Regulates Programmed Death Ligand-1 Expression by Suppressing the EGFR–STAT3 Signaling Pathway in Canine Mammary Tumors

by Chen Mei, Xue Zhang, Yan Zhi, Zhixuan Liang, Haojun Xu, Zhenyi Liu, Ying Liu, Yanli Lyu and Hongjun Wang

Int. J. Mol. Sci. 2024, 25(1), 670; https://doi.org/10.3390/ijms25010670 - 4 Jan 2024

Cited by 2 | Viewed by 2242

Abstract

Programmed death ligand-1 (PD-L1) is highly expressed in a variety of cancer cells and suggests a poorer prognosis for patients. The natural compound isorhamnetin (ISO) shows promise in treating cancers and causing damage to canine mammary tumor (CMT) cells. We investigated the mechanism [...] Read more.

Programmed death ligand-1 (PD-L1) is highly expressed in a variety of cancer cells and suggests a poorer prognosis for patients. The natural compound isorhamnetin (ISO) shows promise in treating cancers and causing damage to canine mammary tumor (CMT) cells. We investigated the mechanism of ISO in reducing PD-L1 expression in CMT cells. Clustered, regularly interspaced short palindromic repeat-associated protein 9 (CRISPR/Cas9) was used to mediate CD274 knockout in U27 cells. Then, monoclonal cells were screened and cultured. Nucleotide sequencing and expression of PD-L1 were detected. Additionally, we examined cell migration, invasion, and damage. Immunofluorescent staining of PD-L1 was examined in U27 cells. The signaling pathways were measured by Western blotting. Murine xenotransplantation models and murine immunocompetent allograft mammary tumor models were established to evaluate the effect of ISO therapy. Expression of Ki-67, caspase3, and PD-L1 were analyzed by immunohistochemistry. A pull-down assay was used to explore which proteins could bind to ISO. Canine EGFR protein was purified and used to detect whether it directly binds to ISO using a surface plasmon resonance assay. ISO inhibited the EGFR-STAT3-PD-L1 signaling pathway and blocked cancer growth, significantly increasing the survival rate of healthy cells. The cell membrane receptor EGFR was identified as a direct target of ISO. ISO could be exploited as an antineoplastic treatment of CMT by targeting EGFR to suppress PD-L1 expression. Full article

(This article belongs to the Section Molecular Oncology)

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16 pages, 3239 KiB

Open AccessArticle

H₂O₂ Significantly Affects Larix kaempferi × Larix olgensis Somatic Embryogenesis

by Junjie Zhu, Kaikai Zhang, Huiru Xiong, Yunhui Xie, Rui Li, Xinru Wu, Yun Yang, Hua Wu, Zhaodong Hao, Xiaomei Sun and Jinhui Chen

Int. J. Mol. Sci. 2024, 25(1), 669; https://doi.org/10.3390/ijms25010669 - 4 Jan 2024

Cited by 3 | Viewed by 1559

Abstract

Larch is widely distributed throughout the world and is an important species for timber supply and the extraction of industrial raw materials. In recent years, the hybrid breeding of Larix kaempferi and Larix olgensis has shown obvious heterosis in quick-growth, stress resistance and [...] Read more.

Larch is widely distributed throughout the world and is an important species for timber supply and the extraction of industrial raw materials. In recent years, the hybrid breeding of Larix kaempferi and Larix olgensis has shown obvious heterosis in quick-growth, stress resistance and wood properties. However, its growth and development cycle is too long to meet general production needs. In order to shorten the breeding cycle, we have for the first time successfully established and optimized a somatic embryogenesis system for Larix kaempferi × Larix olgensis. We found that the highest rate of embryonal-suspensor mass (ESM) induction was observed when late cotyledonary embryos were used as explants. The induced ESMs were subjected to stable proliferation, after which abscisic acid (ABA) and polyethylene glycol (PEG) were added to successfully induce somatic embryos. Treatment with PEG and ABA was of great importance to somatic embryo formation and complemented each other’s effect. ABA assisted embryo growth, whereas PEG facilitated the formation of proembryo-like structures. On top of this, we studied in more detail the relationship between redox homeostasis and the efficiency of somatic embryogenesis (frequency of ESM induction). During subculture, we observed the gradual formation of three distinct types of ESM. The Type I ESM is readily able to form somatic embryos. In contrast to type I, the type III ESM suffers from severe browning, contains a higher level of hydrogen peroxide (H₂O₂) and demonstrates a decreased ability to form somatic embryos. External treatment with H₂O₂ decreased the somatic embryogenesis efficiency of Type I and type III ESMs, or the higher the exogenous H₂O₂ content, the lower the resulting somatic embryogenesis efficiency. We found that treatment with the H₂O₂ scavenger DMTU (dimethylthiourea) could significantly increase the somatic embryogenesis efficiency of the type III ESM, as a result of a decline in endogenous H₂O₂ content. Overall, these findings have contributed to setting up a successful somatic embryogenesis system for larch production. Full article

(This article belongs to the Section Molecular Biology)

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21 pages, 4095 KiB

Open AccessReview

Catastrophic Antiphospholipid Syndrome

by Victoria Bitsadze, Fidan Yakubova, Jamilya Khizroeva, Arina Lazarchuk, Polina Salnikova, Alexander Vorobev, Maria Tretyakova, Natalia Degtyareva, Kristina Grigoreva, Nilufar Gashimova, Margaret Kvaratskheliia, Nataliya Makatsariya, Ekaterina Kudryavtseva, Anna Tomlenova, Jean-Christophe Gris, Ismail Elalamy, Cihan Ay and Alexander Makatsariya

Int. J. Mol. Sci. 2024, 25(1), 668; https://doi.org/10.3390/ijms25010668 - 4 Jan 2024

Cited by 10 | Viewed by 4385

Abstract

Unlike classic APS, CAPS causes multiple microthrombosis due to an increased inflammatory response, known as a “thrombotic storm”. CAPS typically develops after infection, trauma, or surgery and begins with the following symptoms: fever, thrombocytopenia, muscle weakness, visual and cognitive disturbances, abdominal pain, renal [...] Read more.

Unlike classic APS, CAPS causes multiple microthrombosis due to an increased inflammatory response, known as a “thrombotic storm”. CAPS typically develops after infection, trauma, or surgery and begins with the following symptoms: fever, thrombocytopenia, muscle weakness, visual and cognitive disturbances, abdominal pain, renal failure, and disseminated intravascular coagulation. Although the presence of antiphospholipid antibodies in the blood is one of the diagnostic criteria, the level of these antibodies can fluctuate significantly, which complicates the diagnostic process and can lead to erroneous interpretation of rapidly developing symptoms. Triple therapy is often used to treat CAPS, which includes the use of anticoagulants, plasmapheresis, and high doses of glucocorticosteroids and, in some cases, additional intravenous immunoglobulins. The use of LMWH is recommended as the drug of choice due to its anti-inflammatory and anticoagulant properties. CAPS is a multifactorial disease that requires not only an interdisciplinary approach but also highly qualified medical care, adequate and timely diagnosis, and appropriate prevention in the context of relapse or occurrence of the disease. Improved new clinical protocols and education of medical personnel regarding CAPS can significantly improve the therapeutic approach and reduce mortality rates. Full article

(This article belongs to the Special Issue Molecular Mechanisms of the Pathogenesis of Antiphospholipid Syndrome (APS))

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16 pages, 10753 KiB

Open AccessArticle

by Jie Li, Xuefeng Shang, Sen Zhang, Qiaoli Yang, Zunqiang Yan, Pengfei Wang, Xiaoli Gao, Shuangbao Gun and Xiaoyu Huang

Int. J. Mol. Sci. 2024, 25(1), 667; https://doi.org/10.3390/ijms25010667 - 4 Jan 2024

Cited by 1 | Viewed by 2091

Abstract

Breast milk, an indispensable source of immunological and nutrient components, is essential for the growth and development of newborn mammals. MicroRNAs (miRNAs) are present in various tissues and body fluids and are selectively packaged inside exosomes, a type of membrane vesicle. Milk exosomes [...] Read more.

Breast milk, an indispensable source of immunological and nutrient components, is essential for the growth and development of newborn mammals. MicroRNAs (miRNAs) are present in various tissues and body fluids and are selectively packaged inside exosomes, a type of membrane vesicle. Milk exosomes have potential regulatory effects on the growth, development, and immunity of newborn piglets. To explore the differences in milk exosomes related to the breed and milk type, we isolated exosomes from colostrum and mature milk from domestic Bamei pigs and foreign Landrace pigs by using density gradient centrifugation and then characterized them by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Furthermore, the profiles and functions of miRNAs in the two types of pig milk exosomes were investigated using miRNA-seq and bioinformatics analysis. We identified a total of 1081 known and 2311 novel miRNAs in pig milk exosomes from Bamei and Landrace pigs. These differentially expressed miRNAs (DE-miRNAs) are closely associated with processes such as cell signaling, cell physiology, and immune system development. Functional enrichment analysis showed that DE-miRNA target genes were significantly enriched in endocytosis, the T cell receptor signaling pathway, and the Th17 cell differentiation signaling pathway. The exosomal miRNAs in both the colostrum and mature milk of the two pig species showed significant differences. Based on related signaling pathways, we found that the colostrum of local pig breeds contained more immune-system-development-related miRNAs. This study provides new insights into the possible function of milk exosomal miRNAs in the development of the piglet immune system. Full article

(This article belongs to the Section Molecular Informatics)

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28 pages, 4636 KiB

Open AccessArticle

In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates

by Ahmer Bin Hafeez, Karolina Pełka, Randy Worobo and Piotr Szweda

Int. J. Mol. Sci. 2024, 25(1), 666; https://doi.org/10.3390/ijms25010666 - 4 Jan 2024

Cited by 2 | Viewed by 2142

Abstract

Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence [...] Read more.

Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites. Full article

(This article belongs to the Special Issue Molecular Research in Prebiotics, Probiotics and Postbiotics)

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54 pages, 15946 KiB

Open AccessReview

Brief Electrical Stimulation Promotes Recovery after Surgical Repair of Injured Peripheral Nerves

by Tessa Gordon

Int. J. Mol. Sci. 2024, 25(1), 665; https://doi.org/10.3390/ijms25010665 - 4 Jan 2024

Cited by 3 | Viewed by 2648

Abstract

Injured peripheral nerves regenerate their axons in contrast to those in the central nervous system. Yet, functional recovery after surgical repair is often disappointing. The basis for poor recovery is progressive deterioration with time and distance of the growth capacity of the neurons [...] Read more.

Injured peripheral nerves regenerate their axons in contrast to those in the central nervous system. Yet, functional recovery after surgical repair is often disappointing. The basis for poor recovery is progressive deterioration with time and distance of the growth capacity of the neurons that lose their contact with targets (chronic axotomy) and the growth support of the chronically denervated Schwann cells (SC) in the distal nerve stumps. Nonetheless, chronically denervated atrophic muscle retains the capacity for reinnervation. Declining electrical activity of motoneurons accompanies the progressive fall in axotomized neuronal and denervated SC expression of regeneration-associated-genes and declining regenerative success. Reduced motoneuronal activity is due to the withdrawal of synaptic contacts from the soma. Exogenous neurotrophic factors that promote nerve regeneration can replace the endogenous factors whose expression declines with time. But the profuse axonal outgrowth they provoke and the difficulties in their delivery hinder their efficacy. Brief (1 h) low-frequency (20 Hz) electrical stimulation (ES) proximal to the injury site promotes the expression of endogenous growth factors and, in turn, dramatically accelerates axon outgrowth and target reinnervation. The latter ES effect has been demonstrated in both rats and humans. A conditioning ES of intact nerve days prior to nerve injury increases axonal outgrowth and regeneration rate. Thereby, this form of ES is amenable for nerve transfer surgeries and end-to-side neurorrhaphies. However, additional surgery for applying the required electrodes may be a hurdle. ES is applicable in all surgeries with excellent outcomes. Full article

(This article belongs to the Special Issue Plasticity of the Nervous System after Injury)

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30 pages, 1622 KiB

Open AccessReview

Targeted Radium Alpha Therapy in the Era of Nanomedicine: In Vivo Results

by György Trencsényi, Csaba Csikos and Zita Képes

Int. J. Mol. Sci. 2024, 25(1), 664; https://doi.org/10.3390/ijms25010664 - 4 Jan 2024

Cited by 2 | Viewed by 3230

Abstract

Targeted alpha-particle therapy using radionuclides with alpha emission is a rapidly developing area in modern cancer treatment. To selectively deliver alpha-emitting isotopes to tumors, targeting vectors, including monoclonal antibodies, peptides, small molecule inhibitors, or other biomolecules, are attached to them, which ensures specific [...] Read more.

Targeted alpha-particle therapy using radionuclides with alpha emission is a rapidly developing area in modern cancer treatment. To selectively deliver alpha-emitting isotopes to tumors, targeting vectors, including monoclonal antibodies, peptides, small molecule inhibitors, or other biomolecules, are attached to them, which ensures specific binding to tumor-related antigens and cell surface receptors. Although earlier studies have already demonstrated the anti-tumor potential of alpha-emitting radium (Ra) isotopes—Radium-223 and Radium-224 (^223/224Ra)—in the treatment of skeletal metastases, their inability to complex with target-specific moieties hindered application beyond bone targeting. To exploit the therapeutic gains of Ra across a wider spectrum of cancers, nanoparticles have recently been embraced as carriers to ensure the linkage of ^223/224Ra to target-affine vectors. Exemplified by prior findings, Ra was successfully bound to several nano/microparticles, including lanthanum phosphate, nanozeolites, barium sulfate, hydroxyapatite, calcium carbonate, gypsum, celestine, or liposomes. Despite the lengthened tumor retention and the related improvement in the radiotherapeutic effect of ^223/224Ra coupled to nanoparticles, the in vivo assessment of the radiolabeled nanoprobes is a prerequisite prior to clinical usage. For this purpose, experimental xenotransplant models of different cancers provide a well-suited scenario. Herein, we summarize the latest achievements with ^223/224Ra-doped nanoparticles and related advances in targeted alpha radiotherapy. Full article

(This article belongs to the Collection Feature Papers in Molecular Nanoscience)

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15 pages, 18133 KiB

Open AccessArticle

Combination Therapy with a TLR7 Agonist and a BRD4 Inhibitor Suppresses Tumor Growth via Enhanced Immunomodulation

by Yong-Si Liu, Jia-Xin Wang, Guang-Yi Jin, Ming-Hao Hu and Xiao-Dong Wang

Int. J. Mol. Sci. 2024, 25(1), 663; https://doi.org/10.3390/ijms25010663 - 4 Jan 2024

Viewed by 1866

Abstract

JQ-1 is a typical BRD4 inhibitor with the ability to directly fight tumor cells and evoke antitumor immunity via reducing the expression of PD-L1. However, problems arise with the development of JQ-1 in clinical trials, such as marked lymphoid and hematopoietic toxicity, leading [...] Read more.

JQ-1 is a typical BRD4 inhibitor with the ability to directly fight tumor cells and evoke antitumor immunity via reducing the expression of PD-L1. However, problems arise with the development of JQ-1 in clinical trials, such as marked lymphoid and hematopoietic toxicity, leading to the investigation of combination therapy. SZU-101 is a TLR7 agonist designed and synthesized by our group with potent immunostimulatory activity. Therefore, we hypothesized that combination therapy of SZU-101 and JQ-1 would target innate immunity and adaptive immunity simultaneously, to achieve a better antitumor efficacy than monotherapy. In this study, the repressive effects of the combination administration on tumor growth and metastasis were demonstrated in both murine breast cancer and melanoma models. In 4T1 tumor-bearing mice, i.t. treatment with SZU-101 in combination with i.p. treatment with JQ-1 suppressed the growth of tumors at both injected and uninjected sites. Combination therapy increased M1/M2 ratio in TAMs, decreased PD-L1 expression and promoted the recruitment of activated CD8⁺ T cells in the TME. In summary, the improved therapeutic efficacy of the novel combination therapy appears to be feasible for the treatment of a diversity of cancers. Full article

(This article belongs to the Special Issue Molecular Mechanisms and New Therapies for Breast Cancer)

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16 pages, 16061 KiB

Open AccessArticle

Identification of Muscle Strength-Related Gut Microbes through Human Fecal Microbiome Transplantation

by Ji-Seon Ahn, Bon-Chul Koo, Yu-Jin Choi, Woon-Won Jung, Hyun-Sook Kim, Suk-Jun Lee, Seong-Tshool Hong and Hea-Jong Chung

Int. J. Mol. Sci. 2024, 25(1), 662; https://doi.org/10.3390/ijms25010662 - 4 Jan 2024

Cited by 1 | Viewed by 1806

Abstract

The gut microbiome is well known for its influence on human physiology and aging. Therefore, we speculate that the gut microbiome may affect muscle strength in the same way as the host’s own genes. To demonstrate candidates for gut microbes affecting muscle strength, [...] Read more.

The gut microbiome is well known for its influence on human physiology and aging. Therefore, we speculate that the gut microbiome may affect muscle strength in the same way as the host’s own genes. To demonstrate candidates for gut microbes affecting muscle strength, we remodeled the original gut microbiome of mice into human intestinal microbiome through fecal microbiome transplantation (FMT), using human feces and compared the changes in muscle strength in the same mice before and three months after FMT. After comparing before and after FMT, the mice were divided into three groups based on the observed changes in muscle strength: positive, none, and negative changes in muscle strength. As a result of analyzing the α-diversity, β-diversity, and co-occurrence network of the intestinal microbial community before and after FMT, it was observed that a more diverse intestinal microbial community was established after FMT in all groups. In particular, the group with increased muscle strength had more gut microbiome species and communities than the other groups. Fold-change comparison showed that Eisenbergiella massiliensis and Anaeroplasma abactoclasticum from the gut microbiome had positive contributions to muscle strength, while Ileibacterium valens and Ethanoligenens harbinense had negative effects. This study identifies candidates for the gut microbiome that contribute positively and those that contribute negatively to muscle strength. Full article

(This article belongs to the Special Issue Gut Microbiota in Human Health)

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16 pages, 5662 KiB

Open AccessArticle

Systemic Treatment with Fas-Blocking Peptide Attenuates Apoptosis in Brain Ischemia

by Sungeun Chung, Yujong Yi, Irfan Ullah, Kunho Chung, Seongjun Park, Jaeyeoung Lim, Chaeyeon Kim, Seon-Hong Pyun, Minkyung Kim, Dokyoung Kim, Minhyung Lee, Taiyoun Rhim and Sang-Kyung Lee

Int. J. Mol. Sci. 2024, 25(1), 661; https://doi.org/10.3390/ijms25010661 - 4 Jan 2024

Cited by 3 | Viewed by 2232

Abstract

Apoptosis plays a crucial role in neuronal injury, with substantial evidence implicating Fas-mediated cell death as a key factor in ischemic strokes. To address this, inhibition of Fas-signaling has emerged as a promising strategy in preventing neuronal cell death and alleviating brain ischemia. [...] Read more.

Apoptosis plays a crucial role in neuronal injury, with substantial evidence implicating Fas-mediated cell death as a key factor in ischemic strokes. To address this, inhibition of Fas-signaling has emerged as a promising strategy in preventing neuronal cell death and alleviating brain ischemia. However, the challenge of overcoming the blood–brain barrier (BBB) hampers the effective delivery of therapeutic drugs to the central nervous system (CNS). In this study, we employed a 30 amino acid-long leptin peptide to facilitate BBB penetration. By conjugating the leptin peptide with a Fas-blocking peptide (FBP) using polyethylene glycol (PEG), we achieved specific accumulation in the Fas-expressing infarction region of the brain following systemic administration. Notably, administration in leptin receptor-deficient db/db mice demonstrated that leptin facilitated the delivery of FBP peptide. We found that the systemic administration of leptin-PEG-FBP effectively inhibited Fas-mediated apoptosis in the ischemic region, resulting in a significant reduction of neuronal cell death, decreased infarct volumes, and accelerated recovery. Importantly, neither leptin nor PEG-FBP influenced apoptotic signaling in brain ischemia. Here, we demonstrate that the systemic delivery of leptin-PEG-FBP presents a promising and viable strategy for treating cerebral ischemic stroke. Our approach not only highlights the therapeutic potential but also emphasizes the importance of overcoming BBB challenges to advance treatments for neurological disorders. Full article

(This article belongs to the Special Issue Drug Delivery to the Central Nervous System: From Design, Synthesis, and Evaluation)

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16 pages, 4629 KiB

Open AccessArticle

Increased Dentate Gyrus Excitability in the Intrahippocampal Kainic Acid Mouse Model for Temporal Lobe Epilepsy

by Marijke Vergaelen, Simona Manzella, Kristl Vonck, Erine Craey, Jeroen Spanoghe, Mathieu Sprengers, Evelien Carrette, Wytse Jan Wadman, Jean Delbeke, Paul Boon, Lars Emil Larsen and Robrecht Raedt

Int. J. Mol. Sci. 2024, 25(1), 660; https://doi.org/10.3390/ijms25010660 - 4 Jan 2024

Cited by 3 | Viewed by 2242

Abstract

The intrahippocampal kainic acid (IHKA) mouse model is an extensively used in vivo model to investigate the pathophysiology of mesial temporal lobe epilepsy (mTLE) and to develop novel therapies for drug-resistant epilepsy. It is characterized by profound hippocampal sclerosis and spontaneously occurring seizures [...] Read more.

The intrahippocampal kainic acid (IHKA) mouse model is an extensively used in vivo model to investigate the pathophysiology of mesial temporal lobe epilepsy (mTLE) and to develop novel therapies for drug-resistant epilepsy. It is characterized by profound hippocampal sclerosis and spontaneously occurring seizures with a major role for the injected damaged hippocampus, but little is known about the excitability of specific subregions. The purpose of this study was to electrophysiologically characterize the excitability of hippocampal subregions in the chronic phase of the induced epilepsy in the IHKA mouse model. We recorded field postsynaptic potentials (fPSPs) after electrical stimulation in the CA1 region and in the dentate gyrus (DG) of hippocampal slices of IHKA and healthy mice using a multielectrode array (MEA). In the DG, a significantly steeper fPSP slope was found, reflecting higher synaptic strength. Population spikes were more prevalent with a larger spatial distribution in the IHKA group, reflecting a higher degree of granule cell output. Only minor differences were found in the CA1 region. These results point to increased neuronal excitability in the DG but not in the CA1 region of the hippocampus of IHKA mice. This method, in which the excitability of hippocampal slices from IHKA mice is investigated using a MEA, can now be further explored as a potential new model to screen for new interventions that can restore DG function and potentially lead to novel therapies for mTLE. Full article

(This article belongs to the Special Issue Focus on Hippocampus Biology: From Neurophysiology to Dysfunctions)

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14 pages, 3937 KiB

Open AccessArticle

Characterization of the Effect of N-(2-Methoxyphenyl)-1-methyl-1H-benzimidazol-2-amine, Compound 8, against Leishmania mexicana and Its In Vivo Leishmanicidal Activity

by Rocío Nieto-Meneses, Rafael Castillo, Alicia Hernández-Campos, Benjamín Nogueda-Torres, Edgar Oliver López-Villegas, Adriana Moreno-Rodríguez, Félix Matadamas-Martínez and Lilián Yépez-Mulia

Int. J. Mol. Sci. 2024, 25(1), 659; https://doi.org/10.3390/ijms25010659 - 4 Jan 2024

Viewed by 1347

Abstract

Chemotherapy currently available for leishmaniasis treatment has many adverse side effects and drug resistance. Therefore, the identification of new targets and the development of new drugs are urgently needed. Previously, we reported the synthesis of a N-(2-methoxyphenyl)-1-methyl-1H-benzimidazol-2-amine, named compound 8 [...] Read more.

Chemotherapy currently available for leishmaniasis treatment has many adverse side effects and drug resistance. Therefore, the identification of new targets and the development of new drugs are urgently needed. Previously, we reported the synthesis of a N-(2-methoxyphenyl)-1-methyl-1H-benzimidazol-2-amine, named compound 8, with an IC₅₀ value in the micromolar range against L. mexicana, it also inhibited 68.27% the activity of recombinant L. mexicana arginase. Herein, we report studies carried out to characterize the mechanism of action of compound 8, as well as its in vivo leishmanicidal activity. It was shown in our ultrastructural studies that compound 8 induces several changes, such as membrane blebbing, the presence of autophagosomes, membrane detachment and mitochondrial and kinetoplast disorganization, among others. Compound 8 triggers the production of ROS and parasite apoptosis. It reduced 71% of the parasite load of L. mexicana in an experimental model of cutaneous leishmaniasis in comparison with a control. Altogether, the data obtained suggest the potential use of compound 8 in the treatment of cutaneous leishmaniasis. Full article

(This article belongs to the Special Issue New Strategies for the Diagnosis and Treatment of Diseases Caused by Parasites)

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21 pages, 1961 KiB

Open AccessReview

The Current Situation and Development Prospect of Whole-Genome Screening

by Caiting Yang, Yu Lei, Tinglin Ren and Mingze Yao

Int. J. Mol. Sci. 2024, 25(1), 658; https://doi.org/10.3390/ijms25010658 - 4 Jan 2024

Cited by 1 | Viewed by 2448

Abstract

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on [...] Read more.

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening. Full article

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

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21 pages, 10106 KiB

Open AccessArticle

Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants (Camellia sinensis)

by Zhihang Hu, Nan Zhang, Zhiyuan Qin, Jinwen Li, Ni Yang, Yi Chen, Jieyu Kong, Wei Luo, Aisheng Xiong and Jing Zhuang

Int. J. Mol. Sci. 2024, 25(1), 657; https://doi.org/10.3390/ijms25010657 - 4 Jan 2024

Cited by 3 | Viewed by 1988

Abstract

The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible ‘clock’ in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor [...] Read more.

The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible ‘clock’ in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor is involved in plant growth and development. MYB is also inextricably correlated with the circadian rhythm. In this study, the transcriptome data of the tea plant ‘Baiyeyihao’ were measured at a photoperiod interval of 4 h (24 h). A total of 25,306 unigenes were obtained, including 14,615 unigenes that were annotated across 20 functional categories within the GO classification. Additionally, 10,443 single-gene clusters were annotated to 11 sublevels of metabolic pathways using KEGG. Based on the results of gene annotation and differential gene transcript analysis, 22 genes encoding MYB transcription factors were identified. The G10 group in the phylogenetic tree had 13 members, of which 5 were related to the circadian rhythm, accounting for 39%. The G1, G2, G8, G9, G15, G16, G18, G19, G20, G21 and G23 groups had no members associated with the circadian rhythm. Among the 22 differentially expressed MYB transcription factors, 3 members of LHY, RVE1 and RVE8 were core circadian rhythm genes belonging to the G10, G12 and G10 groups, respectively. Real-time fluorescence quantitative PCR was used to detect and validate the expression of the gene transcripts encoding MYB transcription factors associated with the circadian rhythm. Full article

(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)

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20 pages, 4503 KiB

Open AccessArticle

Molecular Signal Transfer of Highly Diluted Antibodies to Interferon-Gamma Regarding Kind, Time, and Distance of Exposition

by Igor Jerman, Linda Ogrizek, Vesna Periček Krapež and Luka Jan

Int. J. Mol. Sci. 2024, 25(1), 656; https://doi.org/10.3390/ijms25010656 - 4 Jan 2024

Cited by 1 | Viewed by 1323

Abstract

Physicochemical examinations of very high dilution (UHD) solutions subjected to certain physical factors (such as shaking) are becoming more frequent and are increasingly producing conclusive results. A much less studied phenomenon is the transfer of molecular information (i.e., UHD signals of dilute substances) [...] Read more.

Physicochemical examinations of very high dilution (UHD) solutions subjected to certain physical factors (such as shaking) are becoming more frequent and are increasingly producing conclusive results. A much less studied phenomenon is the transfer of molecular information (i.e., UHD signals of dilute substances) from one liquid to another without an intermediate liquid phase. The aim of this study was to investigate the possibility of such a transfer of the UHD signal from the UHD solutions to the receiver solution, in particular, if the molecular source used in the donor solutions was the biologically active antibodies to interferon-gamma molecule. We were especially interested in how the transfer of the UHD signal is affected by the time of exposure of the receiver to the donor, the distance between the two, and how the transfer is affected by activation (striking) versus exposure alone. Signal transfer was evaluated by differential measurements of electrical conductivity, ORP, pH, and UV/VIS spectroscopy of the exposed liquid. The results showed that activation strongly influences signal transfer and that this can be compensated to some extent by prolonged direct exposure. In principle, exposure time has a positive effect on signal transfer. Interestingly, the results of different distances between the donor and receiver showed similar changes in the parameters in the range of 0–4 cm, as estimated in this study. While the study mainly confirms the two hypotheses, it also raises a number of new questions and provides clues for further research. Full article

(This article belongs to the Special Issue The Emerging Role of Quantum Sciences and Radiation Biology in Biomedical Applications)

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22 pages, 6377 KiB

Open AccessArticle

Anti-Aging Effect of Hemerocallis citrina Baroni Polysaccharide-Rich Extract on Caenorhabditis elegans

by Yunxia Zou, Xiyue Qin, Wenli Wang, Qingyong Meng and Yali Zhang

Int. J. Mol. Sci. 2024, 25(1), 655; https://doi.org/10.3390/ijms25010655 - 4 Jan 2024

Cited by 3 | Viewed by 1838

Abstract

Plant polysaccharides are important for anti-aging research. Polysaccharides from Hemerocallis citrina Baroni (H. citrina) have been reported to have antioxidant activity; however, their anti-aging roles and mechanisms are not clear. In this study, we extracted polysaccharides from H. citrina by an [...] Read more.

Plant polysaccharides are important for anti-aging research. Polysaccharides from Hemerocallis citrina Baroni (H. citrina) have been reported to have antioxidant activity; however, their anti-aging roles and mechanisms are not clear. In this study, we extracted polysaccharides from H. citrina by an ultrasonic-assisted water extraction–alcohol precipitation method and chemically determined the physicochemical properties such as extraction yield, content, and in vitro antioxidant properties of H. citrina polysaccharide-rich extract (HCPRE). Using Caenorhabditis elegans (C. elegans) as a model animal, the anti-aging effect of HCPRE was investigated, and the mechanism of action of HCPRE was explored by the in vivo antioxidant level assay of C. elegans and the related gene expression assay. The extraction yield of HCPRE was 11.26%, the total polysaccharide content was 77.96%, and the main monosaccharide components were glucose and galactose. In addition, HCPRE exhibited good antioxidant activity both in vitro and in vivo. Under normal thermal stress and oxidative stress conditions, being fed 1200 µg/mL of HCPRE significantly prolonged the life span of C. elegans by 32.65%, 17.71%, and 32.59%, respectively. Our study showed that HCPRE exerted an anti-aging effect on C. elegans, and its mechanism involves increasing the activities of catalase (CAT) and superoxide dismutase (SOD), reducing the level of reactive oxygen species (ROS) and regulating the expression of related genes. Full article

(This article belongs to the Section Molecular Plant Sciences)

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17 pages, 10696 KiB

Open AccessArticle

Large-Scale Biogeographical Shifts of Abundance of Antibiotic Resistance Genes and Marine Bacterial Communities as Their Carriers along a Trophic Gradient

by Mia Dželalija, Željana Fredotović, Nikolina Udiković-Kolić, Hrvoje Kalinić, Slaven Jozić, Ivica Šamanić, Marin Ordulj and Ana Maravić

Int. J. Mol. Sci. 2024, 25(1), 654; https://doi.org/10.3390/ijms25010654 - 4 Jan 2024

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Abstract

The role of marine environments in the global spread of antibiotic resistance still remains poorly understood, leaving gaps in the One Health-based research framework. Antibiotic resistance genes (ARGs) encoding resistance to five major antibiotic classes, including sulfonamides (sul1, sul2), tetracyclines [...] Read more.

The role of marine environments in the global spread of antibiotic resistance still remains poorly understood, leaving gaps in the One Health-based research framework. Antibiotic resistance genes (ARGs) encoding resistance to five major antibiotic classes, including sulfonamides (sul1, sul2), tetracyclines (tetA, tetB), β-lactams (bla_CTX-M, bla_TEM bla_VIM), macrolides (ermB, mphA), aminoglycosides (aac3-2), and integrase gene (intl1) were quantified by RT-qPCR, and their distribution was investigated in relation to environmental parameters and the total bacterial community in bottom layer and surface waters of the central Adriatic (Mediterranean), over a 68 km line from the wastewater-impacted estuary to coastal and pristine open sea. Seasonal changes (higher in winter) were observed for antibiotic resistance frequency and the relative abundances of ARGs, which were generally higher in eutrophic coastal areas. In particular, intl1, followed by bla_TEM and bla_VIM, were strongly associated with anthropogenic influence and Gammaproteobacteria as their predominant carriers. Water column stratification and geographic location had a significant influence on ARGs distribution in the oligotrophic zone, where the bacterial community exhibited a seasonal shift from Gammaproteobacteria in winter to Marine group II in summer. Full article

(This article belongs to the Special Issue Microbial Omics)

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Int. J. Mol. Sci., Volume 25, Issue 1 (January-1 2024) – 683 articles

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