International Journal of Molecular Sciences

11 pages, 3033 KiB

Open AccessArticle

Bolus Effect Caused by Use of Thermoplastic Masks in Head and Neck Radiotherapy Treatments

by Diego A. Barajas-Lopez, Cristian C. Castellanos-Jerez, José A. Diaz-Merchan and S. A. Martinez-Ovalle

Int. J. Mol. Sci. 2024, 25(16), 9133; https://doi.org/10.3390/ijms25169133 - 22 Aug 2024

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Abstract

This paper examines the dosimetric uncertainty arising from the use of thermoplastic masks in the treatment of head and neck cancer through radiotherapy. This study was conducted through Monte Carlo simulations using the Monte Carlo N-Particle eXtended (MCNPX code), and the theoretical results [...] Read more.

This paper examines the dosimetric uncertainty arising from the use of thermoplastic masks in the treatment of head and neck cancer through radiotherapy. This study was conducted through Monte Carlo simulations using the Monte Carlo N-Particle eXtended (MCNPX code), and the theoretical results are compared with radiochromic films. Using material characterization techniques, the compounds of the thermoplastic mask were identified, confirming that most of the material corresponds to the polymer C₁₀H₁₆O₄. The theoretical results show increases ranging from 42% to 57.4% in the surface absorbed dose for 6 and 15 MV photon beams, respectively, compared to the absorbed dose without the mask. The experimental data corroborate these findings, showing dose increases ranging from 18.4% to 52.1% compared to the expected surface absorbed dose without the mask. These results highlight the need to consider the bolus effect induced by thermoplastic masks during the precise and safe planning and application of radiotherapy treatment in order to ensure its therapeutic efficacy and minimize the associated risks to patients. Full article

(This article belongs to the Special Issue Nanotechnology in the Treatment and Diagnosis of Cancer: Opportunities and Challenges)

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13 pages, 4759 KiB

Open AccessArticle

Isolation and Characterization of a Novel Phage against Vibrio alginolyticus Belonging to a New Genus

by Jie Gao, Yuang Zhu, Rui Zhang, Juntian Xu, Runjie Zhou, Meiqi Di, Di Zhang, Wenxin Liang, Xing Zhou, Xing Ren, Huifang Li and Yunlan Yang

Int. J. Mol. Sci. 2024, 25(16), 9132; https://doi.org/10.3390/ijms25169132 - 22 Aug 2024

Cited by 1 | Viewed by 994

Abstract

Vibrio alginolyticus causes substantial economic losses in the aquaculture industry. With the rise of multidrug-resistant Vibrio strains, phages present a promising solution. Here, a novel lytic Vibrio phage, vB_ValC_RH2G (RH2G), that efficiently infects the pathogenic strain V. alginolyticus ATCC 17749^T, was [...] Read more.

Vibrio alginolyticus causes substantial economic losses in the aquaculture industry. With the rise of multidrug-resistant Vibrio strains, phages present a promising solution. Here, a novel lytic Vibrio phage, vB_ValC_RH2G (RH2G), that efficiently infects the pathogenic strain V. alginolyticus ATCC 17749^T, was isolated from mixed wastewater from an aquatic market in Xiamen, China. Transmission electron microscopy revealed that RH2G has the morphology of Siphoviruses, featuring an icosahedral head (73 ± 2 nm diameter) and long noncontractile tail (142 ± 4 nm). A one-step growth experiment showed that RH2G had a short latent period (10 min) and a burst size of 48 phage particles per infected cell. Additionally, RH2G was highly species-specific and was relatively stable at 4–55 °C and pH 4–10. A genomic analysis showed that RH2G has a 116,749 bp double-stranded DNA genome with 43.76% GC content. The intergenomic similarity between the genome sequence of RH2G and other phages recorded in the GenBank database was below 38.8%, suggesting that RH2G represents a new genus. RH2G did not exhibit any virulence or resistance genes. Its rapid lysis capacity, lytic activity, environmental resilience, and genetic safety suggested that RH2G may be a safe candidate for phage therapy in combatting vibriosis in aquaculture settings. Full article

(This article belongs to the Section Molecular Microbiology)

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19 pages, 27849 KiB

Open AccessArticle

Combined Multi-Omics Analysis Reveals the Potential Role of ACADS in Yak Intramuscular Fat Deposition

by Fang Xu, Haibo Wang, Chunyu Qin, Binglin Yue, Youzhualamu Yang, Jikun Wang, Jincheng Zhong and Hui Wang

Int. J. Mol. Sci. 2024, 25(16), 9131; https://doi.org/10.3390/ijms25169131 - 22 Aug 2024

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Abstract

The Yak (Bos grunniens) is a special breed of livestock predominantly distributed in the Qinghai–Tibet Plateau of China. Intramuscular fat (IMF) content in beef cattle is a vital indicator of meat quality. In this study, RNA-Seq and Protein-Seq were respectively employed [...] Read more.

The Yak (Bos grunniens) is a special breed of livestock predominantly distributed in the Qinghai–Tibet Plateau of China. Intramuscular fat (IMF) content in beef cattle is a vital indicator of meat quality. In this study, RNA-Seq and Protein-Seq were respectively employed to sequence the transcriptome and proteome of the longissimus dorsi (LD) tissue from 4-year-old yaks with significant differences in IMF content under the same fattening conditions. Five overlapping genes (MYL3, ACADS, L2HGDH, IGFN1, and ENSBGRG00000000-926) were screened using combined analysis. Functional verification tests demonstrated that the key gene ACADS inhibited yak intramuscular preadipocyte (YIMA) differentiation and proliferation, promoted mitochondrial biogenesis gene expression, and increased the mitochondrial membrane potential (MMP). Furthermore, co-transfection experiments further demonstrated that interfering with ACADS reversed the effect of PPARα agonists in promoting lipid differentiation. In conclusion, ACADS potentially inhibits lipid deposition in YIAMs by regulating the PPARα signalling pathway. These findings offer insights into the molecular mechanisms underlying yak meat quality. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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19 pages, 6280 KiB

Open AccessArticle

Shedding Light on Viral Shedding: Novel Insights into Nuclear Assembly, Cytoplasmic Transformation and Extracellular Vesicle Release of the BK Virus

by Daniela Gerges, Karim Abd El-Ghany, Zsofia Hevesi, Monika Aiad, Haris Omic, Clemens Baumgartner, Wolfgang Winnicki, Michael Eder, Alice Schmidt, Farsad Eskandary and Ludwig Wagner

Int. J. Mol. Sci. 2024, 25(16), 9130; https://doi.org/10.3390/ijms25169130 - 22 Aug 2024

Viewed by 904

Abstract

Despite the high prevalence of BK polyomavirus (BKPyV) and the associated risk for BKPyV-associated nephropathy (BKPyVAN) in kidney transplant (KTX) recipients, many details on viral processes such as replication, maturation, assembly and virion release from host cells have not been fully elucidated. VP1 [...] Read more.

Despite the high prevalence of BK polyomavirus (BKPyV) and the associated risk for BKPyV-associated nephropathy (BKPyVAN) in kidney transplant (KTX) recipients, many details on viral processes such as replication, maturation, assembly and virion release from host cells have not been fully elucidated. VP1 is a polyomavirus-specific protein that is expressed in the late phase of its replicative cycle with important functions in virion assembly and infectious particle release. This study investigated the localization and time-dependent changes in the distribution of VP1-positive viral particles and their association within the spectrum of differing cell morphologies that are observed in the urine of KTX patients upon active BKPyV infection. We found highly differing recognition patterns of two anti-VP1 antibodies with respect to intracellular and extracellular VP1 localization, pointing towards independent binding sites that were seemingly associated with differing stages of virion maturation. Cells originating from single clones were stably cultured out of the urine sediment of KTX recipients with suspected BKPyVAN. The cell morphology, polyploidy, virus replication and protein production were investigated by confocal microscopy using both a monoclonal (mAb 4942) and a polyclonal rabbit anti-VP1-specific antibody (RantiVP1 Ab). Immunoblotting was performed to investigate changes in the VP1 protein. Both antibodies visualized VP1 and the mAb 4942 recognized VP1 in cytoplasmic vesicles exhibiting idiomorphic sizes when released from the cells. In contrast, the polyclonal antibody detected VP1 within the nucleus and in cytoplasm in colocalization with the endoplasmic reticulum marker CNX. At the nuclear rim, VP1 was recognized by both antibodies. Immunoblotting revealed two smaller versions of VP1 in urinary decoy cell extracts, potentially from different translation start sites as evaluated by in silico analysis. Oxford Nanopore sequencing showed integration of BKPyV DNA in chromosomes 3, 4 and 7 in one of the five tested primary cell lines which produced high viral copies throughout four passages before transcending into senescence. The different staining with two VP1-specific antibodies emphasizes the modification of VP1 during the process of virus maturation and cellular exit. The integration of BKPyV into the human genome leads to high virus production; however, this alone does not transform the cell line into a permanently cycling and indefinitely replicating one. Full article

(This article belongs to the Special Issue Virus Infection and Infectious Diseases: Unraveling Mechanisms, Innovations, and Therapeutic Strategies)

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18 pages, 2955 KiB

Open AccessArticle

Fungal Diversity and Gibberellin Hormones Associated with Long Whips of Smut-Infected Sugarcanes

by Syeda Wajeeha Gillani, Lixiu Teng, Abdullah Khan, Yuzhi Xu, Charles A. Powell and Muqing Zhang

Int. J. Mol. Sci. 2024, 25(16), 9129; https://doi.org/10.3390/ijms25169129 - 22 Aug 2024

Viewed by 694

Abstract

Sugarcane smut, caused by the fungus Sporisorium scitamineum (Sydow), significantly affects sugarcane crops worldwide. Infected plants develop whip-like structures known as sori. Significant variations in these whip lengths are commonly observed, but the physiological and molecular differences causing these morphological differences remain poorly [...] Read more.

Sugarcane smut, caused by the fungus Sporisorium scitamineum (Sydow), significantly affects sugarcane crops worldwide. Infected plants develop whip-like structures known as sori. Significant variations in these whip lengths are commonly observed, but the physiological and molecular differences causing these morphological differences remain poorly documented. To address this, we employed conventional microbe isolation, metagenomic, and metabolomic techniques to investigate smut-infected sugarcane stems and whips of varying lengths. Metagenomics analysis revealed a diverse fungal community in the sugarcane whips, with Sporisorium and Fusarium genera notably present (>1%) in long whips. Isolation techniques confirmed these findings. Ultra-performance liquid chromatography analysis (UHPLC-MS/MS) showed high levels of gibberellin hormones (GA₃, GA₁, GA₄, GA₈, and GA₇) in long whips, with GA₄ and GA₇ found exclusively in long whips and stems. Among the prominent genera present within long whips, Fusarium was solely positively correlated with these gibberellin (GA) hormones, with the exception of GA₈, which was positively correlated with Sporisorium. KEGG enrichment analysis linked these hormones to pathways like diterpenoid biosynthesis and plant hormone signal transduction. These findings suggest that Fusarium may influence GA production leading to whip elongation. Our study reveals fungal dynamics and gibberellin responses in sugarcane smut whips. Future research will explore the related molecular gibberellin synthesis mechanisms. Full article

(This article belongs to the Section Molecular Plant Sciences)

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18 pages, 10100 KiB

Open AccessArticle

Integrated Morphological, Comparative Transcriptomic, and Metabolomic Analyses Reveal Mechanisms Underlying Seasonal Patterns of Variation in Spines of the Giant Spiny Frog (Quasipaa spinosa)

by Gang Wan, Ze-Yuan Jiang, Nuo Shi, Yi-Ge Xiong and Rong-Quan Zheng

Int. J. Mol. Sci. 2024, 25(16), 9128; https://doi.org/10.3390/ijms25169128 - 22 Aug 2024

Viewed by 687

Abstract

Quasipaa spinosa, commonly known as the spiny frog, is an economically valued amphibian in China prized for its tender meat and nutritional value. This species exhibits marked sexual dimorphism, most notably the prominent spiny structures on males that are pivotal for mating [...] Read more.

Quasipaa spinosa, commonly known as the spiny frog, is an economically valued amphibian in China prized for its tender meat and nutritional value. This species exhibits marked sexual dimorphism, most notably the prominent spiny structures on males that are pivotal for mating success and species identification. The spines of Q. spinosa exhibit strong seasonal variation, changing significantly with the reproductive cycle, which typically spans from April to October. Sexually mature males develop densely packed, irregularly arranged round papillae with black spines on their chests during the breeding season, which may then reduce or disappear afterward, while females have smooth chest skin. Despite their ecological importance, the developmental mechanisms and biological functions of these spines have been inadequately explored. This study integrates morphological, transcriptomic, and metabolomic analyses to elucidate the mechanisms underlying the seasonal variation in spine characteristics of Q. spinosa. Our results demonstrate that spine density inversely correlates with body size and that spine development is accompanied by significant changes in epidermal thickness and keratinization during the breeding season. Comparative transcriptomic analysis across different breeding stages revealed significant gene expression alterations in pathways related to extracellular matrix interactions, tyrosine metabolism, Wnt signaling, and melanogenesis. Metabolomic analysis further identified significant seasonal shifts in metabolites essential for energy metabolism and melanin synthesis, including notable increases in citric acid and β-alanine. These molecular changes are consistent with the observed morphological adaptations, suggesting a complex regulatory mechanism supporting spine development and functionality. This study provides novel insights into the molecular basis of spine morphogenesis and its seasonal dynamics in Q. spinosa, contributing valuable information for the species’ conservation and aquaculture. Full article

(This article belongs to the Section Molecular Biology)

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18 pages, 2355 KiB

Open AccessArticle

Pitfalls When Determining HNA-1 Genotypes and Finding Novel Alleles

by Kirstine Kløve-Mogensen, Tom Browne, Thure Mors Haunstrup and Rudi Steffensen

Int. J. Mol. Sci. 2024, 25(16), 9127; https://doi.org/10.3390/ijms25169127 - 22 Aug 2024

Viewed by 662

Abstract

Genetic variation in the FCGR3B gene is responsible for different variants of human neutrophil antigen 1 (HNA-1). Laboratory techniques currently utilized for routine HNA-1 genotyping, predominantly PCR-sequence-specific primer (PCR-SSP) and PCR-sequence-based typing (PCR-SBT), lack specificity for FCGR3B. This study compares the capabilities [...] Read more.

Genetic variation in the FCGR3B gene is responsible for different variants of human neutrophil antigen 1 (HNA-1). Laboratory techniques currently utilized for routine HNA-1 genotyping, predominantly PCR-sequence-specific primer (PCR-SSP) and PCR-sequence-based typing (PCR-SBT), lack specificity for FCGR3B. This study compares the capabilities and limitations of existing technologies including an in-house TaqMan PCR, a commercial PCR-SSP test, PCR-SBT and multiplex ligation-dependent probe amplification (MLPA) with those of a long-read nanopore sequencing assay. Testing was performed with both related and unrelated Danish samples with different copy numbers and/or rare alleles. Long-read nanopore sequencing was validated by blind testing of ten English samples. The results showed that FCGR3B copy numbers correlate with a dose-dependent distribution of alleles that complicates genotyping by TaqMan PCR, PCR-SSP and PCR-SBT, due to co-amplification of the homologous FCGR3A gene. MLPA can correctly quantify the dose-dependent distribution but not detect novel variants. Long-read nanopore sequencing showed high specificity for FCGR3B and was able to detect dosage-dependent distribution, and rare and novel variants that were previously not described. Current HNA-1 genotyping methods cannot produce unambiguous allele-level results, whereas long-read nanopore sequencing has shown the potential to resolve observed ambiguities, identify new HNA-1 variants and allow definitive allele assignment. Full article

(This article belongs to the Special Issue Neutrophil in Cell Biology and Diseases 2.0)

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25 pages, 10051 KiB

Open AccessReview

Functional Materials from Biomass-Derived Terpyridines: State of the Art and Few Possible Perspectives

by Jérôme Husson

Int. J. Mol. Sci. 2024, 25(16), 9126; https://doi.org/10.3390/ijms25169126 - 22 Aug 2024

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Abstract

This review focuses on functional materials that contain terpyridine (terpy) units, which can be synthesized from biomass-derived platform chemicals. The latter are obtained by the chemical conversion of raw biopolymers such as cellulose (e.g., 2-furaldehyde) or lignin (e.g., syringaldehyde). These biomass-derived platform chemicals [...] Read more.

This review focuses on functional materials that contain terpyridine (terpy) units, which can be synthesized from biomass-derived platform chemicals. The latter are obtained by the chemical conversion of raw biopolymers such as cellulose (e.g., 2-furaldehyde) or lignin (e.g., syringaldehyde). These biomass-derived platform chemicals serve as starting reagents for the preparation of many different terpyridine derivatives using various synthetic strategies (e.g., Kröhnke reaction, cross-coupling reactions). Chemical transformations of these terpyridines provide a broad range of different ligands with various functionalities to be used for the modification or construction of various materials. Either inorganic materials (such as oxides) or organic ones (such as polymers) can be combined with terpyridines to provide functional materials. Different strategies are presented for grafting terpy to materials, such as covalent grafting through a carboxylic acid or silanization. Furthermore, terpy can be used directly for the elaboration of functional materials via complexation with metals. The so-obtained functional materials find various applications, such as photovoltaic devices, heterogeneous catalysts, metal–organic frameworks (MOF), and metallopolymers. Finally, some possible developments are presented. Full article

(This article belongs to the Special Issue Biomass-Derived Materials: Synthesis and Applications)

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10 pages, 2547 KiB

Open AccessArticle

Sirtuin 5 (SIRT5) Suppresses Tumor Growth by Regulating Mitochondrial Metabolism and Synaptic Remodeling in Gliomas

by Wanjun Tang, Bo Chen, Gilberto Ka-Kit Leung and Karrie M. Kiang

Int. J. Mol. Sci. 2024, 25(16), 9125; https://doi.org/10.3390/ijms25169125 - 22 Aug 2024

Viewed by 798

Abstract

Sirtuin 5 (SIRT5) is increasingly recognized as a key regulator of cellular metabolism, which is commonly dysregulated in cancer cells, resulting in enhanced proliferation and tumor progression. To investigate the clinicopathologic implications of SIRT5 dysregulation in glioblastoma, we performed comprehensive analyses of transcriptomic [...] Read more.

Sirtuin 5 (SIRT5) is increasingly recognized as a key regulator of cellular metabolism, which is commonly dysregulated in cancer cells, resulting in enhanced proliferation and tumor progression. To investigate the clinicopathologic implications of SIRT5 dysregulation in glioblastoma, we performed comprehensive analyses of transcriptomic data and functional verifications using in vitro and in vivo glioblastoma models. We found that higher SIRT5 expression levels were associated with a favorable prognosis in glioma patients. Knockdown of SIRT5 significantly enhanced glioblastoma cell growth. Our data suggest its potential role in regulating mitochondrial metabolism in gliomas. Furthermore, SIRT5 is also significantly correlated with synaptic remodeling pathways. Our findings indicate a tumor-suppressive role for SIRT5 that extends beyond regulating cancer metabolism, by which it may function through modulating neuroplasticity. Understanding these cellular interactions provides nuanced insights into the multifaceted role of SIRT5 and the broader therapeutic implications of this for the development of novel treatment strategies. Full article

(This article belongs to the Special Issue Molecular Targeted Therapy for Gliomas)

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27 pages, 10586 KiB

Open AccessArticle

Integrative Analyses Reveal the Physiological and Molecular Role of Prohexadione Calcium in Regulating Salt Tolerance in Rice

by Rui Deng, Yao Li, Nai-Jie Feng, Dian-Feng Zheng, You-Wei Du, Aaqil Khan, Ying-Bin Xue, Jian-Qin Zhang and Ya-Nan Feng

Int. J. Mol. Sci. 2024, 25(16), 9124; https://doi.org/10.3390/ijms25169124 - 22 Aug 2024

Cited by 1 | Viewed by 675

Abstract

Salinity stress severely restricts rice growth. Prohexadione calcium (Pro-Ca) modulation can effectively alleviate salt stress in rice. In this study, we explored the effects of Pro-Ca on enhancing salt tolerance in two rice varieties, IR29 and HD96-1. The results revealed that Pro-Ca [...] Read more.

Salinity stress severely restricts rice growth. Prohexadione calcium (Pro-Ca) modulation can effectively alleviate salt stress in rice. In this study, we explored the effects of Pro-Ca on enhancing salt tolerance in two rice varieties, IR29 and HD96-1. The results revealed that Pro-Ca markedly enhanced root and shoot morphological traits and improved plant biomass under salt stress. Chlorophyll a and b content were significantly increased, which improved photosynthetic capacity. Transcriptomic and metabolomic data showed that Pro-Ca significantly up-regulated the expression of genes involved in E3 ubiquitin ligases in IR29 and HD96-1 by 2.5-fold and 3-fold, respectively, thereby maintaining Na⁺ and K⁺ homeostasis by reducing Na⁺. Moreover, Pro-Ca treatment significantly down-regulated the expression of Lhcb1, Lhcb2, Lhcb3, Lhcb5, and Lhcb6 in IR29 under salt stress, which led to an increase in photosynthetic efficiency. Furthermore, salt stress + Pro-Ca significantly increased the A-AAR of IR29 and HD96-1 by 2.9-fold and 2.5-fold, respectively, and inhibited endogenous cytokinin synthesis and signal transduction, which promoted root growth. The current findings suggested that Pro-Ca effectively alleviated the harmful effects of salt stress on rice by maintaining abscisic acid content and by promoting oxylipin synthesis. This study provides a molecular basis for Pro-Ca to alleviate salt stress in rice. Full article

(This article belongs to the Section Molecular Plant Sciences)

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23 pages, 2639 KiB

Open AccessArticle

The Impact of the Major Endoribonucleases RNase E and RNase III and of the sRNA StsR on Photosynthesis Gene Expression in Rhodobacter sphaeroides Is Growth-Phase-Dependent

by Janek Börner, Julian Grützner, Florian Gerken and Gabriele Klug

Int. J. Mol. Sci. 2024, 25(16), 9123; https://doi.org/10.3390/ijms25169123 - 22 Aug 2024

Viewed by 603

Abstract

Rhodobacter sphaeroides is a facultative phototrophic bacterium that performs aerobic respiration when oxygen is available. Only when oxygen is present at low concentrations or absent are pigment–protein complexes formed, and anoxygenic photosynthesis generates ATP. The regulation of photosynthesis genes in response to oxygen [...] Read more.

Rhodobacter sphaeroides is a facultative phototrophic bacterium that performs aerobic respiration when oxygen is available. Only when oxygen is present at low concentrations or absent are pigment–protein complexes formed, and anoxygenic photosynthesis generates ATP. The regulation of photosynthesis genes in response to oxygen and light has been investigated for decades, with a focus on the regulation of transcription. However, many studies have also revealed the importance of regulated mRNA processing. This study analyzes the phenotypes of wild type and mutant strains and compares global RNA-seq datasets to elucidate the impact of ribonucleases and the small non-coding RNA StsR on photosynthesis gene expression in Rhodobacter. Most importantly, the results demonstrate that, in particular, the role of ribonuclease E in photosynthesis gene expression is strongly dependent on growth phase. Full article

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

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12 pages, 3497 KiB

Open AccessArticle

Automatic Detection of the EEG Spike–Wave Patterns in Epilepsy: Evaluation of the Effects of Transcranial Current Stimulation Therapy

by Elzbieta Olejarczyk, Aleksander Sobieszek and Giovanni Assenza

Int. J. Mol. Sci. 2024, 25(16), 9122; https://doi.org/10.3390/ijms25169122 - 22 Aug 2024

Viewed by 757

Abstract

This study aims to develop a detection method based on morphological features of spike–wave (SW) patterns in the EEG of epilepsy patients and evaluate the effect of cathodal transcranial direct current stimulation (ctDCS) treatment. The proposed method is based on several simple features [...] Read more.

This study aims to develop a detection method based on morphological features of spike–wave (SW) patterns in the EEG of epilepsy patients and evaluate the effect of cathodal transcranial direct current stimulation (ctDCS) treatment. The proposed method is based on several simple features describing the shape of SW patterns and their synchronous occurrence on at least two EEG channels. High sensitivity, specificity and selectivity values were achieved for each patient and condition. ctDCS resulted in a significant reduction in the number of detected patterns, a decrease in spike duration and amplitude, and an increased spike mobility. The proposed method allows efficient identification of SW patterns regardless of brain condition, although the recruitment of patterns may be modified by ctDCS. This method can be useful in the clinical evaluation of ctDCS effects. Full article

(This article belongs to the Special Issue Epilepsy: From Molecular Basis to Therapy)

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13 pages, 15408 KiB

Open AccessArticle

Expression in Pichia pastoris of Thermostable Endo-1,4-β-xylanase from the Actinobacterium Nocardiopsis halotolerans: Properties and Use for Saccharification of Xylan-Containing Products

by Alexander V. Lisov, Oksana V. Belova, Andrey A. Belov, Zoya A. Lisova, Alexey S. Nagel, Andrey M. Shadrin, Zhanna I. Andreeva-Kovalevskaya, Maxim O. Nagornykh, Marina V. Zakharova and Alexey A. Leontievsky

Int. J. Mol. Sci. 2024, 25(16), 9121; https://doi.org/10.3390/ijms25169121 - 22 Aug 2024

Viewed by 776

Abstract

A gene encoding a polysaccharide-degrading enzyme was cloned from the genome of the bacterium Nocardiopsis halotolerans. Analysis of the amino acid sequence of the protein showed the presence of the catalytic domain of the endo-1,4-β-xylanases of the GH11 family. The gene was [...] Read more.

A gene encoding a polysaccharide-degrading enzyme was cloned from the genome of the bacterium Nocardiopsis halotolerans. Analysis of the amino acid sequence of the protein showed the presence of the catalytic domain of the endo-1,4-β-xylanases of the GH11 family. The gene was amplified by PCR and ligated into the pPic9m vector. A recombinant producer based on Pichia pastoria was obtained. The production of the enzyme, which we called NhX1, was carried out in a 10 L fermenter. Enzyme production was 10.4 g/L with an activity of 927 U/mL. Purification of NhX1 was carried out using Ni-NTA affinity chromatography. The purified enzyme catalyzed the hydrolysis of xylan but not other polysaccharides. Endo-1,4-β-xylanase NhX1 showed maximum activity and stability at pH 6.0–7.0. The enzyme showed high thermal stability, remaining active at 90 °C for 20 min. With beechwood xylan, the enzyme showed K_m 2.16 mg/mL and V_max 96.3 U/mg. The products of xylan hydrolysis under the action of NhX1 were xylobiose, xylotriose, xylopentaose, and xylohexaose. Endo-1,4-β-xylanase NhX1 effectively saccharified xylan-containing products used for the production of animal feed. The xylanase described herein is a thermostable enzyme with biotechnological potential produced in large quantities by P. pastoria. Full article

(This article belongs to the Section Macromolecules)

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15 pages, 5472 KiB

Open AccessArticle

Elucidating Chiral Resolution of Aromatic Amino Acids Using Glycopeptide Selectors: A Combined Molecular Docking and Chromatographic Study

by Dehbiya Gherdaoui, Madiha Melha Yahoum, Selma Toumi, Sabrina Lekmine, Sonia Lefnaoui, Ouided Benslama, Rachida Bouallouche, Hichem Tahraoui, Mohammad Shamsul Ola, Ahmad Ali, Jie Zhang and Abdeltif Amrane

Int. J. Mol. Sci. 2024, 25(16), 9120; https://doi.org/10.3390/ijms25169120 - 22 Aug 2024

Viewed by 834

Abstract

An asymmetric synthesis is a favorable approach for obtaining enantiomerically pure substances, but racemic resolution remains an efficient strategy. This study aims to elucidate the chiral resolution of aromatic amino acids and their elution order using glycopeptides as chiral selectors through molecular docking [...] Read more.

An asymmetric synthesis is a favorable approach for obtaining enantiomerically pure substances, but racemic resolution remains an efficient strategy. This study aims to elucidate the chiral resolution of aromatic amino acids and their elution order using glycopeptides as chiral selectors through molecular docking analysis. Chiral separation experiments were conducted using Vancomycin as a chiral additive in the mobile phase (CMPA) at various concentrations, coupled with an achiral amino column as the stationary phase. The Autodock Vina 1.1.2 software was employed to perform molecular docking simulations between each enantiomer (ligand) and Vancomycin (receptor) to evaluate binding affinities, demonstrate enantiomeric resolution feasibility, and elucidate chiral recognition mechanisms. Utilizing Vancomycin as CMPA at a concentration of 1.5 mM enabled the separation of tryptophan enantiomers with a resolution of 3.98 and tyrosine enantiomers with a resolution of 2.97. However, a poor chiral resolution was observed for phenylalanine and phenylglycine. Molecular docking analysis was employed to elucidate the lack of separation and elution order for tryptophan and tyrosine enantiomers. By calculating the binding energy, docking results were found to be in good agreement with experimental findings, providing insights into the underlying mechanisms governing chiral recognition in this system and the interaction sites. This comprehensive approach clarifies the complex relationship between chiral discrimination and molecular architecture, offering valuable information for creating and improving chiral separation protocols. Full article

(This article belongs to the Special Issue Molecular Novelties in Chiral Enantioseparation and Discrimination)

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12 pages, 988 KiB

Open AccessArticle

Transferrin-Conjugated Nanostructured Lipid Carriers for Targeting Artemisone to Melanoma Cells

by Njoud Altuwaijri and Eman Atef

Int. J. Mol. Sci. 2024, 25(16), 9119; https://doi.org/10.3390/ijms25169119 - 22 Aug 2024

Viewed by 819

Abstract

We report a successful formulation of Artemisone (ATM) in transferrin (Tf)-conjugated nanostructured lipid carriers (NLCs), achieving nearly a five-times increase in cell toxicity. The escalating cost of new drug discoveries led to the repurposing of approved drugs for new indications. This study incorporated [...] Read more.

We report a successful formulation of Artemisone (ATM) in transferrin (Tf)-conjugated nanostructured lipid carriers (NLCs), achieving nearly a five-times increase in cell toxicity. The escalating cost of new drug discoveries led to the repurposing of approved drugs for new indications. This study incorporated Artemisone, an antimalarial drug, into a nanostructured lipid carrier (NLC) and tested for possible anticancer effects. The aim was to develop NLCs, and transferrin-conjugated NLCs (NLC-Tf) encapsulating Artemisone to enhance its delivery and anticancer activity. NLC formulations were prepared using high-pressure homogenization followed by ultrasonication and were characterized by particle size, zeta potential, and PDI. The conjugation of (Tf) to (NLC) was confirmed using IR, and the anticancer activity was tested using MTS assay. All formulations were in the nanometer size range (140–167 nm) with different zeta potential values. IR spectroscopy confirmed the successful conjugation of transferrin to NLC. Upon testing the formulations on melanoma cell lines using MTS assay, there was a significant decrease in viability and an increase in the encapsulated ATM-Tf toxicity compared to positive control ATM. The NLCs presented a promising potential carrier for delivering ATM to melanoma cells, and further conjugation with Tf significantly improved the ATM cytotoxicity. Full article

(This article belongs to the Special Issue Functional Molecules in Tracing and Cancer Therapeutics)

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26 pages, 2740 KiB

Open AccessReview

Dietary Polyphenols and Gut Microbiota Cross-Talk: Molecular and Therapeutic Perspectives for Cardiometabolic Disease: A Narrative Review

by Raquel Cano, Valmore Bermúdez, Nestor Galban, Bermary Garrido, Raquel Santeliz, Maria Paula Gotera, Pablo Duran, Arturo Boscan, Ana-Karina Carbonell-Zabaleta, Samuel Durán-Agüero, Diana Rojas-Gómez, Jorge González-Casanova, Waldo Díaz-Vásquez, Maricarmen Chacín and Lissé Angarita Dávila

Int. J. Mol. Sci. 2024, 25(16), 9118; https://doi.org/10.3390/ijms25169118 - 22 Aug 2024

Cited by 1 | Viewed by 1838

Abstract

The intricate interplay between the gut microbiota and polyphenols has emerged as a captivating frontier in understanding and potentially harnessing the therapeutic potential of these bioactive compounds. Phenolic compounds, renowned for their antioxidant, anti-inflammatory, antidiabetic, and anticancer properties, are subject to intricate transformations [...] Read more.

The intricate interplay between the gut microbiota and polyphenols has emerged as a captivating frontier in understanding and potentially harnessing the therapeutic potential of these bioactive compounds. Phenolic compounds, renowned for their antioxidant, anti-inflammatory, antidiabetic, and anticancer properties, are subject to intricate transformations within the gut milieu, where the diverse microbial ecosystem exerts profound effects on their metabolism and bioavailability. Conversely, polyphenols exhibit a remarkable capacity to modulate the composition and activity of the gut microbiota, fostering a bidirectional relationship that extends beyond mere nutrient processing. This symbiotic interaction holds significant implications for human health, particularly in cardiometabolic diseases such as diabetes mellitus, metabolic-dysfunction-associated steatotic liver disease, and cardiovascular disease. Through a comprehensive exploration of molecular interactions, this narrative review elucidates the reciprocal dynamics between the gut microbiota and polyphenols, unveiling novel avenues for therapeutic intervention in cardiometabolic disorders. By unravelling the intricate cross-talk between these two entities, this review underscores the multifaceted roles of polyphenols in overall health and the pivotal role of gut microbiota modulation as a promising therapeutic strategy in mitigating the burden of cardiometabolic diseases. Full article

(This article belongs to the Special Issue The Role of Dysbiosis in Chronic Diseases)

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13 pages, 3589 KiB

Open AccessArticle

Integrated Analysis of Phagocytic and Immunomodulatory Markers in Cervical Cancer Reveals Constellations of Potential Prognostic Relevance

by Angel Yordanov, Polina Damyanova, Mariela Vasileva-Slaveva, Ihsan Hasan, Stoyan Kostov and Velizar Shivarov

Int. J. Mol. Sci. 2024, 25(16), 9117; https://doi.org/10.3390/ijms25169117 - 22 Aug 2024

Viewed by 922

Abstract

Despite improvements in vaccination, screening, and treatment, cervical cancer (CC) remains a major healthcare problem on a global scale. The tumor microenvironment (TME) plays an important and controversial role in cancer development, and the mechanism of the tumor’s escape from immunological surveillance is [...] Read more.

Despite improvements in vaccination, screening, and treatment, cervical cancer (CC) remains a major healthcare problem on a global scale. The tumor microenvironment (TME) plays an important and controversial role in cancer development, and the mechanism of the tumor’s escape from immunological surveillance is still not clearly defined. We aim to investigate the expression of CD68 and CD47 in patients with different histological variants of CC, tumor characteristics, and burden. This is a retrospective cohort study performed on paraffin-embedded tumor tissues from 191 patients diagnosed with CC between 2014 and 2021 at the Medical University Pleven, Bulgaria. Slides for immunohistochemical (IHC) evaluation were obtained, and the expression of CD68 was scored in intratumoral (IT) and stromal (ST) macrophages (CD68+cells) using a three-point scoring scale. The CD47 expression was reported as an H-score. All statistical analyses were performed using R v. 4.3.1 for Windows. Infiltration by CD68-IT cells in the tumor depended on histological type and the expression of CD47. Higher levels of the CD47 H-score were significantly more frequent among patients in the early stage. Higher levels of infiltration by CD68-ST cells were associated with worse prognosis, and the infiltration of CD68-IT cells was associated with reduced risk of death from neoplastic disease. TME is a complex ecosystem that has a major role in the growth and development of tumors. Macrophages are a major component of innate immunity and, when associated with a tumor process, are defined as TAM. Tumor cells try to escape immunological surveillance in three ways, and one of them is reducing immunogenicity by the overexpression of negative coreceptors by T-lymphocytes and their ligands on the surface of tumor cells. One such mechanism is the expression of CD47 in tumor cells, which sends a “don’t eat me” signal to the macrophages and, thus, prevents phagocytosis. To our knowledge, this is the first study that has tried to establish the relationship between the CD47 and CD68 expression levels and some clinicopathologic features in CC. We found that the only clinicopathological feature implicating the level of CD68 infiltration was the histological variant of the tumor, and only for CD68-IT–high levels were these observed in SCC. High levels of CD47 expression were seen more frequently in pT1B than pT2A and pT2B in the FIGO I stage than in the FIGO II and III stages. Infiltration by large numbers of CD68-IT cells was much more common among patients with a high expression of CD47 in tumor cells. A high level of infiltration by CD68-ST cells was associated with a worse prognosis, and a high level of infiltration by CD68-ST cells was associated with a lower risk of death from cancer. Full article

(This article belongs to the Special Issue Role of Immune Cells in Non-infectious Inflammatory Diseases and Cancers)

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25 pages, 6239 KiB

Open AccessReview

Dietary Exposure to Pesticide and Veterinary Drug Residues and Their Effects on Human Fertility and Embryo Development: A Global Overview

by Ambra Colopi, Eugenia Guida, Silvia Cacciotti, Serena Fuda, Matteo Lampitto, Angelo Onorato, Alice Zucchi, Carmela Rita Balistreri, Paola Grimaldi and Marco Barchi

Int. J. Mol. Sci. 2024, 25(16), 9116; https://doi.org/10.3390/ijms25169116 - 22 Aug 2024

Viewed by 1548

Abstract

Drug residues that contaminate food and water represent a serious concern for human health. The major concerns regard the possible irrational use of these contaminants, since this might increase the amplitude of exposure. Multiple sources contribute to the overall exposure to contaminants, including [...] Read more.

Drug residues that contaminate food and water represent a serious concern for human health. The major concerns regard the possible irrational use of these contaminants, since this might increase the amplitude of exposure. Multiple sources contribute to the overall exposure to contaminants, including agriculture, domestic use, personal, public and veterinary healthcare, increasing the possible origin of contamination. In this review, we focus on crop pesticides and veterinary drug residues because of their extensive use in modern agriculture and farming, which ensures food production and security for the ever-growing population around the world. We discuss crop pesticides and veterinary drug residues with respect to their worldwide distribution and impacts, with special attention on their harmful effects on human reproduction and embryo development, as well as their link to epigenetic alterations, leading to intergenerational and transgenerational diseases. Among the contaminants, the most commonly implicated in causing such disorders are organophosphates, glyphosate and antibiotics, with tetracyclines being the most frequently reported. This review highlights the importance of finding new management strategies for pesticides and veterinary drugs. Moreover, due to the still limited knowledge on inter- and transgenerational effects of these contaminants, we underlie the need to strengthen research in this field, so as to better clarify the specific effects of each contaminant and their long-term impact. Full article

(This article belongs to the Section Biochemistry)

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21 pages, 8172 KiB

Open AccessArticle

Differentiation of Spiral Ganglion Neurons from Human Dental Pulp Stem Cells: A Further Step towards Autologous Auditory Nerve Recovery

by Yassine Messat, Marta Martin-Fernandez, Said Assou, Keshi Chung, Frederic Guérin, Csilla Gergely, Frederic Cuisinier and Azel Zine

Int. J. Mol. Sci. 2024, 25(16), 9115; https://doi.org/10.3390/ijms25169115 - 22 Aug 2024

Viewed by 1026

Abstract

The degeneration of spiral ganglion neurons (SGNs), which convey auditory signals from hair cells to the brain, can be a primary cause of sensorineural hearing loss (SNHL) or can occur secondary to hair cell loss. Emerging therapies for SNHL include the replacement of [...] Read more.

The degeneration of spiral ganglion neurons (SGNs), which convey auditory signals from hair cells to the brain, can be a primary cause of sensorineural hearing loss (SNHL) or can occur secondary to hair cell loss. Emerging therapies for SNHL include the replacement of damaged SGNs using stem cell-derived otic neuronal progenitors (ONPs). However, the availability of renewable, accessible, and patient-matched sources of human stem cells is a prerequisite for successful replacement of the auditory nerve. In this study, we derived ONP and SGN-like cells by a reliable and reproducible stepwise guidance differentiation procedure of self-renewing human dental pulp stem cells (hDPSCs). This in vitro differentiation protocol relies on the modulation of BMP and TGFβ pathways using a free-floating 3D neurosphere method, followed by differentiation on a Geltrex-coated surface using two culture paradigms to modulate the major factors and pathways involved in early otic neurogenesis. Gene and protein expression analyses revealed efficient induction of a comprehensive panel of known ONP and SGN-like cell markers during the time course of hDPSCs differentiation. Atomic force microscopy revealed that hDPSC-derived SGN-like cells exhibit similar nanomechanical properties as their in vivo SGN counterparts. Furthermore, spiral ganglion neurons from newborn rats come in close contact with hDPSC-derived ONPs 5 days after co-culturing. Our data demonstrate the capability of hDPSCs to generate SGN-like neurons with specific lineage marker expression, bipolar morphology, and the nanomechanical characteristics of SGNs, suggesting that the neurons could be used for next-generation cochlear implants and/or inner ear cell-based strategies for SNHL. Full article

(This article belongs to the Special Issue Hearing Loss: Molecular Biological Insights)

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14 pages, 3683 KiB

Open AccessArticle

Analysis of Correlation Effects of Double Mutations in Enzymes: A Revised Residual-Contact Network Clique Model

by Xianbo Zhang, Junpeng Xu and Dengming Ming

Int. J. Mol. Sci. 2024, 25(16), 9114; https://doi.org/10.3390/ijms25169114 - 22 Aug 2024

Viewed by 1026

Abstract

The relationship between amino acid mutations and enzyme bioactivity is a significant challenge in modern bio-industrial applications. Despite many successful designs relying on complex correlations among mutations at different enzyme sites, the underlying mechanisms of these correlations still need to be explored. In [...] Read more.

The relationship between amino acid mutations and enzyme bioactivity is a significant challenge in modern bio-industrial applications. Despite many successful designs relying on complex correlations among mutations at different enzyme sites, the underlying mechanisms of these correlations still need to be explored. In this study, we introduced a revised version of the residual-contact network clique model to investigate the additive effect of double mutations based on the mutation occurrence topology, secondary structures, and physicochemical properties. The model was applied to a set of 182 double mutations reported in three extensively studied enzymes, and it successfully identified over 90% of additive double mutations and a majority of non-additive double mutations. The calculations revealed that the mutation additivity depends intensely on the studied mutation sites’ topology and physicochemical properties. For example, double mutations on irregular secondary structure regions tend to be non-additive. Our method provides valuable tools for facilitating enzyme design and optimization. The code and relevant data are available at Github. Full article

(This article belongs to the Special Issue Structural and Functional Analysis of Amino Acids and Proteins)

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26 pages, 1831 KiB

Open AccessReview

Molecular Aspects in the Development of Type 2 Diabetes and Possible Preventive and Complementary Therapies

by Laura Simon-Szabó, Beáta Lizák, Gábor Sturm, Anikó Somogyi, István Takács and Zsuzsanna Németh

Int. J. Mol. Sci. 2024, 25(16), 9113; https://doi.org/10.3390/ijms25169113 - 22 Aug 2024

Viewed by 1204

Abstract

The incidence of diabetes, including type 2 diabetes (T2DM), is increasing sharply worldwide. To reverse this, more effective approaches in prevention and treatment are needed. In our review, we sought to summarize normal insulin action and the pathways that primarily influence the development [...] Read more.

The incidence of diabetes, including type 2 diabetes (T2DM), is increasing sharply worldwide. To reverse this, more effective approaches in prevention and treatment are needed. In our review, we sought to summarize normal insulin action and the pathways that primarily influence the development of T2DM. Normal insulin action involves mitogenic and metabolic pathways, as both are important in normal metabolic processes, regeneration, etc. However, through excess energy, both can be hyperactive or attenuated/inactive leading to disturbances in the cellular and systemic regulation with the consequence of cellular stress and systemic inflammation. In this review, we detailed the beneficial molecular changes caused by some important components of nutrition and by exercise, which act in the same molecular targets as the developed drugs, and can revert the damaged pathways. Moreover, these induce entire networks of regulatory mechanisms and proteins to restore unbalanced homeostasis, proving their effectiveness as preventive and complementary therapies. These are the main steps for success in prevention and treatment of developed diseases to rid the body of excess energy, both from stored fats and from overnutrition, while facilitating fat burning with adequate, regular exercise in healthy people, and together with necessary drug treatment as required in patients with insulin resistance and T2DM. Full article

(This article belongs to the Section Biochemistry)

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17 pages, 5868 KiB

Open AccessArticle

Revisiting the Injury Mechanism of Goat Sperm Caused by the Cryopreservation Process from a Perspective of Sperm Metabolite Profiles

by Chunyan Li, Chunrong Lv, Allai Larbi, Jiachong Liang, Qige Yang, Guoquan Wu and Guobo Quan

Int. J. Mol. Sci. 2024, 25(16), 9112; https://doi.org/10.3390/ijms25169112 - 22 Aug 2024

Viewed by 747

Abstract

Semen cryopreservation results in the differential remodeling of the molecules presented in sperm, and these alterations related to reductions in sperm quality and its physiological function have not been fully understood. Given this, this study aimed to investigate the cryoinjury mechanism of goat [...] Read more.

Semen cryopreservation results in the differential remodeling of the molecules presented in sperm, and these alterations related to reductions in sperm quality and its physiological function have not been fully understood. Given this, this study aimed to investigate the cryoinjury mechanism of goat sperm by analyzing changes of the metabolic characteristics in sperm during the cryopreservation process. The ultra-high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) technique was performed to explore metabolite profiles of fresh sperm (C group), equilibrated sperm (E group), and frozen–thawed sperm (F group). In total, 2570 metabolites in positive mode and 2306 metabolites in negative mode were identified, respectively. After comparative analyses among these three groups, 374 differentially abundant metabolites (DAMs) in C vs. E, 291 DAMs in C vs. F, and 189 DAMs in E vs. F were obtained in the positive mode; concurrently, 530 DAMs in C vs. E, 405 DAMs in C vs. F, and 193 DAMs in E vs. F were obtained in the negative mode, respectively. The DAMs were significantly enriched in various metabolic pathways, including 31 pathways in C vs. E, 25 pathways in C vs. F, and 28 pathways in E vs. F, respectively. Among them, 65 DAMs and 25 significantly enriched pathways across the three comparisons were discovered, which may be tightly associated with sperm characteristics and function. Particularly, the functional terms such as TCA cycle, biosynthesis of unsaturated fatty acids, sphingolipid metabolism, glycine, serine and threonine metabolism, alpha-linolenic acid metabolism, and pyruvate metabolism, as well as associated pivotal metabolites like ceramide, betaine, choline, fumaric acid, L-malic acid and L-lactic acid, were focused on. In conclusion, our research characterizes the composition of metabolites in goat sperm and their alterations induced by the cryopreservation process, offering a critical foundation for further exploring the molecular mechanisms of metabolism influencing the quality and freezing tolerance of goat sperm. Additionally, the impacts of equilibration at low temperature on sperm quality may need more attentions as compared to the freezing and thawing process. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Mechanisms of Sperm Metabolism and Development)

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22 pages, 16202 KiB

Open AccessArticle

Multi-Omics Integrative Analysis to Reveal the Impacts of Shewanella algae on the Development and Lifespan of Marine Nematode Litoditis marina

by Yiming Xue, Beining Xue and Liusuo Zhang

Int. J. Mol. Sci. 2024, 25(16), 9111; https://doi.org/10.3390/ijms25169111 - 22 Aug 2024

Viewed by 972

Abstract

Understanding how habitat bacteria affect animal development, reproduction, and aging is essential for deciphering animal biology. Our recent study showed that Shewanella algae impaired Litoditis marina development and lifespan, compared with Escherichia coli OP50 feeding; however, the underlying mechanisms remain unclear. Here, multi-omics [...] Read more.

Understanding how habitat bacteria affect animal development, reproduction, and aging is essential for deciphering animal biology. Our recent study showed that Shewanella algae impaired Litoditis marina development and lifespan, compared with Escherichia coli OP50 feeding; however, the underlying mechanisms remain unclear. Here, multi-omics approaches, including the transcriptome of both L. marina and bacteria, as well as the comparative bacterial metabolome, were utilized to investigate how bacterial food affects animal fitness and physiology. We found that genes related to iron ion binding and oxidoreductase activity pathways, such as agmo-1, cdo-1, haao-1, and tdo-2, were significantly upregulated in L. marina grown on S. algae, while extracellular structural components-related genes were significantly downregulated. Next, we observed that bacterial genes belonging to amino acid metabolism and ubiquinol-8 biosynthesis were repressed, while virulence genes were significantly elevated in S. algae. Furthermore, metabolomic analysis revealed that several toxic metabolites, such as puromycin, were enriched in S. algae, while many nucleotides were significantly enriched in OP50. Moreover, we found that the “two-component system” was enriched in S. algae, whereas “purine metabolism” and “one-carbon pool by folate” were significantly enriched in E. coli OP50. Collectively, our data provide new insights to decipher how diet modulates animal fitness and biology. Full article

(This article belongs to the Special Issue Host-Pathogen Interaction, 6th Edition)

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25 pages, 15243 KiB

Open AccessArticle

Integrated Multi-Omics Analysis Reveals Mountain-Cultivated Ginseng Ameliorates Cold-Stimulated Steroid-Resistant Asthma by Regulating Interactions among Microbiota, Genes, and Metabolites

by Daohao Tang, Chao Wang, Hanlin Liu, Junzhe Wu, Luying Tan, Sihan Liu, Haoming Lv, Cuizhu Wang, Fang Wang and Jinping Liu

Int. J. Mol. Sci. 2024, 25(16), 9110; https://doi.org/10.3390/ijms25169110 - 22 Aug 2024

Cited by 1 | Viewed by 1112 | Correction

Abstract

Steroid-resistant asthma (SRA), resisting glucocorticoids such as dexamethasone (DEX), is a bottleneck in the treatment of asthma. It is characterized by a predominantly neutrophilic inflammatory subtype and is prone to developing into severe refractory asthma and fatal asthma. Currently, there is a lack [...] Read more.

Steroid-resistant asthma (SRA), resisting glucocorticoids such as dexamethasone (DEX), is a bottleneck in the treatment of asthma. It is characterized by a predominantly neutrophilic inflammatory subtype and is prone to developing into severe refractory asthma and fatal asthma. Currently, there is a lack of universally effective treatments for SRA. Moreover, since cold stimulation does increase the risk of asthma development and exacerbate asthma symptoms, the treatment of cold-stimulated SRA (CSRA) will face greater challenges. To find effective new methods to ameliorate CSRA, this study established a CSRA mouse model of allergic airway inflammation mimicking human asthma for the first time and evaluated the alleviating effects of 80% ethanol extract of mountain-cultivated ginseng (MCG) based on multi-omics analysis. The results indicate that cold stimulation indeed exacerbated the SRA-related symptoms in mice; the DEX individual treatment did not show a satisfactory effect; while the combination treatment of DEX and MCG could dose-dependently significantly enhance the lung function; reduce neutrophil aggregation; decrease the levels of LPS, IFN-γ, IL-1β, CXCL8, and IL-17; increase the level of IL-10; alleviate the inflammatory infiltration; and decrease the mucus secretion and the expression of MUC5AC. Moreover, the combination of DEX and high-dose (200 mg/kg) MCG could significantly increase the levels of tight junction proteins (TJs), regulate the disordered intestinal flora, increase the content of short-chain fatty acids (SCFAs), and regulate the abnormal gene profile and metabolic profile. Multi-omics integrated analysis showed that 7 gut microbes, 34 genes, 6 metabolites, and the involved 15 metabolic/signaling pathways were closely related to the pharmacological effects of combination therapy. In conclusion, integrated multi-omics profiling highlighted the benefits of MCG for CSRA mice by modulating the interactions of microbiota, genes, and metabolites. MCG shows great potential as a functional food in the adjuvant treatment of CSRA. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

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27 pages, 5112 KiB

Open AccessReview

Cell-Free Systems: Ideal Platforms for Accelerating the Discovery and Production of Peptide-Based Antibiotics

by Hyeongwoo Park, Haneul Jin, Dayeong Kim and Joongoo Lee

Int. J. Mol. Sci. 2024, 25(16), 9109; https://doi.org/10.3390/ijms25169109 - 22 Aug 2024

Viewed by 1288

Abstract

Peptide-based antibiotics (PBAs), including antimicrobial peptides (AMPs) and their synthetic mimics, have received significant interest due to their diverse and unique bioactivities. The integration of high-throughput sequencing and bioinformatics tools has dramatically enhanced the discovery of enzymes, allowing researchers to identify specific genes [...] Read more.

Peptide-based antibiotics (PBAs), including antimicrobial peptides (AMPs) and their synthetic mimics, have received significant interest due to their diverse and unique bioactivities. The integration of high-throughput sequencing and bioinformatics tools has dramatically enhanced the discovery of enzymes, allowing researchers to identify specific genes and metabolic pathways responsible for producing novel PBAs more precisely. Cell-free systems (CFSs) that allow precise control over transcription and translation in vitro are being adapted, which accelerate the identification, characterization, selection, and production of novel PBAs. Furthermore, these platforms offer an ideal solution for overcoming the limitations of small-molecule antibiotics, which often lack efficacy against a broad spectrum of pathogens and contribute to the development of antibiotic resistance. In this review, we highlight recent examples of how CFSs streamline these processes while expanding our ability to access new antimicrobial agents that are effective against antibiotic-resistant infections. Full article

(This article belongs to the Special Issue Versatility of Protein Synthesis in a Test Tube)

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11 pages, 1220 KiB

Open AccessArticle

An IL-5 Single-Nucleotide Polymorphism Influences Neuroinflammation and Prospective Disease Activity in Multiple Sclerosis

by Ettore Dolcetti, Fabio Buttari, Antonio Bruno, Federica Azzolini, Luana Gilio, Angela Borrelli, Veronica Di Caprio, Gianluca Lauritano, Giovanni Galifi, Stefano Gambardella, Rosangela Ferese, Emiliano Giardina, Valentina Rovella, Roberto Furlan, Annamaria Finardi, Alessandra Musella, Sara Balletta, Georgia Mandolesi, Diego Centonze and Mario Stampanoni Bassi

Int. J. Mol. Sci. 2024, 25(16), 9108; https://doi.org/10.3390/ijms25169108 - 22 Aug 2024

Viewed by 737

Abstract

(1) Multiple sclerosis (MS) is identified by a complex interaction between central inflammation and neurodegeneration. Genetic individual variability could play a significative role in clinical presentation. The interleukin-5 (IL-5) rs2069812 single-nucleotide polymorphism (SNP) seems to define the clinical course of Th2 autoimmune diseases, [...] Read more.

(1) Multiple sclerosis (MS) is identified by a complex interaction between central inflammation and neurodegeneration. Genetic individual variability could play a significative role in clinical presentation. The interleukin-5 (IL-5) rs2069812 single-nucleotide polymorphism (SNP) seems to define the clinical course of Th2 autoimmune diseases, while its role in MS has never been investigated. (2) In a group of 230 patients diagnosed with relapsing–remitting MS (RR-MS) or progressive MS (P-MS) and controls (IC), rs2069812 polymorphism, cerebrospinal fluid (CSF) levels of inflammatory mediators, and clinical and demographic characteristics were determined. In RR-MS patients, No Evidence of Disease Activity (NEDA-3) at three years of follow-up was detected. (3) We identified higher levels of proinflammatory cytokines, particularly IL-2 (median [IQR], RR-MS = 0.2 [0–0.7]; P-MS = 0.1 [0–1.6]; IC = 0.1 [0.0–0.1]; p < 0.005), IL-6 (RR-MS = 0.9 [0.3–2.3]; P-MS = 0.8 [0.1–2.7]; IC = 0.1 [0.0–0.5]; p < 0.005), IL-12 (RR-MS = 0.5 [0–1.1]; P-MS = 0.5 [0–1.1]; IC = 0.0 [0.0–0.3]; p < 0.005), and GM-CSF (RR-MS = 15.6 [4.8–26.4]; P-MS = 14 [3.3–29.7]; IC = 8.9 [4.7–11.7]; p < 0.005) in MS patients compared with IC. Conversely, anti-inflammatory cytokines, specifically IL-5 (RR-MS = 0.65 [0–2.4]; P-MS = 0.1 [0–0.8]; IC = 1.7 [0.6–2.8]; p < 0.005) and IL-1ra (RR-MS = 14.7 [4.9–26.4]; P-MS = 13.1 [4.7–22.2]; IC = 27.8 [17.7–37.6]; p < 0.005) were higher in controls. According to rs2069812, in MS patients, the T-allele was associated with higher concentrations of proinflammatory mediators (IL-2, CT/TT = 0.2 [0.0–2.0]; CC = 0.1 [0.0–0.4], p = 0.015; IL-6, CT/TT = 1.2 [0.4–3.2] vs. CC = 0.7 [0.1–1.7], p = 0.007; IL-15, CT/TT = 0.1 [0.0–9.5] vs. CC = 0.0 [0.0–0.1], p = 0.019; and GM-CSF, CT/TT = 0.1 [0.0–0.6] vs. CC = 0.05 [0.0–0.1], p < 0.001), and CC was associated with anti-inflammatory mediators (IL-5, CT/TT = 0.03 [0.0–1.9] vs. CC = 1.28 [0.0–2.7], p = 0.001; IL-1ra, CT/TT = 12.1 [4.1–25.9] vs. CC = 18.1 [12.1–26.9], p = 0.006). We found the same differences in RR-MS patients (IL-2, T-allele median [IQR] = 0.3 [0.0–2.0] vs. C-allele, median [IQR] = 0.04 [0.0–0.3]; p = 0.005; IL-6, T-allele, median [IQR] = 1.3 [0.4–3.3] vs. C-allele, median [IQR] = 0.6 [0.03–1.5]; p = 0.001; IL-15, T-allele, median [IQR] = 0.1 [0.0–9.5] vs. C-allele, median [IQR] = 0.0 [0.0–0.1]; p = 0.008; GM-CSF, T-allele, median [IQR] = 0.1 [0.0–97.9] vs. C-allele, median [IQR] = 0.0 [0.0–0.001]; p < 0.001; IL-5, T-allele, median [IQR] = 0.02 [0.0–2.2] vs. C-allele, median [IQR] = 1.5 [0.0–2.9]; p = 0.016; and IL-1ra, T-allele, median [IQR] = 12.1 [4.3–26.4] vs. C-allele, median [IQR] = 18.5 [12.7–28.3]; p = 0.006) but not in P-MS, except for IL-5 (T-allele, median [IQR] = 0.1 [0–0.23] vs. C-allele, median [IQR] = 0.6 [0.0–2.5]; p = 0.022). Finally, we identified an association between CC in RR-MS patients and NEDA-3 after three years of follow-up (p = 0.007). (4) We describe, for the first time, the role of an SNP of the IL-5 gene in regulating central neuroinflammation and influencing clinical course in MS patients. Full article

(This article belongs to the Special Issue Molecular Mechanism in Multiple Sclerosis and Related Disorders: 2nd Edition)

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24 pages, 3003 KiB

Open AccessReview

Fenestrated Endothelial Cells across Organs: Insights into Kidney Function and Disease

by Xingrui Mou, Sophia M. Leeman, Yasmin Roye, Carmen Miller and Samira Musah

Int. J. Mol. Sci. 2024, 25(16), 9107; https://doi.org/10.3390/ijms25169107 - 22 Aug 2024

Viewed by 1642

Abstract

In the human body, the vascular system plays an indispensable role in maintaining homeostasis by supplying oxygen and nutrients to cells and organs and facilitating the removal of metabolic waste and toxins. Blood vessels—the key constituents of the vascular system—are composed of a [...] Read more.

In the human body, the vascular system plays an indispensable role in maintaining homeostasis by supplying oxygen and nutrients to cells and organs and facilitating the removal of metabolic waste and toxins. Blood vessels—the key constituents of the vascular system—are composed of a layer of endothelial cells on their luminal surface. In most organs, tightly packed endothelial cells serve as a barrier separating blood and lymph from surrounding tissues. Intriguingly, endothelial cells in some tissues and organs (e.g., choroid plexus, liver sinusoids, small intestines, and kidney glomerulus) form transcellular pores called fenestrations that facilitate molecular and ionic transport across the vasculature and mediate immune responses through leukocyte transmigration. However, the development and unique functions of endothelial cell fenestrations across organs are yet to be fully uncovered. This review article provides an overview of fenestrated endothelial cells in multiple organs. We describe their development and organ-specific roles, with expanded discussions on their contributions to glomerular health and disease. We extend these discussions to highlight the dynamic changes in endothelial cell fenestrations in diabetic nephropathy, focal segmental glomerulosclerosis, Alport syndrome, and preeclampsia, and how these unique cellular features could be targeted for therapeutic development. Finally, we discuss emerging technologies for in vitro modeling of biological systems, and their relevance for advancing the current understanding of endothelial cell fenestrations in health and disease. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Endothelial Dysfunction 3.0)

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25 pages, 10825 KiB

Open AccessArticle

Nuclear Localization of Human SOD1 in Motor Neurons in Mouse Model and Patient Amyotrophic Lateral Sclerosis: Possible Links to Cholinergic Phenotype, NADPH Oxidase, Oxidative Stress, and DNA Damage

by Lee J. Martin, Shannon J. Koh, Antionette Price, Dongseok Park and Byung Woo Kim

Int. J. Mol. Sci. 2024, 25(16), 9106; https://doi.org/10.3390/ijms25169106 - 22 Aug 2024

Viewed by 1106

Abstract

Amyotrophic lateral sclerosis (ALS) is a fatal disease that causes degeneration of motor neurons (MNs) and paralysis. ALS can be caused by mutations in the gene that encodes copper/zinc superoxide dismutase (SOD1). SOD1 is known mostly as a cytosolic antioxidant protein, but SOD1 [...] Read more.

Amyotrophic lateral sclerosis (ALS) is a fatal disease that causes degeneration of motor neurons (MNs) and paralysis. ALS can be caused by mutations in the gene that encodes copper/zinc superoxide dismutase (SOD1). SOD1 is known mostly as a cytosolic antioxidant protein, but SOD1 is also in the nucleus of non-transgenic (tg) and human SOD1 (hSOD1) tg mouse MNs. SOD1’s nuclear presence in different cell types and subnuclear compartmentations are unknown, as are the nuclear functions of SOD1. We examined hSOD1 nuclear localization and DNA damage in tg mice expressing mutated and wildtype variants of hSOD1 (hSOD1-G93A and hSOD1-wildtype). We also studied ALS patient-derived induced pluripotent stem (iPS) cells to determine the nuclear presence of SOD1 in undifferentiated and differentiated MNs. In hSOD1-G93A and hSOD1-wildtype tg mice, choline acetyltransferase (ChAT)-positive MNs had nuclear hSOD1, but while hSOD1-wildtype mouse MNs also had nuclear ChAT, hSOD1-G93A mouse MNs showed symptom-related loss of nuclear ChAT. The interneurons had preserved parvalbumin nuclear positivity in hSOD1-G93A mice. hSOD1-G93A was seen less commonly in spinal cord astrocytes and, notably, oligodendrocytes, but as the disease emerged, the oligodendrocytes had increased mutant hSOD1 nuclear presence. Brain and spinal cord subcellular fractionation identified mutant hSOD1 in soluble nuclear extracts of the brain and spinal cord, but mutant hSOD1 was concentrated in the chromatin nuclear extract only in the spinal cord. Nuclear extracts from mutant hSOD1 tg mouse spinal cords had altered protein nitration, footprinting peroxynitrite presence, and the intact nuclear extracts had strongly increased superoxide production as well as the active NADPH oxidase marker, p47phox. The comet assay showed that MNs from hSOD1-G93A mice progressively (6–14 weeks of age) accumulated DNA single-strand breaks. Ablation of the NCF1 gene, encoding p47phox, and pharmacological inhibition of NADPH oxidase with systemic treatment of apocynin (10 mg/kg, ip) extended the mean lifespan of hSOD1-G93A mice by about 25% and mitigated genomic DNA damage progression. In human postmortem CNS, SOD1 was found in the nucleus of neurons and glia; nuclear SOD1 was increased in degenerating neurons in ALS cases and formed inclusions. Human iPS cells had nuclear SOD1 during directed differentiation to MNs, but mutant SOD1-expressing cells failed to establish wildtype MN nuclear SOD1 levels. We conclude that SOD1 has a prominent nuclear presence in the central nervous system, perhaps adopting aberrant contexts to participate in ALS pathobiology. Full article

(This article belongs to the Special Issue Genotoxicity in Neurodegenerative Disease and Neuropsychiatric Disorders)

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15 pages, 2823 KiB

Open AccessArticle

Comprehensive Analysis of Methylome and Transcriptome to Identify Potential Genes Regulating Porcine Testis Development

by Yue Feng, Yu Zhang, Junjing Wu, Mu Qiao, Jiawei Zhou, Zhong Xu, Zipeng Li, Hua Sun, Xianwen Peng and Shuqi Mei

Int. J. Mol. Sci. 2024, 25(16), 9105; https://doi.org/10.3390/ijms25169105 - 22 Aug 2024

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Abstract

DNA methylation plays a critical role in regulating gene expression during testicular development. However, few studies report on candidate genes related to the DNA methylation regulation of porcine testicular development. This study examined the differentially expressed genes (DEGs) and their methylation levels in [...] Read more.

DNA methylation plays a critical role in regulating gene expression during testicular development. However, few studies report on candidate genes related to the DNA methylation regulation of porcine testicular development. This study examined the differentially expressed genes (DEGs) and their methylation levels in testicular tissues from pigs at 60 days of age (60 d) and 180 days of age (180 d) using RNA-Seq and whole genome bisulfite sequencing (WGBS). It was determined that DNA methylation primarily occurs in the cytosine–guanine (CG) context, and the analysis identified 106,282 differentially methylated regions (DMRs) corresponding to 12,385 differentially methylated genes (DMGs). Further integrated analysis of RNA-Seq and WGBS data revealed 1083 DMGs negatively correlated with the expression of DEGs. GO analysis showed that these genes were significantly enriched in spermatogenesis, germ cell development, and spermatid differentiation. The screening of enriched genes revealed that hyper-methylation repressed ADAM30, ADAM3A, DPY19L2, H2BC1, MAK, RPL10L, SPATA16, and YBX2, while hypo-methylation elevated CACNA1I, CADM1, CTNNB1, JAM2, and PAFAH1B3 expression. Additionally, the methylation status of the key genes ADAM3A, ADAM30, YBX2, JAM2, PAFAH1B3, and CTNNB1 was detected by bisulfite sequencing PCR (BSP). This study offers insights into the epigenetic regulation mechanisms underlying porcine testicular development. Full article

(This article belongs to the Section Molecular Biology)

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17 pages, 8992 KiB

Open AccessArticle

Evaluation of the Ameliorative Potential of 3,5-bis(2-hydroxyethyl)-1,3,5-thiadiazinane-2-thione against Scopolamine-Induced Alzheimer’s Disease

by Shagufta, Gowhar Ali, Adnan Khan, Abdur Rasheed, Farah Deeba, Rahim Ullah, Muhammad Shahid, Haleema Ali, Rasool Khan, Najeebullah Shamezai and Naveed Sharif

Int. J. Mol. Sci. 2024, 25(16), 9104; https://doi.org/10.3390/ijms25169104 - 22 Aug 2024

Viewed by 645

Abstract

Alzheimer’s disease (AD) is the most common neurodegenerative disorder, marked by cognitive impairment. Currently, the available treatment provides only symptomatic relief and there is a great need to design and formulate new drugs to stabilize AD. In the search for a new anti-Alzheimer’s [...] Read more.

Alzheimer’s disease (AD) is the most common neurodegenerative disorder, marked by cognitive impairment. Currently, the available treatment provides only symptomatic relief and there is a great need to design and formulate new drugs to stabilize AD. In the search for a new anti-Alzheimer’s drug, 3,5-bis(2-hydroxyethyl)-1,3,5-thiadiazinane-2-thione (THTT), a tetrahydro-2H-1,3,5-thiadiazine-2-thione derivative, was investigated against a scopolamine-induced Alzheimer’s model. The selected test compound was administered intraperitoneally in three doses (15 mg/kg, 30 mg/kg, and 45 mg/kg). The test compound exhibited an IC50 value of 69.41 µg/mL, indicating its ability to inhibit the acetylcholinesterase enzyme. An antioxidant DPPH assay revealed that the IC50 value of the test compound was 97.75 µg/mL, which shows that the test compound possesses antioxidant activity. The results of behavior tests including the Y-maze and elevated plus maze (EPM) show that the test compound improved short-term memory and spatial memory, respectively. Furthermore, in the Morris water maze (MWM) and light/dark model, the test compound shows improvements in learning and memory. Moreover, the results of histological studies show that the test compound can protect the brain against the harmful effects of scopolamine. Overall, the findings of our investigation suggest that our chosen test compound has disease-modifying and neuroprotective activities against the scopolamine-induced Alzheimer’s model. The test compound may be beneficial, subject to further elaborate investigation for anti-amyloid disease-modifying properties in AD. Full article

(This article belongs to the Special Issue New Trends in Alzheimer's Disease Research: From Molecular Mechanisms to Therapeutics)

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Int. J. Mol. Sci., Volume 25, Issue 16 (August-2 2024) – 579 articles

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