International Journal of Molecular Sciences

13 pages, 2938 KiB

Open AccessArticle

The Amino Acid Permease MoGap1 Regulates TOR Activity and Autophagy in Magnaporthe oryzae

by Changli Huang, Lin Li, Lei Wang, Jiandong Bao, Xiaozhi Zhang, Jiongyi Yan, Jiaqi Wu, Na Cao, Jiaoyu Wang, Lili Zhao, Xiaohong Liu, Xiaoping Yu, Xueming Zhu and Fucheng Lin

Int. J. Mol. Sci. 2022, 23(21), 13663; https://doi.org/10.3390/ijms232113663 - 7 Nov 2022

Cited by 2 | Viewed by 2982

Abstract

Rice is an important food crop all over the world. It can be infected by the rice blast fungus Magnaporthe oryzae, which results in a significant reduction in rice yield. The infection mechanism of M. oryzae has been an academic focus for [...] Read more.

Rice is an important food crop all over the world. It can be infected by the rice blast fungus Magnaporthe oryzae, which results in a significant reduction in rice yield. The infection mechanism of M. oryzae has been an academic focus for a long time. It has been found that G protein, AMPK, cAMP-PKA, and MPS1-MAPK pathways play different roles in the infection process. Recently, the function of TOR signaling in regulating cell growth and autophagy by receiving nutritional signals generated by plant pathogenic fungi has been demonstrated, but its regulatory mechanism in response to the nutritional signals remains unclear. In this study, a yeast amino acid permease homologue MoGap1 was identified and a knockout mutant of MoGap1 was successfully obtained. Through a phenotypic analysis, a stress analysis, autophagy flux detection, and a TOR activity analysis, we found that the deletion of MoGap1 led to a sporulation reduction as well as increased sensitivity to cell wall stress and carbon source stress in M. oryzae. The ΔMogap1 mutant showed high sensitivity to the TOR inhibitor rapamycin. A Western blot analysis further confirmed that the TOR activity significantly decreased, which improved the level of autophagy. The results suggested that MoGap1, as an upstream regulator of TOR signaling, regulated autophagy and responded to adversities such as cell wall stress by regulating the TOR activity. Full article

(This article belongs to the Special Issue Regulation Mechanism of Autophagy in Pathogen and Pathogen-Host Interaction)

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Figure 1
Identification of MoGap1 in M. oryzae. (A) Gap1 proteins of M. oryzae, S. cerevisiae, S. pombe, C. truncatum, and F. graminearum shown using IBS 1.0 software. Lysp: amino acid permease domain. (B) Schematic diagram of a Gap1 protein that contained 13 transmembrane regions. (C) Phylogenetic trees of the Gap1 proteins constructed using MEGA 7.0. (D) Multiple sequence alignment shown using DNAMAN software. Full article ">Figure 2
Colony morphology and sporulation of M. oryzae. (A) Colony morphology of Guy11, ΔMogap1, and ΔMogap1-C after 9 days of culture. (B) The conidia of Guy11, ΔMogap1, and ΔMogap1-C stained using DAPI and CFW on a scale of 10 μm. (C) Relative spore formation of Guy11, ΔMogap1, and ΔMogap1-C after 9 days of culture, the first of which differed significantly from the others. ** p < 0.01. Full article ">Figure 3
MoGap1 responses to rapamycin stress. (A) The growth of Guy11, ΔMogap1, and ΔMogap1-C for 8 days of culture on CM and Rap for 8 days, respectively. (B) The inhibition rates of rapamycin in Guy11, ΔMogap1, and ΔMogap1-C calculated by measuring the growth diameters, which were significantly different between MoGap1 and Guy11 (** p < 0.01). (C) The growth rate was observed in CM liquid medium. The dry weights of Guy11 and ΔMogap1 were calculated after being cultured in CM liquid medium for 2 days. (D) Virulence detection in ΔMogap1 mutant. The conidia (1 × 105 spores/mL) were incubated on 2-week-old barley and cultured at 25 °C for 4 days. Full article ">Figure 4
MoGap1 negatively regulates autophagy. (A) MoRps6 phosphorylation levels of Guy11 and ΔMogap1 after 0 h and 4 h of 30 ng/mL rapamycin induction with GAPDH as internal reference. (B) The phosphorylation levels of MoRps6 were calculated and graphed using Prism 7.0 software (t-test; ns: no significant, ** p < 0.01). (C) Autophagy flux was observed in the wild-type Guy11 and ΔMogap1 strain in CM and starvation conditions. Bar = 10 μm. (D) Expression levels of GFP-MoAtg8 and GFP in Guy11 and ΔMogap1, respectively, after SD-N starvation with GAPDH as internal reference. Full article ">Figure 5
Effect of MoGap1 on CWI. (A) The growth performance of Guy11, ΔMogap1, and ΔMogap1-C under hypertonic stress (NaCl medium, KCl medium, and SBT medium), cell wall stress (SDS medium and CR medium), or starvation stress (SD-N medium). (B) The inhibition rates of Guy11, ΔMogap1, and ΔMogap1-C in different stress media, in which those between ΔMogap1 by CR and Guy11 were significantly different (* p < 0.05). Full article ">Figure 6
Utilization of different carbon sources in ΔMogap1. (A) The growth of Guy11, ΔMogap1, and ΔMogap1-C with different C sources. (B) The relative growth rates of Guy11, ΔMogap1, and ΔMogap1-C with different C sources. With oleic acid, mandelic acid, or palmitic acid as the C source, the relative growth rates of Guy11 and ΔMogap1 were significantly different from each other. ** p < 0.01. Full article ">

16 pages, 40300 KiB

Open AccessArticle

Phosphorylcholine Monoclonal Antibody Therapy Decreases Intraplaque Angiogenesis and Intraplaque Hemorrhage in Murine Vein Grafts

by Fabiana Baganha, Thijs J. Sluiter, Rob C. M. de Jong, Louise A. van Alst, Hendrika A. B. Peters, J. Wouter Jukema, Mirela Delibegovic, Knut Pettersson, Paul H. A. Quax and Margreet R. de Vries

Int. J. Mol. Sci. 2022, 23(21), 13662; https://doi.org/10.3390/ijms232113662 - 7 Nov 2022

Cited by 3 | Viewed by 2507

Abstract

Phosphorylcholine (PC) is one of the main oxLDL epitopes playing a central role in atherosclerosis, due to its atherogenic and proinflammatory effects. PC can be cleared by natural IgM antibodies and low levels of these antibodies have been associated with human vein graft [...] Read more.

Phosphorylcholine (PC) is one of the main oxLDL epitopes playing a central role in atherosclerosis, due to its atherogenic and proinflammatory effects. PC can be cleared by natural IgM antibodies and low levels of these antibodies have been associated with human vein graft (VG) failure. Although PC antibodies are recognized for their anti-inflammatory properties, their effect on intraplaque angiogenesis (IPA) and intraplaque hemorrhage (IPH)—interdependent processes contributing to plaque rupture—are unknown. We hypothesized that new IgG phosphorylcholine antibodies (PC-mAb) could decrease vulnerable lesions in murine VGs.Therefore, hypercholesterolemic male ApoE3*Leiden mice received a (donor) caval vein interposition in the carotid artery and weekly IP injections of (5 mg/kg) PCmAb (n = 11) or vehicle (n = 12) until sacrifice at day 28. We found that PCmAb significantly decreased vein graft media (13%), intima lesion (25%), and increased lumen with 32% compared to controls. PCmAb increased collagen content (18%) and decreased macrophages presence (31%). PCmAb resulted in 23% decreased CD163+ macrophages content in vein grafts whereas CD163 expression was decreased in Hb:Hp macrophages. PCmAb significantly lowered neovessel density (34%), EC proliferation and migration with/out oxLDL stimulation. Moreover, PCmAb enhanced intraplaque angiogenic vessels maturation by increasing neovessel pericyte coverage in vivo (31%). Together, this resulted in a 62% decrease in IPH. PCmAb effectively inhibits murine atherosclerotic lesion formation in vein grafts by reducing IPA and IPH via decreased neovessel density and macrophages influx and increased neovessel maturation. PC-mAb therefore holds promise as a new therapeutic approach to prevent vein graft disease. Full article

(This article belongs to the Special Issue Contribution of Dysfunctional Microvasculature to Cardiovascular Diseases)

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17 pages, 1070 KiB

Open AccessReview

Vitamin D-Related Genes and Thyroid Cancer—A Systematic Review

by Adam Maciejewski and Katarzyna Lacka

Int. J. Mol. Sci. 2022, 23(21), 13661; https://doi.org/10.3390/ijms232113661 - 7 Nov 2022

Cited by 4 | Viewed by 3159

Abstract

Vitamin D, formerly known for its role in calcium-phosphorus homeostasis, was shown to exert a broad influence on immunity and on differentiation and proliferation processes in the last few years. In the field of endocrinology, there is proof of the potential role of [...] Read more.

Vitamin D, formerly known for its role in calcium-phosphorus homeostasis, was shown to exert a broad influence on immunity and on differentiation and proliferation processes in the last few years. In the field of endocrinology, there is proof of the potential role of vitamin D and vitamin D-related genes in the pathogenesis of thyroid cancer—the most prevalent endocrine malignancy. Therefore, the study aimed to systematically review the publications on the association between vitamin D-related gene variants (polymorphisms, mutations, etc.) and thyroid cancer. PubMed, EMBASE, Scopus, and Web of Science electronic databases were searched for relevant studies. A total of ten studies were found that met the inclusion criteria. Six vitamin D-related genes were analyzed (VDR—vitamin D receptor, CYP2R1—cytochrome P450 family 2 subfamily R member 1, CYP24A1—cytochrome P450 family 24 subfamily A member 1, CYP27B1—cytochrome P450 family 27 subfamily B member 1, DHCR7—7-dehydrocholesterol reductase and CUBN—cubilin). Moreover, a meta-analysis was conducted to summarize the data from the studies on VDR polymorphisms (rs2228570/FokI, rs1544410/BsmI, rs7975232/ApaI and rs731236/TaqI). Some associations between thyroid cancer risk (VDR, CYP24A1, DHCR7) or the clinical course of the disease (VDR) and vitamin D-related gene polymorphisms were described in the literature. However, these results seem inconclusive and need validation. A meta-analysis of the five studies of common VDR polymorphisms did not confirm their association with increased susceptibility to differentiated thyroid cancer. Further efforts are necessary to improve our understanding of thyroid cancer pathogenesis and implement targeted therapies for refractory cases. Full article

(This article belongs to the Special Issue Advances in Metabolism, Immunology, Genetics in Thyroid Cancer and Thyroid Disease: From Bench to Therapy)

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Figure 1
Known pathways mediating vitamin D action in thyroid cancer cells. CCL2—C-C motif chemokine ligand 2; ERK—extracellular signal-regulated kinase; FN—fibronectin; FOXO3a—forkhead box protein O3a; MEK—mitogen-activated protein kinase kinase 1; PI3K—phosphoinositide 3-kinase; PTEN—phosphatase and tensin homolog; PTPN2—protein tyrosine phosphatase N 2; SIRT1—sirtuin 1 histon deacethylase; STAT3—signal transducer and activator of transcription 3; VDR—vitamin D receptor. Red lines—inhibition; blue lines—stimulation. Full article ">Figure 2
Vitamin D metabolism (including molecules/enzymes involved, coding genes in brackets): Cubilin (CUBN); DBP—vitamin D binding protein (GC); Megalin (LRP2); VDR—vitamin D receptor (VDR); 1—UVB radiation, 290–315 mm wavelength; 2—nonenzymatic isomerization reaction under the temperature; 3—25-hydroxylase (main enzyme—CYP2R1—cytochrome P450 family 2 subfamily R member 1, minor role of CYP27A1—cytochrome P450 family 27 subfamily A member 1); 4—1α-hydroxylase (CYP27B1—cytochrome P450 family 27 subfamily B member 1); 5—24-hydroxylase (CYP24A1—cytochrome P450 family 24 subfamily A member 1); 6—7-dehydrocholesterol reductase (DHCR7); 7—cholesterol side-chain cleavage enzyme (CYP11A1—cytochrome P450 family 11 subfamily A member 1). Full article ">Figure 3
Flow diagram demonstrating the search and selection process for articles. Full article ">

17 pages, 3307 KiB

Open AccessArticle

De Novo Transcriptome Assembly and Analysis of Longevity Genes Using Subterranean Termite (Reticulitermes chinensis) Castes

by Haroon, Yu-Xin Li, Chen-Xu Ye, Jian Su, Ghulam Nabi, Xiao-Hong Su and Lian-Xi Xing

Int. J. Mol. Sci. 2022, 23(21), 13660; https://doi.org/10.3390/ijms232113660 - 7 Nov 2022

Cited by 1 | Viewed by 2010

Abstract

The longevity phenomenon is entirely controlled by the insulin signaling pathway (IIS-pathway). Both vertebrates and invertebrates have IIS-pathways that are comparable to one another, though no one has previously described de novo transcriptome assembly of IIS-pathway-associated genes in termites. In this research, we [...] Read more.

The longevity phenomenon is entirely controlled by the insulin signaling pathway (IIS-pathway). Both vertebrates and invertebrates have IIS-pathways that are comparable to one another, though no one has previously described de novo transcriptome assembly of IIS-pathway-associated genes in termites. In this research, we analyzed the transcriptomes of both reproductive (primary kings “PK” and queens “PQ”, secondary worker reproductive kings “SWRK” and queens “SWRQ”) and non-reproductive (male “WM” and female “WF” workers) castes of the subterranean termite Reticulitermes chinensis. The goal was to identify the genes responsible for longevity in the reproductive and non-reproductive castes. Through transcriptome analysis, we annotated 103,589,264 sequence reads and 184,436 (7G) unigenes were assembled, GC performance was measured at 43.02%, and 64,046 sequences were reported as CDs sequences. Of which 35 IIS-pathway-associated genes were identified, among 35 genes, we focused on the phosphoinositide-dependent kinase-1 (Pdk1), protein kinase B2 (akt2-a), tuberous sclerosis-2 (Tsc2), mammalian target of rapamycin (mTOR), eukaryotic translation initiation factor 4E (EIF4E) and ribosomal protein S6 (RPS6) genes. Previously these genes (Pdk1, akt2-a, mTOR, EIF4E, and RPS6) were investigated in various organisms, that regulate physiological effects, growth factors, protein translation, cell survival, proliferation, protein synthesis, cell metabolism and survival, autophagy, fecundity rate, egg size, and follicle number, although the critical reason for longevity is still unclear in the termite castes. However, based on transcriptome profiling, the IIS-pathway-associated genes could prolong the reproductive caste lifespan and health span. Therefore, the transcriptomic shreds of evidence related to IIS-pathway genes provide new insights into the maintenance and relationships between biomolecular homeostasis and remarkable longevity. Finally, we propose a strategy for future research to decrypt the hidden costs associated with termite aging in reproductive and non-reproductive castes. Full article

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

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KEGG classifications of the R. chinensis unigenes. (A) PK-vs-SWRK; (B) PQ-vs-SWRQ; (C) SWRK-vs-SWRQ; (D) WF-vs-SWRQ; (E) WM-vs-SWRK. PKs (primary king), PQs (primary queen), SWRK (secondary worker reproductive king), SWRQ (secondary worker reproductive queen), WMs (workers male), and WFs (female workers), with 93,078 unigenes were assigned to 343 pathways. Full article ">Figure 2
Histogram presentation of the Gene Ontology (GO) classification in each caste. (A) PK-vs-SWRK; (B) PQ-vs-SWRQ; (C) SWRK-vs-SWRQ; (D) WF-vs-SWRQ; (E) WM-vs-SWRK. PKs (primary king), PQs (primary queen), SWRK (secondary worker reproductive king), SWRQ (secondary worker reproductive queen), WMs (workers male), and WFs (female workers). The figure represents the up (red) and down (green) categorical presentation of biological processes, cellular components, and molecular functions. The x-axis indicates the names of genes in a category, and the y-axis shows the number of genes in the main category. Full article ">Figure 3
Differential expression of genes (DEGs) analysis across distinct castes of R. chinensis (SWRQ-vs-SWRK, PQ-vs-PK, and WM-vs-WF). The red column represents DEGs that are down-regulated, whereas the green column indicates DEGs that are up-regulated. To determine the significance of gene expression changes, FDR ≤ 0.001 and log2Ratio ≥ 1 were employed as thresholds. Full article ">Figure 4
Analysis of DEGs for enhancement across different castes (A–E). PK (primary king), PQ (primary queen), SWRK (secondary worker reproductive king), SWRQ (secondary worker reproductive queen), WM (male worker), and WF (female worker). The volcano plots indicate enriched DEGs expressing genes in the PK, PQ, SWRK, SWRQ, WM, and WF, with a significantly up-regulated (red) and down-regulated (blue). The threshold level for judging the significance of differences in gene expression, FDR ≤ 0.001 and log2Ratio ≥ 1 parameter were used. Full article ">Figure 5
The heat map indicates the differentially expressed gene (DEGs) involved in the insulin signaling pathway in different castes of R. chinensis. The castes are SWRK, SWRQ, PQ, PK, WM, and WF. A change in color from red to blue indicates the gene expression level. Full article ">Figure 6
Log2 fold changes in the insulin signaling pathway in R. chinensis castes SWRK, SWRQ, PK, PQ, WM, and WF. Differential expression of genes in each group is shown as log2 fold changes compared to the reference group. The y-axis represents the log2 fold changes, and the x-axis shows the gene name and individual caste name. Full article ">

17 pages, 2190 KiB

Open AccessArticle

Fine Mapping and Candidate Gene Analysis of Pm36, a Wild Emmer-Derived Powdery Mildew Resistance Locus in Durum Wheat

by Domenica Nigro, Antonio Blanco, Luciana Piarulli, Massimo Antonio Signorile, Pasqualina Colasuonno, Emanuela Blanco and Rosanna Simeone

Int. J. Mol. Sci. 2022, 23(21), 13659; https://doi.org/10.3390/ijms232113659 - 7 Nov 2022

Cited by 4 | Viewed by 2173

Abstract

Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region [...] Read more.

Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region harboring the wild emmer PM resistance locus Pm36 and to identify candidate genes by exploiting the improved tetraploid wheat genomic resources. A set of backcross inbred lines (BILs) of durum wheat were genotyped with the SNP 25K chip array and comparison of the PM-resistant and susceptible lines defined a 1.5 cM region (physical interval of 1.08 Mb) harboring Pm36. The genetic map constructed with F_2:3 progenies derived by crossing the PM resistant line 5BIL-42 and the durum parent Latino, restricted to 0.3 cM the genetic distance between Pm36 and the SNP marker IWB22904 (physical distance 0.515 Mb). The distribution of the marker interval including Pm36 in a tetraploid wheat collection indicated that the positive allele was largely present in the domesticated and wild emmer Triticum turgidum spp. dicoccum and ssp. dicoccoides. Ten high-confidence protein coding genes were identified in the Pm36 region of the emmer, durum and bread wheat reference genomes, while three added genes showed no homologous in the emmer genome. The tightly linked markers can be used for marker-assisted selection in wheat breeding programs, and as starting point for the Pm36 map-based cloning. Full article

(This article belongs to the Special Issue Plant Genomics and Bioinformatics)

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22 pages, 6732 KiB

Open AccessArticle

Preliminary Expression Analysis of the OSCA Gene Family in Maize and Their Involvement in Temperature Stress

by Yuanyang Li, Yubin Zhang, Bin Li, Liyuan Hou, Jianing Yu, Chengguo Jia, Zhe Wang, Siqi Chen, Mingzhe Zhang, Jianchun Qin, Ning Cao, Jinhu Cui and Wuliang Shi

Int. J. Mol. Sci. 2022, 23(21), 13658; https://doi.org/10.3390/ijms232113658 - 7 Nov 2022

Cited by 9 | Viewed by 2785

Abstract

Hyperosmolality-gated calcium-permeable channels (OSCA) are characterized as an osmosensor in plants; they are able to recognize and respond to exogenous and endogenous osmotic changes, and play a vital role in plant growth and adaptability to environmental stress. To explore the potential biological functions [...] Read more.

Hyperosmolality-gated calcium-permeable channels (OSCA) are characterized as an osmosensor in plants; they are able to recognize and respond to exogenous and endogenous osmotic changes, and play a vital role in plant growth and adaptability to environmental stress. To explore the potential biological functions of OSCAs in maize, we performed a bioinformatics and expression analysis of the ZmOSCA gene family. Using bioinformatics methods, we identified twelve OSCA genes from the genome database of maize. According to their sequence composition and phylogenetic relationship, the maize OSCA family was classified into four groups (Ⅰ, Ⅱ, Ⅲ, and Ⅳ). Multiple sequence alignment analysis revealed a conserved DUF221 domain in these members. We modeled the calcium binding sites of four OSCA families using the autodocking technique. The expression profiles of ZmOSCA genes were analyzed in different tissues and under diverse abiotic stresses such as drought, salt, high temperature, and chilling using quantitative real-time PCR (qRT-PCR). We found that the expression of twelve ZmOSCA genes is variant in different tissues of maize. Furthermore, abiotic stresses such as drought, salt, high temperature, and chilling differentially induced the expression of twelve ZmOSCA genes. We chose ZmOSCA2.2 and ZmOSCA2.3, which responded most strongly to temperature stress, for prediction of protein interactions. We modeled the calcium binding sites of four OSCA families using autodocking tools, obtaining a number of new results. These results are helpful in understanding the function of the plant OSCA gene family for study of the molecular mechanism of plant osmotic stress and response, as well as exploration of the interaction between osmotic stress, high-temperature stress, and low-temperature stress signal transduction mechanisms. As such, they can provide a theoretical basis for crop breeding. Full article

(This article belongs to the Special Issue Response to Environmental Stress in Plants)

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0 pages, 2535 KiB

Open AccessReview

RETRACTED: Impact of Histone Modifications and Their Therapeutic Targeting in Hematological Malignancies

by Mariam Markouli, Dimitrios Strepkos and Christina Piperi

Int. J. Mol. Sci. 2022, 23(21), 13657; https://doi.org/10.3390/ijms232113657 - 7 Nov 2022

Cited by 3 | Viewed by 2552 | Retraction

Abstract

Hematologic malignancies are a large and heterogeneous group of neoplasms characterized by complex pathogenetic mechanisms. The abnormal regulation of epigenetic mechanisms and specifically, histone modifications, has been demonstrated to play a central role in hematological cancer pathogenesis and progression. A variety of epigenetic [...] Read more.

Hematologic malignancies are a large and heterogeneous group of neoplasms characterized by complex pathogenetic mechanisms. The abnormal regulation of epigenetic mechanisms and specifically, histone modifications, has been demonstrated to play a central role in hematological cancer pathogenesis and progression. A variety of epigenetic enzymes that affect the state of histones have been detected as deregulated, being either over- or underexpressed, which induces changes in chromatin compaction and, subsequently, affects gene expression. Recent advances in the field of epigenetics have revealed novel therapeutic targets, with many epigenetic drugs being investigated in clinical trials. The present review focuses on the biological impact of histone modifications in the pathogenesis of hematologic malignancies, describing a wide range of therapeutic agents that have been discovered to target these alterations and are currently under investigation in clinical trials. Full article

(This article belongs to the Special Issue Advances in Molecular Research and Novel Diagnostic Technics of Hematological Malignancies)

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Full article ">Figure 1
Chromatin landscape indicating histone methylation changes related to hematological malignancies. EZH2 methyltransferase regulates the differentiation, proliferation, and apoptosis of the adult hematopoietic stem cells by repressing CDKN2A, BLIMP, and IRF4, as well as pro-apoptotic genes, NOX and p21. EZH2 overexpression or gain-of-function mutations have been detected in high-grade follicular lymphoma, DLBCL, and NKT lymphomas. Loss-of-function EZH2 mutations have been observed in MDSs, atypical CML, myelofibrosis, and T-ALL. Mutations in other PRC2 members, such as EED, and SUZ12, have been observed in some MDS and T-ALL cases, whereas ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Frequent MLL1 translocations have been detected in AML and ALL. Most common fusion partners accounting for approximately 80% of MLL rearrangements are AFF1/AF4, MLLT3/AF9, MLLT1/ENL, and MLLT10/AF10, which interact with DOT1L that further sustains the expression of key pro-leukemic genes HOXA and MEIS1. PRMT4 knockdown inhibits cell-cycle progression and promotes apoptosis by downregulating E2F and MYC target genes in leukemic cell lines. PRMT5 is overexpressed in DLBCL and MCL via regulation of p5, p21, GADD45, and PUMA genes. MECOM and PRDM16 are rearranged in AML. PHD finger proteins recognize lysine methylation, upregulating HOXA9 and MEIS1 gene activity in AML. Lysine demethylase UTX is also frequently mutated in MM and ALL, and LSD1 is overexpressed in ALL, AML, CML, MPNs, and MDSs, repressing p53, STAT3, and DNMT1 activity. Full article ">Figure 2
Histone acetylation events related to hematological malignancies. CBP and p300 are often dysregulated in lymphoid neoplasms, leading to abnormal acetylation of histones, as well as nonhistone targets, such as BCL-6 and p53. KAT7, KAT2A, KAT6B, and CSRP2BP are overexpressed in B-ALL and may interact with MYC, implicating them in tumor development. BRD4 further associates with p300/CBP-mediated acetylation-enhanced regions, controlling genes associated with cell renewal and pluripotency, such as Nanog and OCT4. MOZ-TIF2 and MLL-CBP are commonly rearranged in myeloid malignancies, resulting in the respective FPs that have been implicated in leukemic transformation. Increased HDAC expression is also common in ALL, regulating RARb, CYP26 Pax5, IKZF3, CXCR4, IL-16, IL-4R, and Bcl-2 gene expression. HDACs, and in particular HDAC9, also interact with the PML-RARα and PLZF-RARα FPs, as well as with BCL-6 to promote the development of hematologic malignancies. Full article ">Figure 3
Histone phosphorylation and SUMOylation alterations related to hematological malignancies. JAK2 kinase is commonly activated in MPNs, resulting in histone phosphorylation, which induces the disassembly of HP1α from chromatin and the activation of LMO2 oncogene. Phosphorylated genes also attract STAT family members, enabling a functional interaction between JAK kinases and STAT proteins. PIM1 kinase, when simultaneously overexpressed with MYC, promotes lymphomagenesis. It can form complexes with MYC and MAX, activating IEGs, FOSL1, and ID2. Finally, SUMOylation reduces gene expression of the E3 ubiquitin ligase TRAF6 in DLBCL and further represses gene transcription. Full article ">Figure 4
Structure of small-molecule inhibitors targeting epigenetic alterations. Several drugs targeting epigenetic enzymes have been developed and are currently being studied in preclinical and clinical studies. These include small molecules inhibiting CARM-1, PRMT5, DOT1L, EZH2 methyltransferases LSD1, HATs, HDACs, and BET. Full article ">Figure 5
Diagram indicating the status of drugs targeting epigenetic alterations. Currently, only the EZH2 inhibitor tazemetostat and the DNMT inhibitors azacytidine and decitabine have received FDA approval. However, an increasing number of BET, DOT1L, LSD1, HAT, and HDAC inhibitors are already in phase II/III clinical trials with promising results, and several more are under evaluation in phase I trials. Full article ">

21 pages, 2117 KiB

Open AccessReview

Emerging Effects of IL-33 on COVID-19

by Yuan Gao, Luwei Cai, Lili Li, Yidan Zhang, Jing Li, Chengliang Luo, Ying Wang and Luyang Tao

Int. J. Mol. Sci. 2022, 23(21), 13656; https://doi.org/10.3390/ijms232113656 - 7 Nov 2022

Cited by 14 | Viewed by 3176

Abstract

Since the start of COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more than 6 million people have lost their lives worldwide directly or indirectly. Despite intensified efforts to clarify the immunopathology of COVID-19, the key factors and processes that [...] Read more.

Since the start of COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more than 6 million people have lost their lives worldwide directly or indirectly. Despite intensified efforts to clarify the immunopathology of COVID-19, the key factors and processes that trigger an inflammatory storm and lead to severe clinical outcomes in patients remain unclear. As an inflammatory storm factor, IL-33 is an alarmin cytokine, which plays an important role in cell damage or infection. Recent studies have shown that serum IL-33 is upregulated in COVID-19 patients and is strongly associated with poor outcomes. Increased IL-33 levels in severe infections may result from an inflammatory storm caused by strong interactions between activated immune cells. However, the effects of IL-33 in COVID-19 and the underlying mechanisms remain to be fully elucidated. In this review, we systematically discuss the biological properties of IL-33 under pathophysiological conditions and its regulation of immune cells, including neutrophils, innate lymphocytes (ILCs), dendritic cells, macrophages, CD4⁺ T cells, Th17/Treg cells, and CD8⁺ T cells, in COVID-19 phagocytosis. The aim of this review is to explore the potential value of the IL-33/immune cell pathway as a new target for early diagnosis, monitoring of severe cases, and clinical treatment of COVID-19. Full article

(This article belongs to the Section Molecular Immunology)

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Molecular biological characteristics of IL-33 (A) The gene spans of human IL-33 (approximately 48 kb) contain eight exons, which are transcribed and translated into proteins containing 270 amino acids. (B) The full length of IL-33 is sheared to obtain different levels of active fragments. Cleaved by cathepsin, elastase, and proteinase released from neutrophils or chymase, Genzyme B, and tryptase released from mast cells, the highly active fragments of IL-33 (IL-3395-270, IL-3399-270, IL-33107-270, IL-33109-270, IL-33111-270) can bind to the ST2L/IL-1RAcP dimer and activate downstream signaling pathways. In contrast, when the full length of IL-33 is cleaved by casepase3/7 released by apoptotic cells, it forms a fragment (IL-33179-270) without biological activity. (C) The 3D structure of the IL-33/ST2 complex (Protein Data Bank ID:4KC3). IL-33 mediates cytokine activity through the structural domain with three Ig-like structural domains in the extracellular domain of ST2 on target cells. At Site 1, the acidic residues Glu144, Glu148, Asp149, and Asp244 of IL-33 interact with the ST2 basic residues Arg38, Lys22, Arg198, and Arg35, respectively, via a critical salt bridge. At Site 2, the acidic residue Glu165 of IL-33 interacts with Arg313 of ST2 via a salt bridge, and Tyr163 and Leu182 of IL-33 form significant hydrophobic structures with Leu246, Leu306, and Leu311 of ST2. Full article ">Figure 2
The effects and putative mechanisms of the involvement of IL-33 in neutrophils and T helper cells in COVID-19. In response to SAS-CoV-2, IL-33 is released as an alarmin from epithelial cells due to disruption of the epithelial barrier and cell damage. This promotes rapid neutrophil infiltration, migration, and activation via macrophage-derived CXCL1 and CXCL2 while inducing massive accumulation of ROS via the IL-33/ST2 signaling pathway, which in turn induces the excessive release of NETs. Additionally, IL-33 dose dependently upregulates MHC-II class and co-stimulatory molecules to induce maturation and activation of immature DCs and then stimulates activation of CD4+ T cells and induces their differentiation to Th17 cells instead of Treg cells through secretion of IL-1β and IL-6. Finally, a large number of NETs and inflammatory cells enter the bloodstream, triggering serious complications, such as vasoembolic conditions and inflammatory reactions. Full article ">Figure 3
Potential mechanisms by which IL-33 regulates ILC2 and macrophages in COVID-19. SAS-CoV-2 infects cells via ACE2 on the surface of type II alveolar epithelial cells with the assistance of TMPRSS2. IL-33 acts as an alarmin in response to viral infection and is secreted in large quantities by apoptotic alveolar epithelial cells. The released IL-33 acts on the specific receptor of ST2L on the surface of the ILC2 membrane and recruits its accessory receptor IL-1RAcP to form the functional IL-33 receptor complex. Following binding of IL-33 to IL-1RAcP, the receptor complex is activated by exposure of the TIR domain of IL-1RAcP and recruitment of myeloid differentiation primary response gene 88 (MyD88) into the heterodimeric IL-33R1 complex. Recruitment of MyD88 results in the recruitment of IL-1 receptor-associated kinase 1 (IRAK1) and IRAK4 through their death domains. This complex then activates downstream signaling pathways, including mitogen-activated protein kinases MAPK (such as ERK, JNK, p38), GATA3, and NF-κB, and enhances cellular respiration and ATP production, which induces an elevated level of the histone modification H3K4me3. Activation of NF-κB, GATA3, and H3K4me3 in the nuclear membrane further promotes the production of inflammatory cytokines, such as IL-5 and IL-13, and enhances viral recruitment by TMPRSS2. On the other hand, the release of IL-33 directly reduces phagocytosis by macrophages and the antiviral effects of NK cells. In contrast, IL-33 and IL-13 bind to ST2L and IL-4R, respectively, on the surface of macrophage membranes, thereby promoting the activation of macrophage differentiation toward AAMs and damage to alveolar tissue. Full article ">Figure 4
Interaction mechanism between IL-33 and IFN-I released by pDCs during COVID-19 infection. After the lung epithelium is infected with SARS-CoV-2, the replicating virus can cause epithelial cell apoptosis and directly damage the epithelium. Dendritic cells present antigens to helper T cells. Immature DCs differentiate into conventional DCs (cDCs) and plasmacytoid DCs (pDCs). IFN-I specificity derived from pDCs is dependent on the Toll-like receptor-7 (TLR7)/TLR9 pathway. Upon COVID-19 infection, TLR7 or TLR9 activates MyD88 and IL-1 receptor-associated kinase 4 (IRAK-4), which then interact with tumor necrosis factor receptor-associated factor-6 (TRAF6), TRAF3, IRAK1, IKKα, and interferon regulatory factor 7 (IRF7) interaction. Ultimately, IRAK-1 and IKKα phosphorylate IRF7, leading to IRF7 activation and induction of IFN-I gene transcription and massive IFN-I production. Additionally, IL-33, an important inflammatory storm cytokine, is abundantly released from apoptotic epithelial cells and inhibits pDC-dependent IFN-I by rapidly depleting the intracellular adaptor molecules IRAK1 and viperin, resulting in a hyporesponsive state of TLR7. Meanwhile, IL-33 induces the expression of a large number of cytokines by interacting with immune cells, such as macrophages, ILC2 cells, Th2 cells, Th17 cells, and Treg cells, which ultimately leads to abnormal inflammatory damage and decreased antiviral capacity in COVID-19 patients. Full article ">

15 pages, 2858 KiB

Open AccessArticle

Influence of Acidic pH on Wound Healing In Vivo: A Novel Perspective for Wound Treatment

by Pivian Sim, Xanthe L. Strudwick, YunMei Song, Allison J. Cowin and Sanjay Garg

Int. J. Mol. Sci. 2022, 23(21), 13655; https://doi.org/10.3390/ijms232113655 - 7 Nov 2022

Cited by 53 | Viewed by 5840

Abstract

There has been little understanding of acidification functionality in wound healing, highlighting the need to study the efficacy of wound acidification on wound closure and cellular activity in non-infected wounds. This study is focused on establishing the healing potential of wound acidification in [...] Read more.

There has been little understanding of acidification functionality in wound healing, highlighting the need to study the efficacy of wound acidification on wound closure and cellular activity in non-infected wounds. This study is focused on establishing the healing potential of wound acidification in non-infected wounds. Acidic buffers, constituting either phosphoric or citric acid, were employed to modify the physiological pH of non-infected full-thickness excisional murine wounds. Acidification of the wound by acidic buffers was found to be an effective strategy to improve wound healing. A significant improvement in wound healing parameters was observed as early as 2 days post-treatment with acidic buffers compared to controls, with faster rate of epithelialization, wound closure and higher levels of collagen at day 7. pH is shown to play a role in mediating the rate of wound healing, with acidic buffers formulated at pH 4 observed to stimulate faster recovery of wounded tissues than pH 6 buffers. Our study shows the importance of maintaining an acidic wound microenvironment at pH 4, which could be a potential therapeutic strategy for wound management. Full article

(This article belongs to the Special Issue Recent Approaches for Wound Treatment)

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10 pages, 1480 KiB

Open AccessReview

Activity-Dependent Neuroprotective Protein (ADNP): An Overview of Its Role in the Eye

by Grazia Maugeri, Agata Grazia D’Amico, Benedetta Magrì, Giuseppe Musumeci and Velia D’Agata

Int. J. Mol. Sci. 2022, 23(21), 13654; https://doi.org/10.3390/ijms232113654 - 7 Nov 2022

Cited by 4 | Viewed by 2397

Abstract

Vision is one of the dominant senses in humans and eye health is essential to ensure a good quality of life. Therefore, there is an urgent necessity to identify effective therapeutic candidates to reverse the progression of different ocular pathologies. Activity-dependent neuroprotective protein [...] Read more.

Vision is one of the dominant senses in humans and eye health is essential to ensure a good quality of life. Therefore, there is an urgent necessity to identify effective therapeutic candidates to reverse the progression of different ocular pathologies. Activity-dependent neuroprotective protein (ADNP) is a protein involved in the physio-pathological processes of the eye. Noteworthy, is the small peptide derived from ADNP, known as NAP, which shows protective, antioxidant, and anti-apoptotic properties. Herein, we review the current state of knowledge concerning the role of ADNP in ocular pathologies, while providing an overview of eye anatomy. Full article

(This article belongs to the Special Issue The Roles of VIP and PACAP: From Molecular and Genetic Studies)

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54 pages, 991 KiB

Open AccessReview

Mitochondrial Effects of Common Cardiovascular Medications: The Good, the Bad and the Mixed

by Alina M. Bețiu, Lavinia Noveanu, Iasmina M. Hâncu, Ana Lascu, Lucian Petrescu, Christoph Maack, Eskil Elmér and Danina M. Muntean

Int. J. Mol. Sci. 2022, 23(21), 13653; https://doi.org/10.3390/ijms232113653 - 7 Nov 2022

Cited by 15 | Viewed by 6279

Abstract

Mitochondria are central organelles in the homeostasis of the cardiovascular system via the integration of several physiological processes, such as ATP generation via oxidative phosphorylation, synthesis/exchange of metabolites, calcium sequestration, reactive oxygen species (ROS) production/buffering and control of cellular survival/death. Mitochondrial impairment has [...] Read more.

Mitochondria are central organelles in the homeostasis of the cardiovascular system via the integration of several physiological processes, such as ATP generation via oxidative phosphorylation, synthesis/exchange of metabolites, calcium sequestration, reactive oxygen species (ROS) production/buffering and control of cellular survival/death. Mitochondrial impairment has been widely recognized as a central pathomechanism of almost all cardiovascular diseases, rendering these organelles important therapeutic targets. Mitochondrial dysfunction has been reported to occur in the setting of drug-induced toxicity in several tissues and organs, including the heart. Members of the drug classes currently used in the therapeutics of cardiovascular pathologies have been reported to both support and undermine mitochondrial function. For the latter case, mitochondrial toxicity is the consequence of drug interference (direct or off-target effects) with mitochondrial respiration/energy conversion, DNA replication, ROS production and detoxification, cell death signaling and mitochondrial dynamics. The present narrative review aims to summarize the beneficial and deleterious mitochondrial effects of common cardiovascular medications as described in various experimental models and identify those for which evidence for both types of effects is available in the literature. Full article

(This article belongs to the Special Issue Targeting Mitochondria in Metabolic Diseases 2.0)

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23 pages, 4042 KiB

Open AccessArticle

Dynamical Mechanism Analysis of Three Neuroregulatory Strategies on the Modulation of Seizures

by Honghui Zhang, Zhuan Shen, Yuzhi Zhao, Lin Du and Zichen Deng

Int. J. Mol. Sci. 2022, 23(21), 13652; https://doi.org/10.3390/ijms232113652 - 7 Nov 2022

Cited by 3 | Viewed by 1903

Abstract

This paper attempts to explore and compare the regulatory mechanisms of optogenetic stimulation (OS), deep brain stimulation (DBS) and electromagnetic induction on epilepsy. Based on the Wilson–Cowan model, we first demonstrate that the external input received by excitatory and inhibitory neural populations can [...] Read more.

This paper attempts to explore and compare the regulatory mechanisms of optogenetic stimulation (OS), deep brain stimulation (DBS) and electromagnetic induction on epilepsy. Based on the Wilson–Cowan model, we first demonstrate that the external input received by excitatory and inhibitory neural populations can induce rich dynamic bifurcation behaviors such as Hopf bifurcation, and make the system exhibit epileptic and normal states. Then, both OS and DBS are shown to be effective in controlling the epileptic state to a normal low-level state, and the stimulus parameters have a broad effective range. However, electromagnetic induction cannot directly control epilepsy to this desired state, even if it can significantly reduce the oscillation frequency of neural populations. One main difference worth noting is that the high spatiotemporal specificity of OS allows it to target inhibitory neuronal populations, whereas DBS and electromagnetic induction can only stimulate excitatory as well as inhibitory neuronal populations together. Next, the propagation behavior of epilepsy is explored under a typical three-node feedback loop structure. An increase in coupling strength accelerates and exacerbates epileptic activity in other brain regions. Finally, OS and DBS applied to the epileptic focus play similar positive roles in controlling the behavior of the area of seizure propagation, while electromagnetic induction still only achieves unsatisfactory effects. It is hoped that these dynamical results can provide insights into the treatment of epilepsy as well as other neurological disorders. Full article

(This article belongs to the Special Issue Neural Dynamics and Regulation in Epilepsy)

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29 pages, 4124 KiB

Open AccessArticle

Modulation of the Functional State of Mouse Neutrophils by Selenium Nanoparticles In Vivo

by Valentina N. Mal’tseva, Sergey V. Gudkov and Egor A. Turovsky

Int. J. Mol. Sci. 2022, 23(21), 13651; https://doi.org/10.3390/ijms232113651 - 7 Nov 2022

Cited by 8 | Viewed by 2119

Abstract

This study aimed to discover the immunomodulatory effect of selenium nanoparticles (SeNPs) on the functional state of neutrophils in vivo. Intraperitoneal injections of SeNPs (size 100 nm) 2.5 mg/kg/daily to BALB/c mice for a duration of 7–28 days led to the development of [...] Read more.

This study aimed to discover the immunomodulatory effect of selenium nanoparticles (SeNPs) on the functional state of neutrophils in vivo. Intraperitoneal injections of SeNPs (size 100 nm) 2.5 mg/kg/daily to BALB/c mice for a duration of 7–28 days led to the development of an inflammatory reaction, which was registered by a significant increase in the number of neutrophils released from the peritoneal cavity, as well as their activated state, without additional effects. At the same time, subcutaneous injections of the same SeNPs preparations at concentrations of 0.1, 0.5, and 2.5 mg/kg, on the contrary, modulated the functional state of neutrophils depending on the concentration and duration of SeNPs administration. With the use of fluorescence spectroscopy, chemiluminescence, biochemical methods, and PCR analysis, it was found that subcutaneous administration of SeNPs (0.1, 0.5, and 2.5 mg/kg) to mice for a short period of time (7–14 days) leads to modification of important neutrophil functions (adhesion, the number of migrating cells into the peritoneal cell cavity, ROS production, and NET formation). The obtained results indicated the immunostimulatory and antioxidant effects of SeNPs in vivo during short-term administration, while the most pronounced immunomodulatory effects of SeNPs were observed with the introduction of a low concentration of SeNPs (0.1 mg/kg). Increase in the administration time of SeNPs (0.1 mg/kg or 2.5 mg/kg) up to 28 days led to a decrease in the adhesive abilities of neutrophils and suppression of the expression of mRNA of adhesive molecules, as well as proteins involved in the generation of ROS, with the exception of NOX2; there was a tendency to suppress gene expression pro-inflammatory factors, which indicates the possible manifestation of immunosuppressive and anti-inflammatory effects of SeNPs during their long-term administration. Changes in the expression of selenoproteins also had features depending on the concentration and duration of the administered SeNPs. Selenoprotein P, selenoprotein M, selenoprotein S, selenoprotein K, and selenoprotein T were the most sensitive to the introduction of SeNPs into the mouse organism, which indicates their participation in maintaining the functional status of neutrophils, and possibly mediated the immunomodulatory effect of SeNPs. Full article

(This article belongs to the Special Issue Interaction of Nanomaterials with the Immune System 2.0)

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26 pages, 11747 KiB

Open AccessArticle

In Silico Identification of Multi-Target Ligands as Promising Hit Compounds for Neurodegenerative Diseases Drug Development

by Petko Alov, Hristo Stoimenov, Iglika Lessigiarska, Tania Pencheva, Nikolay T. Tzvetkov, Ilza Pajeva and Ivanka Tsakovska

Int. J. Mol. Sci. 2022, 23(21), 13650; https://doi.org/10.3390/ijms232113650 - 7 Nov 2022

Cited by 2 | Viewed by 2462

Abstract

The conventional treatment of neurodegenerative diseases (NDDs) is based on the “one molecule—one target” paradigm. To combat the multifactorial nature of NDDs, the focus is now shifted toward the development of small-molecule-based compounds that can modulate more than one protein target, known as [...] Read more.

The conventional treatment of neurodegenerative diseases (NDDs) is based on the “one molecule—one target” paradigm. To combat the multifactorial nature of NDDs, the focus is now shifted toward the development of small-molecule-based compounds that can modulate more than one protein target, known as “multi-target-directed ligands” (MTDLs), while having low affinity for proteins that are irrelevant for the therapy. The in silico approaches have demonstrated a potential to be a suitable tool for the identification of MTDLs as promising drug candidates with reduction in cost and time for research and development. In this study more than 650,000 compounds were screened by a series of in silico approaches to identify drug-like compounds with predicted activity simultaneously towards three important proteins in the NDDs symptomatic treatment: acetylcholinesterase (AChE), histone deacetylase 2 (HDAC2), and monoamine oxidase B (MAO-B). The compounds with affinities below 5.0 µM for all studied targets were additionally filtered to remove known non-specifically binding or unstable compounds. The selected four hits underwent subsequent refinement through in silico blood-brain barrier penetration estimation, safety evaluation, and molecular dynamics simulations resulting in two hit compounds that constitute a rational basis for further development of multi-target active compounds against NDDs. Full article

(This article belongs to the Collection Computational Studies of Biomolecules)

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20 pages, 5781 KiB

Open AccessArticle

The Cysteine Protease Giardipain-1 from Giardia duodenalis Contributes to a Disruption of Intestinal Homeostasis

by Rodrigo Quezada-Lázaro, Yessica Vázquez-Cobix, Rocío Fonseca-Liñán, Porfirio Nava, Daniel Dimitri Hernández-Cueto, Carlos Cedillo-Peláez, Yolanda López-Vidal, Sara Huerta-Yepez and M. Guadalupe Ortega-Pierres

Int. J. Mol. Sci. 2022, 23(21), 13649; https://doi.org/10.3390/ijms232113649 - 7 Nov 2022

Cited by 3 | Viewed by 2100

Abstract

In giardiasis, diarrhoea, dehydration, malabsorption, weight loss and/or chronic inflammation are indicative of epithelial barrier dysfunction. However, the pathogenesis of giardiasis is still enigmatic in many aspects. Here, we show evidence that a cysteine protease of Giardia duodenalis called giardipain-1, contributes to the [...] Read more.

In giardiasis, diarrhoea, dehydration, malabsorption, weight loss and/or chronic inflammation are indicative of epithelial barrier dysfunction. However, the pathogenesis of giardiasis is still enigmatic in many aspects. Here, we show evidence that a cysteine protease of Giardia duodenalis called giardipain-1, contributes to the pathogenesis of giardiasis induced by trophozoites of the WB strain. In an experimental system, we demonstrate that purified giardipain-1 induces apoptosis and extrusion of epithelial cells at the tips of the villi in infected jirds (Meriones unguiculatus). Moreover, jird infection with trophozoites expressing giardipain-1 resulted in intestinal epithelial damage, cellular infiltration, crypt hyperplasia, goblet cell hypertrophy and oedema. Pathological alterations were more pronounced when jirds were infected intragastrically with Giardia trophozoites that stably overexpress giardipain-1. Furthermore, Giardia colonization in jirds results in a chronic inflammation that could relate to the dysbiosis triggered by the protist. Taken together, these results reveal that giardipain-1 plays a key role in the pathogenesis of giardiasis. Full article

(This article belongs to the Special Issue Gut Microbiota and Immunity 2.0)

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18 pages, 14811 KiB

Open AccessArticle

E3 Ubiquitin Ligase FBXO3 Drives Neuroinflammation to Aggravate Cerebral Ischemia/Reperfusion Injury

by Yu Gao, Xinyu Xiao, Jing Luo, Jianwei Wang, Qiling Peng, Jing Zhao, Ning Jiang and Yong Zhao

Int. J. Mol. Sci. 2022, 23(21), 13648; https://doi.org/10.3390/ijms232113648 - 7 Nov 2022

Cited by 6 | Viewed by 2588

Abstract

Ischemic stroke, one of the most universal causes of human mortality and morbidity, is pathologically characterized by inflammatory cascade, especially during the progression of ischemia/reperfusion (I/R) injury. F-Box Protein 3 (FBXO3), a substrate-recognition subunit of SKP1-cullin 1-F-box protein (SCF) E3 ligase complexes, has [...] Read more.

Ischemic stroke, one of the most universal causes of human mortality and morbidity, is pathologically characterized by inflammatory cascade, especially during the progression of ischemia/reperfusion (I/R) injury. F-Box Protein 3 (FBXO3), a substrate-recognition subunit of SKP1-cullin 1-F-box protein (SCF) E3 ligase complexes, has recently been proven to be severed as an underlying pro-inflammatory factor in pathological processes of diverse diseases. Given these considerations, the current study aims at investigating whether FBXO3 exerts impacts on inflammation in cerebral I/R injury. In this study, first, it was verified that FBXO3 protein expression increased after a middle cerebral artery occlusion/reperfusion (MCAO/R) model in Sprague–Dawley (SD) rats and was specifically expressed in neurons other than microglia or astrocytes. Meanwhile, in mouse hippocampal neuronal cell line HT22 cells, the elevation of FBXO3 protein was observed after oxygen and glucose deprivation/reoxygenation (OGD/R) treatment. It was also found that interference of FBXO3 with siRNA significantly alleviated neuronal damage via inhibiting the inflammatory response in I/R injury both in vivo and in vitro. The FBXO3 inhibitor BC-1215 was used to confirm the pro-inflammatory effect of FBXO3 in the OGD/R model as well. Furthermore, by administration of FBXO3 siRNA and BC-1215, FBXO3 was verified to reduce the protein level of Homeodomain-Interacting Protein Kinase 2 (HIPK2), likely through the ubiquitin–proteasome system (UPS), to aggravate cerebral I/R injury. Collectively, our results underline the detrimental effect FBXO3 has on cerebral I/R injury by accelerating inflammatory response, possibly through ubiquitylating and degrading HIPK2. Despite the specific interaction between FBXO3 and HIPK2 requiring further study, we believe that our data suggest the therapeutic relevance of FBXO3 to ischemic stroke and provide a new perspective on the mechanism of I/R injury. Full article

(This article belongs to the Special Issue Advances in Molecular Mechanisms of Stroke)

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17 pages, 3488 KiB

Open AccessArticle

Biological Solubilisation of Leather Industry Waste in Anaerobic Conditions: Effect of Chromium (III) Presence, Pre-Treatments and Temperature Strategies

by Juana Fernández-Rodríguez, Beñat Lorea and Gustavo González-Gaitano

Int. J. Mol. Sci. 2022, 23(21), 13647; https://doi.org/10.3390/ijms232113647 - 7 Nov 2022

Cited by 7 | Viewed by 2188

Abstract

Collagen-based polymers and their blends have attracted considerable interest for new materials development due to their unique combination of biocompatibility, physical and mechanical properties and durability. Leather, a modified natural biopolymer made from animal rawhide and the first synthetic collagen-based polymer known since [...] Read more.

Collagen-based polymers and their blends have attracted considerable interest for new materials development due to their unique combination of biocompatibility, physical and mechanical properties and durability. Leather, a modified natural biopolymer made from animal rawhide and the first synthetic collagen-based polymer known since the dawn of civilization, combines all these features. Rawhide is transformed into leather by tanning, a process in which the collagen is cross-linked with different agents to make it stronger and more durable and to prevent its decay. Research on the development of environmentally friendly procedures and sustainable materials with higher efficiency and lower costs is a rapidly growing field, and leather industry is not an exemption. Chrome-tanned and vegetable-tanned (chromium-free) shavings from the leather industry present a high content of organic matter, yet they are considered recalcitrant waste to be degraded by microbiological processes like anaerobic digestion (AD), a solid technology to treat organic waste in a circular economy framework. In this technology however, the solubilisation of organic solid substrates is a significant challenge to improving the efficiency of the process. In this context, we have investigated the process of microbial decomposition of leather wastes from the tannery industry to search for the conditions that produce optimal solubilisation of organic matter. Chrome-tanned and chromium-free leather shavings were pre-treated and anaerobically digested under different temperature ranges (thermophilic–55 °C-, intermediate–42 °C- and mesophilic–35 °C) to evaluate the effect on the solubilisation of the organic matter of the wastes. The results showed that the presence of chromium significantly inhibited the solubilization (up to 60%) in the mesophilic and intermediate ranges; this is the fastest and most efficient solubilization reached under thermophilic conditions using the chromium-free leather shaving as substrates. The most suitable temperature for the solubilization was the thermophilic regime (55 °C) for both chromium-free and chrome-tanned shavings. No significant differences were observed in the thermophilic anaerobic digestion of chromium-free shavings when a pre-treatment was applied, since the solubilisation was already high without pre-treatment. However, the pre-treatments significantly improved the solubilisation in the mesophilic and intermediate configurations; the former pre-treatment was better suited in terms of performance and cost-effectiveness compared to the thermophilic range. Thus, the solubilisation of chromium-free tannery solid wastes can be significantly improved by applying appropriate pre-treatments at lower temperature ranges; this is of utter importance when optimizing anaerobic processes of recalcitrant organic wastes, with the added benefit of substantial energy savings in the scaling up of the process in an optimised circular economy scenario. Full article

(This article belongs to the Special Issue Biosynthesis and Biodegradation—Eco-Concept for Polymer Materials)

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Thermogravimetric profiles (TGA and DTG) of chrome-tanned (C) and chromium-free (NC) leather wastes. Full article ">Figure 2
(a) ATR-FTIR spectra of Cr(III)-free leather waste as a function of the temperature; and (b) zoomed-in view of the amide III zone of the FTIR spectra of Cr(III)-free leather waste as a function of the temperature. Full article ">Figure 3
Shift of the amide III band as a function of the temperature (heating and cooling runs), showing the structural hysteresis. Full article ">Figure 4
Evolution of organic matter solubilisation at thermophilic (55 °C), intermediate (42 °C) and mesophilic (35 °C) temperature regimes: (a) CODs from chrome-tanned (C); (b) DOC from chrome-tanned (C); (c) CODs from chromium-free (NC); and (d) DOC from chromium-free (NC) leather shavings. Full article ">Figure 5
Evolution of organic matter solubilisation at thermophilic (55 °C), intermediate (42 °C) and mesophilic (35 °C) temperature regimes: (a) CODs from pre-treated chrome-tanned (C-P); (b) DOC from pre-treated chrome-tanned (C-P); (c) CODs from pre-treated chromium-free (NC-P); and (d) DOC from pre-treated chromium-free (NC-P) leather shavings. Full article ">Figure 6
Solubilisation of the leather shavings expressed as CODs (mg/L) at different temperatures (55, 42, 35 °C). Not pre-treated (-); pre-treated (P); with Cr(III) (C) and without Cr(III) (NC). On top of bars, increments over the not pre-treated substrates. Full article ">Figure 7
Micrographs of the leather shavings used: (a) Chrome-tanned (C), tanned from the wet blue industrial process; and (b) chromium-free (NC), from the wet white industrial process. Full article ">Figure 8
Scheme of the experimental setup for the AD. Full article ">

19 pages, 1006 KiB

Open AccessReview

Helicobacter pylori in the Oral Cavity: Current Evidence and Potential Survival Strategies

by Lin Zhang, Xi Chen, Biao Ren, Xuedong Zhou and Lei Cheng

Int. J. Mol. Sci. 2022, 23(21), 13646; https://doi.org/10.3390/ijms232113646 - 7 Nov 2022

Cited by 20 | Viewed by 8260

Abstract

Helicobacter pylori (H. pylori) is transmitted primarily through the oral–oral route and fecal–oral route. The oral cavity had therefore been hypothesized as an extragastric reservoir of H. pylori, owing to the presence of H. pylori DNA and particular antigens in [...] Read more.

Helicobacter pylori (H. pylori) is transmitted primarily through the oral–oral route and fecal–oral route. The oral cavity had therefore been hypothesized as an extragastric reservoir of H. pylori, owing to the presence of H. pylori DNA and particular antigens in distinct niches of the oral cavity. This bacterium in the oral cavity may contribute to the progression of periodontitis and is associated with a variety of oral diseases, gastric eradication failure, and reinfection. However, the conditions in the oral cavity do not appear to be ideal for H. pylori survival, and little is known about its biological function in the oral cavity. It is critical to clarify the survival strategies of H. pylori to better comprehend the role and function of this bacterium in the oral cavity. In this review, we attempt to analyze the evidence indicating the existence of living oral H. pylori, as well as potential survival strategies, including the formation of a favorable microenvironment, the interaction between H. pylori and oral microorganisms, and the transition to a non-growing state. Further research on oral H. pylori is necessary to develop improved therapies for the prevention and treatment of H. pylori infection. Full article

(This article belongs to the Special Issue New Advances on Helicobacter pylori Research)

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23 pages, 5974 KiB

Open AccessArticle

EMT Molecular Signatures of Pancreatic Neuroendocrine Neoplasms

by Abhirami Venugopal, Agnes Michalczyk, Mustafa Khasraw and M. Leigh Ackland

Int. J. Mol. Sci. 2022, 23(21), 13645; https://doi.org/10.3390/ijms232113645 - 7 Nov 2022

Cited by 4 | Viewed by 1899

Abstract

Neuroendocrine neoplasms (NENs) are relatively rare neoplasms occurring predominantly in the gastrointestinal tract and pancreas. Their heterogeneity poses challenges for diagnosis and treatment. There is a paucity of markers for characterisation of NEN tumours. For routine diagnosis, immunohistochemistry of the NEN-specific markers CgA [...] Read more.

Neuroendocrine neoplasms (NENs) are relatively rare neoplasms occurring predominantly in the gastrointestinal tract and pancreas. Their heterogeneity poses challenges for diagnosis and treatment. There is a paucity of markers for characterisation of NEN tumours. For routine diagnosis, immunohistochemistry of the NEN-specific markers CgA and synaptophysin and the proliferation marker Ki-67 are used. These parameters, however, are qualitative and lack the capacity to fully define the tumour phenotype. Molecules of epithelial–mesenchymal transition (EMT) are potential candidates for improved tumour characterisation. Using qRT-PCR, we measured mRNA levels of 27 tumour markers, including 25 EMT-associated markers, in tumour tissue and matched non-tumour tissues for 13 patients with pancreatic NENs. Tissue from patients with three different grades of tumour had distinctly different mRNA profiles. Of the 25 EMT-associated markers analysed, 17 were higher in G3 tissue relative to matched non-tumour tissue, including CD14, CD24, CD31, CD44, CD45, CD56, CK6, CK7, CK13, CK20, NSE, CDX2, CgA, DAXX, PCNA, laminin and Ki-67. The differences in levels of seven EMT-associated markers, Ki-67, DAXX, CD24, CD44, vimentin, laminin and PDX1 plus CgA and NSE (neuroendocrine markers) enabled a distinct molecular signature for each tumour grade to be generated. EMT molecules differentially expressed in three tumour grades have potential for use in tumour stratification and prognostication and as therapeutic targets for treatment of neuroendocrine cancers, following validation with additional samples. Full article

(This article belongs to the Special Issue Tumor Microenvironment: Molecular Mechanisms and Signaling Pathways Involved in Metastatic Progression)

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22 pages, 2388 KiB

Open AccessArticle

Altered Expression of Genes Associated with Major Neurotransmitter Systems in the Reward-Related Brain Regions of Mice with Positive Fighting Experience

by Dmitry A. Smagin, Anna G. Galyamina, Irina L. Kovalenko and Natalia N. Kudryavtseva

Int. J. Mol. Sci. 2022, 23(21), 13644; https://doi.org/10.3390/ijms232113644 - 7 Nov 2022

Cited by 7 | Viewed by 2347

Abstract

The main neurotransmitters in the brain—dopamine, γ-aminobutyric acid (GABA), glutamate, and opioids—are recognized to be the most important for the regulation of aggression and addiction. The aim of this work was to study differentially expressed genes (DEGs) in the main reward-related brain regions, [...] Read more.

The main neurotransmitters in the brain—dopamine, γ-aminobutyric acid (GABA), glutamate, and opioids—are recognized to be the most important for the regulation of aggression and addiction. The aim of this work was to study differentially expressed genes (DEGs) in the main reward-related brain regions, including the ventral tegmental area (VTA), dorsal striatum (STR), ventral striatum (nucleus accumbens, NAcc), prefrontal cortex (PFC), and midbrain raphe nuclei (MRNs), in male mice with 20-day positive fighting experience in daily agonistic interactions. Expression of opioidergic, catecholaminergic, glutamatergic, and GABAergic genes was analyzed to confirm or refute the influence of repeated positive fighting experience on the development of “addiction-like” signs shown in our previous studies. High-throughput RNA sequencing was performed to identify differentially expressed genes in the brain regions of chronically aggressive mice. In the aggressive mice, upregulation of opioidergic genes was shown (Oprk1 in VTA, Pdyn in NAcc, Penk in PFC, and Oprd1 in MRNs and PFC), as was downregulation of genes Opcml and Oprk1 in STR and Pomc in VTA and NAcc. Upregulation of catecholaminergic genes in VTA (Ddc and Slc6a2) and in NAcc (Th and Drd2) and downregulation of some differentially expressed genes in MRNs (Th, Ddc, Dbh, Drd2, Slc18a2, and Sncg) and in VTA (Adra2c, Sncg, and Sncb) were also documented. The expression of GABAergic and glutamatergic genes that participate in drug addiction changed in all brain regions. According to literature data, the proteins encoded by genes Drd2, Oprk1, Oprd1, Pdyn, Penk, and Pomc are directly involved in drug addiction in humans. Thus, our results confirm our earlier claim about the formation of addiction-like signs following repeated positive fighting experience in mice, as shown previously in our biobehavioral studies. Full article

(This article belongs to the Section Molecular Neurobiology)

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Figure 1
DEGs in the VTA of highly aggressive mice. (A) FPKM of the DEGs in the VTA (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S1</a>). White bars—controls; colored bars—winners: brown—opioidergic genes; pink—CAergic genes; lilac—GABAergic genes; violet—glutamatergic genes. * p < 0.05; ** p < 0.01; *** p < 0.001. (B) AHC based on 13 reference DEGs’ expression profiles (additional information: <a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S2</a>). Similarity: Pearson’s correlation coefficient. Agglomeration method: unweighted pair-group average. The main clusters are highlighted with a blue rounded rectangle. Full article ">Figure 2
DEGs in the NAcc of highly aggressive mice. (A) FPKM of the DEGs in the NAcc (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S1</a>). White bars: controls; colored bars—winners: brown—opioidergic genes; pink - CAergic genes; lilac—GABAergic genes; violet—glutamatergic genes. * p < 0.05; ** p < 0.01; *** p < 0.001. (B) AHC based on expression profiles of eight reference DEGs (additional information: <a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S2</a>). Similarity: Pearson’s correlation coefficient. Agglomeration method: Unweighted pair-group average. The main clusters are highlighted with a blue rounded rectangle. Full article ">Figure 3
DEGs in the STR of highly aggressive mice. (A) FPKM of opioidergic, GABAergic, and glutamatergic DEGs in the STR. White bars—controls; colored bars—winners: brown—opioidergic genes; lilac—GABAergic genes; violet—glutamatergic genes. * p < 0.05; ** p < 0.01 (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S1</a>). (B) AHC based on expression profiles of eight reference DEGs (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S2</a>). Similarity: Pearson’s correlation coefficient. Agglomeration method: Unweighted pair-group average. The main clusters are highlighted with a blue rounded rectangle. Full article ">Figure 4
DEGs in the PFC of highly aggressive mice. (A) FPKM of opioidergic and glutamatergic DEGs in the PFC of mice. White bars—controls; colored bars—winners: brown—opioidergic genes; violet—glutamatergic genes (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S1</a>). * p < 0.05; *** p < 0.001. (B) AHC based on five reference DEGs’ expression profiles (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S2</a>). Similarity: Pearson’s correlation coefficient. Agglomeration method: Unweighted pair-group average. The main clusters are highlighted with a blue rounded rectangle. Full article ">Figure 5
DEGs in the MRNs of highly aggressive mice. (A) FPKM of opioidergic, CAergic, GABAergic and glutamatergic DEGs in the MRNs (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S1</a>). White bars—controls; colored bars—winners: brown—opioidergic genes; pink—CAergic genes; lilac—GABAergic genes; violet—glutamatergic genes. * p < 0.05; ** p < 0.01; *** p < 0.001. (B) AHC based on expression profiles of 18 reference DEGs (<a href="#app1-ijms-23-13644" class="html-app">Supplementary Table S2</a>). Similarity: Pearson’s correlation coefficient. Agglomeration method: Unweighted pair-group average. The main clusters are highlighted with a blue rounded rectangle. Full article ">Figure 6
PCA plots based on covariation of genes on the basis of expression profiles of 15 CAergic and opioidergic DEGs across 30 samples, which comprise RNA-Seq FPKM data for five brain regions. (A) Active observations. W1, W2, and W3: winners; C1, C2, and C3: controls; VTA: ventral tegmental area, NAcc: nucleus accumbens, MRN: midbrain raphe nuclei, STR: dorsal striatum, and PFC: prefrontal cortex. Ovals denote brain regions. (B) Active variables. The graph illustrates distinct clustering of DEGs. Full article ">Figure 7
FPKM values of five CAergic- and opioid-specific DEGs across 30 samples on the basis of the included RNA-Seq FPKM data for five brain regions. C1, C2, and C3: controls; W1, W2, and W3: winners; VTA: ventral tegmental area, NAcc: nucleus accumbens, MRN: midbrain raphe nuclei, STR: dorsal striatum, and PFC: prefrontal cortex. Full article ">Figure 8
The experimental cage. Full article ">

19 pages, 1937 KiB

Open AccessReview

Interplay between Autophagy and Herpes Simplex Virus Type 1: ICP34.5, One of the Main Actors

by Inés Ripa, Sabina Andreu, José Antonio López-Guerrero and Raquel Bello-Morales

Int. J. Mol. Sci. 2022, 23(21), 13643; https://doi.org/10.3390/ijms232113643 - 7 Nov 2022

Cited by 5 | Viewed by 3330

Abstract

Herpes simplex virus type 1 (HSV-1) is a neurotropic virus that occasionally may spread to the central nervous system (CNS), being the most common cause of sporadic encephalitis. One of the main neurovirulence factors of HSV-1 is the protein ICP34.5, which although it [...] Read more.

Herpes simplex virus type 1 (HSV-1) is a neurotropic virus that occasionally may spread to the central nervous system (CNS), being the most common cause of sporadic encephalitis. One of the main neurovirulence factors of HSV-1 is the protein ICP34.5, which although it initially seems to be relevant only in neuronal infections, it can also promote viral replication in non-neuronal cells. New ICP34.5 functions have been discovered during recent years, and some of them have been questioned. This review describes the mechanisms of ICP34.5 to control cellular antiviral responses and debates its most controversial functions. One of the most discussed roles of ICP34.5 is autophagy inhibition. Although autophagy is considered a defense mechanism against viral infections, current evidence suggests that this antiviral function is only one side of the coin. Different types of autophagic pathways interact with HSV-1 impairing or enhancing the infection, and both the virus and the host cell modulate these pathways to tip the scales in its favor. In this review, we summarize the recent progress on the interplay between autophagy and HSV-1, focusing on the intricate role of ICP34.5 in the modulation of this pathway to fight the battle against cellular defenses. Full article

(This article belongs to the Special Issue Alphaherpesviruses)

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Degradation of HSV-1 by selective autophagy. The ULK complex initiates the formation of the phagophore by phosphorylating components of the PI3KC3 complex I and mediating the trafficking of ATG9-containing vesicles. The LC3-PE conjugation system participates in the elongation and closure of the double membrane, resulting in the formation of the autophagosome. The selective autophagy receptors (SARs) p62/SQSTM1 [<a href="#B21-ijms-23-13643" class="html-bibr">21</a>] and optineurin (OPTN) [<a href="#B22-ijms-23-13643" class="html-bibr">22</a>] and the autophagy receptor-like factors Fanconi anemia group C protein (FANCC) [<a href="#B23-ijms-23-13643" class="html-bibr">23</a>] and SMAD ubiquitin regulatory factor 1 (SMURF-1) [<a href="#B21-ijms-23-13643" class="html-bibr">21</a>] can interact with HSV-1 and mediate the recruitment of HSV-1 virions and/or viral cytoplasmic components into the autophagosomes. Once cargo has been engulfed, the external membrane of the autophagosome fuses with a lysosome for degradation of viral components. Full article ">Figure 2
ICP34.5 of HSV-1 strain 17. HSV-1 ICP34.5 is a protein with 248 amino acids that can be divided into three regions: the amino and the carboxyl terminal domains, and a linked tandem of five ATP repeats (161–175 aa) (orange box). The N-terminal region of ICP34.5 contains a nucleolar localization and nuclear export signals, and the C-terminal domain includes a nuclear localization signal (red boxes). Three binding domains (green boxes) have been characterized: the Beclin-1-binding domain (BBD) in the N-terminus, and the PP1α- and elF2α-binding domains in the C-terminus. Full article ">Figure 3
Functions of ICP34.5 in HSV-1 infected cells. Functions of ICP34.5 can be classified according to the cellular location of the protein, which shuttles between the cytoplasm and the nucleus. The amino and the carboxyl domains of ICP34.5 play different roles in infected cells. The C-terminus prevents the translational arrest by the binding of PP1α and the subsequent dephosphorylation of elF2α. The N-terminus is involved in the suppression of Beclin-1-autophagy, the degradation of the nuclear lamina to facilitate nucleocapsid egress from the nucleus, and the blockade of IFN response by the inhibition of the dsDNA-sensing pathway. The full-length protein plays a role in virus replication in non-dividing cells, in the prevention of DCs maturation, and in the suppression of the IFN response by blocking the RNA-sensing pathway. Full article ">Figure 4
Autophagy modulation by ICP34.5 in HSV-1 infection. Early in HSV-1 infection, detection of the virus by host cell promotes the stimulation of macroautophagy. This pathway may act as a cellular defense mechanism involved in virophagy and the processing of viral antigen for MHC presentation. Autophagic flux can be induced in manner that is dependent on viral gene expression by the PKR/elF2α pathway. Autophagy may be enhanced through the recognition of PAMPs by the surface receptor TLR2. Activated TLR2 recruits the adaptor MyD88, which causes the dissociation of Beclin-1 from the BCL-2 inhibitory complex, resulting in the induction of autophagy. Finally, HSV-1 dsDNA may be recognized by the cytosolic dsDNA-sensing cGAS, which produces cGAMP to activate STING and TBK1. Activation of TBK1 promotes autophagy stimulation. Full article ">Figure 5
HSV-1 mechanisms for autophagy inhibition. HSV-1 proteins Us3 and ICP34.5 can inhibit macroautophagy by binding to Beclin-1, which is required for autophagosome formation. Us3 can also suppress the pathway by the activation of the negative regulator of autophagy mTORC1 or by the inactivation of the ULK1 complex, which is involved in phagophore initiation. The HSV-1 protein Us11 can prevent the induction of autophagy mediated by the PKR/elF2α pathway. Besides, Us11 inhibits virus-induced autophagy by the disassembly of the TRIM23-Hsp90-TBK1 complex. Finally, the HSV-1 protein ICP0 promotes the degradation in the proteasome of the selective autophagy receptors p62/SQSTM1 and OPTN, which are implied in the recruitment of HSV-1 in autophagosomal membranes. The TRIM23-TBK1 complex is involved in the phosphorylation and activation of these selective receptors. However, the inhibitory role of Us11 on the TRIM23-TBK1 complex has not been directly associated with a possible SARs inactivation. Full article ">

7 pages, 889 KiB

Open AccessCase Report

Changes in Brain Volumes Are Relevant during Natalizumab-Associated Progressive Multifocal Leukoencephalopathy: Lessons from a Case Report

by Roberto De Masi, Stefania Orlando, Silvia Armenise, Pantaleo Spagnolo, Ruggero Capra and Maria Carmela Costa

Int. J. Mol. Sci. 2022, 23(21), 13642; https://doi.org/10.3390/ijms232113642 - 7 Nov 2022

Cited by 1 | Viewed by 1419

Abstract

This is a case report concerning a Natalizumab-associated Progressive Multifocal Leukoencephalopathy (PML) with cerebellar localization and wakefulness disturbances. Awakening and clinical improvement dramatically occurred as soon as the immune reconstitution inflammatory syndrome (IRIS) took place, being it mild in nature and colocalizing with [...] Read more.

This is a case report concerning a Natalizumab-associated Progressive Multifocal Leukoencephalopathy (PML) with cerebellar localization and wakefulness disturbances. Awakening and clinical improvement dramatically occurred as soon as the immune reconstitution inflammatory syndrome (IRIS) took place, being it mild in nature and colocalizing with the PML lesion. In these ideal experimental conditions, we applied brain magnetic resonance imaging post-analysis in order to know changes in brain volumes underlying the pathological process over the infection period. White matter volume increased with a decrease in grey matter during IRIS. Conversely, we found a constant increase in cerebrospinal fluid volume throughout the duration of PML, suggesting a widespread abiotrophic effect, far from the lesion. Furthermore, brain parenchymal fraction significantly decreased as expected while the total brain volume remained stable at all times. Neurodegeneration is the main contributor to the steady disability in Natalizumab-associated PML. This process is thought to be widespread and inflammatory in nature as well as sustained by IRIS and humoral factors derived from the PML lesion. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Neurobiology in Italy)

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Figure 1
Timeline of changes in brain and PML lesion volumes. Volume (in ml) of total brain (TBV), cerebrospinal fluid (CSF), grey (GM) and white matter (WM), and PML lesion are shown in (A); fraction of grey matter (GMF), white matter (WMF), and brain parenchymal (BPF) are shown in (B). In both graphs, volumes and fractions curves regarding the entire observation period are represented. Specifically, T0: baseline, T1–T5: PML, T6*–T8*: IRIS, T9: recovery from IRIS. The numerical value of each point is expressed with the same color code as the corresponding curve. PML: progressive multifocal leukoencephalopathy; IRIS: immune reconstitution inflammatory syndrome. Full article ">Figure 2
Timeline of evolution of PML, IRIS, and EDSS. Axial brain MRI on FLAIR and T1-weighted post-contrast sequence showing the evolution of PML (top) and IRIS (bottom), respectively. Specifically, T0 shows the baseline MRI, T1 the first MRI suggestive of PML, T2–T5 the progression of PML, T6*–T8* IRIS, and T9 the recovery from IRIS. Note the cerebellar colocalization of PML and IRIS as well as the progressive enlargement of PML lesion from T1 to T5, expressing, the latter, an involvement similar to that of T9, when the infection is over. EDSS is also represented, as well as the time-period characterized by the wakefulness disturbances. Note the progressive accumulation of PML lesion volume and the concomitant worsening of EDSS, from T1 to T5. Wakefulness disturbances manifest in T3 and regress in T6, as soon as IRIS occurs. PML: progressive multifocal leukoencephalopathy; IRIS: immune reconstitution inflammatory syndrome; EDSS: expanded disability status scale. Full article ">

14 pages, 2495 KiB

Open AccessArticle

Non-Muscle MLCK Contributes to Endothelial Cell Hyper-Proliferation through the ERK Pathway as a Mechanism for Vascular Remodeling in Pulmonary Hypertension

by Mariam Anis, Janae Gonzales, Rachel Halstrom, Noman Baig, Cat Humpal, Regaina Demeritte, Yulia Epshtein, Jeffrey R. Jacobson and Dustin R. Fraidenburg

Int. J. Mol. Sci. 2022, 23(21), 13641; https://doi.org/10.3390/ijms232113641 - 7 Nov 2022

Cited by 4 | Viewed by 2129

Abstract

Pulmonary arterial hypertension (PAH) is characterized by endothelial dysfunction, uncontrolled proliferation and migration of pulmonary arterial endothelial cells leading to increased pulmonary vascular resistance resulting in great morbidity and poor survival. Bone morphogenetic protein receptor II (BMPR2) plays an important role in the [...] Read more.

Pulmonary arterial hypertension (PAH) is characterized by endothelial dysfunction, uncontrolled proliferation and migration of pulmonary arterial endothelial cells leading to increased pulmonary vascular resistance resulting in great morbidity and poor survival. Bone morphogenetic protein receptor II (BMPR2) plays an important role in the pathogenesis of PAH as the most common genetic mutation. Non-muscle myosin light chain kinase (nmMLCK) is an essential component of the cellular cytoskeleton and recent studies have shown that increased nmMLCK activity regulates biological processes in various pulmonary diseases such as asthma and acute lung injury. In this study, we aimed to discover the role of nmMLCK in the proliferation and migration of pulmonary arterial endothelial cells (HPAECs) in the pathogenesis of PAH. We used two cellular models relevant to the pathobiology of PAH including BMPR2 silenced and vascular endothelial growth factor (VEGF) stimulated HPAECs. Both models demonstrated an increase in nmMLCK activity along with a robust increase in cellular proliferation, inflammation, and cellular migration. The upregulated nmMLCK activity was also associated with increased ERK expression pointing towards a potential integral cytoplasmic interaction. Mechanistically, we confirmed that when nmMLCK is inhibited by MLCK selective inhibitor (ML-7), proliferation and migration are attenuated. In conclusion, our results demonstrate that nmMLCK upregulation in association with increased ERK expression may contribute to the pathogenesis of PAHby stimulating cellular proliferation and migration. Full article

(This article belongs to the Special Issue Arteriogenesis, Angiogenesis and Vascular Remodeling)

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Figure 1
BMPR2 silencing in human pulmonary artery endothelial cells (HPAECs) is associated with ERK/MAPK activation. Representative Western blot images denoting BMPR2 and p-ERK (A) as well as p-MLC (B) protein expression between HPAECs transfected with BMPR2 siRNA or control siRNA for 48 h. Bar graphs summarizing relative BMPR2 (C), phosphorylated ERK (D), and phosphorylated MLC (E) protein expression at 48 h in BMPR2 silenced HPAECs compared to control (n = 3). * indicates p < 0.05; **, p ≤ 0.01; BMPR2, Bone morphogenetic protein receptor type II; p-ERK, phosphorylated extracellular signal-regulated kinase; p-MLC, phosphorylated myosin light-chain; siRNA, small interfering (silencing) RNA. Full article ">Figure 2
BMPR2 silencing increases HPAEC proliferation and cytokine release which is attenuated by inhibition of myosin light chain kinase (MLCK). Representative Western blot (A) and accompanying bar graph (B) depicting PCNA protein expression at 48 h between HPAECs transfected with BMPR2 or control siRNA (n = 3). (C) Bar graph representing changes in proliferation and viability as measured by WST-1 assay in HPAECs transfected with BMPR2 siRNA, control siRNA, and BMPR2 siRNA with ML-7 (10 μM) pre-treatment for 48 h (n = 9). Bar graph measuring IL-6 (D) and IL-8 (E) concentrations in the media of HPAECs transfected with BMPR2 siRNA, control siRNA, and BMPR2 siRNA with ML-7 (10 μM) pre-treatment for 48 h (n = 3). * indicates p < 0.05; **, p ≤ 0.01; ***, p ≤ 0.001; PCNA, proliferating cell nuclear antigen; BMPR2, Bone morphogenetic protein receptor type II; siRNA, small interfering (silencing) RNA; ML-7, myosin light chain kinase specific inhibitor; IL-6, Interleukin-6; IL-8, Interleukin-8. Full article ">Figure 3
BMPR2 silencing increases HPAEC migration which is attenuated by MLCK inhibition. (A) Plot demonstrating the transendothelial resistance by ECIS-based wounding over time in HPAECs transfected with BMPR2 siRNA, control siRNA, BMPR2 siRNA with ML-7 (10 μM), and control siRNA with ML-7 (10 μM) (n = 2). (B) Bar graph denoting the area under the curve measurements at 12 h for the ECIS-based wounding experiments (n = 2). (C) Representative images of wound healing assay depicting scratches created in confluent cultures of HPAECs transfected with BMPR2 siRNA, control siRNA, and BMPR2 siRNA with ML-7 (10 μM) at 0 h and 24 h time points; scale bar = 100 μm. (D) Bar graph summarizing percent gap closure at 24 h for the wound healing assay experiments (n = 3). * indicates p < 0.05; **, p ≤ 0.01; BMPR2, Bone morphogenetic protein receptor type II; siRNA, small interfering (silencing) RNA; ML-7, myosin light chain kinase specific inhibitor. Full article ">Figure 4
VEGF stimulation in HPAECs leads to upregulation of ERK/MAPK, which is abrogated by MLCK inhibition. (A) Representative Western blot images denoting p-ERK and p-MLC protein expression in HPAECs treated with VEGF (100 ng/mL), control (PBS vehicle), and VEGF with ML-7 (10 μM) pre-treatment for 72 h. Bar graphs summarizing relative phosphorylated ERK (B) and phosphorylated MLC (C) protein expression at 72 h in HPAECs treated with VEGF, control, and VEGF with ML-7 (n = at least 4 for p-ERK, n = at least 7 for p-MLC). ** indicates p ≤ 0.01; ***, p ≤ 0.001; VEGF, vascular endothelial growth factor; p-ERK, phosphorylated extracellular signal-regulated kinase; p-MLC, phosphorylated myosin light-chain; ML-7, myosin light chain kinase specific inhibitor. Full article ">Figure 5
VEGF treatment increases HPAEC proliferation and cytokine release which is attenuated by inhibition of myosin light chain kinase (MLCK). Representative Western blot (A) and accompanying bar graph (B) depicting PCNA protein expression at 72 h between HPAECs treated with VEGF (100 ng/mL), control (PBS vehicle), and VEGF with ML-7 (10 μM) pre-treatment (n = at least 2). β-actin loading control is identical to <a href="#ijms-23-13641-f004" class="html-fig">Figure 4</a>A as the representative blot was derived from the same experiment. (C) Bar graph denoting changes in proliferation and viability as measured by WST-1 assay in HPAECs treated with VEGF, control, and VEGF with ML-7 for 72 h (n = 4). ** indicated p ≤ 0.01; *** indicates p ≤ 0.001; PCNA, proliferating cell nuclear antigen; VEGF, vascular endothelial growth factor; ML-7, myosin light chain kinase specific inhibitor; IL-6, Interleukin-6; IL-8, Interleukin-8. Full article ">Figure 6
VEGF treatment increases HPAEC migration which is attenuated by MLCK inhibition. (A) Plot demonstrating the transendothelial resistance by ECIS-based wounding over time in HPAECs treated with VEGF (100 ng/mL), control (PBS vehicle), VEGF with ML-7 (10 μM) pre-treatment, and control with ML-7 (n = at least 3). (B) Bar graph denoting the area under the curve measurements at 12 h for the ECIS-based wounding experiments (n = at least 3). (C) Representative images of wound healing assays depicting scratches created in confluent cultures of HPAECs treated with VEGF (100 ng/mL), control (PBS vehicle), VEGF with ML-7 (10 μM) pre-treatment at 0 h and 24 h time points; scale bar = 100 μm. (D) Bar graph summarizing percent gap closure at 24 h for the wound healing assay experiments (n = 2). * indicates p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001 VEGF, vascular endothelial growth factor; ML-7, myosin light chain kinase specific inhibitor. Full article ">Figure 7
Schematic representation of our findings demonstrating that nmMLCK activation due to BMPR2 downregulation or VEGF stimulation is associated with increased ERK phosphorylation, potentially directly or indirectly, contributing to the pathogenesis of PAH by stimulating cellular proliferation and migration. Full article ">

17 pages, 2575 KiB

Open AccessArticle

Exploring the RNA Editing Events and Their Potential Regulatory Roles in Tea Plant (Camellia sinensis L.)

by Mengyuan Zhang, Zhuo Li, Zijian Wang, Yao Xiao, Lu Bao, Min Wang, Chuanjing An and Yuefang Gao

Int. J. Mol. Sci. 2022, 23(21), 13640; https://doi.org/10.3390/ijms232113640 - 7 Nov 2022

Cited by 3 | Viewed by 1712

Abstract

RNA editing is a post-transcriptional modification process that alters the RNA sequence relative to the genomic blueprint. In plant organelles (namely, mitochondria and chloroplasts), the most common type is C-to-U, and the absence of C-to-U RNA editing results in abnormal plant development, such [...] Read more.

RNA editing is a post-transcriptional modification process that alters the RNA sequence relative to the genomic blueprint. In plant organelles (namely, mitochondria and chloroplasts), the most common type is C-to-U, and the absence of C-to-U RNA editing results in abnormal plant development, such as etiolation and albino leaves, aborted embryonic development and retarded seedling growth. Here, through PREP, RES-Scanner, PCR and RT-PCR analyses, 38 and 139 RNA editing sites were identified from the chloroplast and mitochondrial genomes of Camellia sinensis, respectively. Analysis of the base preference around the RNA editing sites showed that in the −1 position of the edited C had more frequent occurrences of T whereas rare occurrences of G. Three conserved motifs were identified at 25 bases upstream of the RNA editing site. Structural analyses indicated that the RNA secondary structure of 32 genes, protein secondary structure of 37 genes and the three-dimensional structure of 5 proteins were altered due to RNA editing. The editing level analysis of matK and ndhD in six tea cultivars indicated that matK-701 might be involved in the color change of tea leaves. Furthermore, 218 PLS-CsPPR proteins were predicted to interact with the identified RNA editing sites. In conclusion, this study provides comprehensive insight into RNA editing events, which will facilitate further study of the RNA editing phenomenon of the tea plant. Full article

(This article belongs to the Collection Genetics and Molecular Breeding in Plants)

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Figure 1
RNA editing sites predicted by PREP suite in tea chloroplast and mitochondria. (A) Amino acid residue substitutions resulting from RNA editing; the letters are the abbreviations for amino acid residues, and the block size represents the number of RNA editing sites. (B) Position of RNA editing sites in codons. The outer pie charts represent chloroplasts, and the inner pie charts represent mitochondria. Full article ">Figure 2
Distribution of RNA editing sites on the tea chloroplast (A) and mitochondria (B) genome. PREP suite and RES-Scanner represent the results predicted by PREP-suite and RES-Scanner, respectively. RT-PCR represents these RNA editing sites that were validated by RT-PCR. Full article ">Figure 3
Features of sequences around RNA editing sites. (A) The base preference around edited C. A, C, G and T are abbreviation for nucleotide. The numbers represent the flanking base positions of the edited Cs. (B) Conserved motifs around RNA editing sites. The horizontal axis is the base position in the corresponding motif. The vertical axis is the fraction of bits per base. Full article ">Figure 4
The 3-D structure of proteins were changed by RNA editing events. (A) Before cox2 is edited. (B) After cox2 is edited. Red circle indicates monomer introduced after RNA editing. (C) Before cob is edited. (D) After cob is edited. Red circles show monomers introduced after RNA editing. (E) Before ccmB is edited. (F) After ccmB is edited. (G) Before nad5 is edited. (H) After nad5 is edited. Full article ">Figure 5
Editing levels of 4 RNA editing events in 6 varieties (LJ43 and SC1 with normal green leaves, HJYA and ZH3 with etiolation leaves and HB1 and BY1 with albino leaves) of tea plants. HJYA represents C. sinensis cv. ‘Huangjinya’; ZH3 represents C. sinensis cv. ‘Zhonghuang 3’; SC1 represents C. sinensis cv. ‘Shaancha 1’; LJ43 represents C. sinensis cv. ‘Longjing 43’; HB1 represents C. sinensis cv. ‘Huabai 1’; BY1 represents C. sinensis cv. ‘Baiye 1’. The matk-445 represents 445 position of matK. The matk-701 represents 701 position of matK. The ndhD-674 represents 674 position of ndhD. The ndhD-1310 represents 1310 position of ndhD. Red boxes indicate the RNA editing sites in the gDNA and cDNA. Full article ">

17 pages, 2916 KiB

Open AccessArticle

Effects of Two Bacillus Velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana

by Huimin Shi, Lanxiang Lu, Jianren Ye and Lina Shi

Int. J. Mol. Sci. 2022, 23(21), 13639; https://doi.org/10.3390/ijms232113639 - 7 Nov 2022

Cited by 12 | Viewed by 2385

Abstract

Microbial inoculants, as harmless, efficient, and environmentally friendly plant growth promoters and soil conditioners, are attracting increasing attention. In this study, the effects of Bacillus velezensis YH-18 and B. velezensis YH-20 on Prunus davidiana growth and rhizosphere soil bacterial community in continuously cropped [...] Read more.

Microbial inoculants, as harmless, efficient, and environmentally friendly plant growth promoters and soil conditioners, are attracting increasing attention. In this study, the effects of Bacillus velezensis YH-18 and B. velezensis YH-20 on Prunus davidiana growth and rhizosphere soil bacterial community in continuously cropped soil were investigated by inoculation tests. The results showed that in a pot seedling experiment, inoculation with YH-18 and YH-20 resulted in a certain degree of increase in diameter growth, plant height, and leaf area at different time periods of 180 days compared with the control. Moreover, after 30 and 90 days of inoculation, the available nutrients in the soil were effectively improved, which protected the continuously cropped soil from acidification. In addition, high-throughput sequencing showed that inoculation with microbial inoculants effectively slowed the decrease in soil microbial richness and diversity over a one-month period. At the phylum level, Proteobacteria and Bacteroidetes were significantly enriched on the 30th day. At the genus level, Sphingomonas and Pseudomonas were significantly enriched at 15 and 30 days, respectively. These bacterial phyla and genera can effectively improve the soil nutrient utilization rate, antagonize plant pathogenic bacteria, and benefit the growth of plants. Furthermore, inoculation with YH-18 and inoculation with YH-20 resulted in similar changes in the rhizosphere microbiome. This study provides a basis for the short-term effect of microbial inoculants on the P. davidiana rhizosphere microbiome and has application value for promoting the cultivation and production of high-quality fruit trees. Full article

(This article belongs to the Section Molecular Plant Sciences)

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Figure 1
Effects of inoculation with YH-18 and YH-20 on (A) ground diameter growth, (B) height growth, (C) chlorophyll content and (D) leaf area of P. davidiana. Different letters indicate significant differences between different treatments in a group within the same period at a confidence level of p < 0.05. Full article ">Figure 2
Effects of YH-18 and YH-20 microbial inoculants on (A) OM, (B) AN, (C) AP, (D) AK, and (E) pH in soil. Full article ">Figure 3
The 20 most abundant bacterial groups at the phylum level. Full article ">Figure 4
The 30 most abundant bacterial groups at the genus level. Full article ">Figure 5
Venn diagram of different combinations: (A) Venn diagram of different treatments 15 days after inoculation. (B) Venn diagram of different treatments 30 days after inoculation. Full article ">Figure 6
Principal coordinate analysis of 16S rRNA genes of total bacteria based on the weighted similarity index at 97% identity (operational taxonomic unit level). PC1 and PC2 explained 25.9% and 12.3%, respectively, of the variance. Full article ">Figure 7
Redundancy analysis of the soil bacterial community composition at the genus level and soil environmental parameters. Soil environmental parameters are represented by red lines and bacterial genera are represented by blue lines (1: Sphingomonas, 2: Pseudomonas, 3: Flavobacterium, 4: RB41, 5: Dongia, 6: Gemmatimonas, 7: Haliangium, 8: MND1, 9: Acidibacter, 10: Arenimonas, 11: Bryobacter, 12: Flavisolibacter, 13: Ellin6067; 14: Steroidobacter, 15: Ferruginibacter). Full article ">

36 pages, 1047 KiB

Open AccessReview

Vulnerable Atherosclerotic Plaque: Is There a Molecular Signature?

by Roxana Mihaela Chiorescu, Mihaela Mocan, Andreea Ioana Inceu, Andreea Paula Buda, Dan Blendea and Sonia Irina Vlaicu

Int. J. Mol. Sci. 2022, 23(21), 13638; https://doi.org/10.3390/ijms232113638 - 7 Nov 2022

Cited by 17 | Viewed by 4619

Abstract

Atherosclerosis and its clinical manifestations, coronary and cerebral artery diseases, are the most common cause of death worldwide. The main pathophysiological mechanism for these complications is the rupture of vulnerable atherosclerotic plaques and subsequent thrombosis. Pathological studies of the vulnerable lesions showed that [...] Read more.

Atherosclerosis and its clinical manifestations, coronary and cerebral artery diseases, are the most common cause of death worldwide. The main pathophysiological mechanism for these complications is the rupture of vulnerable atherosclerotic plaques and subsequent thrombosis. Pathological studies of the vulnerable lesions showed that more frequently, plaques rich in lipids and with a high level of inflammation, responsible for mild or moderate stenosis, are more prone to rupture, leading to acute events. Identifying the vulnerable plaques helps to stratify patients at risk of developing acute vascular events. Traditional imaging methods based on plaque appearance and size are not reliable in prediction the risk of rupture. Intravascular imaging is a novel technique able to identify vulnerable lesions, but it is invasive and an operator-dependent technique. This review aims to summarize the current data from literature regarding the main biomarkers involved in the attempt to diagnose vulnerable atherosclerotic lesions. These biomarkers could be the base for risk stratification and development of the new therapeutic drugs in the treatment of patients with vulnerable atherosclerotic plaques. Full article

(This article belongs to the Collection Feature Papers in Molecular Pathology, Diagnostics, and Therapeutics)

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24 pages, 2032 KiB

Open AccessReview

Extracellular Vesicle (EVs) Associated Non-Coding RNAs in Lung Cancer and Therapeutics

by Anjugam Paramanantham, Rahmat Asfiya, Siddharth Das, Grace McCully and Akhil Srivastava

Int. J. Mol. Sci. 2022, 23(21), 13637; https://doi.org/10.3390/ijms232113637 - 7 Nov 2022

Cited by 16 | Viewed by 3134

Abstract

Lung cancer is one of the most lethal forms of cancer, with a very high mortality rate. The precise pathophysiology of lung cancer is not well understood, and pertinent information regarding the initiation and progression of lung cancer is currently a crucial area [...] Read more.

Lung cancer is one of the most lethal forms of cancer, with a very high mortality rate. The precise pathophysiology of lung cancer is not well understood, and pertinent information regarding the initiation and progression of lung cancer is currently a crucial area of scientific investigation. Enhanced knowledge about the disease will lead to the development of potent therapeutic interventions. Extracellular vesicles (EVs) are membrane-bound heterogeneous populations of cellular entities that are abundantly produced by all cells in the human body, including the tumor cells. A defined class of EVs called small Extracellular Vesicles (sEVs or exosomes) carries key biomolecules such as RNA, DNA, Proteins and Lipids. Exosomes, therefore, mediate physiological activities and intracellular communication between various cells, including constituent cells of the tumor microenvironment, namely stromal cells, immunological cells, and tumor cells. In recent years, a surge in studying tumor-associated non-coding RNAs (ncRNAs) has been observed. Subsequently, studies have also reported that exosomes abundantly carry different species of ncRNAs and these exosomal ncRNAs are functionally involved in cancer initiation and progression. Here, we discuss the function of exosomal ncRNAs, such as miRNAs and long non-coding RNAs, in the pathophysiology of lung tumors. Further, the future application of exosomal-ncRNAs in clinics as biomarkers and therapeutic targets in lung cancer is also discussed due to the multifaceted influence of exosomes on cellular physiology. Full article

(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)

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16 pages, 2482 KiB

Open AccessArticle

Hypo-Osmoregulatory Roles of Vasotocinergic and Isotocinergic Systems in the Intestines of Two European Sea Bass Lineages

by Quanquan Cao, Eva Blondeau-Bidet and Catherine Lorin-Nebel

Int. J. Mol. Sci. 2022, 23(21), 13636; https://doi.org/10.3390/ijms232113636 - 7 Nov 2022

Cited by 2 | Viewed by 1489

Abstract

European sea bass (Dicentrarchus labrax) are a major aquaculture species that live in habitats with fluctuating salinities that are sometimes higher than in seawater (SW). Atlantic and West-Mediterranean genetic lineages were compared regarding intestinal neuropeptide receptor expression in SW (36%) and [...] Read more.

European sea bass (Dicentrarchus labrax) are a major aquaculture species that live in habitats with fluctuating salinities that are sometimes higher than in seawater (SW). Atlantic and West-Mediterranean genetic lineages were compared regarding intestinal neuropeptide receptor expression in SW (36%) and following a two-week transfer to hypersalinity (HW, 55%). Phylogenetic analysis revealed seven neuropeptide receptors belonging to the arginine vasotocine (AVTR) family and two isotocin receptors (ITR). Among AVTR paralogs, the highest mRNA levels were recorded for v1a2, with a two- to fourfold upregulation in the European sea bass intestinal sections after transfer of fish to HW. Principal component analysis in posterior intestines showed that v1a2 expression grouped together with the expression and activity of main ion transporters and channels involved in solute-coupled water uptake, indicating a possible role of this receptor in triggering water absorption. v1a1 expression, however, was decreased or did not change after transfer to hypersaline water. Among ITR paralogs, itr1 was the most expressed paralog in the intestine and opposite expression patterns were observed following salinity transfer, comparing intestinal sections. Overall, different expression profiles were observed between genetic lineages for several analyzed genes which could contribute to different osmotic stress-related responses in D. labrax lineages. Full article

(This article belongs to the Collection 21st Anniversary of IJMS: Advances in Molecular Endocrinology and Metabolism)

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Figure 1
Phylogenetic tree of AVTRV-1A1, -1A2, -2A1, -2A2, -2B1, -2B2, -2C, ITR1 and ITR2. Sequences from European sea bass are indicated in blue. Branch lengths represent the degree of divergence. Bayesian posterior probabilities (bpp) are indicated in nodes as red asterisks (if bpp ≥0.99) and in black asterisks (if 0.95 ≤ bpp ≥ 0.98). Nodes with bpp <0.95 are not annotated. Full article ">Figure 2
Relative avtrv and itr mRNA expression in the anterior (AI) and posterior (PI) intestines of Mediterranean European sea bass maintained in seawater. Within the intestinal region, columns displaying different letters are significantly different. Upper letters were indicated for anterior intestines and lower letters were indicated for posterior intestines. Asterisks indicated expression differences between AI and PI for a given gene (two-way ANOVA followed by Tukey’s test, p < 0.05, n = 11). Full article ">Figure 3
Relative avtrv1a1 (A), avtrv1a2 (B), avtrv2a1 (C), avtrv2b1 (D) and itr1 (E) mRNA expression were measured in the anterior intestines of Mediterranean (M) and Atlantic (A) European sea bass maintained in seawater (SW) and hypersaline water (HW). Different letters denote significant differences between groups (two-way ANOVA followed by Tukey’s test, p < 0.05, n = 11). Data are represented as the median, first and third quartiles (box), minimum and maximum values. ns: non significant. Full article ">Figure 4
Relative avtrv1a1 (A), avtrv1a2 (B), avtrv2b1 (C) and itr1 (D) mRNA expression were measured in the posterior intestines of Mediterranean (M) and Atlantic (A) European sea bass maintained in seawater (SW) and hypersaline water (HW). Different letters denote significant differences between groups (two-way ANOVA followed by Tukey’s test, p < 0.05, n = 11). Data are represented as the median, first and third quartile (box), minimum and maximum values. ns: non significant. Full article ">Figure 5
Loading plot of principal component analysis (PCA) representing the individuals (A) and measured variables (B) based on NKA activity, nkaα1a, aqp8ab, aqp8aa, aqp8b, aqp10b, aqp1a, aqp1b, nkcc2, avtrv1a2, avtrv1a1, itr1 and avtrv2b1 gene expressions in posterior intestines. Four conditions were compared (Mediterranean (M) and Atlantic (A) European sea bass maintained in seawater (SW) and hypersaline water (HW) in the (Dim1 × Dim2) coordination plane. Orange and green colors in (B) respectively represent strong and weak cos2 values. Ellipses in (A) group D. labrax from the four conditions (MSW in blue crosses, MHW in red squares, ASW in yellow triangles and AHW in green circles). Full article ">

11 pages, 1948 KiB

Open AccessArticle

Effects of Biochar and Nitrogen Application on Rice Biomass Saccharification, Bioethanol Yield and Cell Wall Polymers Features

by Izhar Ali, Muhammad Adnan, Anas Iqbal, Saif Ullah, Muhammad Rafiullah Khan, Pengli Yuan, Hua Zhang, Jamal Nasar, Minghua Gu and Ligeng Jiang

Int. J. Mol. Sci. 2022, 23(21), 13635; https://doi.org/10.3390/ijms232113635 - 7 Nov 2022

Cited by 2 | Viewed by 1595

Abstract

Rice is a major food crop that produces abundant biomass wastes for biofuels. To improve rice biomass and yield, nitrogen (N) fertilizer is excessively used, which is not eco-friendly. Alternatively, biochar (B) application is favored to improve rice biomass and yield under low [...] Read more.

Rice is a major food crop that produces abundant biomass wastes for biofuels. To improve rice biomass and yield, nitrogen (N) fertilizer is excessively used, which is not eco-friendly. Alternatively, biochar (B) application is favored to improve rice biomass and yield under low chemical fertilizers. To minimize the reliance on N fertilizer, we applied four B levels (0, 10, 20, and 30 t B ha⁻¹) combined with two N rates (low-135 and high-180 kg ha⁻¹) to improve biomass yield. Results showed that compared to control, the combined B at 20–30 t ha⁻¹ with low N application significantly improved plant dry matter and arabinose (Ara%), while decreasing cellulose crystallinity (Crl), degree of polymerization (DP), and the ratio of xylose/arabinose (Xyl/Ara), resulting in high hexoses (% cellulose) and bioethanol yield (% dry matter). We concluded that B coupled with N can alter cell wall polymer features in paddy rice resulting in high biomass saccharification and bioethanol production. Full article

(This article belongs to the Collection Feature Papers in 'Macromolecules')

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Total biomass production in rice plants under different biochar and nitrogen fertilizer treatments during 2019 and 2020. Different letters on bars are not significantly different at p < 0.05.; Bars indicate means ± SD (n = 3). Full article ">Figure 2
Changes in hexose yields (% cellulose) released with tween (A) and without tween (B) of rice straw treated with biochar and nitrogen fertilizers. Different letters on bars are not significantly different at p < 0.05. (n = 3). Full article ">Figure 3
Impact of biochar and nitrogen fertilizer on bioethanol yields from biomass process in rice. ** above the column represent significant difference among the biochar and biochar treatments by t-test at p < 0.05 or p < 0.01 (n = 3). % value indicates the increase in the same treatment with Tween-80 from without Tween-80. Full article ">Figure 4
Biochar and nitrogen fertilizer effect on cell wall polymers feature (A) crystalline index (CrI) of cellulose, (B) degree of polymerization of cellulose, (C) arabinose proportion of hemicellulose, (D) ratio of xylose and arabinose. Different letters on bars are not significantly different at p < 0.05. (n = 3). Full article ">Figure 5
Mechanism involving the primary wall polymer characteristics has an influence on biomass enzymatic saccharification in rice under biochar and nitrogen fertilizer. (A) The correlation coefficient between biochar + N fertilizers, cellulose, hemicelluloses, lignin, and DM. (B) Correlation analysis between hexoses, Crl, Dp, Ara, Xyl/Ara, and DM. (C) A model for improving biomass yield and enzymatic digestibility with biochar and N fertilizer by changing wall polymer characteristics. * and ** indicate a significant coefficient correlation value at p < 0.005 and 0.001. (+) and (−) represented increased and reduced effects, respectively. Full article ">

13 pages, 2040 KiB

Open AccessArticle

Magnetic Multi-Enzymatic System for Cladribine Manufacturing

by Guillermo Cruz, Laura Pilar Saiz, Muhammad Bilal, Lobna Eltoukhy, Christoph Loderer and Jesús Fernández-Lucas

Int. J. Mol. Sci. 2022, 23(21), 13634; https://doi.org/10.3390/ijms232113634 - 7 Nov 2022

Cited by 5 | Viewed by 1975

Abstract

Enzyme-mediated processes have proven to be a valuable and sustainable alternative to traditional chemical methods. In this regard, the use of multi-enzymatic systems enables the realization of complex synthetic schemes, while also introducing a number of additional advantages, including the conversion of reversible [...] Read more.

Enzyme-mediated processes have proven to be a valuable and sustainable alternative to traditional chemical methods. In this regard, the use of multi-enzymatic systems enables the realization of complex synthetic schemes, while also introducing a number of additional advantages, including the conversion of reversible reactions into irreversible processes, the partial or complete elimination of product inhibition problems, and the minimization of undesirable by-products. In addition, the immobilization of biocatalysts on magnetic supports allows for easy reusability and streamlines the downstream process. Herein we have developed a cascade system for cladribine synthesis based on the sequential action of two magnetic biocatalysts. For that purpose, purine 2′-deoxyribosyltransferase from Leishmania mexicana (LmPDT) and Escherichia coli hypoxanthine phosphoribosyltransferase (EcHPRT) were immobilized onto Ni²⁺-prechelated magnetic microspheres (MagReSyn^®NTA). Among the resulting derivatives, MLmPDT3 (activity: 11,935 IU/g_support, 63% retained activity, operational conditions: 40 °C and pH 5–7) and MEcHPRT3 (12,840 IU/g_support, 45% retained activity, operational conditions: pH 5–8 and 40–60 °C) emerge as optimal catalysts for further synthetic application. Moreover, the MLmPDT3/MEcHPRT3 system was biochemically characterized and successfully applied to the one-pot synthesis of cladribine under various conditions. This methodology not only displayed a 1.67-fold improvement in cladribine synthesis (compared to MLmPDT3), but it also implied a practically complete transformation of the undesired by-product into a high-added-value product (90% conversion of Hyp into IMP). Finally, MLmPDT3/MEcHPRT3 was reused for 16 cycles, which displayed a 75% retained activity. Full article

(This article belongs to the Special Issue Biocatalysis: An Eco-Friendly Scenario for the Manufacturing of APIs)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Enzymatic synthesis of Cladribine catalyzed by: (A) LmPDT. (B) LmPDT/EcHPRT. dIno: 2′-deoxyinosine; 2-ClAde: 2-chloroadenine; Hyp: hypoxanthine; PRPP: 5-phospho-α-D-ribosyl-1-pyrophosphate; LmPDT: Leishmania mexicana purine 2′-deoxyribosyltransferase; EcHPRT; Escherichia coli hypoxanthine phosphoribosyltransferase. Full article ">Figure 2
Biochemical characterization of MLmPDT3 and MEcHPRT3. (A) Effect of temperature on MLmPDT3 activity (●). (B) Effect of pH on MLmPDT3 activity, (●) 50 mM sodium citrate (pH 4–6), (△) 50 mM sodium phosphate (pH 6–8), (○) 50 mM MES (pH 6–7), (■) 50 mM Tris-HCl (pH 7–9), (□) 50 mM sodium borate (pH 8–10). (C) Effect of temperature MEcHPRT3 activity (●). (D) Effect of pH on MEcHPRT3 activity, (●) 12 mM sodium citrate (pH 4–6), (△) 12 mM sodium phosphate (pH 6–8), (○) 12 mM MES (pH 6–7), (■) 12 mM Tris-HCl (pH 7–9), (□) 12 mM sodium borate (pH 8–10). Full article ">Figure 3
Biochemical characterization of the MLmPDT3/MEcHPRT3 system. (A) Effect of temperature on cladribine synthesis (●). (B) Effect of pH on cladribine synthesis, (●) 50 mM sodium citrate (pH 4–6), (△) 50 mM sodium phosphate (pH 6–8), (○) 50 mM MES (pH 6–7), (■) 50 mM Tris-HCl (pH 7–9), (□) 50 mM sodium borate (pH 8–10). Full article ">Figure 4
Thermal inactivation profile of MLmPDT3/MEcHPRT3 on cladribine synthesis at 40 °C (●) and 50 °C (○). Full article ">Figure 5
Effect of MLmPDT3/MEcHPRT3 ratio (μg of immobilized LmPDT/μg of immobilized EcHPRT) in the product formation. (A) cladribine (reaction 1). (B) Hyp converted into IMP (reaction 2). Full article ">Figure 6
Reusability of the MLmPDT3/MEcHPRT3 system. 2′-deoxyribosyltransferase activity, reaction 1 (black bar); phosphoribosyltransferase activity, reaction 2 (white bar). Full article ">

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Int. J. Mol. Sci., Volume 23, Issue 21 (November-1 2022) – 954 articles

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