Search Results (52)

Increasing evidence points to members of the chloride intracellular ion channel (CLIC) protein family performing a variety of functions within cells—classifying them as moonlighting proteins—and serving as natural cellular antioxidant protective agents. Apart from their role as membrane-inserting ion channels, members of the CLIC family also possess enzymatic oxidoreduction activity in their soluble form. The current study is the first to specifically examine the S-glutathionylation catalytic activity of several purified recombinant CLIC protein members (rCLIC1, rCLIC3, and rCLIC4) by directly measuring their ability to deglutathionylate and glutathionylate a synthetic model peptide via an in vitro tryptophan fluorescence quenching assay. Effects of pH and temperature on this activity were also assessed. Our findings provide insights into a likely previously uncharacterised mechanism by which CLIC proteins serve as cellular antioxidant protective enzymes via their S-glutathionylation capabilities. Full article

Endocytosis is a specialized transport mechanism in which the cell membrane folds inward to enclose large molecules, fluids, or particles, forming vesicles that are transported within the cell. It plays a crucial role in nutrient uptake, immune responses, and cellular communication. However, many pathogens exploit the endocytic pathway to invade and survive within host cells, allowing them to evade the immune system and establish infection. Endocytosis can be classified as clathrin-mediated (CME) or clathrin-independent (CIE), based on the mechanism of vesicle formation. Unlike CME, which involves the formation of clathrin-coated vesicles that bud from the plasma membrane, CIE does not rely on clathrin-coated vesicles. Instead, other mechanisms facilitate membrane invagination and vesicle formation. CIE encompasses a variety of pathways, including caveolin-mediated, Arf6-dependent, and flotillin-dependent pathways. In this review, we discuss key features of CIE pathways, including cargo selection, vesicle formation, routes taken by internalized cargo, and the regulatory mechanisms governing CIE. Many viruses and bacteria hijack host cell CIE mechanisms to facilitate intracellular trafficking and persistence. We also revisit the exploitation of CIE by bacterial and viral pathogens, highlighting recent discoveries in entry mechanisms, intracellular fate, and host-pathogen interactions. Understanding how pathogens manipulate CIE in host cells can inform the development of novel antimicrobial and immunomodulatory interventions, offering new avenues for disease prevention and treatment. Full article

Knowledge of how novel antigens or dietary stimuli affect stomach development and function in pigs remains limited. This study aimed to investigate stomach characteristics, parietal cell numbers, and the expression of genes essential to the functioning of the fundic and pyloric gland regions at weaning compared to seven days post-weaning and to examine whether maternal probiotic supplementation or piglet dietary tryptophan (Trp) levels influence these stomach parameters. This study has a 2 × 3 factorial design, with 48 sows assigned to one of two diets: basal or basal supplemented with Bacillus subtilis and Bacillus amyloliquefaciens. Their litters received creep diets containing 0.22, 0.27, or 0.33% standardized ileal digestible (SID) Trp. In total, 96 pigs were sacrificed for gastric sampling, 48 on the day of weaning and 48 on day 7 post-weaning. At 7 days post-weaning, pigs had an increased number of parietal cells and expression of parietal cell activity and digestive enzyme (PGA5 and CHIA) genes in the fundic gland region (p < 0.05), although the expression of signaling molecules involved in the regulation of acid secretion was unchanged in the fundic gland region (p > 0.05) and reduced in the pyloric gland region (p < 0.05), compared to the day of weaning. Overall, maternal probiotic supplementation had a significant impact on gene expression in the fundic gland region of the offspring, elevating several genes related to parietal cell activity (CLIC6, HRH2, KCNE1, KCNQ1, CHRM3, CCKBR, and SSTR2) (p < 0.05). Additionally, there were time × maternal interactions, where certain acid secretion pathway (ATP4A and HDC), chitinase enzyme (CHIA), and ghrelin (GHRL) genes were increased in offspring from probiotic sows compared to control sows at weaning (p < 0.05), but not at 7 days post-weaning (p > 0.05). Maternal probiotic supplementation did not influence growth performance pre-weaning or during the 7-day post-weaning period. There was a limited effect of creep Trp level or maternal × creep interactions on performance, gene expression, or parietal cell counts. Low pre-weaning creep intake may have confounded this analysis. In conclusion, maternal probiotic supplementation accelerated the maturation of the offspring’s stomach, particularly in terms of the expression of genes linked to acid secretion from parietal cells. Full article

Background: Idiopathic epilepsy (IE) disproportionately affects Belgian shepherd dogs and although genomic risk markers have been identified previously in the breed, causative variants have not been described. Methods: The current study analyzed differences in whole blood RNA expression associated with IE and with a previously identified IE risk haplotype on canine chromosome (CFA) 14 using a transcriptomics RNA-seq approach. Results: MFSD2A and a likely pseudogene of RPL19, both of which are genes implicated in seizure activity, were upregulated in dogs with IE. Genes in the interferon signaling pathway were downregulated in Belgian shepherds with IE. The CFA14 risk haplotype was associated with upregulation of CLIC1, ACE2, and PIGN and downregulation of EPDR1, all known to be involved with epilepsy or the Wnt/β-catenin signaling pathway. Conclusions: These results highlight the value of assessing gene expression in canine IE research to uncover genomic contributory factors. Full article

Background: Chloride Intracellular Channel 4 (CLIC4) plays a versatile role in cellular functions beyond its role in primary chloride ion transport. Notably, many studies found an association between CLIC4 expression and cancers. However, the correlation between CLIC4 and glioma remains to be uncovered. Methods: A total of 3162 samples from nine public datasets were analyzed to reveal the relationship between CLIC4 expression and glioma malignancy or prognosis. Immunohistochemistry (IHC) staining was performed to examine the results in an in-house cohort. A nomogram model was constructed to predict the prognosis. Functional enrichment analysis was employed to find CLIC4-associated differentially expressed genes in glioma. Immune infiltration analysis, correlation analysis, and IHC staining were employed, aiming to examine the correlation between CLIC4 expression, immune cell infiltration, and ECM (extracellular matrix)-related genes. Results: The expression level of CLIC4 was correlated with the malignancy of glioma and the prognosis of patients. More aggressive gliomas and mesenchymal GBM are associated with a high expression of CLIC4. Gliomas with IDH mutation or 1p19q codeletion express a low level of CLIC4, and a high expression of CLIC4 correlates with poor prognosis. The nomogram model shows a good predictive performance. The DEGs (differentially expressed genes) in gliomas with high and low CLIC4 expression are enriched in extracellular matrix and immune functions. On the one hand, gliomas with high CLIC4 expression have a greater presence of macrophages, neutrophils, and eosinophils; on the other hand, a high CLIC4 expression in gliomas is positively associated with ECM-related genes. Conclusions: Compared to glioma cells with low CLIC4 expression, gliomas with high CLIC4 expression exhibit greater malignancy and poorer prognosis. Our findings indicate that a high level of CLIC4 correlates with high expression of ECM-related genes and the infiltration of macrophages, neutrophils, and eosinophils within glioma tissues. Full article

The breeding of disease-resistant pigs has consistently been a topic of significant interest and concern within the pig farming industry. The study of pig blood indicators has the potential to confer economic benefits upon the pig farming industry, whilst simultaneously providing valuable insights that can inform the study of human diseases. In this study, an F2 resource population of 489 individuals was generated through the intercrossing of Large White boars and Min pig sows. A total of 17 haematological parameters and T lymphocyte subpopulations were measured, including white blood cell count (WBC), lymphocyte count (LYM), lymphocyte count percentage (LYM%), monocyte count (MID), monocyte count percentage (MID%), neutrophilic granulocyte count (GRN), percentage of neutrophils (GRN%), mean platelet volume (MPV), platelet distribution width (PDW), platelet count (PLT), CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8−CD3+, CD4−CD8+CD3+, CD4−CD8−CD3+, and CD3+. The Illumina PorcineSNP60 Genotyping BeadChip was obtained for all of the F2 animals. Subsequently, a genome-wide association study (GWAS) was conducted using the TASSEL 5.0 software to identify associated variants and candidate genes for the 17 traits. Significant association signals were identified for PCT and PLT on SSC7, with 1 and 11 significant SNP loci, respectively. A single nucleotide polymorphism (SNP) on SSC12 was identified as a significant predictor of the white blood cell (WBC) trait. Significant association signals were detected for the T lymphocyte subpopulations, namely CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8−CD3+, and CD4−CD8+CD3+, with the majority of these signals observed on SSC7. The genes CLIC5, TRIM15, and SLC17A4 were identified as potential candidates for influencing CD4+/CD8+ and CD4−CD8+CD3+. A missense variant, c.2707 G>A, in the SLC17A4 gene has been demonstrated to be significantly associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Three missense variants (c.425 A>C, c.500 C>T, and c.733 A>G) have been identified in the TRIM15 gene as being linked to the CD4+/CD8+ trait. Nevertheless, only c.425 A>C has been demonstrated to be significantly associated with CD4-CD8+CD3+. In the CLIC5 gene, one missense variant (c.957 T>C) has been identified as being associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Additionally, significant association signals were observed for CD4+CD8+CD3+ and CD4+CD8−CD3+ on SSC2 and 5, respectively. Subsequently, a gene ontology (GO) enrichment analysis was conducted on all genes within the quantitative trait loci (QTL) intervals of platelet count, CD4+/CD8+, and CD4−CD8+CD3+. The MHC class II protein complex binding pathway was identified as the most significant pathway among the three immune traits. These results provide guidance for further research in the field of breeding disease-resistant pigs. Full article

Energy modelling plays a crucial role in assisting governmental and policymaking bodies to strategise long-term investments within the context of energy transition. Among the well-established open-source optimisation models, OSeMOSYS—the Open-Source Energy Modelling System—stands out. This paper introduces clicSAND, a novel user interface designed for OSeMOSYS, aimed at reducing the learning curve and supporting novice energy modelers in efficiently conducting long-term investment analyses. clicSAND, freely available and open-source, features a user-friendly Excel interface for data input, integrated solvers, and a visualisation dashboard for result interpretation. The outcomes, projected up to 2070, hold the potential to inform policy decisions and mobilise financial resources for sustainable development endeavors, such as ensuring affordable and secure energy supply and mitigating climate change impacts. This advancement not only democratises access to energy modelling tools but also empowers policymakers and stakeholders to conduct thorough long-term investment analyses with ease. This paper elaborates on clicSAND’s key advantages, architecture, and functionalities. Additionally, it discusses the evolutionary journey from clicSAND 1.0 to 3.0, emphasising a commitment to continuous improvement and user-centric adaptation, thereby enhancing its utility and relevance. The inclusion of a South African case study, conducted during the EMP-A (Energy Modelling Platform for Africa) 2021 international capacity-building event, showcases clicSAND’s efficacy in facilitating knowledge transfer and skill development among inexperienced users, while providing a tangible example of its application in addressing specific regional energy challenges and policy contexts. Finally, current applications and future extensions of the software are also presented. Full article

Egypt has the potential to generate a significant amount of energy from renewable technologies, in particular solar PV, concentrated solar power (CSP), and onshore and offshore wind. The energy sector is reliant on fossil fuels, particularly natural gas, for electricity production and is at risk of locking itself into a high carbon pathway. Globally, reducing greenhouse gas (GHG) emissions associated with national energy sectors is a target outlined in the UN’s Paris Agreement. To reduce carbon dioxide (CO₂) emissions associated with a higher dependence on fossil fuels, Egypt must consider upscaling renewable energy technologies (RETs) to achieve a clean energy transition (CET). This research modelled six scenarios using clicSAND for OSeMOSYS to identify the technologies and policy target improvements that are needed to upscale RETs within Egypt’s energy sector. The results showed that solar PV and onshore wind are key technologies to be upscaled to contribute towards Egypt’s CET. The optimal renewable target is the International Renewable Energy Agency’s (IRENA) target of 53% of electricity being sourced from RETs by 2030, which will cost USD 16.4 billion more up to 2035 than Egypt’s current Integrated Sustainable Energy Strategy (ISES) target of 42% by 2035; it also saves 732.0 MtCO₂ over the entire modelling period to 2070. Socio-economic barriers to this transition are considered, such as recent discoveries of natural gas reserves combined with a history of energy insecurity, political instability impacting investor confidence, and a lack of international climate funding. The paper concludes with policy recommendations that would enable Egypt to progress towards achieving a CET. Full article

Down syndrome is a well-studied aneuploidy condition in humans, which is associated with various disease phenotypes including cardiovascular, neurological, haematological and immunological disease processes. This review paper aims to discuss the research conducted on gene expression studies during fetal development. A descriptive review was conducted, encompassing all papers published on the PubMed database between September 1960 and September 2022. We found that in amniotic fluid, certain genes such as COL6A1 and DSCR1 were found to be affected, resulting in phenotypical craniofacial changes. Additionally, other genes such as GSTT1, CLIC6, ITGB2, C21orf67, C21orf86 and RUNX1 were also identified to be affected in the amniotic fluid. In the placenta, dysregulation of genes like MEST, SNF1LK and LOX was observed, which in turn affected nervous system development. In the brain, dysregulation of genes DYRK1A, DNMT3L, DNMT3B, TBX1, olig2 and AQP4 has been shown to contribute to intellectual disability. In the cardiac tissues, dysregulated expression of genes GART, ETS2 and ERG was found to cause abnormalities. Furthermore, dysregulation of XIST, RUNX1, SON, ERG and STAT1 was observed, contributing to myeloproliferative disorders. Understanding the differential expression of genes provides insights into the genetic consequences of DS. A better understanding of these processes could potentially pave the way for the development of genetic and pharmacological therapies. Full article

(1) Background: Influenza A Virus (IAV) uses host cellular proteins during replication in host cells. IAV infection causes elevated expression of chloride intracellular channel protein 1 (CLIC1) in lung epithelial cells, but the importance of this protein in IAV replication is unknown. (2) In this study, we determined the role of CLIC1 in IAV replication by investigating the effects of CLIC1 knockdown (KD) on IAV viral protein translation, genomic RNA transcription, and host cellular proteome dysregulation. (3) Results: CLIC1 KD in A549 human lung epithelial cells resulted in a significant decrease in progeny supernatant IAV, but virus protein expression was unaffected. However, a significantly larger number of viral RNAs accumulated in CLIC1 KD cells. Treatment with a CLIC1 inhibitor also caused a significant reduction in IAV replication, suggesting that CLIC1 is an important host factor in IAV replication. SomaScan^®, which measures 1322 proteins, identified IAV-induced dysregulated proteins in wild-type cells and in CLIC1 KD cells. The expression of 116 and 149 proteins was significantly altered in wild-type and in CLIC1 KD cells, respectively. A large number of the dysregulated proteins in CLIC1 KD cells were associated with cellular transcription and predicted to be inhibited during IAV replication. (4) Conclusions: This study suggests that CLIC1 is involved in later stages of IAV replication. Further investigation should clarify mechanism(s) for the development of anti-IAV drugs targeting CLIC1 protein. Full article

With ambitious targets to drastically increase economic activity over the next decade, Kenya’s future is undoubtedly energy-intensive. Current power capacity expansion plans will see Kenya considerably ramp up fossil fuel generation, significantly increasing emissions. Therefore, Kenya is at a crucial stage of its national development, with critical decisions to make regarding its future power expansion and production. OSeMOSYS modelling software (clicSAND version v1.1) is employed to produce a series of possible clean energy transition pathways to increase renewable power production under rapidly intensifying demand. This study integrates existing national priorities and policies into six modelled scenarios to provide insights into their generation, total production, and costs, which can assist future policymaking and capacity-building efforts. The high-level insights gained in this research were employed to suggest key recommendations for Kenya’s power sector. Most notably, policy alignment, increased wind power production, energy-efficiency penetration, finance and investment securement, the development of storage technologies, power transmission, and distribution improvements should be prioritised. Full article

Chloride intracellular ion channel (CLIC) proteins exist as both soluble and integral membrane proteins, with CLIC1 capable of shifting between two distinct structural conformations. New evidence has emerged indicating that members of the CLIC family act as moonlighting proteins, referring to the ability of a single protein to carry out multiple functions. In addition to their ion channel activity, CLIC family members possess oxidoreductase enzymatic activity and share significant structural and sequence homology, along with varying overlaps in their tissue distribution and cellular localization. In this study, the 2-hydroxyethyl disulfide (HEDS) assay system was used to characterize kinetic properties, as well as the temperature and pH profiles of three CLIC protein family members (CLIC1, CLIC3, CLIC4). We also assessed the effects of the drugs rapamycin and amphotericin B, on the three CLIC proteins’ enzymatic activity in the HEDS assay. Our results demonstrate CLIC1 to be highly heat-sensitive, with optimal enzymatic activity observed at neutral pH7 and at a temperature of 37 °C, while CLIC3 had higher oxidoreductase activity in more acidic pH5 and was found to be relatively heat stable. CLIC4, like CLIC1, was temperature sensitive with optimal enzymatic activity observed at 37 °C; however, it showed optimal activity in more alkaline conditions of pH8. Our current study demonstrates individual differences in the enzymatic activity between the three CLIC proteins, suggesting each CLIC protein is likely regulated in discrete ways, involving changes in the subcellular milieu and microenvironment. Full article

Despite playing a key role in digestion, there is only a broad characterization of the spatiotemporal development of the three glandular regions of the stomach (cardiac, fundic and pyloric) in the weaned pig. Hence, the objective of this experiment was to explore the differential expression (DE) of a panel of key genes within the three glandular regions of the stomach. Eight pigs were sacrificed at d 8 post-weaning, and three mucosal samples were collected from each stomach’s glandular regions. The expression of a panel of genes were measured using QPCR. The true cardiac gland region was characterized by increased expression of PIGR, OLFM4, CXCL8 and MUC2 relative to the two other regions (p < 0.05). The fundic gland region was characterized by increased expression of ATP4A, CLIC6, KCNQ1, HRH2, AQP4, HDC, CCKBR, CHIA, PGA5, GHRL and MBOAT4 compared to the two other regions (p < 0.05). The pyloric gland region was characterized by exclusive expression of GAST (p < 0.05). A transition region between the cardiac and fundic region (cardiac-to-oxyntic transition) was observed with a gene expression signature that resembles a cross of the signatures found in the two regions. In conclusion, unique gene expression signatures were identifiable in each of the glandular regions, with a cardiac-to-oxyntic transition region clearly identifiable in the post-weaned pigs’ stomachs. Full article

Non-syndromic pediatric cataracts are defined as opacification of the crystalline lens that occurs during the first years of life without affecting other organs. Given that this disease is one of the most frequent causes of reversible blindness in childhood, the main objective of this study was to propose new responsible gene candidates that would allow a more targeted genetic approach and expand our genetic knowledge about the disease. We present a whole exome sequencing (WES) study of 20 Spanish families with non-syndromic pediatric cataracts and a previous negative result on an ophthalmology next-generation sequencing panel. After ophthalmological evaluation and collection of peripheral blood samples from these families, WES was performed. We were able to reach a genetic diagnosis in 10% of the families analyzed and found genes that could cause pediatric cataracts in 35% of the cohort. Of the variants found, 18.2% were classified as pathogenic, 9% as likely pathogenic, and 72.8% as variants of uncertain significance. However, we did not find conclusive results in 55% of the families studied, which suggests further studies are needed. The results of this WES study allow us to propose LONP1, ACACA, TRPM1, CLIC5, HSPE1, ODF1, PIKFYVE, and CHMP4A as potential candidates to further investigate for their role in pediatric cataracts, and AQP5 and locus 2q37 as causal genes. Full article

Molecular heterogeneity in prostate cancer (PCa) is one of the key reasons underlying the differing likelihoods of recurrence after surgical treatment in individual patients of the same clinical category. In this study, we performed RNA-Seq profiling of 58 localized PCa and 43 locally advanced PCa tissue samples obtained as a result of radical prostatectomy on a cohort of Russian patients. Based on bioinformatics analysis, we examined features of the transcriptome profiles within the high-risk group, including within the most commonly represented molecular subtype, TMPRSS2-ERG. The most significantly affected biological processes in the samples were also identified, so that they may be further studied in the search for new potential therapeutic targets for the categories of PCa under consideration. The highest predictive potential was found with the EEF1A1P5, RPLP0P6, ZNF483, CIBAR1, HECTD2, OGN, and CLIC4 genes. We also reviewed the main transcriptome changes in the groups at intermediate risk of PCa—Gleason Score 7 (groups 2 and 3 according to the ISUP classification)—on the basis of which the LPL, MYC, and TWIST1 genes were identified as promising additional prognostic markers, the statistical significance of which was confirmed using qPCR validation. Full article