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1.
Cell Mol Biol Lett ; 29(1): 66, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38724931

ABSTRACT

The development of compact CRISPR systems has facilitated delivery but has concurrently reduced gene editing efficiency, thereby limiting the further utilization of CRISPR systems. Enhancing the efficiency of CRISPR systems poses a challenging task and holds significant implications for the advancement of biotechnology. In our work, we report a synthetic dual-antibody system that can stably exist in the intracellular environment, specifically inhibiting the functions of NF-κB and ß-catenin. This not only elevates the transgenic expression of the CRISPR system by suppressing the innate immune response within cells to enhance the gene editing efficiency but also demonstrates a notable tumor inhibitory effect. Based on the specific output expression regulation of CRISPR-CasΦ, we constructed a CRISPR-based gene expression platform, which includes sensor modules for detecting intracellular ß-catenin and NF-κB, as well as an SDA module to enhance overall efficiency. In vitro experiments revealed that the CRISPR-based gene expression platform exhibited superior CDK5 expression inhibition efficiency and specific cytotoxicity towards tumor cells. In vitro experiments, we found that CRISPR-based gene expression platforms can selectively kill bladder cancer cells through T cell-mediated cytotoxicity. Our design holds significant assistant potential of transgene therapy and may offer the capability to treat other diseases requiring transgene therapy.


Subject(s)
CRISPR-Cas Systems , Gene Editing , Urinary Bladder Neoplasms , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/therapy , Urinary Bladder Neoplasms/metabolism , Humans , CRISPR-Cas Systems/genetics , Cell Line, Tumor , Gene Editing/methods , beta Catenin/metabolism , beta Catenin/genetics , NF-kappa B/metabolism , NF-kappa B/genetics , Gene Expression/genetics , Gene Expression Regulation, Neoplastic , Clustered Regularly Interspaced Short Palindromic Repeats/genetics
2.
Appl Microbiol Biotechnol ; 108(1): 329, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38727750

ABSTRACT

Xylanases are key biocatalysts in the degradation of the ß-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-ß-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-ß-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.


Subject(s)
Composting , Endo-1,4-beta Xylanases , Escherichia coli , Metagenomics , Phylogeny , Endo-1,4-beta Xylanases/genetics , Endo-1,4-beta Xylanases/metabolism , Endo-1,4-beta Xylanases/chemistry , Endo-1,4-beta Xylanases/isolation & purification , Escherichia coli/genetics , Escherichia coli/metabolism , Metagenome , Gene Library , Soil Microbiology , Xylans/metabolism , Cloning, Molecular , Fermentation , Gene Expression , Molecular Docking Simulation
3.
Mol Biol Rep ; 51(1): 652, 2024 May 11.
Article in English | MEDLINE | ID: mdl-38734792

ABSTRACT

OBJECTIVE: To compare the mRNA expression of placental iron transporters (TfR-1 and FPN), markers of placental vascularization (VEGF and sFLT1) and marker of structural integrity (LMN-A) in term women with and without iron deficiency anemia. MATERIALS AND METHODS: A total of 30 pregnant women were enrolled; 15 cases of iron deficiency anemia (Hb 7-10.9 gm/dL) and 15 gestational age matched healthy controls (Hb ≥ 11 gm/dL). Peripheral venous blood was collected for assessment of hemoglobin levels and serum iron profile. Placental tissue was used for assessing the mRNA expression of TfR-1, FPN, VEGF, sFLT-1 and LMN-A via real time PCR. RESULTS: Placental expression of TfR-1, VEGF and LMN-A was increased in pregnant women with anemia compared to healthy pregnant controls. Placental expression of sFLT-1 was decreased in pregnant women with anemia compared to healthy pregnant controls. There was no change in the placental expression of FPN. CONCLUSION: The increased expression of TfR-1, VEGF and LMN-A in cases of iron deficiency anemia are most likely to be compensatory in nature to help maintain adequate fetal iron delivery. WHAT DOES THIS STUDY ADDS TO THE CLINICAL WORK: Compensatory changes in the placenta aimed at buffering transport of iron to the fetus are seen in pregnant women with anemia compared to healthy pregnant controls.


Subject(s)
Anemia, Iron-Deficiency , Biomarkers , Cation Transport Proteins , Iron , Placenta , Receptors, Transferrin , Vascular Endothelial Growth Factor A , Humans , Female , Pregnancy , Placenta/metabolism , Adult , Receptors, Transferrin/metabolism , Receptors, Transferrin/genetics , Anemia, Iron-Deficiency/genetics , Anemia, Iron-Deficiency/metabolism , Vascular Endothelial Growth Factor A/genetics , Vascular Endothelial Growth Factor A/metabolism , Cation Transport Proteins/genetics , Cation Transport Proteins/metabolism , Iron/metabolism , Biomarkers/metabolism , Biomarkers/blood , Vascular Endothelial Growth Factor Receptor-1/genetics , Vascular Endothelial Growth Factor Receptor-1/metabolism , Case-Control Studies , Antigens, CD/metabolism , Antigens, CD/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Gene Expression/genetics
4.
Curr Microbiol ; 81(6): 167, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38727744

ABSTRACT

Diabetes mellitus represents a persistent metabolic condition marked by heightened levels of blood glucose, presenting a considerable worldwide health concern, and finding targeted treatment for it is a crucial priority for global health. Gram-positive aerobic bacteria, predominantly inhabiting water and soil, are known carriers of various enzyme-encoding genetic material, which includes the malic enzyme gene that plays a role in insulin secretion. Corynebacterium glutamicum bacteria (ATCC 21799) were acquired from the Pasteur Institute and confirmed using microbiological and molecular tests, including DNA extraction. After identification, gene purification and cloning of the maeB gene were performed using the TA Cloning method. Additionally, the enhancement of enzyme expression was assessed using the expression vector pET-28a, and validation of simulation results was monitored through a real-time PCR analysis. Based on previous studies, the malic enzyme plays a pivotal role in maintaining glucose homeostasis, and increased expression of this enzyme has been associated with enhanced insulin sensitivity. However, the production of malic enzyme has encountered numerous challenges and difficulties. This study successfully isolated the malic enzyme genes via Corynebacterium glutamicum and introduced them into Escherichia coli for high-yield production. According to the results, the optimum temperature for the activity of enzymes has been identified as 39 °C.


Subject(s)
Cloning, Molecular , Corynebacterium glutamicum , Escherichia coli , Malate Dehydrogenase , Malate Dehydrogenase/genetics , Malate Dehydrogenase/metabolism , Escherichia coli/genetics , Corynebacterium glutamicum/genetics , Corynebacterium glutamicum/enzymology , Diabetes Mellitus/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Gene Expression , Temperature , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
5.
Front Endocrinol (Lausanne) ; 15: 1383772, 2024.
Article in English | MEDLINE | ID: mdl-38715799

ABSTRACT

Background: ASCVD is the primary cause of mortality in individuals with T2DM. A potential link between ASCVD and T2DM has been suggested, prompting further investigation. Methods: We utilized linear and multivariate logistic regression, Wilcoxon test, and Spearman's correlation toanalyzethe interrelation between ASCVD and T2DM in NHANES data from 2001-2018.The Gene Expression Omnibus (GEO) database and Weighted Gene Co-expression Network Analysis (WGCNA) wereconducted to identify co-expression networks between ASCVD and T2DM. Hub genes were identified using LASSO regression analysis and further validated in two additional cohorts. Bioinformatics methods were employed for gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, along with the prediction of candidate small molecules. Results: Our analysis of the NHANES dataset indicated a significant impact of blood glucose on lipid levels within diabetic cohort, suggesting that abnormal lipid metabolism is a critical factor in ASCVD development. Cross-phenotyping analysis revealed two pivotal genes, ABCC5 and WDR7, associated with both T2DM and ASCVD. Enrichment analyses demonstrated the intertwining of lipid metabolism in both conditions, encompassing adipocytokine signaling pathway, fatty acid degradation and metabolism, and the regulation of adipocyte lipolysis. Immune infiltration analysis underscored the involvement of immune processes in both diseases. Notably, RITA, ON-01910, doxercalciferol, and topiramate emerged as potential therapeutic agents for both T2DM and ASCVD, indicating their possible clinical significance. Conclusion: Our findings pinpoint ABCC5 and WDR7 as new target genes between T2DM and ASCVD, with RITA, ON-01910, doxercalciferol, and topiramate highlighted as promising therapeutic agents.


Subject(s)
Cardiovascular Diseases , Diabetes Mellitus, Type 2 , Humans , Diabetes Mellitus, Type 2/genetics , Diabetes Mellitus, Type 2/metabolism , Female , Cardiovascular Diseases/genetics , Cardiovascular Diseases/epidemiology , Male , Middle Aged , Heart Disease Risk Factors , Lipid Metabolism/genetics , Gene Expression
6.
Methods Mol Biol ; 2799: 29-46, 2024.
Article in English | MEDLINE | ID: mdl-38727901

ABSTRACT

The expression and activity of ionotropic glutamate receptors control signal transduction at the excitatory synapses in the CNS. The NMDAR comprises two obligatory GluN1 subunits and two GluN2 or GluN3 subunits in different combinations. Each GluN subunit consists of four domains: the extracellular amino-terminal and agonist-binding domains, the transmembrane domain, and the intracellular C-terminal domain (CTD). The CTD interaction with various classes of intracellular proteins is critical for trafficking and synaptic localization of NMDARs. Amino acid mutations or the inclusion of premature stop codons in the CTD could contribute to the emergence of neurodevelopmental and neuropsychiatric disorders. Here, we describe the method of preparing primary hippocampal neurons and lentiviral particles expressing GluN subunits that can be used as a model to study cell surface expression and synaptic localization of NMDARs. We also show a simple method of fluorescence immunostaining of eGFP-tagged GluN2 subunits and subsequent microscopy technique and image analysis to study the effects of disease-associated mutations in the CTDs of GluN2A and GluN2B subunits.


Subject(s)
Hippocampus , Neurons , Receptors, N-Methyl-D-Aspartate , Receptors, N-Methyl-D-Aspartate/metabolism , Receptors, N-Methyl-D-Aspartate/genetics , Hippocampus/metabolism , Hippocampus/cytology , Neurons/metabolism , Animals , Protein Subunits/metabolism , Protein Subunits/genetics , Cells, Cultured , Rats , Humans , Lentivirus/genetics , Primary Cell Culture/methods , Gene Expression
7.
Methods Mol Biol ; 2799: 13-27, 2024.
Article in English | MEDLINE | ID: mdl-38727900

ABSTRACT

N-methyl-D-aspartate (NMDA) receptors are critical for brain function and serve as drug targets for the treatment of neurological and psychiatric disorders. They typically form the tetrameric assembly of GluN1-GluN2 (2A to 2D) subtypes, with their diverse three-dimensional conformations linked with the physiologically relevant function in vivo. Purified proteins of tetrameric assembled NMDA receptors have broad applications in the structural elucidation, hybridoma technology for antibody production, and high-throughput drug screening. However, obtaining sufficient quantity and monodisperse NMDA receptor protein is still technically challenging. Here, we summarize a paradigm for the expression and purification of diverse NMDA receptor subtypes, with detailed descriptions on screening constructs by fluorescence size-exclusion chromatography (FSEC), generation of recombinant baculovirus, expression in the eukaryotic expression system, protein purification by affinity chromatography and size-exclusion chromatography (SEC), biochemical and functional validation assays.


Subject(s)
Baculoviridae , Chromatography, Affinity , Chromatography, Gel , Receptors, N-Methyl-D-Aspartate , Receptors, N-Methyl-D-Aspartate/metabolism , Receptors, N-Methyl-D-Aspartate/genetics , Receptors, N-Methyl-D-Aspartate/isolation & purification , Receptors, N-Methyl-D-Aspartate/chemistry , Animals , Baculoviridae/genetics , Chromatography, Affinity/methods , Humans , Recombinant Proteins/isolation & purification , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Gene Expression , Sf9 Cells
8.
Methods Mol Biol ; 2799: 55-77, 2024.
Article in English | MEDLINE | ID: mdl-38727903

ABSTRACT

NMDA-type ionotropic glutamate receptors are critically involved in many brain functions and are implicated in a variety of brain disorders. Seven NMDA receptor subunits exist (GluN1, GluN2A-D, and GluN3A-B) that assemble into tetrameric receptor subtypes with distinct functional properties and physiological roles. The majority NMDA receptors are composed of two GluN1 and two GluN2 subunits, which can assemble into four diheteromeric receptors subtypes composed of GluN1 and one type of GluN2 subunit (e.g., GluN1/2A), and presumably also six triheteromeric receptor subtypes composed of GluN1 and two different GluN2 subunits (e.g., GluN1/2A/2B). Furthermore, the GluN1 subunit exists as eight splice variants (e.g., GluN1-1a and GluN1-1b isoforms), and two different GluN1 isoforms can co-assemble to also form triheteromeric NMDA receptors (e.g., GluN1-1a/1b/2A). Here, we describe a method to faithfully express triheteromeric NMDA receptors in heterologous expression systems by controlling the identity of two of the four subunits. This method overcomes the problem that co-expression of three different NMDA receptor subunits generates two distinct diheteromeric receptor subtypes as well as one triheteromeric receptor subtype, thereby confounding studies that require a homogenous population of triheteromeric NMDA receptors. The method has been applied to selectively express recombinant triheteromeric GluN1/2A/2B, GluN1/2A/2C, GluN1/2B/2D, GluN1-1a/GluN1-1b/2A, GluN1-1a/GluN1-1b/2B receptors with negligible co-expression of the respective diheteromeric receptor subtypes. This method therefore enables quantitative evaluation of functional and pharmacological properties of triheteromeric NMDA receptors, some of which are abundant NMDA receptor subtypes in the adult brain.


Subject(s)
Protein Isoforms , Protein Subunits , Receptors, N-Methyl-D-Aspartate , Receptors, N-Methyl-D-Aspartate/metabolism , Receptors, N-Methyl-D-Aspartate/genetics , Humans , Protein Subunits/metabolism , Protein Subunits/genetics , Protein Isoforms/genetics , Protein Isoforms/metabolism , HEK293 Cells , Animals , Cell Membrane/metabolism , Gene Expression
9.
Appl Microbiol Biotechnol ; 108(1): 320, 2024 May 06.
Article in English | MEDLINE | ID: mdl-38709366

ABSTRACT

The unspecific peroxygenase (UPO) from Cyclocybe aegerita (AaeUPO) can selectively oxidize C-H bonds using hydrogen peroxide as an oxygen donor without cofactors, which has drawn significant industrial attention. Many studies have made efforts to enhance the overall activity of AaeUPO expressed in Komagataella phaffii by employing strategies such as enzyme-directed evolution, utilizing appropriate promoters, and screening secretion peptides. Building upon these previous studies, the objective of this study was to further enhance the expression of a mutant of AaeUPO with improved activity (PaDa-I) by increasing the gene copy number, co-expressing chaperones, and optimizing culture conditions. Our results demonstrated that a strain carrying approximately three copies of expression cassettes and co-expressing the protein disulfide isomerase showed an approximately 10.7-fold increase in volumetric enzyme activity, using the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) as the substrate. After optimizing the culture conditions, the volumetric enzyme activity of this strain further increased by approximately 48.7%, reaching 117.3 U/mL. Additionally, the purified catalytic domain of PaDa-I displayed regioselective hydroxylation of R-2-phenoxypropionic acid. The results of this study may facilitate the industrial application of UPOs. KEY POINTS: • The secretion of the catalytic domain of PaDa-I can be significantly enhanced through increasing gene copy numbers and co-expressing of protein disulfide isomerase. • After optimizing the culture conditions, the volumetric enzyme activity can reach 117.3 U/mL, using the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) as the substrate. • The R-2-phenoxypropionic acid can undergo the specific hydroxylation reaction catalyzed by catalytic domain of PaDa-I, resulting in the formation of R-2-(4-hydroxyphenoxy)propionic acid.


Subject(s)
Mixed Function Oxygenases , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Saccharomycetales/genetics , Saccharomycetales/enzymology , Saccharomycetales/metabolism , Gene Dosage , Protein Disulfide-Isomerases/genetics , Protein Disulfide-Isomerases/metabolism , Gene Expression , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/chemistry
10.
Anim Sci J ; 95(1): e13951, 2024.
Article in English | MEDLINE | ID: mdl-38703069

ABSTRACT

Intramuscular fat (IMF) is a crucial determinant of meat quality and is influenced by various regulatory factors. Despite the growing recognition of the important role of long noncoding RNAs (lncRNAs) in IMF deposition, the mechanisms underlying buffalo IMF deposition remain poorly understood. In this study, we identified and characterized a lncRNA, lncFABP4, which is transcribed from the antisense strand of fatty acid-binding protein 4 (FABP4). lncFABP4 inhibited cell proliferation in buffalo intramuscular preadipocytes. Moreover, lncFABP4 significantly increased intramuscular preadipocyte differentiation, as indicated by an increase in the expression of the adipogenic markers peroxisome proliferator-activated receptor gamma (PPARG), CCAAT enhancer binding protein alpha (C/EBPα), and FABP4. Mechanistically, lncFABP4 was found to have the potential to regulate downstream gene expression by participating in protein-protein interaction pathways. These findings contribute to further understanding of the intricate mechanisms through which lncRNAs modulate intramuscular adipogenesis in buffaloes.


Subject(s)
Adipocytes , Adipogenesis , Buffaloes , Cell Differentiation , Cell Proliferation , Fatty Acid-Binding Proteins , PPAR gamma , RNA, Long Noncoding , Animals , Buffaloes/genetics , Buffaloes/metabolism , Adipogenesis/genetics , Adipocytes/metabolism , Adipocytes/cytology , Fatty Acid-Binding Proteins/metabolism , Fatty Acid-Binding Proteins/genetics , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Cell Differentiation/genetics , PPAR gamma/metabolism , PPAR gamma/genetics , Gene Expression , Cells, Cultured , CCAAT-Enhancer-Binding Protein-alpha/metabolism , CCAAT-Enhancer-Binding Protein-alpha/genetics , Food Quality
11.
J Psychiatry Neurosci ; 49(3): E157-E171, 2024.
Article in English | MEDLINE | ID: mdl-38692693

ABSTRACT

BACKGROUND: Critical adolescent neural refinement is controlled by the DCC (deleted in colorectal cancer) protein, a receptor for the netrin-1 guidance cue. We sought to describe the effects of reduced DCC on neuroanatomy in the adolescent and adult mouse brain. METHODS: We examined neuronal connectivity, structural covariance, and molecular processes in a DCC-haploinsufficient mouse model, compared with wild-type mice, using new, custom analytical tools designed to leverage publicly available databases from the Allen Institute. RESULTS: We included 11 DCC-haploinsufficient mice and 16 wild-type littermates. Neuroanatomical effects of DCC haploinsufficiency were more severe in adolescence than adulthood and were largely restricted to the mesocorticolimbic dopamine system. The latter finding was consistent whether we identified the regions of the mesocorticolimbic dopamine system a priori or used connectivity data from the Allen Brain Atlas to determine de novo where these dopamine axons terminated. Covariance analyses found that DCC haploinsufficiency disrupted the coordinated development of the brain regions that make up the mesocorticolimbic dopamine system. Gene expression maps pointed to molecular processes involving the expression of DCC, UNC5C (encoding DCC's co-receptor), and NTN1 (encoding its ligand, netrin-1) as underlying our structural findings. LIMITATIONS: Our study involved a single sex (males) at only 2 ages. CONCLUSION: The neuroanatomical phenotype of DCC haploinsufficiency described in mice parallels that observed in DCC-haploinsufficient humans. It is critical to understand the DCC-haploinsufficient mouse as a clinically relevant model system.


Subject(s)
Brain , DCC Receptor , Dopamine , Haploinsufficiency , Animals , DCC Receptor/genetics , Brain/metabolism , Brain/growth & development , Brain/anatomy & histology , Dopamine/metabolism , Mice , Male , Gene Expression , Neural Pathways , Age Factors , Female , Mice, Inbred C57BL , Aging/genetics , Aging/physiology
12.
Anim Biotechnol ; 35(1): 2344208, 2024 Nov.
Article in English | MEDLINE | ID: mdl-38741260

ABSTRACT

Garlic, known for its immune-modulating and antibiotic properties, contains lectins that possess antimicrobial and immunomodulatory effects. Galectins (Gals), which bind ß-galactosides, play a role in modulating immunity and pathological processes. It is hypothesized that garlic's lectin components interfere with animal lectins. St. Croix sheep, known for their resistance to parasites and adaptability, are influenced by dietary supplements for innate immunity. This study evaluated the impact of garlic drench on Galectin gene expression in St. Croix sheep. Adult non-lactating ewes received either garlic juice concentrate or sterile distilled water for four weeks. Blood samples were collected, and plasma and whole blood cells were separated. Galectin secretion was assessed using a Sheep-specific ELISA, while Galectin gene transcription was analyzed through real-time PCR. Garlic administration upregulated LGALS-3 gene expression and significantly increased total plasma protein concentration. Garlic supplementation also affected Galectin secretion, with Gal-1, Gal-3, and Gal-9 showing differential effects.


Subject(s)
Galectins , Garlic , Animals , Garlic/chemistry , Galectins/genetics , Galectins/metabolism , Sheep , Female , Dietary Supplements , Gene Expression Regulation/drug effects , Gene Expression/drug effects , Animal Feed/analysis
13.
Environ Sci Technol ; 58(19): 8169-8181, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38690750

ABSTRACT

Climate change-induced stressors are contributing to the emergence of infectious diseases, including those caused by marine bacterial pathogens such as Vibrio spp. These stressors alter Vibrio temporal and geographical distribution, resulting in increased spread, exposure, and infection rates, thus facilitating greater Vibrio-human interactions. Concurrently, wildfires are increasing in size, severity, frequency, and spread in the built environment due to climate change, resulting in the emission of contaminants of emerging concern. This study aimed to understand the potential effects of urban interface wildfire ashes on Vibrio vulnificus (V. vulnificus) growth and gene expression using transcriptomic approaches. V. vulnificus was exposed to structural and vegetation ashes and analyzed to identify differentially expressed genes using the HTSeq-DESeq2 strategy. Exposure to wildfire ash altered V. vulnificus growth and gene expression, depending on the trace metal composition of the ash. The high Fe content of the vegetation ash enhanced bacterial growth, while the high Cu, As, and Cr content of the structural ash suppressed growth. Additionally, the overall pattern of upregulated genes and pathways suggests increased virulence potential due to the selection of metal- and antibiotic-resistant strains. Therefore, mixed fire ashes transported and deposited into coastal zones may lead to the selection of environmental reservoirs of Vibrio strains with enhanced antibiotic resistance profiles, increasing public health risk.


Subject(s)
Vibrio vulnificus , Vibrio vulnificus/genetics , Wildfires , Gene Expression
14.
Ecol Evol Physiol ; 97(2): 81-96, 2024.
Article in English | MEDLINE | ID: mdl-38728692

ABSTRACT

AbstractTropical ectotherms are thought to be especially vulnerable to climate change because they have evolved in temporally stable thermal environments and therefore have decreased tolerance for thermal variability. Thus, they are expected to have narrow thermal tolerance ranges, live close to their upper thermal tolerance limits, and have decreased thermal acclimation capacity. Although models often predict that tropical forest ectotherms are especially vulnerable to rapid environmental shifts, these models rarely include the potential for plasticity of relevant traits. We measured phenotypic plasticity of thermal tolerance and thermal preference as well as multitissue transcriptome plasticity in response to warmer temperatures in a species that previous work has suggested is highly vulnerable to climate warming, the Panamanian slender anole lizard (Anolis apletophallus). We found that many genes, including heat shock proteins, were differentially expressed across tissues in response to short-term warming. Under long-term warming, the voluntary thermal maxima of lizards also increased, although thermal preference exhibited only limited plasticity. Using these data, we modeled changes in the activity time of slender anoles through the end of the century under climate change and found that plasticity should delay declines in activity time by at least two decades. Our results suggest that slender anoles, and possibly other tropical ectotherms, can alter the expression of genes and phenotypes when responding to shifting environmental temperatures and that plasticity should be considered when predicting the future of organisms under a changing climate.


Subject(s)
Climate Change , Lizards , Thermotolerance , Tropical Climate , Animals , Lizards/genetics , Lizards/physiology , Thermotolerance/genetics , Forests , Acclimatization/genetics , Acclimatization/physiology , Transcriptome , Gene Expression
15.
Molecules ; 29(9)2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38731523

ABSTRACT

This study reports an innovative approach for producing nanoplastics (NP) from various types of domestic waste plastics without the use of chemicals. The plastic materials used included water bottles, styrofoam plates, milk bottles, centrifuge tubes, to-go food boxes, and plastic bags, comprising polyethylene terephthalate (PET), polystyrene (PS), polypropylene (PP), high-density polyethylene (HDPE), and Poly (Ethylene-co-Methacrylic Acid) (PEMA). The chemical composition of these plastics was confirmed using Raman and FTIR spectroscopy, and they were found to have irregular shapes. The resulting NP particles ranged from 50 to 400 nm in size and demonstrated relative stability when suspended in water. To assess their impact, the study investigated the effects of these NP particulates on cell viability and the expression of genes involved in inflammation and oxidative stress using a macrophage cell line. The findings revealed that all types of NP reduced cell viability in a concentration-dependent manner. Notably, PS, HDPE, and PP induced significant reductions in cell viability at lower concentrations, compared to PEMA and PET. Moreover, exposure to NP led to differential alterations in the expression of inflammatory genes in the macrophage cell line. Overall, this study presents a viable method for producing NP from waste materials that closely resemble real-world NP. Furthermore, the toxicity studies demonstrated distinct cellular responses based on the composition of the NP, shedding light on the potential environmental and health impacts of these particles.


Subject(s)
Cell Survival , Macrophages , Microplastics , Cell Survival/drug effects , Macrophages/drug effects , Macrophages/metabolism , Animals , Mice , Nanoparticles/chemistry , Plastics/chemistry , RAW 264.7 Cells , Gene Expression/drug effects , Cell Line , Gene Expression Regulation/drug effects , Waste Products/analysis , Particle Size
16.
Bull Math Biol ; 86(6): 74, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38740619

ABSTRACT

Many imaging techniques for biological systems-like fixation of cells coupled with fluorescence microscopy-provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. These snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.


Subject(s)
Mathematical Concepts , Models, Biological , Stochastic Processes , Poisson Distribution , Computer Simulation , Microscopy, Fluorescence/statistics & numerical data , Gene Expression
17.
Int J Mol Sci ; 25(7)2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38612818

ABSTRACT

Many genomic, anatomical and functional differences exist between the medullary (MTAL) and the cortical thick ascending limb of the loop of Henle (CTAL), including a higher expression of claudin-10 (CLDN10) in the MTAL than in the CTAL. Therefore, we assessed to what extent the Cldn10 gene expression is a determinant of differential gene expression between MTAL and CTAL. RNAs extracted from CTAL and MTAL microdissected from wild type (WT) and Cldn10 knock out mice (cKO) were analyzed by RNAseq. Differential and enrichment analyses (GSEA) were performed with interactive R Shiny software. Between WT and cKO MTAL, 637 genes were differentially expressed, whereas only 76 were differentially expressed between WT and cKO CTAL. Gene expression patterns and GSEA analyses in all replicates showed that WT MTAL did not cluster with the other replicates; no hierarchical clustering could be found between WT CTAL, cKO CTAL and cKO MTAL. Compared to WT replicates, cKO replicates were enriched in Cldn16, Cldn19, Pth1r, (parathyroid hormone receptor type 1), Casr (calcium sensing receptor) and Vdr (Vitamin D Receptor) mRNA in both the cortex and medulla. Cldn10 is associated with gene expression patterns, including genes specifically involved in divalent cations reabsorption in the TAL.


Subject(s)
Adrenal Medulla , Extremities , Animals , Mice , Claudins/genetics , Mice, Knockout , Gene Expression
18.
Viruses ; 16(4)2024 Mar 23.
Article in English | MEDLINE | ID: mdl-38675835

ABSTRACT

Many protein expression systems are primarily utilised to produce a single, specific recombinant protein. In contrast, most biological processes such as virus assembly rely upon a complex of several interacting proteins rather than the activity of a sole protein. The high complexity of the baculovirus genome, coupled with a multiphase replication cycle incorporating distinct transcriptional steps, made it the ideal system to manipulate for high-level expression of a single, or co-expression of multiple, foreign proteins within a single cell. We have developed and utilised a series of recombinant baculovirus systems to unravel the sequential assembly process of a complex non-enveloped model virus, bluetongue virus (BTV). The high protein yields expressed by the baculovirus system not only facilitated structure-function analysis of each viral protein but were also advantageous to crystallography studies and supported the first atomic-level resolution of a recombinant viral protein, the major BTV capsid protein. Further, the formation of recombinant double-shelled virus-like particles (VLPs) provided insights into the structure-function relationships among the four major structural proteins of the BTV whilst also representing a potential candidate for a viral vaccine. The baculovirus multi-gene expression system facilitated the study of structurally complex viruses (both non-enveloped and enveloped viruses) and heralded a new generation of viral vaccines.


Subject(s)
Baculoviridae , Recombinant Proteins , Baculoviridae/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Animals , Gene Expression , Bluetongue virus/genetics , Genetic Vectors/genetics , Virus Assembly , Viral Proteins/genetics , Viral Proteins/metabolism , Capsid Proteins/genetics , Capsid Proteins/metabolism , Capsid Proteins/chemistry
19.
Mol Biochem Parasitol ; 258: 111618, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38588892

ABSTRACT

Trypanosoma cruzi is a parasite with a high capacity to adapt to the host. Animal models have already demonstrated that the tropism of this parasite occurs not only in cardiac/digestive tissues but also in adipose tissue (AT). That said, the consequences ofT. cruziinfection for AT and the implications of treatment with Benzonidazole in this tissue are under discussion. Here, we tested the hypothesis that T. cruzi infection in adipose tissue upon treatment with Benzonidazole (Bz) and the interaction of mononuclear immune cells (PBMC) influences the relative expression of ACAT1, FASN, and PNPLA2 genes. Thus, stem cells derived from adipose tissue (ADSC) after adipogenic differentiation were indirectly cultivated with PBMC after infection with the T. cruzi Y strain and treatment with Bz. We use the TcSAT-IAM system and RT-qPCR to evaluate the parasite load and the relative quantification (ΔCt) of the ACAT1, FASN, and PNPLA2 genes. Our results demonstrate that treatment with Bz did not reduce adipocyte infection in the presence (p-value: 0.5796) or absence (p-value: 0.1854) of cultivation with PBMC. In addition, even though there is no statistical difference when compared to the control group (AT), T. cruzi induces the FASN expression (Rq: 14.00). However, treatment with Bz in AT suggests the increases of PNPLA2 expression levels (Rq: 12.58), even in the absence of T. cruzi infection. During indirect cultivation with PBMC, T. cruzi smooths the expression of PNPLA2 (Rq: 0.824) and instigates the expression of ACAT1 (Rq: 1.632) and FASN (Rq: 1.394). Furthermore, the treatment with Bz during infection induces PNPLA2 expression (Rq: 1.871), maintaining FASN expression levels (Rq: 1.334). Given this, our results indicate that treatment with Benzonidazole did not decrease T. cruzi infection in adipose tissue. However, treating the adipocyte cells with Bz during the interaction with PBMC cells influences the lipid pathways scenario, inducing lipolytic metabolism through the expression of PNPLA2.


Subject(s)
Acyltransferases , Adipose Tissue , Fatty Acid Synthase, Type I , Leukocytes, Mononuclear , Lipase , Trypanosoma cruzi , Humans , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/parasitology , Adipose Tissue/parasitology , Adipose Tissue/metabolism , Trypanosoma cruzi/drug effects , Trypanosoma cruzi/genetics , Lipase/genetics , Lipase/metabolism , Fatty Acid Synthase, Type I/genetics , Fatty Acid Synthase, Type I/metabolism , Acetyl-CoA C-Acetyltransferase/genetics , Acetyl-CoA C-Acetyltransferase/metabolism , Chagas Disease/drug therapy , Chagas Disease/parasitology , Chagas Disease/genetics , Membrane Proteins/genetics , Membrane Proteins/metabolism , Parasite Load , Gene Expression , Cells, Cultured
20.
Protein Expr Purif ; 219: 106480, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38588871

ABSTRACT

Mpox is a zoonotic disease that was once endemic in Africa countries caused by mpox virus. However, cases recently have been confirmed in many non-endemic countries outside of Africa. The rapidly increasing number of confirmed mpox cases poses a threat to the international community. In-depth studies of key viral factors are urgently needed, which will inform the design of multiple antiviral agents. Mpox virus A41L gene encodes a secreted protein, A41, that is nonessential for viral replication, but could affect the host response to infection via interacting with chemokines. Here, mpox virus A41 protein was expressed in Sf9 cells, and purified by affinity chromatography followed by gel filtration. Surface plasmon resonance spectroscopy showed that purified A41 binds a certain human chemokine CXCL8 with the equilibrium dissociation constant (KD) being 1.22 × 10-6 M. The crystal structure of mpox virus A41 protein was solved at 1.92 Å. Structural analysis and comparison revealed that mpox virus A41 protein adopts a characteristic ß-sheet topology, showing minor differences with that of vaccinia virus. These preliminary structural and functional studies of A41 protein from mpox virus will help us better understand its role in chemokine subversion, and contributing to the knowledge to viral chemokine binding proteins.


Subject(s)
Viral Proteins , Humans , Viral Proteins/genetics , Viral Proteins/chemistry , Viral Proteins/metabolism , Viral Proteins/biosynthesis , Viral Proteins/isolation & purification , Crystallography, X-Ray , Animals , Interleukin-8/genetics , Interleukin-8/chemistry , Interleukin-8/metabolism , Gene Expression , Sf9 Cells , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/biosynthesis , Yatapoxvirus/genetics , Yatapoxvirus/chemistry , Yatapoxvirus/metabolism
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