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Biosensors & Bioelectronics Oct 2024In this work, we present an electrochemical sensor for fast, low-cost, and easy detection of the SARS-CoV-2 spike protein in infected patients. The sensor is based on a...
In this work, we present an electrochemical sensor for fast, low-cost, and easy detection of the SARS-CoV-2 spike protein in infected patients. The sensor is based on a selected combination of nanomaterials with a specific purpose. A bioconjugate formed by Few-layer bismuthene nanosheets (FLB) and tetrahedral DNA nanostructures (TDNs) is immobilized on Carbon Screen-Printed Electrodes (CSPE). The TDNs contain on the top vertex an aptamer that specifically binds to the SARS-CoV-2 spike protein, and a thiol group at the three basal vertices to anchor to the FLB. The TDNs are also marked with a redox indicator, Azure A (AA), which allows the direct detection of SARS-CoV-2 spike protein through changes in the current intensity of its electrolysis before and after the biorecognition reaction. The developed sensor can detect SARS-CoV-2 spike protein with a detection limit of 1.74 fg mL directly in nasopharyngeal swab human samples. Therefore, this study offers a new strategy for rapid virus detection since it is versatile enough for different viruses and pathogens.
Topics: SARS-CoV-2; Biosensing Techniques; Humans; Spike Glycoprotein, Coronavirus; COVID-19; Limit of Detection; Electrochemical Techniques; Nanostructures; DNA; Aptamers, Nucleotide
PubMed: 38896979
DOI: 10.1016/j.bios.2024.116500 -
Physiologia Plantarum 2024RNA-seq data is currently generated in numerous non-model organisms that lack a reference genome. Nevertheless, the confirmation of gene expression levels using RT-qPCR...
RNA-seq data is currently generated in numerous non-model organisms that lack a reference genome. Nevertheless, the confirmation of gene expression levels using RT-qPCR remains necessary, and the existing techniques do not seamlessly interface with the omics pipeline workflow. Developing primers for many targets by utilising orthologous genes can be a laborious, imprecise, and subjective process, particularly for plant species that are not commonly studied and do not have a known genome. We have developed a primer design tool, named PABLOG, that analyses the alignments generated from long or short RNA-seq reads and a reference orthologous gene. PABLOG scans, much like a bee searching several flowers for pollen, and presents a sorted list of potential exon-exon junction locations, ranked according to their reliability. Through computational analysis across the whole genomes of several non-model species, we demonstrate that PABLOG performs more effectively than other methods in identifying exon-exon junctions since it generates significantly fewer false-positive results. Examination of candidate regions at the gene level, in conjunction with laboratory studies, shows that the suggested primers successfully amplified particular targets in non-model plants without any presence of genomic contamination. Our tool includes a consensus sequence feature that enables the complete process of primer design, from aligning with the target gene to determining amplification parameters. The utility can be accessed via the GitHub repository located at: https://github.com/tools4plant-omics/PABLOG.
Topics: Bees; DNA Primers; Exons; Software; Animals; Genes, Plant; Genome, Plant; Computational Biology
PubMed: 38894544
DOI: 10.1111/ppl.14398 -
Molecules (Basel, Switzerland) Jun 2024Spinal muscular atrophy (SMA) is a severe neuromuscular disorder that is caused by mutations in the survival motor neuron 1 () gene, hindering the production of... (Review)
Review
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder that is caused by mutations in the survival motor neuron 1 () gene, hindering the production of functional survival motor neuron (SMN) proteins. Antisense oligonucleotides (ASOs), a versatile DNA-like drug, are adept at binding to target RNA to prevent translation or promote alternative splicing. Nusinersen is an FDA-approved ASO for the treatment of SMA. It effectively promotes alternative splicing in pre-mRNA transcribed from the gene, an analog of the gene, to produce a greater amount of full-length SMN protein, to compensate for the loss of functional protein translated from . Despite its efficacy in ameliorating SMA symptoms, the cellular uptake of these ASOs is suboptimal, and their inability to penetrate the CNS necessitates invasive lumbar punctures. Cell-penetrating peptides (CPPs), which can be conjugated to ASOs, represent a promising approach to improve the efficiency of these treatments for SMA and have the potential to transverse the blood-brain barrier to circumvent the need for intrusive intrathecal injections and their associated adverse effects. This review provides a comprehensive analysis of ASO therapies, their application for the treatment of SMA, and the encouraging potential of CPPs as delivery systems to improve ASO uptake and overall efficiency.
Topics: Cell-Penetrating Peptides; Humans; Muscular Atrophy, Spinal; Oligonucleotides, Antisense; Animals; Oligonucleotides; Survival of Motor Neuron 2 Protein; Survival of Motor Neuron 1 Protein; Blood-Brain Barrier
PubMed: 38893532
DOI: 10.3390/molecules29112658 -
International Journal of Molecular... Jun 2024Aging, marked by a gradual decline in physiological function and heightened vulnerability to age-related diseases, remains a complex biological process with multifaceted...
Aging, marked by a gradual decline in physiological function and heightened vulnerability to age-related diseases, remains a complex biological process with multifaceted regulatory mechanisms. Our study elucidates the critical role of poly(ADP-ribose) glycohydrolase (PARG), responsible for catabolizing poly(ADP-ribose) (pADPr) in the aging process by modulating the expression of age-related genes in . Specifically, we uncover the regulatory function of the uncharacterized PARG C-terminal domain in controlling PARG activity. Flies lacking this domain exhibit a significantly reduced lifespan compared to wild-type counterparts. Furthermore, we observe progressive dysregulation of age-related gene expression during aging, accelerated in the absence of PARG activity, culminating in a premature aging phenotype. Our findings reveal the critical involvement of the pADPr pathway as a key player in the aging process, highlighting its potential as a therapeutic target for mitigating age-related effects.
Topics: Animals; Longevity; Drosophila melanogaster; Drosophila Proteins; Glycoside Hydrolases; Aging; Gene Expression Regulation; Poly Adenosine Diphosphate Ribose
PubMed: 38892377
DOI: 10.3390/ijms25116189 -
International Journal of Molecular... Jun 2024Periostin, a multifunctional 90 kDa protein, plays a pivotal role in the pathogenesis of fibrosis across various tissues, including skeletal muscle. It operates within...
Periostin, a multifunctional 90 kDa protein, plays a pivotal role in the pathogenesis of fibrosis across various tissues, including skeletal muscle. It operates within the transforming growth factor beta 1 (Tgf-β1) signalling pathway and is upregulated in fibrotic tissue. Alternative splicing of Periostin's C-terminal region leads to six protein-coding isoforms. This study aimed to elucidate the contribution of the isoforms containing the amino acids encoded by exon 17 (e17+ Periostin) to skeletal muscle fibrosis and investigate the therapeutic potential of manipulating exon 17 splicing. We identified distinct structural differences between e17+ Periostin isoforms, affecting their interaction with key fibrotic proteins, including Tgf-β1 and integrin alpha V. In vitro mouse fibroblast experimentation confirmed the TGF-β1-induced upregulation of e17+ Periostin mRNA, mitigated by an antisense approach that induces the skipping of exon 17 of the gene. Subsequent in vivo studies in the D2. mouse model of Duchenne muscular dystrophy (DMD) demonstrated that our antisense treatment effectively reduced e17+ Periostin mRNA expression, which coincided with reduced full-length Periostin protein expression and collagen accumulation. The grip strength of the treated mice was rescued to the wild-type level. These results suggest a pivotal role of e17+ Periostin isoforms in the fibrotic pathology of skeletal muscle and highlight the potential of targeted exon skipping strategies as a promising therapeutic approach for mitigating fibrosis-associated complications.
Topics: Animals; Cell Adhesion Molecules; Mice; Fibrosis; Exons; Mice, Inbred mdx; Oligonucleotides, Antisense; Alternative Splicing; Muscular Dystrophy, Duchenne; Muscle, Skeletal; Transforming Growth Factor beta1; Fibroblasts; Disease Models, Animal; Protein Isoforms; Male
PubMed: 38892298
DOI: 10.3390/ijms25116113 -
International Journal of Molecular... May 2024Type 2 diabetes mellitus (T2DM) is a risk factor for male infertility, but the underlying molecular mechanisms remain unclear. Advanced glycation end products (AGEs) are...
DNA Aptamer Raised against Advanced Glycation End Products Improves Sperm Concentration, Motility, and Viability by Suppressing Receptors for Advanced Glycation End Product-Induced Oxidative Stress and Inflammation in the Testes of Diabetic Mice.
Type 2 diabetes mellitus (T2DM) is a risk factor for male infertility, but the underlying molecular mechanisms remain unclear. Advanced glycation end products (AGEs) are pathogenic molecules for diabetic vascular complications. Here, we investigated the effects of the DNA aptamer raised against AGEs (AGE-Apt) on testicular and sperm abnormalities in a T2DM mouse model. KK-Ay (DM) and wild-type (non-DM) 4- and 7-week-old male mice were sacrificed to collect the testes and spermatozoa for immunofluorescence, RT-PCR, and histological analyses. DM and non-DM 7-week-old mice were subcutaneously infused with the AGE-Apt or control-aptamer for 6 weeks and were then sacrificed. Plasma glucose, testicular AGEs, and gene expression in 4-week-old DM mice and plasma glucose, testicular AGEs, oxidative stress, and pro-inflammatory gene expressions in 7-week-old DM mice were higher than those in age-matched non-DM mice, the latter of which was associated with seminiferous tubular dilation. AGE-Apt did not affect glycemic parameters, but it inhibited seminiferous tubular dilation, reduced the number of testicular macrophages and apoptotic cells, and restored the decrease in sperm concentration, motility, and viability of 13-week-old DM mice. Our findings suggest that AGEs-Apt may improve sperm abnormality by suppressing AGE-RAGE-induced oxidative stress and inflammation in the testes of DM mice.
Topics: Animals; Male; Oxidative Stress; Glycation End Products, Advanced; Mice; Aptamers, Nucleotide; Testis; Receptor for Advanced Glycation End Products; Diabetes Mellitus, Experimental; Sperm Motility; Diabetes Mellitus, Type 2; Inflammation; Spermatozoa; Sperm Count
PubMed: 38892134
DOI: 10.3390/ijms25115947 -
International Journal of Molecular... May 2024There is great concern in equine sport over the potential use of pharmaceutical agents capable of editing the genome or modifying the expression of gene products....
There is great concern in equine sport over the potential use of pharmaceutical agents capable of editing the genome or modifying the expression of gene products. Synthetic oligonucleotides are short, single-stranded polynucleotides that represent a class of agents capable of modifying gene expression products with a high potential for abuse in horseracing. As these substances are not covered by most routine anti-doping analytical approaches, they represent an entire class of compounds that are not readily detectable. The nucleotide sequence for each oligonucleotide is highly specific, which makes targeted analysis for these agents problematic. Accordingly, we have developed a non-targeted approach to detect the presence of specific product ions that are not naturally present in ribonucleic acids. Briefly, serum samples were extracted using solid-phase extraction with a mixed-mode cartridge following the disruption of protein interactions to isolate the oligonucleotides. Following the elution and concentration steps, chromatographic separation was achieved utilizing reversed-phase liquid chromatography. Following an introduction to a Thermo Q Exactive HF mass spectrometer using electrospray ionization, analytes were detected utilizing a combination of full-scan, parallel reaction monitoring and all ion fragmentation scan modes. The limits of detection were determined along with the accuracy, precision, stability, recovery, and matrix effects using a representative 13mer oligonucleotide. Following method optimization using the 13mer oligonucleotide, the method was applied to successfully detect the presence of specific product ions in three unique oligonucleotide sequences targeting equine-specific transcripts.
Topics: Animals; Horses; Oligonucleotides; Doping in Sports; Chromatography, Liquid; Mass Spectrometry; Solid Phase Extraction; Limit of Detection
PubMed: 38891955
DOI: 10.3390/ijms25115752 -
International Journal of Molecular... May 2024In aquaculture, viral diseases pose a significant threat and can lead to substantial economic losses. The primary defense against viral invasion is the innate immune...
In aquaculture, viral diseases pose a significant threat and can lead to substantial economic losses. The primary defense against viral invasion is the innate immune system, with interferons (IFNs) playing a crucial role in mediating the immune response. With advancements in molecular biology, the role of non-coding RNA (ncRNA), particularly microRNAs (miRNAs), in gene expression has gained increasing attention. While the function of miRNAs in regulating the host immune response has been extensively studied, research on their immunomodulatory effects in teleost fish, including silver carp (), is limited. Therefore, this research aimed to investigate the immunomodulatory role of microRNA-30b-5p (miR-30b-5p) in the antiviral immune response of silver carp () by targeting cytokine receptor family B5 (CRFB5) via the JAK/STAT signaling pathway. In this study, silver carp were stimulated with polyinosinic-polycytidylic acid (poly (I:C)), resulting in the identification of an up-regulated miRNA (miR-30b-5p). Through a dual luciferase assay, it was demonstrated that CRFB5, a receptor shared by fish type I interferon, is a novel target of miR-30b-5p. Furthermore, it was found that miR-30b-5p can suppress post-transcriptional CRFB5 expression. Importantly, this study revealed for the first time that miR-30b-5p negatively regulates the JAK/STAT signaling pathway, thereby mediating the antiviral immune response in silver carp by targeting CRFB5 and maintaining immune system stability. These findings not only contribute to the understanding of how miRNAs act as negative feedback regulators in teleost fish antiviral immunity but also suggest their potential therapeutic measures to prevent an excessive immune response.
Topics: Animals; MicroRNAs; Carps; Poly I-C; Signal Transduction; Janus Kinases; STAT Transcription Factors; Fish Proteins; Fish Diseases; Immunity, Innate; Gene Expression Regulation
PubMed: 38891899
DOI: 10.3390/ijms25115712 -
International Journal of Molecular... May 2024Dysferlin is a large transmembrane protein involved in critical cellular processes including membrane repair and vesicle fusion. Mutations in the dysferlin gene () can... (Review)
Review
Dysferlin is a large transmembrane protein involved in critical cellular processes including membrane repair and vesicle fusion. Mutations in the dysferlin gene () can result in rare forms of muscular dystrophy; Miyoshi myopathy; limb girdle muscular dystrophy type 2B (LGMD2B); and distal myopathy. These conditions are collectively known as dysferlinopathies and are caused by more than 600 mutations that have been identified across the gene to date. In this review, we discuss the key molecular and clinical features of LGMD2B, the causative gene , and the associated dysferlin protein structure. We also provide an update on current approaches to LGMD2B diagnosis and advances in drug development, including splice switching antisense oligonucleotides. We give a brief update on clinical trials involving adeno-associated viral gene therapy and the current progress on CRISPR/Cas9 mediated therapy for LGMD2B, and then conclude by discussing the prospects of antisense oligomer-based intervention to treat selected mutations causing dysferlinopathies.
Topics: Humans; Muscular Dystrophies, Limb-Girdle; Dysferlin; Genetic Therapy; Mutation; Oligonucleotides, Antisense; Animals
PubMed: 38891760
DOI: 10.3390/ijms25115572 -
Cells May 2024Respiratory viruses cause airway inflammation, resulting in epithelial injury and repair. miRNAs, including miR-149-5p, regulate different pathological conditions. We...
Respiratory viruses cause airway inflammation, resulting in epithelial injury and repair. miRNAs, including miR-149-5p, regulate different pathological conditions. We aimed to determine how miR-149-5p functions in regulating pro-inflammatory IL-6 and p63, key regulators of airway epithelial wound repair, in response to viral proteins in bronchial (BEAS-2B) and alveolar (A549) epithelial cells. BEAS-2B or A549 cells were incubated with poly (I:C, 0.5 µg/mL) for 48 h or SARS-CoV-2 spike protein-1 or 2 subunit (S1 or S2, 1 μg/mL) for 24 h. miR-149-5p was suppressed in BEAS-2B challenged with poly (I:C), correlating with IL-6 and p63 upregulation. miR-149-5p was down-regulated in A549 stimulated with poly (I:C); IL-6 expression increased, but p63 protein levels were undetectable. miR-149-5p remained unchanged in cells exposed to S1 or S2, while S1 transfection increased IL-6 expression in BEAS-2B cells. Ectopic over-expression of miR-149-5p in BEAS-2B cells suppressed and mRNA levels and inhibited poly (I:C)-induced and mRNA expressions. miR-149-5p directly suppressed mRNA in BEAS-2B cells. Hence, BEAS-2B cells respond differently to poly (I:C), S1 or S2 compared to A549 cells. Thus, miR-149-5p dysregulation may be involved in poly (I:C)-stimulated but not S1- or S2-stimulated increased IL-6 production and p63 expression in BEAS-2B cells.
Topics: Humans; MicroRNAs; Interleukin-6; A549 Cells; Epithelial Cells; Poly I-C; SARS-CoV-2; COVID-19; Tumor Suppressor Proteins; Transcription Factors; Gene Expression Regulation
PubMed: 38891051
DOI: 10.3390/cells13110919