UNLABELLED: The aim of this study was to identify parameters influencing DNA extraction and PCR amplification efficiencies in an attempt to standardize Mucorales qPCR. The Fungal PCR Initiative Mucorales Laboratory Working Group distributed two panels of simulated samples to 26 laboratories: Panel A (six sera spiked with Mucorales DNA and one negative control serum) and Panel B (six Mucorales DNA extracts). Panel A underwent DNA extraction in each laboratory according to the local procedure and were sent to a central laboratory for testing using three different qPCR techniques: one in-house qPCR assay and two commercial assays (MucorGenius and Fungiplex). Panel B DNA extracts were PCR amplified in each laboratory using local procedures: nine in-house qPCR assays and two commercial kits (MucorGenius and MycoGENIE). All data were compiled and anonymously analyzed at the central laboratory. For Panel A, a total of six different automated platforms and five manual extraction methods were used. Positive rates were 64%, 70%, and 89%, for the MucorGenius, Fungiplex, and the in-house qPCR assay, respectively. Using a large volume of serum for DNA extraction provided the highest analytical sensitivity (82.5% for 1 mL compared with 62.7% for smaller volumes, P < 0.01). For Panel B, five in-house qPCR assays and two commercial kits had >78% positivity. Using larger PCR input volumes (≥7 μL) was associated with the highest sensitivity at 95.5% compared to 58.3% when lower input volumes were used (P < 0.01). Using larger sample volumes for nucleic acid extraction and DNA template volumes for PCR amplification significantly improves the performance of Mucorales qPCR when testing serum. IMPORTANCE: Mucormycosis is a life-threatening mold infection affecting immunosuppressed patients but also other patients with diabetes or trauma. Better survival is linked to shorter delays in diagnosis and treatment initiation. Detection of Mucorales-free DNA in serum or plasma using quantitative PCR allows a prompt diagnosis and earlier treatment. Several techniques and protocols of quantitative Mucorales PCR are used in Europe, and improving performance remains a common objective of laboratories participating in the fungal PCR Initiative Working Group. This study, which combined results from 26 laboratories in Europe, showed that the main parameters underpinning sensitivity are the preanalytical variables (volume of serum used for DNA extraction and DNA template volume), irrespective of the extraction platforms and qPCR assay/platform.
- MeSH
- Molecular Diagnostic Techniques standards methods MeSH
- DNA, Fungal * blood genetics MeSH
- Real-Time Polymerase Chain Reaction * standards methods MeSH
- Humans MeSH
- Mucorales * genetics isolation & purification MeSH
- Mucormycosis * diagnosis microbiology blood MeSH
- Sensitivity and Specificity * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Evaluation Study MeSH
The largest obstacle in the promotion of biopesticides is the existence of counterfeit products available in the market. Identification and quantification of antagonistic organisms in biopesticide products are the key to the reduction of spurious microbial pesticides. In this study, we have developed a simple, sensitive, isothermal-based colourimetric assay for specific detection of Bacillus subtilis from the biopesticide formulations and soil samples. A region specific to B. subtilis which codes for shikimate dehydrogenase was identified through in silico analysis. We employed conventional PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and qPCR for specific detection of B. subtilis in soil samples and biopesticide formulations. Specificity tests showed that the PCR primers amplified an amplicon of 521 bp in four strains of B. subtilis only, and no amplification was found in negative control samples. Similarly, the LAMP assay showed sky blue colour in all four strains of B. subtilis and violet colour in negative control samples. Whereas in the RPA assay, upon the addition of SYBR Green dye, a bright green colour was seen in B. subtilis strains, while a brick-red colour was observed in negative control samples by visualizing under a UV transilluminator. The qPCR assay showed specific amplifications with a Ct value of 12 for B. subtilis strains and no amplification in negative control samples. In the sensitivity test, PCR could amplify DNA of B. subtilis up to 500 pg/μL. DNA concentration as low as 10 pg/μL was enough to show the colour change in the LAMP as well as the RPA assays, whereas the qPCR assay showed sensitivity till 100 pg/μL. All four diagnostic assays developed in the study have been validated in soil samples and B. subtilis-based biopesticides. Compared to conventional PCR, the qPCR assay has the advantage of quantification and visualizing the result in real-time, whereas LAMP and RPA assays have the benefits of being colourimetric and less time-consuming. The other advantages are that the results can be visualized with the naked eye, and these assays do not require a costly thermal cycler and gel documentation system. Hence, LAMP and RPA assays are highly suitable for developing point-of-need diagnostic kits and, in turn, help regulators assess the quality of biopesticides in the market.
- MeSH
- Alcohol Oxidoreductases * genetics MeSH
- Bacillus subtilis * genetics isolation & purification enzymology MeSH
- Bacterial Proteins genetics MeSH
- Molecular Diagnostic Techniques * methods MeSH
- Colorimetry * methods MeSH
- Real-Time Polymerase Chain Reaction MeSH
- Soil Microbiology MeSH
- Sensitivity and Specificity MeSH
- Nucleic Acid Amplification Techniques * methods MeSH
- Publication type
- Journal Article MeSH
BACKGROUND: Severe combined immunodeficiency (SCID) is a fatal but treatable inborn error of immunity (IEI). Newborn screening (NBS) using T-cell receptor excision circles (TREC) has been adopted globally, with very few countries incorporating kappa recombination excision circles (KREC) to also detect early B-cell development disorders, such as X-linked agammaglobulinemia (XLA). OBJECTIVE: To evaluate the effectiveness of a 2-year pilot SCID NBS program in the Czech Republic, emphasising the utility of combined TREC/KREC screening. METHODS: Between January 2022 and December 2023, a dual TREC/KREC NBS pilot was conducted across the Czech Republic, alongside spinal muscular atrophy (SMA) screening. Approximately 200,000 newborns were screened using quantitative real-time PCR on dried blood spots collected 48-72 h after birth. RESULTS: The pilot referred 58 newborns, identifying 21 cases of IEI, including two SCID cases, with an overall incidence of TREC/KREC screenable IEI of 10.5/100,000 newborns. SCID incidence was 1/100,000. KREC screening proved invaluable, detecting 10 cases of congenital agammaglobulinemia including novel non-XLA forms, which increased the estimated incidence of agammaglobulinemia in the Czech Republic sixfold. Over one-third of low KREC results were linked to maternal immunosuppression. CONCLUSION: The Czech pilot demonstrated the effectiveness of integrated TREC/KREC NBS in detecting both T- and B-cell immunodeficiencies. As of 2024, SCID and SMA screening are included in the nationwide NBS, with KREC screening significantly improving early detection of B-cell disorders.
- MeSH
- Agammaglobulinemia diagnosis MeSH
- B-Lymphocytes immunology MeSH
- Genetic Diseases, X-Linked MeSH
- Humans MeSH
- Infant, Newborn MeSH
- Neonatal Screening * methods MeSH
- Pilot Projects MeSH
- Receptors, Antigen, T-Cell * genetics MeSH
- Severe Combined Immunodeficiency * diagnosis genetics epidemiology MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Infant, Newborn MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Bats are the natural reservoirs for a variety of emerging and re-emerging viruses. Among them, rabies virus (genus Lyssavirus, family Rhabdoviridae) is one of the first and most emblematic described in these animals. Since its first description, several new bat lyssaviruses have been regularly identified. In addition to lyssaviruses, other bat rhabdoviruses have also been discovered, including members of the genera Vesiculovirus, Ledantevirus and, more recently, Alphanemrhavirus and Tupavirus. However, the family Rhabdoviridae is one of the most abundant and diverse viral families, with 434 officially recognized species, divided into 5 subfamilies and 56 different genera. The number of rhabdoviruses associated with bats is therefore probably higher than that currently available. In this study, we first developed and validated a combined nested RT-qPCR technique (pan-rhabdo RT-nqPCR) dedicated to the broad detection of animal rhabdoviruses. After validation, this technique was used for a large retrospective screening of archival bat samples (n = 1962), including blood (n = 816), brain (n = 723) and oral swab (n = 423). These samples were collected from various bat species over a 12-year period (2007-2019) in 9 different countries in Europe and Africa. A total of 23 samples (1.2%) from bat species Miniopterus schreibersii, Rhinolophus euryale and Rhinolophus ferrumequinum tested positive for rhabdovirus infection, including 17 (2.1%) blood and 6 (1.4%) oral swab samples, all collected from bats originating from the Mediterranean region. Complete virus genome sequences were obtained by next-generation sequencing for most of the positive samples. Molecular and phylogenetic analysis of these sequences demonstrated that the virus isolates, named Mediterranean bat virus (MBV), were closely related and represented a new species, Mediterranean vesiculovirus, within the genus Vesiculovirus. MBV was more specifically related to other bat vesiculoviruses previously described from China and North America, together clustering into a distinct group of bat viruses within this genus. Interestingly, our results suggest that MBV is widespread, at least in the western part of the Mediterranean region, where it circulates in the blood of several bat species. These results expand the host range and viral diversity of bat vesiculoviruses, and pave the way for further studies to determine the transmission route and dissemination dynamics of these viruses in bat colonies, as well as to assess their potential threat to public health.
- MeSH
- Chiroptera * virology MeSH
- Phylogeny MeSH
- Genome, Viral MeSH
- Rhabdoviridae Infections * veterinary epidemiology virology MeSH
- Real-Time Polymerase Chain Reaction MeSH
- Vesiculovirus * genetics isolation & purification classification MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Mediterranean Region MeSH
BACKGROUND: The progression and recurrence are the fatal prognostic factors in glioma patients. However, the therapeutic role and potential mechanism of TRAF7 in glioma patients remain largely unknown. METHODS: TRAF7 RNA-seq was analysed with the TCGA and CGGA databases between glioma tissues and normal brain tissues. The expression of TRAF7, cellular senescence and cell cycle arrest pathways in glioma tissues and cell lines was detected by real-time quantitative PCR (RT-qPCR), western blotting and immunohistochemistry. The interaction between TRAF7 and KLF4 was determined by Co-immunoprecipitation (Co-IP) assays. The functions of TRAF7 combined with lomustine in glioma were assessed by both in vitro, in vivo and patient-derived primary and recurrent glioma stem cell (GSC) assays. RESULTS: High TRAF7 expression is closely associated with a higher recurrence rate and poorer overall survival (OS). In vitro, TRAF7 knockdown significantly inhibits glioma cell proliferation, invasion, and migration. RNA-seq analysis revealed that TRAF7 inhibition activates pathways related to cellular senescence and cell cycle arrest. In both in vitro and patient-derived GSC assays, the combination of sh-TRAF7 and lomustine enhanced therapeutic efficacy by inducing senescence and G0/G1 cell cycle arrest, surpassing the effects of lomustine or TRAF7 inhibition alone. Mechanistically, TRAF7 interacts with KLF4, and a rescue assay demonstrated that KLF4 overexpression could reverse the effects of TRAF7 depletion on proliferation and cellular senescence. In vivo, TRAF7 knockdown combined with lomustine treatment effectively suppressed glioma growth. CONCLUSION: TRAF7 could be used as a predictive biomarker and the potential therapeutic target among National Comprehensive Cancer Network (NCCN) treatment guidelines in the progression and recurrence of glioma. Lomustine, regulating cellular senescence and cell cycle could be the priority choice in glioma patients with high-level TRAF7 expression.
- MeSH
- Gene Knockdown Techniques MeSH
- Glioma * pathology genetics drug therapy metabolism MeSH
- Kruppel-Like Factor 4 MeSH
- Humans MeSH
- Neoplasm Recurrence, Local * genetics pathology MeSH
- Lomustine * pharmacology therapeutic use MeSH
- Mice MeSH
- Cell Line, Tumor MeSH
- Brain Neoplasms * pathology genetics drug therapy metabolism MeSH
- Tumor Necrosis Factor Receptor-Associated Peptides and Proteins * genetics metabolism MeSH
- Prognosis MeSH
- Disease Progression MeSH
- Cell Proliferation MeSH
- Gene Expression Regulation, Neoplastic MeSH
- Cellular Senescence * drug effects MeSH
- Xenograft Model Antitumor Assays MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Mice MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
OBJECTIVES: The aim of the study was to evaluate the efficiency of molecular diagnostics of tick-borne encephalitis (TBE) and to correlate viral RNA (vRNA) detection with the clinical and laboratory data. METHODS: Clinical samples from 1125 patients from South Bohemia, Czech Republic, a highly endemic TBE region, were screened for TBE virus (TBEV) RNA by RT-qPCR. Samples included blood, serum, cerebrospinal fluid (CSF), and urine. RESULTS: TBEV RNA was detected in 14 patients with clinically proven TBE. TBEV RNA was most frequently detected in sera during early infection (11/37 patients tested, 29.7%) but decreased with rising IgG antibody response (3/228, 1.3%). Detection in CSF and urine was infrequent (1/30, 3.3% and 1/52, 1.9%, respectively). Additionally, five patients initially not diagnosed with TBE were retrospectively found to have TBEV RNA in serum, indicating possible underdiagnosis, particularly in mild or atypical presentations. The study also highlighted the diagnostic challenge of an immunocompromised patient whose delayed antibody response hindered timely diagnosis. In such cases, RT-qPCR could significantly shorten the diagnostic timeline. CONCLUSIONS: These findings underscore the value of early RNA detection in improving the diagnosis of TBE and may in the future facilitate the early administration of potential treatment, thereby improving patient outcomes.
- MeSH
- Molecular Diagnostic Techniques methods MeSH
- Child MeSH
- Adult MeSH
- Immunoglobulin G blood MeSH
- Encephalitis, Tick-Borne * diagnosis virology MeSH
- Real-Time Polymerase Chain Reaction MeSH
- Middle Aged MeSH
- Humans MeSH
- Adolescent MeSH
- Young Adult MeSH
- Child, Preschool MeSH
- Antibodies, Viral blood MeSH
- RNA, Viral * blood cerebrospinal fluid isolation & purification MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Encephalitis Viruses, Tick-Borne * isolation & purification genetics MeSH
- Check Tag
- Child MeSH
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Adolescent MeSH
- Young Adult MeSH
- Male MeSH
- Child, Preschool MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Applications like drug development need simple and streamlined methods to process samples from 96-well cell culture plates for gene expression measurements. Unfortunately, current options are expensive for such processing. Therefore, our aim was to develop a method that would allow streamlined analysis of mRNA from 96-well cell culture plates while being relatively cheap and simple. We developed a method based on the qPCR 'Cells-to-cDNA' approach and validated it against commercially available kits using the same approach or spin columns-based RNA purification. For this purpose, we conducted a series of comparisons of gene expression from peripheral blood mononuclear cells, SK-HEP-1 and U-87 cell cultures in 96-well plates. Our final method involved lysing cells with 25-100 μl solution of 0.5% SDS, 10 mM DTT, 1 mg ml-1 proteinase K dissolved in water, 1 h incubation at 50°C, followed by proteinase K inactivation at 90°C for 5 min and lysate neutralization with 1 : 1 dilution by 20% Tween 20 solution. Reverse transcription and qPCR were carried out using standard methods. This method showed a mean reduction of Ct ± s.d. value by 2.4 ± 1.3 compared with the 'Cells-to-cDNA' kit and by 1.4 ± 0.5 compared with the RNA purification kit with lower variability.
- MeSH
- Cost-Benefit Analysis MeSH
- Cell Culture Techniques methods economics MeSH
- DNA, Complementary * genetics MeSH
- Real-Time Polymerase Chain Reaction methods MeSH
- Leukocytes, Mononuclear cytology metabolism MeSH
- Humans MeSH
- RNA, Messenger genetics metabolism MeSH
- Cell Line, Tumor MeSH
- Gene Expression Profiling methods economics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
Aging and age-related neurodegenerative disorders are characterized by the dysfunction or loss of brain nicotinic acetylcholine receptors (nAChRs), and these changes may be related to other senescence markers, such as oxidative stress and DNA repair dysfunction. However, the mechanism of nAChR loss in the aging brain and the modification of this process by drugs (e.g., memantine, Mem) are not yet fully understood. To study whether the differences in nAChR expression in the rat brain occur due to aging or oxidative stress and are modulated by Mem, we analyzed nAChR subunits (at RNA and protein levels) and other biomarkers by real-time quantitative polymerase chain reaction (RQ-PCR) and Western blot validation. Twenty-one female Wistar rats were divided into four groups, depending on age, and the oldest group received injections of Mem or water with the use of intragastric catheters. We studied the cerebral grey matter (CGM), subcortical white matter (SCWM), and cerebellum (Ce). Results showed an age-related decrease of α7 nAChR mRNA level in SCWM. The α7 nAChR mRNA loss was accompanied by reduced expression of 8-oxoguanine DNA glycosylase 1 (OGG1) and an increased tumor necrosis factor alpha (TNFα) level. In the water group, we observed a higher level of α7 nAChR protein in the SCWM and Ce. Biomarker levels changed, but to a different extent depending on the brain area. Importantly, the dysfunction in antioxidative status was stopped and even regressed under Mem treatment. After two weeks of treatment, an increase in TP53 protein level and a decrease in 8-oxo-2'deoxyguanosine (8-oxo-2'dG) level were observed. We conclude that Mem administration may be protective against the senescence process by antioxidative mechanisms.
- MeSH
- alpha7 Nicotinic Acetylcholine Receptor metabolism genetics MeSH
- DNA Glycosylases metabolism genetics MeSH
- Rats MeSH
- Memantine * pharmacology MeSH
- Brain * metabolism drug effects pathology MeSH
- Neurons metabolism drug effects MeSH
- Receptors, Nicotinic * metabolism genetics MeSH
- Oxidative Stress * drug effects MeSH
- DNA Damage * drug effects MeSH
- Rats, Wistar * MeSH
- Aging * metabolism MeSH
- Animals MeSH
- Check Tag
- Rats MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
A huge number of inbred mouse strains with different bone properties have become available for musculoskeletal research. C57Bl/6J and C3H/HeOuJ mice show a significant difference in their bone characteristics. Nevertheless, there is a lack of knowledge on the molecular basis of these strain differences. The aim of this study is to determine the gene expression of selected regulators expressed in the bone marrow as well as bone microstructure of C57Bl/6J and C3H/HeOuJ mice. Bone properties were investigated in 20-week-old female C57Bl/6J and C3H/HeOuJ mice. Total RNA was extracted from the bone marrow of the tibia and gene expression of the following genes was determined by quantitative real-time PCR: SOST, DKK1, OPN, FGF23, RANKL, IL6, TNF, IL17a, and OPG. The femur and third lumbar vertebral body (L3) were investigated by μCT. Bone histomorphometric evaluations were performed in tartrate-resistant acid phosphatase/toluidine blue stained fourth lumbar vertebral bodies (L4). C57Bl/6J and C3H/HeOuJ mice showed significant differences in the gene expression of DKK1, FGF23, IL-6, TNF, and OPG. When compared with C57Bl/6J mice, C3H/HeOuJ mice had a stronger cortical and trabecular bone microstructure at the femur. In contrast, at L3 bone volume/total volume (BV/TV) and trabecular number were significantly higher in C57Bl/6J than in C3H/HeOuJ mice. Bone histomorphometry of L4 revealed significantly higher BV/TV, trabecular number, and thickness in C57Bl/6J mice. Furthermore, the number of osteoblasts and the number of osteoclasts/bone perimeter were higher in the C57Bl/6J mice. This study shows that C57Bl/6J and C3H/HeOuJ mice exhibit a differential expression of cytokines present in the bone marrow. Bone properties differ not only between both strains but also in relation to the investigated bone region.
- Publication type
- Journal Article MeSH
PURPOSE: This study aimed to evaluate early-phase safety of subretinal application of AAVanc80.CAG.USH1Ca1 (OT_USH_101) in wild-type (WT) pigs, examining the effects of a vehicle control, low dose, and high dose. METHODS: Twelve WT pigs (24 eyes) were divided into three groups: four pigs each received bilateral subretinal injections of either vehicle, low dose (3.3 × 1010 vector genomes [vg] per eye), or high dose (1.0 × 1011 vg per eye). Total retinal thickness (TRT) was evaluated using optical coherence tomography and retinal function was assessed with full-field electroretinography (ff-ERG) at baseline and two months post-surgery. After necropsy, retinal changes were examined through histopathology, and human USH1C_a1/harmonin expression was assessed by quantitative PCR (qPCR) and Western blotting. RESULTS: OT_USH_101 led to high USH1C_a1 expression in WT pig retinas without significant TRT changes two months after subretinal injection. The qPCR revealed expression of the human USH1C_a1 transgene delivered by the adeno-associated virus vector. TRT changes were minimal across groups: vehicle (256 ± 21 to 243 ± 18 μm; P = 0.108), low dose (251 ± 32 to 258 ± 30 μm; P = 0.076), and high dose (242 ± 24 to 259 ± 28 μm; P = 0.590). The ff-ERG showed no significant changes in rod or cone responses. Histopathology indicated no severe retinal adverse effects in the vehicle and low dose groups. CONCLUSIONS: Early-phase clinical imaging, electrophysiology, and histopathological assessments indicated that subretinal administration of OT_USH_101 was well tolerated in the low-dose treatment arm. OT_USH_101 treatment resulted in high expression of human USH1C_a1. Although histopathological changes were not severe, more frequent changes were observed in the high-dose group.
- MeSH
- Cytoskeletal Proteins genetics MeSH
- Dependovirus genetics MeSH
- Electroretinography * MeSH
- Genetic Therapy methods MeSH
- Genetic Vectors * MeSH
- Injections, Intraocular * MeSH
- Real-Time Polymerase Chain Reaction MeSH
- Humans MeSH
- Disease Models, Animal MeSH
- Tomography, Optical Coherence * MeSH
- Swine MeSH
- Cell Cycle Proteins genetics MeSH
- Gene Expression Regulation MeSH
- Retina * metabolism pathology MeSH
- Transgenes * MeSH
- Blotting, Western MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
