Search Results (10)

Reverse transcriptases (RT) are essential tools in BCR::ABL1 fusion transcript monitoring in chronic myeloid leukemia (CML). The RT type and cDNA priming method may impair the stoichiometry of cDNA synthesis, thereby potentially introducing a bias in BCR::ABL1 qRT-PCR data. Using the Acrometrix™ BCR::ABL1 reference panel and 37 clinical specimens, we have comparatively investigated the performance of the RTs MLV and SuperScript IV with random hexamer vs. target-specific priming. Quantitative RT-PCR results identified the priming type and RT type as major factors for diagnostic data variation, mainly due to the different efficacies of processing BCR::ABL1 low-copy-numbers (<50) compared to GUSB or ABL1 high-copy targets. The impairment of SuperScript IV in processing low- and high-copy-number RNA targets equally was not reflected by the diagnostically relevant Log (BCR::ABL1/GUSB%) values. Therefore, the correct representation of housekeeping and BCR::ABL1 target genes should have priority when aiming at as high a number of housekeeping gene copies as possible. Our data suggest that for improving BCR::ABL1 assay sensitivity, increased RNA/cDNA amounts and the use of distinct RT/priming combinations are advantageous. However, for inter-laboratory harmonization, the proper conversion factor according to the CML international standard (IS) has to be reevaluated each time the grade of RT is changed. Full article

RNA purification and cDNA synthesis represents the starting point for molecular analyses of snake venom proteins-enzymes. Usually, the sacrifice of snakes is necessary for venom gland extraction to identify protein-coding transcripts; however, the venom can be used as a source of transcripts. Although there are methods for obtaining RNA from venom, no comparative analysis has been conducted in the Bothrops genus. In the present study, we compared four commercial methods for RNA purification and cDNA synthesis from venom (liquid, lyophilized, or long-term storage) of four clinically relevant species of Peruvian Bothrops. Our results show that the TRIzol method presents the highest yield of RNA purified from venom (59 ± 11 ng/100 µL or 10 mg). The SuperScript First-Strand Synthesis System kit produced high amounts of cDNA (3.2 ± 1.2 ng cDNA/ng RNA), and the highest value was from combination with the Dynabeads mRNA DIRECT kit (4.8 ± 2.0 ng cDNA/ng RNA). The utility of cDNA was demonstrated with the amplification of six relevant toxins: thrombin-like enzymes, P-I and P-III metalloproteinases, acid and basic phospholipases A2, and disintegrins. To our knowledge, this is the first comparative study of RNA purification and cDNA synthesis methodologies from Bothrops genus venom. Full article

The treatment and outcome of respiratory virus infections differ. SARS-CoV-2, as well as other respiratory viruses such as influenza virus (A and B) and respiratory syncytial virus (RSV), require simultaneous, cost-effective, and rapid differential detection. We used a gold standard five-target single-step RT-PCR to detect influenza viruses, RSV, and SARS-CoV-2, and this method can be extended to detect influenza virus subtypes. As a result, this five-target single-step RT-PCR method is ideal for differentiating respiratory viruses. The 5’ nuclease activity of Taq DNA polymerase is used in the real-time reverse transcription PCR assay. The Taq man fast viral 1-step enzyme is a 4× Master mix and five-target primer probe mix that detects influenza A, influenza B, SARS-CoV-2 ORF1ab, respiratory syncytial viruses A/B and actin. When compared with TaqMan ^TM and Invitrogen superscript ^TM III Platinum and the Meril Kit for SARS-CoV-2, the assay demonstrated 100% sensitivity, specificity, and amplification efficiency of 90.1% for target genes. In conclusion, our one-tube multiplex RT-PCR assay offers a rapid and reliable method for the simultaneous detection of influenza A/B, RSV, and SARS-CoV-2 from nasopharyngeal swabs. This assay has the potential to enhance diagnostic capabilities and improve public health responses during respiratory outbreaks, enabling timely interventions and informed decision making. Full article

Chemical probing, for decades, has been one of the most popular tools for studying the secondary structure of RNA molecules. Recently, protocols for simultaneous analysis of multiple RNAs have been developed, enabling in vivo transcriptome-wide interrogation of the RNA structure dynamics. One of the most popular methods is the selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP). In this study, we describe the evaluation of this protocol by addressing the influence of the reverse transcription enzymes, buffer conditions, and chemical probes on the properties of the cDNA library and the quality of mutational profiling-derived structural signals. Our results reveal a SuperScript IV (SSIV) reverse transcriptase as a more efficient enzyme for mutational profiling of SHAPE adducts and shed new light on the role of Mn²⁺ cations in the modulation of SSIV readthrough efficiency. Full article

Reverse transcriptases (RTs) are a family of enzymes synthesizing DNA using RNA as a template and serving as indispensable tools in studies related to RNA. M-MuLV RT and its analogs are the most commonly used RTs. RTs are widely applied in various diagnostics methods, including reverse-transcription loop-mediated isothermal amplification (RT-LAMP). However, the performance of different RTs in LAMP remains relatively unknown. Here, we report on the first direct comparison of various M-MuLV RTs in RT-LAMP, including enzymes with a different number of mutations and fusions with Sto7d. Several parameters were assessed, namely: optimal reaction temperature, enzyme concentration, reverse transcription time, a minimal amount of RNA template, and tolerance to inhibitors. Mutations increased the optimal reaction temperature from 55 °C to 60–65 °C. All of the RTs were suitable for RT-LAMP with RNA templates in the range of 10¹–10⁶ copies per reaction. Highly mutated enzymes were 1.5–3-fold more tolerant to whole blood, blood plasma, and guanidinium, but they were two-fold more sensitive to high concentrations of NaCl. The comparison of different RTs presented here could be helpful for selecting the optimal enzyme when developing novel LAMP-based diagnostic tests. Full article

Metallothioneins (MTs) are low molecular weight cysteine-rich proteins that can bind up to seven zinc ions. Among their numerous functions, MTs appear to act as protectors against oxidative and inflammatory injury. In our first published study, we reported downregulation of the isoforms MT1B (fold distance (FD) −2. 95; p = 0.0024), MT1F (FD −1.72; p = 0.0276), MT1X (FD −3.09; p = 0.0021), MT1H (FD −2.39; p = 0.0018), MT1M (FD −2.37; p = 0.0092), MT1L (FD −2. 55; p = 0.0048), MT1E (FD −2.71; p = 0.0014), MT2A (FD −2.35; p = 0.0072), MT1G (FD −2.24; p = 0.0118), and MT1A (FD −2.82; p = 0.0023) by comparing Down’s syndrome patients with periodontal disease and implant failure to those without periodontal disease and with a positive progression of their implants. In this gene validation study, we intended to verify the results of our first gene expression analysis. Materials and Methods: In our retrospective case–control study, we performed retrotranscription (RT-qPCR) of 11 RNA-to-cDNA samples using the SuperScript™ VILO™ kit (50; reference 1,176,605) from Thermo Fisher. We conducted the study using the real-time PCR technique on the q-PCR ViiA 7 platform from Thermo Fisher. We chose the format of the Taqman Array Plate 16 Plus (reference 4,413,261) from Thermo Fisher, which accommodates 12 genes plus four controls (GAPDH, 18S, ACTB, and HPRT1). We conducted the analysis of the plates using the Thermo Fisher Cloud Web Software. Results: The results obtained through gene validation analysis show that in PD+RI+ patients, the genes encoding the isoforms MT1F (FD 0.3; p = 0.039), MT1X (FD 338; p = 0.0078), MT1E (FD 307; p = 0.0358), and MT2A (FD 252; p = 0.0428) continue to show downregulation, whereas MT1B (FD 2.75; p = 0.580), MT1H (FD 281; p = 0.152), MT1L (FD 354; p = 0.0965), and MT1G (FD 336; p = 0.0749) no longer show statistically significant results. Full article

The objective of this work was to analyze the effect of carbon support on the activity and selectivity of N-doped TiO₂ nanoparticles. Thus, N-doped TiO₂ and two types of composites, N-doped TiO₂/CNT and N-doped TiO₂/rGO, were prepared by a new environmentally friendly one-pot method. CNT and rGO were used as supports, triethylamine and urea as N doping agents, and titanium (IV) tetraisopropoxide and ethanol as Ti precursor and hydrolysis agent, respectively. The as-prepared photocatalysts exhibited enhanced photocatalytic performance compared to TiO₂ P25 commercial catalyst during the photoreduction of CO₂ with water vapor. It was imputed to the synergistic effect of N doping (reduction of semiconductor band gap energy) and carbon support (enlarging e⁻-h⁺ recombination time). The activity and selectivity of catalysts varied depending on the investigated material. Thus, whereas N-doped TiO₂ nanoparticles led to a gaseous mixture, where CH₄ formed the majority compared to CO, N-doped TiO₂/CNT and N-doped TiO₂/rGO composites almost exclusively generated CO. Regarding the activity of the catalysts, the highest production rates of CO (8 µmol/gTiO₂/h) and CH₄ (4 µmol/gTiO₂/h) were achieved with composite N¹/TiO₂/rGO and N¹/TiO₂ nanoparticles, respectively, where superscript represents the ratio mg N/g TiO₂. These rates are four times and almost forty times higher than the CO and CH₄ production rates observed with commercial TiO₂ P25. Full article

A methylene blue (MB) indicator embedded in sodium alginate (SA) film was previously examined for detecting active oxygen species. In a previous study, spectrometry was used to identify and characterize the MB/SA complex. However, the decolorization mechanism was not fully assessed. In this study, our aim is to conduct computational calculations at the B3LYP/6-31G(d) level to clarify the exact types and positions of the interaction that cause the decolorization in MB. The results demonstrate that MB/SA interacts with carboxylates (-COO(superscript)-(superscript)) of SA and the N, C, and S atoms of MB, confirming previous experimental observations. Full article

The morphology and crystallization behavior of two triblock terpolymers of polymethylene, equivalent to polyethylene (PE), poly (ethylene oxide) (PEO), and poly (ε-caprolactone) (PCL) are studied: PE₂₂^7.1-b-PEO₄₆^15.1-b-PCL₃₂^10.4 (T1) and PE₃₇^9.5-b-PEO₃₄^8.8-b-PCL₂₉^7.6 (T2) (superscripts give number average molecular weights in kg/mol and subscripts composition in wt %). The three blocks are potentially crystallizable, and the triple crystalline nature of the samples is investigated. Polyhomologation (C1 polymerization), ring-opening polymerization, and catalyst-switch strategies were combined to synthesize the triblock terpolymers. In addition, the corresponding PE-b-PEO diblock copolymers and PE homopolymers were also analyzed. The crystallization sequence of the blocks was determined via three independent but complementary techniques: differential scanning calorimetry (DSC), in situ SAXS/WAXS (small angle X-ray scattering/wide angle X-ray scattering), and polarized light optical microscopy (PLOM). The two terpolymers (T1 and T2) are weakly phase segregated in the melt according to SAXS. DSC and WAXS results demonstrate that in both triblock terpolymers the crystallization process starts with the PE block, continues with the PCL block, and ends with the PEO block. Hence triple crystalline materials are obtained. The crystallization of the PCL and the PEO block is coincident (i.e., it overlaps); however, WAXS and PLOM experiments can identify both transitions. In addition, PLOM shows a spherulitic morphology for the PE homopolymer and the T1 precursor diblock copolymer, while the other systems appear as non-spherulitic or microspherulitic at the last stage of the crystallization process. The complicated crystallization of tricrystalline triblock terpolymers can only be fully grasped when DSC, WAXS, and PLOM experiments are combined. This knowledge is fundamental to tailor the properties of these complex but fascinating materials. Full article

Facioscapulohumeral muscular dystrophy (FSHD) is believed to be caused by aberrant expression of double homeobox 4 (DUX4) due to epigenetic changes of the D4Z4 region at chromosome 4q35. Detecting DUX4 is challenging due to its stochastic expression pattern and low transcription level. In this study, we examined different cDNA synthesis strategies and the sensitivity for DUX4 detection. In addition, we investigated the effects of dexamethasone and knockout serum replacement (KOSR) on DUX4 expression in culture. Our data showed that DUX4 was consistently detected in cDNA samples synthesized using Superscript III. The sensitivity of DUX4 detection was higher in the samples synthesized using oligo(dT) primers compared to random hexamers. Adding dexamethasone to the culture media significantly suppressed DUX4 expression in immortalized (1.3 fold, p < 0.01) and primary (4.7 fold, p < 0.01) FSHD myoblasts, respectively. Culture medium with KOSR increased DUX4 expression and the response is concentration dependent. The findings suggest that detection strategies and culture conditions should be carefully considered when studying DUX4 in cultured cells. Full article