Methods and Protocols最新文献

This differential extraction protocol details the steps for isolating DNA from sample pads used in lateral flow immunochromatographic (LFI) tests, particularly for cases involving mixed biological samples such as semen and menstrual blood, or other evidence related to sexual assault. This procedure utilizes a differential extraction technique applied to sample pads from immunochromatographic tests, where the sample pads serve as the substrate. The method involves two sequential lysis steps to effectively separate non-sperm and sperm fractions, enabling the targeted isolation of distinct cell types for downstream DNA analysis. The efficiency of this procedure is demonstrated by the results within this paper, which highlights the successful recovery of both male autosomal and Y-STR profiles, even in mixed samples with a high female presence. Overall, this protocol demonstrates the effective recovery of DNA from sample pads, which is beneficial for forensic practitioners dealing with limited sample quantities, underscoring the value of using these pads in forensic analysis.

Culex pipiens is a major vector of pathogens, including West Nile and Usutu viruses, that poses a significant public health risk. Monitoring pyrethroid resistance in mosquito populations is essential for effective vector control. This study aims to evaluate four DNA extraction protocols-QIAsymphony, DNAzol^® Direct reagent, PrepMan^® Ultra Sample Preparation Reagent (USPR), and Chelex^® 100-to identify an optimal method to extract DNA from individual Culex pipiens, as part of a high-throughput surveillance of pyrethroid resistance using Real-Time Genotyping PCR. The target is the L1014F mutation in the voltage-sensitive sodium channel (VSSC) gene, which confers knockdown (kdr) resistance to pyrethroids. Mosquitoes were collected from wintering and summer habitats in Lazio and Tuscany, Italy, and DNA was extracted using the four methods. The quality, quantity, extraction time, and cost of the DNA were compared among the various methods. The PrepMan^® USPR protocol was the most efficient, providing high-quality DNA with a 260/280 purity ratio within the optimal range at the lowest cost and in a short time. This method also demonstrated the highest amplification success rate (77%) in subsequent real-time PCR assays, making it the preferred protocol for large-scale genotyping studies.

Recommendations released by the CDC in 2023 address the need to demonstrate that the RNA genome of positive-strand RNA viruses is inactivated in addition to viral particles. This recommendation is in response to the similarities between host mRNA and the viral genome that allow the viral RNA to be used as a template by host replication mechanisms to produce infectious viruses; therefore, there is concern that through artificial introduction into host cells, active positive-strand RNA genomes can be utilized to produce infectious viruses out of a containment facility. Utilizing 10% formalin for 7 days or 2.5% glutaraldehyde/2% paraformaldehyde in 0.1 M cacodylate buffer (glut/PFA) for 2 days to fix eastern equine encephalitis virus (EEEV)-infected non-human primate (NHP) brain tissue was found to effectively inactivate EEEV particles and genomic RNA. The methods assessed in this paper outline an effective means to validate both genomic RNA and viral particle inactivation.

The accurate measurement of spatiotemporal parameters, such as step length and step frequency, is crucial for analyzing running and sprinting performance. Traditional methods like video analysis and force platforms are either time consuming or limited in scope, prompting the need for more efficient technologies. This study evaluates the effectiveness of a commercial Global Positioning System (GPS) unit integrated with an Inertial Measurement Unit (IMU) in capturing these parameters during sprints at varying velocities. Five experienced male runners performed six 40 m sprints at three velocity conditions (S: Slow, M: Medium, F: Fast) while equipped with a GPS-IMU system and an optical system as the gold standard reference. A total of 398 steps were analyzed for this study. Step frequency, step length and step velocity were extracted and compared using statistical methods, including the coefficient of determination (r²) and root mean square error (RMSE). Results indicated a very large agreement between the embedded system and the reference system, for the step frequency (r² = 0.92, RMSE = 0.14 Hz), for the step length (r² = 0.91, RMSE = 0.07 m) and the step velocity (r² = 0.99, RMSE = 0.17 m/s). The GPS-IMU system accurately measured spatiotemporal parameters across different running velocities, demonstrating low relative errors and high precision. This study demonstrates that GPS-IMU systems can provide comprehensive spatiotemporal data, making them valuable for both training and competition. The integration of these technologies offers practical benefits, helping coaches better understand and enhance running performance. Future improvements in sample rate acquisition GPS-IMU technology could further increase measurement accuracy and expand its application in elite sports.

High-grade serous ovarian cancer (HGSOC) remains the most lethal gynecological malignancy, and there is still an unmet medical need to deepen basic research on its origins and mechanisms of progression. Patient-derived organoids of high-grade serous ovarian cancer (HGSOC-PDO) are a powerful model to study the complexity of ovarian cancer as they maintain, in vitro, the mutational profile and cellular architecture of the cancer tissue. Genetic modifications by lentiviral transduction allow novel insights into signaling pathways and the potential identification of biomarkers regarding the evolution of drug resistance. Here, we provide an in-depth and detailed protocol to successfully modify the gene expression of HGSOC-PDOs by lentiviral transduction. As an example, we validate our protocol and create a stable knockdown of the MACC1 oncogene with an efficacy of ≥72% in two HGSOC-PDO lines, which remained stable for >3 months in culture. Moreover, we explain step-by-step the sample preparation for the validation procedures on transcriptional (qPCR) and protein (Western Blot) levels. Sustained downregulation of specific genes by lentiviral transduction enables the analysis of the resulting phenotypic and morphological changes. It serves as a valuable in-vitro model to study the mechanisms of ovarian cancer pathogenesis and allows for the evaluation of therapeutic approaches.

An electrochemical investigation of 1,2- and 1,4-dihydroxybenzenes was carried out with platinum macro- and microelectrodes using square wave and cyclic voltammetry techniques. Furthermore, the effect of the two solvents-acetic acid and ethyl acetate-was compared. When using square wave voltammetry, signals only appeared at lower frequencies and only when the supporting electrolyte was in excess, as expected due to the relatively low permittivity of the used solvents. The behavior of hydroquinone and catechol did not differ significantly from that of their derivatives (dihydroxybenzaldehydes, dihydroxybenzoic acids and 2',5'-dihydroxyacetophenone). When the cyclic voltammetric experiments using a microelectrode were extended to higher anodic potentials, electrode fouling was very significant in ethyl acetate after the potential region where steady-state oxidation to the corresponding quinone occurs. The substituent effect was not significant here either, which was proven by using different functional groups in different positions. In contrast, the position had a dramatic influence on the susceptibility to electropolymerization, as 1,2-dihydroxybenzenes-independent of the nature of the substituent on the benzene ring-deactivated the electrode, while 1,4-dihydroxybenzenes did not, possibly due to the different solubilities of the polymers formed from the primary oxidation product (quinones). A user-friendly analytical procedure is also proposed that uses an electropolymerization reaction and does not require frequent cleaning of the electrode via polishing, which is required usually especially with a microelectrode.

High-quality RNA is crucial in clinical diagnostics and precision medicine. Formalin-fixed and paraffin-embedded (FFPE) tissues pose a challenge due to nucleic acid fragmentation and crosslinking. In this pilot study, various commercially available techniques for extracting RNA from small FFPE samples were compared. We evaluated the KingFisher Duo automated system or the manual MagMAX FFPE DNA/RNA Ultra Kit as an RNA extraction method combined with either a xylene, d-limonene, or AutoLys M tubes deparaffinization method. Additionally, the automated Maxwell RSC RNA FFPE kit and the High Pure FFPET RNA Isolation Kit were examined using FFPE samples from inflammatory bowel disease (IBD) patients, as well as samples from ovarian, kidney, and breast cancer and the skin. The KingFisher Duo system gave a higher yield and more consistent RNA quantities, especially from small volumes of IBD samples, compared to manual extraction. The deparaffinization method also impacted results, with AutoLys M tubes proving effective in combination with the KingFisher Duo system. Conversely, the High Pure kit exhibited higher yields for larger FFPE samples. While RNA integrity is a critical factor, particularly for messenger RNA (mRNA) expression studies, its role is less prominent in microRNA (miRNA) analyses. Recognizing this, our study focused on RNA yield and purity (A260/A230) to evaluate RNA extraction methods for various sample types. These findings emphasize the importance of selecting appropriate RNA extraction methods based on sample characteristics and research goals, highlighting the performance of automated methods and the impact of deparaffinization choices. The findings contribute to refining RNA extraction for molecular biology analyses, suggesting avenues for further exploration, including cost-effectiveness under specific experimental conditions.

Both the prevalence and mortality of liver cancers continue to rise. Early surgical interventions, including liver transplantation or resection, remain the only curative treatment. Nerves in the periphery influence tumor growth within visceral organs. Emerging cancer neuroscience efforts linked parasympathetic vagus nerves with tumor pathology, underscoring the value of vagal nerve denervation methods within cancer mouse models. Here, we describe a selective hepatic vagotomy that largely maintains non-liver parasympathetic innervation in mice. To address vagal interactions in hepatic tumor pathology, we provide an adapted methodology utilizing an established liver metastatic model. We anticipate that this methodology will expand the burgeoning field of cancer neuroscience, enabling the study of the neuroimmune, neurometabolic, and/or nerve-microbiota interactions shaping liver cancer progression and treatment.

The multifunctional catalytic hemoglobin from the terebellid polychaete Amphitrite ornata, also named dehaloperoxidase (AoDHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. The multifunctional ability of AoDHP is presently a rare observation, and there exists a limitation for how novel dehaloperoxidases can be identified from macrobenthic infauna. In order to discover more infaunal DHP-bearing candidates, we have devised a facilitated method for an accurate taxonomic identification that places visual and molecular taxonomic approaches in parallel. Traditional visual taxonomic species identification by the non-specialist, at least for A. ornata or even for other marine worms, is a very difficult and time-consuming task since a large diversity is present and the method is restricted to adult worm specimens. The work herein aimed to describe a method that simplifies the taxonomic identification of A. ornata in particular through the assessment of its mitochondrial cytochrome c oxidase subunit I gene by employing the DNA barcoding technique. Furthermore, whole-worm specimens of A. ornata were used to extract and purify AoDHP followed by an H₂O₂-dependent peroxidase activity assay evaluation against substrate 2,4,6-trichlorophenol. AoDHP isoenzyme A was also overexpressed as the recombinant protein in Escherichia coli, and its peroxidase activity parameters were compared to AoDHP from the natural source. The activity assay assessment indicated a tight correlation for all Michaelis-Menten parameters evaluated. We conclude that the method described herein exhibits a streamlined approach to identify the polychaete A. ornata, which can be adopted by the non-specialist, and the full procedure is predicted to facilitate the discovery of novel dehaloperoxidases from other marine invertebrates.

Background: About 287,000 women died globally during their pregnancy journey in 2020, yet most of these deaths could have been prevented. In Uganda, studies show that using Community Health Worker (CHW) visits to households with a pregnant woman can support the prevention of adverse maternal and neonatal outcomes. One such intervention is through the timed and targeted counselling (ttC) approach, where CHWs deliver tailored messages to mothers and their male caregivers at key stages of pregnancy. This study aims to evaluate the impact of the ttC approach on maternal health in Northern Uganda. The main outcomes include antenatal care attendance, advised place of delivery, and postnatal care visit.

Methods: We will employ a cross-sectional quasi-experimental design, with retrospective data to compare an intervention group (where ttC is implemented) to a control group (without intervention) using the propensity score matching (PSM) technique applying a 1:1 ratio with a caliper width of 20% of the standard deviation to estimate the average treatment effects. Adjusted odds ratios after generating matched pairs will be reported with 95% confidence intervals with Rosenbaum sensitivity analysis carried out for robustness.

Discussion: These findings can be used to modify the implementation of the ttC approach, thereby enhancing its efficiency and effectiveness.