Methods and Protocols最新文献

The high quantity of polyphenols and polysaccharides present in the tissues of Musa spp. often leads to the degradation of nucleic acids, which is why all previously established methods resulted in lesser yield and poor quality of RNA. In this study, we present a modified SDS-based RNA extraction method to improve the quality and yield of RNA from different tissues of Musa spp. for downstream applications. The modification of RNA extraction buffer, SDS, heat incubation, and use of LiCl resulted in high-intensity RNA bands and increased RNA yield. The clear ribosomal RNA bands ensured the high quality of intact RNA without genomic DNA contamination, along with A260/A280 and A260/A230 ratios ranging from 1.83 to 2.25, which indicated the high quality of RNA across different banana varieties and tissue types. This method was found to be very effective when RNA was extracted from drought-stressed plants yielding 2.92 to 6.30 µg/100 mg fresh weight with high RNA integrity and quality (RNA IQ) 7.8-9.9 from the different groups of Musa tissues. Additionally, the RNA was successfully applied in PCR and quantitative real-time PCR (qRT-PCR), confirming downstream application in gene expression analysis. This method is a reliable and efficient technique for RNA extraction methods like Trizol, NucleoSpin, RNeasy, and CTAB procedures reported so far.

The family Phenuiviridae, part of the order Hareavirales, includes arboviruses and arthropod-associated viruses, with sandflies, mosquitoes, and ticks as primary vectors. Historically, only sandfly/mosquito-borne phenuiviruses were associated with human diseases, but the emergence of severe fever with thrombocytopenia syndrome (SFTS) has highlighted the potential of tick-borne phenuiviruses as human pathogens. Recent discoveries of new arthropod-associated viruses, some of which remain unclassified, underscore the need for sensitive detection and differentiation methods, particularly in regions where these viruses may co-circulate. This study aimed to develop real-time PCR test systems for identifying and differentiating unclassified viruses within the Phenuiviridae family. In this study, tick suspensions containing phenuiviruses, previously obtained during the screening of ticks from various regions of Russia using pan-phenuivirus primers, were used. Specific primers and probes were designed to differentiate five Phenuiviridae viruses of genera Uukuvirus, Ixovirus, Phlebovirus and one unclassified phenuivirus, and their analytical sensitivity and specificity were evaluated. These PCR-based tools provide a robust method for detecting and classifying uncharacterized phenuiviruses, contributing to improved surveillance and understanding their potential epidemiological and epizootological impacts.

This study explores the application of the Least Squares Method to analyze and model the kinematic parameters in monofin swimming, focusing on stroke rate, stroke length, and the amplitudes of joint displacements at the hip, knee, and ankle. The primary aim is to evaluate whether this method provides an objective and diagnostic tool for assessing monofin swimming techniques. Three elite monofin swimmers were evaluated under a progressive fatigue test. Results indicated that the stroke rate increases velocity by 0.95, 0.23, and 0.96 units (for the estimated models respectively). Optimized stroke length (0.01-0.12 units) also significantly correlates with velocity improvements. Joint amplitude reductions, particularly at the hip and ankle, enhanced propulsion by minimizing drag. This study highlights the Least Squares Method as a diagnostic tool for optimizing swimming techniques, with potential applications in performance training.

Many endodontic procedures within the pediatric population are performed with patients aged 12 years and older, using intracanal irrigants to complement mechanical debridement for the removal of debris and to disinfect the root canal system. The use of antimicrobial irrigants that limit damage to the dental pulp are the goals of endodontic biomaterials research. Using an existing biorepository of dental pulp stem cells (DPSCs), Endocyn was evaluated in varying concentrations in proliferation and viability assays, and compared with positive (sodium hypochlorite or bleach) and negative (phosphate-buffered saline) controls. The DPSC viability was reduced in the range of -8.3% to -15.8%, p = 0.22 to p = 0.042, while the growth inhibition varied between -29.7% and -63%, p = 0.041 to p = 0.022. However, the RNA analysis revealed that no significant changes in biomarker mRNA expression (Nestin, NANOG, Sox2, Oct4, CD73, CD90, and CD105) were observed. These data demonstrated that all of the concentrations of Endocyn inhibited the DPSC viability and growth, although only high concentrations were statistically significant. Moreover, the administration of Endocyn did not alter the DPSC biomarker expression, which are novel and important findings not previously observed or reported that may assist with the development of clinical decision protocols and methods for the treatment of vital pulp tissue.

Follicular cells represent a valuable resource for genetic research, biotechnology and cryopreservation in biobanks, particularly for the conservation of endangered species. They offer a more practical alternative to gametes, embryos and fibroblasts. Collection of these cells can be achieved through feather plucking. Feather samples were opened with a scalpel and the feather pulp was washed with PBS, cut into cubes and digested in collagenase type IV. Cultivation was carried out in DMEM culture medium with 15% fetal bovine serum, 1% penicillin/streptomycin and 0.5% amphotericin, under incubation conditions of 39.5 °C and 5% CO₂. Passages were carried out with 5% EDTA for 5 min. The culture was successful, with great cell proliferation, adherence to plastic and aggregation into cell colonies. This method was effective in obtaining feather follicle cells from wild birds, especially when collected up to 6 h after their death, and can serve as a base protocol for research with feather follicle cells aiming to create biobanks.

DNA-free genome editing by the direct delivery of CRISPR-associated nucleases has emerged as a promising technology due to its precision and reduced risk of off-target effects. However, existing purification protocols for native Cas proteins require the use of complex instrumentation, which limits their application. Here, we present a simplified protocol for the purification of native Cas9, Cas12RR and dCas9-VP64 nucleases optimized for DNA-free genome editing. Our approach leverages a streamlined affinity and ion exchange chromatography coupled with minimal downstream processing, ensuring a good yield and activity of the purified proteins. The in vitro analysis of the purified ribonucleoprotein complex demonstrated a good efficiency of DNA target cleavage. This simplified protocol increases the opportunity to adopt CRISPR technology, and enables broader access to DNA-free genome editing tools also for laboratories that are not specifically equipped for protein purification.

Primary dysmenorrhea (PD) is a common gynecological condition characterized by menstrual pain without underlying pelvic pathology. It has been linked to functional and structural changes in the core musculature, but limited evidence exists regarding its association with diaphragmatic and respiratory mechanics. This study aimed to elaborate on these potential associations by assessing the diaphragmatic structure and respiratory function in women with PD compared to healthy controls, utilizing ultrasound imaging, spirometry and respiratory pressure measurements.

Methods: An observational, cross-sectional study was conducted with 44 female participants (22 with PD and 22 healthy controls). Diaphragmatic structure was evaluated through ultrasound, measuring the intercostal distance, diaphragmatic thickness, and diaphragmatic excursion at rest and during maximum voluntary contraction. Spirometric assessments included forced vital capacity (FVC), forced expiratory volume in the first second (FEV1), and the FVC/FEV1 ratio, along with measurements of maximum inspiratory pressure (MIP) and maximum expiratory pressure (MEP). Group differences were analyzed using Student's t-test and effect sizes were reported with Cohen's d.

Results: No significant differences were observed between the groups in diaphragmatic thickness, diaphragmatic excursion, or global respiratory capacity (p > 0.05). However, women with PD presented a significant reduction in the left intercostal distance both at rest (p = 0.035, d = 0.56) and during contraction (p = 0.039, d = 0.54). No other significant group differences were detected.

Conclusions: While primary dysmenorrhea does not appear to affect overall diaphragmatic function or respiratory capacity, it is associated with subtle localized changes in the left intercostal dynamics. These findings suggest a potential compensatory mechanical adaptation rather than global respiratory dysfunction. Further longitudinal studies with larger sample sizes are needed to explore the clinical significance of these findings.

The human immunodeficiency virus (HIV) is a type of retrovirus that infects humans and belongs to the Lentivirus group. Despite the availability of effective treatments, HIV infections are still increasing in some parts of the world, according to the World Health Organization (WHO). Another major challenge is the growing problem of HIV becoming resistant to drugs. This highlights the importance of ongoing research to better understand HIV and find new ways to stop the virus from spreading in the body. Scientists use a variety of methods to study HIV, including techniques from molecular and cellular biology. Many of these methods rely on fluorescent dyes to help visualize specific parts of the virus or infected cells. This article focuses on a technique called imaging flow cytometry, which is particularly useful for studying HIV. Imaging flow cytometry is unique because it not only measures fluorescence (light emitted by the dyes) but also captures images of each cell being analyzed. This allows researchers to see where the fluorescence is located within the cell and to study the cell's shape and structure in detail. Additionally, this method can be combined with machine learning to analyze large amounts of data more efficiently.

The IPDfromKM method, or Shiny method, is an artificial intelligence tool that enables indirect comparisons between studies by reconstructing individual patient data (IPD) from Kaplan-Meier (KM) curves. The IPDfromKM method is generally used for superiority analyses, but a further application could be represented by non-inferiority analyses. However, there are no studies supporting this methodological hypothesis. The aim of this work was to validate the IPDfromKM method for non-inferiority analyses by "exploiting" the well-described non-inferiority of implantable devices occluding the left atrial appendage compared to oral anticoagulants in patients with atrial fibrillation. We performed a systematic review searching for randomized controlled trials (RCTs) in the PubMed database and found five studies. The R software (version 4.3.3) was used to perform a standard survival analysis comparing Watchman and Amlet devices with warfarin. The hazard ratio (HR), with 95% confidence interval (CI), was the main parameter of our analysis. The results confirmed the non-inferiority of Amlet and Watchman compared to warfarin (HR of Watchman vs. warfarin: 1.23, 95% CI 0.80 to 1.9; HR of Amlet vs. warfarin: 1.05, 95% CI 0.61 to 1.80). Therefore, we proposed a new application of the IPDfromKM method that could be potentially relevant in decision-making for the management of this common cardiac arrhythmia and a wide range of other pathological conditions.

The human amniotic membrane (hAM) has been used as an implant to enhance the regenerative process and control inflammation in different diseases, given their structure, biocompatibility, presence of stem cells and multiple growth factors. The objective of this study was to generate a standardized protocol for obtaining, processing, and storing hAMs that guarantee the conservation of their structural and cellular characteristics as well as their mechanical properties, ensuring their ease of handling, sterility, and quality that allows their implementation for therapeutic purposes in the field of regenerative medicine. The hAMs were obtained from mothers with healthy, full-term, controlled pregnancies and by cesarean section. The hAMs were processed under sterile conditions, manually separated from the placenta and, subsequently, they were frozen in a solution of culture medium plus 50% v/v glycerol. The protocol allows obtaining sterile hAMs composed of both epithelium and stroma with adequate preservation of the amniotic cells. The glycerol's impact on the mechanical properties may enhance the membrane's adaptability and conformability to diverse wound surfaces, potentially improving the healing process. It is necessary to repeat microbiological, cell viability and mechanical studies at 6 and 12 months to ensure that long-term frozen conditions do not affect the quality of the hAMs.