BioTechniques最新文献

Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is widely used for nucleic acid quantification. The use of technical triplicates in RT-qPCR aims to minimize variability and improve reliability but increases reagent consumption, labor, and time. This study systematically evaluates the necessity of technical replicates by analyzing 71,142 cycle threshold (Ct) values from 1,113 RT-qPCR runs across three instruments, two detection chemistries, and 30 operators. Variability within replicates was assessed using metrics such as the coefficient of variation (CV), while the impacts of operator expertise, detection chemistry, instrument calibration, and initial template concentration were explored. The findings challenge the assumption that variability increases at low template concentrations, revealing no correlation between Ct values and CV. While inexperienced operators exhibited slightly higher variability, their replicates were still consistent, with acceptable CVs and low outlier frequencies. Dye-based detection showed greater variability than probe-based. Time since calibration had negligible effects on replicate consistency. Notably, duplicate or single replicates sufficiently approximated triplicate means. These results challenge traditional assumptions about RT-qPCR variability and provide a data-driven framework for optimizing experimental design. This study offers potential for resource savings without compromising data quality, particularly in high-throughput applications or laboratories with limited funds. The data underlying this article are available at https://doi.org/10.5281/zenodo.15072870.

Mitophagy, a crucial mitochondrial quality control system for cellular stress adaptation, is a key focus in pathophysiology and drug discovery. Developing a simple and versatile mitophagy flux assay is vital for advancing our understanding of cellular responses. Addressing a gap in systematic methods, we employ the photoactivatable fluorescent protein mito-Kaede in C2C12 myocytes, demonstrating its remarkable versatility in quantifying mitophagy flux responses under various stimuli, including carbonyl cyanide m-chlorophenyl hydrazone (CCCP), TNF-α, lipopolysaccharide (LPS), and hypoxia. This study underscores the validity and distinctive advantages of the mito-Kaede assay through comparative analysis with conventional assays including Western blotting (WB), potentially providing valuable insights for both mitophagy flux analysis and drug development.

Three-dimensional (3D) cell culture is a more physiologically relevant model for drug development than two-dimensional (2D) cell culture. A common method to culture cells in 3D consists in embedding cells in synthetic or animal-based matrices that provide structural support for cell growth. They partially mimic in vivo conditions and enable scalable culture. Here, we introduce an alcohol-based Solution for Harvesting Organoids Efficiently, denoted SHOE. We tested its harvesting potential on 2 cell lines grown as spheroids and 2 patient-derived organoids. It enables rapid, high-yield cell recovery, at room temperature (RT), and bypasses prolonged cold incubation of standard protocols. It preserves 3D structure and growth in subsequent passages.

Protein phosphatase 2A (PP2A), a pivotal serine/threonine phosphatase, plays a crucial role in cellular regulation and tumor suppression. Dysregulation of PP2A complex, particularly the Aα subunit and B56 family, is linked to malignancies through altered substrate interactions, exemplified by c-MYC dynamics. Given the challenges in identifying PP2A substrates-owing to the enzyme's expansive substrate range, transient interaction profiles, and complex regulatory mechanisms-we employed bioluminescence resonance energy transfer (BRET) sensors. These advanced molecular tools facilitate the real-time detection of protein-protein interactions within live cells. This investigation details the creation and application of a novel PPP2R5A (B56α) BRET sensor tailored for cytosolic and nuclear environments, effectively distinguishing specific PP2A interactions. The nuclear sensor, enhanced with a nuclear localization signal, enabled probing of targets like c-MYC. The dual compartmental utility of these sensors underscores their significant potential in elucidating PP2A's regulatory roles and their implications in oncogenesis. Our study highlights the efficacy of BRET sensors in formulating precision therapeutic strategies. This advancement provides a robust framework for deeper investigations into the multifaceted roles of PP2A in both normal physiological and pathological contexts, paving the way for future explorations into its intricate molecular interactions.

Single-cell RNA sequencing (sc-RNA-seq) is a popular method for characterization of cell populations. However, the relationship between RNA and protein expression in cells is often discordant. Protein-based detection methods, such as cytometry by time-of-flight (CyTOF), can provide complementary data to sc-RNA-seq. We collected bronchoalveolar lavage (BAL) from healthy participants and co-evaluated cell populations and gene/protein expression by applying sc-RNA-seq and CyTOF to the same samples. Cell populations were well correlated between these two platforms, but differences emerged at the sub-population level. Notably, macrophage subtypes did not correlate well; whereas T-lymphocytes did. Gene and protein expression levels were significantly correlated (p < .01). Overall, we recommend CyTOF as a tool to validate sc-RNA-seq data for select proteins and cell populations in BAL samples.

Total protein isolation followed by quantitation using a colorimetric method, such as the bicinchoninic acid (BCA) assay is a common laboratory protocol. Protein concentrations are determined by comparing extracted samples to a standard curve generated from serial dilutions of a reference protein, such as bovine serum albumin (BSA). This study aimed to identify the most reproducible and accurate method for quantifying protein concentrations in an experimental series over time. We analyzed the effect of serial freeze-thaws, inter-person and intra-person variability in standard preparation and assay execution. Absorbance was measured at 565 nanometers (nm) using an Epoch Microplate Spectrophotometer (Agilent Technologies, Inc., Santa Clara, CA) with Gen5 Data Analysis software. The most consistent and accurate method for determining the protein concentrations over time is to prepare a large batch of diluted BSA standards, aliquot them into small portions, and store them frozen.

Circulating cell-free DNA (ccfDNA) can be found in blood and other biofluids and is a minimally invasive biomarker for several pathological processes. As tumors become more invasive, an increasing amount of circulating tumor DNA (ctDNA) is also shed into the peripheral circulation. Combined analysis of ccfDNA and ctDNA has demonstrated prognostic and predictive value in metastatic disease. However, localized tumors shed significantly less ccfDNA/ctDNA and accurate detection remains a technical challenge. To overcome this barrier, droplet preamplification has been used to perform robust multiplexed analysis of low-input samples. To reduce false positives, it is essential to use a high-fidelity polymerase with 3'-5' exonuclease activity. However, attempts to combine high-fidelity polymerases with commercial droplet digital chemistries have had limited success. There is also no standardized method for efficient amplicon recovery from droplets. In this work, we present a method to reliably stabilize emulsions and recover preamplified templates. We systematically compared our protocol with different destabilization methods and found an average 41% improvement in recovery efficiency. We anticipate that this standardized method will increase the consistency and reproducibility of ccfDNA/ctDNA analyses. This technique could be readily translated to other low-input or low-biomass samples, such as urine, saliva, or archived biopsy specimens.

Determining large structural variations is difficult and time-consuming without long molecules to aid in the genome assembly. One issue is the fragility of large DNA molecules during routine molecular biology techniques. A novel inverted agarose insert was created to protect and make accessing large DNA easier. The inverted agarose insert has the cell solution in the middle and the agarose on the outside rather than the cells embedded in the agarose (plug inserts). Multiple agarose concentrations were tested to determine the best percentage of agarose to create the inverted insert. A proof-of-principle inverted insert was tested with S. cerevisiae cells to show that cells could be lysed inside the inverted insert, allowing the DNA to remain at full length in the middle.