Molecular Biology Techniques and Applications

Reference-Gene Stability for RT-qPCR in the Medial Prefrontal Cortex and Hippocampal Subregions of the 5xFAD Mouse Brain

The paper evaluates reference gene stability for RT-qPCR in specific brain regions of 5xFAD mice and recommends gene pairs for accurate normalization.

Surfactant-Enhanced Hybridization Capture for Direct Sequence-Specific RNA Extraction from Plasma and Whole Blood

This paper introduces a surfactant-based method for direct RNA extraction from plasma and whole blood, achieving high recovery of low-abundance RNA and outperforming existing silica-based kits.

qPyCR: A qPCR Data Analyzer for Template Quantification and the Detection of Performance Outliers

qPyCR is a Python tool for analyzing qPCR data that computes Cq values, performs background subtraction, and provides global fitting to quantify template abundance and assess reaction quality.

Efficient primer design for broad-range virus detection: A semi-automated workflow using sequence clustering and varVAMP

This paper presents a semi-automated workflow using sequence clustering and varVAMP to design broad-range RT-qPCR primers for diverse viruses, improving representation and reducing redundancy.

homeRNA Just Dropped! Streamlining Remote Blood Collection and RNA Stabilization for Smaller Sample Volumes with homeRNAdrop

homeRNAdrop simplifies remote blood collection and RNA stabilization for small samples, with successful pilot testing showing adequate RNA quality and yield.

Multi-agentic system for primer design in qPCR and LAMP diagnostics tests

This study develops an AI-orchestrated workflow using multiple agents to automate primer design for qPCR and LAMP assays by integrating bioinformatics tools and databases.

Click-Prep: An Interactive Data Preparation Tool for Click-qPCR

Click-Prep simplifies creating Click-qPCR input files by automating data formatting, quality control, and mean Cq calculation from qPCR instrument outputs.

High thoughput fluorometric nucleic acid quantification using qPCR instruments

This study demonstrates the use of qPCR instruments with SYTO-9 dye for high-throughput nucleic acid quantification, showing stable and accurate results across a range of concentrations and conditions.

Enhancing Recombinant Vector Assembly Efficiency: A Novel Methodological Approach

This paper introduces a method to improve recombinant vector assembly efficiency using high-temperature treatment followed by cooling, enhancing PCR product-vector connection.

A long-hidden prevalent PCR artifact and its application in DNA library screening

The paper identifies a new PCR artifact called 'PCR leaping' and develops a DNA library screening method using it for natural product discovery.

qPCR Guru, a free browser-based platform, strengthens microRNA analyses using full-curve Cq estimation

qPCR Guru provides a platform for improved qPCR analysis by comparing instrument-derived and full-curve Cq estimates, enhancing accuracy for low-expressing targets.

Scaling Multiplex qPCR Primer Design to 1000-plex using the Degenerate Incomplete Multiplex Primer List Extension (DIMPLE) Algorithm

The paper introduces DIMPLE, a scalable qPCR primer design algorithm that enables 10,000+ primers in a single reaction, achieving low VAF detection and multiplex applications.

A Poisson-multinomial model for quantifying gene therapy vector integrity using quadplex digital PCR

This paper introduces a Poisson-multinomial model for quantifying gene therapy vector integrity using quadplex digital PCR, enabling accurate analysis of sequence integrity and genetic linkage across four targets.

Determination of suitable reference genes for RT-qPCR analysis in Gryllodes sigillatus (Orthoptera: Gryllidae)

This study identifies stable reference genes for RT-qPCR in Gryllodes sigillatus, improving gene expression analysis and supporting diagnostic tool development.

miRNova: A Next-Generation Platform for Ultra-Precise and Highly Specific MicroRNA Quantification Integrating a Tailored Stem Loop RT-qPCR and a Robust Analytical Framework

The paper introduces miRNova, a platform for precise miRNA quantification using tailored stem-loop RT-qPCR and an analytical framework, showing superior specificity and accuracy in saliva samples.

Enhancing Transcriptional Data Reliability in Fish Oogenesis Using cDNA-Based Normalization

This study evaluates normalization strategies for transcriptomic data in fish oogenesis, finding that cDNA-based normalization improves reliability compared to single or combined reference genes.

Fluorometric DNA Polymerase Activity Assay for Resource-Limited Enzyme Manufacturing

The paper develops a fluorometric DNA polymerase activity assay that is cost-effective and accessible for resource-limited settings by using in-house reagent synthesis and low-cost equipment.

Modified RNA Extraction Methods to Eliminate Agarose Impurities in Precision-Cut Lung Slices

This study evaluates modified RNA extraction methods to remove agarose impurities from precision-cut lung slices, showing improved RNA quantity and integrity using a plant kit and agarose dissolution.

Quantal PCR: A Calibrator-Free Method for Determining the Unit for Nucleic Acid Quantification

This paper introduces quPCR, a calibrator-free method for absolute nucleic acid quantification by defining an intrinsic quantal unit based on replication system properties.

Autolab HBH: A Rapid Hyperbaric Heating Device for Streamlined, PCR-Ready Sample Preparation Across Diverse Biological Matrices and Organisms

The paper introduces a rapid hyperbaric heating device for nucleic acid extraction, demonstrating its effectiveness across diverse biological samples and organisms.

A simple and efficient CTAB plate-based protocol for genomic DNA extraction from crop plants

This paper develops a scalable, cost-effective DNA extraction method using CTAB plates for crop plants, enabling high-throughput PCR-based genotyping.

Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification.

The paper describes an automated workflow for high-throughput plasmid DNA preparation and quantification using a robotic workstation, achieving high yields and quality with minimal human intervention.

ratioPCR delivers precise real-time quantification from multi-template PCR via mechanistic bias correction

ratioPCR improves qPCR precision by correcting mechanistic biases, enabling accurate quantification of nucleic acid ratios in high-throughput applications.

Gene expression profiling for forensic age assessment of porcine skin wounds

This study develops and validates a gene expression signature using qPCR to assess the age of porcine wounds, finding that 14 genes can reflect wound age but are not sufficient for forensic use alone.

Quantification of Human DNA from Century-Old Archived FFPE Samples for Retrospective Genomic Studies

This paper quantifies DNA from century-old FFPE samples and shows that storage time is less impactful on DNA quality than initial fixation time, requiring NGS for analysis.

SAND-MEDIATED DNA EXTRACTION FROM ORCHIDS FOR GENOMIC APPLICATIONS

The paper describes a non-organic DNA extraction protocol for orchids using CTAB-based gel preservation, sterile sand, and stabilization buffers, enabling high-quality DNA extraction from fresh and stored samples for genomic applications.

Stable reference genes for 24-hour circadian profiling of core clock genes in the blood of obstructive sleep apnea patients

The paper identifies ACTB and RPL13A as stable reference genes for circadian gene expression analysis in blood samples from OSA patients.

Cross-platform digital PCR evaluation of bovine papilloma virus quantification: introducing PCR-ValiPal for Standardized guided assay validation

The paper introduces PCR-ValiPal, a web tool for standardized dPCR assay validation, and evaluates its performance across four platforms for BPV quantification.

Enhanced detection of low-expressed miRNAs in Leishmania-infected macrophages through RNA fractionation and RT-qPCR optimization

Elucidation of the mechanism of byproduct DNA synthesis in whole-transcript amplification by poly-A tagging and development of its specific suppression

This paper elucidates the mechanism of byproduct DNA synthesis in poly-A tagging and develops SupTag to suppress it, improving transcriptomic analysis accuracy.