Molecular Biology Techniques and Applications

Digital PCR quantification of DNA, RNA and extracellular microRNA of mouse oocytes

This paper develops an optimized digital PCR method for rapid, absolute quantification of DNA, RNA, and extracellular microRNA in mouse oocytes, demonstrating high accuracy and reproducibility.

Dissecting and Tuning Primer Editing by Proofreading Polymerases

The paper develops synthetic DNA standards to measure primer editing by proofreading polymerases and shows it can be tuned to improve microbiome profiling.

Comparison of real-time quantitative Polymerase Chain Reaction (PCR) and digital droplet PCR for quantification of hormone membrane receptor FSHR, GPER and LHCGR transcripts in human primary granulosa lutein cells

This study compares qPCR and ddPCR for quantifying hormone receptor transcripts in human granulosa cells, finding ddPCR more accurate for low-expression genes.

Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses

The paper identifies and evaluates nine reference genes for qPCR analysis in Fucus distichus under various abiotic stresses, recommending condition-specific normalization strategies.

Quantifying 35 transcripts in a single tube: Model-based calibration of the GeXP RT-PCR assay

The paper develops a kinetic model and data processing workflow to calibrate the GeXP RT-PCR assay for precise transcript quantification in Physarum polycephalum.

PCRedux: A Data Mining and Machine Learning Toolkit for qPCR Experiments

PCRedux analyzes qPCR amplification curves to calculate interpretable features for machine learning, achieving high sensitivity and specificity in classification.

Ultra-precise quantification of mRNA targets across a broad dynamic range with nanoreactor beads

This paper introduces a nanoreactor bead-based assay for ultra-precise RNA quantification across a seven-order-of-magnitude dynamic range, validated for BCR-ABL1 fusion transcripts in CML patients.

barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection

barCoder generates unique genetic tags for qPCR detection, ensuring specificity and minimizing cross-reactivity with contaminants.

PANDAA-monium: Intentional violations of conventional qPCR design enables rapid, HIV-1 subtype-independent drug resistance SNP detection

PANDAA-monium uses intentional qPCR design violations to detect HIV-1 drug resistance SNPs rapidly and subtype-independently with high sensitivity and specificity.

Selection and Validation of Reference Genes Desirable for Gene Expression Analysis by qRT-PCR on Seed Germination of Castanea henryi

The paper identifies stable reference genes for qRT-PCR analysis of gene expression during seed germination in Castanea henryi using computational and experimental validation.

Accurate bulk quantitation of droplet digital PCR

The paper presents a method to perform droplet digital PCR without microfluidics, enabling accurate quantitation of SARS-CoV-2 sequences using bulk analysis.

PCR procedures to amplify GC-rich DNA sequences of Mycobacterium bovis

The paper develops PCR protocols for amplifying GC-rich DNA sequences from Mycobacterium bovis, showing that a 2-step protocol with high-fidelity polymerases and enhancer improves amplification of large GC-rich genes.

Lessons and considerations for the creation of universal primers targeting non-conserved, horizontally mobile genes

The paper develops a method for designing universal primers for non-conserved, horizontally mobile genes and evaluates its effectiveness compared to traditional methods.

One enzyme reverse transcription qPCR using Taq DNA polymerase

The paper demonstrates that Taq DNA polymerase can be optimized for reverse transcriptase activity, enabling its use as the sole enzyme in TaqMan RT-qPCR assays for detecting SARS-CoV-2 RNA.

Auto-regressive modeling and diagnostics for qPCR amplification

The paper introduces a Smooth Transition Autoregressive model to improve qPCR data analysis by addressing autocorrelation in residuals caused by sequential dependence in fluorescence measurements.

Streamlined and quantitative detection of chimerism in mouse tissue using digital PCR

This paper develops a droplet digital PCR assay to quantify chimerism in mouse tissues, showing it is robust, minimally biased, and compatible with crude lysates.

Identification of qPCR reference genes suitable for normalising gene expression in the developing mouse embryo

The paper identifies suitable reference genes for normalizing qPCR data in developing mouse embryos using multiple algorithms and shows that AP3D1, RPL13A, and PAK1IP1 are consistently reliable.

NormiRazor: Tool Applying GPU-accelerated Computing for Determination of Internal References in MicroRNA Transcription Studies

NormiRazor accelerates normalization in miRNA studies by parallelizing reference gene selection methods on a GPU, reducing computation time significantly.

The attachment of Sso7d-like protein improves processivity and resistance to inhibitors of M-MuLV reverse transcriptase

This study creates chimeric reverse transcriptases by fusing M-MuLV RT with DNA-binding domains, improving processivity and inhibitor resistance.

Optimization of On-Bead Emulsion Polymerase Chain Reaction Based on Single Particle Analysis

This study optimizes ePCR by analyzing single particles to determine effective conditions and success criteria for amplifying DNA libraries.

A rapid, super-selective method for detection of single nucleotide variants in C. elegans

The paper introduces a method for detecting single nucleotide variants in C. elegans using optimized SuperSelective primers for endpoint PCR.

The Macerprep: a minimalist kit- and enzyme-free high-yield miniprep utilising alkaline lysis and alkaline hydrolysis principles

The paper introduces a cost-effective, kit- and enzyme-free plasmid DNA isolation method using alkaline lysis and hydrolysis to address issues with commercial miniprep kits.

HRT Atlas v1.1 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

HRT Atlas v1.1 provides a database of human and mouse housekeeping genes and transcripts by analyzing large RNA-seq datasets, offering improved normalization tools for qPCR experiments.

A simple method for isolating high-quality RNA from kenaf containing high polysaccharide and polyphenol contents

This paper presents a simple, low-cost RNA extraction method for kenaf plants with high polysaccharide and polyphenol content, yielding high-quality RNA suitable for downstream applications.

DEBay: a computational tool for deconvolution of quantitative PCR data for estimation of cell type-specifc gene expression in a mixed population

DEBay estimates cell type-specific gene expression from mixed qPCR data using Bayesian methods and provides a GUI and source code.

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye, and inhibitor-resistant high-fidelity DNA polymerase

The paper introduces a sensitive microplate assay for quantifying dNTPs using long synthetic oligonucleotides, EvaGreen dye, and inhibitor-resistant DNA polymerase, enabling reliable measurement in mouse tissues.

A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

The paper compares DNA stains and staining methods for agarose gel electrophoresis, finding that some alternatives are more cost-effective and less impactful on DNA migration than traditional methods.

The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data

The paper introduces the Gini coefficient as a method to select stable reference genes for normalizing expression data, showing it outperforms traditional methods across multiple datasets.

Identification of suitable reference genes for qPCR expression analysis on the gonads of the invasive mussel Limnoperna fortunei

The paper identifies stable reference genes for qPCR analysis of gonads in the invasive mussel Limnoperna fortunei, recommending NAPA, UBE2F, and RPS3 for sex comparisons and HS6ST3B and NAPA for female-specific studies.

Performance comparison of reverse transcriptases for single-cell studies

The paper compares 11 reverse transcriptases for single-cell RNA quantification, identifying two top performers that improve sensitivity and clustering resolution in low RNA concentration experiments.