Molecular Biology Techniques and Applications

Exposure to graphene oxide sheets alters the expression of reference genes used for real-time RT-qPCR normalization

This study evaluates the impact of graphene oxide exposure on reference gene expression in human and mouse cells, showing significant dysregulation in ribosomal proteins and common calibrators.

Targeted transcript quantification in single disseminated cancer cells after whole transcriptome amplification

The paper develops a single-cell qPCR assay to accurately quantify ERBB2 expression in disseminated cancer cells, showing it can detect expression even in HER2-negative cells.

A new set of endogenous control genes for use in quantitative real-time PCR experiments show that formin Ldia2dex transcripts are enriched in the early pond snail embryo

The paper identifies six new endogenous control genes for qRT-PCR in pond snails and shows that Ldia2dex transcripts are enriched in early embryos compared to other tissues.

Optimal use of statistical methods to validate reference gene stability in longitudinal studies

The paper evaluates four statistical methods for validating reference gene stability in longitudinal studies and proposes a combined workflow for improved accuracy.

A framework for analysis of real-time nucleic acid amplification data using novel multidimensional standard curves

This paper introduces a framework for analyzing real-time nucleic acid amplification data using multidimensional standard curves to improve absolute quantification and detect outliers.

Selection of appropriate reference genes for quantitative real-time PCR in Clerodendrum trichotomum

This study identifies stable reference genes for qRT-PCR in Clerodendrum trichotomum across tissues and abiotic stresses to improve gene expression analysis accuracy.

Quality assessment of tissue samples stored in a specialized human lung biobank

The paper assesses the impact of delays and RNAlater use on tissue sample quality using mRNA expression analysis.

A Pipeline for Fecal Host DNA Analysis by Absolute Quantification of LINE-1 and Mitochondrial Genomic Elements Using ddPCR

The paper develops a ddPCR-based pipeline for absolute quantification of host DNA in stool samples, validated across human and mouse specimens.

Selection and validation of reference genes for quantitative Real-Time PCR in Arabis alpina

This study identifies and validates reference genes for qPCR normalization in Arabis alpina under various stress conditions.

Evaluation of DNA extracted from blood filter spots and eluates processed for enzyme linked immunosorbent assay (ELISA)

This paper evaluates DNA extraction from blood filter spots and eluates used for ELISA, finding higher DNA concentration in PBS compared to SDB, with 85% PCR success rate.

Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation

The paper introduces an open-source platform for high-throughput nucleic acid extraction and manipulation using magnetic beads, highlighting their cost-effectiveness and versatility.

Optimization of the experimental parameters of the ligase cycling reaction

This study optimizes LCR experimental parameters to improve plasmid assembly efficiency by analyzing the effects of BO melting temperatures and secondary structure inhibitors.

Identification of reference genes for real-time PCR gene expression studies during seed development and under abiotic stresses in Cyamopsis tetragonoloba (L.) Taub.

The paper identifies stable reference genes for qRT-PCR in guar under different conditions and validates them using the CtMT1 gene.

Filter paper-based spin column for low throughput nucleic acid purification

The paper describes a method to recharge used spin columns or build homemade ones using filter paper for low-throughput nucleic acid purification, showing its effectiveness for various nucleic acids.

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

This paper introduces third-generation in situ HCR with automatic background suppression, enabling multiplexed, quantitative mRNA imaging and flow cytometry with improved performance and ease-of-use.

A novel PCR method directly quantifies sequence features that block primer extension

This paper introduces a novel qPCR method that directly quantifies DNA sequence features blocking primer extension, improving sensitivity over traditional negative assays.

A robust method for RNA extraction and purification from a single adult mouse tendon

The paper develops a method for extracting high-quality RNA from single adult mouse tendons, reducing biological variation and costs for RNA analysis.

Quantification of DNA samples by Ethidium Bromide Spot Technique

The paper optimizes an inexpensive DNA concentration quantification method using Ethidium Bromide spot technique with UV visualization.

Identification of stable reference genes for quantitative PCR in koalas

This study identifies the most stable reference genes for quantitative PCR in koala lymph node tissues across two populations using multiple statistical methods.

Enzyme-based synthesis of single molecule RNA FISH probes

This paper describes an enzyme-based method to synthesize single molecule RNA FISH probes, which performs as well as conventional chemical synthesis methods but is cheaper and more flexible.

Statistical Approaches to Decreasing the Discrepancy of Non-detects in qPCR Data

The paper introduces statistical methods to handle non-detects in qPCR data by modeling missing data mechanisms and using multiple imputation to reduce bias in gene expression estimation.

A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species

The paper introduces a urea-based in situ hybridization method that improves gene expression detection and reduces non-specific staining across multiple animal species.

Improved DOP-PCR (iDOP-PCR): a robust and simple WGA method for efficient amplification of low copy number genomic DNA

The paper introduces an improved DOP-PCR method (iDOP-PCR) that provides better quality DNA amplification for low copy number genomic DNA compared to existing techniques.

Systematic selection of reference genes for normalization of circulating RNA transcripts in pregnant women based on RNA-seq data

The paper identifies a panel of stably expressed genes for normalizing circulating RNA transcripts in maternal blood using RNA-seq data from preterm labor samples.

Flexible, multi-use, PCR-based nucleic acid integrity assays based on the ubiquitin C gene

The paper develops PCR-based assays using the ubiquitin C gene to assess nucleic acid integrity across multiple species and sample types.

Capture and Purification of Plant Genomic DNA on a Readily-available Cellulose Matrix

The paper presents a low-cost method for long-term storage of plant genomic DNA using cellulose-based paper instead of commercial FTA cards.

Synthetic DNA templates for the production of in situ hybridization probes

The paper describes a method to generate DNA templates for in vitro transcription of RNA probes using synthetic DNA, bypassing the need for plasmid-based workflows.

Efficient and flexible strategies for gene cloning and vector construction using overlap PCR

The paper presents efficient and flexible strategies for gene cloning and vector construction using overlap PCR, demonstrating applications for cloning genes and assembling functional cassettes.