Molecular Biology Techniques and Applications

Propidium monoazide is unreliable for quantitative live-dead molecular assays

This study shows that propidium monoazide (PMA) is unreliable for quantitative viability assays when bacterial concentration and composition are unknown, but suitable for qualitative assessment with known dead microbes or extracellular DNA.

Age-Invariant Genes: Multi-Tissue Identification and Characterization of Murine Reference Genes

The paper identifies and characterizes age-invariant genes across multiple tissues in mice, finding they are stable across the lifespan and have distinct molecular features.

Comparison of Commercially Available Thermostable DNA Polymerases with Reverse-Transcriptase Activity in Coupled Reverse-Transcription Polymerase Chain Reaction Assays

This study compares artificial thermostable DNA polymerases with reverse-transcriptase activity to conventional enzyme mixtures in RT-PCR assays for SARS-CoV2 RNA and endogenous mRNA.

P3 site-directed mutagenesis: An efficient method based on primer pairs with 3' overhangs

The paper develops an optimized site-directed mutagenesis method using primer pairs with 3' overhangs, achieving higher efficiency and lower time requirements compared to existing methods.

Identification of robust RT-qPCR reference genes for studying changes in gene expression in response to hypoxia in breast cancer cell lines

This study identifies RPLP1 and RPL27 as robust reference genes for RT-qPCR analysis of gene expression in hypoxic breast cancer cell lines.

Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood

This study evaluates RNA degradation in homeRNA-stabilized blood under varying shipping times and temperatures, finding that samples remain suitable for RNA sequencing under typical shipping conditions.

ThermoPlex: An Automated Design Tool for Target-specific Multiplex PCR Primers based on DNA Thermodynamics

ThermoPlex automates the design of target-specific multiplex PCR primers using DNA thermodynamics, showing reliable performance through theoretical and experimental analysis.

Click-qPCR: an ultra-simple tool for interactive qPCR data analysis

Click-qPCR provides an interactive, web-based tool for analyzing qPCR data without programming skills, enabling efficient processing and visualization of results.

qDATA - an R application implementing a practical framework for analyzing quantitative Real-Time PCR data

qDATA provides an R-based tool for analyzing qRT-PCR data, offering statistical analysis and visualization of Ct values with a focus on improving reliability through biological replicates and technical replicates.

An analysis of RNA quality metrics in human brain tissue

The paper evaluates how pre-sequencing RNA quality metrics (PMI and RIN) correlate with post-sequencing RNA quality metrics and gene expression in human brain tissue.

Superhelicase-driven isothermal amplification of repetitive and low-complexity DNA

This study demonstrates that SHARP, a helicase-driven isothermal amplification method, effectively amplifies repetitive and compositionally extreme DNA sequences that are challenging for conventional PCR.

Advancing Remote and Low-Resource Healthcare Delivery with Microbiopsy Skin Sample mRNA Housekeeping Gene Stability Analysis Across Various Temperatures

The paper evaluates the stability of mRNA housekeeping genes in microbiopsy skin samples stored at various temperatures, showing they remain detectable despite uncontrolled shipping conditions.

A Rapid, Cost-Effective Method for High-Yield DNA Purification from PCR Products and Agarose Gels.

The paper develops a cost-effective in-house DNA purification protocol for PCR products and agarose gels, showing improved clarity and purity compared to commercial kits.

Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mtDNA copy number in songbird blood and sperm cells

This study compares qPCR, dPCR, and ddPCR for mtDNA copy number estimation in songbird blood and sperm, finding ddPCR most reliable for low-abundance samples.

Improving inference in environmental surveillance by modeling the statistical features of digital PCR

The paper introduces a likelihood model for digital PCR data to improve statistical inference in environmental applications by addressing non-normal error structures.

Evaluation of suitable reference genes for qPCR normalisation of gene expression in a Achilles tendon injury model.

The paper evaluates reference genes for qPCR normalization in a rat tendon injury model, identifying stable genes and highlighting unstable ones.

Comparative Analysis of Gene Expression Analysis Methods for RNA In Situ Hybridization Images

The paper compares RNA-ISH quantification methods in ovarian cancer samples, finding good concordance between automated tools and RNAscope, with RT-ddPCR showing less agreement.

Mathematical modeling using box-behnken response surface design for optimal DNA yield with variable parameters of time, temperature, and proteinase K concentration

The paper uses Box-Behnken Design to optimize DNA extraction parameters for maximum yield from whole blood.

Identification of stable reference genes for quantitative real-time PCR in human fibroblasts from lymph nodes and synovium

This study identifies stable reference genes for RT-qPCR normalization in human fibroblasts from lymph nodes and synovium under different experimental conditions.

Biotin based Northern Blotting (BiNoB): A Robust and Efficient Alternative

This paper introduces BiNoB, a biotin-based Northern blotting method that improves sensitivity and cost-effectiveness for RNA detection.

Integrity assay for messenger RNA in mouse and human brain samples and synaptosomal preparations

The paper introduces a RT-qPCR assay to assess mRNA integrity in brain and subcellular samples, showing it outperforms RIN in correlation with housekeeping gene expression.

Evaluation of short-term hair follicle storage conditions for maintenance of RNA integrity.

This study evaluates RNA integrity in horse hair follicles stored in RNAlater at different temperatures and finds no significant differences in RNA quality or quantity across conditions.

Generic workflow for a rapid and easy design of strain-specific PCR and qPCR primers, applied to the assessment of bacterial strains survival in soil

The paper introduces a web-based workflow for designing strain-specific PCR/qPCR primers using microbial genomes, applied to assess Bacillus strain survival in soil.

Rectal Swab DNA Collection Protocol for PCR Genotyping in Rats

The paper develops a non-invasive DNA collection protocol for rat genotyping using rectal swabs, showing it produces reliable PCR results comparable to traditional methods.

A modified dual preparatory method for improved isolation of nucleic acids from laser microdissected fresh-frozen human cancer tissue specimens

The paper describes a modified dual preparatory method to improve RNA yield from laser microdissected human cancer tissue samples.

A novel thermostable and processive reverse transcriptase from a group II intron of Anoxybacillus flavithermus

The paper characterizes a novel thermostable and processive reverse transcriptase from Anoxybacillus flavithermus, showing its potential for applications requiring heat-resistant RTs.

Cross-Species Evaluation of qPCR Reference Genes in Diabrotica speciosa (Coleoptera: Chrysomelidae) using Diabrotica virgifera virgifera sequences.

This study evaluates qPCR reference genes across species in Diabrotica speciosa using Diabrotica virgifera virgifera sequences to normalize gene expression data across developmental stages.

gQuant: A Robust and Generalizable Algorithm for Identifying Normalizer Genes in qRT-PCR Data: A Case Study on Urinary Exosomal miRNAs

gQuant improves normalizer gene identification in qRT-PCR data by using ensemble voting classifiers, showing better consistency and accuracy than existing tools.

Comparison of gene expression in living and postmortem human brain

The paper re-analyzes RNA sequencing data comparing gene expression in living and postmortem human brain tissue, finding that living samples had lower quality, and questions the validity of previous conclusions about postmortem studies.

InterOpt: Improved gene expression quantification in qPCR experiments using weighted aggregation of reference genes

The paper introduces a mathematical framework for improving qPCR gene expression normalization by optimizing weighted aggregation of reference genes using scale-invariant functions.