Enzymatic amplification of DNA by PCR: standard procedures and optimization

Genetic Manipulation of Neisseria gonorrhoeae and Commensal Neisseria Species

The sexually transmitted pathogen, Neisseria gonorrhoeae, undergoes natural transformation at high frequency. This property has led to the rapid dissemination of antibiotic resistance markers and the panmictic structure of the gonococcal population. However, high-frequency transformation also makes N. gonorrhoeae one of the easiest bacterial species to manipulate genetically in the laboratory. Techniques have been developed that result in transformation frequencies >50%, allowing the identification of mutants by screening and without selection. Constructs have been created to take advantage of this high-frequency transformation, facilitating genetic mutation, complementation, and heterologous gene expression. Similar methods have been developed for N. meningitidis and nonpathogenic Neisseria including N. mucosa and N. musculi. Techniques are described for genetic manipulation of N. gonorrhoeae and commensal Neisseria species, as well as for growth of these fastidious organisms. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Spot transformation of Neisseria gonorrhoeae on agar plates Basic Protocol 2: Spot transformation of commensal Neisseria on agar plates Basic Protocol 3: Transformation of Neisseria gonorrhoeae in liquid culture Basic Protocol 4: Electroporation of Neisseria gonorrhoeae Basic Protocol 5: Creation of unmarked mutations using a positive and negative selection cassette Basic Protocol 6: In vitro mutagenesis of Neisseria gonorrhoeae chromosomal DNA using EZ-Tn5 Basic Protocol 7: Chemical mutagenesis Basic Protocol 8: Complementation on the Neisseria gonorrhoeae chromosome Alternate Protocol 1: Complementation with replicating plasmids Alternate Protocol 2: Complementation on the Neisseria musculi or Neisseria mucosa chromosome Basic Protocol 9: Preparation of chromosomal DNA from Neisseria gonorrhoeae grown on solid medium Alternate Protocol 3: Preparation of chromosomal DNA from Neisseria gonorrhoeae grown in broth Support Protocol: Preparing PCR templates from Neisseria gonorrhoeae colonies.

Transcription Factor-Mediated Differentiation of Human iPSCs into Neurons

Accurate modeling of human neuronal cell biology has been a long-standing challenge. However, methods to differentiate human induced pluripotent stem cells (iPSCs) to neurons have recently provided experimentally tractable cell models. Numerous methods that use small molecules to direct iPSCs into neuronal lineages have arisen in recent years. Unfortunately, these methods entail numerous challenges, including poor efficiency, variable cell type heterogeneity, and lengthy, expensive differentiation procedures. We recently developed a new method to generate stable transgenic lines of human iPSCs with doxycycline-inducible transcription factors at safe-harbor loci. Using a simple two-step protocol, these lines can be inducibly differentiated into either cortical (i³ Neurons) or lower motor neurons (i³ LMN) in a rapid, efficient, and scalable manner (Wang et al., 2017). In this manuscript, we describe a set of protocols to assist investigators in the culture and genetic engineering of iPSC lines to enable transcription factor-mediated differentiation of iPSCs into i³ Neurons or i³ LMNs, and we present neuronal culture conditions for various experimental applications. © 2018 by John Wiley & Sons, Inc.

Proximity-Dependent Biotinylation for Identification of Interacting Proteins

Complex interaction networks orchestrate key cellular processes including but not limited to transcription, translation, metabolism, and cell signaling. Delineating these interactions will aid in deciphering the regulation and function of these pathways and potential for manipulation. Proximity-dependent biotin identification (BioID) is quickly gaining popularity as a powerful tool for identifying novel protein-protein and proximity-based interactions in live cells. This technique relies on a promiscuous biotin ligase, which is fused to a protein of interest and, upon expression in the desired cell, will biotinylate proximal endogenous proteins. In vivo protein-protein interactions can be very transient and occur momentarily to facilitate signaling or a metabolic function. BioID is useful in identifying these weak and/or transient interactions that are not detected by traditional methods such as yeast two-hybrid or affinity purification. Here, we outline a BioID protocol that can be used as a workflow to guide a new application. © 2016 by John Wiley & Sons, Inc.

Bovine serum albumin further enhances the effects of organic solvents on increased yield of polymerase chain reaction of GC-rich templates

BACKGROUND

While being a standard powerful molecular biology technique, applications of the PCR to the amplification of high GC-rich DNA samples still present challenges which include limited yield and poor specificity of the reaction. Organic solvents, including DMSO and formamide, have been often employed as additives to increase the efficiency of amplification of high GC content (GC > 60%) DNA sequences. Bovine serum albumin (BSA) has been used as an additive in several applications, including restriction enzyme digestions as well as in PCR amplification of templates from environmental samples that contain potential inhibitors such as phenolic compounds.

FINDINGS

Significant increase in PCR amplification yields of GC-rich DNA targets ranging in sizes from 0.4 kb to 7.1 kb were achieved by using BSA as a co-additive along with DMSO and formamide. Notably, enhancing effects of BSA occurs in the initial PCR cycles with BSA additions having no detrimental impact on PCR yield or specificity. When a PCR was set up such that the cycling parameters paused after every ten cycles to allow for supplementation of BSA, combining BSA and organic solvent produced significantly higher yields relative to conditions using the solvent alone. The co-enhancing effects of BSA in presence of organic solvents were also obtained in other PCR applications, including site-directed mutagenesis and overlap extension PCR.

CONCLUSIONS

BSA significantly enhances PCR amplification yield when used in combination with organic solvents, DMSO or formamide. BSA enhancing effects were obtained in several PCR applications, with DNA templates of high GC content and spanning a broad size range. When added to the reaction buffer, promoting effects of BSA were seen in the first cycles of the PCR, regardless of the size of the DNA to amplify. The strategy outlined here provides a cost-effective alternative for increasing the efficiency of PCR amplification of GC-rich DNA targets over a broad size range.

The possibility of a false positive arising from sperm DNA in genetic diagnosis of bovine embryos

The present study was conducted to evaluate the effect of accessory sperm cells that adhered to the zona pellucida or blastomeres on the accuracy of genetic diagnosis of preimplantation embryos. The properties of sperm cells as a template for DNA amplification were examined using bovine sperm cells frozen-thawed or incubated in PBS after thawing for 7 days at 39 C. Sexing by loop-mediated isothermal amplification (LAMP) and claudin-16 genotyping by polymerase chain reaction (PCR) were performed using 10, 50 and 100 sperm cells. When sexing based on LAMP was performed, no amplified DNA was detected in 10 sperm-derived samples, whereas male-specific (10-60%) and gender-natural DNA (30-100%) sequences were detected in 50 and 100 sperm-derived samples. The detection rates for gender-natural DNA sequences were higher in incubated sperm samples than in sperm samples immediately after freeze-thawing. The detection rates for claudin-16 were low (7-13%) regardless of the concentration of sperm cells and the period of incubation after thawing. The present results showed that male-specific DNA, gender-natural DNA and claudin-16 sequences were not usually amplified from a small number of sperm cells (< or =10 cells). However, when a large number of sperm cells (> or =50 cells) were present, male-specific and gender-natural DNA sequences were amplified at a high rate, and claudin-16 DNA sequences were also occasionally detected. These results raise the possibility that accessory sperm cells may reduce the accuracy of the genetic diagnosis of bovine embryos. Therefore, steps to prevent the contamination of sperm cells, such as removal of the zona pellucida and washing of sample blastomeres, are necessary to obtain an accurate result.