Analysis of DNA by Southern Blotting

Long-term labelling and tracing of endodermal cells using a perpetual cycling Gal4-UAS system

Cell labelling and lineage tracing are indispensable tools in developmental biology, offering powerful means with which to visualise and understand the complex dynamics of cell populations during embryogenesis. Traditional cell labelling relies heavily on signal stability, promoter strength and stage specificity, limiting its application in long-term tracing. In this report, we optimise and reconfigure a perpetual cycling Gal4-UAS system employing a previously unreported Gal4 fusion protein and the autoregulatory Gal4 expression loop. As validated through heat-shock induction, this configuration ensures sustained transcription of reporter genes in target cells and their descendant cells while minimising cytotoxicity, thereby achieving long-term labelling and tracing. Further exploiting this system, we generate zebrafish transgenic lines with continuous fluorescent labelling specific to the endoderm, and demonstrate its effectiveness in long-term tracing by showing the progression of endoderm development from embryo to adult, providing visualisation of endodermal cells and their derived tissues. This continuous labelling and tracing strategy can span the entire process of endodermal differentiation, from progenitor cells to mature functional cells, and is applicable to studying endoderm patterning and organogenesis.

Efficient solid-phase extraction of oligo-DNA from complex media using a nitrocellulose membrane modified with carbon nanotubes and aminated reduced graphene oxide

Oligonucleotides are essential for gene regulation, expression, and disease biomarker identification, yet their small size presents challenges due to lower abundance and increased susceptibility to degradation in biological samples. Addressing these challenges, a novel approach was developed for effective oligonucleotide extraction, consisting of a commercially available nitrocellulose (NC) membrane non-covalently modified with a combination of single-walled carbon nanotubes (SWCNTs) and polyethylene glycol (PEG) aminated reduced graphene oxide (GA). The membrane was evaluated for the extraction of a fluorescent labelled single-stranded deoxyribonucleic acid (ssDNA), with fewer than 30 nucleotides, from complex solutions containing various ionic species (MnCl2, MgCl2, and MnCl2/MgCl2). Fourier transform infrared spectroscopy confirmed successful modification, revealing characteristic peaks of NC, SWCNT, and GA. Raman spectroscopy and X-ray photoelectron spectroscopy showed distinctive changes after the membrane interaction with divalent cations and ssDNA. Scanning electron microscopy revealed morphological changes in the SWCNTs/GA-NC hybrid membrane, showing a smoother surface compared to the porous structure of the unmodified NC membrane. Wettability assays indicated hydrophobic properties for the SWCNT/GA-NC hybrid membrane, with a water contact angle exceeding 110°, contrasting with the hydrophilic nature of the NC membrane, which exhibits a contact angle of 26.7°. Optimal performance of the SWCNTs/GA-NC hybrid membrane was observed when incubated in MgCl2, demonstrating the highest fluorescence emission at approximately 670 relative fluorescence units. This corresponded to the extraction of approximately 781 pg (≈ 16%) of the total oligo-DNA, highlighting the enhanced efficacy of the hybrid material compared to the unmodified NC membrane, which extracted only 318 pg (≈ 7%) of oligo-DNA.

Dissemination of virulence and resistance genes among Klebsiella pneumoniae via outer membrane vesicle: An important plasmid transfer mechanism to promote the emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae

Klebsiella pneumoniae is well-known opportunistic enterobacteria involved in complex clinical infections in humans and animals. The domestic animals might be a source of the multidrug-resistant virulent K. pneumoniae to humans. K. pneumoniae infections in domestic animals are considered as an emergent global concern. The horizontal gene transfer plays essential roles in bacterial genome evolution by spread of virulence and resistance determinants. However, the virulence genes can be transferred horizontally via K. pneumoniae-derived outer membrane vesicles (OMVs) remains to be unreported. In this study, we performed complete genome sequencing of two K. pneumoniae HvK2115 and CRK3022 with hypervirulent or carbapenem-resistant traits. OMVs from K. pneumoniae HvK2115 and CRK3022 were purified and observed. The carriage of virulence or resistance genes in K. pneumoniae OMVs was identified. The influence of OMVs on the horizontal transfer of virulence-related or drug-resistant plasmids among K. pneumoniae strains was evaluated thoroughly. The plasmid transfer to recipient bacteria through OMVs was identified by polymerase chain reaction, pulsed field gel electrophoresis and Southern blot. This study revealed that OMVs could mediate the intraspecific and interspecific horizontal transfer of the virulence plasmid phvK2115. OMVs could simultaneously transfer two resistance plasmids into K. pneumoniae and Escherichia coli recipient strains. OMVs-mediated horizontal transfer of virulence plasmid phvK2115 could significantly enhance the pathogenicity of human carbapenem-resistant K. pneumoniae CRK3022. The CRK3022 acquired the virulence plasmid phvK2115 could become a CR-hvKp strain. It was critically important that OMVs-mediated horizontal transfer of phvK2115 lead to the coexistence of virulence and carbapenem-resistance genes in K. pneumoniae, resulting in the emerging of carbapenem-resistant hypervirulent K. pneumoniae.

Southern Hybridization of Radiolabeled Probes to Nucleic Acids Immobilized on Membranes

In this protocol, restriction fragments that have been transferred to a membrane by Southern blotting are hybridized to a labeled probe. Methods for stripping the probe from the membrane are also included.

Southern Blotting

In Southern blotting, DNA is digested with one or more restriction enzymes, and the resulting fragments are separated according to size by electrophoresis through a standard agarose gel. The DNA is then denatured in situ and transferred from the gel to a solid support (usually a nylon or nitrocellulose membrane). The relative positions of the DNA fragments are preserved during their transfer to the membrane. The DNA is then fixed to the membrane and prepared for hybridization. Alternatively, DNA can be simultaneously transferred from the top and bottom surfaces of a single agarose gel to two membranes. This procedure is useful when the need arises to analyze the same set of restriction fragments with two different probes. Transfer of DNA fragments is rapid, but the efficiency is low because the agarose gel quickly becomes dehydrated as fluid is withdrawn from both sides. The method therefore works best when the target sequences are present in high concentration (e.g., when analyzing cloned DNAs [plasmids, bacteriophages, cosmids, PACs, or BACs] or less complex genomes [those of Saccharomyces cerevisiae or Drosophila]). Too little mammalian genomic DNA is transferred to allow signals from single-copy sequences to be detected in a reproducible or timely fashion.