An SPRI beads-based DNA purification strategy for flexibility and cost-effectiveness

Draft genome sequence of carbapenems-resistant Acinetobacter baumannii Hakim RU_CBWP strain isolated from a pond surface water in Bangladesh

We have revealed the genomic sequence of Acinetobacter baumannii strain Hakim RU_CBWP isolated from pond surface water. Our assembled genome covers 3.787 Mb with 45.5629× coverage, showcasing an average GC content of 38.60%. This genome contains two CRISPR arrays, 17 prophages, 22 antibiotic resistance genes, and 20 virulence factor genes.

Draft genome sequence of multidrug-resistant Klebsiella pneumoniae Hakim-RU strain isolated from a patient with urinary tract infections in Bangladesh

We unveil the genomic sequence of the Klebsiella pneumoniae Hakim-RU strain isolated from a patient with urinary tract infections. Our assembled genome spans 4.3 Mb with 73.0× coverage, an average GC content of 57.41%, 4 plasmids, 2 CRISPR arrays, 10 prophages, 41 antibiotic resistance genes, and 6 virulence factor genes.

Ampholytic ion-exchange magnetic beads: a promising tool for selecting short fragments in circulating cell-free DNA analysis

Objective

For liquid biopsy of cancer, the extraction of circulating cell-free DNA (cfDNA) from plasma is required. We evaluated the efficacy of use of magnetic submicron particles coated with abundant small zwitterions (MSP-ZEWBs) for extracting short fragments of cfDNA.

Methods

We developed and optimized an MSP-ZEWB-based cfDNA extraction method using ampholytic ion-exchange materials and compared its results with those using a control kit. We measured the cfDNA concentration by quantitative polymerase-chain-reaction and using the Qubit method and analyzed cfDNA fragmentation patterns using a bioanalyzer.

Results

The fragment size of cfDNA isolated from glycine hydrochloric acid at a pH of 2.2 exhibited a better alignment with the DNA marker. The highest DNA intensity was observed at the final concentration of 0.8% polyethylene glycol 8000. The intensity of cfDNA decreased significantly when isolated from plasma with DNA marker using MSP-ZEWBs with an adsorption buffer containing guanidine hydrochloride or isothiocyanoguanidine. All fragments were successfully extracted using MSP-ZEWBs from both plasma and phosphate-buffered saline. Notably, the intensity of short cfDNA fragments isolated using MSP-ZEWBs remained consistent for recovery of long DNA fragments. indicating a potential selective of small fragments.

Conclusion

The extraction of plasma cfDNA with MSP-ZEWBs requires no protein denaturation, shows resistance to cells remaining in plasma, and demonstrates higher overall efficiency and better reproducibility than other extraction methods. Use of MSP-ZEWBs may greatly enhance liquid biopsy of cancers through the analysis of plasma cfDNA in clinical practice.

Automated Purification of DNA Origami with SPRI Beads

DNA origami synthesis is a well-established technique with wide-ranging applications. In most cases, the synthesized origami must be purified to remove excess materials such as DNA oligos and other functional molecules. While several purification techniques are routinely used, all have limitations, and cannot be integrated with robotic systems. Here the use of solid-phase reversible immobilization (SPRI) beads as a scalable, high-throughput, and automatable method to purify DNA origami is demonstrated. Not only can this method remove unreacted oligos and biomolecules with yields comparable to existing methods while maintaining the high structural integrity of the origami, but it can also be integrated into an automated workflow to purify simultaneously large numbers and quantities of samples. It is envisioned that the SPRI beads purification method will improve the scalability of DNA nanostructures synthesis both for research and commercial applications.

Draft genome sequence of multidrug-resistant Citrobacter portucalensis BAU_133-2 strain isolated from a domestic duck (Anas platyrhynchos domesticus) in Bangladesh

We announce the genome sequence of the Citrobacter portucalensis BAU_133-2 strain isolated from a domestic duck. Our assembled genome contained a length of 4.8 Mb, 110.0× genome coverage, 51.91% of an average GC content, 1 plasmid, 1 CRISPR array, 8 prophages, 27 antibiotic resistance genes, and 75 virulence factor genes.

Pneumatic nano-sieve for CRISPR-based detection of drug-resistant bacteria

The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieved an on-chip concentration factor of ∼15-fold for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU mL-1. This developed approach provides a rapid, precise, and centrifuge-free solution suitable for point-of-care diagnostics, with the potential to significantly improve patient outcomes in resource-limited medical conditions.

Pneumatic Nano-Sieve for CRISPR-based Detection of Drug-resistant Bacteria

The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieve an on-chip concentration factor of 15 for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU/mL. This developed approach provides a rapid, precise, and centrifuge-free solution suitable for point-of-care diagnostics, with the potential to significantly improve patient outcomes in resource-limited medical conditions.

Shaking Device for Homogeneous Dispersion of Magnetic Beads in Droplet Microfluidics

Magnetic beads (or particles) having a size between 1 and 5 µm are largely used in many biochemical assays devoted to both purification and quantification of cells, nucleic acids, or proteins. Unfortunately, the use of these beads within microfluidic devices suffers from natural precipitation because of their size and density. The strategies applied thus far to cells or polymeric particles cannot be extended to magnetic beads, mainly due to their magnetization and their higher densities. We report an effective shaking device capable of preventing the sedimentation of beads that are stored in a custom PCR tube. After the characterization of the operating principle, the device is validated for magnetic beads in droplets, leading to an equal distribution between the droplets, barely affecting their generation.