Comparative DNA isolation behaviours of silica and polymer based sorbents in batch fashion: monodisperse silica microspheres with bimodal pore size distribution as a new sorbent for DNA isolation

Novel 3D-Printed Microfluidic Magnetic Platform for Rapid DNA Isolation

This study presents a novel miniaturized device as a 3D-printed microfluidic magnetic platform specifically designed to manipulate magnetic microparticles in a microfluidic chip for rapid deoxyribonucleic acid (DNA) isolation. The novel design enables the movement of the magnetic particles in the same or opposite directions with the flow or suspends them in continuous flow. A computational model was developed to assess the effectiveness of the magnetic manipulation of the particles. Superparamagnetic monodisperse silica particles synthesized in-house are utilized for the isolation of fish sperm DNA and human placenta DNA. It was demonstrated that the proposed platform can perform DNA isolation within 10 min with an isolation efficiency of 50% at optimum operating conditions.

Cibacron Blue F3GA ligand dye-based magnetic silica particles for the albumin purification

Dye-ligand affinity chromatography is among the increasingly popular affinity chromatography based on molecular recognition for the purification of albumin. This study focuses on the binding of Cibacron Blue F3GA ligand dye with magnetic silica particles and purification by separation. Mono-disperse silica particles with bimodal pore size distribution were employed as a high-performance adsorbent for human serum albumin (HSA) protein purification under equilibrium conditions. The synthesized ligand-dye affinity based magnetic silica particles were characterized by electron spin resonance, Fourier-transform infrared spectroscopy, scanning electron microscopy, vibrating sample magnetometer, elemental analysis, and dispersive X-ray analysis. The HSA purification performance of the proposed material in the presence of a magnetic field was relatively investigated using magnetic-based particles with similar morphologies. The maximum adsorption capacity for HSA in an artificial plasma medium was defined as 48.6 mg/g magnetic silica particle. By using the designed magnetic silica particles, 1.0 M NaCl solution was successfully utilized for obtaining quantitative desorption with HSA. However, continued HSA purification performances of magnetic-based particles were significantly lower concerning the ligand-dye magnetic silica particles. The purity of the removed albumin was about 97%. The magnetic silica particles could be utilized many times without decreasing their protein adsorption capacities remarkably.

Distribution Behavior of Single-Stranded DNA Molecules in an Amino-Group-Functionalized Silica Microparticle

In this study, we investigated the distribution behavior of single-stranded DNA molecules with 20 bases in silica particles (particle size: ∼30 μm) using confocal fluorescence microspectroscopy. The distribution kinetics was investigated under various conditions, such as the type of base (adenine, thymine, guanine, and cytosine), pore size of the particle (30 and 50 nm), and salt concentration (100, 200, and 500 mM), which changed the distribution behavior. At high salt concentrations, we observed sigmoidal kinetic behavior, which does not occur in the general distribution of small organic molecules but is often observed in protein aggregation and nuclear growth. An analytical model based on DNA aggregation explained the sigmoidal distribution behavior well, and this model also worked well when the number of DNA molecules involved in DNA aggregation was greater than two. The intraparticle diffusion of DNA molecules was analyzed using the pore and surface diffusion model. As a result, the intraparticle diffusion of DNA aggregates mainly occurs according to surface diffusion, and the surface diffusion coefficient has the same value ((2.4-6.7) × 10^-9 cm² s^-1) independent of the pore size and type of base.

Comparison of three commercial DNA extraction kits for the enhancement of PCR assay sensitivity for Xanthomonas euvesicatoria pv. allii

AIM

The study was carried out to evaluate three commercial DNA extraction kits, Probe GS, FitoSorb and Sorb GMO, thus identifying the most suitable for isolating the phytopathogenic bacteria Xanthomonas euvesicatoria pv. allii.

MATERIALS AND METHODS

Onion seed samples were prepared which were inoculated with bacterial concentrations ranging from 10¹ to 10⁷  CFU per ml. Real-time PCR was performed to determine the efficacy of the isolated DNA in enhancing the sensitivity of the assay. The DNA extracted by Probe GS had the best detectability, having been detected at the lowest concentration used in the study 10¹  × 3 CFU per ml. FitoSorb and Sorb GMO yielded DNA with a higher and similar limit of detection 10³  × 3 CFU per ml. Furthermore, Probe GS had the lowest cycle at every concentration tested as compared to the other methods.

CONCLUSION

Therefore, Probe GS proved to be the most optimized kit for the extraction of X. euvesicatoria pv. allii, hence enhanced degree of sensitivity for the assay.

IMPACT AND SIGNIFICANCE OF THE STUDY

The findings generated in this study can be used by phytosanitary laboratories to develop highly rapid and accurate diagnostic protocols for X. euvesicatoria pv. allii.

Recent trends in sorbents for bioaffinity chromatography

Isolation or enrichment of biological molecules from complex biological samples is mostly a prerequisite in proteomics, genomics, and glycomics. Different techniques have been used to advance the efficiency of the purification of biological molecules. Bioaffinity chromatography is one of the most powerful technique that plays an important role in the isolation of target biological molecules by the specific interactions with ligands that are immobilized on different support materials. This review examines the recent developments in bioaffinity chromatography particularly over the past 5 years in the literature. Also properties of supports, immobilization techniques, types of binding agents, and methods used in bioaffinity chromatography applications are summarized.

Efficiency of DNA Isolation Methods Based on Silica Columns and Magnetic Separation Tested for the Detection of Mycobacterium avium Subsp. Paratuberculosis in Milk and Faeces

Timely and reliable detection of animals shedding Mycobacterium avium subsp. paratuberculosis (MAP) should help to effectively identify infected animals and limit infection transmission at early stages to ensure effective control of paratuberculosis. The aim of the study was to compare DNA extraction methods and evaluate isolation efficiency using milk and faecal samples artificially contaminated by MAP with a focus on modern instrumental automatic DNA isolation procedures based on magnetic separation. In parallel, an automatic and manual version of magnetic separation and two methods of faecal samples preparation were compared. Commercially available DNA isolation kits were evaluated, and the selected kits were used in a trial of automatic magnetic beads-based isolation and compared with the manual version of each kit. Detection of the single copy element F57 was performed by qPCR to quantify MAP and determine the isolation efficiency. The evaluated kits showed significant differences in DNA isolation efficiencies. The best results were observed with the silica column Blood and Tissue kit for milk and Zymo Research for faeces. The highest isolation efficiency for magnetic separation was achieved with MagMAX for both matrices. The magnetic separation and silica column isolation methods used in this study represent frequently used methods in mycobacterial diagnostics.

Surface-imprinted silica particles for Concanavalin A purification from Canavalia ensiformis

Concanavalin A is a representative of the plant protein group known as lectins. Many lectin proteins have useful characteristics for studies on cell division and cell surfaces. In this study, a new adsorbent for the specific separation of Concanavalin A was prepared by applying a silica particle surface imprinting method. First, silica particles were activated via acidic treatment, and then, 3-methacryloyloxypropyl trimethoxysilane (MPTMS) was used for modification. For the preparation of Concanavalin A surface-imprinted silica particles (Con A-MISPs), N-methacryloyl-l-histidine methyl ester (MAH) was used as a functional monomer. The silica particles were characterized using a Zetasizer, scanning electron microscopy equipment (SEM), and Fourier transform infrared spectroscopy (FTIR). The effects of parameters such as the pH, initial concentration of Concanavalin A, and temperature on the adsorption of Concanavalin A were determined. The maximum Concanavalin A adsorption onto Con A-MISPs was observed to be 305.2 mg/g at a pH of 6. The reusability of the Con A-MISPs was approximately 93.5%. The non-imprinted silica particles (NISPs) were prepared in the same manner without Concanavalin A to compare the surface imprinting factor. Selective binding studies were carried out with lysozyme and hemoglobin molecules. The selectivity of the Con A-MISPs was also investigated by isolating Concanavalin A from Canavalia ensiformis. The purity of the Concanavalin A was shown by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE).

Isolation of RNA and beta-NAD by phenylboronic acid functionalized, monodisperse-porous silica microspheres as sorbent in batch and microfluidic boronate affinity systems

Monodisperse-porous silica microspheres 5.5 μm in size were obtained by a staged shape templated hydrolysis-condensation method, with a bimodal pore-size distribution. 3-aminophenylboronic acid (APBA) was covalently attached onto the silica microspheres with a capacity of 0.476 mmol APBA/g microspheres. The boronate affinity isolation behaviour of ribonucleic acid (RNA) containing cis-diol at 3'-end was investigated by using APBA attached-silica microspheres as the sorbent in batch fashion. A short-chain diol carrying agent, β-nicotinamide adenine dinucleotide (β-NAD) was used as a target molecule with stronger affinity for phenylboronic acid ligand. The maximum equilibrium adsorptions for RNA and β-NAD were determined as 60 and 159 mg/g sorbent, respectively. By using the synthesized sorbent, phosphate buffer at pH 7.0 containing sorbitol was successfuly used as a mild elution medium for obtaining quantitative desorptions with both RNA and β-NAD. RNA isolations from mammalian and bacterial cells were successfully performed while protecting the structural integrity of RNA via boronate affinity interaction in batch fashion. A microfluidic boronate affinity system including a microcolumn 300 μm in diameter was also constructed using APBA attached-silica microspheres as the stationary phase. The breakthrough curves of microfluidic system were obtained by studying with different feed concentrations of RNA and β-NAD. Quantitative desorptions and satisfactory isolation yields were obtained with RNA and β-NAD in the microfluidic system. The proposed system is useful for boronate affinity applications in genomics or proteomics in which valuable cis-diols at low concentrations are recovered from low-volume samples.

Next-generation sequencing yields the complete mitogenome of red-crowned crane (G. japonensis)

In this study, the complete mitogenome sequence of red-crowned crane (G. japonensis) has been decoded by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 16,727 bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for red-crowned crane phylogeny.

Next-generation sequencing yields the complete mitogenome of wattled crane (Bugeranus carunculatus)

In this study, the complete mitogenome sequence of wattled crane (Bugeranus carunculatus) has been decoded by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 16,679 bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for wattled crane phylogeny.

Complete mitochondrial genome of a Siberian Crane (Grus leucogeranus)

The complete mitochondrial genome (mtDNA) of hemocyte from Siberian Crane (Grus leucogeranus) was sequenced using high-throughput genetic sequencing, and mitochondrial genome was assembled using MITObim tools according complete mitochondrial genome of Grus leucogeranus (NCBI Reference Sequence: NC_020574.1). The assembled mitogenome, consisting of 16,747 bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Siberian Crane phylogeny.