Circulating Cell-Free DNA Extraction from Liquid Biopsy for Cancer Research.

As the number of cancer patients globally increases, a need for reliable biomarkers including circulating tumour DNA from liquid biopsy for diagnosis, prognosis and monitoring of the disease is rising. Currently, mainly tissue samples from biopsy are used, but there are certain limitations: firstly, it is an invasive technique, and secondly, in some cases it is almost impossible to obtain an acceptable tissue sample. This could be changed by using circulating cell-free DNA from liquid biopsy, which also gives the possibility of repeated examination. Here, we focus on the options of isolating circulating cell-free DNA from plasma samples using two isolation techniques: precision manual QIAamp Circulating Nucleic Acid Kit and automatic MagNA Pure Compact (MPC) using Nucleic Acid Isolation Kit I. Manual extraction gave significantly better yields of circulating tumour DNA (P < 0.05). This DNA also had less contaminants (organic compounds or proteins). DNA obtained by both tested methods of isolation is suitable for subsequent molecular genetic methods.

The Effects of Different Storage Conditions and Repeated Freeze/Thaw Cycles on the Concentration, Purity and Integrity of Genomic DNA.

The crucial requirement of molecular genetic methods is high-quality input material. The key question is "how to preserve DNA during long-term storage." Biobanks are recommended to aliquot isolated DNA into provided volumes. The aim of this study was to analyse the effect of repeated freezing and thawing on the genomic DNA integrity, quality and concentration. The aliquoted DNA isolated from blood cells using the automatic MagNA system and manual salting out method underwent freeze/thaw cycles at different storage conditions (-20 °C, -80 °C and liquid nitrogen). The average initial concentrations were 270.6 ng/µl (salting out method) and 125.0 ng/µl (MagNA). All concentration deviations relative to the concentration after the first freeze/ thaw cycle were less than 5 % for -20 °C and -80 °C cycling with both isolation methods. The average percentage differences of liquid nitrogen samples were higher, and the MagNA isolation method showed significant differences. There were no significant changes in the DNA purity or quality. The repeating freeze/ thaw up to 100 cycles (through -20 °C and -80 °C, respectively) did not significantly influence the integrity, concentration, or purity of genomic DNA, suggesting that storage of samples in high-volume pools without multiple aliquoting is possible. Storage in a freezer seems to be the most suitable way of long-term DNA preservation, because liquid nitrogen storage leads to formation of DNA clumps.

Plasma osteopontin levels, but not its myocardial expression, reflect heart failure severity in recently diagnosed dilated cardiomyopathy.

BACKGROUND: Elevated levels of the extracellular matrix glycoprotein osteopontin (OPN) may be detected in both myocardium and plasma under various pathological conditions affecting the heart. Several studies demonstrated increased plasma OPN levels in patients with heart failure due to dilated cardiomyopathy (DCM), while other studies showed high OPN expression levels in the myocardium of such patients. However, very little is known about OPN levels in both plasma and myocardium of the same individual with DCM. Therefore, we aimed to compare plasma OPN levels and levels of myocardial OPN expression in patients with recent-onset DCM (Ro-DCM). METHODS: We examined plasma OPN as well as creatinine, C­reactive protein (CRP), brain natriuretic peptide (BNP), and troponin I levels in 25 patients with Ro-DCM. Furthermore, all subjects underwent transthoracic echocardiography, selective coronary angiography, and endomyocardial biopsy (EMB) for the assessment of myocardial OPN expression. RESULTS: No significant correlation between myocardial OPN expression and clinical, biochemical, or echocardiographic parameters was found. In log transformation analysis, plasma OPN levels correlated significantly with BNP levels (r = 0.46, p = 0.031), with CRP levels (r = 0.52, p = 0.015), and with early diastolic mitral annular velocity (r = -0.57, p = 0.009). There was a borderline association between the plasma OPN log value and New York Heart Association class (p = 0.053). CONCLUSION: Plasma OPN levels reflect heart failure severity in patients with Ro-DCM. Myocardial OPN expression is not associated with either plasma OPN levels or markers of heart failure in these individuals.

Mutational analysis of ACTN4, encoding α-actinin 4, in patients with focal segmental glomerulosclerosis using HRM method.

α-Actinin 4, encoded by ACTN4, is an F-actin crosslinking protein which belongs to the spectrin gene superfamily. It has a head-to-tail homodimer structure with three main domains. Mutations in ACTN4 are associated with idiopathic nephrotic syndrome (NS). However, until today only a few mutations have been described in this gene. We used genomic DNA of 48 patients with focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD) to screen for ACTN4 mutations by high-resolution melting analysis (HRM). Suspect samples were sequenced and compared with healthy controls. To investigate the prevalence and possible effect of some substitutions found in FSGS/MCD patients we also looked for these changes in patients with IgA nephropathy (IgAN) and membranous glomerulonephritis (MGN). We found 20 exonic and intronic substitutions in the group of 48 Czech patients. The substitution 2242A>G (p.Asn748Asp) is a candidate mutation which was identified in one patient but not in any of the 200 healthy controls. Exon 19 seems to be a variable region due to the amount of revealed polymorphisms. In this region we also found three unreported substitutions in IgAN patients, c.2351C>T (p.Ala784Val), c.2378G>A (p.Cys793Tyr) and c.2393G>A (p.Gly798Asp). These substitutions were not found in any tested healthy controls. To conclude, the ACTN4 mutations are not a frequent cause of FSGS/MCD in Czech adult patients. One new ACTN4 mutation has been identified.

Biosorption of water-soluble dyes on magnetically modified Saccharomyces cerevisiae subsp. uvarum cells.

Brewer's yeast (bottom yeast, Saccharomyces cerevisiae subsp. uvarum) cells were magnetically modified using water based magnetic fluid stabilized with perchloric acid. Magnetically modified yeast cells efficiently adsorbed various water soluble dyes. The dyes adsorption can be described by the Langmuir adsorption model. The maximum adsorption capacity of the magnetic cells differed substantially for individual dyes; the highest value was found for aniline blue (approx. 220 mg per g of dried magnetic adsorbent).

Magnetic alginate microparticles for purification of alpha-amylases.

Spherical magnetic alginate microparticles (25-60 microm in diameter) were prepared using the microemulsion system, with water-saturated 1-pentanol as the organic phase. The limited solubility of 1-pentanol in water enabled simple removal of the organic solvent from the prepared beads with water solution. The prepared alginate microparticles were used as magnetic affinity adsorbents for specific purification of alpha-amylases. Enzyme activity was eluted by 1.0 M maltose. alpha-Amylases from Bacillus amyloliquefaciens and porcine pancreatic acetone powder were purified 9- and 12-fold with 88 and 96% activity recovery, respectively.

Detection of low concentrations of malachite green and crystal violet in water.

A simple procedure for the detection of low concentrations of malachite green and crystal violet in water is presented. The dyes were preconcentrated from 1,000 ml of water samples with magnetic solid phase extraction using magnetic affinity adsorbent (magnetite with immobilized copper phthalocyanine dye). Due to the magnetic properties of the adsorbent the preconcentration process can also be performed in water samples containing suspended solids. After elution of the captured dyes, their presence in eluates was detected spectrophotometrically. Concentrations of both dyes in the range 0.5-1.0 microgl(-1) of water could be reproducibly detected. The dyes can be detected not only in potable water, but also in river ones.

Immunomagnetic separation of Escherichia coli O26, O111 and O157 from vegetables.

AIMS: Raw fruits and vegetables have been increasingly associated with human infections caused by Shiga toxin-producing Escherichia coli. This study evaluates the isolation and detection of E. coli O26, O111 and O157 from vegetable samples using immunomagnetic particles. METHODS AND RESULTS: Standard cultivation and immunomagnetic separation (IMS) procedures were compared. It was found that immunomagnetic particles could efficiently concentrate E. coli cells, detecting significantly more bacteria than with standard cultivation procedures. CONCLUSION: Bacteria were detected in 93-100% of the inoculated samples using the IMS procedure, but only 36-93% samples tested by standard cultivation procedures were found to be positive. SIGNIFICANCE AND IMPACT OF THE STUDY: The results indicate that E. coli O26, O111 and O157 immunomagnetic particles can be a very useful and efficient tool for the detection of E. coli strains in raw vegetables, and could probably be used with samples of animal origin.

Use of magnetic techniques for the isolation of cells.

Magnetic separation is an emerging technology using magnetism, sometimes in combination with conventional separation or identification methods, to purify cells, cell organelles and biologically active compounds (nucleic acids, proteins, xenobiotics) directly from crude samples. Several magnetic separation procedures have been developed to isolate target cells specifically. The purpose of this short review is to summarize various methodologies, strategies and materials which can be employed for the selection and separation of target cells with the help of magnetic field and thus to help the novices in this field to be able to orient themselves in vast amount of literature available. Immunomagnetic separations employing specific antibodies to label the target cells represent the most often used approach and are discussed in detail.

Spectrophotometric determination of effective proteolytic activity in biodetergents.

A new procedure for the determination of effective proteolytic activity in biodetergents has been developed. Effective enzyme activity is defined as the activity exhibited by the tested enzyme under real washing conditions, i.e., in the water suspensions of the biodetergent tested at the working temperature (usually 40 degrees C). Two insoluble chromolytic substrates, namely black gelatin (gelatin cross-linked with glutaraldehyde in the presence of black drawing ink) and the protease substrate based on the immobilization of dyed casein in the structure of polyacrylamide gel (blue casein-PAAG) were successfully used. It was found that there is a great difference in effective proteolytic activity among various biodetergents. The proposed procedure is suitable both for the manufacturers for a quick control of their products and for the quality control laboratories.

Batch isolation of hen egg white lysozyme with magnetic chitin.

Biospecific magnetic sorbent for lysozyme isolation (magnetic chitin) has been prepared from magnetic chitosan after acetylation with acetic anhydride. The capacity of magnetic chitin was 2.5 mg of lysozyme per 1 ml of sorbent.

Black substrate for spectrophotometric determination of cellulase activity in coloured solutions.

A simple procedure for spectrophotometric determination of cellulase activity in coloured solutions is described. CM-cellulose, cross-linked with epichlorhydrin in the presence of black drawing ink, is used as an insoluble chromolytic substrate. The absorbance of reaction mixture filtrates are read in the near infra-red region (at 800-900 nm) where the absorbances of contaminating coloured substances are substantially lowered; by contrast, black drawing ink released from the substrate during the action of cellulases absorbs strongly at these wavelengths.