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We demonstrate that gDNA can be conveniently and efficiently isolated and purified using standard agarose gel electrophoresis, band excision and gel purification. This method yields a substantial amount at microgram levels of gDNA per gel cleanup with high purity. An RNase A treatment step can be omitted. The quality of gDNA is suitable for next-generation sequencing, resulting in >10 Mb reads and high-quality read data (Phred score >28 up to 100 of 150 base reads). Furthermore, the gDNA can be kept intact in a gel slice for several days. This method has been tested for dictyostelids, bacteria and plants.

Analysis of several parameters is required for adequate quality control in umbilical cord blood units (UCBU) when used for therapeutic purposes.To optimize colony-forming units (CFU) from clonogenic cultures and to detect the human papillomavirus (HPV) genome in UCBU.One hundred and forty-one umbilical cord blood (UCB), segment or CFU samples from UCBU clonogenic cultures were included. DNA extraction, quantification and endogenous GAPDH gene PCR amplification were carried out. Subsequently, HPV L1 gene was detected using the MY09/MY11 and GP5/GP6+ oligonucleotides. PCR products were analyzed with electrophoresis in agarose gel. CFU-extracted purified DNA was analyzed by electrophoresis in agarose gel, as well as some DNAs, using the sequence-specific priming technique.CFU-extracted DNA concentration was higher in comparison with that of UCB (p = 0.0041) and that of the segment (p0.0001), as well as that of UCB in comparison with that of the segment (p0.0001). All samples were positive for GAPDH amplification and negative for MY09/MY/11 and GP5/GP6+.Cryopreserved UCBUs were HPV-negative. Obtaining CFU DNA from clonogenic cultures with high concentrations and purity is feasible.Se requiere analizar diversos parámetros para el control de calidad adecuado de las unidades de sangre de cordón umbilical (USCU) cuando se utilizan con fines terapéuticos.Optimizar las unidades formadoras de colonias (UFC) de cultivos clonogénicos y detectar el genoma del virus del papiloma humano (VPH) en USCU.Se incluyeron 141 muestras de sangre de cordón umbilical (SCU), de segmento y de UFC de cultivos clonogénicos de USCU. Se realizó extracción de ADN, cuantificación y amplificación por PCR del gen endógeno GAPDH. Se detectó el gen L1 del VPH con los oligonucleótidos MY09/MY11 y GP5/GP6+; los productos de PCR se migraron en electroforesis de agarosa. El ADN purificado de las UFC se analizó mediante electroforesis de agarosa y algunos ADN, con la técnica sequence specific priming.La concentración de ADN extraído de UFC fue superior comparada con la de SCU (p = 0.0041) y la de segmento (p0.0001); así como la de SCU comparada con la de segmento (p0.0001). Todas las muestras fueron positivas para la amplificación de GAPDH y negativas para MY09/MY11 y GP5/GP6+.Las USCU criopreservadas fueron VPH netativas; además, es factible obtener ADN en altas concentraciones y con alta pureza a partir de UFC de los cultivos clonogénicos.

In the production of novel biological products, plasmids are often engineered into delivery vectors for target genes, which can be used directly as vaccines or as intermediate products for gene/cell therapy. Plasmid DNA exists in several topological forms such as supercoiled, linear, and open circular. As supercoiled plasmid shows the highest efficiency in transfecting eukaryotic cells, the content of supercoiled plasmids becomes an important indicator of plasmid quality. CGE is an effective analysis method for separating different topological structures of plasmids. For the purpose of providing plasmid manufacturers and regulatory agencies with an efficient and readily used tool for monitoring the quality of plasmids, this article identifies the optimal separation and detection conditions of CGE, presents a platform-based plasmid analytical method, and uses plasmid of different sizes to verify the feasibility of this method. In terms of detector, the LIF detector has obvious advantages over the ultraviolet detector in sensitivity and resolution. Using the optimal CE condition (10× gel buffer), baseline separation of different topological forms and impurities can be achieved for different plasmid sizes (5.9, 7.8, 15.4 kb). In addition, 6.5 kb plasmid was used to compare the different separation technologies such as CGE-LIF, ion exchange chromatography and agarose gel electrophoresis. The result shows that CGE-LIF can provide better resolution and quantitation accuracy than ion exchange chromatography and agarose gel electrophoresis. CGE-LIF, as a quick and convenient method to separate and quantify plasmids, has the advantages of high sensitivity, high resolution, and high quantitative accuracy. Therefore, it is ideal for analysis of plasmids with different sizes, and it can also be used as a platform method for manufacturers and regulatory agencies to monitor the purity and stability of plasmids.

Capillary electrophoresis is a method with a long history of developments which enables monitoring of several pathological processes and has an irreplaceable role in screening for presence of M- protein. The aim of this study was to assess analytical performance of Sebia and Helena systems, as well as their screening efficiency for M-protein by identifying characteristic electrophoretic pattern abnormalities. The controls were analyzed in triplicate over a five- day period. Comparability testing was performed on 46 (Capillarys3Octa) and 49 (V8Nexus) serum samples with routinely used Capillarys2. Electropherograms (EPGs) were reviewed by two specialists independently to select samples for further processing by immunofixation. All precision test results met the eligibility criteria by Ricos et al. The correlation coefficients higher than 0.8 indicated excellent comparability although the results were slightly more comparable among the same manufacturer systems. There were no variations in observed abnormalities in EPGs when Capillarys systems were compared, but a disparity was detected in 11/49 EPGs on comparing Capillarys2 and V8Nexus. The cause of the detected difference could be in a different graphical presentation of the findings and in a lesser resolution of the applied buffer. The impression is that the V8Nexus system combined with the utilized buffer provides greater resolution in the alpha-1 and alpha-2 globulin fractions, but that it declines in the gamma globulin fraction. The precision and estimated accuracy criteria were met by both systems. Comparison results implied that capillary systems are not equally effective in M-protein screening, highlighting the necessity to include system screening efficiency in analytical evaluation.

Low-cost analytical solutions built around microcomputers like the Raspberry Pi help to facilitate laboratory investigations in resource limited venues. Here, three camera modules (V1.3 with and without filter, as well as NoIR) that work with this microcomputer were assessed for their suitability in imaging fluorescent DNA following agarose gel electrophoresis. Evaluation of their utility was based on signal-to-noise (SNR) and noise variance metrics that were developed. Experiments conducted with samples were subjected to Polymerase Chain Reaction (PCR), and the amplified products were separated using gel electrophoresis and stained with Midori green. Image analysis revealed the NoIR camera performed the best with SNR and noise variance values of 21.7 and 0.222 respectively. In experiments conducted using UV LED lighting to simulate ethidium bromide (EtBr) excitation, the NoIR and V1.3 with filter removed cameras showed comparable SNR values.

Occult Hepatitis B Infection (OBI) is a critical risk factor for triggering post-transfusion hepatitis (PTH), cirrhosis, hepatocellular carcinoma, and hepatitis B virus (HBV) reactivation, which β-thalassemia major (BTM) patients are at risk of it due to multiple blood transfusions. This study was aimed at determining the prevalence of OBI among BTM patients from Khuzestan Province, Iran. In this cross-sectional study, 90 thalassemia patients, who have received blood 36 to 552 times, participated referred to the Shafa hospital of Ahvaz city from January 2018 to April 2019. ELISA for determining serological markers (HBsAg, anti-HBc, anti-HBs, and anti-HCV) and real-time PCR for detecting HBV-DNA were performed; Nested PCR was conducted for DNA sequencing and determining the genotype of OBI case. Phylogenetic and statistical analyses were done by R package. Of 90 subjects enrolled in this study; 95.5% (86/90) were HBsAg negative, and the frequency of OBI among them was 1.16% (1/86). The anti-HBs, anti-HBc, and anti-HCV were detected in 80.00%, 7.78%, and 12.2% of patients, respectively. HBV-DNA was assessed at four HBsAg-positive subjects as well, and all of them were negative. The phylogenetic analysis showed that the detected HBV DNA in the OBI case belongs to the genotype D. This research, for the first time, demonstrated that OBI is present among β-thalassemia patients in Iran. Also, further studies are necessary to determine the actual prevalence of OBI among BTM patients in Iran to decisions concerning OBI screening, especially in transfusion centers.

EPH has been demonstrated to be a useful tool in companion animals while providing an opportunity to characterize globulinemias, including paraproteinemia. In EPH of non-traditional species, these same applications are important, but the primary use is to gauge the acute-phase and humoral immune responses. This includes the valid quantitation of albumin as well as the examination of fractions reflective of increases in acute-phase reactants and immunoglobulins. Agarose gel EPH and, more recently, capillary zone EPH have been applied to samples from these species. Performing these analyses provides special challenges in the placement of fraction delimits, generation of RIs, and interpretation of results. Recommended as part of routine bloodwork, EPH can also provide key results that are helpful in clinical and field-based health assessments as well as in prognostication.

BACKGROUND Densitometric quantification of myeloma paraproteins (M-proteins) is used to monitor secretory myeloma related disorders in humans and dogs. The previous work in dogs used agarose gel electrophoresis (AGE) but did not establish if other methods of serum protein electrophoresis, such as capillary zone electrophoresis (CZE), were comparable. OBJECTIVES We aimed to determine if the densitometric quantification of M-proteins using CZE would yield results comparable to AGE methods. METHODS Fifty-one serum samples from 22 dogs and 18 cats with confirmed monoclonal gammopathies and previously performed AGE were evaluated using CZE on a Sebia Minicap system. Samples were run in duplicate, and their M-proteins were densitometrically measured using the corrected perpendicular drop method previously described. Human-based quality control samples were used to determine the inter-run coefficient of variation (CV). Patient samples were used to calculate the intra-run CV. Method comparison was performed using simple linear regression, Passing-Bablok regression, and Bland-Altman analyses, and Medx evaluations. RESULTS Inter-run and intra-run CVs for CZE were 3.71%-7.65% and 2.89%-4.74%, respectively. Simple linear regression demonstrated an excellent correlation (r > 0.98). Passing-Bablok regression was compatible with the presence of proportional bias in the entire population, and Bland-Altman plots revealed a proportional bias in the feline cases. The Medx evaluation suggested that the two methods did not perform similarly in clinical samples with poor performance at a decision limit of 0.5 gm/dL. CONCLUSIONS Capillary zone electrophoresis is an acceptable method for M-protein densitometric quantification in canine and feline sera but cannot be used interchangeably with AGE-based evaluations.

Nucleic acids dye Goldview is widely used in agarose gel electrophoresis (AGE). However, in this study, a sample of multiplasmid DNA (multi-pDNA) stained with Goldview analyzed by AGE showed its instability at low temperature. Three types of DNA samples were analyzed, including linear DNA (ladder), single-plasmid DNA (single-pDNA), and multi-pDNA, electrophoretic conditions were optimized by adjusting the dye, the buffer, and the temperature (1-50°C). The results showed that the light intensity of Gelred is 2.2-times higher than that of Goldview in staining multi-pDNA. Compared with the single-pDNA and the linear DNA, the multi-pDNA stained with Goldview was greatly affected by temperature. This short communication indicated that Gelred is a highly applicable dye for analyzing multiplasmid samples. The degree and the way of binding of Goldview to multi-pDNA are greatly affected by temperature.

Electrophoresis is one of the major techniques to analyze macromolecular structure and interaction. Its capability depends on the sensitivity and specificity of the staining methods. We have here examined silver staining of proteins and nucleic acids separated by agarose native gel electrophoresis. By comparing five commercial kits, we identified Silver Stain Plus from Bio-Rad most adequate, as it provided little background staining and reasonable band staining. One of the disadvantages of the Silver Stain Plus kit is its variable staining of glycoproteins as tested with several model samples, including hen egg white proteins, α1-acid glycoprotein and SARS-CoV-2 Spike protein. One of the advantages of silver staining is its ability to stain nucleic acids as demonstrated here for a model nucleic acid with two kits. It was then used to monitor the removal of nucleic acids from the affinity-purified maltose binding protein and monoclonal antibody. It also worked well on staining proteins on agarose gels prepared in the vertical mode, although preparation of the vertical agarose gels required technological modifications described in this report. With the silver staining method optimized here, it should be possible in the future to analyze biological samples that may be available in limited quantity.

While conducting recombinant DNA technology procedures, such as DNA purification, agarose gel electrophoresis is often used for identification, characterization and quantification of DNA. The collection of data for experiments involving such techniques frequently involves capturing images using systems that are expensive and/or proprietary, such that they are not user-serviceable when they malfunction or become antiquated. In response to these limitations, work was done to replace the authors' existing aging Mac OS-based modular system with open-source software and generic hardware. Several versions of a modular imaging system that can be adjusted to fit nearly all use cases are described. The systems developed can accommodate diverse uses from research laboratories to educational environments where commercial systems could be unaffordable.

The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In molecular biology, enzymatic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnology, the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed analysis and optimization of the conditions for the enzymatic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temperature, and typically requires much higher concentration of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a maximum ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concentration-dependent manner.

It is hypothesized that nonlinear solid friction between the gel matrix and DNA molecules inhibits the motion of DNA through the nanopores of the gel during electrophoresis. In this article, it is demonstrated that external noise can alleviate the effect of solid friction, thus enhancing the mobility of DNA in an electrophoretic setting. In the presence of noise, the mobility of DNA increases by more than ∼113% compared to conventional electrophoresis. Although at a high power of noise, DNA exhibits Arrhenius kinetics, at a low power of noise, super-Arrhenius kinetics suggests the collective behavior of the activated motion of DNA molecules. A stochastic simulation following modified Langevin dynamics with the asymmetric pore size distribution of the agarose gel successfully predicts the mobility of DNA molecules and reveals the salient features of the overall dynamics. This "noise lubricity" may have a broader applicability from molecular to macroscopic locomotion.

Purpose: Purpose of the current study was to assess the presence and functionality of the nucleoside transporters in the lacrimal gland for the tear disposition of its substrate given intravenously...

Routine electrophoresis [agarose gel electrophoresis (AGE) and capillary zone electrophoresis (CZE)] and species-specific immunofixation (IF) can be used alone or in combination to detect immunoglobulin paraprotein (M-protein) and diagnose secretory myeloma-related disorders (sMRD).We aimed to evaluate the performance of AGE, CZE, CZE plus IF (CZE-IF), and AGE plus IF (AGE-IF) for detecting canine serum M-proteins.One hundred canine cases that had AGE, CZE, and routine IF performed on serum, and where B-cell lineage neoplasia (such as B-cell lymphoma and plasma cell tumors) had been diagnosed or excluded, were evaluated. Routine IF protocols targeted IgG-FC, IgA, and IgM heavy chains and light chains. IgG4 IF and free light chain IF were also performed. B-cell lineage neoplasms with an M-protein detected, using any available method, were classified as sMRD. Datasets from AGE, CZE, IF, CZE-IF, and AGE-IF (electrophoretograms, gel images, and fraction concentrations) were composed and reviewed. The sensitivity, specificity, and Youden's index for M-protein detection were determined for each dataset.The combination of AGE-IF or CZE-IF was more sensitive (82.9%) than CZE alone (72.0%) or AGE alone (64.6%) and more specific (66.1%, 48.3%, 51.7%, respectively). Immunofixation could be used alone to detect M-proteins (sensitivity 82.9%, specificity 61.9%), but there were technical challenges that complicated the performance and evaluation of the test. Myeloma with free light chains only was found in 5/41 cases of sMRD.Adding routine IF to routine electrophoresis increases the ability to accurately identify M-proteins; however, there is still room for further diagnostic performance improvements.

Context.— In laboratory testing for monoclonal gammopathies, paraproteins are identified via serum immunofixation or serum immunosubtraction, and immunoturbidimetric quantitation of serum immunoglobulins is often used. Objective.— To evaluate methodologic differences between serum immunofixation and serum immunosubtraction, as well as in the quantitation of serum immunoglobulins on different clinical chemical platforms. Design.— Three hundred twenty-two unique routine patient samples were blinded and used for comparison between serum immunofixation on Sebia's HYDRASIS 2 and serum immunosubtraction on Sebia's CAPILLARYS 2, as well as between quantitation results of immunoglobulin A, G, and M on Abbott's ARCHITECT c16000PLUS and Roche's Cobas c 502 module. Microsoft Excel 2019 with the add-on Abacus 2.0 and MedCalc were used for statistical analysis and graphic depiction via bubble diagram, Passing-Bablok regressions, and Bland-Altman plots. Results.— The median age of patients was 75 years, and samples with paraproteinemia were nearly evenly split between sexes. Paraprotein identification differed remarkably between immunofixation and immunosubtraction. Quantitation of serum immunoglobulins showed higher values on Abbott's ARCHITECT c16000PLUS when compared with Roche's Cobas c 502 module. Conclusions.— Identification of paraproteins via serum immunosubtraction is inferior to serum immunofixation, which can have implications on the diagnosis and monitoring of patients with monoclonal gammopathy. If immunoturbidimetric quantitation of immunoglobulins is used for follow-up, the same clinical-chemical platform should be used consistently.

Background: Plasmid DNA has been widely used in vaccination as well as in cell and gene therapy. It exists in multiple isoforms, including supercoiled, nicked or open circular and linear forms. Regulatory agencies recommend having more than 80% of the supercoiled isoform for the bulk release of plasmid products; thus, it should be analyzed accordingly. Methods and Results: The traditional analysis method for plasmid DNA is agarose gel electrophoresis. However, due to time-consuming manual sample loading, visualization, and data analysis, it has limitations in obtaining consistently quantitative results. In this short communication, we introduced a fast, sensitive, and robust plasmid analysis method using capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF). CGE-LIF analysis of the supercoiled isoform and its open circular counterpart was completed in 20 minutes with excellent sensitivity by using a common fluorescent DNA binding dye. The advantage of the method was demonstrated by the purity analysis of two large plasmids (7 kb and 10 kb). The fully automated sample loading, separation and data analysis featured enhanced assay repeatability and ease of quantitation over agarose gel electrophoresis. Conclusion: As a worked example, analysis of plasmid samples treated at elevated temperature during an accelerated stability test also demonstrated the applicability of CGE-LIF to monitor plasmid topology and possible degradation.

Objectives On agarose gel electrophoresis, IgA paraprotein has a tendency to polymerise and form multiple bands on immunofixation. We decided to investigate if there are any differences in clinical parameters with monomeric vs. polymeric IgA paraprotein multiple myeloma (MM) patients. Methods During an 18-month retrospective and prospective cross-sectional audit review period at one Australian laboratory, we identified 92 IgA MM patients that were divided up according to monomeric or polymeric IgA paraproteins based on their appearance on IFE. Medical and pathology records were reviewed for demographic details, and laboratory data to examine for end-organ manifestations of MM. Results After correcting for age, polymeric IgA MM patients had a greater degree of proteinuria and hence, higher incidence of hypogammaglobulinaemia. The patients tended to have a higher quantity of paraprotein as well. No difference in mortality was seen. Conclusions Our study is the first to stratify IgA MM patients according to the laboratory appearance of their paraprotein and may hold important prognostic and predictive clues for these patients.

Western blotting was attempted to analyze proteins separated by agarose native gel electrophoresis that was previously developed on His/Mes buffer system. This report shows a simple protocol for blotting agarose native gel to a PVDF membrane by soaking the gel in sodium dodecylsulfate-containing transfer buffer and 3 examples of such analysis. First example showed expression of a recombinant antibody in HEK293 cells by direct staining of the agarose native gels for both proteins and nucleic acids and staining of the blots for proteins and host cell proteins. These analyses demonstrated usefulness of agarose native gel electrophoresis, confirming that the recombinant antibody migrates toward the cathode while nucleic acids and a majority of host cell proteins migrate toward the anode. Second example demonstrated the phosphorylation state of MAP kinase in human lymphocyte cell line. Namely, agarose native gel can separate kinase, whose phosphorylation can be analyzed by Western blotting. Third example showed correlation of Escherichia coli β-galactosidase expression between the oligomerization and enzyme activity using antibody and substrate staining.

Damage from ultraviolet (UV)B exposure is cumulative and proceeds via augmenting cellular oxidative stress. The present study investigates UVB-protective effects of Sargassum confusum derived fucoidans in human keratinocytes. Algae was extracted using Celluclast, and fucoidan fractions were recovered by step gradient ethanol precipitation. Refined fucoidan fractions were treated to human HaCaT keratinocytes and exposed to UVB (50 mJ cm−2). Among fucoidan fractions, SCFC4, the lowest molecular weight (MW) fraction indicated better UVB-protective effects with dose-dependent reduction of intracellular ROS levels, while recovering the cell viability. SCFC4 suppressed UVB-induced apoptotic body formation, sub-G1 cell content, and DNA damage by hindering the mitochondria-mediated apoptotic pathway. Also, SCFC4 repressed upstream mediators of UVB-induced inflammatory responses, which would impair stratum corneum hydration. The above therapeutic effects of SCFC4 could be attributed to suppression of nuclear factor (NF)-κB and mitogen-activated protein kinase (MAPK) pathways while activating nuclear factor erythroid 2-related factor 2 (Nrf2) mediated production of antioxidant enzymes. SCFC4 was identified as a fucoidan (MW ≈ 20 kDa) with a 64.64% fucose and 23.62% sulfate contents. Further analysis of shelf life, safety, and efficacy could promote SCFC4's use as a cosmetic ingredient.

The clock neurons of the fruit fly Drosophila melanogaster have become a useful model for expressing misfolded protein aggregates that accumulate in several human neurodegenerative diseases. One advantage of such an approach is that the behavioral effects can be readily quantified on circadian locomotor rhythms, sleep or activity levels via automated, highly reliable and objective procedures. Therefore, a rapid assay is required to visualize whether these neurons develop aggregates. Here we describe a modified immunoblot method, agarose gel electrophoresis (AGERA) that has been optimized for resolving aggregates from fly clock neurons.

An attempt was made to specifically stain unfolded proteins on agarose native gels. SYPRO Orange is routinely used to detect unfolded protein in differential scanning fluorimetry, which is based on the enhanced fluorescence intensity upon binding to the unfolded protein. We demonstrated that this dye barely bound to the native proteins, resulting in no or faint staining of the native bands, but bound to and stained the unfolded proteins, on agarose native gels. Using bovine serum albumin (BSA), it was shown that staining did not depend on whether BSA was thermally unfolded in the presence of SYPRO Orange or stained after electrophoresis. On the contrary, SYPRO Orange dye stained protein bands in the presence of sodium dodecylsulfate (SDS) due to incorporation of the dye into SDS micelles that bound to the unfolded proteins. This staining resulted in detection of new, intermediately unfolded structure of BSA during thermal unfolding. Such intermediate structure occurred at higher temperature in the presence of ATP.

We have developed a new Western blotting method of native proteins from agarose-based gel electrophoresis using a buffer at pH 6.1 containing basic histidine and acidic 2-( N-morpholino)ethanesulfonic acid. This gel electrophoresis successfully provided native structures for a variety of proteins and macromolecular complexes. This paper is focused on the Western blotting of native protein bands separated on agarose gels. Two blotting methods from agarose gel to PVDF membrane are introduced here, one by contact (diffusion) blotting and another by electroblotting after pre-treating the agarose gels with SDS. The contact blotting resulted in the transfer of native GFP, native human plexin domain containing protein 2 (PLXDC2) and native SARS-CoV-2 spike protein, which were detected by conformation-specific antibodies generated in-house.

A commercially available bovine serum albumin (BSA) was examined by agarose native gel electrophoresis using two different agarose sources, UltraPure and MetaPhor agarose. While UltraPure agarose up to 5 % showed no clear separation of BSA oligomers, MetaPhor agarose clearly demonstrated oligomer bands above 4 %, indicating that the latter agarose has greater molecular sieving effects and is hence characterized to have high resolution for size differences, as probed by a greater slope of Ferguson plot. Physical properties are different between two agaroses. In general, UltraPure agarose has physical strength, while MetaPhor agarose is considerably fragile, but MetaPhor agarose solution is less viscous so that even 10 % gel can be made. Cause of oligomers was shown to be not associated with inter-chain disulfide bonds, but is due to association of native or native-like molecules.

Agarose gel electrophoresis is a relatively easy to use method, commonly applied to evaluate PCR reaction success. Intercalating agents or dyes are used to visualize the amplified fragments. However, it is uncertain to what extent the brightness of bands is informative about the concentration of the amplicons. To more closely examine the suitability of agarose gel electrophoresis to assess PCR product yield, we quantified the brightness of bands on a gel and compared these data with the results from spectrophotometry, fluorometry and qPCR. Evaluation of the results suggests that assessment of the relative quantity of amplicons by band brightness is precise enough even for post-PCR analysis steps requiring PCR product concentrations within a certain range to function properly.

Capillary zone electrophoresis (CZE) and an immunoassay for serum amyloid A (SAA) were used to examine serum samples from clinically normal and abnormal southern white rhinoceros (

Background Although not fully understood, oxidative stress has been implicated in the pathogenesis of different autoimmune diseases such as systemic sclerosis. Accumulating evidence indicates that oxidative stress can induce mitochondrial DNA (mtDNA) damage and variations in mtDNA copy number (mtDNAcn). Objective The aim of this study was to explore mtDNAcn and oxidative DNA damage byproducts in peripheral blood of patients with systemic sclerosis and healthy controls. Methods Forty six patients with systemic sclerosis and forty nine healthy subjects were studied. Quantitative real-time PCR used to measure the relative mtDNAcn and the oxidative damage (oxidized purines) of each sample. Results The mean mtDNAcn was lower in patients with systemic sclerosis than in healthy controls whereas the degree of mtDNA damage was significantly higher in cases as compared to controls. Moreover, there was a negative correlation between mtDNAcn and oxidative DNA damage. Study limitations The lack of simultaneous analysis and quantification of DNA oxidative damage markers in serum or urine of patients with systemic sclerosis and healthy controls. Conclusion These data suggest that alteration in mtDNAcn and increased oxidative DNA damage may be involved in the pathogenesis of systemic sclerosis.

Biomimetic synthesis of gold nanoparticles (GNPs) is critical in biomedical applications. Gold bioconjugates were fabricated by capping the water-dispersible gold-carbon nanoparticles with tyrosine, tryptophan and cysteine amino acids. Incubation of the water-soluble and easily reducible aryldiazonium gold(III) salt [HOOC-4-C6H4N≡N]AuCl4 with amino acids at room temperature formed a purple color over a few minutes with tryptophan and tyrosine and over two hours with cysteine. Rarely that cysteine is capable of reducing gold(III) precursors; however, a cysteine capped gold bioconjugate was synthesized and characterized in this study. Capping GNPs with amino acids was confirmed by high resolution transmission electron microscopy (TEM) and agarose gel electrophoresis. Depending on the amino acid, synthesized particles size was 27.2 ± 5.4 nm, 14.6 ± 7.7 nm and 8.6 ± 2.6 nm for tyrosine, tryptophan and cysteine, respectively. The amino acids capped GNPs showed negligible cytotoxicity to human dermal normal fibroblast cell lines. The highly water dispersible bioconjugates were studied for in vitro cellular uptake by HeLa cancer cells using confocal laser scan microscopy (CLSM) after being labelled with FITC (GNPs-COOH-FITC) and the nuclei were counter stained with DAPI fluorescent dyes. The biomimetic route for the synthesis of the amino acids reduced gold-carbon nanoparticles will benefit the applications in biomedical devices and biosensors.

BACKGROUND The bromocresol green (BCG) method has been reported to overestimate serum albumin concentration in several species due to non-specific binding to globulins. As the white rhinoceros has high concentrations of serum globulins, significant differences in albumin measured by the BCG method, and the field method of agarose gel serum protein electrophoresis (SPE) are expected. OBJECTIVES We aimed to compare the BCG and SPE methods for albumin determination in the serum of white rhinoceroses. METHODS SPE and BCG albumin were measured in 82 white rhinoceros serum samples. Results were compared using Bland-Altman difference plots and Passing-Bablok regression analysis. RESULTS BCG albumin showed a significant mean constant positive bias of 7 g/L, or 36%, which was more than the total allowable error of 15% and was clinically significant. Methods were not comparable within the inherent imprecision of each method. CONCLUSIONS The BCG method overestimated albumin concentrations in this species compared with agarose gel SPE, and method-specific reference intervals should be used.

The lipoproteinogram (or lipidogram) consists in an electrophoretic separation of the main classes of serum lipoproteins. Separation was done in agarose gel using the Sebia Hydragel Lipo + Lp(a)® kit. A repeatability study (n=6) was conducted on 3 sera (1 normolipidemic, 1 hypertriglyceridemic and 1 with a high Lp(a) concentration). The reproducibility was studied on these 3 sera and on an ascites liquid containing chylomicrons, upon 6 days (n=6). A quantitative approach was made by studying areas under the curve and percentages of fractions. In both cases (repeatability and reproducibility), the revelation of the lipoproteins in the gel after electrophoretic migration was made either by staining with Sudan Black (procedure recommended by Sebia), or with Fat Red 7B. Regardless of staining, both repeatability and reproducibility studies show that all lipoprotein fractions were correctly detected at their respective positions, leading to satisfactory interpretations of lipoproteinograms. Our reproducibility study also confirmed a good stability of the fractions over 6 days (storage at +5 ± 3̊C). In addition, the Fat Red 7B staining leads to a shorter technical time (about 40 min) for the gel drying and staining/destaining phases, which allows us to respond more quickly to certain urgent requests such as chylothorax diagnosis.

Cancer is the uncontrolled growth of abnormal cells via malignant cell division and rapid DNA replication. While DNA damaging molecules can cause cancer, their role as anticancer drugs are very significant. For this purpose, the novel series of paraben substituted spermine bridged(dispirobino) cyclotriphosphazene compounds 2-6 were synthesized for the first time, and their structures were characterized by various spectroscopic techniques. The solid-state structures and geometries of compounds 2-6 were determined using single-crystal X-ray structural analysis. In addition, it was confirmed by TGA that all compounds 1-6 showed high thermal stability. Two methods were used in order to investigate DNA interaction properties of the targeted molecules. While biosensor-based screening test that measures DNA hybridization efficiency on a biochip surface, the agarose gel electrophoresis method examines the effect of compounds on plasmid DNA structure. The results collected from the automated biosensor device and agarose gel electrophoresis have indicated that compounds 1, 5, and 6 showed higher DNA damage than the compounds 2-4. According to the biosensor results, compounds 1, 5, and 6 showed 85%, 69%, and 77% activity, respectively.

Phosphorene, a monolayer of black phosphorus, has emerged as one of the most promising two-dimensional (2D) nanomaterials for various applications in the post-graphene-discovery period due to its highly anisotropic structure and novel properties. In order to apply phosphorene in biomedical fields, it is crucial to understand how it interacts with biomolecules. Herein, we use both molecular dynamics (MD) simulations and experimental techniques to investigate the interactions of phosphorene with a dsDNA segment. Our results reveal that dsDNA can form a stable binding on the phosphorene surface through the terminal base pairs and adopt an upright orientation regardless of its initial configurations. Moreover, the binding strength of dsDNA with phosphorene is found to be mild and does not cause significant distortion in the internal structure of dsDNA. This phenomenon is attributed to the weaker dispersion interaction between dsDNA and phosphorene. Further analysis of the free energy profile calculated by the umbrella sampling technique suggests that the puckered surface morphology significantly reduces the adsorption free energy of DNA bases to phosphorene. Compared to graphene, phosphorene is found to show a milder attraction to DNA, which is confirmed by our electrophoresis experiments. We believe that these findings provide valuable insight into the molecular interactions between phosphorene and dsDNA which may prompt further investigation of phosphorene for future biomedical applications.

Summary Secreted polypeptides represent a fundamental axis of intercellular communication. Here, we present a protocol for the cell type-specific biotinylation, enrichment, and proteomic profiling of secreted plasma proteins directly in mice. This protocol uses conditional “turn-on” adeno-associated viruses expressing an endoplasmic reticulum-targeted biotin ligase to globally biotinylate proteins of the secretory pathway in a cell type-specific manner. Biotinylated secreted proteins can be directly purified from blood plasma and analyzed by SDS-PAGE gel or shotgun proteomics. For complete information on the generation and use of this protocol, please refer to Wei et al. (2021)., Graphical abstract, Highlights • Protocol for cell type-specific biotinylation of secreted proteins directly in mice • Secreted proteins can be directly enriched from blood and profiled by proteomics • This protocol is applicable to any cell type for which a Cre mouse line is available, Secreted polypeptides represent a fundamental axis of intercellular communication. Here, we present a protocol for the cell type-specific biotinylation, enrichment, and proteomic profiling of secreted plasma proteins directly in mice. This protocol uses conditional “turn-on” adeno-associated viruses expressing an endoplasmic reticulum-targeted biotin ligase to globally biotinylate proteins of the secretory pathway in a cell type-specific manner. Biotinylated secreted proteins can be directly purified from blood plasma and analyzed by SDS-PAGE gel or shotgun proteomics.

The genus Trichoderma is ubiquitous in various niches and is currently used for biocontrol, biofertilizer, enzyme production and bioremediation. However, molecular mechanisms underlying its diverse biological functions are yet not fully elucidated. Extraction of high-quality RNA for downstream applications such as quantitative polymerase chain reaction is a prerequisite. The current study aims to optimize a total RNA extraction protocol for high-quality and quantity RNA from Trichoderma atrobrunneum. Seven RNA extraction protocols including Trizol, RiboEx PureLink RNA mini kit, high salt CTAB (cetyltrimethylammonium bromide), modified high salt CTAB, SDS (sodium dodecyl sulfate) and CTAB-PVP (polyvinylpyrrolidone) were performed separately, to extract RNA. Quality and quantity of extracted RNA samples were further analyzed by Nanodrop spectrophotometry, agarose gel electrophoresis and RT-PCR analysis. The results of quantitative and qualitative analysis of RNA samples showed that more intact, high-quality RNA was extracted using the modified high salt CTAB as compared to other methods. The RT-PCR results for the amplification of the genes encoding β-tubulin and Ubiquitin carrier protein also showed lowest threshold cycle (Ct) and coefficient of variation (CV) for RNA samples extracted with the modified high salt CTAB method as compared to RNA samples extracted with other protocols. Therefore, it is proposed that the modified high salt CTAB protocol is an excellent method to obtain high-quality RNA with good yield from T. atrobrunneum for its downstream applications. Moreover, the optimized protocol is very economical and can be used to extract total RNA from a large number of samples.

More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.

Alkaline agarose gels are run at high pH, which causes each thymine and guanine residue to lose a proton and thus prevents the formation of hydrogen bonds with their adenine and cytosine partners. The denatured DNA is maintained in a single-stranded state and migrates through an alkaline agarose gel as a function of its size. Other denaturants such as formamide and urea do not work well because they cause the agarose to become rubbery.

International audience; In the present study, three biodegradable block copolymers composed of a poly(ethylene glycol) block and a copolypeptide block with varying compositions of cationic L-lysine (L-Lys) and hydrophobic benzyl-L-glutamate (Bzl-L-Glu) were designed for gene delivery applications. The polypeptides were synthesized by ring opening polymerization (ROP) and after orthogonal deprotection of Boc-L-Lys side chains, the polymer exhibited an amphiphilic character. To bind or encapsulate plasmid DNA (pDNA), different formulations were investigated: a nanoprecipitation and an emulsion technique using various organic solvents as well as an aqueous pH-controlled formulation method. The complex and nanoparticle (NP) formations were monitored by dynamic light scattering (DLS), and pDNA interaction was shown by gel electrophoresis and subsequent controlled release with heparin. The polypeptides were further tested for their cytotoxicity as well as biodegradability. The complexes and NPs presentingthe most promising size distributions and pDNA binding ability were subsequently evaluated for their transfection efficiency in HEK293T cells. The highest transfection efficiencies were obtained with an aqueous formulation of the polypeptide containing the highest L-Lys content and lowest proportion of hydrophobic, helical structures (P1*), which is therefore a promising candidate for efficient gene delivery by biodegradable gene delivery vectors.

R-loops are a major source of genome instability associated with transcription-induced replication stress. However, how R-loops inherently impact replication fork progression is not understood. Here, we characterize R-loop-replisome collisions using a fully reconstituted eukaryotic DNA replication system. We find that RNA:DNA hybrids and G-quadruplexes at both co-directional and head-on R-loops can impact fork progression by inducing fork stalling, uncoupling of leading strand synthesis from replisome progression, and nascent strand gaps. RNase H1 and Pif1 suppress replication defects by resolving RNA:DNA hybrids and G-quadruplexes, respectively. We also identify an intrinsic capacity of replisomes to maintain fork progression at certain R-loops by unwinding RNA:DNA hybrids, repriming leading strand synthesis downstream of G-quadruplexes, or utilizing R-loop transcripts to prime leading strand restart during co-directional R-loop-replisome collisions. Collectively, the data demonstrates that the outcome of R-loop-replisome collisions is modulated by R-loop structure, providing a mechanistic basis for the distinction of deleterious from non-deleterious R-loops.

Canine babesiosis is a serious disease among tick-borne haemoprotozoan diseases that threaten dog health. To find out the prevalence of canine babesiosis and its main pathogenic species in Shaanxi Province, the study was centered on the infection of babesiosis in dogs in different regions of the Province. First, a total of 367 blood samples were collected in Shaanxi Province, and 53 Babesia nucleic-acid-positive samples were found by polymerase chain reaction (PCR) identification, with a positive rate of 14.44%, and Babesia gibsoni was found by sequencing analysis. Further analysis showed that the prevalence of canine babesiosis was significantly different in 5 regions. There was no significant difference in infection rates between age groups, with the lowest prevalence in young dogs (10.81%) and the highest in adult dogs (17.29%). The infection rate in male dogs was higher than in female dogs. The morbidity of canine Babesia spp. was significantly different between different seasons, with the highest infection rate in autumn (27.78%) and the lowest in winter (6.10%). In conclusion, the epidemicity of canine Babesia spp. in dogs was mainly affected by region and season, and B. gibsoni was the most common canine Babesia spp. within Shaanxi Province in our study. These results provide basic data for the prevention and control of canine babesiosis in this region.

Glycosylated PD-L1 is a more reliable biomarker for immune checkpoint therapy and plays important roles in tumor immunity. Glycosylation of PD-L1 hinders antibody-based detection, which is partially responsible for the inconsistency between PD-L1 immunohistochemical results and therapeutic treatment response. Herein, we present a proximity ligation assay mediated rolling circle amplification (PLA-RCA) strategy for amplified imaging of glycosylated PD-L1 in situ. The strategy relies on a pair of DNA probes: an aptamer probe to specifically recognize cellular surface protein PD-L1 and a glycan conversion (GC) probe for metabolic glycan labeling. Upon proximity ligation of sequence binding to the two probes, the proximity ligation-triggered RCA occurs. The feasibility of the as-proposed strategy has been validated as it realized the visualization of PD-L1 glycosylation in different cancer cells and the monitoring of the variation of PD-L1 glycosylation during drug treatment. Thus, we envision the present work offers a useful alternative to track protein-specific glycosylation and potentially advances the investigation of the dynamic glycan state associated with the disease process.

The simultaneous detection of multiple mycotoxins is of great significance for food safety and human health. Herein, a simple, convenient and accurate fluorescent aptasensor was designed based on the dual cross DNA nanostructure for the simultaneous detection of ochratoxin A (OTA) and aflatoxin B