Comparison and evaluation of RNA quantification methods using viral, prokaryotic, and eukaryotic RNA over a 10 concentration range

Quantification of RNA is essential for various molecular biology studies. In this work, three quantification methods were evaluated: ultraviolet (UV) absorbance, microcapillary electrophoresis (MCE), and fluorescence-based quantification. Viral, bacterial, and eukaryotic RNA were measured in the 500 to 0.05-ng μl⁻¹ range via an ND-1000 spectrophotometer (UV), Agilent RNA 6000 kits (MCE), and Quant-iT RiboGreen assay (fluorescence). The precision and accuracy of each method were assessed and compared with a concentration derived independently using inductively coupled plasma-optical emission spectroscopy (ICP-OES). Cost, operator time and skill, and required sample volumes were also considered in the evaluation. Results indicate an ideal concentration range for each quantification technique to optimize accuracy and precision. The ND-1000 spectrophotometer exhibits high precision and accurately quantifies a 1-μl sample in the 500 to 5-ng μl⁻¹ range. The Quant-iT RiboGreen assay demonstrates high precision in the 1 to 0.05-ng μl⁻¹ range but is limited to lower RNA concentrations and is more costly than the ND-1000 spectrophotometer. The Agilent kits exhibit less precision than the ND-1000 spectrophotometer and Quant-iT RiboGreen assays in the 500 to 0.05-ng μl⁻¹ range. However, the Agilent kits require 1 μl of sample and can determine the integrity of the RNA, a useful feature for verifying whether the isolation process was successful.     

RESPONSE OF MARINE SYNECHOCOCCUS (CYANOPHYCEAE) CULTURES TO IRON NUTRITION1

Three clones of marine Synechococcus (WH6501, WH7803, and WH8018) were grown through at least three transfers, at 6-day intervals, in synthetic medium with total iron concentrations from 10^?9 to 10^?6 M. After 6 days of exponential growth, these cultures were harvested, and the cell density and protein and pigment concentrations were measured. Aliquots of the culture were assayed for their carbon fixation rates at two light intensities. Cell density and protein concentration increased by up to 7.8 times over a range of iron from the lowest (10^?9 M) to the highest concentrations (10^?6 M). The concentration of chlorophyll-a and phycobiliproteins showed a wider range of response, increasing by up to 48 times. The carbon fixation rate (per mL of culture) also increased approximately 40 times over the total range of iron concentration. The ranges of these biochemical and physiological responses were much lower than the range of total available iron, which was 1000-fold, and the range of total cellular iron, which was estimated to be about 160-fold. This “less-than-linear” relationship indicates that the cells are adapting to make more efficient use of iron under limiting conditions. Our results demonstrate characteristics of iron-limited Synechococcus that may be important in understanding the relationships between primary productivity and iron availability in the oceans.     

Development of a new device for on-line measurement of high cell concentrations

A variable-light-path-length flow-through cell to be installed on a spectrophotometer was developed for on-line measurement of high cell concentrations. Cell concentrations of up to about 100 g l^–1 could be measured without dilution. High concentration of protein solution was also measured. A spectrophotometer system combined with the flow-through cell is considered to be cost effective and durable with a minimal maintenance requirement.     

Utility of solid-phase spectrophotometry to determine trace amounts of zinc in environmental and biological samples

A solid-phase spectrophotometric analysis has been proposed for preconcentration and determination of Zn(II) in real samples. The procedure is based on sorption of zinc(II) as 5-(2-benzothiazolylazo)-8-hydroxyquinoline (BTAHQ) complex on dextran-type anion-exchange gel (Sephadex DEAE A-25). The influences of the analytical parameters, including pH of the aqueous solution, amounts of BTAHQ, and sample volume, were investigated. The absorbance of the gel at 675 and 750 nm, packed in a 1.0-mm cell, was measured directly. The molar absorptivities were found to be 2.50 × 10⁷ and 9.55 × 10⁷ L mol⁻¹ cm⁻¹ for 500 and 1000 ml, respectively. Calibration was linear over the range of 0.05–1.10 μg L⁻¹ with a relative standard deviation of less than 1.60% (n = 10). The detection and quantification limits of the 500-ml sample method were 12 and 40 ng L⁻¹ on using 50 mg. For the 1000-ml sample, the detection and quantification limits were 7.5 and 25 ng L⁻¹ using a 50-mg exchanger. Increasing the sample volume can enhance sensitivity. No considerable interferences were observed from other investigated anions and cations on the Zn(II) determination. The proposed method was applied to determine zinc in environmental samples, including natural water, food, certified reference materials, meat, and biological samples, comparing the results simultaneously with those obtained using a flame atomic absorption spectrophotometer, whereby the validity of the method was tested.     

Mass spectrometric quantification of asparagine synthetase in circulating leukemia cells from acute lymphoblastic leukemia patients

The appearance of asparaginase-resistant acute lymphoblastic leukemia (ALL) in transformed cell lines has been correlated with increased expression of asparagine synthetase (ASNS). Recent measurements using mRNA-based assays have raised doubts, however, as to the importance of ASNS protein in the cellular mechanisms that confer drug resistance upon the leukemic cells. Studies aimed at determining the concentration of ASNS protein in human leukemias are therefore needed to resolve this issue. A mass spectrometry (MS)-based procedure is presented for the direct quantification of ASNS protein concentration in complex sample mixtures. This assay is able to distinguish samples from transformed cell lines that express ASNS over a wide dynamic range of concentration. Importantly, this method directly detects ASNS protein, the functional entity that may be synthesizing sufficient asparagine to render leukemia cells resistant to asparaginase-treatment. We also report the successful use of this MS method, which has lower limits of detection and quantification of 30 and 100 attomoles, respectively, for the first direct measurements of ASNS protein concentrations in four patient blast samples.     

The molecular interaction of a protein in highly concentrated solution investigated by Raman spectroscopy

We used Raman spectroscopy to investigate the structure and interactions of lysozyme molecules in solution over a wide range of concentrations (2.5–300 mg ml^?1). No changes in the amide‐I band were observed as the concentration was increased, but the width of the Trp band at 1555 cm^?1 and the ratios of the intensities of the Tyr bands at 856 and 837 cm^?1, the Trp bands at 870 and 877 cm^?1, and the bands at 2940 (CH stretching) and 3420 cm^?1 (OH stretching) changed as the concentration was changed. These results reveal that although the distance between lysozyme molecules changed by more than an order of magnitude over the tested concentration range, the secondary structure of the protein did not change. The changes in the molecular interactions occurred in a stepwise process as the order of magnitude of the distance between molecules changed. These results suggest that Raman bands can be used as markers to investigate the behavior of high‐concentration solutions of proteins and that the use of Raman spectroscopy will lead to progress in our understanding not only of the basic science of protein behavior under concentrated (i.e., crowded) conditions but also of practical processes involving proteins, such as in the field of biopharmaceuticals. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 237–246, 2015.     

Protein,enzyme and carbohydrate quantification using smartphone through colorimetric digitization technique

In this paper the utilization of smartphone as a detection platform for colorimetric quantification of biological macromolecules has been demonstrated. Using V‐channel of HSV color space, the quantification of BSA protein, catalase enzyme and carbohydrate (using D‐glucose) have been successfully investigated. A custom designed android application has been developed for estimating the total concentration of biological macromolecules. The results have been compared with that of a standard spectrophotometer which is generally used for colorimetric quantification in laboratory settings by measuring its absorbance at a specific wavelength. The results obtained with the designed sensor is found to be similar when compared with the spectrophotometer data. The designed sensor is low cost, robust and we envision that it could promote diverse fields of bio‐analytical investigations.

Schematic illustration of the smartphone sensing mechanism for colorimetric analysis of biomolecular samples.     

New luminometric method for quantification of biological sulfur nucleophiles with the participation of 9-cyano-10-methylacridinium salt

Biologically active compounds containing sulfhydryl groups (RSHs: N-acetyl-l -cysteine, d -penicillamine, glutathione and acetylthiocholine chloride) were used to develop a luminometric method for their quantification. The title substrate capable of chemiluminescence (CL) was isolated in a highly pure state as a chloride salt (99.9% using RP-HPLC) and identified using mass spectrometry (ESI Q-TOF) and ¹H NMR spectroscopy. The cation included in the salt, 9-CMA⁺, underwent oxidation in an alkaline environment containing RSHs by molecular oxygen, generating CL of various intensities, with no need for the use of hydrogen peroxide. The amount of produced light was linearly proportional to the content of investigated analytes in the system over the concentration range ~0.2–2 μM, with the detection limits in the range 0.19–1.73 μM. The mechanism of chemiluminogenic oxidation of 9-CMA⁺ in the presence of RSHs and molecular oxygen is proposed, using computational methods at the density-functional theory level. The presence of RSHs in an alkaline medium seems to be crucial to produce hydroperoxide anions (⁻OOH), which initiate the ‘light path’ of 9-CMA⁺ transformations, ending with the excretion of electronically excited molecules of 10 methyl-acridan-9-one.     

Application of the Bradford Assay for Cell Lysis Quantification: Residual Protein Content in Cell Culture Supernatants

Frequently measured mammalian cell culture process indicators include viability and total cell concentration (TCC). Cell lysis, an additional important process characteristic that substantially contributes to the overall product purity profiles, is often not addressed in detail. In the present study, an inexpensive and simple application of the Bradford assay is developed to determine the residual protein content (RPC) in cell culture supernatants. The reliability and reproducibility of the method are tested in a long‐term study and compared with lysis quantification via the DNA measurement. The results show that its performance is more robust and accurate over time and the respective concentration range. Additionally, both methods are used for cell lysis process monitoring in a recombinant Chinese hamster ovary fed‐batch process. In the presented process, by applying the established assay, the lysis rate k _DL is determined to be constant over time at 4.6 × 10 ^?4 lysed cell concentration (LCC) per TCC and time (LCC/TCC/h). In contrast, DNA data did not confirm the constant lysis rate due to variations of the content per cell during cultivation. Thus, information on the RPC can facilitate the determination of the optimal harvest time point with respect to purity and in improving process characterization.     

IN SITU UPTAKE KINETICS OF AMMONIUM AND PHOSPHATE AND CHEMICAL COMPOSITION OF THE RED SEAWEED GRACILARIA TIKVAHIAE1

The uptake kinetics of ammonium and phosphate by Gracilaria tikvahiae McLachlan were studied under field conditions. Seaweeds, pulse fed once a week for 6 h over a 4-week period, had maximum uptake rates of 19 μmol·g fwt^?1·h^?1 for ammonium and 0.28 μmol·g fwt^?1·h^?1 for phosphate. For both nutrients there was a positive linear correlation between uptake rate (v) and concentration (S) over the entire range of concentration tested. In a nutrient depletion experiment, the phosphate uptake curve determined over a wide range of concentrations consisted of two stages of saturation at low concentrations, and a linear phase at high concentrations. Ash free dry weight, chlorophyll a, phycoerythrin, and protein content were higher in pulse fed plants than in control plants receiving no nutrient additions, while the reverse held true for carbohydrate contents and the C/N ratios. The C/N ratio inversely correlated with ammonium and phosphate uptake rate as well as protein and phycoerythrin content, and positively with carbohydrate content.     

Improved and simplified liquid chromatographic assay for adefovir, a novel antiviral drug, in human plasma using derivatization with chloroacetaldehyde

A rapid and simplified chromatographic assay is reported for the quantification of adefovir (PMEA) utilizing derivatization with chloroacetaldehyde. Adefovir is isolated from plasma using protein precipitation with trichloroacetic acid; next, the fluorescent 1,N⁶-etheno derivative is directly formed at 98°C in the buffered extract with chloroacetaldehyde. This derivative is analyzed using isocratic ion-pair liquid chromatography and fluorescence detection at 254 nm for excitation and 425 nm for emission. In the evaluated concentration range (10–1000 ng/ml) precisions ≤5% and accuracies between 95 and 117% were found, using a 0.2-ml volume of plasma. The lower limit of quantification is 10 ng/ml with a intra-assay precision of 16%. The currently reported bioanalytical method is 20–25-fold more sensitive than previously published assays.     

A protein and peptide monitor with a hollow-cathode light source.

This communication describes an inexpensive system that will monitor protein and peptide concentration in chromatogram eluates by light absorbance at an adjustable wavelength.Proteins in chromatogram eluate streams are commonly metered for concentration by absorbance measurement at 280 nm. Besides a range of commercially manufactured monitors, there is the apparatus described by Bennett et al. (1) which uses a selectively modulated magnesium lamp. Measurements in the region of 280 nm are of no value, however, when the material does not contain aromatic amino acids. Monitoring then becomes necessary at 230 nm in the region of absorption due to the peptide bond. The common resort in such a case is the standard ultraviolet-visible spectrophotometer, which has the disadvantage of being both unnecessarily elaborate and expensive for the purpose required. The deuterium lamps in these instruments require frequent replacement because of the extended periods of operation, adding to the cost factor.We have investigated the use of a hollow-cathode lamp of the type manufactured for use in an atomic absorption spectrophotometer. These lamps have high stability and a long working life, due to the considerably lower level of power dissipation compared with deuterium lamps. Their emission spectra are discontinuous, but the lamp for the element iron provides adequately strong lines at both 229.5 and 279.2 nm, suitable for a protein monitor.     

Conformation of myelin basic protein in aqueous solution from nuclear magnetic resonance spectroscopy

High resolution ¹³C and ¹H NMR spectra of myelin basic protein over a range of pH and concentration indicate that intramolecular folding of the polypeptide chain occurs in the region of residues 8–116. As the pH is raised and the net charge on the protein decreased, intermolecular aggregation occurs between these same regions. The residues 81–118 are invariant in different species and this region is the locus of several chemical specificities of the protein.     

Spectrophotometric and spectrofluorimetric determination of indacaterol maleate in pure form and pharmaceutical preparations: application to content uniformity

Two simple, rapid, sensitive and precise spectrophotometric and spectrofluorimetric methods were developed for the determination of indacaterol maleate in bulk powder and capsules. Both methods were based on the direct measurement of the drug in methanol. In the spectrophotometric merthod (Method I) the absorbance was measured at 259 nm. The absorbance‐concentration plot was rectilinear over the range 1.0–10.0 µg mL^?1 with a lower detection limit (LOD) of 0.078 µg mL^?1 and lower quantification limit (LOQ) of 0.238 µg mL^?1. Meanwhile in the spectrofluorimetric method (Method II) the native fluorescence was measured at 358 nm after excitation at 258 nm. The fluorescence‐concentration plot was rectilinear over the range of 1.0–40.0 ng mL^?1 with an LOD of 0.075 ng mL^?1and an LOQ of 0.226 ng mL^?1. The proposed methods were successfully applied to the determination of indacaterol maleate in capsules with average percent recoveries ± RSD% of 99.94 ± 0.96 for Method I and 99.97 ± 0.81 for Method II. In addition, the proposed methods were extended to a content uniformity test according to the United States Pharmacopoeia (USP) guidelines and were accurate, precise for the capsules studied with acceptance value 3.98 for Method I and 2.616 for Method II. Copyright © 2015 John Wiley & Sons, Ltd.     

Optimization and control of perfusion cultures using a viable cell probe and cell specific perfusion rates

Consistent perfusion culture production requires reliable cell retention and control of feed rates. An on-line cell probe based on capacitance was used to assay viable biomass concentrations. A constant cell specific perfusion rate controlled medium feed rates with a bioreactor cell concentration of ∼5 × 10⁶ cells mL^-1. Perfusion feeding was automatically adjusted based on the cell concentration signal from the on-line biomass sensor. Cell specific perfusion rates were varied over a range of 0.05 to 0.4 nL cell^-1 day^-1. Pseudo-steady-state bioreactor indices (concentrations, cellular rates and yields) were correlated to cell specific perfusion rates investigated to maximize recombinant protein production from a Chinese hamster ovary cell line. The tissue-type plasminogen activator concentration was maximized (∼40 mg L^-1) at 0.2 nL cell^-1 day^-1. The volumetric protein productivity (∼60 mg L^-1 day^-1 was maximized above 0.3 nL cell^-1 day^-1. The use of cell specific perfusion rates provided a straightforward basis for controlling, modeling and optimizing perfusion cultures. This revised version was published online in July 2006 with corrections to the Cover Date.     

Accurate proteome-wide protein quantification from high-resolution <Superscript>15</Superscript>N mass spectra

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of ¹⁵N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing ¹⁵N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.     

Heavy Metals Bioconcentration from Soil to Vegetables and Assessment of Health Risk Caused by Their Ingestion

The present study was undertaken to assess the non-carcinogenic human health risk of heavy metals through the ingestion of locally grown and commonly used vegetables viz. Raphanus sativus (root vegetable), Daucus carota (root vegetable), Benincasa hispida (fruit vegetable) and Brassica campestris leaves (leafy vegetable) in a semi-urbanized area of Haryana state, India. Heavy metal quantification of soil and vegetable samples was done using flame atomic absorption spectrophotometer. Lead, cadmium and nickel concentration in vegetable samples varied in range of 0.12–6.54 mg kg^?1, 0.02–0.67 mg kg^?1 and <0.05–0.41 mg kg^?1, respectively. Cadmium and lead concentration in some vegetable samples exceeded maximum permissible limit given by World Health Organization/Food and Agriculture Organization and Indian standards. Much higher concentrations of Pb (40–190.5 mg kg^?1), Cd (0.56–9.85 mg kg^-1) and Ni (3.21–45.87 mg kg^?1) were reported in corresponding vegetable fields’ soils. Correlation analysis revealed the formation of three primary clusters, i.e. Cu–Cd, Cd–Pb and Ni–Zn in vegetable fields’ soils further supported by cluster analysis and principal component analysis. Bioconcentration factor revealed that heavy metals’ uptake was more by leafy vegetable than root and fruit vegetables. Hazard index of all the vegetables was less than unity; thus, the ingestion of these vegetables is unlikely to pose health risks to the target population.     

Quantification of titanium from TiO2 particles in biological tissue

This study presents the development of a strategy for the quantification of titanium from titanium dioxide polydisperse particles (TiO₂) in dry biological tissue. Calf liver was chosen as laboratory testing material. The challenge was to (i) obtain a complete mineralization of the solid material (biological tissue and TiO₂) and (ii) ensure the accuracy of the determined concentrations with a sufficient sensitivity. Mineralization was performed using a mixture of concentrated nitric and hydrofluoric acids. Atomic mass spectrometry associated with light-scattering technique was used to control the physical state (dissolved and particle forms) of titanium and reliably estimate the total titanium concentration in calf liver. The monitoring of ⁴⁶Ti and ⁴⁹Ti, operating in helium collision/reaction cell mode, and using external calibration with internal standard addition, allowed the quantification of Ti while removing isobaric interferences. The limit of detection and quantification were 0.7 and 2.3 μg (Ti) g⁻¹ (tissue) respectively. The mean analytical recovery over the whole procedure was (103 ± 6)% in a range of concentrations from LOD to 200 μg(Ti) g⁻¹ (tissue).     

High performance liquid chromatography determination of sulphachloropyrazine residues in broiler and turkey edible tissues

A HPLC method to determine and quantify sulphachloropyrazine residues from broilers and turkeys is reported. This procedure permitted sulphachloropyrazine to be separated from muscle tissue, liver, kidneys and fat with skin after extraction with dichloromethane under slightly acidic conditions. The analytical methodology showed a high specificity and sensitivity and an adequate precision and accuracy with a limit of quantification of 56 ng mL^?1. The peak area showed a linear relationship with a concentration over the range 50–750 ng mL^?1 for sulphachloropyrazine standard solutions. Recovery dates were also satisfactory with values between 69.7 and 77.5%.     

Choline-containing compounds quantification by 1H NMR spectroscopy using external reference and noise measurements

Proton magnetic resonance spectroscopy (¹H-MRS) is largely exploited in clinical settings to non-invasively investigate chemical compounds in human tissues. Applications of ¹H-MRS in oncology field are connected to the detection of abnormal levels of choline compounds in more active tumours, providing useful information for cancer diagnosis and treatment monitoring. Since benign lesions may also show presence of a choline peak, implementing absolute evaluation will help differentiating benign from malignant tumours. An external reference procedure was described to provide choline quantification in standard unit of measurements. Spectra were acquired on a 1.5 T scanner using both phantoms and healthy volunteers with a PRESS sequence. The implemented quantification procedure used metabolite and noise measurements on the spectrum to remove large part of scanner settings contributing to metabolites of interest. A standard quantification was also used to compare performances of the noise-based method. In vitro quantification had accuracy and precision in the range (95–99)% and (5–13)%, respectively. When applied to in vivo studies on healthy volunteers, the method provided very close values of choline concentration, more exactly (1.73 ± 0.24) mmol/l. The method proposed can quantify the proper choline content in phantoms as well as in human structures, as brain. The method is ease of use, computational costless and it can be rapidly calibrated and implemented in any centre.