Progressive degradation of serum samples limits proteomic biomarker discovery

Preanalytical variables play a key role in discovery of biomarkers. Although the effect of several preanalytical variables on the mass spectral profiles has been studied extensively, little is known about long-term storage of serum samples. This is important because samples used in case-control or epidemiological studies are usually stored for a long time before analysis. Here we evaluated long-term storage effects on mass spectral peak patterns of serum peptides extracted using weak cation exchange magnetic beads. For this, 20 serum samples stored at −80 °C were divided equally into two groups based on their storage time. We found that intensities of 26 mass spectral peaks significantly varied between these two groups. Intensities of these peaks significantly correlated with storage time. Genetic algorithm-based models generated using these 26 peaks could classify 63 additional samples into these two groups with 100% and 96% accuracy, respectively. We also show that storing samples for 10 months at −80 and −20 °C results in the appearance/disappearance or intensity variation of peaks, some of which were previously reported as disease biomarkers.     

Limited stability of thiopurine metabolites in blood samples: Relevant in research and clinical practise

Background

Monitoring of thiopurine metabolites 6-thioguanine nucleotides (6-TGN) and 6-methylmercaptopurine (6-MMP) is used to assess compliance and explain adverse reactions in IBD-patients. Correlations between dosage, metabolite concentrations and therapeutic efficacy or toxicity are contradictive. Research is complicated by analytical problems as matrices analyzed and analytical procedures vary widely. Moreover, stability of thiopurine metabolites is not well documented, yet pivotal for interpretation of analytical outcomes. Therefore, we prospectively investigated metabolite stability in blood samples under standard storage conditions.

Methods

Stability at room temperature and refrigeration (22 °C, 4 °C) was investigated during 1 week and frozen samples (−20 °C, −80 °C) were analyzed during 6 months storage. Ten patient samples were analyzed for each study period.

Results

Median 6-TGN concentrations on day 7 decreased significantly to 53% and 90% during storage at ambient temperature or refrigeration. Median 6-MMP concentrations on day 7 decreased significantly to 55% and 86%, respectively. Samples stored at −20 °C also showed significant decreases in both 6-TGN and 6-MMP in comparison with baseline values. At −80 °C, only 6-MMP showed a significant decrease in values compared to baseline.

Conclusion

The stability of thiopurine metabolites is clearly a limiting factor in studies investigating utilisation of TDM and correlations with therapeutic outcome in IBD-patients. This has to be accounted for in clinical practice and (multi-center) trials investigating thiopurine drugs.     

Minimizing artifactual elevation of lipid peroxidation products (F2-isoprostanes) in plasma during collection and storage

F₂-isoprostanes (F₂-IsoP’s) are reliable measures of in vivo lipid oxidation, but care is required to prevent artifactual elevation. We examined the effects of blood collection and storage on plasma F₂-IsoP’s. Blood was collected into EDTA/butylated hydroxytoluene/reduced glutathione (EDTA/BHT/GSH) or EDTA, at 4 °C or room temperature. Plasma was stored at −20 or −80 °C for 1 or 6 months before F₂-IsoP’s were assayed by GC–MS. The temperature of blood collection did not affect F₂-IsoP’s. However, storage at −20 °C or collection into EDTA resulted in significant increases in F₂-IsoP’s. Blood collection into EDTA/BHT/GSH and storage at −80 °C minimizes artifactual elevation of plasma F₂-IsoP’s.     

Proteomic analysis of response to long-term continuous stress in roots of germinating soybean seeds

Germination is a complex process, highly dependent on various environmental factors, including temperature and water availability. Germinating soybean seeds are especially vulnerable to unfavorable environmental conditions and exposure to long-term abiotic stresses may result in diminishing much of the yield and most importantly – restrained germination. In the present study, a proteomic approach was employed to analyze influence of cold and osmotic stress on roots of germinated soybean (Glycine max, L.) seeds. Seeds were germinating under continuous conditions of cold stress (+10 °C/H₂O), osmotic stress (+25 °C/−0.2 MPa) as well as cold and osmotic stress combined (+10 °C/−0.2 MPa). Proteome maps established for control samples and stress-treated samples displayed 1272 CBB-stained spots. A total of 59 proteins, present in both control and stress-treated samples and showing significant differences in volume, were identified with LC/nanoESI-MS. Identified proteins divided into functional categories, revealed 9 proteins involved in plant defense, 8 proteins responsible for plant destination and storage and 10 proteins involved in various tracks of carbohydrate metabolism. Furthermore, a number of proteins were assigned to electron transport, range of metabolic pathways, secondary metabolism, protein synthesis, embryogenesis and development, signal transduction, cellular transport, translocation and storage. By analyzing differences in expression patterns, it was possible to trace the soybean response to long-term abiotic stress as well as to distinguish similarities and differences between response to cold and osmotic stress.     

Peptide substrates for G protein-coupled receptor kinase 2

G protein-coupled receptor kinases (GRKs) control the signaling and activation of G protein-coupled receptors through phosphorylation. In this study, consensus substrate motifs for GRK2 were identified from the sequences of GRK2 protein substrates, and 17 candidate peptides were synthesized to identify peptide substrates with high affinity for GRK2. GRK2 appears to require an acidic amino acid at the −2, −3, or −4 positions and its consensus phosphorylation site motifs were identified as (D/E)X_1–3(S/T), (D/E)X_1–3(S/T)(D/E), or (D/E)X_0–2(D/E)(S/T). Among the 17 peptide substrates examined, a 13-amino-acid peptide fragment of β-tubulin (DEMEFTEAESNMN) showed the highest affinity for GRK2 (K_m, 33.9 μM; V_max, 0.35 pmol min⁻¹ mg⁻¹), but very low affinity for GRK5. This peptide may be a useful tool for investigating cellular signaling pathways regulated by GRK2.     

High performance liquid chromatography–tandem mass spectrometry for the determination of bile acid concentrations in human plasma

We report a sensitive and robust method to determine cholic acid (CA), chenodeoxycholic acid (CDCA), deoxycholic acid (DCA), lithocholic acid (LCA), ursodeoxycholic acid (UDCA), and their taurine- and glycine-conjugate concentrations in human plasma using liquid chromatography–tandem mass spectrometry. Activated charcoal was utilized to prepare bile acid-free plasma, which served as the biological matrix for the preparation of standard and quality control samples. Plasma sample preparation involved solid-phase extraction. A total of 16 bile acids and 5 internal standards were separated on a reverse column by gradient elution and detected by tandem mass spectrometry in negative ion mode. The calibration curve was linear for all the bile acids over a range of 0.005–5 μmol/L. The extraction recoveries for all the analytes fell in the range of 88–101%. Intra-day and inter-day coefficients of variation were all below 10%. A stability test showed that all the bile acids were stable in plasma for at least 6 h at room temperature, at least three freeze–thaw cycles, in the −70 °C or −20 °C freezer for 2 months, and also in the reconstitution solution at 8 °C for 48 h. Comparison of the matrix effect of bile acid-free plasma with that of real plasma indicated that the charcoal purification procedure did not affect the properties of charcoal-purified plasma as calibration matrix. This method has been used to determine the bile acid concentrations in more than 300 plasma samples from healthy individuals. In conclusion, this method is suitable for the simultaneous quantification of individual bile acids in human plasma.     

Seed germination in Marathrum schiedeanum and M. rubrum (Podostemaceae)

Marathrum schiedeanum and Marathrum rubrum are annual Podostemaceae, thus their seeds are important to their dispersal and persistence in their habitat. We assessed the effect on germination of (1) light (white, red and far red) and darkness, (2) temperature (15, 20, 25, 30 °C and alternating 20/30 °C), (3) osmotic potential (0 to −0.8 MPa), (4) proximity to moisture sources and (5) seed storage. Seeds of M. schiedeanum and M. rubrum were non-dormant and had a high germination capacity (96%). Seeds were positive photoblastic; at 15 °C germination drop to zero, and germination rate was slower at 20 °C and at 20/30 °C than at 25 °C. A small proportion of seeds of both species germinated even at osmotic potentials as low as −0.6 MPa (11%) for M. rubrum and −0.8 MPa (70%) for M. schiedeanum. Seeds germinated only when near to the source of moisture (91.3–87.1% and 53.3–35.6% for M. schiedeanum and M. rubrum, respectively) and 2 years in dry storage did not modify their capacity to germinate. At the beginning of the rainy season, light and temperature in the rivers may be high enough for germination. The ability to germinate at low osmotic potential may be related to early germination during the rainy season. This may be because the seed mucilage assists in diffusion of water from the substrate to the seed. Both species germinated faster at −0.06 MPa, than in distilled water, which may indicate appropriate conditions for germination of these short-lived species.     

Simplified method for the collection, storage, and comet assay analysis of DNA damage in whole blood

Single-cell gel electrophoresis (comet assay) is one of the most common methods used to measure oxidatively damaged DNA in peripheral blood mononuclear cells (PBMC), as a biomarker of oxidative stress in vivo. However, storage, extraction, and assay workup of blood samples are associated with a risk of artifactual formation of damage. Previous reports using this approach to study DNA damage in PBMC have, for the most part, required the isolation of PBMC before immediate analysis or freezing in cryopreservative. This is very time-consuming and a significant drain on human resources. Here, we report the successful storage of whole blood in ~ 250 μl volumes, at − 80 °C, without cryopreservative, for up to 1 month without artifactual formation of DNA damage. Furthermore, this blood is amenable for direct use in both the alkaline and the enzyme-modified comet assay, without the need for prior isolation of PBMC. In contrast, storage of larger volumes (e.g., 5 ml) of whole blood leads to an increase in damage with longer term storage even at − 80 °C, unless a cryopreservative is present. Our “small volume” approach may be suitable for archived blood samples, facilitating analysis of biobanks when prior isolation of PBMC has not been performed.     

Influence of environmental factors on Vallisneria americana seed germination

Over the course of a growing season (April–October) water quality (water temperature, light, salinity, dissolved oxygen) and reproductive phenology (biomass, production of flowering shoots and seed pods, seed bank densities) were quantified in three Vallisneria americana beds in Nanjemoy Creek, MD, a tributary to the Chesapeake Bay. Clonal production of V. americana biomass increased at all sites when water temperatures rose above 25 °C. Flowering occurred during peak biomass (August–September) and resulted in the production of up to 16,000 seeds m⁻² at the end of the growing season. However, observed seed bank densities represented <1% of seed production. Laboratory experiments quantified the effects of dissolved oxygen (0.29–8.00 mg l⁻¹), light (0–160 μmol m² s⁻¹), temperature (13–29 °C), salinity (0.1–17.4 psu), sediment composition (3–86% sand; 0.9–8.3% sediment organic content), and burial depth (0.2–10 cm) on V. americana seed germination. Germination of V. americana seeds was enhanced (greater overall germination and shorter time to germination) under oxygenated conditions (8.00 mg l⁻¹), temperatures >22 °C, salinities of <1 psu, and in sediments composed of ≤3% organic content and >40% sand. Light (<160 μmol m⁻² s⁻¹) and burial depth (0.2–10 cm) had no significant effects on germination. Temperatures most favorable for seed germination (>22 °C) occurred in June, 2 months in the growing season just prior to development of peak vegetative standing stock. Seedlings were therefore at a distinct disadvantage to plants developed from over wintering buds. A lack of viable seed retention and inadequate environmental conditions at critical times in the growing season may be limiting seed germination success and subsequent seedling establishment within V. americana beds in the Chesapeake Bay. However, ungerminated seeds were found to maintain high viability, especially at salinities of 10 psu that can have significant negative effects of shoot growth survival. This suggests that seeds may serve as a source of reproductive material for bed recovery after periods of drought or other stressful conditions in estuarine systems.     

Performance of sulfidogenic anaerobic baffled reactor (ABR) treating acidic and zinc-containing wastewater

The applicability of anaerobic baffled reactor (ABR) was investigated for the treatment of acidic (pH 4.5–7.0) wastewater containing sulfate (1000–2000 mg/L) and Zn (65–200 mg/L) at 35 °C. The ABR consisted of four equal stages and lactate was supplemented (COD/SO₄²⁻ = 0.67) as carbon and energy source for sulfate reducing bacteria (SRB). The robustness of the system was studied by decreasing pH and increasing Zn, COD, and sulfate loadings. Sulfate-reduction efficiency quickly increased during the startup period and reached 80% within 45 days. Decreasing feed pH, increasing feed sulfate and Zn concentrations did not adversely affect system performance as sulfate reduction and COD removal efficiencies were within 62–90% and 80–95%, respectively. Although feed pH was steadily decreased from 7.0 to 4.5, effluent pH was always within 6.8–7.5. Over 99% Zn removal was attained throughout the study due to formation of Zn-sulfide precipitate.     

Stabilization of human urine doping control samples: II. Microbial degradation of steroids

The transportation of urine samples, collected for doping control analysis, does not always meet ideal conditions of storage and prompt delivery to the World Anti-Doping Agency (WADA) accredited laboratories. Because sample collection is not conducted under sterile conditions, microbial activity may cause changes to the endogenous steroid profiles of samples. In the current work, funded by WADA, a chemical mixture consisting of antibiotics, antimycotic substances and protease inhibitors was applied in urine aliquots fortified with conjugated and deuterated steroids and inoculated with nine representative microorganisms. Aliquots with and without the chemical mixture were incubated at 37 °C for 7 days to simulate the transportation period, whereas another series of aliquots was stored at −20 °C as reference. Microbial growth was assessed immediately after inoculation and at the end of the incubation period. Variations in pH and specific gravity values were recorded. Gas chromatography-mass spectrometry (GC-MS) analysis was performed for the detection of steroids in the free, glucuronide, and sulfate fractions. The addition of the chemical stabilization mixture to urine samples inhibited microorganism growth and prevented steroid degradation at 37 °C. On the other hand, four of the nine microorganisms induced alterations in the steroid profile of the unstabilized samples incubated at 37 °C.     

Biodiesel surrogates: Achieving performance demands

Synthesis of surrogate molecules is particularly useful for generating in sight of structural-activity relationships, understanding processes and improving the performance. In order to improve upon the physico-chemical properties of biodiesel, methyl, ethyl, isopropyl and n-butyl esters of β-branched fatty acid have been synthesized, initiating from β-branched alcohols. β-Branched alcohols upon oxidation gave corresponding acids, which were converted to their esters. The synthesized esters have substantially better oxidative stability, exhibited by Rancimat oxidation induction period of more than 24 h. The cloud point of synthesized esters is <−36 °C, pour point is <−42 °C and CFPP is <−21 °C, which is substantially better than fatty acid methyl esters. Besides achieving the objective of better oxidative stability and improved low temperature properties, the synthesized surrogate esters have viscosity in the range of 4.2–4.6 cSt at 40 °C, meeting the international diesel and biodiesel standards. The cetane number of synthesized esters is 62–69, which is much better than diesel and biodiesel. The blends of the synthesized esters in diesel at 5% and 10% meet Indian standards of diesel.     

Estimation of peptide concentration by a modified bicinchoninic acid assay

Although biuret based protein assays are theoretically applicable to peptide measurement, there is a high level of interpeptide variation, determined largely by peptide hydrophobicity. This variation in peptide reactivity can be significantly reduced by heat-denaturation of peptides at 95 °C for 5 min in the presence of 0.1 M NaOH containing 1% (w/v) SDS, prior to incubation for 30 min at 37 °C in BCA standard working reagent. This modification to the standard bicinchoninic acid (BCA) assay protocol allows for an accurate, rapid, and economical estimation of the peptide concentration within an unknown sample.     

Effect of temperature on chitin and astaxanthin recoveries from shrimp waste using lactic acid bacteria

The chitin and astaxanthin recoveries by lactic acid fermentation of shrimp wastes (Litopenaeus sp) were conducted in bed-column reactors at 15, 20, 25, 30, 35, 40 and 45 °C. The response surface methodology showed that the fermentations carried out in the 27–36 °C temperature range with lactic acid above 0.319 mmol/g resulted in the highest demineralization. The maximal deproteinizations were attained from 30 to 40 °C. The extraction of free-astaxanthin did not present significant differences between 20 and 35 °C and the proportion of cis-stereoisomer forms increased with temperature. The growth rates of Lactobacillus plantarum were estimated in the 15–45 °C range and analyzed by Arrhenius and square root models. The cardinal values were 3.94 and 51.7 °C for minimum and maximum temperatures, respectively, with activation energy of 43.38 Jmol⁻¹.     

Biointeraction analysis by high-performance affinity chromatography: Kinetic studies of immobilized antibodies

A system based on high-performance affinity chromatography was developed for characterizing the binding, elution and regeneration kinetics of immobilized antibodies and immunoaffinity supports. This information was provided by using a combination of frontal analysis, split-peak analysis and peak decay analysis to determine the rate constants for antibody–antigen interactions under typical sample application and elution conditions. This technique was tested using immunoaffinity supports that contained monoclonal antibodies for 2,4-dichlorophenoxyacetic acid (2,4-D). Association equilibrium constants measured by frontal analysis for 2,4-D and related compounds with the immobilized antibodies were 1.7–12 × 10⁶ M⁻¹ at pH 7.0 and 25 °C. Split-peak analysis gave association rate constants of 1.4–12 × 10⁵ M⁻¹ s⁻¹ and calculated dissociation rate constants of 0.01–0.4 s⁻¹ under the application conditions. Elution at pH 2.5 for the analytes from the antibodies was examined by peak decay analysis and gave dissociation rate constants of 0.056–0.17 s⁻¹. A comparison of frontal analysis results after various periods of column regeneration allowed the rate of antibody regeneration to be examined, with the results giving a first-order regeneration rate constant of 2.4 × 10⁻⁴ s⁻¹. This combined approach and the information it provides should be useful in the design and optimization of immunoaffinity chromatography and other analytical methods that employ immobilized antibodies. The methods described are not limited to the particular analytes and antibodies employed in this study but should be useful in characterizing other targets, ligands and supports.     

Cryopreservation of Greenshell™ mussel (Perna canaliculus) trochophore larvae

The Greenshell™ mussel (Perna canaliculus) is the main shellfish species farmed in New Zealand. The aim of this study was to evaluate the effects of cryoprotectant concentration, loading and unloading strategy as well as freezing and thawing method in order to develop a protocol for cryopreservation of trochophore larvae (16–20 h old). Toxicity tests showed that levels of 10–15% ethylene glycol (EG) were not toxic to larvae and could be loaded and unloaded in a single step. Through cryopreservation experiments, we designed a cryopreservation protocol that enabled 40–60% of trochophores to develop to D-larvae when normalized to controls. The protocol involved: holding at 0 °C for 5 min, then cooling at 1 °C min⁻¹ to −10 °C, holding for a further 5 min, then cooling at 0.5 °C min⁻¹ to −35 °C followed by a 5 min hold and then plunging into liquid nitrogen. A final larval rearing experiment of 18 days was conducted to assess the ability of these frozen larvae to develop further. Results showed that only 2.8% of the frozen trochophores were able to develop to competent pediveligers.     

Investigating sperm cryopreservation in a model tunicate, Ciona intestinalis sp. A

In cryopreservation procedures, the capacity to protect the cells from freezing and thawing processes is sensitive to the choice of the cryoprotective agent (CPA) and to its optimal concentration. The advancement of research on Tunicate model species has raised interest in liquid nitrogen cryopreservation for the storage and distribution of genetic resources. Ciona intestinalis (Linnè, 1767) consists of a complex of cryptic taxa that are central to several areas of investigation, from comparative genomics to invasive biology. Here we investigated how five CPAs, three chilling rates and two freezing rates influence semen cryopreservation in C. intestinalis sp. A. By using larval morphology and motility as endpoints, we estimated that long term semen storage requires 10% dimethyl sulfoxide as a protective agent, −1 °C/min chilling rate (18 °C to 5 °C) and −13 °C/min freezing rate (5 °C to −80 °C), followed by immersion in liquid nitrogen.     

Determination of casopitant and its three major metabolites in dog and rat plasma by positive ion liquid chromatography/tandem mass spectrometry

A sensitive, selective and quantitative method for the simultaneous determination of casopitant, a potent and selective antagonist of the human Neurokinin 1 (NK-1) receptor, and its three major metabolites M12, M13 and M31 was developed and validated in dog and rat plasma. Acetonitrile containing stable labeled internal standards for the four analytes was used to precipitate proteins in plasma. Chromatographic separation was obtained using a reversed phase column with multiple reaction monitoring turboionspray positive ion detection. The lower and upper limits of quantification for casopitant and its metabolites were 15 and 15,000 ng/mL, using a 50 μL of dog or rat plasma aliquot, respectively. The inter-day precision (relative standard deviation) and accuracy (relative error) in dog plasma, derived from the analysis of validation samples at 5 concentrations, ranged from 4.1% to 10.0% and −10.8% to 8.7%, respectively, for casopitant and its 3 major metabolites. The intra-day precision (relative standard deviation) and accuracy (relative error) in rat plasma, derived from the analysis of validation samples at 5 concentrations, ranged from 3.9% to 6.6% and −9.6% to 8.3%, respectively, for casopitant and its three metabolites. All analytes were found to be stable in analytical solutions for at least 43 days at 4 °C, in dog and rat plasma at room temperature for at least 24 h, at the storage temperature of −20 °C for at least 6 months, and following the action of three freeze–thaw cycles from −20 °C to room temperature. All analytes were also found to be stable in processed extracts at 4 °C for at least 72 h. This assay proved to be accurate, precise, fast and was used to support long-term toxicology studies in dog and rat.     

Detection of microRNAs in dried serum blots

We observed the preservation of microRNAs in unrefrigerated dried serum blots. Preservation was not adversely affected by drying or storing at 37, 45, or 60 °C instead of room temperature, but it was harmed when blots were dried incompletely before storage. Preservation of microRNAs in serum was not diminished if, instead of being kept frozen at −80 °C, it was stored as dried blots at room temperature for 5 months or at 37 °C for 4 weeks. Thus, dried blots can be a convenient and safer way to save, transport, and store serum for microRNA assays.     

Seed germination at different temperatures and water stress levels,and seedling emergence from different depths of Ziziphus lotus

Ziziphus lotus (L.) Lam. is a deciduous shrub with intricately branched stems in the Rhamnaceae family. It's a dominant and economically important species widely distributed in active sand dunes in the southern desert of Tunisia. To provide basic information for its conservation and reintroduction, we studied the influence of environmental factors on seed germination patterns. The germination responses of seeds were determined over a wide range of constant temperatures (10–50 °C), polyethylene glycol (PEG)-6000 solutions of different osmotic potentials (0 to − 1 MPa) and burial depths (1–10 cm). Temperatures between 15 and 45 °C seem to be favorable for the germination of this species. Germination was inhibited by either an increase or decrease in temperature from the most suitable temperature found (35 °C). The highest germination percentages (100%) were obtained under control conditions without PEG, and increasing moisture stress progressively inhibited seed germination, which was less than 5% at − 1 MPa. When tested for germination in distilled water, after PEG treatments, seeds germinated to the same extent as when fresh. When seeds buried deeply, there was a significant decrease in seedling emergence percentage and rate. Seedlings of Z. lotus emerged well at depths of 1–2 cm and could not emerge when sand burial depth was > 4 cm.