Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR)

MicroRNAs (miRNAs) are small (～22 nt) RNAs that play important roles in gene regulatory networks by binding to and repressing the activity of specific target mRNAs. Recent studies have indicated that miRNAs circulate in a stable, cell-free form in the bloodstream and that the abundance of specific miRNAs in plasma or serum can serve as biomarkers of cancer and other diseases. Measurement of circulating miRNAs as biomarkers is associated with some special challenges, including those related to pre-analytic variation and data normalization. We describe here our procedure for qRT-PCR analysis of circulating miRNAs as biomarkers, and discuss relevant issues of sample preparation, experimental design and data analysis.     

Ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) for the sensitive determination of folates in rice

High-performance liquid chromatography, coupled to tandem mass spectrometry (HPLC–MS/MS) has been established as the method of choice for the sensitive and simultaneous determination of different folates in a particular matrix, especially when only minute quantities of material are available. Using a previously developed and validated HPLC–MS/MS method as a starting point, we here report on the development and validation of an ultra-performance liquid chromatography (UPLC–MS/MS) method for analysis of folates in rice, which allows higher throughput and better resolution. UPLC was performed under gradient conditions on an Acquity HSS T3 column, followed by tandem mass spectrometry detection. The method was validated based on linearity, sensitivity, precision, accuracy and matrix effects. The limits of detection and the lower limits of quantification varied between 0.06 and 0.45 μg/100 g and 0.12 and 0.91 μg/100 g, respectively. Two linear calibration curves were established, one for the low and the other for the high concentration range. Analysis of the distribution and levels of folates in wild-type and folate-biofortified rice showed up to 50-fold enrichment in biofortified rice, with total folate levels of up to 900 μg/100 g rice. This is the first successful implementation of a UPLC method for the rapid and sensitive quantitative determination of folates in plant material.     

Regulation of lipid metabolism in the snow alga Chlamydomonas nivalis in response to NaCl stress: An integrated analysis by cytomic and lipidomic approaches

The cultures of the snow alga Chlamydomonas nivalis in the exponential phage were stressed by NaCl (up to 1.5%) for 0～48 h, followed by Nile Red staining-based cytomic analysis (flow cytometry and confocal laser scanning microscopy). The fluorescent intensities of total lipids, and neutral and polar lipids increased to the maximum within 7 h in the NaCl stressed cells with the highest increase in total lipids by 2-fold (0.75%-NaCl for 7 h), the highest increase in neutral lipids by 68-fold (1%-NaCl for 7 h) and the highest increase in polar lipids by 10-fold (1.25%-NaCl for 5 h), respectively. Seven types and 22 kinds of polar lipid molecules were selected and identified as biomarkers by UPLC/Q-TOF-MS-based lipidomic analysis, which demonstrated differences in total lipids between the stress group (0.75%-NaCl for 7 h) and the control. The biological roles of the biomarkers in the alga under NaCl stress were discussed. The integrated approach based on “omics” technologies developed in the present work is validated as a powerful tool to successfully reveal the regulation of lipid metabolism in microalgae in response to stress stimulation.     

Multimodal information improves the rapid detection of mental fatigue

One of the major challenge in the detection of mental states is improving the accuracy of brain activity-based detectors with additional information from extracranial signals. We assessed the suitability, for real-time mental fatigue detection, of EEG, EOG and ECG measurements, taken separately or together. Thirteen subjects performed six blocks of switching tasks. For each participant, the block with the lowest error rate from the first two blocks and the block with the highest error rate from the last three blocks were discriminated with a machine learning algorithm (support vector machine). The classification scores obtained with ECG or EOG were greater than would be expected by chance (>50%) for time windows of at least 8 s. EEG was the best single mode of detection, with classification scores ranging from 80 ± 3% with a 4 s time window to 94 ± 2% with a 30 s time window. The addition of ECG and EOG features to EEG features significantly increased classification scores for short time windows (e.g., to 86 ± 3% with a 4 s time window, p < 0.001). For short time windows (up to 12 s), ECG significantly increased the discriminatory power of EEG, whereas EOG did not. These results demonstrate that mental state detection on the basis of extracerebral measurements is feasible and that a combination of EEG and ECG is particularly appropriate for the rapid detection of mental fatigue.     

Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput

We report on the development and characterization of automated metal-free multiple-column nanoLC instrumentation for sensitive and high-throughput analysis of phosphopeptides with mass spectrometry. The system employs a multiple-column capillary LC fluidic design developed for high-throughput analysis of peptides (Anal. Chem. 2001, 73, 3011–3021), incorporating modifications to achieve broad and sensitive analysis of phosphopeptides. The integrated nanoLC columns (50 μm i.d. × 30 cm containing 5 μm C18 particles) and the on-line solid phase extraction columns (150 μm i.d. × 4 cm containing 5 μm C18 particles) were connected to automatic switching valves with non-metal chromatographic accessories, and other modifications to avoid the exposure of the analyte to any metal surfaces during handling, separation, and electrospray ionization. The nanoLC developed provided a separation peak capacity of ～250 for phosphopeptides (and ～400 for normal peptides). A detection limit of 0.4 fmol was obtained when a linear ion trap tandem mass spectrometer (Finnegan LTQ) was coupled to a 50-μm i.d. column of the nanoLC. The separation power and sensitivity provided by the nanoLC–LTQ enabled identification of ～4600 phosphopeptide candidates from ～60 μg COS-7 cell tryptic digest followed by IMAC enrichment and ～520 tyrosine phosphopeptides from ～2 mg of human T cells digests followed by phosphotyrosine peptide immunoprecipitation.     

Cellular ATP and biomass of attached and planktonic sulfur-oxidizing Acidithiobacillus ferrooxidans

This study demonstrates differences in ATP levels between attached and planktonic cells of Acidithiobacillus ferrooxidans growing with elemental sulfur. A small fraction of 3.7–14.4% of the bacterial cells was attached to the sulfur particles. The highest cell attachment of 14.4% was at the end of the lag phase, decreasing to 3.7% into the latter part of the active growth phase. Therefore, attached cells and their ATP content made a minor contribution to the total culture biomass in the active growth phase. However, the cellular ATP content was 1.01 amol per attached cell and 0.34 amol per planktonic cell. The significantly (P < 0.01) lower ATP content was attributed to sulfur limitation in the planktonic cells. These results suggest that a negligibly small subpopulation may be a link in cooperative interaction whereby sulfur oxidation by attached cells under boundary conditions provides bioavailable substrates to planktonic cells in the population.     

Optimization of a rapid microwave-assisted extraction method for the simultaneous determination of opiates,cocaine and their metabolites in human hair

A rapid and cleanup-free microwave-assisted extraction (MAE) method is proposed for the simultaneous extraction of six illegal drugs of abuse – cocaine, benzoylecgonine (BZE), cocaethylene (CCE), morphine, 6-monoacethylmorphine (6AM) and codeine – from human hair samples. The analytes were determined using high performance liquid chromatography (HPLC) with photodiode array UV detection. The influence of several variables on the efficiency of the MAE procedure was investigated in detail by a multi-objective optimization approach based on a hybrid experimental design (17 experiments) and desirability functions. Six drugs were successfully extracted from human hair with recoveries close to 100% and good reproducibility (<3.6% RSD) under the optimal MAE conditions: 11 mL dichloromethane (DCM) extraction solvent, 60 °C extraction temperature, 9 min extraction time and 0.5 mL of methanol (MeOH) added to 50 mg of the hair sample in the extraction vessels. Limits of quantification of 0.2 ng mg^?1 were found for the studied compounds. A comparison of sample preparation procedures, including MAE, enzymatic digestion and digestion by aqueous acids, was also conducted. The results indicated that the global behaviour of sample procedures provided similar satisfactory recoveries ranging from 86 to 100%. Indeed, the MAE procedure resulted in a reduction of extraction time by 100-fold and the elimination of cleanup steps. Slightly higher recoveries of morphine, 6AM, BZE and CCE, at 1 ng mg^?1 concentration level and cocaine at 40 ng mg^?1 concentration level, were achieved using MAE. Lastly, the proposed MAE method was applied to several human hair samples from multidrug abusers.     

A simple glutathione transferase-based colorimetric endpoint assay for insecticide detection

The natural ability of the detoxification enzymes glutathione transferases (GSTs) to interact with xenobiotics can be used for the production of colorimetric assays. Detection is usually based on the inhibition of the GST-catalysed reaction, with detection achieved spectrophotometrically or electrochemically. Here we have adopted a chromogenic (visual) activity assay for screening GSTs with alkyltransferase activity for iodoalkene substrates for detection of insecticides. We screened a number of GSTs from insecticide resistant mosquito species for their ability to catalyse iodoalkane biotransformation reactions. AaGSTE2 was found to metabolise iodoethane with high turnover, which resulted in a dark blue colour in the enzymatic reaction. Following assay optimisation we exploited the high recognition affinity of the AgGSTE2 for insecticides to develop a novel colorimetric detection assay for organochlorine and pyrethroid quantification. Calibration curves were obtained for permethirn, deltamethrin, λ-cyhalothrin and DDT, with useful concentration ranges of 0–40 μg/ml (0–100 μM), 0–50 μg/ml (0–100 μM), 0–100 μg/ml (0–220 μM), and 0–50 μg/ml (0–140 μM), respectively. The assay was validated with extracts from insecticide sprayed surfaces and found to be reproducible and reliable compared with HPLC. The assay is therefore suitable for monitoring insecticide residues in insecticide treated materials, and therefore has potential for insect vector control operations.     

Effect of CoCl2 treatment on major and trace elements metabolism and protein concentration in mice

Cobalt (Co) is a transition metal and an essential trace element, required for vitamin B₁₂ biosynthesis, enzyme activation and other biological processes, but toxic in high concentrations. There is lack of data for the effect of long-term Co(II) treatment on the concentrations of other trace elements. We estimate the influence of cobalt chloride (CoCl₂) on the relative content of different metals in mouse plasma using two-jet arc plasmatron atomic emission and on the total protein content. On average, the content of different elements in the plasma of 2-month-old balb/c mice (control group) decreased in the order: Ca > Mg > Si > Fe > Zn > Cu ≥ Al ≥ B. The treatment of mice for 60 days with CoCl₂ (daily dose 125 mg/kg) did not appreciably change the relative content of Ca, Cu, and Zn, while a 2.4-fold statistically significant decrease in the content of B and significant increase in the content of Mg (1.4-fold), Al and Fe (2.0-fold) and Si (3.2-fold) was found. A detectable amount of Mo was observed only for two control mice, while the plasma of 9 out of 16 mice of the treated group contained this metal. The administration of Co made its concentration detectable in the plasma of all mice of the treated group, but the relative content varied significantly. The treatment led to a 2.2-fold decrease in the concentration of the total plasma protein. Chronic exposure to CoCl₂ affects homeostasis as well as the concentrations and metabolism of other essential elements, probably due to competition of Co ions for similar binding sites within cells, altered signal transduction and protein biosynthesis. Long-term treatment also leads to significant weight changes and reduces the total protein concentration.The data may be useful for an understanding of Co toxicity, its effect on the concentration of other metal ions and different physiological processes.     

Freeze-drying of ATP entrapped in cationic,low lipid liposomes

Concerning the instability of ATP liposomes formulated to easily diffuse through the liver (size ～100 nm), this work targets the key parameters that influence the freeze-drying of a preparation that combines cholesterol, DOTAP and phosphatidylcholine (either natural soybean or egg (SPC or EPC) or hydrogenated (HSPC)). After freeze-drying blank liposomes, size increased significantly when initial lipid concentration was lowered from 20 to 5 mM (p = 0.0018). With low lipid concentration preparation (5 mM), SPC limited size increase (SI) more efficiently compared to EPC or HSPC. With SPC and EPC, sucrose showed better size results compared to trehalose (Lyoprotectant/Lipid ratio (w/w) avoiding any SI: ～5 and ～10 (for SPC), ～10 and ～15 (for EPC), for sucrose and trehalose, respectively), but the opposite was evidenced with HSPC liposomes where a Trehalose/Lipid ratio of 25 barely prevented SI. In addition, slow versus quick cooling rate led to limiting SI for HSPC liposomes (p = 0.0035). With sucrose or trehalose at both Lyoprotectant/Lipid ratios ensuring size stabilisation (10:1 and 15:1, respectively), ATP leakage ranged between 38.8 ± 7.9% and 58.2 ± 1.4%. In conclusion, this study emphasizes that using strict size maintenance as the primary objective does not result in drug complete retention inside the liposome core.     

Structure–activity relationships of 2-aminothiazoles effective against Mycobacterium tuberculosis

A series of 2-aminothiazoles was synthesized based on a HTS scaffold from a whole-cell screen against Mycobacterium tuberculosis (Mtb). The SAR shows the central thiazole moiety and the 2-pyridyl moiety at C-4 of the thiazole are intolerant to modification. However, the N-2 position of the aminothiazole exhibits high flexibility and we successfully improved the antitubercular activity of the initial hit by more than 128-fold through introduction of substituted benzoyl groups at this position. N-(3-Chlorobenzoyl)-4-(2-pyridinyl)-1,3-thiazol-2-amine (55) emerged as one of the most promising analogues with a MIC of 0.024 μM or 0.008 μg/mL in 7H9 media and therapeutic index of nearly ～300. However, 55 is rapidly metabolized by human liver microsomes (t_1/2 = 28 min) with metabolism occurring at the invariant aminothiazole moiety and Mtb develops spontaneous low-level resistance with a frequency of ～10^?5.     

Deletion and site-directed mutagenesis of laccase from Shigella dysenteriae results in enhanced enzymatic activity and thermostability

A putative laccase gene was cloned from Shigella dysenteriae W202 and expressed in Escherichia coli as a soluble fusion protein with high yield. The purified product (Wlac) was characterized as the CueO-like laccase from E. coli, a monomer of molecular mass 55 kDa, with a maximum activity of 24.4 U/mg (K_m = 0.086) and a pH optimum of 2.5, in a standard assay using ABTS (2,2′-azino-di(3-ethyl-benzthiazoline-6-sulfonate) as the substrate. Activity was stable at 0–25 °C but inhibited above 40 °C. Purified Wlac was completely inhibited by 200 mM EDTA and partially by 32 mM SDS, 50 mM NaN₃ and 60 mM thioglycolic acid. Activity was stimulated by Cu²⁺; other metal ions had only slight or negative effects. Two mutated variants, WlacS and WlacD, were obtained by substituting Glu 106 with Phe 106, and adding a deletion of an α-helix domain (from Leu 351 to Gly 378). WlacS had a 2.2-fold (52.9 U/mg) and WlacD a 3.5-fold (85.1 U/mg) higher enzyme activity than the wild-type laccase and WlacD showed greater thermostability at higher temperatures. Sce VMA intein-associated fusion proteins maintained ～80% of total enzyme activity. Thus, deletion and site-directed mutagenesis of laccases are capable of promoting both enzymatic activity and thermostability.     

Sensitivity of ruminal bacteria isolates of sheep,cattle and buffalo to some heavy metals

This study was conducted to investigate the toxicity of 12 heavy metals (i.e., HM), namely Hg, Cd, Co, Ni, Cr, Cu, Ag, Mo, Zn, Pb, Li and Na on bacterial isolates from the rumen of sheep, cattle and buffaloes. Rumen samples were collected immediately after slaughter during the dry season. Ruminal bacterial isolates, 59, were obtained from two sheep, five cows and nine buffaloes. Sensitivity of ruminal bacterial isolates to each HM was determined by the clearance zone (CZ) using the Kirby-Bauer disc diffusion susceptibility test. Bacterial populations isolated from the rumens of sheep and buffalo had a lower resistance (P<0.001) to HM toxicity than did cattle. Regardless of ruminant species, bacterial isolates revealed a higher tolerance (P<0.001) to Li and Na, whereas Hg and Cd were the most toxic HM for all isolates. We conclude that inhibition of these HM to the isolated microbial population of sheep, cattle and buffalo is ranked: Hg (most toxic) > Cd > Co ～ Ag ～ Cu ～ Cr ～ Ni > Mo ～ Zn ～ Pb > Li ～ Na. Further research is required to explain the mechanism of toxicity of these HM, and also to explore the variation among ruminant species.     

Proteomics of wine additives: Mining for the invisible via combinatorial peptide ligand libraries

Combinatorial peptide ligand libraries (CPLLs) have been adopted for harvesting and identifying traces of casein (used as a fining agent) present in white wines. Although minute amounts (200 µL) of CPLL beads are added to the entire content of a wine bottle (750 mL), they are able to sequester with high efficiency (up to 80%) residual traces of casein, permitting a signal “amplification” of at least 5000-fold. It is here demonstrated that as little as 1 µg/L of casein can be efficiently detected in white wines, a major improvement over previous investigations in which the lower detection limit had been estimated at 100 µg/L. The fact that such very low levels of fining agents can still be detected in treated white wines should be taken into consideration by winemakers in labelling their products and by EC rulers in issuing proper regulations.     

Expression,purification and partial characterization of a xanthine oxidase (XOD) in Arthrobacter sp.

A xanthine oxidase (XOD) was expressed, purified and partially characterized from Arthrobacter sp. with a negative immune protocol. To determine the optimal inducer for XOD, xanthine, hypoxanthine and uric acid were added into the medium of cultivation. The results revealed that with the inducement of about 14 mM xanthine, the highest XOD activity could be detected. To separate XOD from Arthrobacter sp., the cells were first cultured without any inducement; then the total proteins of the collected cells were extracted and immunized to rabbits for the polyclonal antibodies. These antibodies were then coupled with sepharose CL 6 B, and the medium was further employed to deplete most of the cells’ back ground proteins. Began with ～20 mg crude protein from disrupted cells was subjected to the antibody medium, and ～1.45 mg protein was detected in unbinding fractions with ～92.0% of activity. The extracted xanthine oxidase was ～85% pure with native-PAGE analysis, and ～90% pure with SDS-PAGE analysis, the yield of protein was ～7.4%. The specific activity of the enzyme was 36.0 U/mg. The native enzyme should be a dimer (～280 kDa) of a protein composed with two different peptides with the mass of approximately 55.5 and 85.5 kDa, respectively. The optimal pH and temperature of this enzyme were determined at about pH 7 and 50 °C. Furthermore, EDTA revealed almost no influences on the activity.     

Simultaneous determination of quinolones for veterinary use by high-performance liquid chromatography with electrochemical detection

A selective method based on high-performance liquid chromatography with electrochemical detection (HPLC-ECD) has been developed to enable simultaneous determination of three fluoroquinolones (FQs), namely danofloxacin (DANO), difloxacin (DIFLO) and sarafloxacin (SARA). The fluoroquinolones are separated on a Novapack C-18 column and detected in a high sensitivity amperometric cell at a potential of +0.8 V. Solid-phase extraction was used for the extraction of the analytes in real samples. The range of concentration examined varied from 10 to 150 ng g^?1 for danofloxacin, from 25 to 100 ng g^?1 for sarafloxacin and from 50 to 315 ng g^?1 for difloxacin, respectively. The method presents detection limits under 10 ng g^?1 and recoveries around 90% for the three analytes have been obtained in the experiments with fortified samples. This HPLC-ECD approach can be useful in the routine analysis of antibacterial residues being less expensive and less complicated than other more powerful tools as hyphenated techniques.     

Saxitoxin monitoring in three species of Florida puffer fish

Beginning in April 2002, three species of Florida puffer fish from around the state of Florida, USA were monitored for the presence of saxitoxin (STX). In total, 873 southern (Sphoeroides nephelus), 171 checkered (S. testudineus), and 53 bandtail (S. spengleri) puffer fish were collected between 2002 and 2006 from eight regions: Jacksonville, the Indian River Lagoon, Tequesta, the Florida Keys, Charlotte Harbor, Tampa Bay, Cedar Key, and Apalachicola. Emphasis was placed on collecting specimens from the Indian River Lagoon (IRL), where recreational harvesting of puffer fish led to 28 cases of saxitoxin puffer fish poisoning (SPFP) between January 2002 and May 2004. Southern puffer fish from the northern IRL routinely contained the highest concentrations of STX, with average levels in the skin of 1787 μg STXequiv./100 g tissue. Elevated concentrations were also found in the muscle (1102 μg STXequiv./100 g), gut contents (539 μg STXequiv./100 g), gonads (654 μg STXequiv./100 g), and liver (214 μg STXequiv./100 g). Lower, yet significant (above the action limit of 80 μg STXequiv./100 g tissue), concentrations of STX were also detected in the skin (599 μg STXequiv./100 g), muscle (233 μg STXequiv./100 g), gut contents (197 μg STXequiv./100 g), and gonads (239 μg STXequiv./100 g) of southern puffer fish from Tequesta in the southern IRL, as well as in the gonads (122 μg STXequiv./100 g) of Jacksonville southern puffer fish and the skin (265 μg STXequiv./100 g) of Tampa Bay southern puffer fish. STX concentrations above the action limit were also found in the skin of bandtail puffer fish from the IRL (620 μg STXequiv./100 g), Tequesta (374 μg STXequiv./100 g), and the Florida Keys (230 μg STXequiv./100 g). Checkered puffer fish collected from the IRL, Tequesta, and the Florida Keys on average were nontoxic, containing STX levels below the action limit in all tissues.     

Identification of reference microRNAs and suitability of archived hemopoietic samples for robust microRNA expression profiling

In many cancers, including neuroblastoma, microRNA (miRNA) expression profiling of peripheral blood (PB) and bone marrow (BM) may increase understanding of the metastatic process and lead to the identification of clinically informative biomarkers. The quality of miRNAs in PB and BM samples archived in PAXgene? blood RNA tubes from large-scale clinical studies and the identity of reference miRNAs for standard reporting of data are to date unknown. In this study, we evaluated the reliability of expression profiling of 377 miRNAs using quantitative polymerase chain reaction (qPCR) in PB and BM samples (n = 90) stored at ?80 °C for up to 5 years in PAXgene? blood RNA tubes. There was no correlation with storage time and variation of expression for any single miRNA (r < 0.50). The profile of miRNAs isolated as small RNAs or co-isolated with small/large RNAs was highly correlated (r = 0.96). The mean expression of all miRNAs and the geNorm program identified miR-26a, miR-28-5p, and miR-24 as the most stable reference miRNAs. This study describes detailed methodologies for reliable miRNA isolation and profiling of PB and BM, including reference miRNAs for qPCR normalization, and demonstrates the suitability of clinical samples archived at ?80 °C into PAXgene? blood RNA tubes for miRNA expression studies.     

Activation of cardiac hypertrophic signaling pathways in a transgenic mouse with the human PRKAG2 Thr400Asn mutation

Human mutations in PRKAG2, the gene encoding the γ2 subunit of AMP activated protein kinase (AMPK), cause a glycogen storage cardiomyopathy. In a transgenic mouse with cardiac specific expression of the Thr400Asn mutation in PRKAG2 (TG^T400N), we previously reported initial cardiac hypertrophy (ages 2–8 weeks) followed by dilation and failure (ages 12–20 weeks). We sought to elucidate the molecular mechanisms of cardiac hypertrophy. TG^T400N mice showed significantly increased cardiac mass/body mass ratios up to ～ 3-fold beginning at age 2 weeks. Cardiac expression of ANP and BNP were ～ 2- and ～ 5-fold higher, respectively, in TG^T400N relative to wildtype (WT) mice at age 2 weeks. NF-κB activity and nuclear translocation of the p50 subunit were increased ～ 2- to 3-fold in TG^T400N hearts relative to WT during the hypertrophic phase. Phosphorylated Akt and p70S6K were elevated ～ 2-fold as early as age 2 weeks. To ascertain whether these changes in TG^T400N mice were a consequence of increased AMPK activity, we crossbred TG^T400N with TG^α2DN mice, which express a dominant negative, kinase dead mutant of the AMPK α2 catalytic subunit and have low myocardial AMPK activity. Genetic reversal of AMPK overactivity led to a reduction in hypertrophy, nuclear translocation of NF-κB, phosphorylated Akt, and p70S6K. We conclude that inappropriate activation of AMPK secondary to the T400N PRKAG2 mutation is associated with the early activation of NF-κB and Akt signaling pathway, which mediates cardiac hypertrophy.