The determination of urea in soil extracts and related samples - a review

Although the dominant methods for the determination of urea in clinical applications incorporate selective enzymatic hydrolysis of urea, the determination of urea in soil extracts is complicated by the presence of urease inhibitors. The spectrophotometric determination of urea with an acidic solution diacetyl monoxime and semicarbazide is a viable option but traditional manual procedures are time-consuming. New variations on these procedures, based on microplates or flow-injection analysis methodologies, allow a far greater number of samples to be analysed with high precision and sensitivity.

Effect of crude oil extracts from trout offal as a replacement for fish oil in the diets of the Australian native fish Murray cod Maccullochella peelii peelii

The efficacy of trout oil (TO), extracted from trout offal from the aquaculture industry, was evaluated in juvenile Murray cod Maccullochella peelii peelii (25.4-0.81 g) diets in an experiment conducted over 60 days at 23.7-0.8 °C. Five isonitrogenous (48% protein), isolipidic (16%) and isoenergetic (21.8 kJ gm1) diets, in which the fish oil fraction was replaced in increments of 25% (0-100%), were used. The best growth and feed efficiency was observed in fish fed diets containing 50-75% TO. The relationship of specific growth rate (SGR), food conversion ratio (FCR) and protein efficiency ratio (PER) to the amount of TO in the diets was described in each case by second-order polynomial equations (P<0.05), which were: SGR=-0.44TO2+0.52TO+1.23 (r2=0.90, P<0.05); FCR=0.53TO2-0.64TO+1.21 (r2=0.95, P<0.05); and PER=-0.73TO2+0.90TO+1.54 (r2=0.90, P<0.05). Significant differences in carcass and muscle proximate compositions were noted among the different dietary treatments. Less lipid was found in muscle than in carcass. The fatty acids found in highest amounts in Murray cod, irrespective of the dietary treatment, were palmitic acid (16:0), oleic acid (18:1n-9), linoleic acid (18:2n-6) and eicosapentaenoic acid (20:5n-3). The fatty acid composition of the muscle reflected that of the diets. Both the n-6 fatty acid content and the n-3 to n-6 ratio were significantly (P<0.05) related to growth parameters, the relationships being as follows. Percentage of n-6 in diet (X) to SGR and FCR: SGR=-0.12X2+3.96X-32.51 (r2=0.96) and FCR=0.13X2-4.47X+39.39 (r2=0.98); and n-3:n-6 ratio (Z) to SGR, FCR, PER: SGR=-2.02Z2+5.01Z-1.74 (r2=0.88), FCR=2.31Z2-5.70Z+4.54 (r2=0.93) and PER=-3.12Z2-7.56Z+2.80 (r2=0.88) respectively. It is evident from this study that TO could be used effectively in Murray cod diets, and that an n-3:n-6 ratio of 1.2 results in the best growth performance in Murray cod.

Coupled RNA polymerase II transcription and 3′ end formation with yeast whole-cell extracts

 RNA polymerase II (RNAP II) transcription and pre-mRNA 3' end formation are linked through physical and functional interactions. We describe here a highly efficient yeast in vitro system that reproduces both transcription and 3' end formation in a single reaction. The system is based on simple whole-cell extracts that were supplemented with a hybrid Gal4-VP16 transcriptional activator and supercoiled plasmid DNA templates encoding G-less cassette reporters. We found that the coupling of transcription and processing in vitro enhanced pre-mRNA 3' end formation and reproduced requirements for poly(A) signals and polyadenylation factors. Unexpectedly, however, we show that in vitro transcripts lacked m⁷G-caps. Reconstitution experiments with CF IA factor assembled entirely from heterologous components suggested that the CTD interaction domain of the Pcf11 subunit was required for proper RNAP II termination but not 3' end formation. Moreover, we observed reduced termination activity associated with extracts prepared from cells carrying a mutation in the 5'-3' exonuclease Rat1 or following chemical inhibition of exonuclease activity. Thus, in vitro transcription coupled to pre-mRNA processing recapitulates hallmarks of poly(A)-dependent RNAP II termination. The in vitro transcription/processing system presented here should provide a useful tool to further define the role of factors involved in coupling.

Metabolite profiling of biological extracts

Metabolite profiling, HPLC, LC-QTOF-MS, GC-MS. A workflow will be presented for comprehensive metabolomics using LC- and GC-MS. Metabolomics is an emerging field in the suite of ‘omic’ approaches for Systems Biology. The goal of metabolomics is to detect the presence of all small-molecules in a biological sample. This presents a significant challenge due to the chemical diversity and large concentration range of metabolites. Currently, there is no single method which enables the entire metabolome to be analysed, therefore a suite of analytical approaches are required to increase the coverage of detected metabolites. The routinely used techniques for metabolite profiling are LC- and GC-MS and NMR. Here we present complementary approaches using MS hyphenated to different chromatographic techniques. GC-MS represent the most robust standardised technique for high throughput metabolite profiling however there are still no standard LC-based methods for profiling. Polar compounds represent the most challenging aspect of LC-based metabolomics. A robust chromatographic technique for profiling polar compounds using HILIC chromatography and QTOF-MS will be presented as well as the complimentary reverse phase LC-MS method. The polar separation was carried out using a diamond hydride column. This unique stationary phase provides stable retention times and fast re-equilibration which contrasts to other forms of HILIC stationary phases. These LC-based methods will be compared to the well established GC-MS method as well as NMRbased profiling.

Profiling of polar metabolites in biological extracts using diamond hydride-based aqueous normal phase chromatography

Highly polar metabolites, such as sugars and most amino acids are not retained by conventional RP LC columns. Without sufficient retention low concentration compounds are not detected due ion suppression and structural isomers are not resolved. In contrast, hydrophilic interaction chromatography (HILIC) and aqueous normal phase chromatography (ANP) retain compounds based on their hydrophilicity and therefore provides a means of separating highly polar compounds. Here, an ANP method based on the diamond hydride stationary phase is presented for profiling biological small molecules by LC. A rapid separation system based upon a fast gradient that delivers reproducible chromatography is presented. Approximately 1000 compounds were reproducibly detected in human urine samples and clear differences between these samples were identified. This chromatography was also applied to xylem fluid from soyabean (Glycine max) plants to which 400 compounds were detected. This method greatly increases the metabolite coverage over RP-only metabolite profiling in biological samples. We show that both forms of chromatography are necessary for untargeted comprehensive metabolite profiling and that the diamond hydride stationary phase provides a good option for polar metabolite analysis.

Multiplexed detection: fast comprehensive sample analysis of tobacco leaf extracts using HPLC with AFT columns

Detector-based comprehensive screening analysis of complex samples of natural origin using High Performance Liquid Chromatography (HPLC) can be a complicated and time-consuming task. There are a number of ways multidetection characterization can be achieved; however, there are limitations associated with each technique. Active Flow Technology (AFT) in Parallel Segmented Flow (PSF) mode allows for multiplexed detection HPLC analysis within a single injection, whereas maintaining chromatographic performance and allowing the use of multiple destructive detectors to achieve a comprehensive yet efficient screening of a complex sample. In this study, a comprehensive characterization analysis of tobacco leaf extract was carried out through multiplexed detection using a PSF column for the detection of biomolecules by UV-Vis detection, DPPH• for reactive-oxygen species (ROS) detection, and mass spectrometry, the latter two detection methods being sample destructive.