A comparison of alternative sample preparation procedures for the analysis of swainsonine using LC‐MS/MS

Introduction – Swainsonine, a polyhydroxy indolizidine alkaloid and known glycosidase inhibitor, is found in a number of different plants that cause a lysosomal storage disease known as locoism in the western USA. Most recently swainsonine has been analysed by LC‐MS/MS after sample extraction and preparation from ion‐exchange resins. Objective – To compare previously published sample preparation procedures with several new alternative procedures to provide methods using either commercially available solid‐phase extraction equipment or procedures which significantly reduce sample preparation time. Methodology – A previously reported and validated sample preparation method using ion‐exchange resin was compared with methods using a commercially available solid‐phase extraction cartridge, a solvent partitioning procedure or a single solvent extraction procedure using one of two solvents. Twenty different plant samples of varying swainsonine concentrations were prepared in triplicate and analysed by LC‐MS/MS. The measured concentration of swainsonine was then statistically compared between methods. Results – There were no statistically significant differences found between four of the five different sample preparation methods tested. Conclusion – A commercially available SPE cartridge can be used to replace the previously used ion‐exchange resin for swainsonine analysis. For very rapid analyses the SPE procedure can be eliminated and a simple, single solvent extraction step used for sample preparation. Published in 2010 by John Wiley & Sons, Ltd.     

蚧虫基因组DNA不同提取方法的比较

实验以日本龟蜡蚧CeroplastesjaponicusGreen,白蜡绵粉蚧PhenacoccusfraxinusTang ,朝鲜球蚧DidesmococcuskoreanusBorchseniush和瘤大球坚蚧EulecaniumgiganteaShinji等 4种蚧虫为材料 ,分别用十二烷基硫酸钠 (SDS)法、十六烷基三乙基溴化铵 (CTAB)法、醋酸钾 (KAc)法和氯化钠 (NaCl)法等 4种方法 ,对单只蚧虫进行基因组DNA提取 ,用 0 8%琼脂糖凝胶电泳检测所提DNA。结果表明 ,4种方法都可以提取到基因组DNA ,但是比较而言 ,CTAB法和NaCl法所提取的DNA质量明显优于SDS法和KAc法 ,并适用于PCR。因此认为 ,CTAB法和NaCl法是实验室提取单只蚧虫基因组DNA更有效而实用的方法。     

Investigation of simultaneous lutein and lipid extraction from wet microalgae using Nile Red as solvatochromic shift probe

Microalgae have been proposed as an alternative lutein source due to their high productivity, reliability, and versatility. In this study lutein and lipid extraction from wet Chlorella vulgaris UTEX 265 was investigated. The lutein production was monitored throughout the microalgal growth phase and several extraction parameters such as the sample size, drying method, and cell disruption method were investigated. The performance of solvents on lutein extraction was compared using Nile Red as a solvatochromic polarity probe. The simultaneous lutein and lipid extraction was also studied for different polarities using an ethanol-hexane binary solvent at the optimal solvent compositions suitable for lutein extraction. Among the solvents investigated, 3:1 (v/v) ethanol/hexane was recognized as the optimal solvent for lutein and lipid co-extraction, which contributed to a 13.03 mg g^?1 lutein and 101.8 mg g^?1 FAME yield. The saponifiable lipids content (86.9% w/w) was higher than conventional extraction methods. Based on our results, wet extraction approach exhibits good potential, while the bead-beater is the most suitable technique for cell disruption and lutein extraction.     

松突圆蚧基因组DNA提取方法的比较

分别采用醋酸钾(KAc)法、十二烷基硫酸钠-蛋白酶K(SDS-PK)消化法、十六烷基三乙基溴化铵(CTAB)法及DNA提取试剂盒(吸附柱型)对单只松突圆蚧的基因组DNA进行提取。同时针对盾蚧科昆虫的特点,在提取前利用氯仿和解剖针去除样品表面的介壳。结果表明,用同种提取方法提取的经氯仿处理与未经处理样本的提取效果无明显差异,而采用解剖针去除介壳的样本提取效果较好。所采用的4种提取方法均能从新鲜标本中提取出DNA,其中CTAB法提取的DNA量较多,而SDS-PK法提取的DNA质量较好。     

Application of the standard addition method for the absolute quantification of neutral lipids in microalgae using Nile red

Microalgae are considered one of the best candidates for biofuel production due to their high content in neutral lipids, therefore, an accurate quantification of these lipids in microalgae is fundamental for the identification of the better candidates as biodiesel source.Nile red is a fluorescent dye widely employed for the quantification of neutral lipids in microalgae. Usually, the fluorescence intensity of the stained samples is correlated to the neutral lipid content determined with standard methods, in order to draw a standard curve and deduce the neutral lipids concentration of the unknown samples positioning their fluorescence intensity values on the curve.Standard methods used for the neutral lipids determination are laborious and often implying solvent extraction and/or other transformation (i.e. saponification or transesterification) of the sample. These methods are also time consuming and may give rise to an underestimation of the lipid content due to variable extraction yields.The approach described in this paper combines the standard addition method and the fluorometric staining using Nile red, avoiding the association of traditional neutral lipids quantification methods to the fluorometric determination. After optimization of instrument parameters and staining conditions, a linear correlation between the fluorescence intensity of each sample stained with the Nile red and its neutral lipids content deduced with the standard addition method was identified. The obtained curve allowed the direct determination of neutral lipids content maintaining a linearity range from 0.12 to 12 μg of neutral lipids per ml of sample, without need of pre-concentration. This curve was then used in the quantification of the neutral lipids content in culture of Skeletonema marinoi (Bacillariophyceae) at different days from the inoculum. This method was also successfully applied on Chaetoceros socialis (Bacillariophyceae) and Alexandrium minutum (Dinophyceae).     

Nitrogenous excretory materials from the American cockroach

Excreta obtained from both sexes of the American cockroach, Periplaneta americana, maintained on three different diets was examined for the presence of numerous possible nitrogenous materials in an effort to establish what substances are excreted by this insect. It was found that none of the classical terrestrial insect excretory products, including uric acid, could be detected by the methods employed. Rather, ammonia, amino groups, three tryptophan metabolites, unidentified water soluble materials, and water insoluble components constitute most of the total nitrogen excreted. Ammonia seems to be the largest single component, and it was quantitated in fresh and dried excreta. Upon lyophilization of the excreta more than half of the ammonia is lost.     

High-efficient extraction of principal medicinal components from fresh Phellodendron bark (cortex phellodendri)

There are three key medicinal components (phellodendrine, berberine and palmatine) in the extracts of Phellodendron bark, as one of the fundamental herbs of traditional Chinese medicine. Different extraction methods and solvent combinations were investigated to obtain the optimal technologies for high-efficient extraction of these medicinal components. Results: The results showed that combined solvents have higher extracting effect of phellodendrine, berberine and palmatine than single solvent, and the effect of ultrasonic extraction is distinctly better than those of distillation and soxhlet extraction. Conclusion: The hydrochloric acid/methanol-ultrasonic extraction has the best effect for three medicinal components of fresh Phellodendron bark, providing an extraction yield of 103.12 mg/g berberine, 24.41 mg/g phellodendrine, 1.25 mg/g palmatine.     

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the “gold standard” enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples.     

Improvement of hydrocarbon recovery by spouting solvent into culture of Botryococcus braunii

Botryococcus braunii, a green microalga, is known to produce plentiful liquid hydrocarbons as promising biodiesel resources. However, the hydrocarbon extraction methods that have so far achieved have several problems such as low efficiency and high cost. In our study, a solvent-spouted extraction process integrated with photo-bioculture was designed for simultaneous realization of hydrocarbon extraction and cell culture in two phases. The n-octane was selected as the best solvent among several solvents because its biocompatibility was highest for B. braunii. As a result, high level of biomass and hydrocarbon, 4.17 and 893.79 mg/L, respectively, was attained at 100 mL/min of solvent recycling rate through three times of processes for 66 days. Moreover, formation of cell clump was suppressed in solvent extraction, cells were regenerated after it, and thus cell viability was maintained even after repeated cycles of it. Finally, this solvent-spouted culture process required the smaller cost due to reuse of the less solvent and regenerated cells, compared with the other conventional methods. Accordingly, this technique would be applicable to exploit the continuous extraction of hydrocarbon from the algal biomass, especially for application on a large scale.     

Evaluation of methods for extracting Xylella fastidiosa DNA from the glassy-winged sharpshooter

The recent spread of the plant pathogenic bacterium Xylclla fastidiosa Wells et al. by an invasive vector species, Homalodisca coagulata Say, in southern California has resulted in new epidemics of Pierce's disease of grapevine. Our goal is to develop an efficient method to detect low titers of X. fastidiosa in H. coagulata that is amenable to large sample sizes for epidemiological studies. Detection of the plant pathogenic bacterium X. fastidiosa in its insect vector is complicated by low titers of bacteria, difficulty in releasing it from the insect mouthparts and foregut, and the presence of substances in the insect that inhibit polymerase chain reaction (PCr). To select the optimal protocol for DNA extraction to be used with PCR, we compared three standard methods and 11 commercially available kits for relative efficiency of X. fastidiosa DNA extraction in the presence of insect tissue. All of the protocols tested were proficient at extracting DNA from pure bacterial culture (1 x 10(5) cells), and all but one protocol successfully extracted sufficient bacterial DNA in the presence of insect tissue. Three DNA extraction techniques, immunomagnetic separation, the DNeasy Tissue kit (Qiagen, Hercules, CA), and Genomic DNA Purification kit (Fermentus, Hanover, MD), were compared more closely using a dilution series of X. fastidiosa (5000-0 cells) with and without insect tissue present. The DNeasy Tissue kit was the best kit tested, allowing detection of 5 x 10(3) X. fastidiosa cells with an insect head background.     

Tissue disruption and extraction methods for metabolic profiling of an invertebrate sentinel species

Metabolic profiling of tissues needs special attention, because the compartmentalization of cellular constituents will be abolished by sample homogenization. This loss of partitioning leads to protein and metabolite instability in extracts, and therefore metabolite extraction protocols need to ensure very rapid inactivation of macromolecules as well as solubilization of metabolites. There are many published methods for tissue metabolome analysis, but no universally accepted standard, and a lack of measurable quality benchmarks. We developed a protocol for efficient tissue disruption and metabolite extraction of the earthworm Lumbricus rubellus guided by prior biological knowledge as well as metrics based on the data. In particular, we identified an unusual degree of instability of L. rubellus tissue extracts, and evaluated different approaches such as heating and filtration to counteract this. Finally, we evaluated four different solvent systems for comprehensive metabolite extraction using three analytical platforms (¹H NMR spectroscopy, GC?CMS, and direct-infusion FT-ICR-MS), and also compared bead-beating and cryogenic milling for tissue disruption. Initially we ranked methods by common analytical criteria (e.g. numbers and total intensity of detected peaks) in order to compare protocols. These approaches to assess protocol suitability proved to be inadequate to judge earthworm tissue extraction methods because of sample instability. Existing tissue extraction protocols should not be assumed to be automatically applicable to novel species.     

Comparison of extraction methods for quantifying vitamin E from animal tissues

Four extraction methods: (1) solvent (SOL), (2) ultrasound assisted solvent (UA), (3) saponification and solvent (SP), and (4) saponification and ultrasound assisted solvent (SP-UA), were used in sample preparation for quantifying vitamin E (tocopherols) in chicken liver and plasma samples. The extraction yields of SOL, UA, SP, and SP-UA methods obtained by adding delta-tocopherol as internal reference were 95%, 104%, 65%, and 62% for liver and 98%, 103%, 97%, and 94% for plasma, respectively. The methods with saponification significantly affected the stabilities of tocopherols in liver samples. The measured values of alpha- and gamma-tocopherols using the solvent only extraction (SOL) method were much lower than that using any of the other extraction methods. This indicated that less of the tocopherols in those samples were in a form that could be extracted directly by solvent. The measured value of alpha-tocopherol in the liver sample using the ultrasound assisted solvent (UA) method was 1.5-2.5 times of that obtained from the saponification and solvent (SP) method. The differences in measured values of tocopherols in the plasma samples by using the two methods were not significant. However, the measured value of the saponification and ultrasound assisted solvent (SP-UA) method was lower than either the saponification and solvent (SP) or the ultrasound assisted solvent (UA) method. Also, the reproducibility of the ultrasound assisted solvent (UA) method was greater than any of the saponification methods. Compared with the traditional saponification method, the ultrasound assisted solvent method could effectively extract tocopherols from sample matrix without any chemical degradation reactions, especially for complex animal tissue such as liver.     

Recycling Isolation of Plant DNA,A Novel Method

DNA is one of the most basic and essential genetic materials in the field of molecular biology.To date,isolation of sufficient and good-quality DNA is still a challenge for many plant species,though various DNA extraction methods have been published.In the present paper,a recycling DNA extraction method was proposed.The key step of this method was that a single plant tissue sample was recycled for DNA extraction for up to four times,and correspondingly four DNA precipitations(termed as the 1st,2nd,3rd and 4th DNA sample, respectively) were conducted.This recycling step was integrated into the conventional CTAB DNA extraction method to establish a recycling CTAB method.This modified CTAB method was tested in eight plant species,wheat,sorghum,barley,corn,rice,Brachypodium distachyon,Miscanthus sinensis and tung tree.The results showed that high-yield and good-quality DNA samples could be obtained by using this new method in all the eight plant species.The DNA samples were good templates for PCR amplification of both ISSR and SSR markers.The recycling method can be used in multiple plant species and can be integrated with multiple conventional DNA isolation methods,and thus is an effective and universal DNA isolation method.     

Diethylamine extraction of proteins and peptides isolated with a mono-phasic solution of phenol and guanidine isothiocyanate

Representative extraction of both RNA and protein from a single biological sample is required for reliable assessment of coordinated changes in gene and protein expression. Such a simultaneous extraction can be performed by using Trizol Reagent. Here, we demonstrate that, as an alternative to SDS, 2% diethylamine is an effective solvent, which can be conveniently used in extraction of Trizol-isolated proteins from various tissues. Diethylamine provides efficient extraction of proteins and compatibility with a variety of common downstream analytical applications.     

Water-soluble polysaccharides of antarctic and cultured Phormidium species of the cyanophyceae

Hot water extraction of a Phormidium species from Antarctica and of a sample of Phormïdium foveolarum which had been cultured axenically led to the isolation of a water-soluble polysaccharide from both materials. Acidic hydrolysis of each gave a similar pattern of monosaccharides comprising arabinose, xylose, rhamnose, fucose, galactose, mannose and glucose, and both contained uronic acid. All attempts by a variety of methods to fractionate the Antarctic polysaccharide into more than a single entity were unsuccessful. Periodate oxidation, partial hydrolysis and methylation studies on this polysaccharide supported a highly branched molecule with 1,3-linked glucose and 1,4-linked galactose as dominant features.     

Extraction of chlorophylls and carotenoids from dry and wet biomass of isolated Chlorella Thermophila: Optimization of process parameters and modelling by artificial neural network

Chlorophylls and carotenoids can be extracted from microalgae using various solvents. However, there is lack of studies regarding the comparison of extraction yield of these pigments from wet and dry microalgal biomass using different combination of cell disruption methods. Therefore, in this work, we have investigated the comparison of the extraction yield of chlorophylls and carotenoids from the wet and heat-dried microalgal biomass (isolated Chlorella thermophila) using ethanol. Extraction parameters such as homogenisation time, homogenisation speed, solvent temperature, solid-solvent ratio, boiling time and microwave time have been optimised. Chlorophyll extraction yield was observed to be 2.7 fold higher from wet biomass than dry biomass while carotenoid yield was 6.7 fold higher. Highest chlorophyll yield (∼60 mg/g-dry biomass) was observed at 6 min of homogenisation time, 10,000 rpm, solid solvent ratio of 1 mg/mL and 58 °C of solvent temperature from wet biomass with extraction efficiency of ∼94 %. Highest carotenoid yield was noticed following the same conditions of chlorophyll extraction except 4 °C of solvent temperature. The modelling of the extraction process was performed using artificial neural network (ANN) which may be useful for the scale-up of the extraction process at the industrial level.     

Chemical Analysis and Risk Assessment of Diethyl Phthalate in Alcoholic Beverages with Special Regard to Unrecorded Alcohol

Background

Phthalates are synthetic compounds with a widespread field of applications. For example, they are used as plasticizers in PVC plastics and food packaging, or are added to personal care products. Diethyl phthalate (DEP) may be used to denature alcohol, e.g., for cosmetic purposes. Public health concerns of phthalates include carcinogenic, teratogenic, hepatotoxic and endocrine effects. The aim of this study was to develop and validate a method for determining phthalates in alcohol samples and to provide a risk assessment for consumers of such products.

Methodology/Principal Findings

A liquid-liquid extraction procedure was optimized by varying the following parameters: type of extraction solvent (cyclohexane, n-hexane, 1,1,2-trichlorotrifluoroethane), the ratio extraction solvent/sample volume (1∶1 to 50∶1) and the number of extraction repetitions (1–10). The best extraction yield (99.9%) was achieved with the solvent 1,1,2-trichlorotrifluoroethane, an extraction solvent volume/sample volume ratio of 10∶1 and a double extraction. For quantification, gas chromatography/mass spectrometry with deuterated internal standards was used. The investigated samples were alcoholic beverages and unrecorded alcohol products from different countries (n = 257). Two unrecorded alcohol samples from Lithuania contained diethyl phthalate in concentrations of 608 mg/L and 210 mg/L.

Conclusions/Significance

The consumption of the phthalate-positive unrecorded alcohols would exceed tolerable daily intakes as derived from animal experiments. Both positive samples were labelled as cosmetic alcohol, but had clearly been offered for human consumption. DEP seems to be unsuitable as a denaturing agent as it has no effect on the organoleptic properties of ethanol. In light of our results that DEP might be consumed by humans in unrecorded alcohols, the prohibition of its use as a denaturing agent should be considered.     

Liquid Chromatographic-Fluorescence Determination of Ammonia from Nitrogenase Reactions: A 2-Min Assay

The analytical potential of the reaction of ammonia with o-phthalaldehyde mercaptoethanol reagent at pH 7 (an atypical fluorescence) has already been demonstrated. This, coupled with additional findings reported here, has led to an ammonia determination well suited to nitrogenase studies. As a result, large numbers of samples can be rapidly analyzed by high-pressure liquid chromatrography methods under mild conditions and without prior microdiffusion. Neither sodium dithionite (or other components of the usual nitrogenase assay), nor alternative substrates (cyanide, azide, methyl isonitrile), nor their products (methylamine, dimethylamine, hydrazine) interfere. High-pressure liquid chromatography showed that the fluorescent “product” of the o-phthalaldehyde mercaptoethanol reagent-ammonia reaction was, in fact, more than just a single compound. Despite this, once the proper solvent composition was found, high-pressure liquid chromatography with a small inexpensive C₁₈ “guard” column proved quite fast and reproducible for this measurement. Fluorescence response to ammonia was linear to at least 40 nmol/ml. A previous problem, long-term stability of the fluorescence, was solved by running the reactions in the dark. Background ammonia in the buffer could be substantially reduced by an analogous o-phthalaldehyde mercaptoethanol reagent reaction, using t-butyl mercaptan, and solvent extraction.     

Mechanism of lipid extraction from Botryococcus braunii FACHB 357 in a biphasic bioreactor

Algal lipid of Botryococcus braunii could be produced continuously and in situ extracted in an aqueous-organic bioreactor. In this study, the cell ultra-structure and cell membrane permeability of B. braunii FACHB 357 were investigated to understand the mechanism of lipid extraction within the biphasic system. The results showed that biocompatible solvent of tetradecane could induce algal lipid accumulation, enable the cell membrane more active and the cell wall much looser. The exocytosis process was observed to be one of the mechanisms for lipid cross-membrane extraction in the presence of organic solvent.     

A sample extraction and chromatographic strategy for increasing LC/MS detection coverage of the erythrocyte metabolome

Reproducible and comprehensive sample extraction and detection of metabolites with a broad range of physico-chemical properties from biological matrices can be a highly challenging process. A single LC/MS separation method was developed for a 2.1mmx100mm, 1.8mum ZORBAX SB-Aq column that was used to separate human erythrocyte metabolites extracted under sample extraction solvent conditions where the pH was neutral or had been adjusted to either, pH 2, 6 or 9. Internal standards were included and evaluated for tracking sample extraction efficiency. Through the combination of electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) techniques in both positive (+) and negative (-) ion modes, a total of 2370 features (compounds and associated compound related components: isotopes, adducts and dimers) were detected across all pHs. Broader coverage of the detected metabolome was achieved by observing that (1) performing extractions at pH 2 and 9, leads to a combined 92% increase in detected features over pH 7 alone; and (2) including APCI in the analysis results in a 34% increase in detected features, across all pHs, than the total number detected by ESI. A significant dependency of extraction solvent pH on the recovery of heme and other compounds was observed in erythrocytes and underscores the need for a comprehensive sample extraction strategy and LC/MS analysis in metabolomics profiling experiments.