A simple and general plant tissue extraction procedure for two-dimensional gel electrophoresis

A fast and simple extraction procedure of plant tissue for two-dimensional gel electrophoresis is presented. The procedure is especially useful for the extraction of plant cell suspension cultures, callus and other plant tissues having a high content of phenol oxidases, polysaccharides, polynucleotides, terpenoids and other substances interfering with isoelectric focusing. Due to the speed of the extraction procedure (about 20 min), large numbers of samples containing only milligram amounts of tissue can be easily processed. The simplicity of the method makes it particularly suitable for the extraction of radiolabeled tissues (³⁵S, ³²P). This method is perfectly compatible with silver staining, autoradiography and Western blotting analysis.Abbreviations DTT dithiothreitol - IEF isoelectric focusing - SDS sodium dodecyl sulfate - TEMED N,N,N,N-tetramethylethylenediamine     

谷氨酸提取产业现状与无废化发展方向

谷氨酸提取的工艺路线及其技术对味精生产成本、质量和环境等因素的影响最为重要：现有“等电离交”工艺技术收率高,但存在辅料消耗大、废水多等缺陷;“浓缩等电转晶工艺”辅料消耗低、廒水少且质量好,但存在谷氨酸收率低的缺点;“喷浆造粒工艺”消除了高浓废水的污染,但又造成严重的废气污染,环境问题随着味精制造规模的扩大而呈加重趋势“谷氨酸提取无废低耗工艺”在清洁生产思想指导下,吸收现有技术的优点,整体谋求经济、环境和质量的集成,通过开发关键技术,形成成本低、质量好、无污染且易于工程放大的谷氨酸提取新型工艺路线。     

Extraction of pigments and fatty acids from the green alga Scenedesmus obliquus (Chlorophyceae)

In this paper, the efficiency of pigment and fatty acid extraction from resistant algae using Scenedesmus obliquus as an example was examined. We found that adding quartz sand and solvent to freeze-dried algal material and subsequent extraction in an ultrasound bath for 90min at –4°C resulted in excellent extraction of these compounds. This extraction method was compared with a method regularly used for extraction of fatty acids and pigments, i.e. addition of solvents to algal material with subsequent incubation. Our extraction using the ultrasound and sand method was about twice as efficient as this method for both pigments and fatty acids. The ultrasound method is simple, extracts over 90% of the different substances in one step and conserves the relationships of pigments and fatty acids. In addition, no alteration- or breakdown products were observed with the new method. Thus, this method allows accurate quantitative extraction of both pigments and fatty acids from Scenedesmus obliquus and other algae. The method was also been found to be as effective for Cryptomonas erosa (Cryptophyceae), Cyclotella meneghiniana (Bacillariophyceae), Microcystis aeruginosa (Cyanophyceae), and Staurastrum paradoxum (Chlorophyceae, Desmidiaceae) and is thus applicable to a wide spectrum of algae.     

Comparative assessment of DNA extraction methods for identification of glanders and melioidosis etiological agents by PCR

Pathogenic Burkholderia are considered as a cause of dangerous infections and potential agents of bioterrorism. Comparative assessment of different methods of extraction and purification of DNA for PCR analysis of pure cultures and samples contaminated by etiological agents of glanders and melioidosis was performed. Samples of soil and food artificially contaminated by pathogenic Burkholderia as well as organs of infected animals were tested. DNA was extracted by methods of boiling, nucleosorption with presence of guanidine thiocyanate, guanidine thiocyanatephenol extraction, guanidine thiocyanate-phenol extraction with additional purification of DNA by nucleosorption. Amplification was performed by "Flash" technique and detector of fluorescence was used for analysis of PCR products. Utilization of the recommended methods of preparation depending on the nature of sample let to detect by the "Flash" technique the etiological agents of glanders and melioidosis in concentration =10(3) microbial cells per ml. Choice of DNA extraction and purification methods is determined by type of a sample and presence in it of admixtures inhibiting PCR.     

A comparative methodical study of the faecal steroid analysis on birds: looking for a valid method of testosterone determination

In a comparative study, a relatively simple and high sensitivity method was developed for analysis of testosterone-equivalent(s) in the faeces of different bird species. To determine the recovery of extractions and purifications, tritium-labelled testosterone was added to the wet samples. Then the samples were treated with sodium dodecil sulphate (SDS), an emulsificator to "open-up" the complex, lipid-coated particles of faecal samples. This emulsification resulted in the decrease of the quantity of interfering substances after diethyl-ether extraction and the linearity of the measured testosterone equivalents from aliquots in the range of 2 and 10 mg of faeces. In the RIA, we applied a group specific polyclonal testosterone antibody which cross-reacted with reduced metabolites and at a certain level with sulphate conjugates as well. The use of Helix enzymes did not modified significantly the results of the analysis relating to a low level of conjugated androgens in the faecal extracts. The biological validity of the method was tested on domestic cockerels, where between the plasma and faecal testosterone values a four hours phase shift was observed, with a correlation of 0.6355. This method is suitable for "non invasive", behavioural-ethological studies.     

Quantitative Analysis of Flavonoids in Chamomile Flowers (<Emphasis Type="Italic">Matricaria chamomilla</Emphasis> L.) by Microcolumn HPLC-UV

A reverse-phase microcolumn HPLC method with UV detection (330 nm) was developed for quantitative analysis of flavonoids of Matricaria chamomilla flowers using a ProntoSIL-120-5-C18 AQ column (60 mm × 1 mm × 5 μm), gradient elution system 0.2 M LiClO₄/0.006 M HClO₄–acetonitrile and cosmosiin as a reference compound. Optimal conditions for the hydrolytic process of flavonoids (KOH concentration 0.25%, extraction time 30 min) and the parameters of flavonoids extraction (particle size 0.25 mm, extraction temperature 60°C, a single extraction step lasting 30 min at a ratio 1: 100) were selected. Validation analysis showed that the proposed method is characterized by satisfactory metrological parameters. The limit of detection (LOD) and limit of quantification (LOQ) of cosmosiin were 84 and 255 ng/mL, respectively. The accuracy for cosmosiin content levels 80–120% was less than 101.93–103.00%. The method was used for the analysis of introduced and commercial samples of M. chamomilla flowers.     

Comparative Analysis of the Fatty Acid Composition of Microalgae Obtained by Different Oil Extraction Methods and Direct Biomass Transesterification

One of the main challenges for the successful production and use of microalgae for biodiesel production is to obtain a satisfactory level of fatty acid methyl esters (FAME). The aims of this study are to identify the best method of lipid extraction and provide high FAME levels and to evaluate their fatty acid profiles. Six lipid extraction methodologies in three microalgae species were tested in comparison with the direct transesterification (DT) of microalgal biomass method. The choice of extraction method affected both the oily extract yield and the FAME composition of the microalgae and consequently may affect the properties of biodiesel. The efficiency of different lipid extraction methods is affected by the solvent polarity, which extracts different target compounds from lipid matrix. Dichloromethane/methanol extraction and Folch extraction produced the largest oil extract yields, but extraction with hexane/ethanol resulted in the best ester profile and levels. Performing DT reduces the volume of extractor solvent, the time and cost of FA composition analysis, as well as, presents less steps for fatty acid quantification. DT provided biomass FAME levels of 50.2, 636.4, and 258.2 mg.g^?1 in Nannochlorophisis oculata, Chaetoceros muelleri, and Chlorella sp., respectively. On the basis of an analysis of the fatty acids profiles of different species, C. muelleri is a promising microalga for biodiesel production. Depending on the extraction method, Chlorella sp. and N. oculata can be considered as an alternative in obtaining arachidonic (Aa) and eicosapentaenoic (EPA) acids.     

Sample preparation method for tissue based proteomic analysis of <Emphasis Type="Italic">Azolla microphylla</Emphasis>

The nitrogen fixing aquatic pteridophyte Azolla is used as biofertilizer for rice paddy. It is also used as poultry and cattle feed due to high protein content. However, its mass cultivation and exploitation is constrained due to the abiotic stress conditions it is exposed to. The system is interesting due to the presence of symbiotic nitrogen fixing cyanobacteria and its interaction with the carbon fixing host. Therefore these interactions have to be studied at the molecular level using advanced techniques. Proteomics is a technique which can be employed to reveal the mechanism of cross talk between the host and its symbiont as well as its response to abiotc stress. The primary step that contributes to successful proteomic analysis is standardization of sound protocols for protein extraction and sufficient yield to initiate proteomic studies using 2-dimensional electrophoresis. However, reports are not available on the protein extraction procedures in Azolla. Therefore in the present study we attempted to optimize protein extraction protocol in the whole plant, roots and the chloroplast of Azolla microphylla using phenol extraction, TCA-acetone and phosphate buffer methods. Our studies showed the efficacy of phenol extraction method in terms of maximum yield and resolution of proteins in Azolla.     

Properties and reaction mechanism of mitochondrial menadione reductase]

An isolation procedure of mitochondrial menadione reductase from rat liver using an ethanol-ether extraction for solubilization of the enzyme is described. The enzyme was purified 930-fold. The molecular weight of mitochondrial menadione reductase is 62,000. According to spectroscopic and enzymic analysis the prosthetic group of the enzyme was identified as FAD. Mitochondrial menadione reductase is inhibitied by dicumarol and p-chloromecuribenzoate. The enzyme is characterized by a group substrate specificity towards quinones. A high catalytic activity of menadione reductase towards 4-aniline-5-methoxy-1,2-benzoquinone (AMOBQ), and 4-N-(p-sulfoanilino)-5-methoxy-1,2-benzoquinone (AMOBQS) as acceptors was demonstrated. It was shown that the reduction of these orto-benzoquinones by NAD(P) H follows the "ping-pong" kinetics. The kinetic constants for NAD(P)H,AMOBQ and and AMOBQS were determined.     

Polyomavirus replication in mice: influences of VP1 type and route of inoculation.

Patterns of polyomavirus replication and spread have been studied following inoculation of virus into newborn mice. Levels of virus replication in different tissues were followed in situ by using whole mouse section blots and immunoperoxidase staining for the major capsid protein VP1, as well as by tissue extraction and direct quantitation of viral DNA and infectious virus. Patterns of replication and spread were compared between the "high tumor" strain (inducing a high incidence of tumors) PTA and and the "low tumor" strain (inducing a low incidence of tumors) RA, following different routes of inoculation. The ability to induce a high tumor profile correlated with the ability to establish disseminated productive infection, with the kidney as a major site of amplification. Furthermore, results with PTA-RA recombinant viruses and site-directed mutants showed that the VP1 specificity of PTA, demonstrated earlier to be a critical determinant for induction of a high tumor profile (R. Freund, A. Calderone, C. J. Dawe, and T. L. Benjamin, J. Virol. 65:335-341, 1991), is also critical for amplification in the kidney and for establishment of disseminated infections.     

Microsequence analysis of electroblotted proteins. I. Comparison of electroblotting recoveries using different types of PVDF membranes.

The most effective protein purification method of low picomole amounts for sequence analysis involves polyacrylamide gel electrophoresis followed by electroblotting to polyvinylidene difluoride (PVDF) membranes. Since a critical factor in this procedure is the protein recovery at the blotting step, different types of PVDF membranes were systematically evaluated for their ability to bind proteins during electrotransfer. Differences in electroblotting recoveries occurred between types of PVDF membranes for some proteins. Some variability persisted even when optimized electroblotting procedures were used which reduce the sodium dodecyl sulfate (SDS) concentration in the gel and improve protein-PVDF binding. The membranes which were evaluated could be grouped as either "high retention" membranes (ProBlott, Trans-Blot, and Immobilon-PSQ) or "low retention" membranes (Immobilon-P and Westran). The high retention membranes showed higher protein recoveries under most conditions tested, especially for small proteins or peptides. These high retention membranes were also less sensitive to the exact electroblotting conditions, especially those factors which affect the amount of SDS present during either electrotransfer or direct adsorption from protein solutions. High retention PVDF membranes are therefore preferred in most cases for optimal protein or peptide recovery prior to direct sequence analysis. In contrast, low retention membranes are preferred for procedures where subsequent extraction of the proteins from the membranes is required. Even under identical conditions, substantial protein-to-protein variation for both adsorption and subsequent extraction is routinely observed for both groups of membranes, indicating that the nature of protein-PVDF interactions is more complex than simple hydrophobic interactions.     

Fatty Acid Methyl Ester (FAME) Succession in Different Substrates as Affected by the Co-Application of Three Pesticides

Introduction

In intensive agriculture areas the use of pesticides can alter soil properties and microbial community structure with the risk of reducing soil quality.

Materials and Methods

In this study the fatty acid methyl esters (FAMEs) evolution has been studied in a factorial lab experiment combining five substrates (a soil, two aged composts and their mixtures) treated with a co-application of three pesticides (azoxystrobin, chlorotoluron and epoxiconazole), with two extraction methods, and two incubation times (0 and 58 days). FAMEs extraction followed the microbial identification system (MIDI) and ester-linked method (EL).

Results and Discussion

The pesticides showed high persistence, as revealed by half-life (t_1/2) values ranging from 168 to 298 days, which confirms their recalcitrance to degradation. However, t_1/2 values were affected by substrate and compost age down to 8 days for chlorotoluron in S and up to 453 days for epoxiconazole in 12M. Fifty-six FAMEs were detected. Analysis of variance (ANOVA) showed that the EL method detected a higher number of FAMEs and unique FAMEs than the MIDI one, whereas principal component analysis (PCA) highlighted that the monosaturated 18:1ω9c and cyclopropane 19:0ω10c/19ω6 were the most significant FAMEs grouping by extraction method. The cyclopropyl to monoenoic acids ratio evidenced higher stress conditions when pesticides were applied to compost and compost+soil than solely soil, as well as with final time.

Conclusion

Overall, FAMEs profiles showed the importance of the extraction method for both substrate and incubation time, the t_1/2 values highlighted the effectiveness of solely soil and the less mature compost in reducing the persistence of pesticides.     

Studies in lipid histochemistry

Summary Conditions for a selective extraction of nonpolar lipids from tissue sections with acetone were investigated using methods of lipid chromatography, histochemistry and quantitative determination of lipid phosphorus.Extraction of nonpolar lipids is selective when water (present either in acetone or in tissue sections) is completely excluded from the extraction procedure and the extraction is carried out at 0–4° C for 20–30 minutes. Under these conditions a negligible amount of polar lipids is extracted which cannot be demonstrated histochemically. A very small amount of nonpolar lipids remaining in sections cannot be demonstrated histochemically either.A method for the preparation of anhydrous acetone was recommended and an extraction procedure devised. This is to be applied in cases where nonpolar and polar lipids are to be distinguished and as an integral part of all types of phospholipid stains.When water is present during the extraction procedure (either in acetone or in tissue sections) significant extraction of all polar lipids occurs which is proportional to the content of water, to the length of extraction and to the temperature. Under these conditions the extraction of nonpolar lipids is somewhat slower.The significance of selective extraction with anhydrous acetone in histochemical analysis of lipids is discussed particularly with reference to lipids in atherosclerotic plaques.     

A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems

Background

Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is relation extraction, which aims to identify designated relations among biological entities reported in literature. A relation extraction system achieving high performance is expensive to develop because of the substantial time and effort required for its design and implementation. Here, we report a novel framework to facilitate the development of a pattern-based biomedical relation extraction system. It has several unique design features: (1) leveraging syntactic variations possible in a language and automatically generating extraction patterns in a systematic manner, (2) applying sentence simplification to improve the coverage of extraction patterns, and (3) identifying referential relations between a syntactic argument of a predicate and the actual target expected in the relation extraction task.

Results

A relation extraction system derived using the proposed framework achieved overall F-scores of 72.66% for the Simple events and 55.57% for the Binding events on the BioNLP-ST 2011 GE test set, comparing favorably with the top performing systems that participated in the BioNLP-ST 2011 GE task. We obtained similar results on the BioNLP-ST 2013 GE test set (80.07% and 60.58%, respectively). We conducted additional experiments on the training and development sets to provide a more detailed analysis of the system and its individual modules. This analysis indicates that without increasing the number of patterns, simplification and referential relation linking play a key role in the effective extraction of biomedical relations.

Conclusions

In this paper, we present a novel framework for fast development of relation extraction systems. The framework requires only a list of triggers as input, and does not need information from an annotated corpus. Thus, we reduce the involvement of domain experts, who would otherwise have to provide manual annotations and help with the design of hand crafted patterns. We demonstrate how our framework is used to develop a system which achieves state-of-the-art performance on a public benchmark corpus.     

Experimental Study of Mobility and Kinetic Characterization of Trace Elements in Contaminated Sediments from a River Basin in Northern Peru

In the Jequetepeque basin (Peru), gold extraction activity has been performed in the last decades, leading to a release of metals and metalloids into the environment. Sediment samples were taken in the vicinity of two mines and analyzed. Extraction of metals and metalloids from sediments was carried out using single extraction procedures, acidic (HNO₃), and complexation (EDTA) leaching, in order to determine the mobility of trace elements. Results indicated that acidic extraction at low pH values increased the leachability of trace elements. EDTA showed a higher bioavailability of metals in sediments than acidic extraction under similar pH conditions because of its greater leaching capacity. This is an important issue in view of risk assessment analysis. The highest extractability was observed for Cd in all sediments with up to 90% of extraction after 1 h. The mobility index analysis indicated that faster kinetic leachability of some trace elements leads to a higher mobility in sediments, especially those near the active gold extraction mine. The ecological risk assessment suggested that the four river sediments were at high and very high risk levels, indicating that sediment contamination is an issue of environmental concern in the Jequetepeque basin of northern Peru.     

Restricted access materials and large particle supports for on-line sample preparation: an attractive approach for biological fluids analysis

An analytical process generally involves four main steps: (1) sample preparation; (2) analytical separation; (3) detection; and (4) data handling. In the bioanalytical field, sample preparation is often considered as the time-limiting step. Indeed, the extraction techniques commonly used for biological matrices such as liquid-liquid extraction (LLE) and solid-phase extraction (SPE) are achieved in the off-line mode. In order to perform a high throughput analysis, efforts have been engaged in developing a faster sample purification process. Among different strategies, the introduction of special extraction sorbents, such as the restricted access media (RAM) and large particle supports (LPS), allowing the direct and repetitive injection of complex biological matrices, represents a very attractive approach. Integrated in a liquid chromatography (LC) system, these extraction supports lead to the automation, simplification and speeding up of the sample preparation process. In this paper, RAM and LPS are reviewed and particular attention is given to commercially available supports. Applications of these extraction supports, are presented in single column and column-switching configurations, for the direct analysis of compounds in various biological fluids.     

Axial and radial filamentous components of the neurofilamentous network

Summary The three-dimensional structure of the neurofilamentous network of the giant axon of the squid has been investigated by stereo electron microscopy and optical image analysis. The neurofilamentous network with its structural associations intact was partially purified by means of extraction of extruded axoplasm in a physiological buffer. The authors employed a double-grid mounting technique for critical point drying of axoplasm which provides high contrast preparations having great depth suitable for the analysis of spatial relations. There is a striking improvement in the perception of the continuity and three-dimensionality of the network, particularly in thin areas produced by teasing apart the specimen prior to mounting. Sidearms and cross-bridges are readily identifiable.In 1-m thick preparations of the extracted axoplasm the neurofilamentous network is composed of two structural entities: (i) long 10-nm wide filaments approximately parallel with the long axis of the extracted axoplasmic cylinder (axial), (ii) and short, finer filaments projecting from them as sidearms or crossbridges (radial). Optical analysis of micrographs of extracted axoplasm indicates that the radial filamentous components of the neurofilamentous network are distributed predominantly in the range of 32° to 67° with respect to the long axis of the axial filaments. We tentatively assign the 220,000 mol wt peptide observed by SDS-PAGE in this preparation to the radial filaments and the 68,000 mol wt peptide to the axial filaments.