" 黑美人" 马铃薯中花色苷提取工艺研究

马铃薯(Solanum tuberosum)是一种重要的粮菜兼用型作物,马铃薯传入我国后产生了许多变种、变型和适合当地种植的地方品种,尤其是块茎的皮色和肉色出现了红色、紫色、黑色品种。"黑美人"马铃薯是甘肃省特有的经航空育种技术培育的新型马铃薯品种,经分析测定"黑美人"马铃薯中花色素含量非常丰富,其富含的花青素还具有抗癌、抗衰老、美容和防止高血压等多种保健作用。因此,"黑美人"马铃薯中花色苷提取工艺的研究,对于花色苷的应用与开发具有重要的研究意义。本研究以甘肃"黑美人"马铃薯为原料,对其所含花色苷提取工艺条件(乙醇浓度,温度,pH,提取时间,料液比,提取次数等)进行优化。研究结果显示最佳提取工艺参数为:乙醇浓度80%,温度75℃,pH 1.0,时间1 h,料液比1:20,提取3次。在优化后的提取工艺条件下,"黑美人"马铃薯的花色苷提取率得到提高,花色苷含量可达到33.05 mg/100g。     

Methodological concerns in measuring the lipid fraction of carbon fixation

Carbon fixation into lipid (lipid production) by phytoplankton was measured in 3 lakes on the edge of the Canadian Shield by two different extraction methods. The amount of lipid detected in the plankton samples was generally 11% lower when extracted by a Folch-like lipid solvent (dichloromethane:methanol (2:1)) than with the lipid solvent (80% ethanol and 80% ethanol-diethyl ether) used in a sequential extraction method. The difference between methods was not due to losses of fixed carbon during extraction since the sum of the extraction fractions from both methods were not different from the amount of carbon fixed on a replicate acidified filter. Although more carbon was detected in the lipid fraction of the sequential extraction method, an additional 5% of total carbon fixed was found in the lipid extract of another fraction from the sequential method, the low molecular weight fraction. Our results suggest that accurate comparisons of lipid production data can only occur after compensating for differences in extraction methods while comparing the LFCF determined by different lipid extraction should be avoided.     

Extraction of urinary pregnanediol and estriol by the Bio-Rad column

In the present study, we have evaluated the quality control parameters of a new method for the determination of the urinary Pregnandiol and Estriol using a small column AG 1X2 proposed by Bio-Rad Laboratories. The principle of this method is based on a single extraction of steroids by ion exchange and methanol elution under different pH conditions. Compared to the "classical" methods using solvent extraction, the present method has some advantages mainly the elimination of the use of large volumes of solvents and the reduction of the sample volume to be analyzed. The preliminary results showed a recovery of 89,0% - 98,9% (C.V. = 5%) for Estriol and 83,8% - 93, 2% C.V = 5%) for Pregnandiol . The precision of the method evaluated by its repeatability and between-assay reproductibility showed 4% and 6% variation for Estriol and Pregnandiol . The Comparison of the present method with a classical one using Ether/Ethanol (4/1) for extraction gave us a very good correlation.     

Microvillar membrane microdomains exist at physiological temperature. Role of galectin-4 as lipid raft stabilizer revealed by "superrafts"

Lipid rafts (glycosphingolipid/cholesterol-enriched membrane microdomains) have been isolated as low temperature, detergent-resistant membranes from many cell types, but despite their presumed importance as lateral sorting and signaling platforms, fundamental questions persist concerning raft function and even existence in vivo. The nonionic detergent Brij 98 was used to isolate lipid rafts from microvillar membrane vesicles of intestinal brush borders at physiological temperature to compare with rafts, obtained by "conventional" extraction using Triton X-100 at low temperature. Microvillar rafts prepared by the two protocols were morphologically different but had essentially similar profiles of protein- and lipid components, showing that raft microdomains do exist at 37 degrees C and are not "low temperature artifacts." We also employed a novel method of sequential detergent extraction at increasing temperature to define a fraction of highly detergent-resistant "superrafts." These were enriched in galectin-4, a beta-galactoside-recognizing lectin residing on the extracellular side of the membrane. Superrafts also harbored the glycosylphosphatidylinositol-linked alkaline phosphatase and the transmembrane aminopeptidase N, whereas the peripheral lipid raft protein annexin 2 was essentially absent. In conclusion, in the microvillar membrane, galectin-4, functions as a core raft stabilizer/organizer for other, more loosely raft-associated proteins. The superraft analysis might be applicable to other membrane microdomain systems.     

Application of supercritical fluid extraction in biotechnology

In the present paper recent investigations on the applications of supercritical fluid extraction (SCE) from post fermentation biomass or in situ extraction of inhibitory fermentation products as a promising method for increasing the yield of extraction have been reviewed. Although supercritical CO2 (SC-CO2) is unfriendly, or even toxic, for some living cells and precludes direct fermentation in dense CO2, it does not rule out other useful applications for in situ extraction of inhibitory fermentation products and fractional extraction of biomass constituents. This technique is a highly desirable method for fractional extraction of biomass constituents, and intracellular metabolites due to the potential of system modification by physical parameters and addition of co-solvents to selectively extract compounds of different polarity, volatility and hydrophilicity without any contamination.     

Photosystem II reaction center with altered pigment-composition: reconstitution of a complex containing five chlorophyll a per two pheophytin a with modified chlorophylls

Pigment-depleted Photosystem II reaction centers (PS II-RCs) from a higher plant (pea) containing five chlorophyll a (Chl) per two pheophytin a (Phe), were treated with Chl and several derivatives under exchange conditions [FEBS Lett. 434 (1998) 88]. The resulting reconstituted complexes were compared to those obtained by pigment exchange of "conventional" PS II-RCs containing six Chl per two Phe. (1) The extraction of one Chl is fully reversible. (2) The site of extraction is the same as the one into which previously extraneous pigments have been exchanged, most likely the peripheral D1-H118. (3) Introducing an efficient quencher (Ni-Chl) into this site results in only 25% reduction of fluorescence, indicating incomplete energy equilibration among the "core" and peripheral chlorophylls.     

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.     

Subcellular localisation of lipoproteins of <Emphasis Type="Italic">Vibrio vulnificus</Emphasis> by the identification of outer membrane vesicles components

Vibrio vulnificus, a Gram-negative halophilic bacterium, is an opportunistic human pathogen that is responsible for the majority of seafood-associated deaths worldwide. Lipoproteins are important components of the bacterial cell envelope and have been shown to be involved in a wide variety of cellular processes. Little is known about the localisation or transport mechanism of lipoproteins in V. vulnificus. To assess the localisation of lipoproteins in V. vulnificus, we tested two established techniques for the rapid separation of membrane-associated proteins: detergent extraction with Sarkosyl and outer membrane vesicles (OMVs) preparation. The results showed that Sarkosyl extraction was not useful for the separation of lipoproteins from the different membranes of V. vulnificus. On the other hand, we confirmed that OMVs produced by V. vulnificus contained lipoproteins from the outer but not the inner membrane. Analysis of the OMVs components confirmed the localisation of several well-known lipoproteins to membranes that were different from expected, based on their predicted functions. Using this technique, we found that Asp at position +2 of mature lipoproteins can function as an inner membrane retention signal in V. vulnificus. Interestingly, the Escherichia coli “+2 rule” does not apply to the V. vulnificus lipoprotein IlpA (G2D) mutant, as a Ser to Asp mutation at position +2 of IlpA did not affect its outer membrane localisation. Furthermore, an IlpA tether-mRFP chimeric lipoprotein and its G2D mutant also behaved like IlpA. Together, these results suggest that the sorting rule of lipoproteins in V. vulnificus might be different from that in E. coli.     

Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of <Emphasis Type="Italic">Ganoderma</Emphasis> spp.

Ganoderma species are a group of fungi that have the ability to degrade lignin polymers and cause severe diseases such as stem and root rot and can infect economically important plants and perennial crops such as oil palm, especially in tropical countries such as Malaysia. Unfortunately, very little is known about the complex interplay between oil palm and Ganoderma in the pathogenesis of the diseases. Proteomic technologies are simple yet powerful tools in comparing protein profile and have been widely used to study plant–fungus interaction. A critical step to perform a good proteome research is to establish a method that gives the best quality and a wide coverage of total proteins. Despite the availability of various protein extraction protocols from pathogenic fungi in the literature, no single extraction method was found suitable for all types of pathogenic fungi. To develop an optimized protein extraction protocol for 2-DE gel analysis of Ganoderma spp., three previously reported protein extraction protocols were compared: trichloroacetic acid, sucrose and phenol/ammonium acetate in methanol. The third method was found to give the most reproducible gels and highest protein concentration. Using the later method, a total of 10 protein spots (5 from each species) were successfully identified. Hence, the results from this study propose phenol/ammonium acetate in methanol as the most effective protein extraction method for 2-DE proteomic studies of Ganoderma spp.     

Evaluation of methods for the extraction and purification of DNA from the human microbiome

Background

DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled.

Methodology/Principal Findings

In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used.

Conclusions/Significance

Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.     

Proteomic analysis of the porcine interphotoreceptor matrix

The interphotoreceptor matrix (IPM) is located between photoreceptors and pigment epithelium in the retina and is involved in fundamental functions of the visual cycle. These include visual pigment chromophore exchange, retinal adhesion, metabolite trafficking, and growth factor presentation. In general, IPM preparations are contaminated with intracellular proteins, as has also been described for other body fluids. This study aimed at identifying new components of the IPM by discriminating between truly secreted proteins and proteins that are part of the IPM for secondary reasons. "Soluble" porcine IPM was extracted from retina and pigment epithelium with PBS by two different procedures, followed by extraction with water alone that released "insoluble" IPM matrix sheets. Samples from all preparations were separated by 2-DE and a total of 140 protein spots were identified by MALDI-TOF and/or CapLC Q-TOF MS. Although identified proteins included several already known in the IPM, the majority had not been previously described in this structure. Gene ontology classifications allocated the identified proteins into nine different functional networks. The IPM preparations also included intracellular proteins from cells adjacent to the IPM, which may have resulted from cell disruption. This underlines the experimental difficulties of a biochemical analysis of the IPM as an intact compartment. We show here a strategy for predicting the probability of identified IPM proteins occurring in vivo by combined high-resolution protein separation methods with computational prediction methods. Thus, a set of potentially neuroprotective proteins could be extracted, including PEA-15, peroxiredoxin 5, alpha-B-crystallin, macrophage migration inhibitory factor, 78 kDa glucose-regulated protein (GRP78), protein disulfide-isomerase, and PEP-19, which have not been previously associated with the IPM. Furthermore, with immunohistochemical staining we could confirm the localization of GRP78 in the IPM on porcine eye sections, thus validating the proposed prediction method.     

Efficient extraction of proteins from formalin-fixed paraffin-embedded tissues requires higher concentration of tris(hydroxymethyl)aminomethane

Background

Numerous formaldehyde-fixed and paraffin-embedded clinical tissues have been created in the past decades and stored in pathological depositories at hospitals as well as in clinical laboratories worldwide. In addition to the archived tissues, formaldehyde-fixation is also mandatory for preparing proteomics samples from diseased patients or animal models in order to inactivate contagious agents. Protein extraction from formaldehyde-fixed tissues is hampered by the Schiff base formation between the amino groups of proteins and formaldehyde. Although achievement of the highest extraction efficiency of proteins from the formaldehyde-fixed tissues is essential for obtaining maximum proteomics information, no attention has been paid to the concentration dependence of tris(hydroxymethyl)aminomethane on the extraction efficacy. We suspected that the concentration of tris(hydroxymethyl)aminomethane affects the protein extraction efficiency because of its property as a primary amine that reverses the Schiff base formation between the primary amines of proteins and formaldehyde. Thus we pursued optimization of the component and protocol of protein extraction buffer to achieve better extraction efficiency of proteins from formaldehyde-fixed and paraffin-embedded tissues.

Results

In order to simulate protein extraction from diseased tissues we made formaldehyde-fixed and paraffin-embedded samples from mouse liver slices and investigated the protein extraction efficiency and speed by changing the concentration of the protein extraction buffer component tris(hydroxymethyl)aminomethane under various extraction conditions. We find, as expected, that tris(hydroxymethyl)aminomethane significantly affects the performance of protein extraction from the formaldehyde-fixed and paraffin-embedded samples both in the extraction yield and in the extraction speed.

Conclusions

We recommend the concentration of tris(hydroxymethyl)aminomethane in protein extraction buffer to be higher than 300 mM when extraction is conducted for 90 min at 90°C to achieve the most efficient protein extraction in a shorter time. The information will be essential for performing the most efficient protein extraction from formaldehyde-fixed and paraffin-embedded tissue samples for proteomics analysis.     

Concept recognition for extracting protein interaction relations from biomedical text

Background:

Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present an integrated approach to concept recognition in biomedical text. Concept recognition provides key information that has been largely missing from previous biomedical information extraction efforts, namely direct links to well defined knowledge resources that explicitly cement the concept's semantics. The BioCreative II tasks discussed in this special issue have provided a unique opportunity to demonstrate the effectiveness of concept recognition in the field of biomedical language processing.

Results:

Through the modular construction of a protein interaction relation extraction system, we present several use cases of concept recognition in biomedical text, and relate these use cases to potential uses by the benchside biologist.

Conclusion:

Current information extraction technologies are approaching performance standards at which concept recognition can begin to deliver high quality data to the benchside biologist. Our system is available as part of the BioCreative Meta-Server project and on the internet http://bionlp.sourceforge.net.

     

Solid-phase extraction-electrospray ionization mass spectrometry for the quantification of folate in human plasma or serum

The measurement of 5-methyltetrahydrofolic acid (5 MT) blood levels is one of several factors used to diagnose folate deficiency in humans. 5 can be selectively purified from either human plasma or human serum via solid-phase extraction procedures and specifically detected and quantified in the extracts with liquid chromatography/isotope-dilution electrospray-ionization mass spectrometry. Two different, yet complementary, solid-phase extraction-liquid chromatography/mass spectrometry methods have been developed and applied to the quantification of 5 MT from such extracts. One method utilizes the high-affinity folate-binding protein from cow's milk coupled with multiple-reaction-monitoring-mode tandem mass spectrometry while the other method utilizes reversed-phase C(18) extraction followed by selected-ion-monitoring-mode mass spectrometry. The accuracy of each method is assessed through a comparative determination of 5 MT levels in homogenous plasma and serum pools. Additionally, each method is compared and evaluated against the "total folate" results provided by routine radioassay and microbiological assay determinations. On the basis of the experimental data presented in this report, it is suggested that both methods have the capacity to serve as potential reference methods for the quantification of circulating 5MT in plasma or serum.     

Fecal steroid research in the field and laboratory: improved methods for storage, transport, processing, and analysis

Since the pioneering paper "Measurement of Excreted Steroids in Macaca nemestrina" [Risler et al., American Journal of Primatology 12:91-100, 1987] was first published, field primatologists have been using fecal extraction techniques to examine adrenal and gonadal hormones. These techniques have allowed investigators to determine reproductive conditions in wild primates without causing any disruption to the populations. Over the years, many techniques have been developed to improve the ease of analysis, transportation, and purification. More of the processing can now be done in the field. This paper describes the methodology developed or adapted at the Wisconsin National Primate Research Center, and the factors involved in preparing fecal samples for steroid analysis. We provide information on the steps involved in extracting and purifying steroids from feces for measurement. The latest methods include field processing of samples, such as drying collected material or separating steroids from the fecal material by solid phase extraction (SPE). How samples are processed in the field determines the requirements for international transportation and the methods used in the laboratory. The pros and cons of the different processing methods are discussed. We also report on recent advances in laboratory quantification, with implications for steroid isolation prior to analysis. The different processes involved in isolating and measuring fecal steroids discussed here will enable investigators to understand the components necessary to ensure accurate and reliable results.     

Optimal selection of organic solvents for biocompatible extraction of beta-carotene from Dunaliella salina

In the aim of beta-carotene biocompatible extraction, toxicity of various pure solvents belonging to different homologous series has been investigated for Dunaliella salina. The results showed that solvents having logP(oct) > 5 or having a molecular weight over 150 g/mol can be considered biocompatible for this microalga. The membrane critical solvent concentration for each series of solvents has been calculated applying Osborne's model, showing that the aliphatic chlorinated hydrocarbon is the most toxic family studied. Mixtures of a biocompatible solvent (decane) with a toxic solvent (CH(2)Cl(2), MEK, MTBE) have been studied. The beta-carotene extraction ability of CH(2)Cl(2)-decane mixture was found six times more efficient than with pure decane. It has been demonstrated that the extraction ability of solvent depends on its affinity with the product extracted and on its concentration incorporated in the cellular membrane.