A rapid TRIzol-based two-step method for DNA-free RNA extraction from Arabidopsis siliques and dry seeds

Extraction of high-quality RNA from Arabidopsis seeds has been a challenge. Here we report a two-step TRIzol-based procedure for RNA extraction from Arabidopsis siliques and dry seeds. This procedure employs a modified, high pH (pH 9.5) extraction buffer. High pH plus the addition of either DTT or β-mercaptoethanol in the extraction buffer effectively inhibits RNase activity during the extraction, and removes most polysaccharides, polyphenols and other insoluble material. TRIzol reagent was subsequently used to purify the RNA. Using this procedure we isolated high-quality DNA-free RNA samples without DNase I treatment from Arabidopsis seeds or siliques in less than 3 h.     

Comparative studies on citric acid production by Aspergillus niger and Candida lipolytica using molasses and glucose

Citric acid production by Aspergillus niger NCIM 548 and Candida lipolytica NCIM 3472 has been studied in shake culture using glucose and molasses as carbon sources. Methanol addition (3% v/v) at 40 h of fermentation enhanced the production of citric acid by Aspergillus niger whereas a reduction in citric acid production by Candida lipolytica was observed with addition of methanol. Maximum citric acid concentration of 12 kg/m³ was obtained with Aspergillus niger using molasses in the presence of methanol, while maximum citric acid concentration of 8.4 kg/m³ was obtained with Candida lipolytica using glucose without methanol. It appears that product formation by Aspergillus niger is either non-growth associated or partially growth associated depending on the substrate. Methanol addition changes the nature of product formation in case of Candida lipolytica.     

Residual Nuclear structures fromZea mays L.

Nuclei fromZea mays L. root tip meristematic cells were treated according to the conventional method for nuclear matrix isolation and according to a recently adapted procedure for isolation of nuclear shells from plant cells. In the first case, after high salt extraction of proteins and DNase I and RNase digestions, residual structures are obtained consisting of a periferal layer and an internal network. The obtained structures are very similar to the nuclear matrix preparations from animal cells. In case nuclei are swollen in EDTA first, digested with DNase II and RNase prior high salt treatment, structures devoid of internal network are obtained. The analogous residual structures were shown forPhaseolus vulgaris L. meristematic root cells nuclei (Galcheva-Gargovaet al. 1988). The morphology and the protein composition of the two types of residual structures suggest that the organization of scaffold structures from plant nuclei is very similar to the one from animal cell nuclei.     

Comparative studies of four protein preparation methods for proteomic study of the dinoflagellate Alexandrium sp. using two-dimensional electrophoresis

Alexandrium is a wide-spread genus of dinoflagellate causing harmful algal blooms and paralytic shellfish poisoning around the world. Proteomics has been introduced to the study of Alexandrium, but the protein preparation method is still unsatisfactory with respect to protein spot number, separation and resolution, and this has limited the application of a proteomic approach to the study of dinoflagellates. In this study we compared four protein preparation methods for the two-dimensional electrophoresis (2DE) analysis of A. tamarense: (1) urea/Triton X-100 buffer extraction with trichloroacetic acid (TCA)/acetone precipitation; (2) direct precipitation with TCA/acetone; (3) 40 mM Tris (hydroxymethyl) aminomethane (Tris) buffer extraction; and (4) 50 mM Tris/5% glycerol buffer extraction. The results showed that, among the four protein preparation methods, the method combining the urea/Triton X-100 buffer extraction and TCA/acetone precipitation allowed detection of the highest number and quality of protein spots with a clear background. Although the direct TCA/acetone precipitation method also detected a high number of protein spots with a clear background, the spot number, separation and intensity were not as good as those obtained from the urea/Triton X-100 buffer extraction with TCA/acetone precipitation method. The 40 mM Tris buffer and 50 mM Tris/5% glycerol buffer methods allowed the detection of fewer protein spots and a pH range only from 4 to 7. Subsequently, the urea/Triton X-100 buffer extraction with TCA/acetone precipitation method was successfully applied to profiling protein expression in A. catenella under light stress conditions and the differential expression proteins were identified using MALDI TOF–TOF mass spectrometry. The method developed here appears to be promising for further proteomic studies of this organism and related species.     

Fermentation of n-Paraffins by Yeast

α-Ketoglutarate productivity from n-paraffins of 141 strains of identified yeasts was studied. Among the strains tested, only strains of Candida lipolytica exclusively showed a high ability to produce α-ketoglutarale.

It was also observed that these strains of Candida lipolytica required thiamine for their growth and that exegenous thiamine stimulated the activity of α-ketoglutarate dehydrogenase of Candida lipolytica AJ 5004.

From these results, relationship between thiamine requirement and α-ketoglutarate productivity of Candida lipolytica was discussed.

α-Ketoglutarate fermentation by representative strains of Candida lipolytica was also carried out.     

Rapid and Effective Method of RNA Isolation from Green Microalga <Emphasis Type="Italic">Ankistrodesmus convolutus</Emphasis>

The rapid and effective method for the isolation of RNA from green microalga Ankistrodesmus convolutus based on homogenization in a simple CTAB buffer and selective precipitation of RNA with lithium chloride is developed. This procedure avoids the use of toxic chaotropic agents and phenol while high concentration of dithiothreitol is used to inhibit RNase activity and prevent oxidative cross-linking of nucleic acids by phenolics. The extraction procedure was able to produce high quality and intact RNA from A. convolutus. The yield of total RNA was 0.69–0.73 mg/g of fresh weight, with A₂₆₀/A₂₈₀ ratio of 1.79–1.86. The obtained RNA was of sufficient quality and suitable for downstream application such as RT-PCR and cDNA library construction. The procedure may also have wider applicability for total RNA isolation from other green microalgae species.     

Some properties of chrysanthemum stunt, a virus with the characteristics of an uncoated ribonucleic acid

Grafting to virus-free Mistletoe chrysanthemums was the most reliable method of detecting the chrysanthemum stunt agent, but specific light and temperature conditions were required for the diagnostic ‘measles’ symptoms to develop. Although stunt agent was highly infectious, leaf-rubbing inoculations with chrysanthemum sap gave erratic results. Colorimetric and electrophoretic tests were unreliable for indexing chrysanthemums. Stunt agent infected eight of twenty-nine species in the family Compositae, but none of 116 species in forty-seven other families. Stunt spread rapidly by foliage contact and by handling plants, but dipping the hands in 2% trisodium orthophosphate when handling plants increased the amount of spread. Stunt agent was not transmitted by four species of aphids, the glasshouse redspider mite, dodder (Cuscuta campestris) or through chrysanthemum seed. Stunt agent withstood 10 min at c. 98 °C and dilution to 10^-4, was not pelleted by ultracentrifugation, and was inactivated by RNase in weak, but not strong, buffer, suggestive of an uncoated RNA ‘viroid’. Partially purified preparations were made by homogenizing frozen chrysanthemum leaves in 0.5 m phosphate buffer with antioxidant at c. 2 °C, and clarification by n-but-anol and chloroform, followed by centrifugation. Highly infective RNA was precipitated from the supernant fluid by 2.5 vol. cold ethanol, and resuspended in a small volume of buffer. The u.v. absorption spectra of infective preparations and the u.v. absorbance profiles of density-gradients, were very similar to those of preparations from healthy chrysanthemum. Infective partially purified preparations of stunt agent withstood exposure to 2% formaldehyde or tri-sodium orthophosphate, u.v. irradiation, and sonication. Stunt preparations contained no virus particles recognizable by electron microscopy, gave no distinct peak on analytical ultracentrifugation, and did not consistently contain any specific antigen. Although similar to the ‘viroids’ potato spindle tuber and citrus exocortis, stunt agent did not infect Citrus limon, Gynura aurantiaca or tomato.     

High efficiency transformation by electroporation of <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis>

Yarrowia lipolytica was usually transformed by heat shock, but linearized integrative vectors always resulted in a low transformation efficiency when electroporation was used. To develop a high efficiency integrative transformation method by electroporation of F. lipolytica, we report here that pretreatment of F. lipolytica with 150 mM LiAc for 1 h before electroporation will approximately 30-fold of increase transformation efficiency. A cell concentration of 10¹⁰/ml and instrument settings of 1.5 kV will generate the highest transformation efficiencies. We have developed a procedure to transform F. lipolytica that will be able to yield an efficiency of 2.1 × 10⁴ transformants/ug for integrative linear DNA. With our modifications, the electroporation procedures became a very efficient and reliable tool for F. lipolytica transformation.     

Fermentation of n-Paraffins by Yeast

Screening test for obtaining microorganisms which produce l-amino acids or organic acids from n-paraffins were carried out. Fourteen strains of microorganisms which seemed to belong to the yeast showed strong ability to produce α-ketoglutaric acid. A representative strain of these microorganisms was identified as Candida lipolytica AJ 5004.

Optimal conditions for production of α-ketoglutarate using Candida lipolytica AJ 5004 were also studied. Under the condition thus obtained using a culture medium of 8 weight % of n-paraffins, the yeast accumulated 59% of α-ketoglutarate to the substrate added after three days culture.     

Assimilation of methanol by Yeasts

Candida lipolytica was cultured on a methanol containing medium as the only C source. The influence of different concentrations of methanol and ammonium sulphate and the effect of addition of some biological active materials to the methanol containing medium were studied. Dry cell yield of C. lipolytica and protein content were determined to be 23.1 g of cells/100 g of methanol added and 40.2%, respectively. Total lipids, phospholipids, keto acid and amino acid composition were estimated. The amino acid composition of the protein was comparable to the composition of the other reported single cell proteins (SCP). These results indicate that C. lipolytica is potentially important for fodder use.     

Lipase-catalyzed synthesis of vitamin C fatty acid esters

Fatty acid esters of vitamin C (ascorbic acid) where synthesized in a mainly solid-phase system in the presence of small amounts of organic solvent (acetone or t-butanol) catalyzed by immobilized lipase B from Candida antarctica.Highest reaction rates and yields of isolated products were obtained using fatty acid vinyl esters, e.g., 6-O-palmitoyl-l-ascorbic acid was obtained in 91% isolated yield after 48 h. As vitamin C and its esters are very sensitive to oxidation, a mild extraction method for the isolation of reaction products was developed.     

Effects of ribonucleic acid removal methods on proteolytic activity and protein solubility in Candida utilis

Candida utilis was grown under controlled conditions and nucleic acids were removed from whole cells and homogenates by alkaline hydrolysis techniques, en-zymatic methods, and washing with buffer. Homogenization released hydrolytic enzymes and proteolytic activity increased with incubation at elevated temperatures under acidic conditions. Slight proteolysis occurred in all incubated samples and this may contribute to protein insolubilization. Very little protein was lost during incu-bation when compared to similar processes using bakers' yeast. This can be due to lower levels of protease activities in C. utilis. Alkaline hydrolysis methods resulted in hydrolysis of some proteins and irreversible insolubilization of the protein. These methods also destroyed any residual enzymatic activities. Heat denaturation studies suggest that protein insolubilization occurs at neutral pH when heat treatments equivalent to or greater than 85° C for 15 min are used. SDS-PAGE methods were used to characterize and monitor changes in protein. Eighteen proteins and/or sub-units were present at levels of 1% or greater. Results may help to explain changesin functional properties of sample preparations which accompany RNA removal.     

Homology-independent genome integration enables rapid library construction for enzyme expression and pathway optimization in Yarrowia lipolytica

Yarrowia lipolytica is an important oleaginous industrial microorganism used to produce biofuels and other value-added compounds. Although several genetic engineering tools have been developed for Y. lipolytica, there is no efficient method for genomic integration of large DNA fragments. In addition, methods for constructing multigene expression libraries for biosynthetic pathway optimization are still lacking in Y. lipolytica. In this study, we demonstrate that multiple and large DNA fragments can be randomly and efficiently integrated into the genome of Y. lipolytica in a homology-independent manner. This homology-independent integration generates variation in the chromosomal locations of the inserted fragments and in gene copy numbers, resulting in the expression differences in the integrated genes or pathways. Because of these variations, gene expression libraries can be easily created through one-step integration. As a proof of concept, a LIP2 (producing lipase) expression library and a library of multiple genes in the β-carotene biosynthetic pathway were constructed, and high-production strains were obtained through library screening. Our work demonstrates the potential of homology-independent genome integration for library construction, especially for multivariate modular libraries for metabolic pathways in Y. lipolytica, and will facilitate pathway optimization in metabolic engineering applications.     

Characteristics of copper tolerance in Yarrowia lipolytica

We discovered that a mutant strain of the dimorphic yeast Yarrowia lipolytica could grow in the yeast form in high concentrations of copper sulfate. The amount of metal accumulated by Y. lipolytica increased with increasing copper concentrations in the medium. Washing with 100 mM EDTA released at least 60% of the total metal from the cells, but about 20–25 μmol/g DW persisted, which represented about 30% of the soluble fraction of cultured cells. The soluble fraction (mainly cytosol) contained only about 10% of the total metal content within cells cultured in medium supplemented with 6 mM copper. We suggest that although a high copper concentration induces an efflux mechanism, the released copper becomes entrapped in the periplasm and in other parts of the cell wall. Washing with EDTA liberated not only copper ions, but also melanin, a brown pigment that can bind metal and which located at the cell wall. These findings indicated that melanin participates in the mechanism of metal accumulation. Culture in medium supplemented with copper obviously enhanced the activities of Cu, Zn-SOD, but not of Mn-SOD.     

A simple method for the extraction and quantification of photopigments from Symbiodinium spp.

We have developed a simple, mild extraction procedure using methanol which, when coupled with HPLC analysis and diode array detection (DAD), can be used to quantify the major photopigments found in cultured Symbiodinium spp. Extracts were prepared by suspending, fresh or frozen (− 70 °C), wet cell pellets in methanol and sonicating or not sonicating the cell suspensions before soaking the cells for 2 h in an ice bath. To assist the soaking process, cell suspensions were vortex mixed at 30 min intervals. After soaking, 0.5 M ammonium acetate buffer was added (1 part buffer to 9 parts methanol) before suspensions were stored over night at − 20 °C. Greater than 92% the recoverable pigment was obtained in the initial extraction of the four major photopigments, chlorophyll c, peridinin, diadinoxanthin, and chlorophyll a. Neither sonication nor freezing substantially increased the recovery of photopigments extracted with methanol. Extraction by other commonly used solvents such as acetone or acetone:water with or without freezing and sonication were less effective.     

Chlorophyll-a determination with ethanol – a critical test

Chlorophyll-a content is widely used as an indicator of the quality of freshwater bodies. Quantification of chlorophyll-a is a routine procedure in the test laboratories of water works, and in research laboratories. Although attempts have been made to standardise the measurement procedure, there are nonetheless many procedures currently in use. This work is focused on a careful re-examination of the ISO: 10260, 1992 standard, which prescribes 90% (v/v) ethanol for chlorophyll extraction and measurement. Chlorophyll contents of cultures of the cyanobacterium Synechococcus elongatus Nägeli and the chlorophyte Scenedesmus acutus Meyen were determined by means of a series of concentrations of ethanol/water mixtures which were employed as extracting agents – the water content was gradually decreased from 20 to 0%. The extraction procedure was verified by measuring the amount of retained water after using both water and oil pumps for filtering the samples. The spectroscopic effects of the presence of water were studied and the molecular background of these spectral phenomena is discussed. The extraction yields obtained with 90% ethanol were compared to those obtained with methanol and acetone. On the basis of the calculated error level, improvements to the ISO: 10260, 1992 standard method have been suggested.     

Solubilization of 3-hydroxy-3-methylglutaryl coenzyme A reductase from rat and chicken liver microsomes

A simple, efficient, freeze-thaw procedure for the solubilization of liver 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase has been developed. Microsomes of chicken or rat liver were prepared by homogenization in buffer containing 100 mm sucrose, 50 mm KCl, 40 mm KH₂PO₄, 30 mm EDTA, and 2 mm DTT, pH 7.2 (buffer A). The homogenate was centrifuged at 12,000g (15 min), and the microsomes were separated from the supernatant by centrifugation at 100,000g (60 min). The isolated microsomes were frozen, either by dry ice-acetone or by storage in a freezer at ?20°C. The frozen microsomes were permitted to thaw at room temperature, homogenized in buffer A, and centrifuged at 100,000g (60 min). The extraction was repeated and the combined supernatants contained 70 to 90% of the microsomal HMG-CoA reductase activity. The yield of enzyme activity by the freeze-thaw technique is equal to or greater than previously reported methodologies and is significantly easier to perform. This procedure is particularly suited to the preparation of large quantities of solubilized enzyme for isolation and characterization of HMG-CoA reductase. In addition, this method does not require the use of detergents, sonification, or other procedures which might partially inactivate or alter the molecular properties of the enzyme.     

Biochemical and immuno- and lectin-histochemical studies of solubility and retention of bone matrix proteins during EDTA demineralization

Summary The present study utilized biochemical and immuno-and lectin-histochemical methods to demonstrate solubility and retention of mineral-binding non-collagenous proteins in rat midshaft subperiosteal bone during EDTA demineralization. A monoclonal antibody (9-A-2) specific for chondroitin 4-sulphate and dermatan sulphate and wheat germ agglutinin (WGA) specific forN-acetyl-d-glucosamine,N-acetylneuraminic acid, andN-acetyl-d-galactosamine were used. Bone proteins were extracted from fresh unfixed or aldehyde-fixed specimens with a three step extraction procedure, 4 M guanidine HCl (GdnCl), aqueous EDTA without GdnCl, followed by GdnCl. For comparison with the second extraction step, ethanolic trimethylammonium EDTA (ethanolic EDTA) was substituted for aqueous EDTA. Based on protein staining and Western blot analysis of SDS-polyacrylamide gel electrophoresis of each extract using 9-A-2 and WGA, retention of mineral-binding proteins extractable from fresh specimens with aqueous EDTA was greatly increased in tissue when ethanolic EDTA was used. Their retention was even greater with prior aldehyde fixation. Maximum retention with no detectable solubility of 9-A-2 and WGA reactive proteins was obtained after ethanolic EDTA extraction of aldehyde-fixed specimens, which concomitantly provided the strongest immuno- and lectin staining. These results indicate that this combined method dramatically improves retention of PGs and glycoproteins during demineralization of bone tissues and provides the best method for localizing these glycoconjugates.     

Cherry fruit development: The use of a microassay for studying indoleacetic acid oxidase

An improved procedure is described for extraction and assay of indoleacetic acid oxidase from seeds of sour cherry (Prunus cerasus L.). The extraction procedure was optimized for pH, buffer, polyvinylpolypyrrolidone (PVP) and tissue: buffer ratio. Greatest extraction efficiency was obtained at pH 4.0, 0.2 M acetate buffer, tissue: PVP ratio of 1:2.5 and tissue: buffer ratio of 50 ml per g of seed. The enzyme was assayed at 30°C using indoleacetic acid-1-¹⁴C as substrate and radioassaying the ¹⁴CO₂ evolved. Mn²⁺ and 2,4-dichlorophenol enhanced enzyme activity but were not obligatory. A minimum substrate concentration of 60 M was needed for quantitative evaluation. This assay was sensitive and reproducible, enzyme activity being demonstrated in as little as 0.8 mg of seed tissue with a coefficient of variation of 1 to 9%.     

Utilization of normal alkanes by yeasts

A stable mixed yeast culture designated as Culture 4, consisting of Candida intermedia and Candida lipolytica was investigated. The culture was judged stable based on uniformity of fermentation results and the nearly constant ratio of the two organisms at the completion of fermentations. However, the ratio of the two organisms at different times during the fermentation was not determined. The mixed culture grew more rapidly on n-alkanes than did C. intermedia; C. lipolytica did not grow on unsupplemented mineral salt–n-alkane medium. Solid n-alkanes were dissolved in 2,6,0,14-tetramethylpentadecane (pristane) for investigation as carbon sources. With Culture 4, on n-alkanes ranging from pentadecane (C₁₅) through octacosane (C₂₈), cell yields were 74.2–89.5%; generation times were 3.0–8.0 hr. during the exponential growth phase. The fastest growth rates and highest cell yields were obtained with docosane (C₂₂) as substrate. The cells obtained contained 6.75–8.81% nitrogen and 1.9–13.4% lipid. Crude protein yields were 34.4–47.6%. The oxidation of n-alkanes by C. intermedia was studied manometrically with resting whole cells. The alkaneoxidizing system of this organism appears to be constitutive and nonspecific for alkane substrates.