Simple isolation of functional RNA from woody stems of gymnosperms

Stems of woody conifers contain high levels of polysaccharides and phenolic compounds that complicate the isolation of functional RNA from this highly lignified tissue. These difficulties were overcome by pulverizing the frozen tissue with a stainless-steel mortar and by effectively sequestering interfering phenolic compounds with vinylpyrrolidone polymers, thereby minimizing damage to nucleic acids during extraction. RNases were inhibited by aurintricarboxylic acid, and gelatinous polysaccharides were removed by inclusion of a 10% ethanol precipitation step. RNA was then isolated by precipitation with 33% isopropanol and ultracentrifugation onto a cushion of 5.7 M CsCl. Yields of 10 to 20 μg RNA/g FW were obtained from woody stems of several different gymnosperm species, including grand fir (Abies grandis), lodgepole pine (Pinus contorta), loblolly pine (Pinus taeda), Douglas fir (Pseudotsuga menziesii) and Pacific yew (Taxus brevifolia). The high quality of the RNA obtained was determined by UV-spectrophotometry, denaturing agarose gel electrophoresis, andin-vitro translation, and this material was used to construct cDNA libraries.     

An efficient method for total RNA extraction from peanut seeds

Most of conventional RNA extraction methods failed to extract highly pure and integral RNA from peanut seeds because peanut seeds are extremely rich in lipids, proteins, polysaccharides, and phenolic compounds. Here, we describe a new method, named Peanut Improved Modified RNA extraction method (PIMRNAext), using SDS, Tris-saturated phenol, NaCl, and sarkosyl during the extraction process, which are particularly successful for total RNA extraction from lipid- and polysaccharide-rich materials. The proposed PIMRNAext method is simple and fast. It requires only conventional reagents and is completed within 2 h. Using PIMRNAext gives very good yields of high quality peanut RNA. This method is about ten times more efficient than conventional methods, and the RNA produced by it is compatible with further molecular biology experiments, such as RT-PCR. We propose to use the PIMRNAext method to extract RNA from peanuts and peanut-like plant species not only for RT-PCR, but also for most molecular biology techniques that need copies of pure RNA, such as microarray or cDNA library construction.     

Changes in Formation and Localization of Phenolic Compounds in the Tissues of European and Canadian Yew during Dedifferentiation <Emphasis Type="Italic">In Vitro</Emphasis>

Changes in formation and localizations of phenolic compounds, including flavans, were investigated in the tissues of European and Canadian yew (Taxus baccata L. and T. canadensis Marsh.) during dedifferentiation in vitro. Annual shoots of European yew had the highest capacity for synthesizing these compounds. During the summer growth period, the content of total soluble phenolic compounds and flavans in these shoots was 30–40% higher than in the winter. Cell dedifferentiation and growth in vitro was accompanied by enhanced synthesis of phenolic compounds, including flavans, the change in tissue localization of these compounds, and an increase in the number of cells containing phenolics. Significant accumulation of phenolic compounds in callus cells resulted in necroses following two subcultures in the European and Canadian yew cultures initiated from summer explants, and following seven subcultures of the European yew calli initiated from winter explants. These data allow us to suggest that a high level of phenolic compounds in yew calli could be the reason for their necrosis.     

Enhancement of phenolic compound production in Spirulina platensis by two-step batch mode cultivation

Phenolic compounds regarded as important pharmaceuticals with various biological activities are found in low amounts in microalgae. The objective of this study was to increase the amount of phenolic compounds in Spirulina platensis by a two-step batch mode cultivation. The evaluation of the effect of the sudden shift from low light to high light on phenolic compound production, antioxidant activity, growth, and biomass composition of S. platensis was undertaken. The amount of phenolic compounds was significantly increased by approximately eightfold (p?<?0.01) by the light treatment. There were also increases in total amounts of carbohydrate, phycocyanin, carotenoid, malondialdehyde, and antioxidant activities while there were significant decreases in total protein amounts (p?<?0.05). The relationships between antioxidant activities and total amounts of phenolic compounds were significantly correlated at the 99% confidence level (p?<?0.01) indicating that phenolic compounds were major contributors of antioxidant activities.     

莲藕组织总RNA的快速提取方法

莲藕组织富含多糖、脂质、酚类等物质,用一般的方法较难提取高质量的RNA。在改进前人方法的基础上,建立了一种高效、简单的CTAB-LiCl提取法,能快速提取高质量的莲藕组织总RNA,并且产率高、完整性好、纯度高,能进一步满足RT-PCR等分子生物学实验的需要。此外,该方法也适用于其它富含多糖、脂质、酚类等物质的植物组织总RNA的提取。     

Optimization of RNA Isolation from Brittle Leaf Disease Affected Date Palm Leaves and Construction of a Subtractive cDNA Library

A simple and efficient method was described here for the isolation of high-quality RNA from date palm leaves affected with Brittle Leaf Disease (BLD) and containing high amount of phenolic compounds. The procedure was based on the use of a non-ionic detergent Nonidet-P40 (NP-40), Polyvinylpyrrolidone (PVP), and beta-mercaptoethanol in the extraction buffer in order to isolate cytoplasmic RNA and to prevent the oxidation of phenolic compounds. This method allowed the isolation of intact RNA, suitable for cDNA synthesis and library construction. Differential screening of the subtractive cDNA library from affected leaf RNA led to the identification of some BLD-induced genes.     

Potential of natural phenolic antioxidant compounds from Bersama abyssinica (Meliathacea) for treatment of chronic diseases

Chronic diseases including cardiovascular, diabetes and cancer persist for a long time in the course of treatment affecting health and are currently the cause of many deaths. In most cases, the treatment of chronic infectious diseases especially Tuberculosis relies on conventional drugs which are currently becoming fruitless due to drug resistance and unpredicted complications in course of treatment. However, herbal medicines have for a long time been used in prevention and treatment of chronic diseases including asthma and heart diseases in Africa. In this study, we extracted metabolites and screened for active compounds with potential free radical scavenging and pharmacological activities from Bersama abyssinica, the plant commonly used in traditional medicine in Tanzania. B. abyssinica root, stembark and leaf were air dried, sequentially extracted in various solvents including petroleum ether, dichloromethane, ethylacetate and methanol to yield extracts and fractions. The extracts and fractions were tested for the presence of several metabolites and antioxidant activity. The analysis of chemical compounds from resultant extracts was done by GC–MS for non-polar factions and LC-MS/MC for moderate polar extracts.High amount of phenolic acid, flavonoids and tannin were identified in ethylacetate fraction compared to ethanol, dichloromethane and petroleum ether. The GC–MS analysis of petroleum ether extract of B. abyssinica stem back yielded twelve (12) compounds with varying composition. The most abundant compounds were 2-Butenoic acid, 3-methyl-, ethyl ester comprising 33.8%, n-Hexadecanoic acid comprising 16.7% and Ethanolpentamethyl- yielded in 16.7%.The LC-MS/MS analysis of Ethyl acetate fractions yielded 20 compounds including; Mangiferin and Isoquercitin were abundant in leaves, stembark and roots. Lastly, ethyl vanillate was identified in both roots and leaves whereas Quercitrin and 7,8-Dimethoxycoumarin were found in stembark and root.These findings indicated that B. abyssinica is rich in phenolic compounds ranging from phenolic acids, flavonoids and coumarin that possess high antioxidant and pharmacological properties potential for treatment of chronic diseases.     

The sensing of plant signal molecules by Agrobacterium: genetic evidence for direct recognition of phenolic inducers by the VirA protein

The virulence (vir) genes of Agrobacterium tumefaciens are induced by low-molecular-weight phenolic compounds and monosaccharides through a two-component regulatory system consisting of the VirA and VirG proteins. Although it is clear that the monosaccharides require binding to a periplasmic binding protein before they can interact with the sensor VirA protein, it is not certain whether the phenolic compounds also interact with a binding protein or directly interact with the sensor protein. To shed light on this question, we tested the vir-inducing abilities of several different phenolic compounds using two wild-type strains of A. tumefaciens, KU12 and A6. We found that several compounds such as 4-hydroxyacetophone and p-coumaric acid induced the vir of KU12, but not A6. On the other hand, acetosyringone and several other phenolic compounds induced the vir of A6, but not KU12. By transferring different Ti plasmids into isogenic chromosomal backgrounds, we showed that the phenolic sensing determinant is associated with the Ti plasmid. Subcloning of the Ti plasmid indicated that the virA locus determines which phenolic compounds can function as vir inducers. These results suggest that VirA directly senses the phenolic compounds for vir activation.     

Isolation and Partial Characterization of Transfer RNAs from Astragalus bisulcatus

A procedure has been developed for the isolation of transfer RNA from the selenium accumulator plant Astragalus bisulcatus. This material appears free of interfering phenolic compounds, has a high guanosine to cytidine ratio, shows a major and modified nucleoside composition characteristic of plant transfer RNAs, and exhibits chromatographic and electrophoretic properties similar to transfer RNAs from other well studied bacterial and plant systems. RNAs isolated from A. bisulcatus seedlings incubated in the presence of ⁷⁵Se indicate some incorporation of radioactivity into the transfer RNAs, but at extremely low levels. The transfer RNAs were active in accepting amino acids, although their over-all levels of activity appeared low when compared with those from a homologous Escherichia coli aminoacylation reaction system.     

Probing a family GH11 endo-β-1,4-xylanase inhibition mechanism by phenolic compounds: Role of functional phenolic groups

Phenolic compounds generated from lignin degradation during the pre-treatment step in the process of producing bioethanol from lignocellulosic biomass are known to be inhibitory to enzymatic hydrolysis and fermentation. The inactivation mechanism of a GH11 endoxylanase (Tx-Xyl) by several phenolic compounds varying in their hydroxyl and methoxyl radical content was investigated. Apparent kinetic inactivation parameters were measured as an approximate index of the inhibitory effects. All the tested aromatic compounds had strong negative impact on enzyme activity and kinetic analysis revealed non competitive multi-site inhibition mechanism. The interactions between Tx-Xyl and the phenolic compounds were further studied by steady-state (tryptophan) fluorescence spectroscopy. Changes in λ_max of emission and quenching of fluorescence intensity indicated changes in the microenvironment of tryptophan residues. In agreement with the kinetic parameters, the fluorescence derived binding constants evidenced higher enzyme–phenolics interaction affinity with increasing phenolic hydroxyl radical content, suggesting clear correlations of such radicals with the inhibitory effects. Results indicated that the inhibitory effects of phenolic compounds on Tx-Xyl activity are most likely brought about by conformational alterations of the enzyme protein inducing steric inactivation.     

Characterization of the microbial communities in jet-loop (JACTO) reactors during aerobic olive oil wastewater treatment

The olive oil industry is one of the most typical and economically important Portuguese agro-industries, 29,900 tons of olive oil having been produced in 2002/2003. This industry generates large amounts of olive oil wastewaters (OOWW), which are difficult to degrade and thus cause a negative environmental impact. Jet-loop reactors (JACTO) developed and scaled-up by our group have been successfully used for biological treatment of winery and OOWW. This study aimed to determine the interactions of reactor hydrodynamics with microflora profiles during bio-treatment of OOWW. Bio-treatment was performed using a 20-dm³ JACTO bioreactor achieving a chemical oxygen demand (COD) and phenolic compounds removal rate of 70% at a hydraulic retention time of 12 days. Bio-treatment was scaled-up to 200-dm³ JACTO bioreactor, reaching 87% COD removal and 80% phenolic compounds removal. Microflora present on OOWW were identified on samples taken before, during, and at the end of bio-treatment. Identification of isolates was carried out at genus and/or species level. Samples from the bio-treatments did not show any fungi; most of the isolates belonged to the Bacillus genus (with predominance of Bacillus megaterium, Bacillus sphaericus, and Brevibacillus brevis). The good COD and phenolic compounds removal rate indicates that the microbial community selected during the treatment is well adapted to the stress conditions imposed by this special type of bioreactor.     

The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or “azaaromatics,” trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics.     

Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit

A simple and efficient method is described for isolating high quality RNA from bilberry fruit. The procedure is based on the use of hexadecyltrimethyl ammonium bromide (CTAB), polyvinylpyrrolidone (PVP), and β-mercaptoethanol in an extraction buffer in order to eliminate the polysaccharides and prevent the oxidation of phenolic compounds. This method is a modification of the one described for pine trees, and yields high-quality RNA suitable for cDNA based methodologies. This method is applicable for a variety of plant tissues.     

Accumulation of amino acids and phenolic compounds in biochemical plant responses to feeding of two different herbivorous arthropod pests

The study aimed at comparing the changes in the content of free amino acids, phenolic compounds and the activity of PAL and TAL caused by two piercing-sucking arthropods: the grape mealybug (Pseudococcus maritimus Ehrh.) and the two-spotted spider mite (Tetranychus urticae Koch) in the leaves of orchid and strawberry, respectively. The obtained results show that the amino acid content and the ratio of amino acids to phenolic compounds increased in both plant species infested by the mealybug and the mite. However, such response was weakly dependent on changes in activity of the analysed enzymes. The pest feeding affected accumulation of the phenolic compounds, since the induction of the PAL activity in mealybug-infested orchid leaves during the first 5 h of the experiment preceded the increase in phenolic compounds during the first week of insect feeding. Instead, the increased activity of TAL was accompanied by elevated levels of phenolic compounds in the leaves of strawberry infested by mites. Mechanisms of biochemical plant responses induced by infestation of the studied herbivorous arthropods are discussed.     

Persistence of Anticancer Activity in Berry Extracts after Simulated Gastrointestinal Digestion and Colonic Fermentation

Fruit and vegetable consumption is associated at the population level with a protective effect against colorectal cancer. Phenolic compounds, especially abundant in berries, are of interest due to their putative anticancer activity. After consumption, however, phenolic compounds are subject to digestive conditions within the gastrointestinal tract that alter their structures and potentially their function. However, the majority of phenolic compounds are not efficiently absorbed in the small intestine and a substantial portion pass into the colon. We characterized berry extracts (raspberries, strawberries, blackcurrants) produced by in vitro-simulated upper intestinal tract digestion and subsequent fecal fermentation. These extracts and selected individual colonic metabolites were then evaluated for their putative anticancer activities using in vitro models of colorectal cancer, representing the key stages of initiation, promotion and invasion. Over a physiologically-relevant dose range (0–50 µg/ml gallic acid equivalents), the digested and fermented extracts demonstrated significant anti-genotoxic, anti-mutagenic and anti-invasive activity on colonocytes. This work indicates that phenolic compounds from berries undergo considerable structural modifications during their passage through the gastrointestinal tract but their breakdown products and metabolites retain biological activity and can modulate cellular processes associated with colon cancer.     

Aporphine alkaloids and lignans formed in response to injury of sapwood in Liriodendron tulipifera

Two new phenolic aporphine alkaloids, (+)-lirioferine and (+)liriotulipiferine, were isolated from discolored sapwood of L. tulipifera. Injury to the tree stem greatly stimulated biosynthesis of glaucine and phenolic alkaloids related to glaucine including thaliporphine, predicentrine, N-methylaurotetanine and corunine as well as the above two compounds. Injury also stimulated synthesis of oxoaporphine related and other polymeric pigments. Corunine was responsible for at least part of the color of discolored sapwood. None of the above compounds except glaucine was detected in normal sapwood or heartwood of L. tulipifera. Thus, formation of alkaloids and lignans in discolored sapwood differs both quantitatively and qualitatively from that observed during the normal transition of sapwood to heartwood in this tree. The compounds formed in response to injury differed substantially from one zone of injury to another within the same tree.