Efficient isolation of high quality nucleic acids from different tissues of <Emphasis Type="Italic">Taxus baccata</Emphasis> L.

Improved and efficient methods were developed for isolating high quality DNA and RNA from different sources of Iranian Yew (Taxus baccata L.). The methods were based on CTAB extraction buffer added with high levels of polyvinylpyrrolidone (PVP) and β-mercaptoethanol to properly remove polysaccharides and prevent oxidation of phenolics. The pellets obtained by ethanol precipitation were washed only with Chloroform: isoamyl alcohol (24:1). So, we could successfully eliminate the dangerous phenol/chloroform extraction steps from the isolation procedure. Both spectrophotometric (A₂₆₀/A₂₈₀ and A₂₆₀/A₂₃₀ ratios) and agarose electrophoresis analysis of isolated nucleic acids (DNA and RNA) indicated good results. DNA with the average yield of 100–300 μg/g leaf and stem tissue and total RNA with an average yield of 20–30 μg/g cell culture and 80–100 μg/g leaf and stem tissue of Iranian yew could be obtained. Successful amplification of pam and pds by PCR and RT-PCR, showed the integrity of isolated DNA and RNA, respectively.     

High-Quality RNA Preparation from <Emphasis Type="Italic">Rhodosporidium toruloides</Emphasis> and cDNA Library Construction Therewith

Oleaginous yeast Rhodosporidium toruloides is an excellent microbial lipid producer. Therefore, it is important to develop molecular biology tools to understand the basic mechanism for lipid accumulation and further manipulate the microorganism. High-quality RNA extraction from R. toruloides is particularly challenging due to high level of polysaccharides, lipids, and other secondary metabolites. To obtain an optimal protocol for RNA extraction from R. toruloides, four methods were evaluated. Large difference in RNA yield and quality among these protocols was found. The optimum method was modified RNAiso procedure, where RNA was isolated using liquid nitrogen-RNAiso method with salt precipitation and the addition of β-mercaptoethanol. This method consistently recovered RNA in good quality with high yield. Around 297 μg total RNA per gram of cells was obtained with an average purity measured as A₂₆₀/A₂₈₀ of 2.09. A titer of 10⁵ cfu/ml could be harvested to construct a full-length cDNA library with the RNA sample in this quality. Electrophoresis gel analysis indicated the fragments ranged from 200 bp to 4.0 kb, with the average size of 1000 bp. Randomly picked clones showed the recombination efficiency at 80%. These results showed that RNA of R. toruloides was successfully extracted for the first time using the modified RNAiso method, and the cDNA library was appropriate for screening the genes related to lipid accumulation.     

Improved RNA isolation from Laminaria japonica Aresch (Laminariaceae, Phaeophyta)

RNA isolation is difficult in some plants and algae because phenolics, polysaccharides, or other compounds can bind or co-precipitate with RNA, and because the success of RNA isolation can be strain-specific and species-specific. To create an improved RNA isolation protocol for Laminaria japonica Aresch (Laminariaceae, Phaeophyta), four methods for extracting RNA were tested. A cetyltrimethylammonium bromide (CTAB)-based RNA extraction protocol was developed that clearly showed 28S and 18S ribosomal RNA bands and produced RNA with high yield (68 μg g⁻¹ fresh weight) and high quality (A _260/280 ratio 1.96 ± 0.05). The isolated RNA was intact, and RT-PCR analysis confirmed that further molecular application is feasible.     

Improved procedure for separation and purification of <Emphasis Type="Italic">Arthronema africanum</Emphasis> phycobiliproteins

A rapid, inexpensive and reliable procedure for separation and purification of C-phycocyanin (C-PC) and allophycocyanin (APC) from Arthronema africanum based on a previously described rivanol-sulfate method for C-PC purification was developed. Exclusion of NaCl from the extraction buffer resulted in complete separation of APC and C-PC, two-fold reduction of rivanol treatments, and a higher yield and purity of C-PC. Pure C-PC (A₆₂₀/A₂₈₀ of 4.52) and APC (A₆₅₂/A₂₈₀ of 2.41) were obtained. The estimated molecular masses of the α and β subunits were 17 and 19 kDа for С-phycocyanin and 16 and 18 kDа for APC, respectively. The overall C-PC recovery of 55% (w/w) from its content (100 mg) in the crude extract was 10–20% higher than so far reported. The procedure appears promising for scaling up and broader applications.     

Efficiency of ligation-mediated PCR and TAIL-PCR methods for isolation of <Emphasis Type="Italic">RbcS</Emphasis> promoter sequences from green microalga <Emphasis Type="Italic">Ankistrodesmus convolutus</Emphasis>

Isolation of promoter sequences from known gene sequences is a tedious task in genome-related research. An efficient method of obtaining the promoter sequences is necessary in order to successfully use targeted promoters for genetic manipulations. Here, efficiency and usefulness of two PCR-based methods, namely: ligation-mediated PCR and thermal asymmetric interlaced (TAIL) PCR, for isolation of promoter sequences of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) gene from green microalga Ankistrodesmus convolutus (A. convolutus) were evaluated. The results showed that the amplification efficiency of TAIL-PCR was higher than that of the ligation-mediated PCR method, i.e. the amplified promoter fragments of 1.2 and 0.8 kb in length or promoter sequences of 813 and 606 bp (after eliminating the unreadable sequences). The use of TAIL-PCR described here presents a low cost and efficient strategy for the isolation of promoter sequences of known genes, especially in GC-rich regions, and species with little or no available genome information such as A. convolutus.     

Spatial and Temporal Genetic Variation of Green Mussel, Perna viridis in the Gulf of Thailand and Implication for Aquaculture

The culture of green mussel (Perna viridis) in the Gulf of Thailand depends on natural spat which are believed to come from spawning grounds adjacent to major river mouths. In the present paper, genetic diversity of spatial and temporal populations of green mussel in the Gulf of Thailand was investigated using five microsatellite loci. The results showed moderate genetic variation of all 11 populations (averaged number of alleles per locus, A = 10.4–12.2; effective number of alleles per locus, A _e = 5.36–6.59; mean allelic richness, A _r = 10.23–12.06; observed heterozygosity, H _o = 0.52–0.63, and expected heterozygosity, H _e = 0.66–0.73) without significant differences among populations. No sign of bottleneck or genetic disequilibrium was observed. Genetic differentiation among spatial populations was low (F _ST = 0.0046, CI_0.95 = 0.0020–0.0083 for the samples collected in January, 2007, and F _ST = 0.0088, CI_0.95 = 0.0010–0.0162 for the samples collected in July, 2007) while temporal variation was significant as revealed by the analysis of molecular variance. Multidimensional scaling separated temporal population groups with minor exception. The assignment test revealed that most of the recruits were from other populations.     

A Modified Protocol for RNA Extraction from Different Peach Tissues Suitable for Gene Isolation and Real-Time PCR Analysis

RNA extraction is the first step in the study of gene isolation and expression. However, it is difficult to extract high quantity and quality RNA from tissues containing large quantities of polysaccharides and polyphenols. Peach (Prunus persica), in addition to containing high levels of polysaccharides and polyphenols, is a challenging starting material for RNA isolation using a single method because of different amounts of those substances in diverse tissues. Based on three reported methods, we developed a modified RNA isolation protocol to solve this problem, leading to high quality and quantity of total RNA from peach mesocarp tissues of fruits which were sampled from all developmental stages and different storage periods, as well as from other tissues including flowers, leaves, stems, and roots. With our modified method, 28–650 μg of total RNA was routinely obtained from per gram of fresh material, gave at least a 1.16-fold improvement by compared with those isolated by other seven methods. The RNA extracts were successfully used in downstream applications such as RT-PCR, RACE, and real-time PCR.     

Isolation of RNA of high quality and yield from <Emphasis Type="BoldItalic">Ginkgo biloba</Emphasis> leaves

An improved protocol was developed to isolate total RNA in good yield and integrity from Ginkgo biloba leaves containing high levels of flavonoid glycosides, terpene lactones, carbohydrates and polyphenolic secondary metabolites. Polyvinylpolypyrrolidone at 2% and β-mercaptoethanol at 4% were added to the standard CTAB extraction buffer and, after chloroform and phenol extraction, the pellet obtained by ethanol/acetate precipitation was washed and a second phenol/chloroform extraction was introduced to remove co-precipitated polysaccharides. Both A₂₆₀/A₂₃₀ and A₂₆₀/A₂₈₀ absorbancy ratios of isolated RNA were around 2 and the yield was about 0.4 mg g^--1 fresh weight. At least seven distinct rRNA bands were detected by denaturing gel electrophoresis. Sharp hybridization signals were obtained from Northern blots with both nuclear and plastid gene probes. Two gene fragments: nuclear-encoded cab and chloroplast encoded rbcL were successfully amplified by RT-PCR, suggesting the integrity of isolated RNA. The total RNA isolated by this protocol is of sufficient quality for subsequent molecular applications.     

Voltage-Dependent Behavior of Delayed-Firing Neurons in the Rat <Emphasis Type="Italic">Substantia Gelatinosa</Emphasis>

Upon application of a long-lasting rectangular stimulus, neurons of the substantia gelatinosa (SG) display three main types of intrinsic firing behavior, tonic, adapting, and delayed onset. The electrical landmark of delayed-firing neurons (DFNs), i.e., a significant delay before initiation of action potentials (APs), is believed to result from activation of subthreshold A-type K⁺ current (K_A). We checked out this hypothesis by comparing the voltage dependence of the firing delay with steady-state inactivation of K_A in spinal cord slices of 3- to 5-week-old rats. The delay strongly decreased with membrane depolarization and disappeared at ~ –60 mV; herewith the discharge pattern was transformed to either a tonic or an adapting one. This correlated well with inactivation of K_A recorded in a whole-cell mode in low-Cl^– intracellular solution; inactivation was nearly complete at –60 mV (voltage of half-maximum inactivation, V _1/2 ~ –74.5 mV). Unexpectedly, it was found that filling the cells with high-Cl^– solution, to minimize the liquid junction potential, produced at least a 10 mV-difference between voltage dependences of the firing delay and K_A inactivation; the latter shifted toward negativity (V _1/2 ~ –88.3 mV). The results suggest that the K_A and its inactivation properties determine the appearance and voltage dependence of the firing delay in SG neurons; the apparent influence of intracellular Cl^– on inactivation properties needs further investigation.     

A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites

A protocol is described for rapid RNA isolation from various plant species and tissues rich in polyphenolics and polysaccharides. The method is based on the Nucleon PhytoPure^™ system without the use of phenol. The procedure can be completed within 1 h and many samples can be processed at the same time. The yield ranged from 240 μg up to 3 mg per gram of tissue with an average purity measured as A_260/280 of 1.85. The RNA was of sufficient quality for use in RT-PCR reactions. Quantitation of single-stranded cDNA was carried out with the RiboGreen^™ reagent and of PCR products with the PicoGreen^™ reagent.     

Single-step chromatography for simultaneous purification of C-phycocyanin and allophycocyanin with high purity and recovery from <Emphasis Type="Italic">Spirulina</Emphasis> (<Emphasis Type="Italic">Arthrospira</Emphasis>) <Emphasis Type="Italic">platensis</Emphasis>

The cyanobacterium Spirulina (Arthrospira) platensis is a good source of phycobiliprotein purification. C-phycocyanin (C-PC) is the major phycobiliprotein, while allophycocyanin (APC) is less abundant in S. platensis. Previously reported methods for C-PC purification are only able to offer either high purity or high efficiency. This paper describes one-step anion exchange chromatography method with continuous pH gradient elution for simultaneous purification of C-PC and APC with high purity and high recovery. Crude C-PC and APC were extracted and concentrated by ammonium sulfate fractionation at saturation of 25% and 60%, then purified on a DEAE-Sepharose Fast Flow chromatography column with continuous pH gradient elution from pH 5.0 to 3.6. After this single-step chromatography, C-PC and APC with high purity and recovery were simultaneously obtained. The purity ratios of C-PC and APC reached 5.59 (A₆₂₀/A₂₈₀) and 5.19 (A₆₅₀/A₂₈₀), respectively. Their purity was further demonstrated by electrophoresis and fluorescence emission spectroscopy. Moreover, the total recovery yield of pure C-PC and APC were 67.04% and 80.0%, representing 111.83 and 29.28 mg·g⁻¹ lyophilized weight, respectively. The obtained C-PC and APC remained stable over a pH range of 4–9. This purification method for high purity and recovery of C-PC and APC proved to be fairly efficient compared with previously reported methods.     

Co-isolation of high-quality DNA and RNA from coenocytic green algae

A protocol is presented for the simultaneous isolation of DNA and RNA from giant-celled green algae. The overall quality of the DNA was examined by the A²⁶⁰/A²⁸⁰ ratio, agarose gel electrophoresis, and restriction enzyme analysis. Denaturing gel electrophoresis and cDNA cloning were used to investigate the quality of the RNA. These assays indicated that both the DNA and RNA isolated by this procedure are of high quality, suitable for further molecular analyses. Since many of these algae are slow growing and therefore only a few grams may be available, the isolation of DNA and RNA from the same plant material has obvious advantages.Abbreviations: Etbr, ethidium bromide.     

A simple procedure for the isolation of high quality RNA from ripening banana fruit

Isolation of high quality RNA from ripening banana fruit tissue is difficult due to high levels of polysaccharides and other substances that interfere when using conventional procedures for RNA isolation. These substances not only decrease the yield but the quality of RNA is almost unusable. We describe here a simple RNA procedure that effectively removes these contaminating substances without affecting the yield. Following this procedure, we routinely obtained 80–150 μg of total RNA per g fresh tissue. The RNA is of good quality and suitable for northern analysis, RT-PCR and cDNA library construction. NBRI publication No. 488(NS).     

Rapid aggregation and assembly in aqueous solution of A<Emphasis Type="Italic">β</Emphasis> (25–35) peptide

The highly toxic Aβ(25–35) is a peculiar peptide that differs from all the other commonly studied β-amyloid peptides because of its extremely rapid aggregation properties and enhanced neurotoxicity. We investigated Aβ(25–35) aggregation in H₂O at pH 3.0 and at pH 7.4 by means of in-solution analyses. Adopting UV spectroscopy, Congo red spectrophotometry and thioflavin T fluorimetry, we were able to quantify, in water, the very fast assembling time necessary for Aβ(25–35) to form stable insoluble aggregates and their ability to seed or not seed fibril growth. Our quantitative results, which confirm a very rapid assembly leading to stable insoluble aggregates of Aβ(25–35) only when incubated at pH 7.4, might be helpful for designing novel aggregation inhibitors and to shed light on the in vivo environment in which fibril formation takes place.     

Isolation of C-phycocyanin from <Emphasis Type="Italic">Synechococcus</Emphasis> sp., (<Emphasis Type="Italic">Anacystis nidulans</Emphasis> BD1)

We report a procedure for obtaining fairly pure phycocyanin from a local isolate of the cyanobacterium Synechococcus sp (Anacystis nidulans BD1). Cells were incubated with 1 mg∙mL⁻¹ of lysozyme at 37°C for 16 h with shaking. The cell-free extract was treated with activated charcoal and chitosan. The purity (A _620/280) of phycocyanin obtained after lysozyme treatment was up to 2.18, which could be improved to 4.72 after incubation with activated charcoal and chitosan. The yield of phycocyanin was 80–100 mg∙g⁻¹ dry weight of cells. The method reported here is a single-step and efficient procedure and has the potential to be adopted for large-scale production of phycocyanin.     

Influence of soil porosity on water use in<Emphasis Type="Italic"> Pinus taeda</Emphasis>

We analyzed the hydraulic constraints imposed on water uptake from soils of different porosities in loblolly pine (Pinus taeda L.) by comparing genetically related and even-aged plantations growing in loam versus sand soil. Water use was evaluated relative to the maximum transpiration rate (E _crit) allowed by the soil-leaf continuum. We expected that trees on both soils would approach E _crit during drought. Trees in sand, however, should face greater drought limitation because of steeply declining hydraulic conductivity in sand at high soil water potential (Ψ _S). Transport considerations suggest that trees in sand should have higher root to leaf area ratios (A _R:A _L), less negative leaf xylem pressure (Ψ _L), and be more vulnerable to xylem cavitation than trees in loam. The A _R:A _L was greater in sand versus loam (9.8 vs 1.7, respectively). This adjustment maintained about 86% of the water extraction potential for both soils. Trees in sand were more deeply rooted (>1.9 m) than in loam (95% of roots <0.2 m), allowing them to shift water uptake to deeper layers during drought and avoid hydraulic failure. Midday Ψ _L was constant for days of high evaporative demand, but was less negative in sand (–1.6 MPa) versus loam (–2.1 MPa). Xylem was more vulnerable to cavitation in sand versus loam trees. Roots in both soils were more vulnerable than stems, and experienced the greatest predicted loss of conductivity during drought. Trees on both soils approached E _crit during drought, but at much higher Ψ _S in sand (<–0.4 MPa) than in loam (<–1.0 MPa). Results suggest considerable phenotypic plasticity in water use traits for P. taeda which are adaptive to differences in soil porosity. Received: 28 December 1999 / Accepted: 31 March 2000     

An improved and rapid protocol for the isolation of poly(A)+-RNA from small samples of scots pine seedlings

A simple rapid method for the isolation of poly(A)⁺-RNA from pine seedlings (Pinus sylvestris) was developed. The entire procedure can be carried out in Eppendorf tubes, thus greatly minimizing the time, starting material (as little as 3–5 μg of total RNA) and the amount of chemicals required. The poly(A)⁺-RNA recovered is a suitable substrate for RT-PCR.