Conditions of Phenol Extraction of RNA From Rat Liver Subcellular Cytoplasmic Fractions II. Effect of a Glycine NaOH Buffer on the Separation of Polysomal RNA

A suspension of rat liver ribosomes in glycine NaOH buffer, pH 10. 5, with phenol was prepared after manually shaking for 30 sec with rapid strokes. The RNA was clarified immediately after by centrifugation. This extraction procedure was at 2°C and gave a high yield in RNA. Previous investigators omitted the addition of glycine NaOH buffer, thus preparing their suspension in approximately 10 min at 37°C⁴. Protein determinations and the integrity of RNA on gradients were used to determine the purity and stability of the RNA. A comparison was made between preparations of ribosomal RNA and microsomal RNA. The results showed that the former were much more stable.     

Hydrolysis with lead perchlorate: A new method used to estimate RNA in sugarcane tissues

The precipitation and hydrolysis of RNA by lead perchlorate has been studied and the results have been applied to estimate RNA in three widely different tissues from Saccharum species (sugarcane). This new method makes it possible to estimate RNA in highly lignified tissue for which existing methods using cold perchloric acid or warm alkali are unsuitable. As far as comparisons are possible, lead perchlorate gives the same results as extraction with acid and alkali, except that values are slightly lower in rapidly dividing tissue. Acid-soluble materials are removed by a single extraction with 0.01 m Pb(ClO₄)₂ at pH 2, where RNA and DNA are quantitatively precipitated but not hydrolyzed. Specific hydrolysis of RNA is then carried out at neutral pH with a solution containing 3 m Pb(ClO₄)₂ and 2.5 n NaOH, and the products are extracted at pH 2. DNA and most interfering materials remain insoluble. RNA in the extract is measured by uv absorption versus a combined tissue/reagent blank. The entire procedure can be carried out at room temperature. DNA in the tissue can be estimated as usual (1–3).     

Pretreatment of cellulosic wastes to increase enzyme reactivity

The enzymatic hydrolysis of cellulose to glucose is generally a slow reaction. Different pretreatments, such as ball milling to a ?200 mesh or swelling in 1–2% NaOH are reported to increase the reactivity considerably. In this work a fiber fraction from cattle manure was treated in an autoclave for 5–30 min at temperatures ranging from 130–200°C. The reactivity of the cellulose, measured by incubating samples with a commercial cellulase preparation for one hour at 50°C and pH 4.8, was increased by a factor of 4–6 compared to NaOH treatment and 10–12 compared to untreated fiber. The increased reaction rate is probably mostly due to an increase in cellulose availability to enzymatic attack, as structural hemicellulose is hydrolyzed and removed during the treatment. Sugars, produced by hemicellulosis, hydrolysis, will react further to give caramelization products. These side reactions were shown to be suppressed by short treatment times. The treated fiber could support growth of a mixed culture of Trichoderma viride and Candida utilis only after washing, indicating the formation of water soluble inhibitory products during treatment. The treatment with high-temperature steam can probably be used also with other cellulosic materials to increase reactivity. This may be an attractive way to prepare low-valued wastes such as manure fibers, straw, stalks, or corn cobs for fermentation processes to increase the protein content or for use directly as ruminant animal feed.     

The estimation of the nucleic acids of tissue sections and its use as a unit of comparison for quantitative histochemistry

Summary There are many advantages in using the nucleic acid content of tissue sections as the unit of comparison for quantitative histochemistry. A quick, simple, reliable method for the estimation of DNA and RNA in sections of rat liver is described. The method depends on the differential hydrolysis in IN HCl at 60° C; the RNA is removed after 4 min hydrolysis and the DNA by a further 30 min hydrolysis. The optimum extinction of the hydrolysates is measured in an ultraviolet spectrophotometer. The results show a reproducibility, between serial sections, of better than ±5 %.     

A simple method to recover intact high molecular weight RNA and DNA after electrophoretic separation in low gelling temperature agarose gels.

Defined RNA fractions can be recovered from low gelling temperature agarose gels by a combination of agarose melting at 65°C and phenol extraction. By this approach RNA molecules up to a size of 37 kb can be eluted undegraded with a recovery of 60–90%. The method is applicable also to DNA and the eluted DNA can be correctly cleaved with restriction endonucleases as shown for λDNA using EcoRI.     

Studies on the degradation of HeLa non-histone proteins

The hydrolysis of HeLa non-histone nuclear proteins over 24 h has been monitored in dilute alkali at 4, 15 and 25°C using the standard ninhydrin estimation, dansylation and various electrophoresis techniques. Under conditions (up to 0.2 N NaOH, 4°C) that do not release a significant quantity of ninhydrin-positive material or new N-terminal end group considerable breakdown was observed by two-dimensional electrophoresis analysis. The number of stained spots decreased from approx. 140 to 25–30. No internal protease activity could be found.Labelling studies (¹⁴C-labelled amino acids) showed that much of the hydrolysed material was extracted from the gel during normal staining and destaining procedures. Peptides could be extracted from alkali-hydrolysed non-histone protein with acid/ethanol and could be further separated by thin-layer chromatography on silica gel G. Short-term labelling of HeLa cells (¹⁴C-labelled amino acids for up to 60 min) revealed that these peptides probably have a high rate of turnover. [¹⁴C] Glucosamine studies also indicated the presence of considerable carbohydrate material in the low molecular weight products of this alkaline hydrolysis. Various standard proteins and histones were unaffected by hydrolysis in up to 0.2 N NaOH (4°C, 24 h) as judged by gel electrophoresis.Seven different phosphate-splitting enzymes and an esterase had no effect on the non-histone protein electrophoresis patterns but a preparation of phospholipase C which had no protease activity towards eight standard proteins did produce considerable breakdown in HeLa non-histone proteins similar to that produced by 0.2 N NaOH at 4°C.     

Optimization of the yield and quality of agar from Gracilariopsis lemaneiformis (Gracilariales) from the Gulf of California using an alkaline treatment

The effect of several alkali treatments on the yield, gel strength, rheology, and chemical characteristics (quality) of the agar obtained from Gracilariopsis lemaneiformis from the Gulf of California was analyzed using different alkali concentrations, temperatures and treatment times. In the first stage of the experiment, all treatments lasted 60 min and the NaOH concentrations (2.5, 3.0, 4.0, 5.0, 6.0%) and temperature (80, 90, 100°C) varied. At constant time, temperature played the predominant role, promoting an increase in agar gel strength. Based on the best treatment conditions found (4% and 5% NaOH, and 90°C and 100°C temperature), in the second stage different treatment times (15, 30, 60, 90, 120 min) were used. Since agar yields were not significantly different among temperatures and times, the optimal conditions to obtain best quality agar were those providing the highest gel strength. Treatment time played an important role in increasing gel strength. Maximum gel strength (Nikan, 954 g cm⁻²) was obtained with 5% NaOH at 100°C after 90 min of treatment, though these conditions resulted in an agar yield reduction of 25.5% relative to native agar. This treatment proved to efficiently yield G. lemaneiformis agar that will meet the commercial quality requirements regarding gel strength, 3,6 anhydrogalactose and sulfate content, as well as rheology and hysteresis. Enrique Hernández-Garibay holds a CONACyT scholarship.     

Autohydrolysis extraction process as a pretreatment of lignocelluloses for their enzymatic hydrolysis

Autohydrolysis was studied as a pretreatment to enhance sugar yields from enzymatic hydrolysis of wheat and rape straw, beech, birch and poplar sawdust. Reaction temperatures were 185°C to 212°C and the reaction time 20 min. The pretreated slurries were hydrolyzed with “Novo” cellulase and Fusarium sp. 27 cellulase at 45°C and pH 4.8 for 24 h with addition of Fusarium sp. 27 cellbound cellobiase. From 85% to 90% sugar content of substrates were converted to reducing sugars after 24 h enzymatic hydrolysis, with exception of poplar wood. 10.8 g biomass was obtained after cultivation of Fusarium sp. 27 with water solution hemicellulose fraction from 100 g beech sawdust autohydrolyzed at 200°C during 20 min.     

Fractionation of Chromatin by thermal precipitation in phosphate buffer.

The stability of sonicated rat liver chromatin in sodium phosphate buffer, pH 6.8 was studied as a function of buffer concentration (0.012 to 0.16 m) and temperature (20 to 98 °C). It was found that as the temperature was increased a stepwise precipitation of chromatin took place which was revealed by the presence of three plateaux (20 to 50 °C, 70 to 75 °C and above 90 °C) and two transitional zones (55 to 70 °C and 75 to 90 °C) on the A₃₂₀ curves and on the percentage precipitated nucleoprotein versus temperature curves as well.This permitted the fractionation of chromatin in 0.08 m-phosphate buffer into three fractions by a stepwise heating at 50 °C (50 °C-pellet) and 98 °C (50–98 °C-pellet and post 98 °C-supernatant). DNA isolated from these fractions was characterized in respect to sedimentation velocity and hybridization with heterogeneous nuclear RNA. The hybridization studies showed a different ability of these three DNA preparations in binding nuclear heterogeneous RNA: 16%, 8% and 30% for DNA isolated from 50 °C-pellet, 50–98 °C-pellet and post 98 °C-supernatant, respectively. The results are discussed in terms of chromatin structure and function.     

Enriched arabinoxylan in corn fiber for value-added products

A two-step process is evaluated to separate the hexose component in wet milling corn fibers from the pentose component for production of value-added products. Corn fibers were first pretreated with hot water at 121°C for 1 h followed by glucoamylase hydrolysis to remove starch. The remaining solid was then treated with hot water at 140–170°C followed by an enzymatic hydrolysis to further separate the hexose and pentose components. After the second pretreatment, the enzymatic digestibility of cellulose was much better than that of arabinoxylan. As a result, up to 90% arabinoxylan in corn fibers was retained in a solid form after the enzyme hydrolysis, while most of the hexose components were removed.     

Improvement of radio frequency (RF) heating-assisted alkaline pretreatment on four categories of lignocellulosic biomass

Pretreatment plays an important role in making the cellulose accessible for enzyme hydrolysis and subsequent conversion because it destroys more or less resistance and recalcitrance of biomass. Radio frequency (RF)-assisted dielectric heating was utilized in the alkaline pretreatment on agricultural residues (corn stover), herbaceous crops (switchgrass), hardwood (sweetgum) and softwood (loblolly pine). Pretreatment was performed at 90 °C with either RF or traditional water bath (WB) heating for 1 h after overnight soaking in NaOH solution (0.2 g NaOH/g Biomass). Pretreated materials were characterized by chemical compositional analysis, enzyme hydrolysis, scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The glucan yields of RF-heated four categories of hydrolysates were 89.6, 72.6, 21.7, and 9.9 %. Interestingly, RF heating raised glucan yield on switchgrass and sweetgum but not on corn stover or loblolly pine. The SEM images and FTIR spectra agreed with results of composition analysis and hydrolysis. GC–MS detected some compounds only from RF-heated switchgrass. These compounds were found by other researchers only in high-temperature (150–600 °C) and high-pressure pyrolysis processes.     

Chromosomal DNA denaturation and reassociation in situ.

The degree of chromosomal DNA (cDNA) denaturation and renaturation on polytene chromosomes has been measured by UV microspectrophotometry. Also DNA losses occurring upon denaturation have been quantified by Feulgen, gallocyanin-chromalum and UV. It has been observed that denaturation in alkali (0.07 N NaOH at room temperature) and formamide (90% formamide; 0.1 SSC, pH 7.2) at 65 °C removes about 30% of the DNA. Low DNA loss occurs upon denaturation in HCl (0.24 M) at room temperature and 60% formamide: 2 × 10^?4 M EDTA (pH 8) at 55 °C. The presence of 4% formaldehyde in the denaturation buffer prevents DNA loss. After denaturation of chromosomes in 0.1 × SSC containing 4% formaldehyde at 100 °C for 30 sec, an hyperchromicity of 39 °C is observed. The denaturation efficiency varies with the denaturation treatment. The percentage reassociation was measured from the difference in the UV absorption of renatured chromosomes and that of denatured chromosomes from the same set. It seems that in our conditions DNA:DNA reassociation does not occur. The efficiency of hybridization is proportional to the denaturation extent of the DNA. However, the entire fraction of DNA which has been denatured is not available for hybridization.     

The Impact of Temperature Stress on DNA and RNA Synthesis in Potentially Toxic Dinoflagellates <Emphasis Type="Italic">Prorocentrum minimum</Emphasis>

Biomarkers of temperature stress were studied as major characteristics crucial for the understanding complex processes that underlie the response of marine planktonic microorganisms to environmental factors and their sublethal effects. Using the potentially toxic dinoflagellates Prorocentrum minimum as a model object, the impact of temperature stress on viability, cell cycle, RNA synthesis and DNA replication in these protists was evaluated. It was shown by flow cytometry that stress evoked by a temperature increase from 25°C (control) to 37 or 42°C during 15 to 60 min did not cause any considerable alterations in the cell cycle, while cell death rate increased from ≤ 1% (control) to 2–12% at 37°C and 4–22% at 42°C. Along with a relatively low cell death rate, following a temperature increase to 37 and/or 42°C, P. minimum displayed the ability to boost the synthesis of DNA (1.7–1.9 and 1.2–1.6 times, respectively) and especially RNA (2.5–3.1 and 1.7–2.8 times, respectively) during the first 15–30 min after stress. At certain stages of the life cycle, this effect can be critical for maintaining the viability and normal development of the P. minimum population. The obtained results demonstrate that a significantly elevated synthesis of nucleic acids can serve as an indicator (biomarker) of sublethal environmental stress.     

Comparison of SHF and SSF processes for the bioconversion of steam-exploded wheat straw

Two processes for ethanol production from wheat straw have been evaluated — separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF). The study compares the ethanol yield for biomass subjected to varying steam explosion pretreatment conditions: temperature and time of pretreatment was 200°C or 217°C and at 3 or 10 min. A rinsing procedure with water and NaOH solutions was employed for removing lignin residues and the products of hemicellulose degradation from the biomass, resulting in a final structure that facilitated enzymatic hydrolysis. Biomass loading in the bioreactor ranged from 25 to 100 g l⁻¹ (dry weight). The enzyme-to-biomass mass ratio was 0.06. Ethanol yields close to 81% of theoretical were achieved in the two-step process (SHF) at hydrolysis and fermentation temperatures of 45°C and 37°C, respectively. The broth required addition of nutrients. Sterilisation of the biomass hydrolysate in SHF and of reaction medium in SSF can be avoided as can the use of different buffers in the two stages. The optimum temperature for the single-step process (SSF) was found to be 37°C and ethanol yields close to 68% of theoretical were achieved. The SSF process required a much shorter overall process time (≈30 h) than the SHF process (96 h) and resulted in a large increase in ethanol productivity (0.837 g l⁻¹ h⁻¹ for SSF compared to 0.313 g l⁻¹ h⁻¹ for SHF). Journal of Industrial Microbiology & Biotechnology (2000) 25, 184–192. Received 02 December 1999/ Accepted in revised form 20 July 2000     

Catecholamine content of chromaffin granule ‘ghosts’ isolated from bovine adrenal glands

Studies on the mechanism of catecholamine transport into chromaffin granules is complicated by the release of endogenous catecholamines. To overcome this problem chromaffin granule ghosts have been prepared by many investigators by osmotic lysis of the granules which results in a loss of over 90% of the endogenous catecholamine. However, in the studies reported here, the resulting ghosts still contained 36 ± 3.9 nmol epinephrine/mg of protein if they were lysed by passage through a Sephadex G-50 column preequilibrated with hypoosmtic media. This residual catecholamine was foun the slowly diffuse out of the ghosts in a temperature-dependent process at a rate sufficient to interfere with kinetic analysis of catecholamine transport. Attempts to remove the endogenous catecholamine from the ghosts indicated that most of it could not be removed by further osmotic shock or freeze-thaw treatments, but that over 85% of it was released from the granules by incubating them at 30°C for 90 min or by dialysis with a 35 and 86% loss of rate of catecholamine transport into the ghosts, respectively. If the endogenous catecholamine was removed from chromaffin granule ghosts by preincubating them for 90 min at 30°C, these resulting ghosts transported catecholamine with a linear Lineweaver-Burk plot indicating a K_m of 12±2 μM. In addition, the resulting ghosts did not leak catecholamines over a 10 min period at 30°C, and the transport of catecholamines was blocked by reserpine and enhanced with increasing pH from 6.0 to 8.5.     

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.     

Analysis of mammalian DNA for the presence of carcinogen-induced phosphotriesters: Application of the technique of difference sedimentation

The concentration of alkyl phosphotriesters induced in mammalian DNA by many carcinogens can be determined by measuring the mean sedimentation coefficient of the single strands before and after hydrolysis of the triesters in 0.5 m NaOH at 37°C for 1 h. Experiments show that the difference between hydrolyzed and unhydrolyzed DNA containing methyl phosphotriesters can be quantitatively determined using the technique of difference sedimentation. Theoretical analysis indicates that there is no requirement for the accurate matching of the meniscus positions but that differences in DNA concentration between the two solutions have to be avoided. Practical procedures for the analysis and the calculation of the results are discussed.     

Preparation of corn gluten hydrolysate with angiotensin I converting enzyme inhibitory activity and its solubility and moisture sorption

This study attempted to prepare a hydrolysate of corn gluten containing powerful ACE inhibitory activity and higher solubility, which could be used as a physiologically functional food material. The digestion of starch at 80 °C resulted in more removal of the starch from the corn gluten than that at 60 °C. More than 95% reducing sugars as enzymic digests of starch was removed by washing three-times. As for the thermal treatment effect on the increase of degree of hydrolysis (DH), degree of increase of protein content (slope) was 6.30 mg/ml min at 100 °C, 4.40 mg/ml min at 80 °C and 2.29 mg/ml min without heat treatment. After 45 min of heat treatment the increased ratio of protein content was greater than those by other heat treatments. After the pretreatment of corn gluten, hydrolysis with Flavourzyme, among six commercial proteases, resulted in the production of the hydrolysate with the highest ACE inhibitory activity, and with Protamax, the second highest ACE inhibitory activity was obtained. Flavourzyme hydrolysate of corn gluten at the 4% level was easily and completely soluble between pH 2 and 9. Water sorption of the hydrolysate slowly increased up to 0.8 of water activity and greatly increased at higher than 0.8 of water activity.     

Hepatitis B virus contains protein attached to the 5′ terminus of its complete DNA strand

Hepatitis B virus DNA contains a tightly bound protein which was not removed by heating to 60°C with 2% SDS, 2% mercaptoethanol. The protein was indirectly demonstrated by the extraction of the DNA-protein complex with phenol before but not after its digestion with proteinase K. The DNA-protein complex had a lower buoyant density than protease-treated or free DNA; it was bound to glass fiber filters; it migrated at a slower rate in gel electrophoresis; and it could be radiolabeled by oxidative iodination. The binding site of the protein was mapped by extraction of restriction endonuclease digests with phenol and analysis of the digests for missing DNA fragments. The protein was localized to a site near the 5′ end of the complete viral DNA strand. It remained attached to this strand after heating with SDS to 90°C or treatment with 0.1 N NaOH, suggesting a covalent linkage. The 5′ end of neither viral DNA strand could be phosphorylated in a reaction with polynucleotide kinase, consistent with attachment of protein to the 5′ ends. The incomplete DNA strand, however, which is the strand elongated by the virion DNA polymerase reaction, did not contain a detectable amount of polypeptide as did the complete strand. The reasons for the apparent block of the 5′ end of the incomplete DNA strand is thus not known. The protein bound covalently to HBV DNA could be involved in the replication of the complete viral DNA strand and/or endonucleolytic generation of linear unit-length DNA pieces from replicative intermediates, although its function and origin are not yet known.     

Reduction of RNA and DNA in Methylococcus capsulatus by endogenous nucleases

 A method for reducing RNA and DNA in the bacterium Methylococcus capsulatus (Bath) has been developed. Endogenous RNase and DNase were activated by a 10 s heat shock at 90°C. Cells were then incubated at 60°C for 20 min to allow degradation of the nucleic acids. The optimum pH for the process was 7.0. The protein loss was less than 10% and occurred during the initial heat shock. No protein loss was found during incubation. The total dry-weight loss in connection with an 80% reduction of the nucleic acid content was 20%–25%, giving a final product with a raw protein content of approximately 75%. Reduction of both RNA and DNA was inhibited by CuSO₄ and ZnSO₄. DNA reduction was stimulated by other minerals. Optimal stimulation was found at 1 mM FeSO₄. Reduction of RNA was not increased by any of the minerals tested. Received: 29 June 1995/Received last revision: 2 October 1995/Accepted: 16 October 1995