Simple methods for the orientation of DNA molecules in films suitable for optical studies

Three methods are described for the preparation of oriented samples of DNA molecules in films. The methods involve simple equipment and produce films of good optical qualities, suitable for the determinations of dichroic spectra, for example. To illustrate the quality of the films the dichroism of DNA and of acridine orange–DNA complex are described. Evidence is given that native DNA structure is stabilized by poly-(vinyl alcohol).     

Preparation of films and fibers containing proteolytic enzymes

Immobilization of the proteolytic enzymes trypsin and terrylitin in fluorplastic-42 films and fibers as well as in water-soluble polymeric (polyvinyl alcohol and carboxymethyl cellulose) films was being studied during preparation of the films. The properties of the proteolytic enzymes immobilized in the polymers are dependent on the conditions of preparation of fibers and films.     

Hormonal control of proteinase activity in squash cotyledons

A crude proteolytic enzyme preparation which hydrolyzes casein was isolated from the cotyledons of squash seedlings. The presence of ethylene diamine tetraacetate or cysteine did not appreciably affect the activity of the preparation. During the course of germination, the level of proteolytic activity increased in the cotyledons of intact embryos through the third day and then decreased. The presence of the embryonic axis during the first 32 hours of germination was a prerequisite for the development of maximum proteolytic activity.     

Proteolytic Enzyme Preparation from Pseudomonas fragi: Its Action on Pig Muscle

An extracellular preparation from Pseudomonas fragi with proteolytic enzyme activity was isolated, and its action on meat proteins and meat protein ultrastructure was studied. First, a suitable growth medium for proteolytic enzyme production was determined, and a method for partial purification of the proteolytically active fraction was developed. The enzyme preparation displayed optimal proteolytic activity at neutral pH and 35 C. Proteolytic activity was irreversibly lost by mild heat treatment. The enzyme preparation was tested for its ability to hydrolyze isolated pig muscle proteins. Myofibrillar protein was rapidly degraded, G-actin and myosin were broken down at a slower rate, and the sarcoplasmic proteins were least susceptible to hydrolysis. Electron micrographs of pork muscle showed that the proteolytic enzyme preparation caused a complete loss of dense material from the Z line. Similarities are discussed between the action of P. fragi extracellular proteolytic enzyme(s) on meat and normal bacterial spoilage of meat.     

A new <Emphasis Type="Italic">Bacillus licheniformis</Emphasis> mutant strain producing serine protease efficient for hydrolysis of soy meal proteins

Induced mutagenesis with γ-irradiation of the industrial strain Bacillus licheniformis-60 VKM B-2366 D was used to obtain a new highly active producer of an extracellular serine protease, Bacillus licheniformis-145. Samples of dry concentrated preparations of serine protease produced by the original and mutant strains were obtained, and identity of their protein composition was established. Alkaline serine protease subtilisin DY was the main component of the preparations. The biochemical and physicochemical properties of the Protolicheterm-145 enzyme preparation obtained from the mutant strain were studied. It exhibited proteolytic activity (1.5 times higher than the preparation from the initial strain) within broad ranges of pH (5–11) and temperature (30–70°C). Efficient hydrolysis of extruded soybean meal protein at high concentrations (20 to 50%) in the reaction mixture was the main advantage of the Protolicheterm-145 preparation. Compared to the preparation obtained using the initial strain, the new preparation with increased proteolytic activity provided for more complete hydrolysis of the main non-nutritious anti-nutritional soy proteins (glycinin and β-conglycinin) with the yield of soluble protein increased by 19–28%, which decreased the cost of bioconversion of the proteinaceous material and indicated promise of the new preparation in resource-saving technologies for processing soybean meals and cakes.     

Cytoplasmic origin of the so-called nuclear neutral histone protease.

1. We have investigated the origin of proteolytic activity which causes degradation of histones in chromatin isolated from Xenopus liver and the rat liver at neutral pH. Polyacrylamide disc gel electrophoresis was used for detection of proteolytic products of histones. 2. No proteolytic degradation of histones occurs in chromatin isolated from Xenopus erythrocytes and rat liver according to our procedure even after prolonged incubation at pH 8.0 and pH 5.0. However with chromatin isolated from Xenopus liver a high level of histone degradation is observed under similar conditions. 3. Mixing isolated nuclei from Xenopus erythrocytes with a crude cytoplasmic fraction from Xenopus liver causes histone proteolysis in isolated chromatin at pH 8.0. In similar experiments with corresponding fractions from rat liver histone proteolysis can be introduced only after repeated freezing and thawing of the cytoplasmic fraction. 4. A purified lysosomal preparation from rat liver causes a similar type of histone degradation upon incubation with chromatin from Xenopus erythrocytes and rat liver. 5. The neutral proteolytic activity that can be introduced in isolated chromatin by a crude cytoplasmic fraction and by a purified lysosomal erythrocytes and rat liver. 5. The neutral proteolytic activity that can be introduced in isolated chromatin by a crude cytoplasmic fraction and by a purified lysosomal fraction from rat liver is inhibited by sodium bisulphite. 6. We conclude that the neutral proteolytic activity which causes degradation of histones in isolated chromatin is due to a contamination with neutral protease(s) originating from cytoplasmic organelles.     

Role of the RRM domain in the activity, structure and stability of poly(A)-specific ribonuclease

Poly(A) specific ribonuclease (PARN), which contains a catalytic domain and two RNA-binding domains (R3H and RRM), acts as a key enzyme in eukaryotic organisms to regulate the stability of mRNA by degrading the 3' poly-(A) tail. In this research, the activity, structure and stability were compared between the full-length 74kDa PARN, the proteolytic 54kDa fragment with half of the RRM, and a truncated 46kDa form completely missing the RRM. The results indicated that the 46kDa one had the lowest activity and substrate binding affinity, the most hydrophobic exposure in the native state and the least stability upon denaturation. The dissimilarity in the activity, structure and stability of the three PARNs revealed that the entire RRM domain not only contributed to the substrate binding and efficient catalysis of PARN, but also stabilized the overall structures of the protein. Spectroscopic experiments suggested that the RRM domain might be structurally adjacent to the R3H domain, and thus provide a basis for the cooperative binding of poly(A) by the two RNA-binding domains as well as the catalytic domain.     

Input of protein to lake water microcosms affects expression of proteolytic enzymes and the dynamics of Pseudomonas spp.

The objective of this study was to determine how an input of protein to lake water affects expression of a proteolytic potential and influences the abundance and composition of a specific group of bacteria. Pseudomonas spp. were chosen as a target group that can be recovered on selective growth media and contain both proteolytic and nonproteolytic strains. Amendment with 2 mg of casein per liter increased total proteinase activity (hydrolysis of [(3)H]casein) by 74%, leucine-aminopeptidase activity (hydrolysis of leucine-methyl-coumarinylamide) by 133%, bacterial abundance by 44%, and phytoplankton biomass (chlorophyll a) by 39%. The casein amendment also increased the abundance of culturable Pseudomonas spp. by fivefold relative to control microcosms but did not select for proteolytic isolates. Soluble proteins immunochemically related to the Pseudomonas fluorescens alkaline proteinase, AprX, were detected in amended microcosms but not in the controls. The expression of this class of proteinase was confirmed exclusively for proteolytic Pseudomonas isolates from the microcosms. The population structure of Pseudomonas isolates was determined from genomic fingerprints generated by universally primed PCR, and the analysis indicated that casein amendment led to only minor shifts in population structure. The appearance of AprX-like proteinases in the lake water might thus reflect a general induction of enzyme expression rather than pronounced shifts in the Pseudomonas population structure. The limited effect of casein amendment on Pseudomonas population structure might be due to the availability of casein hydrolysates to bacteria independent of their proteinase expression. In the lake water, 44% of the total proteinase activity was recovered in 0.22-microm-pore-size filtrates and thus without a direct association with the bacteria providing the extracellular enzyme activity. Since all Pseudomonas isolates expressed leucine-aminopeptidase in pure culture, proteolytic as well as nonproteolytic pseudomonads were likely members of the bacterial consortium that metabolized protein in the lake water.     

Investigation of the fibroblast chalone (author's transl)]

By ultrafiltration of a cytoplasm preparation from diploid human fibroblasts (Flow 2000) we obtained a fraction which inhibited the proliferation of the same cells. We succeeded in demonstrating fibroblast chalone, because the activity was endogenous, reversible and affected murine fibroblasts, but not human cervical carcinoma cells (HeLa S3) or neuronal tumor cells of rats (B104). The chalone activity was found in the range of molecular weights between 10 000 and 100 000. The active part was of peptide nature, for proteolytic treatment destroyed the chalone activity.     

Effect of terrilitin on the proteolytic activity of the blood and formation of an immunostimulating factor by spleen cells

Terrilitin is studied for its effect on proteolytic activity of blood and formation of immunostimulating factors by spleen cells. The preparation is shown to induce isolation of the immunostimulating factor (molecular mass 10-15 kDalton) from the spleen cells. The preparation is destroyed by trypsin and RNAase and is stable to the action of lysozyme. Spleen cell factor of the animals with administered terrilitin increases general antiproteolytic activity of the blood serum and concentration of alpha 2-macroglobulins. At the same time, it decreases the general proteolytic activity and callicrein activity of blood serum for syngenic animals.     

Proteolytic degradation of ferredoxin-NADP reductase during purification from spinach

Ferredoxin-NADP reductase (FNR) was rapidly isolated from spinach leaves with special care to suppress proteolytic degradation. The molecular mass of this FNR preparation was estimated to be 35 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Limited proteolysis of 35-kDa FNR to 33-kDa FNR was effectively suppressed by high pH (at pH 9.3), concentrated salts, and low temperature. On the basis of these observations, a new isolation procedure was designed to obtain 35-kDa FNR in a preparative scale. The resulting final preparation still contained two FNR components. One appeared to correspond to the longest polypeptide so far reported for spinach FNR (Karplus et al., 1984, Biochemistry 23, 6576-6583) while the other lacked a gamma-pyroglutamyl residue from its amino terminus. Conventional preparation procedure without suppression of proteolytic action yielded an FNR preparation with a molecular mass of 33 kDa. This FNR preparation consisted of three components. They lacked 11 to 17 amino-terminal residues, while their carboxyl-terminal structure was retained intact. These results showed that proteolytic degradation of the spinach FNR molecule during purification took place exclusively at its amino-terminal moiety and further suggested that 35-kDa FNR with Karplus' structure should be the mature FNR molecule functional in the chloroplast thylakoids.     

Hymenolepis diminuta: interactions of the isolated brush border membrane with proteolytic enzymes

Proteins of the isolated brush border membrane of Hymenolepis diminuta were hydrolyzed in vitro by chymotrypsin, papain, pepsin, subtilopeptidase A (= subtilisin Carlsberg), and trypsin. Neither proteolytic nor amidase activity was demonstrable in the isolated membrane using proteinaceous (casein and hemoglobin) or chromogenic (benzoyl-arginine-p-nitroanilide and succinyl-alanyl-alanyl-propyl-phenylalanine p-nitroanilide) substrates, and the membrane preparation did not inhibit the proteolytic and amidase activities of these enzymes. Thus, the isolated tegumental membrane of H. diminuta is not inherently resistant to the action of proteolytic enzymes, and it does not inhibit proteolytic activity. In control incubations containing only buffer, the alkaline phosphatase activity of the brush border membrane decreased in a time dependent manner, but in the presence of chymotrypsin, subtilopeptidase A, and trypsin, the membrane retained greater alkaline phosphatase activity (pepsin and papain could not be tested for this effect on alkaline phosphatase activity). A similar time dependent decrease in activity was also noted for each of the proteolytic enzymes in control assays, but subtilopeptidase A and papain retained greater activity in the presence of the isolated membrane preparation when these assays were compared to controls.     

The effect of acid proteinases on the activity and stability of glucoamylase preparations

It was demonstrated that the presence of acid proteinases in the preparation isolated from Aspergillus awamori decreased the activity and stability of glucoamylase. Patterns of changes in the enzymatic activity and stability of glucoamylase at increased temperature and various pH values were studied over a long-term storage. A biospecific sorbent for removal of acid proteinases was synthesized, and glucoamylase preparations free of proteolytic activity were produced.     

Biocatalytic surface modification of knitted fabrics made of poly (ethylene terephthalate) with hydrolytic enzymes from Thermobifida fusca KW3b

Knitted fabrics made from poly(ethylene terephthalate) fibres were treated with an enzyme preparation from Thermobifida fusca KW3b showing hydrolytic activity on p-nitrophenyl butyrate. The fabrics were also treated with NaOH and the results were compared. Both enzyme- and alkaline-treated fabrics showed an increase in reactive dye uptake, vertical wicking height and water absorption capacity of the fabrics indicating an increased surface hydrophilicity. However, X-ray photoelectron (XPS) and energy-dispersive spectroscopy (EDS) did not give conclusive results on the presence of newly introduced hydrophilic groups on the surface of the fibres. Analysis of the enzyme-treated poly(ethylene terephthalate) fibres by scanning electron microscopy (SEM) and by atomic force microscopy (AFM) indicated an increase in surface roughness of the fibres, which may contribute to the observed increased hydrophilicity of the PET fabrics. However, much longer treatment times (24 h) were required to obtain these effects with the enzymes compared to the chemical treatment (1 h).     

Selective removal of heparan sulfate chains from proteoheparan sulfate with a commercial preparation of heparitinase

Procedures employing the commercial preparation of heparitinase were developed for isolating a protein-enriched core molecule from proteoheparan sulfate by selective removal of the heparan sulfate chains. Treatment of proteoheparan sulfate with the enzyme preparation caused seriously extensive degradation owing to the presence of proteolytic activity in the enzyme preparation. This effect could be avoided by using a series of protease inhibitors which prevented proteolytic degradation with less significant effect on the heparitinase activity. Application of the procedures to a purified preparation from the Engelbreth-Holm-Swarm tumor yielded a single protein-enriched core fraction with a molecular weight of approximately 450,000, as ascertained by sodium dodceyl sulfate-gel electrophoresis.     

Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls

Synovial fluid (SF) may contain cleavage products of proteolytic activities. Our aim was to characterize the degradome through analysis of proteolytic activity and differential abundance of these components in a peptidomic analysis of SF in knee osteoarthritis (OA) patients versus controls (n = 23). SF samples from end-stage knee osteoarthritis patients undergoing total knee replacement surgery and controls, that is, deceased donors without known knee disease were previously run using liquid chromatography mass spectrometry (LC-MS). This data was used to perform new database searches generating results for non-tryptic and semi-tryptic peptides for studies of degradomics in OA. We used linear mixed models to estimate differences in peptide-level expression between the two groups. Known proteolytic events (from the MEROPS peptidase database) were mapped to the dataset, allowing the identification of potential proteases and which substrates they cleave. We also developed a peptide-centric R tool, proteasy, which facilitates analyses that involve retrieval and mapping of proteolytic events. We identified 429 differentially abundant peptides. We found that the increased abundance of cleaved APOA1 peptides is likely a consequence of enzymatic degradation by metalloproteinases and chymase. We identified metalloproteinase, chymase, and cathepsins as the main proteolytic actors. The analysis indicated increased activity of these proteases irrespective of their abundance.     

Starch-based extruded plastic films and evaluation of their biodegradable properties

Plastic formulations containing up to 40% starch were prepared and blown into thin films using extrusion methods. Extruded films were evaluated for their biodegradability by exposing them to a consortium of starch degrading bacteria in the laboratory for 45 days and in the La Silla river located in Monterrey, N.L. Mexico for up to 60 days. Biodegradability was assessed by measuring changes in weight loss and chemical composition of the films using Fourier transform infrared (FTIR) spectroscopy. While little or no degradation was apparent in control films made up of 100% low density polyethylene (LDPE) or 100% poly-(ethylene-co-acrylic acid) (EAA), most of the starch was depleted in starch-containing films exposed in the river. Starch degradation in films exposed to amylolytic bacteria in the laboratory was relatively slower. Also, increasing the amount of EAA from 25% to 50% substantially reduced starch depletion in these films.Abbreviations FTIR Fourier transform infrared - LDPE low density poly-(ethylene) - EAA poly-(ethyleneco-acrylic acid) - SEM Scanning electron microscopy The mention of firms names or trade products does not imply that they are endorsed or recommended by the U. S. Department of Agriculture over the firms or similar products not mentioned. All programs and services of the U. S. Department of Agriculture are offered on a nondiscriminatory basis without regard to race, color, national origin, religion, sex, marital status, or handicap.     

The effect of acid proteinases on the activity and stability of glucoamylase preparations

It was demonstrated that the presence of acid proteinases in the preparation isolated from Aspergillus awamori decreased the activity and stability of glucoamylase. Patterns of changes in the enzymatic activity and stability of glucoamylase at increased temperature and various pH values were studied over a long-term storage. A biospecific sorbent for removal of acid proteinases was synthesized and glucoamylase preparations free of proteolytic activity were produced.     

Force-induced structural transitions in cross-linked DNA films

We report on the preparation and characterization of wet-spun films of sodium DNA in which intermolecular cross-links were introduced following formaldehyde treatment. Raman scattering shows that the DNA in moderately cross-linked films is mainly in the B conformation. Stretching experiments show a transition from plastic to elastomeric behavior with increasing exposure to the cross-linking agent. Elastomeric DNA films are strongly disordered. X-ray diffraction shows that stretching of moderately cross-linked films under controlled high humidity conditions results in increased molecular orientation as well as the appearance of meridional reflections at 7.4-7.8 and 8.2 A. These reflections are not observed for any of the classical conformations associated with mixed sequence DNA, and may arise from extended base-pair stacking in a stretched DNA structure.