Foam separation of DNA and proteins from solutions

Foam separation on BSA-DNA (bovine serum albumine/deoxyribonucleic acid) and Lysozyme-DNA systems is performed. The separation of the total protein from DNA is evaluated for dissociated chromatin solution. Foam separation for the same systems is done also by a new method of creating a pressure gradient in the Plateau-Gibbs borders in the foam and obtaining a "dry" foam. It is shown that the effectiveness of the foam separation can be improved significantly by the application of the latter method. Some factors (pH, initial concentration of the solution, expansion factor of the foam) influencing the separation of proteins from DNA in the foam and in the residual solution are studied as well.     

Existence of transdominant and potentiating mutants of UL9, the herpes simplex virus type 1 origin-binding protein,suggests that levels of UL9 protein may be regulated during infection

UL9 is a multifunctional protein required for herpes simplex virus type 1 (HSV-1) replication in vivo. UL9 is a member of the superfamily II helicases and exhibits helicase and origin-binding activities. We have previously shown that mutations in the conserved helicase motifs of UL9 can have either a transdominant or potentiating effect on the plaque-forming ability of infectious DNA from wild-type virus (A. J. Malik and S. K. Weller, J. Virol. 70:7859-7866, 1996). In this paper, the mechanisms of transdominance and potentiation are explored. We show that the motif V mutant protein containing a G to A substitution at residue 354 is unstable when expressed by transfection and is either processed to a 38-kDa N-terminal fragment or degraded completely. The overexpression of the MV mutant protein is able to influence the steady-state protein levels of wild-type UL9 and to override the inhibitory effects of wild-type UL9. Potentiation correlates with the ability of the UL9 variants containing the G354A mutation to be processed or degraded to the 38-kDa form. We propose that the MV mutant protein is able to interact with full-length UL9 and that this interaction results in a decrease in the steady-state levels of UL9, which in turn leads to enhanced viral infection. Furthermore, we demonstrate that inhibition of HSV-1 infection can be obtained by overexpression of full-length UL9, the C-terminal third of the protein containing the origin-binding domain, or the N-terminal two-thirds of UL9 containing the conserved helicase motifs and the putative dimerization domain. Our results suggest that transdominance can be mediated by overexpression, origin-binding activity, and dimerization, whereas potentiation is most likely caused by the ability of the UL9 MV mutant to influence the steady-state levels of wild-type UL9. Taken together, the results presented in this paper suggest that the regulation of steady-state levels of UL9 may play an important role in controlling viral infection.     

A challenging insight on the structural unit 1 of molluscan Rapana venosa hemocyanin

Hemocyanins of mollusks are high molecular mass glycoproteins with a complex quaternary structure which still remains to be defined in detail for most of its species as far as number, spatial distribution and interactions of their structural units is concerned. In the present study, we isolated the functional units of the structural subunit RvH1 of Rapana venosa hemocyanin, combining enzymatic and non-enzymatic methods. Our results suggest that Hc's carbohydrate moieties play a basic role in the organization of the structural units, resulting from post-translational polymerization of the 50 kDa functional units and involving sugar moieties that link between them.     

AUGUSTUS at EGASP: using EST,protein and genomic alignments for improved gene prediction in the human genome

Background

A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were systematically evaluated and compared on test data from the human genome. AUGUSTUS was among the tools that were tested in this project.

Results

AUGUSTUS can be used as an ab initio program, that is, as a program that uses only one single genomic sequence as input information. In addition, it is able to combine information from the genomic sequence under study with external hints from various sources of information. For EGASP, we used genomic sequence alignments as well as alignments to expressed sequence tags (ESTs) and protein sequences as additional sources of information. Within the category of ab initio programs AUGUSTUS predicted significantly more genes correctly than any other ab initio program. At the same time it predicted the smallest number of false positive genes and the smallest number of false positive exons among all ab initio programs. The accuracy of AUGUSTUS could be further improved when additional extrinsic data, such as alignments to EST, protein and/or genomic sequences, was taken into account.

Conclusion

AUGUSTUS turned out to be the most accurate ab initio gene finder among the tested tools. Moreover it is very flexible because it can take information from several sources simultaneously into consideration.

     

Seasonal activity of non-specific acid and alkaline phosphatases in beech (<Emphasis Type="Italic">Fagus sylvatica</Emphasis>) leaves

The activities of acid and alkaline phosphatases along with phosphorus content in leaves of European beech (Fagus sylvatica L.) were studied for a period from April to October. The phosphorus content of beech leaves was highest in April, at the beginning of the vegetation period; from May to October it was twofold lower than in April. Acid phosphatase activity (per unit fresh weight) in leaves collected from the middle part of the crown decreased significantly in May and July compared to the enzyme activity in April. In both the low and middle parts of the crown, the acid phosphatase activity had a peak in August, and thereafter decreased in September and October. No correlations between acid phosphatase activity and phosphorus concentrations were found. Alkaline phosphatase activity was very low and in some cases near the detection limit during the whole observation period.     

Neuro-fuzzy prediction of uricase production

Recent biotechnology requires implementation of new modelling methods based on knowledge principles and learning structures, comprised in fuzzy knowledge-based systems (FKBS), neural networks (NN) and different hybrid methods. The intelligent modelling approaches solve sufficiently a very important problem - processing of scarce, uncertainty and incomplete numerical and linguistic information about multivariate non-linear and non-stationary systems as well as biotechnological processes. The paper deals with prediction of an enzyme oxidizing uric acid to alantoin - the uricase, produced by Candida utilis 90-12 employing neuro-fuzzy knowledge-based approach. The implemented predictive technique exploits the fact that the fuzzy model can be seen as a network structure, similar to artificial NN, which on computational level assure a high model accuracy. The predictors implemented are four different by nature variables. The developed predictive model shows that best predictors of uricase production are biomass and limiting substrate concentrations.     

Structure and axon outgrowth inhibitor binding of the Nogo-66 receptor and related proteins

The myelin-derived proteins Nogo, MAG and OMgp limit axonal regeneration after injury of the spinal cord and brain. These cell-surface proteins signal through multi-subunit neuronal receptors that contain a common ligand-binding glycosylphosphatidylinositol-anchored subunit termed the Nogo-66 receptor (NgR). By deletion analysis, we show that the binding of soluble fragments of Nogo, MAG and NgR to cell-surface NgR requires the entire leucine-rich repeat (LRR) region of NgR, but not other portions of the protein. Despite sharing extensive sequence similarity with NgR, two related proteins, NgR2 and NgR3, which we have identified, do not bind Nogo, MAG, OMgp or NgR. To investigate NgR specificity and multi-ligand binding, we determined the crystal structure of the biologically active ligand-binding soluble ectodomain of NgR. The molecule is banana shaped with elongation and curvature arising from eight LRRs flanked by an N-terminal cap and a small C-terminal subdomain. The NgR structure analysis, as well as a comparison of NgR surface residues not conserved in NgR2 and NgR3, identifies potential protein interaction sites important in the assembly of a functional signaling complex.     

Chemical composition and biochemical changes in needles of Scots pine (Pinus sylvestris L.) stands at different stages of decline in Bulgaria

Water content was decreased in the needles of Scots pines (Pinus sylvestris L.) with moderate and slight levels of stress-induced decline. In pines with moderate decline a misbalance of foliar nutritional elements was observed. In 1-year-old needles of afflicted pines, the content of potassium and calcium was decreased, but the content of phosphorus, magnesium, iron, manganese and of the heavy metals cadmium and lead was increased. In 2-year-old needles of damaged pines, the content of calcium, iron and of the heavy metal cadmium was decreased, but the content of phosphorus, magnesium, manganese and zinc was increased. Potassium deficiency and zinc levels above toxicity tolerance characterized the nutrient status of declined Scots pines. In the same pines chlorophyll a/b ratio was diminished in 2-year-old needles and the protein content was increased in 1-year-old needles but was decreased in 2-year-old needles.In the second phase of the study 25- and 40-year-old pines with slight decline were examined. An increase in the protein content of 2-year-old needles of 25-year-old declined pines and of both 1- and 2-year-old needles of older 40-year-old pines was observed. A 280% increase of peroxidase activity in 1-year-old and a 178% increase in 2-year-old needles of 25-year-old damaged pines were shown. In older 40-year-old damaged pines a slight increase only in 1-year-old needles was seen. The observed age-related decrease in peroxidase activity in older 40-year-old symptomatic pines might be responsible for the lower resistance to decline in older pines. Our results show that clear but complex chemical and biochemical changes are observed in the needles of Scots pines in Bulgaria and that these changes hold promise for use as indicators of stress.     

Approaches for yield increase of <Emphasis Type="Italic">β</Emphasis>-cyclodextrin formed by cyclodextrin glucanotransferase from <Emphasis Type="Italic">Bacillus megaterium</Emphasis>

Two methods for increasing β-cyclodextrin yield, achieved with cyclodextrin glucanotransferase from Bacillus megaterium were investigated. A membrane process was performed, allowing a reuse of the enzyme. A process for simultaneous production and isolation of β-cyclodextrin in the presence of complexing agents was conducted. The β-cyclodextrin yield was increased twofold, when the product was precipitated with trichloroethylene or toluene. A change in the product selectivity of cyclodextrin glucanotransferase occurred, resulting in an increase in the relative amount of β-cyclodextrin up to 90% of all cyclodextrins formed. Yield increase was due to the removal of product inhibition and the coupling activity of the enzyme, which limited the full conversion of starch. The isolated cyclodextrin products contained 75–79% β-cyclodextrin, and 4–6% each of α-, and γ-cyclodextrins.     

Optimisation of synthetic medium composition for levorin biosynthesis by Streptomyces levoris 99/23 and investigation of its accumulation dynamics using mathematical modelling methods

The composition of a synthetic culture medium for levorin biosynthesis by Streptomyces levoris 99/23 was optimised using mathematical modelling methods. The optimal concentrations of the medium components were established by means of an optimum composition design at three factor variation levels. An adequate regression model was obtained. Levorin biosynthesis by Streptomyces levoris 99/23 in the optimised synthetic medium was over 38% higher than in the initial medium. The antibiotic biosynthesis dynamics in the optimised culture medium was studied by means of a non-linear differential equation system. The resultant model was valid.