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E Barta

Publications and source records attributed to E Barta.

At least 19 recordsLinked to original sources
PubMed2001

The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments.

SBASE 8.0 is the eighth release of the SBASE library of protein domain sequences that contains 294 898 annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to most major sequence databases and sequence pattern collections. The entries are clustered into over 2005 statistically validated domain groups (SBASE-A) and 595 non-validated groups (SBASE-B), provided with several WWW-based search and browsing facilities for online use. A domain-search facility was developed, based on non-parametric pattern recognition methods, including artificial neural networks. SBASE 8.0 is freely available by anonymous 'ftp' file transfer from ftp.icgeb.trieste.it. Automated searching of SBASE can be carried out with the WWW servers http://www.icgeb.trieste.it/sbase/ and http://sbase.abc. hu/sbase/.

Binding Sites↗
PubMed2001

Proteins of circularly permuted sequence present within the same organism: the major serine proteinase inhibitor from Capsicum annuum seeds.

The major serine proteinase inhibitor from bell pepper (Capsicum annuum, paprika) seeds was isolated, characterized, and sequenced, and its disulfide bond topology was determined. PSI-1.2 is a 52-amino-acid-long, cysteine-rich polypeptide that inhibits both trypsin (K(i) = 4.6 x 10(-9) M) and chymotrypsin (K(i) = 1.1 x 10(-8) M) and is a circularly permuted member of the potato type II inhibitor family. Mature proteins of this family are produced from precursor proteins containing two to eight repeat units that are proteolytically cleaved within, rather than between, the repeats. In contrast, PSI-1.2 corresponds to a complete repeat that was predicted as the putative ancestral protein of the potato type II family. To our knowledge, this is the first case in which two proteins related to each other by circular permutation are shown to exist in the same organism and are expressed within the same organ. PSI-1.2 is not derived from any of the known precursors, and it contains a unique amphiphilic segment in one of its loops. A systematic comparison of the related precursor repeat-sequences reveals common evolutionary patterns that are in agreement with the ancestral gene-duplication hypothesis.

Amino Acid Sequence↗
PubMed2000

The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments.

SBASE 7.0 is the seventh release of the SBASE protein domain library sequences that contains 237 937 annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to all major sequence databases and sequence pattern collections. The entries are clustered into over 1811 groups and are provided with two WWW-based search facilities for on-line use. SBASE 7.0 is freely available by anonymous 'ftp' file transfer from ftp.icgeb. trieste.it. Automated searching of SBASE with BLAST can be carried out with the WWW servers http://www.icgeb.trieste.it/sbase/and http://sbase.abc.hu/sbase/

Amino Acid Sequence↗
PubMed2000

Facilitated diffusion and membrane permeation of fatty acid in albumin solutions.

Facilitated transport is characteristic of most living systems, and usually involves a series of consecutive adjacent transfer regions, each having different transport properties. As a first step in the analysis of the multiregional problem, we consider in a single unstirred layer the facilitated diffusion of fatty acid (F) in albumin (A) solution under conditions of slow versus rapid association-dissociation, accounting for differing diffusivities of the albumin-fatty acid complex (AF). Diffusion gradients become established in an unstirred layer between a source of constant concentration of A, AF, and F in equilibrium, and a membrane permeable to F. The posited system does not reduce to a thin- or thick-layer approximation. The transient state is prolonged by slower on/off binding rates and by increasing the thickness of the unstirred layer. Solutions to transient and steady state depend upon the choice of boundary conditions, especially for thin regions. When there are two regions (each with its specific binding protein) separated by a permeable membrane, the steady-state fluxes and concentration profiles depend on the rates of association and dissociation reactions, on the diffusion coefficients, local consumption rates, and on the membrane permeability. Sensitivity analysis reveals the relative importance of these mechanisms.

Biological Transport, Active↗
PubMed1999

The SBASE protein domain library, release 6.0: a collection of annotated protein sequence segments.

The sixth release of the SBASE protein domain library sequences contains 130 703 annotated and crossreferenced entries corresponding to structural, functional, ligand-binding and topogenic segments of proteins. The entries were grouped based on standard names (2312 groups) and futher classified on the basis of the BLAST similarity (2463 clusters). Automated searching with BLAST and a new sequence-plot representation of local domain similarities are available at the WWW-server http://www.icgeb.trieste.it/sbase. A mirror site is at http://sbase.abc.hu/sbase. The database is freely available by anonymous 'ftp' file transfer from ftp.icgeb.trieste.it

Amino Acid Sequence↗
PubMed1999

Specific amino acid content and codon usage account for the existence of overlapping ORFS.

Here we present a novel hypothesis for the origin of overlapping open reading frames (O-ORFs) observed in the 'non-coding frames' of several genes of yeast chromosome II. By computer analysis it was found that the specific amino acid content and base distribution pattern at certain genomic locations and the presence of O-ORFs were related. This observation prompt us to conclude that these O-ORFs are mere statistical curiosities without any biological function, which is in contrast to the hypotheses proposed by other authors.

Amino Acids↗
PubMed1999

The domain-server: direct prediction of protein domain-homologies from BLAST search.

RESULTS: A WWW server for protein domain homology prediction, based on BLAST search and a simple data-mining algorithm (Hegyi,H. and Pongor,S. (1993) Comput. Appl. Biosci., 9, 371-372), was constructed providing a tabulated list and a graphic plot of similarities. AVAILABILITY: http://www.icgeb.trieste.it/domain. Mirror site is available at http://sbase.abc.hu/domain. A standalone programme will be available on request. SUPPLEMENTARY INFORMATION: A series of help files is available at the above addresses.

Algorithms↗
PubMed1997

Isolation and sequence analysis of a cDNA and a related gene for cytochrome P450 proteins from Solanum chacoense.

Inosine-containing degenerate PCR primers corresponding to the heme-binding domain of cytochrome P450 proteins have been synthesized and used for cloning cDNAs by the RT-PCR technique from Solanum chacoense. One clone in which the primer was immediately followed by sequences corresponding to the remaining part of the conserved domain was obtained. A leaf cDNA and a genomic library were constructed from S. chacoense. Clones homologous to the PCR fragment were isolated by plaque hybridization from both libraries (CYPs.ch-1 and CYPs.ch-2, respectively). Based on DNA sequence analysis, the selected clones are 87.6% identical and belong to the CYP71 family. The CYPs.ch genes are present in multiple copies in the S. chacoense as well as in the S. tuberosum genome with some polymorphisms. The CYPs.ch transcripts are slightly induced by methyl jasmonate and abscisic acid in S. chacoense foliage.

Amino Acid Sequence↗
PubMed1996

Early changes in protein synthesis in epicardial coronary artery of pressure-overloaded heart.

In anesthetized dogs, a 4-h, approximately 30% increase in blood pressure induced by constriction of the abdominal aorta brought about an increase in the total RNA content in the left anterior descending coronary artery (LADCA) and the left ventricular (LV) myocardium (9.05 +/- 1.72 and 11.06 +/- 4.68%, respectively) but not in the left circumflex coronary artery (LCCA). Under the same experimental conditions, [14C]leucine incorporation increased in LADCA and LV myocardium (45.34 +/- 13.54 and 58.07 +/- 11.91%, respectively), but not in LCCA. The data indicate an early shift in protein synthesis in LADCA and simultaneously in the myocardium during a short-term pressor event. The difference in the shift of protein synthesis in the two main branches of the left coronary artery was related to the quantitatively different deformation of the LADCA and LCCA due to different deformation of the underlying myocardium and/or of the annulus fibrosus atrioventricularis during changes in the left or right ventricle volume [M. Gerová, E. Barta, M. Stolárik, and J. Gero, Am. J. Physiol. 262 (Heart Circ. Physiol. 31): H1049-H1053, 1992]. The results support the hypothesis that the deformation and/or rate of deformation of cells in the coronary wall may trigger an increase in protein synthesis. Changes in protein synthesis in the myocardium and LADCA were found to be reversible 2 h after releasing the aortic constriction.

Animals↗
PubMed1995

Isolation and characterization of a water-stress-inducible cDNA clone from Solanum chacoense.

A rich source of valuable genes are wild species. Solanum chacoense Bitter with its extreme resistance to viruses, insects and drought, is a good example. In the present study, a stress gene, designated DS2, has been isolated from S. chacoense. We have shown that the expression of the gene is organ-specific being detected in leaf, stem and stolon, but not in root, tuber or flower. Treatment of detached leaves with abscisic acid (ABA), salicylic acid or methyl jasmonate resulted in only very moderate accumulation of DS2 mRNA. Thus, DS2 represents a very rare type of the water-stress-inducible genes whose signalling pathway is not primarily related to ABA. Based on DNA sequence analysis, DS2 encodes a putative protein starting with 20 amino acids homologous to the ABA- and water-stress-inducible, ripening-related (ASR) proteins of tomato continued by an insert of 155 amino acids structurally similar to certain LEAs (late embryogenesis-abundant proteins) and ending in 88 amino acids homologous again to the ASR sequences and to an unpublished partial cDNA fragment isolated from the root of rice. The N-terminal region of the DS2 protein is hydrophilic with ten 13-mer amino acid motifs and random coil structure. In contrast, the C-terminus predicts an alpha-helix and possesses a bipartite nuclear targeting sequence motif. These data suggest that the function of the DS2 may be the protection of the nuclear DNA from desiccation.

Abscisic Acid↗
PubMed1994

Solanum brevidens possesses a non-sucrose-inducible patatin gene.

The patatin gene is the best known "tuber-specific" gene of potato (Solanum tuberosum). Patatin is encoded by a multigene family that can be divided into two classes. Class I genes are highly expressed in tubers and are sucrose inducible, while class II genes are under developmental control and are expressed mainly in root tips. Here we report the isolation and characterization of cDNA clones corresponding to a patatin gene of the non-tuberizing Solanum species S. brevidens. We show that the gene is 94-100% homologous to the class I type patatin genes of S. tuberosum; the homology includes the sequences in the 5' and the 3' untranslated regions. However, the patatin gene of S. brevidens is regulated like class II type patatin genes and cannot be transcriptionally activated by elevated levels of sucrose. This result further supports the idea that the components required for tuberization may be present in non-tuberizing solanaceous plants, but are regulated differently.

Amino Acid Sequence↗
PubMed1993

[Biochemical parameters in the blood of patients during open-heart surgery. I. Monitoring changes in energy metabolism].

Levels of lactate, inorganic phosphate and uric acid in arterial, mixed venous and coronary sinus blood were studied in patients during open-heart surgery. It was found that the determination of mentioned biochemical parameters can provide information regarding the energetic metabolism status of the whole organism, but selectively, also of the patient's myocardium. The results of biochemical analyses demonstrate a significant loading of the organism manifested by metabolic alterations, especially after long-term cardiopulmonary bypass. The study of mentioned biochemical parameters can be employed for investigation of a more efficient protection of myocardium against ischemia-reperfusion injury. (Fig. 6, Ref. 18).

Cardiac Surgical Procedures↗
PubMed1993

[Biochemical parameters in the blood in patients during open-heart surgery. II. Malondialdehyde, superoxide dismutase and catalase as indicators of formation and elimination of free oxygen radicals].

Investigation of cardiosurgical patients have provided evidence for the generation of free oxygen radicals during open heart surgery. The finding of increased plasma malondialdehyde concentrations, considered to be an indicator of lipid peroxidation in cell membranes, is suggestive of this process. Simultaneously, the antiradical capacity of tissue was found to exhibit a decreasing trend, as established by the levels of superoxide dismutase and catalase in erythrocytes of peripheral blood which tended to diminish. The funding that no changes in the studied parameters were observed in the blood from the coronary sinus taken before and after interruption of coronary blood flow demonstrates that the commonly applied protection of the myocardium by hypothermic cardioplegic solution and topical cooling of the heart is effective in suppressing radical formation. (Fig. 5, Ref. 36.)

Adult↗
PubMed1992

Heterogeneity in geometrical alterations of main branches of left coronary artery induced by increase in ventricle volume.

With the use of ultrasound technique, segment length and diameter of ramus circumflexus (RC) and ramus interventricularis anterior (RIA) in the dog heart, placed in a bath, were monitored under constant pressure. When the left and/or right ventricular volume was increased by 150% of the normal diastolic filling, segment length of RC increased by 2.54 +/- 0.17 and 2.15 +/- 0.06%, respectively, and diameter of RC decreased by 4.72 +/- 0.20% and by 4.60 +/- 0.20%, respectively. The same filling of the left and/or right ventricle induced in the proximal third of RIA an increase in segment length by 11.40 +/- 0.55 and 12.2 +/- 0.42%, respectively, and a decrease in diameter by 9.41 +/- 0.42% and by 10.01 +/- 0.31%, respectively. The latter values of RIA were significantly higher (P less than 0.001) than those registered in RC. The deformations of RIA decreased toward the periphery of the vessel. By the fact that conduit coronary artery tracks instantaneously the increase of the volume of the left and right ventricle, its contribution to the total coronary resistance increases dynamically. With the ventricular volume increased by 150%, the RC contributes to the total coronary resistance by 14% and RIA in the proximal part contributes by 23%, with values significantly higher than control (10%) (Malindzak, G. S. In: The Coronary Artery. London: Croom Helm, 1982, p. 241-267). The results imply a methodical consequence, namely that the diameter of the respective coronary artery is an index of smooth muscle activity only if both perfusion pressure and volume of the heart are maintained constant.

Animals↗
PubMed1991

Complex pattern of alternative splicing generates unusual diversity in the leader sequence of the chicken link protein mRNA.

We report here the isolation of the 5' end and the promoter region of the gene for chicken cartilage link protein, and demonstrate extensive heterogeneity of the leader sequence arising from differential utilization of multiple splice sites within the 5'-most exon. The 500-base pairs (bp) exon 1 consists of solely untranslated sequence and is followed by an intron greater than 33 kilobase pairs (kb). Together, the five exons predict a gene size longer than 100 kb. Multiple transcription initiation sites were mapped 34, 46, 56, 66 and 76 bp downstream of a TATA-like motif. Sequence analysis revealed that in addition to the non-spliced variant, multiple mRNA species were generated by alternative splicing resulting in the exclusion of 92, 166, 170, 174 and 263 nucleotides (nt), respectively, from exon 1. Polymerase chain reaction confirmed the existence of various splice forms, and showed cell type- and developmental stage-specific expression for one group of them. Secondary structure predictions indicated that the leaders of the splice forms could form stable hairpin structures with different free energies of formation (up to delta G = -110 kcal/mol), suggesting translational control. The splice variant detected in the largest amount had the least stable predicted hairpin (delta G = -31.7 kcal/mol).

Animals↗
PubMed1990

Identification of positive and negative regulatory regions controlling expression of the cartilage matrix protein gene.

A complex pattern of regulation of the cartilage matrix protein gene was revealed by transient expression experiments. A minimal promoter from positions -15 to +64 functioned in chondrocytes and fibroblasts. An enhancer located in the first intron exerted chondrocyte-specific stimulation on the minimal promoter activity. The same fragment, however, had a negative effect in fibroblasts. Between -334 and -15, a silencer was found which inhibited the gene expression driven from its homologous as well as heterologous promoters both in chondrocytes and fibroblasts. Additional positive and negative control regions were mapped further upstream of the promoter.

Animals↗