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The genetic code is a set of rules that establishes mapping between triplets in messenger RNA and amino acids in proteins. The most common way to display these rules is the Standard Genetic Code (SGC) table. This paper takes an alternative approach, based on the relational data model by Edgar F. Codd (Commun. ACM, 13:377-387, 1970). The relational model (RM) proposes a distributed storage of data into a collection of tables (called relations), that can be connected by shared communality. Basic elements of the table are rows (called records or tuples), and columns (called fields or attributes). The SGC table, according to the relational data model, represents the so called unnormalized form of a table. Using normalization rules it is possible to subdivide the SGC table into four tables. The rows and columns of single tables are defined by the first and second base and individual tables by the third codon base. The result of this model is an approach to managing genetic code data, represented in terms of tuples and grouped into relations, with table structure and language consistent with first-order (predicate) logic. The RM explains that the final step in the development of the SGC was the adoption of coding function by the third base, which makes an informational/functional unit with the first base, despite the different physical location in a triplet. This enabled the synthesis of specific proteins without ambiguity, in accordance with the concept of ambiguity reduction and five phases of the general model on the origin of biological codes by Marcello Barbieri (BioSystems 181:11-19, 2019).

Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods.

We present the data concerning the clustering of sense and antisense amino acid pairs into polar, nonpolar and neutral groups, as measured using hydrophobicity parameter—logarithmic equilibrium constants (Log10 Kw>c)—at 25 °C and 100 °C (Wolfenden et al., 2015). The Log10 Kw>c, values, of the complementary amino acid pairs are strongly correlated to the central (2nd) purine base of the mRNA codon and the complementary pyrimidine base of the tRNA anticodon. Clustering of amino acids is temperature independent with regard to the direction of translation (3′ → 5′ or 5′ → 3′). The Log10 Kw>c discriminate between artificial Hecht α- and β-protein datasets at 25 °C and 100 °C. Interpretation of this data may be found in the research article entitled “Determining amino acid scores of the genetic code table: complementarity, structure, function and evolution” (Stambuk and Konjevoda, 2020).

The Standard Genetic Code (SGC) table was investigated with respect to the three- dimensional codon arrangement, and all possible 24 hierarchical base partitions (4! = 24). This was done by determining the amino acid scores for each codon hierarchy in relation to the 1st horizontal, 2nd vertical and 3rd horizontal sub-tables. Marked differences were observed for the hydrophobicity and lipophilicity parameters encoded by the second base of the SGC table. The nucleotide hierarchy U < C < G < A and its complement A < G < C < U at the second base correlated best with the amino acid hydrophobicity and polarity. By contrast, the hierarchy C < G < U < A and its backwards transcript A < U < G < C at the second base were associated with the amino acid parameters of lipophilicity and accessible surface area. No association was observed between 24 base hierarchies of the codons at the 1st and 3rd positions with respect to the hydropathy, polarity, lipophilicity and accessible surface area. The results imply that the second base possesses the majority of information content with respect to the physicochemical properties observed. It is shown that amino acid information obtained by determining the scores of the bases and codon weightings in digital form coincides with physicochemical properties, and the temperature range between 25 °C and 100 °C does not affect the hydrophobicity, the related prediction of α- and β-protein structure, codon scores, or the complementarity code for sense and antisense peptide interactions. The amino acid scores determined for the SGC table enable the construction of rules and algorithms for the analysis of the structure, function and evolution of proteins. It has been demonstrated that IUPAC-based encoding of nucleobase and amino acid sequences could be used for the representation of the bases with the Semiotic (Greimas) Square and probabilistic square of opposition. It is concluded that the structural, functional and evolutionary patterns of the protein sequences may be modeled using codon based amino acid information, instead of using the information based on amino acid physicochemical properties only.

The purpose of this paper was to outline the development of short peptide targeting of the human prostate specific antigen (hPSA), and to evaluate its effectiveness in staining PSA in human prostate cancer tissue. The targeting of the hPSA antigen by means of antisense peptide AVRDKVG was designed according to a three-step method involving: 1. The selection of the molecular target (hPSA epitope), 2. the modeling of an antisense peptide (paratope) based on the epitope sequence, and 3. the spectroscopic evaluation of sense&ndash, antisense peptide binding. We then modified standard hPSA immunohistochemical staining practice by using a biotinylated antisense peptide instead of the standard monoclonal antibody and compared the results of both procedures. Immunochemical testing on human tissue showed the applicability of the antisense peptide technology to human molecular targets. This methodology represents a new approach to deriving peptide ligands and potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.

Melanocortins, i.e., melanocyte stimulating hormones (MSH) are peptides with strong antiinflammatory effects. The most investigated aspects of γ2-MSH are related to cardiovascular effects and natriuresis, with limited research available about its anti-inflammatory and cytoprotective effects. The aims of this study were: 1) to examine the effects of γ2-MSH and its derivative [D-Trp(8)]-γ2-MSH on the acetaminophen model of liver damage in CBA mice; 2) to evaluate the modulation of γ2-MSH hepatoprotection by melanocortin subtypes 3 and 4 receptor antagonists SHU 9119 and HS 024; 3) to define the importance of central MSH pharmacophore region (HFRW) by using antisense peptides LVKAT and VKAT. In this study, specific antagonists and antisense peptides were used to target central pharmacophore region of γ2-MSH and [D-Trp(8)]-γ2-MSH, enabling the evaluation of hepatoprotection from the standpoint of the receptor and pharmacophore blockade. The criteria for monitoring the effects of the hormones on the liver damage were alanine transaminase, aspartate transaminase activities (U/L), and pathohistological scoring of liver necrosis (scale 0-5). γ2-MSH (0.24 mg/kg) indicated hepatoprotective effects in comparison to control (p < 0.001). In contrast, [D-Trp(8)]-γ2-MSH did not show any hepatoprotective effects. Application of antagonists SHU 9119 and HS 024, and antisense peptides LVKAT and VKAT, also did not show any hepatoprotective effects. In fact, when combined with γ2-MSH, it annulled its hepatoprotective effect. The results provide evidence for hepatoprotective and antiinflammatory effects of the γ2-MSH in the liver.

Sense and antisense peptides, i.e. peptides specified by complementary DNA and RNA sequences, interact with increased probability. Biro, Blalock, Mekler, Root-Bernstein and Siemion investigated the recognition rules of peptide—peptide interaction based on the complementary coding of DNA and RNA sequences in 3′ → 5′ and 5′ → 3′ directions. After more than three decades of theoretical and experimental investigations, the efficiency of this approach to predict peptide—peptide binding has been experimentally verified for more than 50 ligand—receptor systems, and represents a promising field of research. The natural genetic coding algorithm for sense and antisense peptide interactions combines following elements: of amino acid physico- chemical properties, stereochemical interaction, and bidirectional transcription. The interplay of these factors influences the specificity of sense—antisense peptide interactions, and affects the selection and evolution of peptide ligand—receptor systems. Complementary mRNA codon—tRNA anticodon complexes, and recently discovered Carter- Wolfenden tRNA acceptor-stem code, provide the basis for the rational modeling of peptide interactions based on their hydrophobic and lipophilic amino acid physico-chemical properties. It is shown that the interactions of complementary amino acid pairs according to the hydrophobic and lipophilic properties strongly depend on the central (second) purine base of the mRNA codon and its pyrimidine complement of the tRNA anticodon. This enables the development of new algorithms for the analysis of structure, function and evolution of protein and nucleotide sequences that take into account the residue's tendency to leave water and enter a nonpolar condensed phase considering its mass, size and accessible surface area. The practical applications of the sense—antisense peptide modeling are illustrated using different interaction assay types based on: microscale thermophoresis (MST), tryptophan fluorescence spectroscopy (TFS), nuclear magnetic resonance spectroscopy (NMR), and magnetic particles enzyme immunoassay (MPEIA). Various binding events and circumstances were considered, e.g., in situations with—short antisense peptide ligand (MST), L- and D-enantiomer acceptors (TFS), in low affinity conditions (NMR), and with more than one antisense peptide targeting hormone (MPEIA).

Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide–receptor modulation. It is based on the fact that peptides specified by the complementary (antisense) nucleotide sequences often bind to each other with a higher specificity and efficacy. We tested the validity of this concept on the example of human erythropoietin, a well-characterized and pharmacologically relevant hematopoietic growth factor. The purpose of the work was to present and test simple and efficient three-step procedure for the design of an antisense peptide targeting receptor-binding site of human erythropoietin. Firstly, we selected the carboxyl-terminal receptor binding region of the molecule (epitope) as a template for the antisense peptide modeling, Secondly, we designed an antisense peptide using mRNA transcription of the epitope sequence in the 3'→5' direction and computational screening of potential paratope structures with BLAST, Thirdly, we evaluated sense–antisense (epitope–paratope) peptide binding and affinity by means of fluorescence spectroscopy and microscale thermophoresis. Both methods showed similar Kd values of 850 and 816 µM, respectively. The advantages of the methods were: fast screening with a small quantity of the sample needed, and measurements done within the range of physicochemical parameters resembling physiological conditions. Antisense peptides targeting specific erythropoietin region(s) could be used for the development of new immunochemical methods. Selected antisense peptides with optimal affinity are potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.

The difference between amino acid chemical properties that correlate to the exchangeability of protein sequence residues is often analysed using approach proposed by Grantham (1974). His difference formula, i.e., matrix, for calculating the distances between amino acid pairs of the protein consists of three essential amino acid physicochemical properties – composition, polarity and volume, that are significantly correlated to the substitution frequencies of the protein residues. Miyata et al. (1979) re-evaluated this concept, and showed that the degree of amino acid difference is just as adequately explained by only two physicochemical factors, volume and polarity. Miyazawa-Jernigan relative partition/hydrophobic energies (ε = Δ e ir), and Carter-Wolfenden vapor-to-cyclohexane scale ( G v>c = ΔG v>c ) are two alternative amino acid physicochemical parameters that are strongly correlated to their polarity and volume/mass, respectively. We show that the Miyazawa-Jernigan residue contact potential could be used instead of the Grantham polarity and composition parameters to derive an updated Miyata matrix. This substitution permits Miyata matrix correction for the amino acid parameters of: contact energies, repulsive packing energies, secondary structure energies, and Grantham’s composition property. Distance values calculated between both (classic and updated) Miyata matrices exhibit a strong correlation of r = 0.91. The possibility of analyzing residue distances based on Carter-Wolfenden water-to-cyclohexane (w > c) and vapor- to-cyclohexane (v > c) scales instead of the amino acid polarity and volume parameters is also discussed, and a new distance matrix is derived.

The classic results by Biro, Blalock and Root-Bernstein link genetic code nucleotide patterns to amino acid properties, protein structure and interaction. This study explores the use of the Miyazawa-Jernigan residue contact potential in analyses of protein interaction and recognition between sense and complementary (antisense) peptides. We show that Miyazawa-Jernigan residue contact energies, derived from 3D data, define the recognition rules of peptide-peptide interaction based on the complementary coding of DNA and RNA sequences. The model is strongly correlated with several other chemoinformatic scales often used for the determination of protein antigenic sites and transmembrane regions (Parker et al. r = 0.94 ; Rose et al. r = − 0.92 ; Manavalan-Ponnuswamy r = − 0.92 ; Cornette et al. r = − 0.91 ; Kolaskar-Tongaonkar r = − 0.91 ; Grantham r = 0.90 ; White-Wimley (octanol) r = − 0.88 ; Kyte-Doolittle r = − 0.85). The algorithms presented have important biomedical and proteomic applications related to modulation of the peptide-receptor function and epitope-paratope interaction, the design of lead compounds and the development of new immunochemical assays and diagnostic procedures.

Recently discovered anti-inflammatory and immunomodulatory properties of melanocortin peptides led to the conclusion that they might serve as new anti-inflammatory therapeutics. The purpose of this work was to examine the effectiveness of β-melanocortin (β-MSH) in two experimental models: ethanol-induced gastric lesions and TNBS (2, 4, 6- trinitrobenzenesulfonic acid)-induced colitis in male Wistar rats. Three progressive doses of β-MSH were used: 0.125, 0.250 and 0.500 mg/kg. Our results suggest that β-MSH acts as a protective substance in the gastric lesions model, which can be seen as a statistically significant reduction of hemorrhagic lesions at all three doses, compared to the control group. The most efficient dose was 0.250 mg/kg. Statistically significant reduction in mucosal surface affected by necrosis and the reduction of overall degree of inflammation in the colitis model indicates an anti-inflammatory effect of β-MSH at a dose of 0.250 mg/kg. The results justify further research on β-MSH peptide and its derivates in the inflammatory gastrointestinal diseases, and point out the possibility of using β-MSH in studies of digestive system pharmacology.

Proteins and peptides in mammals are based exclusively on L-amino acids. Recent investigations show that D-amino acids exhibit physiological effects in vivo, despite of their very small quantities. We have investigated the hepatoprotective effects of the Land D-enantiomers of alpha-melanocortin peptide (alpha-MSH). The results showed that peptide-enantiomerism is related to the protective effects of melanocortin peptides in vivo. L-alpha-MSH exhibited potent hepatoprotective effect in the experimental model of acetaminophen induced hepatotoxicity in male CBA mice, while its D-mirror image was inefficient. Furthermore, the antibody to the L-peptide did not recognize the D-structure. The results indicate that the opposite peptide configuration may be used to modulate its function and metabolism in vivo and in vitro.

Background We investigated the possible non-lipid effects of simvastatin (SIMV) on paraoxonase 1 (PON1) and butyrylcholinesterase (BuChE) activity, as well as on malondialdehyde (MDA) levels in normolipidemic rats. Methods Two experimental groups of Wistar rats (10 mg/kg/day of SIMV) and two control groups (saline) underwent a 21-day treatment period (TP). On the 22nd day one experimental and one control group of rats were sacrificed. Remaining groups of animals were sacrificied on the 32nd day of the study (10-day after-treatment period (AT)). Blood samples and slices of liver, heart, kidney, and brain tissue were obtained for the measurement of PON1 and BuChE activity and levels of MDA. Data were analyzed by means of t -test for independent samples. p values ≤ 0.05 were considered as statistically significant. Results SIMV caused a significant decrease of serum and liver PON1 activity (18–24%, p ≤ 0.05) and MDA concentrations in the plasma, heart, liver, kidney, and brain (9–40%, p ≤ 0.05), while plasma and liver BuChE activity increased by 29% ( p ≤ 0.05) and 18%, respectively. All effects of SIMV were largely diminished following AT. The exception was MDA, which remained significantly decreased in plasma and all tissues analyzed. Conclusion SIMV significantly decreased PON1 activity and MDA levels and increased BuChE activity. We suggest that the decrease of MDA levels is a beneficial therapeutic effect of SIMV, for example in cardiovascular disorders, while the increase of BuChE activity, especially in brain, may be a potential adverse effect in patients with Alzheimer disease.

We present binary coding algorithm for the α- and β-protein fold prediction. The method links amino acid molecular polarity patterns and physicochemical properties of nucleotide bases coded by means of a binary addresses. Primary sequences that define secondary protein structure were analyzed with respect to the symbolic oligopeptides (SO) obtained by the reduction of the 20 amino acid letter alphabet into a binary alphabet of nonpolar group 0 (W, C, I, F, M, V, L, Y) and polar group 1 (Q, R, H, K, N, E, D, S, G, T, A, P). The groups were extracted from the Grantham polarity scale with the clustering around medoids procedure. The transformation of protein strings into binary coding patterns of the polar and nonpolar amino acid groups reduced analyzed elements within the protein motif of length n by the factor of 10n. SMO learning algorithm for the support vector machines was applied to classify α-helices and β-strands. It was shown that the relative frequencies of binary hexapeptides classify all 174 nonhomologous α- and β-protein folds from the Jpred database with 100% accuracy. The results of 10-fold cross-validation and leave-one-out test were 86.78%. Classification tree confirmed the results of SMO analysis and correctly classified 100% of the folds by means of 9 binary hexapeptides. Linear block triple-check code was proposed for the description of hexapeptide patterns. The presented method enables simple, quick, and accurate prediction of α- and β-protein folding types from the primary amino acid and nucleotide sequences on a personal computer. Our results imply that few amino acid polarity patterns specified by the nucleotide physicochemical properties describe basic protein folding types with >90% accuracy. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

Recent histopathological investigations in patients with hepatitis suggested possible involvement of Met-enkephalin and its receptors in the pathophysiology of hepatitis. Consequently, we evaluated the potential hepatoprotective effects of this endogenous opioid pentapeptide in the experimental model of acetaminophen induced hepatotoxicity in male CBA mice. Met-enkephalin exhibited strong hepatoprotective effects in a dose of 7.5 mg/kg, which corresponds to the protective dose reported for several different animal disease models. In this group plasma alanine aminotransferase and aspartate aminotransferase enzyme activities, as well as liver necrosis score were significantly reduced in comparison to control animals treated with physiological saline (p &gt, 0.01). The specificity of the peptide hepatoprotection was investigated from the standpoint of the receptor and peptide blockade. It was concluded that Met-enkephalin effects on the liver were mediated via δ and ζ opioid receptors. Genotoxic testing of Met-enkephalin confirmed the safety of the peptide.

In this paper, we present a new rule-based system for an artificial protein design incorporating ternary amino acid polarity (polar, nonpolar, and neutral). It may be used to design de novo alpha and beta protein fold structures and mixed class proteins. The targeted molecules are artificial proteins with important industrial and biomedical applications, related to the development of diagnostic-therapeutic peptide pharmaceuticals, antibody mimetics, peptide vaccines, new nanobiomaterials and engineered protein scaffolds.

Medical differential diagnosis is a method of identifying the presence of a particular entity (disease) within a set of multiple possible alternatives. The significant problem in dermatology and pathology is the differential diagnosis of malignant melanoma and other pigmented skin lesions, especially of dysplastic nevi. Malignant melanoma is the most malignant skin neoplasma, with increasing incidence in various parts of the world. It is hoped that the methods of quantitative pathology, i.e. morphometry, can help objectification of the diagnostic process, since early discovery of melanoma results in 10-year survival rate of 90%. The aim of the study was to use fractal dimension calculated from the perimeter-area relation of the cell nuclei as a tool for the differential diagnosis of pigmented skin lesions. We analyzed hemalaun-eosin stained pathohistological slides of pigmented skin lesions: intradermal naevi (n = 45), dysplastic naevi (n = 47), and malignant melanoma (n = 50). It was found that fractal dimension of malignant melanoma cell nuclei differs significantly from the intradermal and dysplastic naevi (p ≤ 0. 001, Steel-Dwass Multiple Comparison Test). Additionaly, ROC analysis confirmed the value of fractal dimension based evaluation. It is suggested that the estimation of fractal dimension from the perimeter-area relation of the cell nuclei may be a potentially useful morphometric parameter in the medical differential diagnosis of pigmented skin lesions.

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

Background: L-alpha-Melanocortin is a strong inhibitor of inflammation.It is a promising new anti-inflammatory and hepatoprotective peptide. Consequently, its melanocortin receptors (MC1, MC3, MC4 and MC5) could be possible targets for the development of new antiinflammatory drugs for chronic inflammatory liver disease. For a long ime it has been believed that only the L-enantiomers of amino acids are present in higher animals, but recent investigations show that D-amino acids also exhibit physiological effects in vivo, despite their very small quantities. The aim of this study was to compare hepatoprotective effects of L-alphamelanocortin and D-alpha-melanocortin using the acetaminophen model of chemical liver damage in male CBA mice. Methods: Tested substances were applied intraperitoneally 60 minutes prior to the intragastric application of acetaminophen (150 mg/kg). Animals were sacrificed 24 hours after the administration of acetaminophen. The criteria for monitoring hepatoprotective effects of the tested substances were biochemical parameters (AST and ALT) and histopathological analysis. Results: The results obtained by the histopathological analysis and biochemical findings show potent hepatoprotective and anti-inflammatory effects of L-alpha-melanocortin in the liver, and suggest the possibility of modulating liver inflammation by means of melanocortin molecules and related receptors. D-alpha-melanocortin did not show any hepatoprotective effects in vivo. Conclusions: Our results show that peptide enantiomerism influences the protective effects of alpha-melanocortin peptides in vivo. This concept may be used to modulate peptide function in vivo and antibody binding assay in vitro. Acknowledgements: The support of the Croatian Ministry of Science, Education and Sports is gratefully acknowledged (grant no. 098-0982929-2524).

Open-source data mining software is completely comparable to commercial programs according to the criteria of functionality and reliability. Moreover, some of them, such as R and Weka, have become the gold standard for industrial applications. According to Rexer's Annual Data Miner Survey in 2010, R has become the data mining tool used by more data miners (43%) than any other (Rexer Analytics, 2010). Therefore, it can be concluded that the use of open source software for educational purposes is completely justified, because students will be able to continue using the same programs after they graduate.

The genetic code defines nucleotide patterns that code for individual amino acids and their complementary, i.e., antisense, pairs. Peptides specified by the complementary mRNAs often bind to each other with a higher specificity and efficacy. Applications of this genetic code property in biomedicine are related to the modulation of peptide and hormone biological function, selective immunomodulation, modeling of discontinuous and linear epitopes, modeling of mimotopes, paratopes and antibody mimetics, peptide vaccine development, peptidomimetic and drug design. We have investigated sense-antisense peptide interactions and related modulation of the peptide function by modulating the effects of a-MSH on hepatoprotection with its antisense peptide LVKAT. First, transcription of complementary mRNA sequence of a-MSH in 3’→5’ direction was used to design antisense peptide to the central motif that serves as a-MSH pharmacophore for melanocortin receptors. Second, tryptophan spectrofluorometric titration was applied to evaluate the binding of a-MSH and its central pharmacophore motif to the antisense peptide, and it was concluded that this procedure represents a simple and efficient method to evaluate sense-antisense peptide interaction in vitro. Third, we showed that antisense peptide LVKAT abolished potent hepatoprotective effects of a-MSH in vivo.

The testing of a bioinformatics algorithm on the training set is not the best indicator of its future performance because of the misleadingly optimistic results. The optimal method of testing is the calculation of error rate on an independent dataset (test set). We have tested the validity of the FOLD-RATE method for the prediction of protein folding rate constants [ln(k f )] using sequences, structural class information and experimentally verified folding rate constants of the Protein Folding Database (PFD). PFD is a publicly accessible repository of thermodynamic and kinetic data of interest for the researchers of different profiles, standardized by the International Foldeomics Consortium. Our results show that when the standardized PFD dataset is used to test a protein fold rate prediction method, the estimation of validity may differ significantly.

Research over the past decade has indicated that melanocortin peptides are potent inhibitors of inflammation and a promising source of new anti-inflammatory and cytoprotective therapies. The purpose of the present paper is to compare protective effects of alpha-, beta-, and gamma-melanocyte stimulating hormone on acetaminophen induced liver lesions in male CBA mice. Acetaminophen was applied intragastrically in a dose of 150 mg/kg, and tested substances were applied intraperitoneally 1 hour before acetaminophen. Mice were sacrificed after 24 hours and intensity of liver injury was estimated by measurement of plasma transaminase activity (AST and ALT) and histopathological grading of lesions. It was found that alpha-, beta-, and gamma-MSH decrease intensity of lesions by both criteria in a dose-dependent manner.

The authors have tested two formulas by means of which the filtrated and the intraocularly (intrathecally) synthesized fraction of particular protein can be distinguished. The laser nephelometric method was applied to determine the serum (IgG, IgA, IgM, C3, albumin), aqueous humor (IgA, IgM, albumin) and CSF (IgG, IgM, C3, albumin) protein values in 42 subjects to test two models in physiological conditions. It was confirmed that the best results were achieved using the formula after Stambuk. Computer simulation performed to compare the formulas after Stambuk and Reiber & Felgenhauer showed a strong correlation (r greater than 0.98) between the calculated filtrated fractions of both models in a wide range of different barrier permeabilities. Laser nephelometry proved to be a useful method to determine low IgA and IgM values in aqueous humor.

The hydropathic profile, secondary structure, epitope and binding site of the a-melanotropin molecule were investigated. It was shown that the standard algorithm according to Kyte and Doolittle may be combined with complex methods of the secondary structure prediction to extract the information relevant for the epitope location and modeling. The binding ligand-receptor motifs of the hormone were investigated by means of the SSpro8 method. The Molecular Recognition Theory combined with an NCBInr protein database search was applied to find the possible paratope (receptor) structures for the predicted a-melanotropin epitope (ligand). The described concept constitutes a useful and simple set of procedures for deriving new biologically active peptides and antibodies and also for performing modulation of peptide-receptor interaction.

We evaluated the effectiveness of latanoprost (Xalatan) monotherapy in primary open angle glaucoma (POAG). Latanoprost is a prostaglandin analogue, the pure 15(R) epimer of 13,14-dihydro-17-phenyl-18,19,20-trinor-PGF2alpha-isopropyl ester. As a prodrug it is being activated by enzymatic hydrolysis in the cornea after which it becomes active acid of latanoprost. Latanoprost is lowering the intraocular pressure (IOP) by increasing the uveoscleral outflow. In this study, latanoprost was used once daily as monotherapy what offers much better compliance for the patients than other combinations of drugs, preserving good IOP control. Based on the significant reduction of the IOP, measured on the day 60 of the trial (mean change in IOP was -5.1 mmHg, with 95% confidence interval in range from -5.6 to -4.5), it is concluded that use of latanoprost is advisable when calculating better IOP control, few side-effects and reductions in costs of potential surgical procedures.

A large body of literature relates physical and chemical properties of the amino acids and protein folding. However, relatively little is known about the relationships of the codons and secondary protein structure. Nucleotide strings based protein folding prediction is important because the Genome Project has resulted in a large number of gene sequences that code for different proteins, of often unknown structure and function We present a new computational algorithm for the prediction of all alpha- and all beta-protein fold classes from the nucleotide and amino acid sequences. The method is based on the binary and error-control coding of nucleotide and amino acid physicochemical properties. It enables quick, simple and accurate prediction of all alpha- and all beta-protein folds on a personal computer. The analysis of the prediction accuracy and its cross-validations by means of the machine learning SMO classifier and classification trees has confirmed the validity of the procedure. We also investigated how encoding physicochemical parameters of the nucleotides and amino acids influences the structure of protein. Genetic code randomisation analysis with respect to the distinguishing of all alpha- and all beta-protein fold classes indicated that: a) there is a very low chance that a better code than the one specified by the nature is randomly produced, b) basic protein units with respect to the genetic coding of alpha- and beta-protein fold classes are not monomers (single amino acids) but dipeptides and tripeptides.

Molecular Recognition Theory is based on the finding of Blalock et al. (Biochem. Biophys. Res. Commun. 121 (1984) 203-207; Nature Med. 1 (1995) 876-878; Biochem. J. 234 (1986) 679-683) that peptides specified by the complementary RNAs bind to each other with higher specificity and efficacy. This theory is investigated considering the interaction of the sense peptides coded by means of messenger RNA (read in 5'--3' direction) and antisense peptides coded in 3'--5' direction. We analysed the hydropathy of the complementary amino acid pairs and their frequencies in 10 peptide-receptor systems with verified ligand-receptor interaction. An optimization procedure aimed to reduce the number of possible antisense peptides derived from the sense peptide has been proposed. Molecular Recognition Theory was also validated by an "in vivo" experiment. It was shown that 3'--5', peptide antisense of alpha-MSH abolished its cytoprotective effects on the gastric mucosa in rats. Molecular Recognition Theory could be useful method to simplify experimental procedures, reduce the costs of the peptide synthesis, and improve peptide structure modelling.

Large scale preparation of N-1-sulfonylcytosine derivatives has been optimized. The best method was the condensation reaction of silylated cytosine (1) with p-toluenesulfonyl chloride in acetonitrile. Depending on the isolation procedure, 1-(p-toluenesulfonyl)cytosine 2 and 1-(p- -toluenesulfonyl)cytosine hydrochloride 3 were isolated in 80 % and 75 % yields, respectively. The NMR evidence presented shows that 2 appears as a common keto-amino tautomer in DMSO-d6 solution while its hydrochloride 3 forms exclusively the rare keto imino tautomer. N-1-Sulfonylcytosine derivatives 2 and 3 were investigated for possible cytotoxic activity on human normal fibroblasts (WI38), human pancreatic adenocarcinoma cells (MIAPaCa2), poorly differentiated cells from lymph node metastases of colon carcinoma (SW-620), and human Burkitt lymphoma cells (Raji). MTT-cytotoxicity screens in human tissue culture cell lines showed that both investigated compounds demonstrated antiproliferative activity in different histological types of tumors. In comparison with 5-fluorouracil, some of N-1-sulfonylcytosine derivatives showed 10 times stronger activity, with respect IC50. The inhibitory effect of the investigated derivatives on normal human cells was lower compared to their antitumor effects. In addition to antitumor effects, hematological findings following the parenteral administration of substances were also investigated., Optimizirana je priprava većih količina N-1-sulfonilcitozinskih derivata, kondenzacijom sililiranoga citozina i p-toluensulfonil klorida u acetonitrilu. Ovisno o načinu izolacije dobiveni su 1-(p-toluensulfonil)citozin 2 (80 %) i 1-(p-toluensulfonil)citozin hidroklorid 3 (75 %). NMR eksperimenti pokazuju isključivo nastajanje keto-imino tautomera 3 u DMSO-d6 otopini, dok se 2 pojavljuje u uobičajenome keto-amino obliku. Ispitivani su potencijalni citotoksični učinci N-1-sulfonilcitozinskih derivata 2 i 3 na fibroblastima čovjeka (WI38), stanicama adenokarcinoma gušterače (MIAPaCa2), slabo diferenciranim metastazama adenokarcinoma debelog crijeva (SW-620) i stanicama Burkitt-ovog limfoma (Raji). Rezultati dobiveni MTT-testom pokazuju da ispitivani spojevi djeluju antiproliferativno na različite histološke tipove tumora. U usporedbi s 5-fluorouracilom, N-1-sulfonilcitozinski derivati pokazuju 10 puta jaču inhibiciju rasta izloženih tumorskih stanica. Inhibicijski učinci ispitivanih spojeva na normalne stanice značajno su slabiji u odnosu na protutumorske učinke. Osim antitumorskoga učinka, ispitivani su i hematološki parametri poslije parenteralne primjene ispitivanih tvari.

The majority of urinary stones in children are composed of calcium oxalate. To investigate the interaction between urinary calcium, oxalate, and citrate as major risk factors for calcium stones formation, their 24-h urinary excretion was determined in 30 children with urolithiasis and 15 normal healthy children. The cutoff points between children with urolithiasis and healthy children, accuracy, sensitivity, and specificity for each risk factor alone as well as for all three taken together were determined. OneR and J4.8 classifiers as parts of the larger data mining software Weka, based on machine learning algorithms, were used for the determination of the cutoff points for differentiation of the children. The decision tree based on J4.8 classifier analysis of all three risk factors together proved to be the best for differentiating stone formers from normal children. In comparison to the accuracy of the differentiation after calcium and oxalate of 80% and 75.6%, respectively, the decision tree showed an accuracy of 97.8%. Even when its stability was tested by the leave-one-out cross-validation procedure, the accuracy remained at a very acceptable percentage of 93.2% correctly classified patients. J4.8 classifier analysis gave a look inside urinary calcium, oxalate, and citrate interaction. Urinary calcium excretion was shown as the most informative in discrimination of the children with urolithiasis from healthy children. However, it was shown that oxalate and citrate excretions might influence the stone formation in a subpopulation of the stone formers. In patients with low urinary calcium, a major role in lithogenesis belongs to oxalate, in some of them alone and in others in conjunction with citrate. Decreased urinary citrate excretion in the presence of increased oxalate excretion may lead to stone formation.

We used the rat model of ethanol induced gastric lesions to measure cytoprotective effects of neuropeptides met-enkephalin and alpha-melanocyte stimulating hormone (alpha-MSH). The lesions were induced with i.g. application of 1 ml 96% ethanol. The peptides were given i.p. 1 h before the ethanol. Sacrifice was made 1 h after ethanol application and hemorrhagic gastric area was assessed in mm(2). alpha-MSH and met-enkephalin exhibited significant and additive cytoprotective effects. The protective effects of alpha-MSH were significantly stronger than of met-enkephalin. Almost total absence of lesions was obtained with met-enkephalin and alpha-MSH mixture 10:1 (10 mg/kg met-enkephalin and 1 mg/kg alpha-MSH). The addition of indomethacin (5 mg/kg s.c.) almost completely abolished the effect of met-enkaphalin, while alpha-MSH mediated cytoprotection was weakened but still present. Interestingly, indomethacin also blocked almost completely the cytoprotective effects of met-enkephalin and alpha-MSH mixture. The latter result may have a practical consequence for the clinical trials in which met-enkephalin and alpha-MSH could be used in combination with non-steroidal anti-inflammatory drugs.

We applied the machine learning procedure to the analysis of serum and aqueous humor albumin, IgG and interferon-γ patterns. The data were analyzed with respect to the cataract, type of diabetes, retinopathy and blood-aqueous humor barrier damage. Intraocular production of IgG was detected in diabetic patients, since the IgG index values were increased in some diabetic groups (especially those with type I diabetes and retinopathy). Comparison of numerical methods and clonal IgG detection suggested that intraocular IgG patterns in diabetes are predominately polyclonal. Interferon-γ (IFN-γ) was pathological in serum and aqueous humor of patients with type I diabetes and to a lesser extent in the type II diabetes group. Machine learning system based on C5.0 classifier extracted 98.5% accurate rules for discrimination of the senile cataract group, diabetes group and diabetic retinopathy group. Our results confirm that the combination of immunochemical and numerical methods with a proper statistical analysis may contribute to the diagnosis of the pathologic ocular immune response and the related retinal or vascular disorders in diabetes. Significant savings in laboratory material and efforts may be obtained by means of the machine learning based optimization of the tests.

An imbalance between urinary-promoting and -inhibiting factors has been suggested as more important in urinary stone formation than a disturbance of any single substance. To investigate the value of promoter/inhibitor ratios for estimation of the risk of urolithiasis, urinary citrate/calcium, magnesium/calcium oxalate, and oxalate/citrate x glycosaminoglycans ratios were determined in 30 children with urolithiasis, 36 children with isolated hematuria, and 15 healthy control children. The cutoff points between normal children and children with urolithiasis, accuracy, specificity, and sensitivity for each ratio were determined and compared with those of the 24-h urine calcium and oxalate excretion and urine saturation calculated with the computer program EQUIL 2. The neural network application (aiNET Artificial Neural Network, version 1.25) was used for the determination of the cutoff points for the classification of normal children and the urolithiasis group. The best test for differentiating stone formers from non-stone formers proved the aiNET determined cutoff values of oxalate/citrate x glycosaminoglycans ratio. The method showed 97.78% accuracy, 100% sensitivity, and 93.33% specificity. Two cutoff points between normal and urolithiasis groups were found showing that the children with urolithiasis had ratio values either above 34.00 or less than 10.16. Increased oxalate excretion was linked to the first cutoff value (34.00), and decreased glycosaminoglycans excretion was typical of the second cutoff value (10.16).

The algorithms and equations that define and link circular coding properties of the genetic code and amino acid structural properties are derived according to the model of Cantor dynamics based automaton. It is shown that the model defines a unifying concept of the genetic code, which incorporates Crick's code without comma and the evolutionary code concept. Arithmetic for codes is defined via the number theory results in coding theory, Smale's horseshoe map and the dynamics on fractal lattices. The method has been denoted SCA (Symbolic Cantor Algorithm) and defined with respect to the principles of Molecular Recognition Theory, Grafstein's hypothesis of the stereochemical origin of the genetic code and Siemion's mutation ring. Underlying Fibonacci dynamics is extracted and mathematically defined considering the Cantor set and Farey tree codon and amino acid projections. Two digit specification of the codon positions, by means of the binary group subdivision, is particularly analysed with respect to octal coding and defined according to the purine-pyrimidine, amino-keto and strong-week H bonding discrimination principles.

Laser nephelometry (LN) is a rapid and very sensitive method for simultaneous determination of albumin, immunoglobulins, C(3)c and C-4 in diluted serum and paired cerebrospinal fluid (CSF) samples. It is very useful in routine analyses. Determination of C(3)c and C-4 covers classical as well as alternative pathways of complement activation. In CSF, they are mostly derived from and related to serum values. Under physiological conditions, the addition of intrathecal C, synthesis is likely. The incidence of complement activation within CSF is also influenced by the method of choice (native molecules, activation products and complexes, inhibitors) and the mode of interpretation of results according to the functional state of the blood-brain barrier (BBB). Calculation of indexes and the modified Reiber's graph method are valid means of detection of complement activation within CSF. Complement activation within CSF was confirmed in 36% (111/302) of neurological patients examined ; in 55% (48/87) of patients with inflammatory and demyelinating diseases, in 40% (37/94) of patients with CNS infections and complications, in 33% (4/12) of patients with motor neuron diseases, in 27% (11/40) of patients with spinal cord compression and sequelae, in 25% (8/32) of patients with neoplastic disease, and in 17% (6/37) of patients with cerebrovascular accidents.

To investigate the risk for the development of urolithiasis in 30 children with urolithiasis, 36 children with isolated hematuria, and 15 healthy control children, 24-h urinary excretion of calcium, sodium, oxalate, citrate, sulfate, phosphate, magnesium, urate, chloride, ammonium, and glycosaminoglycans was determined and urine saturation for calcium oxalate was calculated with the computer program EQUIL 2. Compared with controls, children with urolithiasis had significantly increased calcium excretion, oxalate excretion, and urine saturation, whereas children with isolated hematuria had significantly increased calcium excretion only. The best estimation of the relative risk of urolithiasis can be made after urine saturation, using logistic regression. The percentage of patients correctly classified after urine saturation is 85.41% in comparison with 80.95% and 73.81% when the estimation was done by calcium excretion and oxalate excretion, respectively. Using the breakpoint value of 4.29 for urine saturation, it was possible to separate children with increased risk of urolithiasis development from the group of children with isolated hematuria.

We prospectively studied and classified 152 cases of endogenous uveitis treated at the Ophthalmological Clinic in Split, Yugoslavia, according to clinical presentation, several immunologic parameters including HLA subtyping, and the presence of an associated systemic disease. Using our diagnostic criteria we successfully classified 91.4% of patients. Anterior uveitis was the most common form of clinical presentation (94 patients, 61.8%), whereas an intermediate uveitis was present in only 5.3% of patients (8 patients). By HLA typing we found that 115 patients (75.7%), were positive for HLA-B27 (57 patients, 50%), B5 (30 patients, 26%) and B35 (28 patients, 24%) risk antigens. Of these patients 96 (83%) had an associated systemic illness. In the 8.6% of cases (13 cases) in which the etiology of an endogenous uveitis was not determined, none were associated with an HLA-B risk antigen. Our study emphasizes the association of HLA-B risk antigens and concurrent systemic disease in patients with endogenous uveitis.