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Article: Extracellular Matrix- and Integrin Adhesion Complexes-Related Genes in the Prognosis of Prostate Cancer Patients' Progression-Free Survival.

Samaržija, Ivana / Konjevoda, Paško

2023 Volume 11, Issue 7

Abstract: Prostate cancer is a heterogeneous disease, and one of the main obstacles in its management is the inability to foresee its course. Therefore, novel biomarkers are needed that will guide the treatment options. The extracellular matrix (ECM) is an ... ...

Abstract	Prostate cancer is a heterogeneous disease, and one of the main obstacles in its management is the inability to foresee its course. Therefore, novel biomarkers are needed that will guide the treatment options. The extracellular matrix (ECM) is an important part of the tumor microenvironment that largely influences cell behavior. ECM components are ligands for integrin receptors which are involved in every step of tumor progression. An underlying characteristic of integrin activation and ligation is the formation of integrin adhesion complexes (IACs), intracellular structures that carry information conveyed by integrins. By using The Cancer Genome Atlas data, we show that the expression of ECM- and IACs-related genes is changed in prostate cancer. Moreover, machine learning methods revealed that they are a source of biomarkers for progression-free survival of patients that are stratified according to the Gleason score. Namely, low expression of
Language	English
Publishing date	2023-07-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines11072006
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Article ; Online: How ambiguity codes specify molecular descriptors and information flow in Code Biology.

Štambuk, Nikola / Konjevoda, Paško / Štambuk, Albert

Bio Systems

2023 Volume 233, Page(s) 105034

Abstract: The article presents IUPAC ambiguity codes for incomplete nucleic acid specification, and their use in Code Biology. It is shown how to use this nomenclature in order to extract accurate information on different properties of the biological systems. We ... ...

Abstract	The article presents IUPAC ambiguity codes for incomplete nucleic acid specification, and their use in Code Biology. It is shown how to use this nomenclature in order to extract accurate information on different properties of the biological systems. We investigated the use of ambiguity codes, as mathematical and logical operators and truth table elements, for the encoding of amino acids by means of the Standard Genetic Code. It is explained how to use ambiguity codes and truth functions in order to obtain accurate information on different properties of the biological systems. Nucleotide ambiguity codes could be applied to: 1. encoding descriptive information of nucleotides, amino acids and proteins (e.g., of polarity, relative solvent accessibility, atom depth, etc.), and 2. system modelling ranging from standard bioinformatics tools to classic evolutionary models (i.e. from Miyazawa-Jernigan statistical potential to Kimura three-substitution-type model, respectively). It is shown that the algorithms based on IUPAC ambiguity codes, Boolean functions and truth table, Probabilistic Square of Opposition/Semiotic Square and Klein 4-groups-could be used for the bioinformatics analyses and Relational data modelling in natural science. Underlying mathematical, logical and semiotic concepts of interest are presented and addressed.
Language	English
Publishing date	2023-09-21
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2023.105034
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Article: Prognostic Significance of Amino Acid Metabolism-Related Genes in Prostate Cancer Retrieved by Machine Learning.

Samaržija, Ivana / Trošelj, Koraljka Gall / Konjevoda, Paško

Cancers

2023 Volume 15, Issue 4

Abstract: Prostate cancer is among the leading cancers according to both incidence and mortality. Due to the high molecular, morphological and clinical heterogeneity, the course of prostate cancer ranges from slow growth that usually does not require immediate ... ...

Abstract	Prostate cancer is among the leading cancers according to both incidence and mortality. Due to the high molecular, morphological and clinical heterogeneity, the course of prostate cancer ranges from slow growth that usually does not require immediate therapeutic intervention to aggressive and fatal disease that spreads quickly. However, currently available biomarkers cannot precisely predict the course of a disease, and novel strategies are needed to guide prostate cancer management. Amino acids serve numerous roles in cancers, among which are energy production, building block reservoirs, maintenance of redox homeostasis, epigenetic regulation, immune system modulation and resistance to therapy. In this article, by using The Cancer Genome Atlas (TCGA) data, we found that the expression of amino acid metabolism-related genes is highly aberrant in prostate cancer, which holds potential to be exploited in biomarker design or in treatment strategies. This change in expression is especially evident for catabolism genes and transporters from the solute carrier family. Furthermore, by using recursive partitioning, we confirmed that the Gleason score is strongly prognostic for progression-free survival. However, the expression of the genes
Language	English
Publishing date	2023-02-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15041309
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Article ; Online: Relational model of the standard genetic code.

Konjevoda, Paško / Štambuk, Nikola

Bio Systems

2021 Volume 210, Page(s) 104529

Abstract: 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, ... ...

Abstract	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).
MeSH term(s)	Animals ; Codon/genetics ; Evolution, Molecular ; Genetic Code/genetics ; Humans ; Models, Genetic
Chemical Substances	Codon
Language	English
Publishing date	2021-08-28
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2021.104529
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Article ; Online: The temperature dependence of amino acid hydrophobicity data is related to the genetic coding algorithm for complementary (sense and antisense) peptide interactions.

Štambuk, Nikola / Konjevoda, Paško

Data in brief

2020 Volume 30, Page(s) 105392

Abstract: 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 ( ... ...

Abstract	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 (Log
Language	English
Publishing date	2020-03-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2020.105392
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Article: The temperature dependence of amino acid hydrophobicity data is related to the genetic coding algorithm for complementary (sense and antisense) peptide interactions

Štambuk, Nikola / Konjevoda, Paško

Data in Brief. 2020 June, v. 30

2020

Abstract	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” (Štambuk and Konjevoda, 2020).
Keywords	algorithms ; amino acids ; data collection ; evolution ; genetic code ; hydrophobicity ; peptides ; purines ; temperature
Language	English
Dates of publication	2020-06
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2020.105392
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Article ; Online: New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group.

Štambuk, Nikola / Konjevoda, Paško / Brčić-Kostić, Krunoslav / Baković, Josip / Štambuk, Albert

Bio Systems

2023 Volume 233, Page(s) 105030

Abstract: Phylogenetics is the study of ancestral relationships among biological species. Such sequence analyses are often represented as phylogenetic trees. The branching pattern of each tree and its topology reflect the evolutionary relatedness between analyzed ... ...

Abstract	Phylogenetics is the study of ancestral relationships among biological species. Such sequence analyses are often represented as phylogenetic trees. The branching pattern of each tree and its topology reflect the evolutionary relatedness between analyzed sequences. We present a Klein four-group algorithm (K4A) for the evolutionary analysis of nucleotide and amino acid sequences. Klein four-group set of operators consists of: identity e (U), and three elements-a = transition (C), b = transversion (G) and c = transition-transversion or complementarity (A). We generated Klein four-group based distance matrices of: 1. Cayley table (CK4), 2. Table rows (K4R), 3. Table columns (K4C), and 4. Euclidean 2D distance (K4E). The performance of the matrices was tested on a dataset of RecA proteins in bacteria, eukaryotes (Rad51 homolog) and archaea (RadA homolog). RecA and its functional homologs are found in all species, and are essential for the repair and maintenance of DNA. Consequently, they represent a good model for the study of evolutionary relationship of protein and nucleotide sequences. The ancestral relationship between the sequences was correctly classified by all K4A matrices concerning general topology. All distance matrices exhibited small variations among species, and overall results of tree classification were in agreement with the general patterns obtained by standard BLOSUM and PAM substitution matrices. During the evolution of a code there is a phase of optimization of system rules, the ambiguity of a code is eliminated, and the system starts producing specific components. Klein four-group algorithm is consistent with the concept of ambiguity reduction. It also enables the use of different genetic code table variants optimized for particular transitions in evolution based on biological specificity.
MeSH term(s)	Amino Acids/genetics ; Nucleotides/genetics ; Phylogeny ; Proteins/chemistry ; Algorithms ; Evolution, Molecular
Chemical Substances	Amino Acids ; Nucleotides ; Proteins
Language	English
Publishing date	2023-09-17
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2023.105030
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Article ; Online: Determining amino acid scores of the genetic code table: Complementarity, structure, function and evolution.

Štambuk, Nikola / Konjevoda, Paško

Bio Systems

2019 Volume 187, Page(s) 104026

Abstract: 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 ... ...

Abstract	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 1
MeSH term(s)	Amino Acids/chemistry ; Amino Acids/physiology ; Evolution, Molecular ; Genetic Code/physiology ; Hydrophobic and Hydrophilic Interactions ; Models, Genetic ; Systems Biology
Chemical Substances	Amino Acids
Language	English
Publishing date	2019-09-11
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2019.104026
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Article ; Online: Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research.

Štambuk, Nikola / Konjevoda, Paško / Pavan, Josip

International journal of molecular sciences

2021 Volume 22, Issue 17

Abstract: 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 ... ...

Abstract	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
MeSH term(s)	Algorithms ; Amino Acid Sequence/genetics ; Binding Sites/genetics ; COVID-19/blood ; COVID-19/diagnosis ; COVID-19/virology ; COVID-19 Serological Testing/methods ; Humans ; Immunochemistry/methods ; Molecular Docking Simulation ; Peptides/genetics ; Peptides/metabolism ; Protein Binding/genetics ; Protein Engineering/methods ; SARS-CoV-2/isolation & purification ; Spike Glycoprotein, Coronavirus/isolation & purification ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Peptides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-08-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22179106
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Article ; Online: The effects of simvastatin and fenofibrate on malondialdehyde and reduced glutathione concentrations in the plasma, liver, and brain of normolipidaemic and hyperlipidaemic rats.

Vukšić, Antonija / Rašić, Dubravka / Žunec, Suzana / Božina, Tamara / Konjevoda, Paško / Lovrić, Jasna / Bilušić, Marinko / Bradamante, Vlasta

Arhiv za higijenu rada i toksikologiju

2023 Volume 74, Issue 1, Page(s) 34–41

Abstract: The objective of study was to investigate the effects of different doses of simvastatin and fenofibrate on malondialdehyde (MDA) and reduced glutathione (GSH) in the plasma, liver, and brain tissue of male normolipidaemic and hyperlipidaemic rats. ... ...

Abstract	The objective of study was to investigate the effects of different doses of simvastatin and fenofibrate on malondialdehyde (MDA) and reduced glutathione (GSH) in the plasma, liver, and brain tissue of male normolipidaemic and hyperlipidaemic rats. Normolipidaemic (Wistar) rats were receiving 10 or 50 mg/kg a day of simvastatin or 30 or 50 mg/kg a day of fenofibrate. Hyperlipidaemic (Zucker) rats were receiving 50 mg/kg/day of simvastatin or 30 mg/kg/day of fenofibrate. Control normolipidaemic and hyperlipidaemic rats were receiving saline. Simvastatin, fenofibrate, and saline were administered by gavage for three weeks. In normolipidaemic rats simvastatin and fenofibrate showed similar and dose-independent effects on plasma and brain MDA and GSH concentrations. Generally, plasma and brain MDA decreased, while brain GSH concentration increased. In hyperlipidaemic rats simvastatin did not affect plasma and brain MDA and GSH concentrations but significantly decreased liver GSH. Fenofibrate decreased plasma and liver MDA but increased brain MDA. In both rat strains fenofibrate significantly decreased liver GSH concentrations, most likely because fenofibrate metabolites bind to GSH. Our findings suggest that simvastatin acts as an antioxidant only in normolipidaemic rats, whereas fenofibrate acts as an antioxidant in both rat strains.
MeSH term(s)	Rats ; Male ; Animals ; Simvastatin/pharmacology ; Simvastatin/therapeutic use ; Fenofibrate/pharmacology ; Glutathione/metabolism ; Antioxidants/pharmacology ; Malondialdehyde/metabolism ; Malondialdehyde/pharmacology ; Rats, Wistar ; Rats, Zucker ; Liver ; Brain
Chemical Substances	Simvastatin (AGG2FN16EV) ; Fenofibrate (U202363UOS) ; Glutathione (GAN16C9B8O) ; Antioxidants ; Malondialdehyde (4Y8F71G49Q)
Language	English
Publishing date	2023-04-04
Publishing country	Croatia
Document type	Journal Article
ZDB-ID	127289-5
ISSN	1848-6312 ; 0004-1254
ISSN (online)	1848-6312
ISSN	0004-1254
DOI	10.2478/aiht-2023-74-3697
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