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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., Competing Interests: Declaration of competing interest Authors declare no conflict of Interest for their article., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Staphylococcus aureus ( S. aureus ) is an aggressive opportunistic pathogen of prominent virulence and antibiotic resistance. These characteristics are due in part to the accessory gene regulator ( agr ) quorum-sensing system, which allows for the rapid adaptation of S. aureus to environmental changes and thus promotes virulence and the development of pathogenesis. AgrA is the agr system response regulator that binds to the P2 and P3 promoters and upregulates agr expression. In this study, we reveal that S. aureus AgrA is modified by covalent binding of CoA (CoAlation) in response to oxidative or metabolic stress. The sites of CoAlation were mapped by liquid chromatography tandem mass spectrometry (LC-MS/MS) and revealed that oxidation-sensing Cys199 is modified by CoA. Surface plasmon resonance (SPR) analysis showed an inhibitory effect of CoAlation on the DNA-binding activity, as CoAlated AgrA had significantly lower affinity towards the P2 and P3 promoters than non-CoAlated AgrA. Overall, this study provides novel insights into the mode of transcriptional regulation in S. aureus and further elucidates the link between the quorum-sensing and oxidation-sensing roles of the agr system.

Coenzyme A (CoA) is an essential cofactor present in all living cells. Under physiological conditions, CoA mainly functions to generate metabolically active CoA thioesters, which are indispensable for cellular metabolism, the regulation of gene expression, and the biosynthesis of neurotransmitters. When cells are exposed to oxidative or metabolic stress, CoA acts as an important cellular antioxidant that protects protein thiols from overoxidation, and this function is mediated by protein CoAlation. CoA and its derivatives are strictly maintained at levels controlled by nutrients, hormones, metabolites, and cellular stresses. Dysregulation of their biosynthesis and homeostasis has deleterious consequences and has been noted in a range of pathological conditions, including cancer, diabetes, Reye's syndrome, cardiac hypertrophy, and neurodegeneration. The biochemistry of CoA biosynthesis, which involves five enzymatic steps, has been extensively studied. However, the existence of a CoA biosynthetic complex and the mode of its regulation in mammalian cells are unknown. In this study, we report the assembly of all five enzymes that drive CoA biosynthesis, in HEK293/Pank1β and A549 cells, using the in situ proximity ligation assay. Furthermore, we show that the association of CoA biosynthetic enzymes is strongly upregulated in response to serum starvation and oxidative stress, whereas insulin and growth factor signaling downregulate their assembly.

Spores of Bacillus species have novel properties, which allow them to lie dormant for years and then germinate under favourable conditions. In the current work, the role of a key metabolic integrator, coenzyme A (CoA), in redox regulation of growing cells and during spore formation in Bacillus megaterium and Bacillus subtilis is studied. Exposing these growing cells to oxidising agents or carbon deprivation resulted in extensive covalent protein modification by CoA (termed protein CoAlation), through disulphide bond formation between the CoA thiol group and a protein cysteine. Significant protein CoAlation was observed during sporulation of B. megaterium, and increased largely in parallel with loss of metabolism in spores. Mass spectrometric analysis identified four CoAlated proteins in B. subtilis spores as well as one CoAlated protein in growing B. megaterium cells. All five of these proteins have been identified as moderately abundant in spores. Based on these findings and published studies, protein CoAlation might be involved in facilitating establishment of spores' metabolic dormancy, and/or protecting sensitive sulfhydryl groups of spore enzymes., (© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.)

The quantity and quality of preoperative material in colorectal cancer is often limiting factor in determination of risk factors and therapy planning. The most important negative prognostic factors are intravascular and perineural invasion, as well as tumor budding. Usually, the only parameter available in preoperative biopsy is tumor budding. However, the growing body of evidence suggests that cancer differentiation based on the poorly differentiated clusters has better prognostic value. The limiting factor in applying of these new parameters is reproducible, simple, cheap and fast method of their determination. In this paper we investigated the prognostic value of lacunarity, determined in preoperative biopsy. Lacunarity is a measure of spatial heterogeneity (inhomogeneity) in an image. It quantifies how objects fill the space, and enables analysis of gaps distribution, homogeneity of gaps, and presence of structures. It was shown that lacunarity and the total number of buds could be combined in a model which clearly divides colorectal cancer patients in low, medium and high risk subgroups. The paper also points out that the quantitative numerical methods are superior to semiquantitative methods, and that individual methods should be combined using algorithms to obtain a more accurate prediction. Because the study described is designed as a pilot study, verification is needed on a larger sample of patients from independent researchers.

Aurora A kinase is a master mitotic regulator whose functions are controlled by several regulatory interactions and post-translational modifications. It is frequently dysregulated in cancer, making Aurora A inhibition a very attractive antitumor target. However, recently uncovered links between Aurora A, cellular metabolism and redox regulation are not well understood. In this study, we report a novel mechanism of Aurora A regulation in the cellular response to oxidative stress through CoAlation. A combination of biochemical, biophysical, crystallographic and cell biology approaches revealed a new and, to our knowledge, unique mode of Aurora A inhibition by CoA, involving selective binding of the ADP moiety of CoA to the ATP binding pocket and covalent modification of Cys290 in the activation loop by the thiol group of the pantetheine tail. We provide evidence that covalent CoA modification (CoAlation) of Aurora A is specific, and that it can be induced by oxidative stress in human cells. Oxidising agents, such as diamide, hydrogen peroxide and menadione were found to induce Thr 288 phosphorylation and DTT-dependent dimerization of Aurora A. Moreover, microinjection of CoA into fertilized mouse embryos disrupts bipolar spindle formation and the alignment of chromosomes, consistent with Aurora A inhibition. Altogether, our data reveal CoA as a new, rather selective, inhibitor of Aurora A, which locks this kinase in an inactive state via a "dual anchor" mechanism of inhibition that might also operate in cellular response to oxidative stress. Finally and most importantly, we believe that these novel findings provide a new rationale for developing effective and irreversible inhibitors of Aurora A, and perhaps other protein kinases containing appropriately conserved Cys residues., (Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.)

Peroxiredoxins (Prdxs) are antioxidant enzymes that catalyse the breakdown of peroxides and regulate redox activity in the cell. Peroxiredoxin 5 (Prdx5) is a unique member of Prdxs, which displays a wider subcellular distribution and substrate specificity and exhibits a different catalytic mechanism when compared to other members of the family. Here, the role of a key metabolic integrator coenzyme A (CoA) in modulating the activity of Prdx5 was investigated. We report for the first time a novel mode of Prdx5 regulation mediated via covalent and reversible attachment of CoA (CoAlation) in cellular response to oxidative and metabolic stress. The site of CoAlation in endogenous Prdx5 was mapped by mass spectrometry to peroxidatic cysteine 48. By employing an in vitro CoAlation assay, we showed that Prdx5 peroxidase activity is inhibited by covalent interaction with CoA in a dithiothreitol-sensitive manner. Collectively, these results reveal that human Prdx5 is a substrate for CoAlation in vitro and in vivo, and provide new insight into metabolic control of redox status in mammalian cells.

Dictyostelium discoideum (D. discoideum) is a simple eukaryote with a unique life cycle in which it differentiates from unicellular amoebae into a fruiting body upon starvation. Reactive oxygen species (ROS) have been associated with bacterial predation, as well as regulatory events during D. discoideum development and differentiation. Coenzyme A (CoA) is a key metabolic integrator in all living cells. A novel function of CoA in redox regulation, mediated by covalent attachment of CoA to cellular proteins in response to oxidative or metabolic stress, has been recently discovered and termed protein CoAlation. In this study, we report that the level of CoA and protein CoAlation in D. discoideum are developmentally regulated, and correlate with the temporal expression pattern of genes implicated in CoA biosynthesis during morphogenesis. Furthermore, treatment of growing D. discoideum cells with oxidising agents results in a dose-dependent increase of protein CoAlation. However, much higher concentrations were required when compared to mammalian cells and bacteria. Increased resistance of D. discoideum to oxidative stress induced by H 2 O 2 has previously been attributed to high levels of catalase activity. In support of this notion, we found that H 2 O 2 -induced protein CoAlation is significantly increased in CatA-deficient D. discoideum cells. Collectively, this study provides insights into the role of CoA and protein CoAlation in the maintenance of redox homeostasis in amoeba and during D. discoideum morphogenesis., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

In all living organisms, coenzyme A (CoA) is an essential cofactor with a unique design allowing it to function as an acyl group carrier and a carbonyl-activating group in diverse biochemical reactions. It is synthesized in a highly conserved process in prokaryotes and eukaryotes that requires pantothenic acid (vitamin B5), cysteine and ATP. CoA and its thioester derivatives are involved in major metabolic pathways, allosteric interactions and the regulation of gene expression. A novel unconventional function of CoA in redox regulation has been recently discovered in mammalian cells and termed protein CoAlation. Here, we report for the first time that protein CoAlation occurs at a background level in exponentially growing bacteria and is strongly induced in response to oxidizing agents and metabolic stress. Over 12% of Staphylococcus aureus gene products were shown to be CoAlated in response to diamide-induced stress . In vitro CoAlation of S. aureus glyceraldehyde-3-phosphate dehydrogenase was found to inhibit its enzymatic activity and to protect the catalytic cysteine 151 from overoxidation by hydrogen peroxide. These findings suggest that in exponentially growing bacteria, CoA functions to generate metabolically active thioesters, while it also has the potential to act as a low-molecular-weight antioxidant in response to oxidative and metabolic stress., (© 2018 The Author(s).)

The study presents the epidemiological features of patients treated with renal replacement therapy (RRT) in Serbia from 1997 to 2009 and compares the results of hemodialysis treatment in 1999 and 2009. Epidemiological data were obtained from the National Registry of RRT patients and data on hemodialysis treatment from special surveys conducted in 1999 and 2009. Within the period 1997-2009 the incidence of patients on RRT increased from 108 to 179 per million population (pmp), prevalence rose from 435 to 699 pmp, while mortality rate fell from 20.7% to 16.7%. The frequency of patients with glomerulonephritis decreased, while that of patients with diabetes and hypertensive nephropathy increased. In late 2009 there were 5208 patients receiving RRT in Serbia. Within the examined period new hemodialysis and reverse osmosis equipment were purchased, high-flux dialyzers with synthetic membranes were increasingly used and the number of patients receiving hemodiafiltration increased to 17.6%. Kt/V greater than 1.2 was recorded in 16% of the patients in 1999 but 52% in 2009. Options for correction of anemia and mineral disorders have also improved. The percentage of patients with HbsAg (13.8% vs. 4.8%) as well as anti-hepatitis C virus antibodies positive patients (23.2% vs. 12.7%) was significantly lower in 2009 than in 1999. Both the incidence and prevalence of RRT patients in Serbia are rising continuously, while the mortality rate is falling. More favorable conditions for dialysis treatment have brought about significant improvement in the results over the last 10 years., (© 2012 The Authors. Hemodialysis International © 2012 International Society for Hemodialysis.)

The term "quality of life" usually describes factors that have an impact on living conditions within the society or on an individual. Generally, the term quality of life refers to the level of the welfare of individuals or group of people. Obesity is a medical condition in which excess body fat has accumulated to the extent that it may have an adverse effect on health and as such is one of the most common pathological conditions of modern society. Almost 10-25% of adult population in Europe, 1/3 population in the USA and 20% of population in Croatia are affected by obesity. In this prospective study we included 30 patients who underwent Sweedish adjustable gastric band procedure (SAGB) (Johnson & Johnson) procedures without complications during the first year of the postoperative period. Body mass index (BMI) was in female patients 40,52174 kg/m2 and in male patients 46,71429 kg/m2. Prior to the surgical procedures 13 patients (43.33%) experienced worse health conditions. Health conditions were equl in 17 patients. The treatment was ineffective in 5 patients (16.67%). In 5 patients health conditions were equal. 6 patients (20%) had good quality of life, 11 patients (36.67%) very good and only 3 patients (10%) had excellent quality of life after the procedure. We noticed body weight reduction in all patients. The quality of life was improved in all patients, except for one 28 years old woman. Body weight loss and quality of life after the procedure are in positive correlation which means that significant body weight loss leads to improved quality of life. Our conclusion is that SAGB is a quality method in obesity treatment which improves quality of life.

Introduction: Adult polycystic kidney disease (APKD) is the most common hereditary kidney disease in humans. The course of the disease is accompanied by numerous complications. OBJECTIVE The aim was to assess the prevalence, clinical course and outcome of adult dominant polycystic kidney disease (ADPKD) patients on renal replacement therapy., Method: Medical data on 700 haemodialyzed (HD) and 500 transplanted patients treated in 10 Serbian centres from 1996 to 2000 were retrospectively analyzed. While ADPKD patients accounted for 13% of HD patients in Serbia in 2000, in the period between 1996 and 2000, the percent of patients with ADPKD in the population of patients starting HD in 8 examined centres changed from 13.5% to 6.9%., Results: The total number of 180 ADPKD patients on HD was analyzed (96 males; aged 55 years at HD onset). Their HD lasted between 1 and 22 years: males started HD 1.3 years earlier and spent on HD 1.1 years less than females. In 53% of HD patients one or more family members had ADPKD but the cause of death was unknown for many family members. Hypertension was present in 75% of ADPKD patients, anaemia in 37% and other organ involvement (usually liver) was found in 53 patients. Fifty patients experienced AV fistula thrombosis and a vascular prosthesis had to be used in 9 of them. A hundred and two HD patients died (aged between 38 and 78 years, on HD for 5.3 years). The causes of death were stroke (19.6%), cardiovascular diseases (29%), infections, while 5% of patients died with the picture of acute abdomen. Among 500 transplanted patients, there were 20 patients with ADPKD (11 males, ages between 35 and 56 years at the time of transplantation) and 14 of them received graft from cadaver donor. Uni- or bilateral nephrectomy was done in 4 patients in the pretransplant preparation, and in another two early after transplantation due to urinary infection. Three patients restarted HD in the first 3 months after transplantation due to acute tubular necrosis and 10 patients died 56.5 months after the transplantation. The known causes of death were cardiovascular disease (3 patients), severe gastrointestinal bleeding (2 patients), infection (2 patients) and cancer (2 patients)., Conclusion: The obtained results showed that it was possible to provide a favourable outcome of patients with APBB on renal replacement therapy in spite of numerous complications.