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Approximately 50% of tumors carry mutations in TP53; thus, evaluation of the features of mutant p53 is crucial to understanding the mechanisms underlying cell transformation and tumor progression. HaCaT keratinocytes represent a valuable model for research in this area since they are considered normal, although they bear two gain-of-function mutations in TP53. In the present study, transcriptomic and proteomic profiling were employed to examine the functions of mutant p53 and to investigate the impact of its complete abolishment. Our findings indicate that CRISPR-mediated TP53 knockout results in significant changes at the transcriptomic and proteomic levels. The knockout of TP53 significantly increased the migration rate and altered the expression of genes associated with invasion, migration, and EMT but suppressed the epidermal differentiation program. These outcomes suggest that, despite being dysfunctional, p53 may still possess oncosuppressive functions. However, despite being considered normal keratinocytes, HaCaT cells exhibit oncogenic properties.

Obesity is a socially significant disease that is characterized by a disproportionate accumulation of fat. It is also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers and pathological processes linked to obesity is especially vital for young individuals, given their increased potential for lifestyle modifications. By comparing the genetic, proteomic, and metabolomic profiles of individuals categorized as underweight, normal, overweight, and obese, we aimed to determine which omics layer most accurately reflects the phenotypic changes in an organism that result from obesity. We profiled blood plasma samples by employing three omics methodologies. The untargeted GC×GC–MS metabolomics approach identified 313 metabolites. To augment the metabolomic dataset, we integrated a label-free HPLC–MS/MS proteomics method, leading to the identification of 708 proteins. The genomic layer encompassed the genotyping of 647,250 SNPs. Utilizing omics data, we trained sparse Partial Least Squares models to predict body mass index. Molecular features exhibiting frequently non-zero coefficients were selected as potential biomarkers, and we further explored enriched biological pathways. Proteomics was the most effective in single-omics analyses, with a median absolute error (MAE) of 5.44 ± 0.31 kg/m2, incorporating an average of 24 proteins per model. Metabolomics showed slightly lower performance (MAE = 6.06 ± 0.33 kg/m2), followed by genomics (MAE = 6.20 ± 0.34 kg/m2). As expected, multiomic models demonstrated better accuracy, particularly the combination of proteomics and metabolomics (MAE = 4.77 ± 0.33 kg/m2), while including genomics data did not enhance the results. This manuscript is the first multiomics study of obesity in a gender-balanced cohort of young adults profiled by genomic, proteomic, and metabolomic methods. The comprehensive approach provides novel insights into the molecular mechanisms of obesity, opening avenues for more targeted interventions.

The contribution of the antimicrobial activity of sIgA, lactoferrin, -lactalbumin, serum albumin, and lysozyme to the total antimicrobial activity of whey was evaluated. 66 breast milk samples from healthy women aged from 23 to 45 years collected at different periods of lactation were studied. It was found that along with proceeding the lactation period, not only the total antimicrobial activity (r = 0.944) decreased, but also the activity of the low molecular weight fraction containing the sum of antimicrobial peptides (r = 0.950). The median lactoferrin level varied from 3.46 mg/ml in colostrum down to 0.94 mg/ml one year after the onset of lactation that correlated with whey activity (r = 0.616). The concentration of sIgA was peaked in the whey of colostrum (5.01 mg/ml) and significantly reduced in mature milk, remaining approximately at the same level in subsequent periods of lactation (1.0 mg/ml). Serum albumin concentration significantly decreased while proceeding through lactation period (from 5.52 to 4.68 mg/ml) and correlated with whey activity (r = 0.589). Evaluating effects of the purified -lactalbumin on C. albicans cells within the range of 520 mg/ml by spectrophotometry and microscopy showed the absence of fungicidal activity. At the same time, purified lactoferrin, IgA, lysozyme, and serum albumin demonstrated a direct fungicidal effect. The activity of the IgA preparation at a concentration relevant to the sIgA content in the whey of the first day colostrum was 50.0%, and in the whey after 12 months 31.0%; lactoferrin 26.7% and 3.4%; serum albumin 15.0% and 17.7%; lysozyme 0.1% and 1.8%. Thus, the sum of the activities of these polypeptides at concentrations typical for the first-day colostrum was 91.7%, which is comparable to the total activity of this whey 82.4%. The sum of the activities of these polypeptides, typical for 12 months of lactation, was 53.9%, and the total whey activity relevant to this period was 64.5%. Therefore, IgA and lactoferrin contribute the most significant antimicrobial activity in the whey of colostrum, whereas after 12 month-breastfeeding IgA and serum albumin become most significant.

Despite their astonishing biological diversity, surprisingly few shared traits connect all or nearly all living organisms. Aging, i.e., the progressive and irreversible decline in the function of multiple cells and tissues, is one of these fundamental features of all organisms, ranging from single-cell creatures to complex animals, alongside variability, adaptation, growth, healing, reproducibility, mobility, and, finally, death. Age is a key determinant for many pathologies, shaping the risks of incidence, severity, and treatment outcomes for cancer, neurodegeneration, heart failure, sarcopenia, atherosclerosis, osteoporosis, and many other diseases. In this review, we aim to systematically investigate the age-related features of the development of several diseases through the lens of multiomics: from genome instability and somatic mutations to pathway alterations and dysregulated metabolism. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides and proteins (AMPs) are endogenous compounds that have a direct antimicrobial effect on bacteria (e.g. by disrupting bacterial membranes) as well as on fungi and viruses. AMPs are the main components of the innate immunity of living organisms and are produced by both epithelial cells (skin cells, cells of respiratory tract, intestines, urinary and genital tracts) and cells of the immune system and are secreted into secretory fluids. AMPs can also act as chemoattractants for immunocompetent cells (neutrophils, monocytes, T lymphocytes, dendritic cells) in the inflammation site and affect the antigen presenting cells by modulating adaptive T cell immune responses. The representatives of the main 15 AMP classes, that we describe in this review, are the most studied group of the large pool of these compounds. We discuss their localization, expression, and concentration in various human biofluids under normal and pathological conditions.

To represent the composition of small molecules circulating in HepG2 cells and the formation of the “core” of characteristic metabolites that often attract researchers’ attention, we conducted a meta-analysis of 56 datasets obtained through metabolomic profiling via mass spectrometry and NMR. We highlighted the 288 most commonly studied compounds of diverse chemical nature and analyzed metabolic processes involving these small molecules. Building a complete map of the metabolome of a cell, which encompasses the diversity of possible impacts on it, is a severe challenge for the scientific community, which is faced not only with natural limitations of experimental technologies, but also with the absence of transparent and widely accepted standards for processing and presenting the obtained metabolomic data. Formulating our research design, we aimed to reveal metabolites crucial to the Hepg2 cell line, regardless of all chemical and/or physical impact factors. Unfortunately, the existing paradigm of data policy leads to a streetlight effect. When analyzing and reporting only target metabolites of interest, the community ignores the changes in the metabolomic landscape that hide many molecular secrets.

The aim was to study the effect of rabbit immunization with different yeasts cells on overall antimicrobial serum activity and specific activity of antimicrobial peptides fraction.Material and methods. Rabbits were immunized with cells of Candida albicans, Rhodotorula mucilaginosa, Malassezia furfur, Cryptococcus neoformans, Geotrichum candidum, Trichosporon cutaneum and Saccharomyces cerevisiae. AMP fractions were obtained by filtration through 100 kDa filters. Overall activities of sera and their AMP-fractions were estimated spectrophotometrically.Results. Overall serum antimicrobial activity had tendency to decrease after immunization independently from yeast species. Activity of AMP-fractions after immunization with C. albicans, Cr. neoformans, G. candi dum и S. ce revisiae increased, but with other yeasts — decreased. The highest sensitivity to AMP fraction cor res ponded to C. albicans, especially for serum of the rabbit immunized with this yeasts — 1,5-fold higher com pare to control. Serum albumin concentration showed the positive correlation with overall antimicrobial activity against C. albicans (r = 0,760), R. mucilaginosa (r = 0,728), M. furfur (r = 0,723) и T. cutaneum (r = 0,588).Discussion. The results confirm our earlier data. Moreover, they expand current views on the effect of yeasts antigens on activity of serum AMP against different yeasts.Conclusion. Serum albumin and serum AMP demonstrated the specificity toward different yeasts: maximal activity they showed towards specia which more often play opportunistic role.

Although modern biology is now in the post-genomic era with vastly increased access to high-quality data, the set of human genes with a known function remains far from complete. This is especially true for hundreds of mitochondria-associated genes, which are under-characterized and lack clear functional annotation. However, with the advent of multi-omics profiling methods coupled with systems biology algorithms, the cellular role of many such genes can be elucidated. Here, we report genes and pathways associated with TOMM34, Translocase of Outer Mitochondrial Membrane, which plays role in the mitochondrial protein import as a part of cytosolic complex together with Hsp70/Hsp90 and is upregulated in various cancers. We identified genes, proteins, and metabolites altered in TOMM34-/- HepG2 cells. To our knowledge, this is the first attempt to study the functional capacity of TOMM34 using a multi-omics strategy. We demonstrate that TOMM34 affects various processes including oxidative phosphorylation, citric acid cycle, metabolism of purine, and several amino acids. Besides the analysis of already known pathways, we utilized de novo network enrichment algorithm to extract novel perturbed subnetworks, thus obtaining evidence that TOMM34 potentially plays role in several other cellular processes, including NOTCH-, MAPK-, and STAT3-signaling. Collectively, our findings provide new insights into TOMM34’s cellular functions.

Metabolomics based on two-dimensional gas chromatography coupled with mass spectrometry is making high demands on accuracy at all stages of sample preparation, up to the storage and injection into the analytical system. In high sample flow conditions, good repeatability in peak areas and a list of detectable metabolites is sometimes challenging to obtain. In this research, we successfully obtained good repeatability for the peak areas of MSFTA-derivatives of 29 core blood plasma metabolites. Six different strategies of storage and injection were investigated and evaluated for the reproducibility of the obtained data. As the essential factors, we considered popular GC-MS syringe washing solvents (methanol and pyridine); storage conditions (freshly prepared samples and stored for 24 h in ambient temperature or in the refrigerator); scheme of injection (one injection per intact vial or three sequential injections per vial). Our GC×GC-MS results demonstrated that the usage of pyridine as a syringe wash solvent and triple injecting the sample from the same vial was the most appropriate for minimizing the coefficient of variation (CV) of the results obtained (in general,

For further development of the theory of entrepreneurship and the operationalization of its concepts, it is important to clarify the content of its fundamental categories «entrepreneurship» and «business activity». It is shown that in Ukraine entrepreneurship is considered in two aspects: as an economic category and as a business activity, in defining the content of which various imperatives are used. The entrepreneurship as an economic category is proposed to be considered as the economic relations of society and economic agents associated with the search, creation and commercialization of innovations that are a powerful driving force in developing the country’s economic system. The concept of «business activity» should objectivize the category of «entrepreneurship», which ensures its use in applied research and practice. The business activity both in the legislation and in scientific literature is considered as a commercial type of economic activity, that is, economic and entrepreneurial activity correlate with each other as a general and a partial one. A number of features are used to separate the general concept of «economic activity» from the concept of «entrepreneurial activity». Therefore, there are grounds to state that there is a certain violation of the relationship between the category of «entrepreneurship» and the concept of «business activity» since innovation as a fundamental feature of entrepreneurship in the interpretation of the content of business activity has lost its decisive significance. The existing identification of the concepts of «business activity» and «business» is shown, which can not be regarded as correct. It is proposed to select from the business activity that part of it, which in fact is focused on innovation (search and commercialization of innovations) and mark such an activity as a venture one.

The number of infections caused by microorganisms that are resistant to antibiotics and synthetic antibacterial drugs is growing fast worldwide. This is one of the most important and urgent problems in health care. The main efforts of researchers around the world are focused on solving this issue. Nitrofurans represent one of the most effective classes of antibacterial drugs. We have synthesized 4 analogues of nifuroxazide – a well known nitrofuran antibiotic – and confirmed their structures by NMR, IR spectroscopy, and mass-spectrometry. All of the obtained compounds were studied for antimicrobial and antifungal activity. Activity against Escherichia coli , Staphylococcus aureus , Staphylococcus haemolyticus , and Pseudomonas aeruginosa was evaluated by the agar diffusion method. The synthesized compounds suppressed the growth of all the studied bacterial strains except Escherichia coli ; the diameter of the inhibition zones ranged from 13.5 to 28 mm depending on the concentration of the tested compound and bacterial strain. One of the compounds studied in this project – the pyridine analogue of nifuroxazide – exceeded the activity of the standard (nifuroxazide) against the Staphylococcus aureus . The inhibitory activity of the synthesized compounds against the Candida albicans and Cryptococcus neoformans yeasts was determined using the microdilution method. The results were assessed according to the indicator color change. None of the studied compounds showed activity against these cultures. The obtained results confirm that substituted nifuroxazides have significant antimicrobial activity and, therefore, can be considered as promising candidates for developing new antibacterial drugs.

Both biological and technical variations can discredit the reliability of obtained data in omics studies. In this technical note, we investigated the effect of prolonged cultivation of the HepG2 hepatoma cell line on its metabolomic profile. Using the GC × GC-MS approach, we determined the degree of metabolic variability across HepG2 cells cultured in uniform conditions for 0, 5, 10, 15, and 20 days. Post-processing of obtained data revealed substantial changes in relative abundances of 110 metabolites among HepG2 samples under investigation. Our findings have implications for interpreting metabolomic results obtained from immortal cells, especially in longitudinal studies. There are still plenty of unanswered questions regarding metabolomics variability and many potential areas for future targeted and panoramic research. However, we suggest that the metabolome of cell lines is unstable and may undergo significant transformation over time, even if the culture conditions remain the same. Considering metabolomics variability on a relatively long-term basis, careful experimentation with particular attention to control samples is required to ensure reproducibility and relevance of the research results when testing both fundamentally and practically significant hypotheses.

Simple Summary: Obesity is a significant health concern associated with fat accumulation and complications like inflammation, cancer, and diabetes. Understanding its molecular roots is crucial, especially for young individuals who are capable of lifestyle changes. Our study examined underweight, lean, overweight, and obese individuals by analyzing blood samples using metabolomics, proteomics, and genomics. Using metabolomics, we identified 313 substances; proteomics revealed 708 proteins, and genomics explored 647,250 point mutations. Models predicting body mass index showed that, individually, proteomics provided more value for prediction, followed by metabolomics and genomics. Combining proteomics and metabolomics in a multiomic approach yielded the best results, surpassing single-factor analyses. This pioneering study is the first to focus on obesity in young people, integrating genomic, proteomic, and metabolomic data. Our findings provide valuable insights into the molecular mechanisms of obesity, offering potential for more targeted interventions. Obesity is a socially significant disease that is characterized by a disproportionate accumulation of fat. It is also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers and pathological processes linked to obesity is especially vital for young individuals, given their increased potential for lifestyle modifications. By comparing the genetic, proteomic, and metabolomic profiles of individuals categorized as underweight, normal, overweight, and obese, we aimed to determine which omics layer most accurately reflects the phenotypic changes in an organism that result from obesity. We profiled blood plasma samples by employing three omics methodologies. The untargeted GC×GC–MS metabolomics approach identified 313 metabolites. To augment the metabolomic dataset, we integrated a label-free HPLC–MS/MS proteomics method, leading to the identification of 708 proteins. The genomic layer encompassed the genotyping of 647,250 SNPs. Utilizing omics data, we trained sparse Partial Least Squares models to predict body mass index. Molecular features exhibiting frequently non-zero coefficients were selected as potential biomarkers, and we further explored enriched biological pathways. Proteomics was the most effective in single-omics analyses, with a median absolute error (MAE) of 5.44 ± 0.31 kg/m2, incorporating an average of 24 proteins per model. Metabolomics showed slightly lower performance (MAE = 6.06 ± 0.33 kg/m2), followed by genomics (MAE = 6.20 ± 0.34 kg/m2). As expected, multiomic models demonstrated better accuracy, particularly the combination of proteomics and metabolomics (MAE = 4.77 ± 0.33 kg/m2), while including genomics data did not enhance the results. This manuscript is the first multiomics study of obesity in a gender-balanced cohort of young adults profiled by genomic, proteomic, and metabolomic methods. The comprehensive approach provides novel insights into the molecular mechanisms of obesity, opening avenues for more targeted interventions. [ABSTRACT FROM AUTHOR]

Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a growing interest to utilize transcriptome data to unravel activated biological processes responsible for disease progression and response to therapies. This trend is of particular interest for precision medicine which aims at single-patient analysis. Here we evaluated whether gene abundances measured by MinION direct RNA sequencing are suited to produce robust estimates of pathway activation for single sample scoring methods. We performed multiple RNA-seq analyses for a single sample that originated from the HepG2 cell line, namely five ONT replicates, and three replicates using Illumina NovaSeq. Two pathway scoring methods were employed—ssGSEA and singscore. We estimated the ONT performance in terms of detected protein-coding genes and average pairwise correlation between pathway activation scores using an exhaustive computational scheme for all combinations of replicates. In brief, we found that at least two ONT replicates are required to obtain reproducible pathway scores for both algorithms. We hope that our findings may be of interest to researchers planning their ONT direct RNA-seq experiments.

Cyanide represents a persistent threat for accidental or malicious misuse due to easy conversion into a toxic gas and access to large quantities through several industries. The high safety index of hydroxocobalamin is a cornerstone quality as a cyanide scavenger. Unfortunately, intravenous infusion of hydroxocobalamin limits the utility in a mass casualty setting. We previously reported platinum(II) [Pt(II)] complexes with trans-directing sulfur ligands as an efficacious alternative to hydroxocobalamin when delivered by a bolus intramuscular (IM) injection in mice and rabbits. Thus, to enable Pt(II) as an alternative to hydroxocobalamin, a high safety factor is needed. The objective is to maintain efficacy and mitigate the risk of nephrotoxicity. Platinum amino acid complexes with the ability to form 5- or 6-membered rings and possessing either carboxylates or carboxamides are evaluated in vitro for cyanide scavenging. In vivo efficacy wa s evaluated in the zebrafish and mice cyanide exposure models. In addition, Pt(II) complex toxicity and pharmacokinetics were evaluated in a cyanide naive Sprague Dawley model. Doses for toxicity are escalated to 5× from the efficacious dose in mice using a body surface area adjustment. The results show the carboxamide ligands display a time and pH dependence on cyanide scavenging in vitro and efficacy in vivo. Additionally, exchanging the carboxylate for carboxamide showed reduced indications of renal injury. A pharmacokinetic analysis of the larger bidentate complexes displayed rapid absorption by IM administration and having similar plasma exposure. These findings point to the importance of pH and ligand structures for methionine carboxamide complexes with Pt(II). [ABSTRACT FROM AUTHOR]

In the paper, we discuss some problems concerning the structural properties of crossed products. While expansions of [C.sup.*]-algebras under group actions have been studied rather extensively, known difficulties in the transition to irreversible dynasmical systems require the development of new methods. The first step in this direction is to study actions of inverse semigroups, whose properties are closest to those of groups. The main tool to achieve the goal is the concept of grading. The detection of the grading structure in the corresponding constructions seems to be very promising. Bibliography: 3 titles., UDC 512.53, 517.986.22, 517.986.24 INTRODUCTION The initial motivation to present these notes was an attempt to find a satisfactory construction of the operator algebra associated with a semigroup dynamical system, [...]