BioChem最新文献

{"title":"pH-Selective Reactions to Selectively Reduce Cancer Cell Proliferation: Effect of CaS Nanostructures in Human Skin Melanoma and Benign Fibroblasts.","authors":"Olga M Rodríguez Martínez, Michelle A Narváez Ramos, Angeliz A Soto Acevedo, Carolina C Colón Colón, Darlene Malavé Ramos, Coral Castro Rivera, Miguel E Castro Rosario","doi":"10.3390/biochem3010002","DOIUrl":"10.3390/biochem3010002","url":null,"abstract":"<p><p>An acidic extracellular pH value (pH_e) is characteristic of many cancers, in contrast to the physiologic pH_e found in most benign cells. This difference in pH offers a unique opportunity to design and engineer chemicals that can be employed for pH-selective reactions in the extracellular fluid of cancer cells. The viability of human skin melanoma and corresponding fibroblasts exposed to CaS dispersions is reported. The viability of melanoma cells decreases with CaS dispersion concentration and reaches 57% at 3%, a value easily distinguishable from melanoma control experiments. In contrast, the viability of benign fibroblasts remains nearly constant within experimental error over the range of dispersion concentrations studied. The CaS dispersions facilitate vinculin delocalization in the cytoplasmic fluid, a result consistent with improved focal adhesion kinase (FAK) regulation in melanoma cells. Thermodynamic considerations are consistent with the formation of <math> <msub><mrow><mi>H</mi></mrow> <mrow><mn>2</mn></mrow> </msub> <mi>S</mi></math> from CaS in the presence of protons. The thermodynamic prediction is verified in independent experiments with solid CaS and acidic aqueous solutions. The amount of <math> <msub><mrow><mi>H</mi></mrow> <mrow><mn>2</mn></mrow> </msub> <mi>S</mi></math> formed decreases with pH. An activation energy for the process of (30 ± 10) kJ/mol in the temperature range of 280 to 330 K is estimated from initial rate measurements as a function of temperature. The total Gibbs energy minimization approach was employed to establish the distribution of sulfides-including <math> <msub><mrow><mi>H</mi></mrow> <mrow><mn>2</mn></mrow> </msub> <mi>S</mi></math> in the gas and aqueous phases-from the dissociation of CaS as a function of pH to mimic physiologically relevant pH values. Theoretical calculations suggest that partially protonated CaS in solution can be stable until the sulfur atom bonds to two hydrogen atoms, resulting in the formation of Ca²⁺ and <math> <msub><mrow><mi>H</mi></mrow> <mrow><mn>2</mn></mrow> </msub> <mi>S</mi></math> , which can be solvated and/or released to the gas phase. Our results are consistent with a model in which CaS is dissociated in the extracellular fluid of melanoma cells selectively. The results are discussed in the context of the potential biomedical applications of CaS dispersions in cancer therapies.</p>","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"3 1","pages":"15-30"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10079261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9274120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intracellular Organization of Proteins and Nucleic Acids via Biomolecular Condensates in Human Health and Diseases","authors":"Raffaella Gallo","doi":"10.3390/biochem3010003","DOIUrl":"https://doi.org/10.3390/biochem3010003","url":null,"abstract":"Eukaryotic cells are intracellularly divided into several compartments that provide spatiotemporal control over biochemical reactions. Phase separation of proteins and RNA is emerging as an important mechanism underlying the formation of intracellular compartments that are not delimited by membranes. These structures are also known as biomolecular condensates and have been shown to serve a myriad of cellular functions, such as organization of cytoplasm and nucleoplasm, stress response, signal transduction, gene regulation, and immune response. Here, the author will summarize our current understanding of intracellular phase separation, its biological functions, and how this phenomenon is regulated in eukaryotic cells. Additionally, the author will review recent evidence of the role of biomolecular condensates in the development of pathophysiological conditions, with special emphasis on cancer and immune signaling.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77995246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Current Technical Approaches to Study RNA–Protein Interactions in mRNAs and Long Non-Coding RNAs","authors":"Johanna Mattay","doi":"10.3390/biochem3010001","DOIUrl":"https://doi.org/10.3390/biochem3010001","url":null,"abstract":"It is commonly understood that RNA-binding proteins crucially determine the fate of their target RNAs. Vice versa, RNAs are becoming increasingly recognized for their functions in protein regulation and the dynamics of RNA-protein complexes. Long non-coding RNAs are emerging as potent regulators of proteins that exert unknown RNA-binding properties and moonlighting functions. A vast array of RNA- and protein-centric techniques have been developed for the identification of protein and RNA targets, respectively, including unbiased protein mass spectrometry and next-generation RNA sequencing as readout. Determining true physiological RNA and protein targets is challenging as RNA–protein interaction is highly dynamic, tissue- and cell-type-specific, and changes with the environment. Here I review current techniques for the analysis of RNA–protein interactions in living cells and in vitro. RNA-centric techniques are presented on the basis of cross-linking or the use of alternative approaches. Protein-centric approaches are discussed in combination with high-throughput sequencing. Finally, the impact of mutations in RNA–protein complexes on human disease is highlighted.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78169878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synergistic Antibacterial Activity of Green Gold Nanoparticles and Tannin-Based Derivatives","authors":"E. Oliveira, S. A. Vieira, F. A. G. da Silva, M. M. da Costa, A. Gomes, H. P. Oliveira","doi":"10.3390/biochem2040019","DOIUrl":"https://doi.org/10.3390/biochem2040019","url":null,"abstract":"The development of composites with antibacterial activity represents an important strategy to avoid side effects such as increasing bacterial resistance to antibiotics. In particular, the green synthesis of metal nanoparticles avoids the use of hazardous chemical compounds and introduces the intrinsic beneficial properties of plant-derived compounds. Herein, the reduction of gold salt into metal nanoparticles was provided by the action of a cationic polymer derived from tannin (Tanfloc®). Comparative activity of antibacterial agents (pure Tanfloc and Au NPs—Tanfloc) at different concentrations were evaluated in terms of the antibiofilm activity, kill-time assays and inhibition haloes confirming the antibacterial activity of the Tanfloc that is reinforced by the incorporation of reduced gold nanoparticles, resulting in the complete elimination of S. aureus from an initial concentration of 108 CFU/mL after 120 min of reaction of Au NPs + Tanfloc solution in association with strong inhibition of the biofilm formation attributed to the Tanfloc.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84724022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oil Spill in Brazil—Analysis of Vulnerabilities and Socio-Environmental Conflicts","authors":"M. O. S. D. Santos, Mariana Nepomuceno, J. Gonçalves, Ana Catarina Leite Véras Medeiros, Rafaella Miranda Machado, Caroline P S Santos, M. J. C. F. Alves, Aline do Monte Gurgel, I. G. D. Gurgel","doi":"10.3390/biochem2040018","DOIUrl":"https://doi.org/10.3390/biochem2040018","url":null,"abstract":"The 2019 oil spill was considered the largest environmental disaster in the Brazilian Northeastern coast. It was associated with mostly ineffective government actions, thus intensifying historical vulnerabilities faced by local populations. We aimed to analyze the environmental conflicts and injustices and the socio-environmental, economic, and health vulnerabilities arising from the oil spill, considering the COVID-19 pandemic, impacting artisanal fishing communities of the Northeastern coast. A document-based, qualitative, cross-sectional research was carried out between September 2019 and October 2022, in open access secondary databases, and using field diaries from research of the Environmental Health and Work Laboratory (LASAT) of the Aggeu Magalhães Institute of the Oswaldo Cruz Foundation. The disaster caused situations of injustice and environmental conflicts that had negative repercussions in the territories with socioeconomic impacts, on the environment, and on the health of the population. The entire marine environment was affected, resulting in physical and chemical alterations. The health vulnerabilities faced by local people were intensified, influencing the social determination of the health–disease process. The local economy was extremely affected, generating job insecurity and several socio-cultural problems. It is essential to build environmental and health diagnoses for remedial measures in disasters such as the oil spill.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81960109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Role of Epitranscriptomic Modifications in the Regulation of RNA–Protein Interactions","authors":"Elżbieta Wanowska, Alexis McFeely, Joanna Sztuba-Solinska","doi":"10.3390/biochem2040017","DOIUrl":"https://doi.org/10.3390/biochem2040017","url":null,"abstract":"Epitranscriptome refers to post-transcriptional modifications to RNA and their associated regulatory factors that can govern changes in an organism’s cells in response to various environmental stimuli. Recent studies have recognized over 170 distinct chemical signatures in RNA, and the list keeps expanding. These modifications are hypothesized to have roles beyond simply fine-tuning the structure and function of RNA, as studies have linked them to various infectious and noninfectious diseases in humans. Dedicated cellular machinery comprising of RNA-binding proteins (RBPs) that can write, erase, and read these modifications drives the regulation of the epitranscriptomic code, and as such influences RNA metabolism and homeostasis. Equally, perturbations in the function of RBPs may disrupt RNA processing, further implicating them in pathogenesis. As such, the mechanisms underlying RNA modifications and their association with RBPs are emerging areas of interest within the field of biomedicine. This review focuses on understanding epitranscriptomic modifications, their effects on RNA–RBPs interactions, and their influence on cellular processes.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87414112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bilayers as Basic Formation of Epimolecular Structure of Mostly Lyotropic (Hydrotropic) Structuralized Liquid Systems Being Influenced Predominantly by the Temperature","authors":"M. Milichovský","doi":"10.3390/biochem2040016","DOIUrl":"https://doi.org/10.3390/biochem2040016","url":null,"abstract":"The bilayer’s formations of amphiphilic molecules or polyions of different ionogenity comprise the basic building units of most organic biological and non-biological systems. A theory has evolved to explain their behaviour during the creation of those organized structures, such as anisotropic liquid crystal (LC) in lyotropic (especially hydrotropic) systems and polyelectrolyte multilayer (PEM) assemblies. Particular attention has been paid to the temperature and the important role of water in the formation and behaviour of the bilayers. A novel insight into the formation of hydrotropic liquid LC systems and their thermotropic behaviour is presented. In this context, the systems PEM assemblies are also discussed. Essentially, a structuralised form of water fills out continuous and discontinuous, i.e., confined, nano-spaces among hydrophilic interfaces of bilayers, controlling their supramolecular structure through a system of attractive and repulsive hydration forces. The character of those sophisticated bonding hydration systems is predestined by the composition and type of these hydrophilic interface groups. The miscellaneous complexity of the bilayer’s aqueous systems suggests the need to study these examples in greater detail. Therefore, the bilayer’s processes connected with disruption as far as destruction of bilayers are mentioned, i.e., the processes with the highest potential to combat bacteria, fungi, and viruses, such as in a situation where a person exhales a breath of micro-droplets containing virus nanoparticles (e.g., the COVID-19 virus).","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81879928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"cEpiderm, a Canine Skin Analog Suitable for In Vivo Testing Replacement","authors":"Mariana Marques, João Nunes, Bárbara Ustymenko, L. Fialho, Luís Martins, A. Burke, Cesar Filho, Alexandre C. Craveiro, Ana R. Costa, S. Branco, C. Antunes","doi":"10.3390/biochem2040015","DOIUrl":"https://doi.org/10.3390/biochem2040015","url":null,"abstract":"Skin is one of the organs most tested for toxicity and safety evaluation during the process of drug research and development and in the past has usually been performed in vivo using animals. Over the last few years, non-animal alternatives have been developed and validated epidermis models for human and rat skin are already available. Our goal was to develop a histotypical canine skin analog, suitable for non-animal biocompatibility and biosafety assessment. Canine keratinocytes were seeded in an air-lift culture using an adapted version of the CELLnTEC protocol. Corrosion and irritation protocols were adapted from human EpiSkinTM. For histological analysis, sample biopsies were fixed in neutral-buffered formalin, and paraffin slices were routinely processed and stained with hematoxylin and eosin. A canine multilayer and stratified epidermal-like tissue (cEpiderm), confirmed by histological analysis, was obtained. The cEpiderm tissue exhibited normal morphological and functional characteristics of epidermis, namely impermeability and an adequate response to stressors. The cEpiderm is a promising canine skin model for non-animal safety testing of veterinary pharmaceuticals and/or cosmetics, significantly contributing to reducing undesirable in vivo approaches. cEpiderm is therefore a valid canine skin model and may be made commercially available either as a service or as a product.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85174094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testicular Glycogen Metabolism: An Overlooked Source of Energy for Spermatogenesis?","authors":"Ricardo Silva, D. Carrageta, M. Alves, P. Oliveira","doi":"10.3390/biochem2030014","DOIUrl":"https://doi.org/10.3390/biochem2030014","url":null,"abstract":"The incidence of male infertility has been increasing over the years and is now becoming a serious health problem. This trend has been followed by an increase in metabolic diseases, which are known to induce clear alterations in testicular metabolism, although the underlying mechanismremain unclear. Testicular metabolism displays several unique features, with testicular somatic cells being central in providing the conditions needed for spermatogenesis, including its nutritional and hormonal support. In addition to glucose and lactate, the two main energy sources used by the testis, glycogen is also present in testicular cells. Glycogen metabolism is a potential source of glucose to both testicular somatic (namely Sertoli and Leydig cells) and germ cells. Many of the enzymes involved in the pathways of the synthesis and degradation of glycogen were identified in these cells, emphasising the relevance of this complex carbohydrate. Glycogen, however, has other non-canonical functions in testicular cells; besides its role as a source of energy, it is also associated with events such as cellular differentiation and apoptosis. In this review, we address the relevance of testicular glycogen metabolism, focusing on its role in Sertoli and Leydig cells and spermatogenesis. In addition, all the available information on the role of glycogen and related pathways in male infertility cases is discussed. Our discussion highlights that glycogen metabolism has been somewhat overlooked in testis and its contribution to spermatogenesis may be underestimated.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90933574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Native Protein Template Assisted Synthesis of Non-Native Metal-Sulfur Clusters","authors":"B. Maiti, J. Moura","doi":"10.3390/biochem2030013","DOIUrl":"https://doi.org/10.3390/biochem2030013","url":null,"abstract":"Metalloenzymes are the most proficient nature catalysts that are responsible for diverse biochemical transformations introducing excellent selectivity and performing at high rates, using intricate mutual relationships between metal ions and proteins. Inspired by nature, chemists started using naturally occurring proteins as templates to harbor non-native metal catalysts for the sustainable synthesis of molecules for pharmaceutical, biotechnological and industrial purposes. Therefore, metalloenzymes are the relevant targets for the design of artificial biocatalysts. The search and development of new scaffolds capable of hosting metals with high levels of selectivity could significantly expand the scope of bio-catalysis. To meet this challenge, herein, three native scaffolds: [1Fe-4Cys] (rubredoxin), [3Fe-4S] (ferredoxin), and [S2MoS2CuS2MoS2]-ORP (orange protein) protein scaffolds are case studies describing templates for the synthesis of non-native monomeric to mixed metal–sulfur clusters, which mimic native Ni containing metalloenzymes including [Ni-Fe] Hydrogenase and [Ni-Fe] CO Dehydrogenase. The non-native metal-substituted metalloproteins are not only useful for catalysis but also as spectroscopic probes.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87316691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}