BioChem最新文献

{"title":"Cytotoxic Effects of Indonesian Betel Quid Components on Oral Keratinocytes and Fibroblasts","authors":"Elizabeth Fitriana Sari, Ali I. Mohammed, Antonio Celentano, Michael John McCullough, Nicola Cirillo","doi":"10.3390/biochem3040011","DOIUrl":"https://doi.org/10.3390/biochem3040011","url":null,"abstract":"A betel quid (BQ) chewing habit has been strongly associated with the development of several oral mucosal diseases. In order to investigate whether individual components of BQ mixtures have distinct physio-pathological effects on oral mucosal cells, we examined the impact of areca nut (AN), Piper betle leaf (Leaf), Piper betle stem inflorescence (SI), areca husk (Husk) and the complete BQ mixture on the growth of oral keratinocytes (OKF-6) and primary oral fibroblasts (MMF-1). Based on their known chemical properties, we selected BQ samples from Banda Aceh (BA) and West Papua (WP) regions for our in vitro study. We used a fluorescein diacetate assay (FDA) to assess the cell viability of BQ components on OKF-6 and MMF-1 cells. The cytotoxic effect of WP-AN on the OKF-6 cell line was observed at a concentration of 100 μg/mL, resulting in a 50% reduction in cell viability (IC50) after a 2-day incubation. Similarly, BA-AN exhibited cytotoxic effect, although at a higher concentration (500 μg/mL). WP-SI also displayed cytotoxic effects at a concentration of 500 μg/mL following 2 days of incubation. In contrast, Leaf, BQ mixture and husk extracts did not show any cytotoxic effects even after 3 days of incubation. No cytotoxic effects were observed at any concentration of BQ components when exposed to MMF-1 cells. Regarding cell proliferation, MMF-1 cells exposed to BA-AN and WP-AN showed increased growth on day 1, followed by decreased growth on day 2, in a dose- and time-dependent manner. Overall, our study indicates that BQ components induce distinctive cytotoxic effects on stromal and epithelial cells from the oral cavity.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135413392","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":"New Method of Isothermal, Hairpin Assisted, Primer Independent Amplification of DNA","authors":"Denis Sergeevich Naberezhnov, Alexander Andreevich Alferov, Yuriy Borisovich Kuzmin, Nikolay Evgenievich Kushlinskii","doi":"10.3390/biochem3030010","DOIUrl":"https://doi.org/10.3390/biochem3030010","url":null,"abstract":"The isothermal amplification of nucleic acids refers to processes that quickly increase the amount of DNA at a constant temperature. These methods are mainly developed as alternatives to PCR for cases in which the application of a thermal cycler is not possible or the assay method must be as rapid as possible. We have developed a new method of isothermal amplification based on the formation of hairpins at the ends of DNA fragments containing palindromic sequences and increased by the hydrolysis of one or both DNA strands by restriction endonuclease, known as hairpin-assisted isothermal reaction (HAIR). The key steps in HAIR are the formation of a self-complementary hairpin and the DNA breakage introduced by nickase. The end hairpins facilitate primer-free amplification, the amplicon strand cleavage by nickase produces additional 3′ ends that serve as new amplification points, and the amount of DNA can increase exponentially. The rate of amplification in HAIR is more than five times the rate of loop-mediated isothermal amplification (LAMP), and the total amount of DNA product of HAIR is more than double the amount of the LAMP product.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135106634","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":"Combined Therapies with Taxane-Based Chemotherapeutic Drugs in Prostate Cancer: Novel Insights and Future Directions","authors":"Rafaella S. Coelho, S. M. Rocha, Cláudio J. Maia","doi":"10.3390/biochem3030009","DOIUrl":"https://doi.org/10.3390/biochem3030009","url":null,"abstract":"Oncologic disease is a significant global health issue that causes thousands of deaths annually, and it has a significant impact on the quality of life of patients. Prostate cancer (PCa) is the second most diagnosed cancer and the fourth leading cause of cancer-related death in men in the Western world. Delineation of pathogenetic pathways and key driver molecular alterations involved in PCa development has provided a roadmap for the evaluation of biomarkers in predicting disease outcome and to identify potential therapeutic targets. Chemotherapeutic agents introduced from the 1990s include the taxanes (paclitaxel, docetaxel, and cabazitaxel), which are the anticancer drugs used most frequently for PCa treatment. This review presents the current knowledge about the onset and development of PCa, the state of the art of the use of taxane-based therapy, and their combination with targeting different transmembrane oncoproteins in PCa. The silencing of some transmembrane proteins can improve taxane sensitivity, and therefore may be a mechanism to improve the effectiveness of these drugs in PCa treatment. This combined therapy needs to be explored as a potential therapeutic agent for reducing cell proliferation, migration, and invasiveness in PCa.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83495555","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":"Qualitative Shotgun Proteomics Strategy for Protein Expression Profiling of Fish Otoliths","authors":"R. Rideout, Trevena N. Youssef, Aaron T. Adamack, R. John, Alejandro M. Cohen, T. D. Fridgen, J. Banoub","doi":"10.3390/biochem3030008","DOIUrl":"https://doi.org/10.3390/biochem3030008","url":null,"abstract":"Despite decades of research on fish otoliths and their capacity to serve as biochronological recorders, much remains unknown about their protein composition, the mechanisms by which proteins are incorporated into the otolith matrix, or the potential for using otolith proteins to provide insight into aspects of fish life history. We examined the protein composition of Atlantic cod (Gadus morhua) otoliths using a state-of-the-art shotgun proteomics approach with liquid chromatography coupled to an electrospray ionization-orbitrap tandem mass spectrometer. In addition to previously known otolith matrix proteins, we discovered over 2000 proteins not previously identified in cod otoliths and more than 1500 proteins not previously identified in any fish otoliths. These included three novel proteins (Somatolactin, F-actin-capping protein subunit beta, Annexin) primarily involved in binding calcium ions and likely mediating crystal nucleation. However, most of the otolith proteins were not necessarily related to otolith formation but rather to other aspects of fish physiology. For example, we identified sex-related biomarkers for males (SPATA6 protein) and females (Vitellogenin-2-like protein). We highlight some noteworthy classes of proteins having diverse functions; however, the primary goal here is not to discuss each protein separately. The number and diverse roles of the proteins discovered in the otoliths suggest that proteomics could reveal critical life history information from archived otolith collections that could be invaluable for understanding aspects of fish biology and population ecology. This proof-of-concept methodology paper provides a novel methodology whereby otolith proteomics can be further explored.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85574590","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":"DMSO Alleviates LPS-Induced Inflammatory Responses in RAW264.7 Macrophages by Inhibiting NF-κB and MAPK Activation","authors":"Hyun-Gyu Han, J. Kang, K. Ahn, C. Hyun","doi":"10.3390/biochem3020007","DOIUrl":"https://doi.org/10.3390/biochem3020007","url":null,"abstract":"Dimethyl sulfoxide (DMSO), an amphipathic molecule composed of one highly polar sulfinyl group and two nonpolar methyl groups, is considered an excellent solvent due to its capability to dissolve many polar and nonpolar compounds. Therefore, DMSO is widely used to solubilize drugs for therapeutic applications. DMSO is reported to possess anti-inflammatory, anticancer, and antioxidative capacities, and the anti-inflammatory efficacy of DMSO has been intensively studied in various cell lines and animal models. An in vitro model of mouse macrophage RAW 264.7 cells has been widely used, among several experimental designs, for evaluation during the development of new anti-inflammatory drugs. DMSO, which is used to dissolve samples, is also prone to experimental errors because of its anti-inflammatory properties. Therefore, we systematically confirmed the cytotoxic and anti-inflammatory effects of DMSO and the related signaling pathways in RAW 264.7 cells. The results show that DMSO at 0.25% to 1.5% did not result in cellular toxicity, with results comparable to the control group where DMSO is absent; at concentrations 2.0%, however, it inhibited the viability of RAW264.7 cells (13.25%). The results demonstrate that pretreatment with DMSO profoundly attenuates the lipopolysaccharide (LPS)-stimulated levels of nitric oxide (NO) and prostaglandin (PG)E2, as well as the levels of pro-inflammatory cytokines, cyclooxygenase-2 (COX-2) protein, and inducible nitric oxide synthase (iNOS). Collectively, the DMSO pretreatments appear to notably alleviate LPS-induced damage by reducing phosphorylation of p38, c-Jun N-terminal kinase (JNK), and extracellular signal-regulated kinase proteins (ERKs), nuclear factor-kappa-B (NF-κB) in addition to NF-κB/p65 nuclear translocation. Taken together, the results clearly show that DMSO attenuates the inflammatory response in LPS-induced RAW264.7 cells by regulating the activation of the MAPK and NF-κB signaling pathways. These results contribute to potentially reducing experimental errors or misjudgments when using the LPS-induced RAW 264.7 macrophage cell model for evaluation during the development of new anti-inflammatory drugs.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82604571","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":"Nitric Oxide Production from Nitrite plus Ascorbate during Ischemia upon Hippocampal Glutamate NMDA Receptor Stimulation","authors":"Carla Nunes, J. Laranjinha","doi":"10.3390/biochem3020006","DOIUrl":"https://doi.org/10.3390/biochem3020006","url":null,"abstract":"Nitric oxide (•NO), a diffusible free radical, is an intercellular messenger, playing a crucial role in several key brain physiological processes, including in neurovascular coupling (NVC). In the brain, glutamatergic activation of the neuronal nitric oxide synthase (nNOS) enzyme constitutes its main synthesis pathway. However, when oxygen (O2) supply is compromised, such as in stroke, ischemia, and aging, such •NO production pathway may be seriously impaired. In this context, evidence suggests that, as already observed in the gastric compartment, the reduction of nitrite by dietary compounds (such as ascorbate and polyphenols) or by specific enzymes may occur in the brain, constituting an important rescuing or complementary mechanism of •NO production. Here, using microsensors selective for •NO, we show that nitrite enhanced the •NO production in a concentration-dependent manner and in the presence of ascorbate evoked by N-methyl-D-aspartate (NMDA) and glutamate stimulation of rat hippocampal slices. Additionally, nitrite potentiated the •NO production induced by oxygen-glucose deprivation (OGD). Overall, these observations support the notion of a redox interaction of ascorbate with nitrite yielding •NO upon neuronal glutamatergic activation and given the critical role of NO as the direct mediator of neurovascular coupling may represents a key physiological mechanism by which •NO production for cerebral blood flow (CBF) responses to neuronal activation is sustained under hypoxic/acidic conditions in the brain.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87258512","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":"Fluorinated Derivatives of Digalloyl-Flavan-3-ol Induce Autophagic Cell Death by Forming Granular Aggregates Containing Mitochondria","authors":"Ryo Doge, Y. Nishino, Akiko Saito","doi":"10.3390/biochem3020005","DOIUrl":"https://doi.org/10.3390/biochem3020005","url":null,"abstract":"Flavan-3-ol derivatives are polyphenolic compounds with multifunctional properties. One of the flavan-3-ol derivatives, green tea catechin epigallocatechin gallate, is known to have anticancer activity as one of its multifunctional properties. We have studied the synthesis of flavan-3-ol derivatives and conducted structure-activity relationship studies; we found that the fluorinated derivatives exhibited high toxicity against HeLa and A549 cells. It was confirmed that the cytotoxicity was affected by the conformation of the flavan-3-ol skeleton and that the 2,3-cis form was dominant. The addition of fluorinated compounds increased the amount of intracellular mitochondrial superoxide, abolished the membrane potential of mitochondria, and, interestingly, formed granular aggregates containing mitochondria. When the level of LC3-II, a marker of autophagy induction, was confirmed, it suggested that the addition of the fluorinated compounds promoted autophagy. These results suggest that the novel highly cytotoxic fluorinated flavan-3-ol compound synthesized in this study promotes autophagy and induces cell death by triggering mitochondrial dysfunction. We believe that these results suggest the possibility of conferring more functionality through structural transformations of flavan-3-ol derivatives.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87737805","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 Cross-Talk between Microbiome and Metabolome in Rheumatoid Arthritis","authors":"L. La Barbera, C. Rizzo, G. Grasso, F. Macaluso, F. Camarda, F. Ciccia, G. Guggino","doi":"10.3390/biochem3010004","DOIUrl":"https://doi.org/10.3390/biochem3010004","url":null,"abstract":"Modern “omics” sciences, including metabolomics and microbiomics, are currently being applied to inflammatory autoimmune diseases, such as rheumatoid arthritis (RA), to investigate the interplay between microbiota, metabolic function, and the immune system. In recent decades, robust evidence has suggested that disruption of the normal composition of the microbiome, known as dysbiosis, in the gut and mouth of RA patients contributes to immune dysregulation and alterations in the metabolic pathways, shaping the pathogenesis of the disease and playing a central role in the risk and progression of RA. Metabolic pathways can be influenced by various agents such as the surrounding environment, lifestyle, and exposure to microbiota imbalance. In turn, the body’s metabolic homeostasis influences the immune response, making metabolomics helpful not only to understand pathogenesis pathways, but also to improve early disease detection and therapeutic chances. Combined gut microbiome and metabolome studies set out to unravel the interactions between these two entities, providing insights to discover new treatment targets and potential biomarkers to prevent joint damage. The purpose of this review is to summarize the main recent findings that suggest promising new research directions for the pathogenesis of RA.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84777591","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":"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":null,"pages":null},"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":null,"pages":null},"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}