Biomolecular Concepts最新文献_第2页

A novel approach for protein secondary structure prediction using encoder-decoder with attention mechanism model. 利用编码器-解码器和注意力机制模型预测蛋白质二级结构的新方法。

Biomolecular Concepts Pub Date : 2024-03-13 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0043

Pravinkumar M Sonsare, Chellamuthu Gunavathi

{"title":"A novel approach for protein secondary structure prediction using encoder-decoder with attention mechanism model.","authors":"Pravinkumar M Sonsare, Chellamuthu Gunavathi","doi":"10.1515/bmc-2022-0043","DOIUrl":"10.1515/bmc-2022-0043","url":null,"abstract":"Computational biology faces many challenges like protein secondary structure prediction (PSS), prediction of solvent accessibility, etc. In this work, we addressed PSS prediction. PSS is based on sequence-structure mapping and interaction among amino acid residues. We proposed an encoder-decoder with an attention mechanism model, which considers the mapping of sequence structure and interaction among residues. The attention mechanism is used to select prominent features from amino acid residues. The proposed model is trained on CB513 and CullPDB open datasets using the Nvidia DGX system. We have tested our proposed method for Q 3 and Q 8 accuracy, segment of overlap, and Mathew correlation coefficient. We achieved 70.63 and 78.93% Q 3 and Q 8 accuracy, respectively, on the CullPDB dataset whereas 79.8 and 77.13% Q 3 and Q 8 accuracy on the CB513 dataset. We observed improvement in SOV up to 80.29 and 91.3% on CullPDB and CB513 datasets. We achieved the results using our proposed model in very few epochs, which is better than the state-of-the-art methods.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140120951","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}

引用次数: 0

β-Amyloid peptide modulates peripheral immune responses and neuroinflammation in rats. β-淀粉样肽可调节大鼠的外周免疫反应和神经炎症。

Biomolecular Concepts Pub Date : 2024-03-07 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0042

Krishnendu Adhikary, Satyajit Mohanty, Bidyut Bandyopadhyay, Rajkumar Maiti, Koushik Bhattacharya, Prithviraj Karak

{"title":"β-Amyloid peptide modulates peripheral immune responses and neuroinflammation in rats.","authors":"Krishnendu Adhikary, Satyajit Mohanty, Bidyut Bandyopadhyay, Rajkumar Maiti, Koushik Bhattacharya, Prithviraj Karak","doi":"10.1515/bmc-2022-0042","DOIUrl":"10.1515/bmc-2022-0042","url":null,"abstract":"Alzheimer's disease (AD) is characterized by immune system dysregulation, impacting both central and peripheral immune responses. The study aimed to investigate the mechanism behind the neurotoxic effects of β-amyloid (Aβ) peptide in the rat brain including the study of neuroinflammation, neurodegeneration, and alterations in peripheral immune responses (PIR). The neuroinflammation brought on by Aβ1-42 and is unknown to influence PIR. Animal models were prepared, after 28 days, control, sham, and treated rats were anaesthetized and inflammatory markers of hippocampus and serum levels (reactive oxygen species, nitrite, tumor necrosis factor-α, and interleukin-1β), and some markers of PIR (splenic mononuclear cells or MNC, cytotoxicity and phagocytic index of the white blood cells leukocyte adhesion inhibition index or LAI), as well as polymorphonuclear cells of the spleen, were assessed. In addition to changes in peripheral immune responses, the present study found that AD rats had higher blood levels of inflammatory markers. Based on the study, the immune system irregularities observed in AD rats in the peripheral regions might be connected to neuroinflammation, which is facilitated by a compromised blood-brain barrier. Hence, it is viable to propose that the neuroinflammatory condition in rats with Aβ-induced AD could modify immune responses in the peripheral areas with significantly higher levels of inflammatory cytokines markers in the hippocampal tissue in Aβ-injected AD rats.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060761","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}

引用次数: 0

Synergistic effects of essential oils and phenolic extracts on antimicrobial activities using blends of Artemisia campestris, Artemisia herba alba, and Citrus aurantium. 使用野蒿、白花蒿和枳壳的混合物，研究精油和酚类提取物对抗菌活性的协同效应。

Biomolecular Concepts Pub Date : 2024-02-14 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0040

Boualem Benamar-Aissa, Nadhir Gourine, Mohamed Ouinten, Mohamed Yousfi

{"title":"Synergistic effects of essential oils and phenolic extracts on antimicrobial activities using blends of Artemisia campestris, Artemisia herba alba, and Citrus aurantium.","authors":"Boualem Benamar-Aissa, Nadhir Gourine, Mohamed Ouinten, Mohamed Yousfi","doi":"10.1515/bmc-2022-0040","DOIUrl":"10.1515/bmc-2022-0040","url":null,"abstract":"This study explores the synergistic antibacterial effects of essential oils (EOs) and phenolic extracts from three plants against foodborne pathogenic bacteria. The present work aimed to investigate the synergistic effects of the binary and the ternary combinations of extracts using different blend proportions of the following plant extracts: Artemisia campestris (AC), Artemisia herba alba (AHA), and Citrus aurantium (CA). The antimicrobial activities of EOs and phenolic extracts were determined and evaluated against five strains. For the EOs, the results of the DIZ showed the existence of synergism for different combinations of binary blends, such as AC/AHA or AHA/CA against Escherichia coli, and AC/CA against Enterobacter faecalis. In addition, ternary blends of AC:AHA:CA at a ratio of 1/6:2/3:1/6 exhibited a synergy effect, as measured by the CI, against E. coli. On the other hand, for the phenolic extracts, synergistic effects were noticed for binary blends of AC/CA at different ratios against E. coli, E. faecalis, and Pseudomonas aeruginosa strains. Similarly, ternary blends of phenolic extracts presented synergy against E. coli, E. faecalis, P. aeruginosa strains, and even C. albicans. In this case, the blending ratios were crucial determining factors for maximizing the synergy effect. The study established that the proportion of a single drug could play an essential role in determining the bioefficacy of a drug combination treatment. Therefore, the results showed the importance of studying the modulation of antibacterial activities based on the proportions of extracts in the mixture and finding the range of proportions (as determined by SLMD) that have a synergistic/additive/antagonistic effect with no or low side effects, which can be used in a food preservation system.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139730702","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}

引用次数: 0

Digital methylation-specific PCR: New applications for liquid biopsy. 数字甲基化特异性 PCR：液体活检的新应用

Biomolecular Concepts Pub Date : 2024-02-12 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0041

Gabriela Casani Cardoso, Fernando Augusto de Oliveira Ganzella, Guilherme Miniskiskosky, Regiane Stafim da Cunha, Edneia Amancio de Souza Ramos

{"title":"Digital methylation-specific PCR: New applications for liquid biopsy.","authors":"Gabriela Casani Cardoso, Fernando Augusto de Oliveira Ganzella, Guilherme Miniskiskosky, Regiane Stafim da Cunha, Edneia Amancio de Souza Ramos","doi":"10.1515/bmc-2022-0041","DOIUrl":"10.1515/bmc-2022-0041","url":null,"abstract":"Epigenetic analysis is a fundamental part of understanding pathophysiological processes with potential applications in diagnosis, prognosis, and assessment of disease susceptibility. Epigenetic changes have been widely studied in chronic obstructive pulmonary disease (COPD), but currently, there is no molecular marker used to improve the treatment of patients. Furthermore, this progressive disease is a risk factor for the development of more severe COVID-19. Methylation-specific polymerase chain reaction (MSP-PCR) plays an important role in the analysis of DNA methylation profiles, and it is one of the most widely used techniques. In this context, the combination of MSP-PCR with emerging PCR technologies, such as digital PCR (dPCR), results in more accurate analyses of the DNA methylation profile of the genes under study. In this study, we propose the application of the MSP-dPCR technique to evaluate the methylation profile of the ADAM33 gene from saliva samples and lung tissue biopsies of patients with COPD and COVID-19. MSP-dPCR generated a measurable prediction of gene methylation rate, with the potential application of this combined technology for diagnostic and prognostic purposes. It has also proven to be a powerful tool for liquid biopsy applications.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139724361","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}

引用次数: 0

Antitumor activity of 5-hydroxy-3',4',6,7-tetramethoxyflavone in glioblastoma cell lines and its antagonism with radiotherapy. 5-羟基-3',4',6,7-四甲氧基黄酮在胶质母细胞瘤细胞系中的抗肿瘤活性及其与放疗的拮抗作用。

Biomolecular Concepts Pub Date : 2024-02-12 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0039

Panagiota Papapetrou, Kyriakos Dimitriadis, Vasiliki Galani, Vasiliki Zoi, Maria Giannakopoulou, Vasiliki A Papathanasopoulou, Chrissa Sioka, Pericles Tsekeris, Athanassios P Kyritsis, Diamanto Lazari, George A Alexiou

{"title":"Antitumor activity of 5-hydroxy-3',4',6,7-tetramethoxyflavone in glioblastoma cell lines and its antagonism with radiotherapy.","authors":"Panagiota Papapetrou, Kyriakos Dimitriadis, Vasiliki Galani, Vasiliki Zoi, Maria Giannakopoulou, Vasiliki A Papathanasopoulou, Chrissa Sioka, Pericles Tsekeris, Athanassios P Kyritsis, Diamanto Lazari, George A Alexiou","doi":"10.1515/bmc-2022-0039","DOIUrl":"10.1515/bmc-2022-0039","url":null,"abstract":"5-Hydroxy-3',4',6,7-tetramethoxyflavone (TMF) is a plant-origin flavone known for its anti-cancer properties. In the present study, the cytotoxic effect of TMF was evaluated in the U87MG and T98G glioblastoma (GBM) cell lines. The effect of TMF on cell viability was assessed with trypan blue exclusion assay and crystal violet staining. In addition, flow cytometry was performed to examine its effect on the different phases of the cell cycle, and in vitro scratch wound assay assessed the migratory capacity of the treated cells. Furthermore, the effect of in vitro radiotherapy was also evaluated with a combination of TMF and radiation. In both cell lines, TMF treatment resulted in G0/G1 cell cycle arrest, reduced cell viability, and reduced cell migratory capacity. In contrast, there was an antagonistic property of TMF treatment with radiotherapy. These results demonstrated the antineoplastic effect of TMF in GBM cells in vitro, but the antagonistic effect with radiotherapy indicated that TMF should be further evaluated for its possible antitumor role post-radiotherapy.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139724360","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}

引用次数: 0

Polycystic ovary syndrome and its management: In view of oxidative stress. 多囊卵巢综合征及其治疗：氧化应激。

Biomolecular Concepts Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0038

Koushik Bhattacharya, Rajen Dey, Debanjana Sen, Nimisha Paul, Asim Kumar Basak, Mohuya Patra Purkait, Nandini Shukla, Gargi Ray Chaudhuri, Aniruddha Bhattacharya, Rajkumar Maiti, Krishnendu Adhikary, Prity Chatterjee, Prithviraj Karak, Alak Kumar Syamal

{"title":"Polycystic ovary syndrome and its management: In view of oxidative stress.","authors":"Koushik Bhattacharya, Rajen Dey, Debanjana Sen, Nimisha Paul, Asim Kumar Basak, Mohuya Patra Purkait, Nandini Shukla, Gargi Ray Chaudhuri, Aniruddha Bhattacharya, Rajkumar Maiti, Krishnendu Adhikary, Prity Chatterjee, Prithviraj Karak, Alak Kumar Syamal","doi":"10.1515/bmc-2022-0038","DOIUrl":"10.1515/bmc-2022-0038","url":null,"abstract":"In the past two decades, oxidative stress (OS) has drawn a lot of interest due to the revelation that individuals with many persistent disorders including diabetes, polycystic ovarian syndrome (PCOS), cardiovascular, and other disorders often have aberrant oxidation statuses. OS has a close interplay with PCOS features such as insulin resistance, hyperandrogenism, and chronic inflammation; there is a belief that OS might contribute to the development of PCOS. PCOS is currently recognized as not only one of the most prevalent endocrine disorders but also a significant contributor to female infertility, affecting a considerable proportion of women globally. Therefore, the understanding of the relationship between OS and PCOS is crucial to the development of therapeutic and preventive strategies for PCOS. Moreover, the mechanistic study of intracellular reactive oxygen species/ reactive nitrogen species formation and its possible interaction with women's reproductive health is required, which includes complex enzymatic and non-enzymatic antioxidant systems. Apart from that, our current review includes possible regulation of the pathogenesis of OS. A change in lifestyle, including physical activity, various supplements that boost antioxidant levels, particularly vitamins, and the usage of medicinal herbs, is thought to be the best way to combat this occurrence of OS and improve the pathophysiologic conditions associated with PCOS.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139503068","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}

引用次数: 0

⁷Be and ²²Na radionuclides for a new therapy for cancer. 用于癌症新疗法的 7Be 和 22Na 放射性核素。

Biomolecular Concepts Pub Date : 2023-12-31 eCollection Date: 2023-01-01 DOI: 10.1515/bmc-2022-0028

Vladimir I Kukulin, Anton V Bibikov, Eugene V Tkalya, Matteo Ceccarelli, Igor V Bodrenko

引用次数: 0

Mitigation of the hyperglycemic effect of streptozotocin-induced diabetes albino rats using biosynthesized copper oxide nanoparticles. 利用生物合成的纳米氧化铜颗粒缓解链脲佐菌素诱导的白化糖尿病大鼠的高血糖效应。

Biomolecular Concepts Pub Date : 2023-12-31 eCollection Date: 2023-01-01 DOI: 10.1515/bmc-2022-0037

Ahmed Saber Hussein, Amr H Hashem, Salem S Salem

{"title":"Mitigation of the hyperglycemic effect of streptozotocin-induced diabetes albino rats using biosynthesized copper oxide nanoparticles.","authors":"Ahmed Saber Hussein, Amr H Hashem, Salem S Salem","doi":"10.1515/bmc-2022-0037","DOIUrl":"10.1515/bmc-2022-0037","url":null,"abstract":"Diabetes mellitus is a metabolic disorder described by compromised insulin synthesis or resistance to insulin inside the human body. Diabetes is a persistent metabolic condition defined by elevated amounts of glucose in the bloodstream, resulting in a range of potential consequences. The main purpose of this study was to find out how biosynthesized copper oxide nanoparticles (CuONPs) affect the blood sugar levels of diabetic albino rats induced by streptozotocin (STZ). In the current study, CuONPs were successfully biosynthesized using Saccharomyes cervisiae using an eco-friendly method. Characterization results revealed that biosynthesized CuONPs appeared at 376 nm with a spherical shape with sizes ranging from 4 to 47.8 nm. Furthermore, results illustrated that administration of 0.5 and 5 mg/kg CuONP in diabetic rats showed a significant decrease in blood glucose levels accompanied by elevated insulin levels when compared to the diabetic control group; however, administration of 0.5 mg/kg is the best choice for diabetic management. Furthermore, it was found that the group treated with CuONPs exhibited a noteworthy elevation in the HDL-C level, along with a depletion in triglycerides, total cholesterol, LDL-C, and VLDL-cholesterol levels compared to the diabetic control group. This study found that administration of CuONPs reduced hyperglycemia and improved pancreatic function as well as dyslipidemia in diabetic rats exposed to STZ, suggesting their potential as a promising therapeutic agent for diabetes treatment.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479439","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}

引用次数: 0

Potential PDE4B inhibitors as promising candidates against SARS-CoV-2 infection. 潜在的PDE4B抑制剂是对抗严重急性呼吸系统综合征冠状病毒2型感染的有前景的候选者。

Biomolecular Concepts Pub Date : 2023-11-01 eCollection Date: 2023-01-01 DOI: 10.1515/bmc-2022-0033

Federica Giuzio, Maria Grazia Bonomo, Alessia Catalano, Vittoria Infantino, Giovanni Salzano, Magnus Monné, Athina Geronikaki, Anthi Petrou, Stefano Aquaro, Maria Stefania Sinicropi, Carmela Saturnino

{"title":"Potential PDE4B inhibitors as promising candidates against SARS-CoV-2 infection.","authors":"Federica Giuzio, Maria Grazia Bonomo, Alessia Catalano, Vittoria Infantino, Giovanni Salzano, Magnus Monné, Athina Geronikaki, Anthi Petrou, Stefano Aquaro, Maria Stefania Sinicropi, Carmela Saturnino","doi":"10.1515/bmc-2022-0033","DOIUrl":"10.1515/bmc-2022-0033","url":null,"abstract":"Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an RNA virus belonging to the coronavirus family responsible for coronavirus disease 2019 (COVID-19). It primarily affects the pulmonary system, which is the target of chronic obstructive pulmonary disease (COPD), for which many new compounds have been developed. In this study, phosphodiesterase 4 (PDE4) inhibitors are being investigated. The inhibition of PDE4 enzyme produces anti-inflammatory and bronchodilator effects in the lung by inducing an increase in cAMP concentrations. Piclamilast and rolipram are known selective inhibitors of PDE4, which are unfortunately endowed with common side effects, such as nausea and emesis. The selective inhibition of the phosphodiesterase 4B (PDE4B) subtype may represent an intriguing technique for combating this highly contagious disease with fewer side effects. In this article, molecular docking studies for the selective inhibition of the PDE4B enzyme have been carried out on 21 in-house compounds. The compounds were docked into the pocket of the PDE4B catalytic site, and in most cases, they were almost completely superimposed onto piclamilast. Then, in order to enlarge our study, drug-likeness prediction studies were performed on the compounds under study.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71427582","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}

引用次数: 0

Proteins turn "Proteans" - The over 40-year delayed paradigm shift in structural biology: From "native proteins in uniquely defined configurations" to "intrinsically disordered proteins". 蛋白质转变为“变形体”-结构生物学中超过40年的延迟范式转变:从“独特定义结构的天然蛋白质”到“内在无序的蛋白质”。

Biomolecular Concepts Pub Date : 2023-01-01 DOI: 10.1515/bmc-2022-0030

Eugenio Frixione, Lourdes Ruiz-Zamarripa

引用次数: 0