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Anti-arthritic potential of crude sulfated polysaccharide from marine macroalgae Sargassum ilicifolium (Turner) C. Agardh: Regulation of cytokine cascade.
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2025-01-23 eCollection Date: 2025-01-01 DOI: 10.1515/bmc-2022-0050
Lavanya Ramamoorthi, Srikanth Jeyabalan, Seethalakshmi Sankar, M Yasmin Begum, Chamundeeswari Duraipandian, Mahendran Sekar, Ling Shing Wong, Vetriselvan Subramaniyan

Seaweeds have been utilized as food, fodder, fertilizer, and medicine since ancient times; nevertheless, they have received only a little attention. In the current work, we extracted the sulfated polysaccharide from a marine source and investigated its anti-arthritic potential in vivo. The isolated and freeze-dried polysaccharide was tested for acute oral toxicity based on OECD 423. This step was followed by investigations on clinical signs and gross pathological alterations seen. A complete Freund's adjuvant-induced arthritis was used to test the in vivo activity in female Sprague-Dawley rats, which were divided into five groups: (1) normal control, (2) arthritic control, (3) methotrexate treatment (0.1 mg/kg), (4) crude sulfated polysaccharide (CSP) (5 mg/kg), and (5) CSP (10 mg/kg). CSP was from the marine brown algae Sargassum ilicifolium from the Gulf of Mannar. The body weight, paw volume, and biochemical markers (alanine aminotransferase, aspartate aminotransferase, creatinine, urea, and C-reactive protein levels) were also measured for each group coupled with histopathological and immunohistochemistry studies. The acute toxicity investigation indicated that the lethal dose of 50% (LD50) of the polysaccharide was more than 2,000 mg/kg. In addition, animals from the methotrexate and CSP (5 mg/kg, p.o.) groups had a substantial reduction in paw volume compared to other treatment groups. Methotrexate and CSP treatment dramatically decreased the levels of the investigated marker enzymes. Histopathology revealed that low-dose CSP (5 mg/kg, p.o.) significantly reduced the severity of synovitis, panniculitis, liver necrosis, inflammatory cell infiltration, and cortical and paracortical necrotic foci in node, compared to the high dose (10 mg/kg, p.o.). Immunohistochemical studies revealed that CSP (5 mg/kg) significantly inhibited pro-inflammatory cytokines such as tumor necrosis factor-alpha, interleukin-2, and CD4 cells. Overall, it can be concluded that a low-dose CSP (5 mg/kg) is an efficient anti-arthritic agent that confers its effects via the cytokine pathway.

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引用次数: 0
Exploring cardiovascular implications in systemic lupus erythematosus: A holistic analysis of complications, diagnostic criteria, and therapeutic modalities, encompassing pharmacological and adjuvant approaches. 探索系统性红斑狼疮对心血管的影响:综合分析并发症、诊断标准和治疗方法,包括药物和辅助方法。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-27 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0051
John Dawi, Scarlet Affa, Yura Misakyan, Sabrina Fardeheb, Samuel Kades, Anthony Kiriaki, Aishvaryaa Shree Mohan, Brandon Norris, Sonyeol Yoon, Vishwanath Venketaraman

Systemic lupus erythematosus (SLE) poses a diagnostic challenge due to its heterogeneity. This study examines the cardiac complications of SLE comprehensively, covering pericarditis, myocarditis, pleural effusion, valvular disease, atherosclerosis, and cardiac arrhythmias. Nearly one-third of SLE-related deaths are attributed to cardiovascular diseases, necessitating a deeper understanding of cardiac pathophysiology. The impact of SLE on the cardiovascular system manifests in various ways, including recurrent and resistant pericarditis, severe myocarditis, and pleural effusion. Valvular diseases, atherosclerosis, and cardiac arrhythmias are prevalent, with immune complex deposition playing a role in atherosclerosis. Diagnostic criteria involve clinical features, laboratory findings, and autoantibodies, emphasizing the need for early diagnosis and a multidisciplinary diagnostic approach. The review explores pharmacological and non-pharmacological modalities for managing cardiac manifestations in SLE. Recommendations include NSAIDs, colchicine, and proton pump inhibitors for acute pericarditis, while selective immunosuppressive therapy is emerging for myocarditis. Valvular diseases require individualized treatment approaches, and careful corticosteroid management is crucial to avoid increased cardiovascular events. Anti-malarial therapy, particularly hydroxychloroquine, shows promise in mitigating cardiovascular risk factors. Non-pharmacological modifications, such as diet, exercise, and smoke cessation, significantly contribute to cardiovascular health in SLE patients. Adjuvant therapies involving glutathione and glutathione peroxidase focus on redox balance, offering potential interventions. This integrated approach combines diagnostic insights with diverse treatment modalities, providing a holistic strategy for managing cardiac complications in SLE. Ongoing research is essential to refine these strategies and optimize individualized treatment plans for improved patient outcomes.

系统性红斑狼疮(SLE)的异质性给诊断带来了挑战。本研究全面探讨了系统性红斑狼疮的心脏并发症,包括心包炎、心肌炎、胸腔积液、瓣膜病、动脉粥样硬化和心律失常。在与系统性红斑狼疮相关的死亡病例中,近三分之一归因于心血管疾病,因此有必要加深对心脏病理生理学的了解。系统性红斑狼疮对心血管系统的影响表现在多个方面,包括复发性和耐药性心包炎、严重心肌炎和胸腔积液。瓣膜疾病、动脉粥样硬化和心律失常很常见,免疫复合物沉积在动脉粥样硬化中起了一定作用。诊断标准涉及临床特征、实验室检查结果和自身抗体,强调了早期诊断和多学科诊断方法的必要性。该综述探讨了治疗系统性红斑狼疮心脏表现的药物和非药物方法。针对急性心包炎的推荐药物包括非甾体抗炎药、秋水仙碱和质子泵抑制剂,而针对心肌炎的选择性免疫抑制疗法正在兴起。瓣膜疾病需要个体化的治疗方法,而谨慎的皮质类固醇管理对于避免心血管事件的增加至关重要。抗疟疾疗法,尤其是羟氯喹,有望减轻心血管风险因素。饮食、运动和戒烟等非药物疗法对系统性红斑狼疮患者的心血管健康大有裨益。涉及谷胱甘肽和谷胱甘肽过氧化物酶的辅助疗法侧重于氧化还原平衡,提供了潜在的干预措施。这种综合方法将诊断见解与多种治疗方式相结合,为控制系统性红斑狼疮的心脏并发症提供了一种整体策略。持续的研究对于完善这些策略和优化个体化治疗方案以改善患者预后至关重要。
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引用次数: 0
Toxicity of bisphenol A and p-nitrophenol on tomato plants: Morpho-physiological, ionomic profile, and antioxidants/defense-related gene expression studies. 双酚 A 和对硝基苯酚对番茄植物的毒性:形态生理学、基因组学和抗氧化剂/防御相关基因表达研究。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-06-26 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0049
Mahmoud S Abdelmoneim, Elsayed E Hafez, Mona F A Dawood, Sherif F Hammad, Mohamed A Ghazy

Bisphenol A (BPA) and p-nitrophenol (PNP) are emerging contaminants of soils due to their wide presence in agricultural and industrial products. Thus, the present study aimed to integrate morpho-physiological, ionic homeostasis, and defense- and antioxidant-related genes in the response of tomato plants to BPA or PNP stress, an area of research that has been scarcely studied. In this work, increasing the levels of BPA and PNP in the soil intensified their drastic effects on the biomass and photosynthetic pigments of tomato plants. Moreover, BPA and PNP induced osmotic stress on tomato plants by reducing soluble sugars and soluble proteins relative to control. The soil contamination with BPA and PNP treatments caused a decline in the levels of macro- and micro-elements in the foliar tissues of tomatoes while simultaneously increasing the contents of non-essential micronutrients. The Fourier transform infrared analysis of the active components in tomato leaves revealed that BPA influenced the presence of certain functional groups, resulting in the absence of some functional groups, while on PNP treatment, there was a shift observed in certain functional groups compared to the control. At the molecular level, BPA and PNP induced an increase in the gene expression of polyphenol oxidase and peroxidase, with the exception of POD gene expression under BPA stress. The expression of the thaumatin-like protein gene increased at the highest level of PNP and a moderate level of BPA without any significant effect of both pollutants on the expression of the tubulin (TUB) gene. The comprehensive analysis of biochemical responses in tomato plants subjected to BPA and PNP stress illustrates valuable insights into the mechanisms underlying tolerance to these pollutants.

双酚 A(BPA)和对硝基苯酚(PNP)是土壤中新出现的污染物,因为它们广泛存在于农产品和工业产品中。因此,本研究旨在整合番茄植物对双酚 A 或对硝基苯酚胁迫的反应中的形态生理、离子平衡以及防御和抗氧化相关基因,这是一个鲜有研究的领域。在这项研究中,土壤中双酚 A 和全氟辛基苯酚含量的增加加剧了它们对番茄植株生物量和光合色素的剧烈影响。此外,与对照组相比,BPA 和 PNP 会降低可溶性糖和可溶性蛋白质,从而诱发番茄植株的渗透胁迫。双酚 A 和 PNP 污染土壤会导致番茄叶片组织中的宏量和微量元素含量下降,同时增加非必需微量元素的含量。对番茄叶片中有效成分的傅立叶变换红外分析表明,双酚 A 影响了某些官能团的存在,导致某些官能团缺失,而在 PNP 处理中,与对照组相比,某些官能团发生了变化。在分子水平上,双酚 A 和 PNP 诱导了多酚氧化酶和过氧化物酶基因表达的增加,只有 POD 基因表达在双酚 A 胁迫下有所增加。在最高水平的 PNP 和中等水平的双酚 A 诱导下,thaumatin 样蛋白基因的表达增加,而这两种污染物对微管蛋白(TUB)基因的表达没有明显影响。对受到 BPA 和 PNP 胁迫的番茄植株的生化反应进行全面分析,有助于深入了解这些污染物的耐受机制。
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引用次数: 0
A comprehensive review of the interaction between COVID-19 spike proteins with mammalian small and major heat shock proteins. 全面回顾 COVID-19 尖峰蛋白与哺乳动物小型和大型热休克蛋白之间的相互作用。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-06-14 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0027
Liberty T Navhaya, Dzveta Mutsawashe Blessing, Mthembu Yamkela, Sesethu Godlo, Xolani Henry Makhoba

Coronavirus disease 2019 (COVID-19) is a novel disease that had devastating effects on human lives and the country's economies worldwide. This disease shows similar parasitic traits, requiring the host's biomolecules for its survival and propagation. Spike glycoproteins severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 spike protein) located on the surface of the COVID-19 virus serve as a potential hotspot for antiviral drug development based on their structure. COVID-19 virus calls into action the chaperonin system that assists the attacker, hence favoring infection. To investigate the interaction that occurs between SARS-CoV-2 spike protein and human molecular chaperons (HSPA8 and sHSP27), a series of steps were carried out which included sequence attainment and analysis, followed by multiple sequence alignment, homology modeling, and protein-protein docking which we performed using Cluspro to predict the interactions between SARS-CoV-2 spike protein and human molecular chaperones of interest. Our findings depicted that SARS-CoV-2 spike protein consists of three distinct chains, chains A, B, and C, which interact forming hydrogen bonds, hydrophobic interactions, and electrostatic interactions with both human HSPA8 and HSP27 with -828.3 and -827.9 kcal/mol as binding energies for human HSPA8 and -1166.7 and -1165.9 kcal/mol for HSP27.

冠状病毒病 2019(COVID-19)是一种新型疾病,对全球人类生命和国家经济造成了毁灭性影响。这种疾病表现出类似的寄生特性,需要宿主的生物大分子才能生存和繁殖。位于 COVID-19 病毒表面的尖峰糖蛋白严重急性呼吸系统综合征冠状病毒 2(SARS-CoV-2 尖峰蛋白)是根据其结构开发抗病毒药物的潜在热点。COVID-19 病毒唤醒了辅助攻击者的伴侣蛋白系统,从而有利于感染。为了研究 SARS-CoV-2 穗状病毒蛋白与人类分子伴侣(HSPA8 和 sHSP27)之间的相互作用,我们进行了一系列步骤,包括序列获取和分析,然后进行多序列比对、同源建模和蛋白质-蛋白质对接,我们使用 Cluspro 预测了 SARS-CoV-2 穗状病毒蛋白与感兴趣的人类分子伴侣之间的相互作用。我们的研究结果表明,SARS-CoV-2 穗状病毒蛋白由三条不同的链 A、B 和 C 组成,它们与人类 HSPA8 和 HSP27 相互作用,形成氢键、疏水作用和静电作用,人类 HSPA8 的结合能分别为 -828.3 和 -827.9 kcal/mol,HSP27 的结合能分别为 -1166.7 和 -1165.9 kcal/mol。
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引用次数: 0
Biochemical dynamics during postharvest: Highlighting the interplay of stress during storage and maturation of fresh produce. 收获后的生化动态:突出新鲜农产品贮藏和成熟过程中各种压力的相互作用。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-08 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0048
Ernesto Alonso Lagarda-Clark, Charles Goulet, Arturo Duarte-Sierra

The lifecycle of fresh produce involves a sequence of biochemical events during their ontology, and these events are particularly significant for climacteric fruits. A high demand during ripening is observed in these plant products, which is reflected in a high rate of respiration and ethylene production. Increased respiratory demand triggers the activation of secondary pathways such as alternate oxidase, which do not experience critical increases in energy consumption in non-climacteric fruit. In addition, biochemical events produced by external factors lead to compensatory responses in fresh produce to counteract the oxidative stress caused by the former. The dynamics of these responses are accompanied by signaling, where reactive oxygen species play a pivotal role in fresh product cell perception. This review aims to describe the protection mechanisms of fresh produce against environmental challenges and how controlled doses of abiotic stressors can be used to improve quality and prolong their shelf-life through the interaction of stress and defense mechanisms.

新鲜农产品的生命周期涉及其本体过程中的一系列生化事件,这些事件对气候性水果尤为重要。这些植物产品在成熟期的需求量很大,这反映在呼吸作用和乙烯的高产率上。呼吸需求的增加会引发交替氧化酶等次级途径的激活,而在非成熟期果实中,这些途径的能量消耗不会出现关键性的增加。此外,外部因素产生的生化事件会导致新鲜农产品产生补偿反应,以抵消前者造成的氧化压力。这些反应的动态伴随着信号传递,其中活性氧在新鲜产品的细胞感知中起着关键作用。本综述旨在介绍新鲜农产品应对环境挑战的保护机制,以及如何通过应激和防御机制的相互作用,利用可控剂量的非生物应激源来提高农产品质量和延长货架期。
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引用次数: 0
Seeing beyond the blot: A critical look at assumptions and raw data interpretation in Western blotting. 透过印迹看本质:对 Western 印迹分析中的假设和原始数据解释的批判性审视。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-01 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0047
Maxwell S DeNies, Allen P Liu, Santiago Schnell

Rapid advancements in technology refine our understanding of intricate biological processes, but a crucial emphasis remains on understanding the assumptions and sources of uncertainty underlying biological measurements. This is particularly critical in cell signaling research, where a quantitative understanding of the fundamental mechanisms governing these transient events is essential for drug development, given their importance in both homeostatic and pathogenic processes. Western blotting, a technique developed decades ago, remains an indispensable tool for investigating cell signaling, protein expression, and protein-protein interactions. While improvements in statistical analysis and methodology reporting have undoubtedly enhanced data quality, understanding the underlying assumptions and limitations of visual inspection in Western blotting can provide valuable additional information for evaluating experimental conclusions. Using the example of agonist-induced receptor post-translational modification, we highlight the theoretical and experimental assumptions associated with Western blotting and demonstrate how raw blot data can offer clues to experimental variability that may not be fully captured by statistical analyses and reported methodologies. This article is not intended as a comprehensive technical review of Western blotting. Instead, we leverage an illustrative example to demonstrate how assumptions about experimental design and data normalization can be revealed within raw data and subsequently influence data interpretation.

技术的飞速发展完善了我们对错综复杂的生物过程的理解,但重点仍然是理解生物测量的假设和不确定性来源。这一点在细胞信号传导研究中尤为重要,鉴于瞬时事件在平衡和致病过程中的重要性,定量了解这些瞬时事件的基本机制对药物开发至关重要。几十年前开发的 Western 印迹技术仍然是研究细胞信号传导、蛋白质表达和蛋白质间相互作用不可或缺的工具。虽然统计分析和方法报告的改进无疑提高了数据质量,但了解 Western 印迹技术的基本假设和目视检查的局限性也能为评估实验结论提供有价值的额外信息。我们以激动剂诱导的受体翻译后修饰为例,强调了与 Western 印迹相关的理论和实验假设,并展示了原始印迹数据如何为统计分析和报告方法可能无法完全捕捉的实验变异性提供线索。本文无意作为一篇全面的 Western 印迹技术综述。相反,我们利用一个示例来说明实验设计和数据归一化的假设是如何在原始数据中显现出来并进而影响数据解读的。
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引用次数: 0
Senescent adipocytes and type 2 diabetes - current knowledge and perspective concepts. 衰老脂肪细胞与 2 型糖尿病--当前知识和前景概念。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-03-26 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0046
Weronika Kruczkowska, Julia Gałęziewska, Mateusz Kciuk, Adrianna Gielecińska, Elżbieta Płuciennik, Zbigniew Pasieka, Lin-Yong Zhao, Yi-Jin Yu, Damian Kołat, Żaneta Kałuzińska-Kołat

Among civilization diseases, the number of individuals suffering from type 2 diabetes (T2DM) is expected to increase to more than a billion in less than 20 years, which is associated with, e.g., populational aging, poor diet, sedentary lifestyle, genetic predispositions, and immunological factors. T2DM affects many organs and is characterized by insulin resistance, high glucose levels, and adipocyte dysfunction, which are related to senescence. Although this type of cellular aging has beneficial biological functions, it can also act unfavorable since senescent adipocytes resist apoptosis, enhance cytokine secretion, downregulate cell identity genes, and acquire the senescence-associated secretory phenotype that renders a more oxidative environment. Opposing T2DM is possible via a wide variety of senotherapies, including senolytics and senomorphics; nevertheless, further research is advised to expand therapeutic possibilities and benefits. Consequences that ought to be deeply researched include secretory phenotype, chronic inflammation, increasing insulin resistance, as well as impairment of adipogenesis and functioning of adipocyte cells. Herein, despite reviewing T2DM and fat tissue senescence, we summarized the latest adipocyte-related anti-diabetes solutions and suggested further research directions.

在文明病中,2 型糖尿病(T2DM)患者的人数预计将在不到 20 年的时间内增加到 10 亿以上,这与人口老龄化、不良饮食习惯、久坐不动的生活方式、遗传倾向和免疫因素等有关。T2DM 影响许多器官,其特点是胰岛素抵抗、高血糖和脂肪细胞功能障碍,这些都与衰老有关。虽然这种细胞衰老具有有益的生物功能,但也可能产生不利影响,因为衰老的脂肪细胞会抵制细胞凋亡,增强细胞因子分泌,下调细胞特征基因,并获得衰老相关的分泌表型,使氧化环境更加恶化。通过各种衰老疗法,包括衰老溶解剂和衰老蜕变剂,可以对抗 T2DM;不过,建议进一步开展研究,以扩大治疗的可能性和益处。需要深入研究的后果包括分泌表型、慢性炎症、胰岛素抵抗增加以及脂肪生成和脂肪细胞功能受损。在此,我们回顾了 T2DM 和脂肪组织衰老,总结了与脂肪细胞相关的最新抗糖尿病方案,并提出了进一步的研究方向。
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引用次数: 0
Withaferin A alters the expression of microRNAs 146a-5p and 34a-5p and associated hub genes in MDA-MB-231 cells. Withaferin A 可改变 MDA-MB-231 细胞中 microRNA 146a-5p 和 34a-5p 以及相关枢纽基因的表达。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-03-25 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0045
Mohd Shuaib, Smriti Chaudhri, Shashank Kumar

Triple-negative breast cancer (TNBC) is a highly metastatic subtype of breast cancer. Due to the absence of obvious therapeutic targets, microRNAs (miRNAs) provide possible hope to treat TNBC. Withaferin A (WA), a steroidal lactone, possesses potential anticancer activity with lesser side effects. The present study identifies hub genes (CDKN3, TRAF6, CCND1, JAK1, MET, AXIN2, JAG1, VEGFA, BRCA1, E2F3, WNT1, CDK6, KRAS, MYB, MYCN, TGFβR2, NOTCH1, SIRT1, MYCN, NOTCH2, WNT3A) from the list of predicted targets of the differentially expressed miRNAs (DEMs) in WA-treated MDA-MB-231 cells using in silico protein-protein interaction network analysis. CCND1, CDK6, and TRAF6 hub genes were predicted as targets of miR-34a-5p and miR-146a-5p, respectively. The study found the lower expression of miR-34a-5p and miR-146a-5p in MDA-MB-231 cells, and further, it was observed that WA treatment effectively restored the lost expression of miR-34a-5p and miR-146a-5p in MDA-MB-231 cells. An anti-correlation expression pattern was found among the miR-34a-5p and miR-146a-5p and the respective target hub genes in WA-treated TNBC cells. In conclusion, WA might exert anti-cancer effect in TNBC cells by inducing miR-34a-5p and miR-146a-5p expressions and decreasing CCND1, CDK6, and TARF6 target hub genes in TNBC cells.

三阴性乳腺癌(TNBC)是一种高度转移性乳腺癌亚型。由于缺乏明显的治疗靶点,microRNA(miRNA)为治疗 TNBC 带来了可能的希望。Withaferin A(WA)是一种甾体内酯,具有潜在的抗癌活性,且副作用较小。本研究确定了中心基因(CDKN3、TRAF6、CCND1、JAK1、MET、AXIN2、JAG1、VEGFA、BRCA1、E2F3、WNT1、CDK6、KRAS、MYB、MYCN、TGFβR2、NOTCH1、SIRT1、MYCN、NOTCH2、在 WA 处理过的 MDA-MB-231 细胞中,利用硅学蛋白-蛋白相互作用网络分析,从差异表达 miRNAs(DEMs)的预测靶标列表中筛选出 CDK6、KRAS、MYB、MYCN、TGFβR2、NOTCH1、SIRT1、MYCN、NOTCH2、WNT3A。CCND1、CDK6 和 TRAF6 中枢基因分别被预测为 miR-34a-5p 和 miR-146a-5p 的靶标。研究发现,miR-34a-5p和miR-146a-5p在MDA-MB-231细胞中的表达量较低,而且WA处理能有效恢复MDA-MB-231细胞中miR-34a-5p和miR-146a-5p的表达量。在WA处理的TNBC细胞中,miR-34a-5p和miR-146a-5p与各自的靶中心基因之间存在反相关表达模式。总之,WA可能通过诱导TNBC细胞中miR-34a-5p和miR-146a-5p的表达以及降低CCND1、CDK6和TARF6靶中心基因的表达,对TNBC细胞产生抗癌作用。
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引用次数: 0
Diurnal and circadian regulation of opsin-like transcripts in the eyeless cnidarian Hydra. 无眼刺胞动物水螅中类视蛋白转录本的昼夜节律调控
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-03-19 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0044
Silvia Santillo, Luciano De Petrocellis, Carlo Musio

Opsins play a key role in the ability to sense light both in image-forming vision and in non-visual photoreception (NVP). These modalities, in most animal phyla, share the photoreceptor protein: an opsin-based protein binding a light-sensitive chromophore by a lysine (Lys) residue. So far, visual and non-visual opsins have been discovered throughout the Metazoa phyla, including the photoresponsive Hydra, an eyeless cnidarian considered the evolutionary sister species to bilaterians. To verify whether light influences and modulates opsin gene expression in Hydra, we utilized four expression sequence tags, similar to two classic opsins (SW rhodopsin and SW blue-sensitive opsin) and two non-visual opsins (melanopsin and peropsin), in investigating the expression patterns during both diurnal and circadian time, by means of a quantitative RT-PCR. The expression levels of all four genes fluctuated along the light hours of diurnal cycle with respect to the darkness one and, in constant dark condition of the circadian cycle, they increased. The monophasic behavior in the L12:D12 cycle turned into a triphasic expression profile during the continuous darkness condition. Consequently, while the diurnal opsin-like expression revealed a close dependence on light hours, the highest transcript levels were found in darkness, leading us to novel hypothesis that in Hydra, an "internal" biological rhythm autonomously supplies the opsins expression during the circadian time. In conclusion, in Hydra, both diurnal and circadian rhythms apparently regulate the expression of the so-called visual and non-visual opsins, as already demonstrated in higher invertebrate and vertebrate species. Our data confirm that Hydra is a suitable model for studying ancestral precursor of both visual and NVP, providing useful hints on the evolution of visual and photosensory systems.

在形成图像的视觉和非视觉光感受(NVP)中,眼色素在感光能力中都发挥着关键作用。在大多数动物门类中,这些模式都有共同的光感受器蛋白质:一种基于视蛋白的蛋白质,通过赖氨酸(Lys)残基与光敏发色团结合。迄今为止,已在整个后生动物门中发现了视觉和非视觉的视蛋白,其中包括具有光感受器的水螅,它是一种无眼的刺胞动物,在进化过程中被认为是双翅目动物的姊妹物种。为了验证光是否会影响和调节水螅的视蛋白基因表达,我们利用四个表达序列标签(类似于两种经典视蛋白(SW rhodopsin 和 SW blue-sensitive opsin)和两种非视蛋白(melanopsin 和 peropsin)),通过定量 RT-PCR 技术研究了昼夜节律时间内的表达模式。这四个基因的表达水平在昼夜循环的光照时间内相对于黑暗时间有所波动,而在昼夜循环的恒定黑暗条件下则有所上升。在持续黑暗条件下,L12:D12 周期中的单相表达变成了三相表达。因此,虽然类视蛋白的昼夜表达与光照时间密切相关,但最高的转录水平是在黑暗条件下发现的,这使我们提出了一个新的假设,即在水螅中,"内部 "生物节律在昼夜节律期间自主提供视蛋白的表达。总之,在水螅中,昼夜节律显然可以调节所谓的视觉和非视觉蛋白的表达,这在高等无脊椎动物和脊椎动物中已经得到证实。我们的数据证实水螅是研究视觉和非视觉蛋白祖先前体的合适模型,为视觉和光感系统的进化提供了有用的提示。
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引用次数: 0
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。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-03-13 eCollection Date: 2024-01-01 DOI: 10.1515/bmc-2022-0043
Pravinkumar M Sonsare, Chellamuthu Gunavathi

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.

计算生物学面临着许多挑战,如蛋白质二级结构预测(PSS)、溶剂可及性预测等。在这项工作中,我们研究了蛋白质二级结构预测。PSS 基于氨基酸残基之间的序列结构映射和相互作用。我们提出了一种带有注意机制模型的编码器-解码器,该模型考虑了序列结构和残基间相互作用的映射。注意力机制用于从氨基酸残基中选择突出特征。我们使用 Nvidia DGX 系统在 CB513 和 CullPDB 开放数据集上训练了所提出的模型。我们对提出的方法进行了 Q 3 和 Q 8 准确率、重叠段和 Mathew 相关系数测试。我们在 CullPDB 数据集上的 Q 3 和 Q 8 准确率分别为 70.63% 和 78.93%,而在 CB513 数据集上的 Q 3 和 Q 8 准确率分别为 79.8% 和 77.13%。在 CullPDB 和 CB513 数据集上,我们观察到 SOV 分别提高到 80.29% 和 91.3%。使用我们提出的模型,我们只用了很少的时间就取得了这样的结果,这比最先进的方法要好。
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Biomolecular Concepts
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