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Syzygium aromaticum as a possible source of SARS-CoV-2 main protease inhibitors: Evidence from a computational investigation 丁香作为SARS-CoV-2主要蛋白酶抑制剂的可能来源:来自计算调查的证据
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d109
M. Ali, A-Zha Nur, Rubaeit Rakib, M. Khatun, R. Hasib, M. Rahman, M. Alam, Md Abdullah Al Mashud, Mohammad Jamal
SARS-CoV-2, a new and fast circulating coronavirus strain, infected over 214 countries and territories worldwide and caused global health emergencies. The absence of appropriate medicines and vaccinations has further complicated the condition. SARS-CoV-2 main protease (Mpro) is crucial for its propagation, and it is considered a striking target. This study used several computational approaches to determine the probable antagonist of SARS-CoV-2 Mpro from bioactive phytochemicals of Syzygium aromaticum. A total of 20 compounds were screened through in silico approach. The molecular dynamics simulation studies were then carried out for further insights. We found crategolic acid, oleanolic acid, and kaempferol have considerable binding affinity and important molecular contacts with catalytic pocket residues, His41-Cys145. The pharmacological properties through ADMET analysis also showed that these compounds could be used as safe drug candidates. The molecular dynamics simulation study further confirmed these compound's stability with Mpro. However, further detailed in-vitro and in-vivo analyses are compulsory to evaluate the real potentiality of identified compounds.
SARS-CoV-2是一种快速传播的新型冠状病毒毒株,已在全球214多个国家和地区感染,并引发全球突发卫生事件。缺乏适当的药物和疫苗接种使病情进一步复杂化。SARS-CoV-2主蛋白酶(Mpro)对其繁殖至关重要,被认为是一个引人注目的靶标。本研究使用了几种计算方法,从丁香的生物活性植物化学物质中确定可能的SARS-CoV-2 Mpro拮抗剂。通过硅法共筛选了20个化合物。然后进行分子动力学模拟研究以进一步了解。我们发现,十一烯酸、齐墩果酸和山奈酚与催化口袋残基His41-Cys145具有相当大的结合亲和力和重要的分子接触。通过ADMET分析的药理学性质也表明这些化合物可以作为安全的候选药物。分子动力学模拟研究进一步证实了这些化合物与Mpro的稳定性。然而,进一步详细的体外和体内分析是必要的,以评估鉴定的化合物的真正潜力。
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引用次数: 0
HPTLC Fingerprinting analysis of phytoconstituents from Bixa orellana and Beta vulgaris plant 薄层色谱(HPTLC)指纹图谱分析薄层色谱法测定苦参和甜菜的成分
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d116
Mrunal Patel, Priti Patel
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引用次数: 1
Optimization of surface sterilization method for the isolation of endophytic fungi associated with Curcuma longa L. and their antibacterial activity. 姜黄内生真菌表面灭菌方法的优化及其抑菌活性研究。
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d119
Himani Deepak, Verinder Virk
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引用次数: 0
Characterization of virulence gene distribution and antibiotic susceptibility profiles of diarrheagenic Escherichia coli from chicken faeces 鸡粪致泻性大肠埃希菌毒力基因分布及抗生素敏感性分析
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d104
S. Giri, Sanath H. Kumar, G. K, V. Shetty
{"title":"Characterization of virulence gene distribution and antibiotic susceptibility profiles of diarrheagenic Escherichia coli from chicken faeces","authors":"S. Giri, Sanath H. Kumar, G. K, V. Shetty","doi":"10.5455/jabet.2022.d104","DOIUrl":"https://doi.org/10.5455/jabet.2022.d104","url":null,"abstract":"","PeriodicalId":36275,"journal":{"name":"Journal of Advanced Biotechnology and Experimental Therapeutics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70796036","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: 1
Antimicrobial and Phytochemical screening of selected wild mushrooms naturally found in Garhwal Himalayan region, Uttarakhand, India 印度北阿坎德邦加尔瓦尔喜马拉雅地区天然野生蘑菇的抗菌和植物化学筛选
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d125
Gaurav Kothiyal, Keerti Singh
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引用次数: 1
Protective effect of L-carnitine nanoparticles Vs carnitine on lead acetate-induced toxicity in male rats. 左旋肉碱纳米颗粒与左旋肉碱对醋酸铅致雄性大鼠毒性的保护作用。
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d138
Hayder Mahdi, R. Ghadhban
Chitosan nanoparticles are important materials that are widely used in many biological, engineering and food industries and are also used as plant growth stimulants as well as use as vectors for drug delivery to target cells. Whereas L-carnitine (LC) is a water-soluble compound that contributes to the transport of long-chain fatty acids across the mitochondrial membranes and the oxidation of β-lipids. Methods: 60 male rats (Rattus Rattus) were divided into six equal groups. The first group (control group): Animals received orally distilled water. The second group. Animals received 1ml orally lead acetate at a dose of 30 mg/kg of body weight daily for 30 days. Third group: Animals received 1ml (lead acetate 30mg/kg B.W + L-carnitine (100mg/ kg B.W. /daily). The fourth group. Animals received 1ml (lead acetate 30mg/kg B.W. + Nano L-carnitine 100mg/ kg B.W./ daily). The fifth group: Animals received 1ml of L-Carnitine orally at a dose of 100mg/ kg B.W /daily. The sixth group: Animals received 1ml of L-Carnitine-NPs orally at 100mg/ kg B.W /daily. Results: Our findings demonstrated that exposure to lead acetate caused a significant increase in liver-enzymes Aspartate Transaminase (AST), Alanine Transaminase (ALT), and Alkaline Phosphatase (ALP) and renal function enzymes (creatinine and urea) in the lead acetate group. Whereas, lead treatment increased oxidative stress and reactive oxygen species (ROS), which can be removed through decreased glutathione (GHPX) and increased malondialdehyde (MDA). Conclusions: Histopathological study showed significant changes in the brain (cerebellum) that disrupted the normal arrangement of the three layers, with large distances between the Purkinje cell layer and the molecular or granular layer. According to the study, we can conclude that the Nano L-Carnitine had a greater role in protecting against the effect of lead at the haematological parameters and a clear role in the protection against histopathology change of lead poisoning. L-Carnitine and Nano L-Carnitine had an active role in protecting against lead acetate toxicity.
壳聚糖纳米颗粒是一种重要的材料,广泛应用于生物、工程和食品工业,也可作为植物生长刺激剂和药物载体递送到靶细胞。而左旋肉碱(LC)是一种水溶性化合物,有助于长链脂肪酸在线粒体膜上的运输和β-脂质的氧化。方法:雄性Rattus Rattus大鼠60只,随机分为6组。第一组(对照组):动物口服蒸馏水。第二组。动物每日口服醋酸铅1ml,剂量为30 mg/kg体重,连续30天。第三组:每日给予醋酸铅30mg/kg体重1ml +左旋肉碱100mg/ kg体重/d。第四组。动物每天服用1ml(醋酸铅30mg/kg体重+纳米左旋肉碱100mg/ kg体重/天)。第五组:动物口服左旋肉碱1ml,剂量为100mg/ kg体重/天。第六组:每日口服左旋肉碱- nps 1ml,剂量为100mg/ kg B.W。结果:我们的研究结果表明,暴露于醋酸铅导致醋酸铅组肝脏酶(天冬氨酸转氨酶(AST)、丙氨酸转氨酶(ALT)、碱性磷酸酶(ALP)和肾功能酶(肌酐和尿素)显著增加。然而,铅处理增加了氧化应激和活性氧(ROS),这可以通过降低谷胱甘肽(GHPX)和增加丙二醛(MDA)来去除。结论:组织病理学研究显示,脑(小脑)发生了明显的变化,破坏了三层的正常排列,浦肯野细胞层与分子或颗粒层之间距离较大。由此可见,纳米左旋肉碱在血液学参数上对铅的影响具有较大的保护作用,对铅中毒的组织病理学变化具有明显的保护作用。左旋肉碱和纳米左旋肉碱对醋酸铅中毒具有积极的保护作用。
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引用次数: 2
Molecular and immunological effect of Terminalia chebula extracts 诃子提取物的分子和免疫作用
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d106
Haider Mousawi, A. Mushtaq, Alyaa Bohan
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引用次数: 2
Validation Study of c.746A>G SNP of BMPR1B Gene Associated with Litter Size in Sheep Genetic Resources of Bangladesh 孟加拉国绵羊遗传资源中BMPR1B基因c.746A>G SNP与产仔数相关的验证研究
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d149
S. Mony, T. Maruf, N. Desha, M. Pabitra, Sadek Ahmed, M. Hossain, M. Bhuiyan
The BMPR1B gene is one of the major fecundity genes that have been investigated in different sheep populations worldwide for its association with prolificacy traits. The present study was performed to validate the association of c.746A>G SNP of BMPR1B gene with litter size trait in different sheep populations of Bangladesh. A total of 192 blood samples were collected from ewes of both farmers’ and institutional flocks comprising sheep populations of Jamuna River Basin (JRB), Barendra (BAT), Coastal (COR), Garole (GAR) and Muzaffarnagari (MUZ). Genotyping of the individuals was performed using PCR-RFLP method and single marker association analysis was carried out to evaluate the relationships between resultant genotypes and litter size trait using agricolae and pastecs packages of R software. The prolificacy attributed homozygous FecBBB genotype frequencies were 66, 50 and 55%, respectively in JRB, BAT and GAR populations whereas it was only 0-2% in MUZ and COR populations. Association analysis revealed highly significant (P<0.001) association of litter size trait with genotypes and populations. The mean litter sizes of JRB, BAT, GAR, COR and MUZ were 2.17±0.15, 1.88±0.07 1.90±0.10, 1.12±0.03 and 1.02±0.02, respectively. The prolific JRB, BAT, GAR ewes produced 0.67 to 0.83 more lambs per lambing than their wild type FecB++ counterparts. Thus, this study validated the potential contribution of the investigated c.746A>G SNP that could be applied in marker assisted selection (MAS) program for identifying high prolific ewes in order to improve litter size trait at the population level
BMPR1B基因是主要的生殖力基因之一,已在世界各地的不同绵羊种群中进行了研究,因为它与繁殖性状有关。本研究旨在验证孟加拉国不同绵羊群体BMPR1B基因c.746A>G SNP与产仔数性状的关系。从贾穆纳河流域(JRB)、巴伦德拉(BAT)、沿海(COR)、加罗尔(GAR)和Muzaffarnagari (MUZ)的农民羊群和机构羊群的母羊中共采集了192份血液样本。采用PCR-RFLP方法对个体进行基因分型,并利用agricolae和pastecs R软件进行单标记关联分析,评价所得基因型与产仔数性状之间的关系。纯合子FecBBB基因型在JRB、BAT和GAR群体中分别为66%、50%和55%,而在MUZ和COR群体中仅为0-2%。关联分析显示,高显著(PG) SNP可应用于标记辅助选择(MAS)程序,以识别高产母羊,以提高群体水平上的产仔数性状
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引用次数: 2
Codon usage bias and purifying selection identified in Cirrhinus reba mitogenome 热螺旋鱼有丝分裂基因组密码子使用偏向和纯化选择的研究
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.5455/jabet.2022.d139
Mohammad Islam, S. Sultana
In our previous study, we described sequence assembly and organization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba (GenBank accession no.: MN862482). In this study, our attempts were to find out any mutation or selection pressures and codon usage patterns existing in the mitogenome of the same fish. We applied bioinformatics tools to measure important gene parameters including AT/GC skewness, codon adaptation index (CAI), the effective number of codons (ENc) and GC percentages of each protein coding gene. We found an overrepresentation of A and C resulting a lower number of T and G bases, respectively, where AT-skew was slightly positive and GC-skew was slightly negative. Except for ND6, all protein coding genes (PCGs) had negative GC-skew, which indicated the higher occurrence of Cs. With reference to other two mitogenomes, the dN/dS or Ka/Ks ratios ranged from the lowest value (0.016) for ND4L to the highest value (0.694) for ND1 gene which indicated that PCGs of this fish evolved under strong purifying selection. We further analyzed the codon frequency and relative synonymous codon usage (RSCU) and observed a total of 3802 codons which were used for coding 20 amino acids by a standard set of 64 codons. The amino acids Leucine and Serine were encoded each by six different codons, whereas rest of the amino acids was encoded by either two or four codons. We identified a total of 25 RSCU values (> 1) and revealed 12 codons as “overpresented” that implied for codon usage bias to engage in highly expressed genes for efficient protein synthesis via translational selection. The existence of codon usage biasness rolling in translational selection and the signs of purifying selection identified in PCGs suggest obvious conservation of this threatened fish species.
在我们之前的研究中,我们描述了一种受威胁的labeonine鱼Cirrhinus reba (GenBank accession no. 1)的全线粒体基因组的序列组装和组织。: MN862482)。在这项研究中,我们试图找出任何突变或选择压力和密码子的使用模式存在于同一鱼类的有丝分裂基因组。我们应用生物信息学工具测量了每个蛋白质编码基因的重要基因参数,包括AT/GC偏度、密码子适应指数(CAI)、有效密码子数(ENc)和GC百分比。我们发现A和C的过度代表分别导致T和G碱基的数量较低,其中at偏偏略为正,gc偏偏略为负。除ND6外,所有蛋白编码基因(PCGs)均呈负gc偏态,表明Cs的发生率较高。与其他两个有丝分裂基因组相比,ND4L基因的dN/dS或Ka/Ks值从最低值(0.016)到ND1基因的最高值(0.694)不等,表明该鱼的PCGs是在强净化选择下进化的。我们进一步分析了密码子频率和相对同义密码子使用(RSCU),发现在64个标准密码子中,共有3802个密码子用于编码20个氨基酸。亮氨酸和丝氨酸分别由6个不同的密码子编码,而其余的氨基酸则由2个或4个密码子编码。我们共鉴定了25个RSCU值(> 1),并揭示了12个密码子“过度呈现”,这意味着密码子使用偏向于通过翻译选择参与高表达基因的高效蛋白质合成。翻译选择中密码子使用偏倚滚动的存在以及在PCGs中发现的净化选择的迹象表明该濒危鱼类存在明显的保护。
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引用次数: 2
In Vivo Antidiabetic Efficacy, Mineral Element Composition, and Qualitative Phytochemistry of the Aqueous Leaf Extracts of Pentas zanzibarica (Klotzsch.) Vatke and Olea europaea subspecies africana (Mill.) 桑给巴尔刺Pentas zanzibarica (Klotzsch.)叶水提取物的体内抗糖尿病功效、矿物元素组成和定性植物化学研究欧洲油橄榄亚种非洲油橄榄亚种
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2021-07-15 DOI: 10.5455/jabet.2021.d134
G. Moriasi, C. Kibiti, M. Ngugi
Persistent hyperglycaemia is the hallmark of diabetes and is accountable for the devastating complications, which cause high morbidity and mortality. Conventional anti-diabetic agents are only palliative and characterised with limited efficacy, adverse effects, high costs, inaccessibility, prompting the need for better alternatives. Therefore, we investigated the in vivo hypoglycaemic activities, elemental composition, and qualitative phytochemistry of the aqueous leaf extracts of P. zanzibarica and O. europaea subspecies africana as potential sources of affordable, safer, accessible, and potent anti-diabetic therapies. In vivo hypoglycaemic activities of the studied plant extracts were evaluated at three dose levels of 50, 100, and 150 mg/Kg body weight (bw) in Alloxan-induced hyperglycaemic Swiss albino mice. The elemental composition of the plant extracts was analysed using the energy dispersive x-ray fluorescence spectroscopy (EDXRF System) and the atomic absorption spectrometry (AAS). Qualitative phytochemical screening was done following standard procedures. In this study, the aqueous leaf extract of P. zanzibarica, significantly (p<0.05) reduced alloxan-induced hyperglycaemia in mice from 163.26±2.24 mg/dL (at 0h) to 52.12±1.16 mg/dL (at the 4th h) at a dose of 50 mg/Kg body weight, 166.98±1.56 mg/dL (at 0h) to 48.90±1.40 mg/dL (at 4th h) at a dose of 100 mg/Kg body weight, and 168.64±2.96 mg/dL (at 0h) to 42.46±1.80 mg/dL (at 4th h) at a dose of 150 mg/Kg body weight, respectively. Similarly, the aqueous leaf extract of O. europaea subspecies africana significantly (p<0.05) reduced hyperglycaemia from 165.74±3.66 mg/dL (at 0h) to 65.26±1.46 mg/dL (at the 4th h) at a dose of 50 mg/Kg body weight, 158.14±3.49 mg/dL (at 0h) to 53.68±1.48 mg/dL (at the 4th h) at a dose of 100 mg/Kg body weight, and from 161.66±2.19 mg/dL (at 0h) to 44.48±1.35 mg/dL (at the 4th h) at a dose of 150 mg/Kg body weight, respectively Furthermore, the extracts contained chromium (Cr), zinc (Zn), magnesium (Mg), among other elements, and phytochemicals like phenols, flavonoids, and alkaloids, among others. Generally, the studied plant extracts exhibited significant hypoglycaemic efficacy in alloxan-induced hyperglycaemic mice, indicating their antidiabetic potential, and possess pharmacologically active phytochemicals and valuable minerals.
持续高血糖是糖尿病的标志,是造成高发病率和高死亡率的毁灭性并发症的原因。传统的抗糖尿病药物只能起到缓解作用,而且疗效有限,副作用大,成本高,难以获得,这促使人们需要更好的替代品。因此,我们研究了zanzibarica和O. europaea非洲亚种的叶片水提取物的体内降糖活性、元素组成和定性植物化学,作为可负担、更安全、可获得和有效的抗糖尿病治疗的潜在来源。在四氧嘧啶诱导的高血糖瑞士白化小鼠体内,研究了所研究的植物提取物在50、100和150 mg/Kg体重(bw)三个剂量水平下的降血糖活性。采用能量色散x射线荧光光谱法(EDXRF)和原子吸收光谱法(AAS)分析了植物提取物的元素组成。按照标准程序进行定性植物化学筛选。在本研究中,桑给桑树叶水提物能显著(p<0.05)降低小鼠四氧胺诱导的高血糖,分别在50 mg/Kg体重剂量下,从163.26±2.24 mg/dL (0h)降至52.12±1.16 mg/dL (4 h);在100 mg/Kg体重剂量下,从166.98±1.56 mg/dL (0h)降至48.90±1.40 mg/dL (4 h);在150 mg/Kg体重剂量下,从168.64±2.96 mg/dL (0h)降至42.46±1.80 mg/dL (4 h)。同样,水叶提取o .欧洲亚种非洲显著(p < 0.05)降低高血糖症从165.74±3.66 mg / dL (0 h) 65.26±1.46 mg / dL (4 h)的剂量50毫克/公斤体重,158.14±3.49 mg / dL (0 h) 53.68±1.48 mg / dL (4 h)的剂量100毫克/公斤体重,和从161.66±2.19 mg / dL (0 h) 44.48±1.35 mg / dL (4 h)的剂量150毫克/公斤体重,此外,分别提取包含铬(Cr)、锌(锌),镁(Mg)和其他元素,以及植物化学物质,如酚类物质、类黄酮和生物碱等。总的来说,所研究的植物提取物在四氧嘧啶诱导的高血糖小鼠中表现出显著的降糖功效,表明它们具有抗糖尿病的潜力,并且具有药理活性的植物化学物质和有价值的矿物质。
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引用次数: 3
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Journal of Advanced Biotechnology and Experimental Therapeutics
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