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Assessment of vitamin D status and vitamin D receptor polymorphism in Egyptian children with Type 1 diabetes 评估埃及 1 型糖尿病患儿的维生素 D 状态和维生素 D 受体多态性
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-22 DOI: 10.1016/j.jgeb.2023.100343
Eman A. Mostafa , Maha M.A. Abo Hashish , Nagwa Abdallah Ismail , Hasanin M. Hasanin , Rasha M. Hasanin , Aliaa Ahmed Wahby , Ingy Ashmawy , Shereen Hamdy Abd El Aziz , Mai Magdy Abdel Wahed

Background

The endocrine system of vitamin D regulates about 3 % of the human genome. Vitamin D exerts its actions via a nuclear vitamin D receptor (VDR) which in turn regulates insulin secretion from the pancreas. VDR gene polymorphisms could have an impact on how autoimmune illnesses like Type 1 diabetes mellitus (T1DM) develop. We aimed to explore the relation between T1DM and VDR gene polymorphisms in Egyptian diabetic children and their siblings.

Methods

Enzyme-linked immunosorbent assay was used to quantify 25(OH) vitamin D in the study, which had 179 participants (group 1 = 85 diabetic children, group 2 = 57 siblings of the patients, group 3 = 37 healthy controls). Real-time polymerase chain reaction (RT-PCR) was used to analyze the genotyping of the VDR gene polymorphisms Apa-I (rs7975232), Fok-I (rs2228570), Taq-I (rs731236) and Bsm-I (rs1544410).

Results

The mean serum 25(OH) vitamin D levels was significantly lower in T1DM patients (14.99 ± 9.24 ng/mL) and siblings (16.31 ± 7.96 ng/mL) compared to the controls (19.48 ± 7.42 ng/mL) (p = 0.031). The genotypes distribution of VDR Fok-I (rs2228570) and Bsm-I (rs1544410) polymorphisms showed a significant difference between patients, siblings and controls as P = 0.001 and 0.026 respectively, while the VDR ApaI and TaqI polymorphisms did not. FokI-A allele frequency was significantly lower in T1DM patients and siblings than in controls (p < 0.001). FokI-AA genotype had a statistical significant higher vitamin D levels than other genotypes with p value of 0.024.

Conclusion

Our study found that T1DM children had lower vitamin D levels, and VDR FokI and BsmI gene polymorphisms were linked to T1DM in Egyptian children. Determining the relationship between vitamin D levels and VDR polymorphisms, particularly the FokI and other genetic analyses may aid in the early diagnosis of T1DM in children.

背景维生素 D 的内分泌系统调节着约 3% 的人类基因组。维生素 D 通过核维生素 D 受体 (VDR) 发挥作用,VDR 反过来又调节胰腺的胰岛素分泌。VDR 基因多态性可能会对 1 型糖尿病(T1DM)等自身免疫性疾病的发病方式产生影响。我们旨在探讨埃及糖尿病儿童及其兄弟姐妹中 T1DM 与 VDR 基因多态性之间的关系。研究采用酶联免疫吸附测定法对 179 名参与者(第 1 组 = 85 名糖尿病儿童,第 2 组 = 57 名患者兄弟姐妹,第 3 组 = 37 名健康对照组)中的 25(OH)维生素 D 进行定量。实时聚合酶链反应(RT-PCR)用于分析 VDR 基因多态性 Apa-I (rs7975232)、Fok-I (rs2228570)、Taq-I (rs731236) 和 Bsm-I (rs1544410) 的基因分型。结果与对照组(19.48 ± 7.42 ng/mL)相比,T1DM 患者(14.99 ± 9.24 ng/mL)和兄弟姐妹(16.31 ± 7.96 ng/mL)的平均血清 25(OH)维生素 D 水平明显较低(p = 0.031)。VDR Fok-I(rs2228570)和 Bsm-I(rs1544410)多态性的基因型分布在患者、兄弟姐妹和对照组之间有显著差异,分别为 P = 0.001 和 0.026,而 VDR ApaI 和 TaqI 多态性没有显著差异。T1DM 患者和兄弟姐妹的 FokI-A 等位基因频率明显低于对照组(P < 0.001)。结论我们的研究发现,T1DM 儿童的维生素 D 水平较低,VDR FokI 和 BsmI 基因多态性与埃及儿童的 T1DM 有关。确定维生素 D 水平与 VDR 多态性之间的关系,尤其是 FokI 和其他基因分析,可能有助于儿童 T1DM 的早期诊断。
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引用次数: 0
Acetaminophen-traces bioremediation with novel phenotypically and genotypically characterized 2 Streptomyces strains using chemo-informatics, in vivo, and in vitro experiments for cytotoxicity and biological activity 利用化学信息学、体内和体外细胞毒性和生物活性实验,利用表型和基因型特征新颖的 2 株链霉菌进行乙酰氨基酚痕迹生物修复
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-19 DOI: 10.1186/s43141-023-00602-w
Donia H. Embarez, Ahmed S. Abdel Razek, Emad B. Basalious, Magdi Mahmoud, Nadia M. Hamdy
We isolated two novel bacterial strains, active against the environmental pollutant acetaminophen/Paracetamol®. Streptomyces chrestomyceticus (symbol RS2) and Flavofuscus (symbol M33) collected from El-Natrun Valley, Egypt—water, sediment, and sand samples, taxonomically characterized using a transmission electron microscope (TEM). Genotypic identification, based on 16S rRNA gene sequence analysis followed by BLAST alignment, were deposited on the NCBI as 2 novel strains https://www.ncbi.nlm.nih.gov/nuccore/OM665324 and https://www.ncbi.nlm.nih.gov/nuccore/OM665325 . The phylogenetic tree was constructed. Acetaminophen secondary or intermediate product’s chemical structure was identified by GC/LC MS. Some selected acetaminophen secondary-product extracts and derived compounds were examined against a panel of test micro-organisms and fortunately showed a good anti-microbial effect. In silico chemo-informatics Swiss ADMET evaluation was used in the selected bio-degradation extracts for absorption (gastric), distribution (to CNS), metabolism (hepatic), excretion (renal), and finally not toxic, being non-mutagenic/teratogenic or genotoxic, virtually. Moreover, in vitro cytotoxic activity of these selected bio-degradation secondary products was examined against HepG2 and MCF7 cancer cell lines, where M33 and RS2 extract effects on acetaminophen/paracetamol bio-degradation products were safe, with higher IC50 on HepG2 and MCF7 than the acetaminophen/paracetamol IC50 of 108.5 μg/ml. Moreover, an in vivo oral acute single-dose toxicity experiment was conducted, to confirm these in vitro and in silico lower toxicity (better safety) than acetaminophen/paracetamol.
我们分离出两种新型细菌菌株,它们对环境污染物对乙酰氨基酚/扑热息痛®具有活性。我们从埃及 El-Natrun 谷地的水、沉积物和沙子样本中分离到两株新型细菌,它们分别是链霉菌(Streptomyces chrestomyceticus,符号 RS2)和黄杆菌(Flavofuscus,符号 M33),并使用透射电子显微镜(TEM)进行了分类鉴定。根据 16S rRNA 基因序列分析和 BLAST 比对进行了基因型鉴定,并将其作为 2 个新菌株 https://www.ncbi.nlm.nih.gov/nuccore/OM665324 和 https://www.ncbi.nlm.nih.gov/nuccore/OM665325 保存在 NCBI 上。构建了系统发生树。通过 GC/LC MS 鉴定了对乙酰氨基酚次级或中间产物的化学结构。对一些精选的对乙酰氨基酚次级产物提取物和衍生化合物进行了抗微生物测试,结果表明它们具有良好的抗微生物效果。对所选生物降解提取物的吸收(胃)、分布(中枢神经系统)、代谢(肝)、排泄(肾)进行了硅化学信息学瑞士 ADMET 评估,最终确定其无毒性、无致突变性/致畸性或无遗传毒性。此外,还针对 HepG2 和 MCF7 癌细胞系检测了所选生物降解二级产物的体外细胞毒性活性,其中 M33 和 RS2 提取物对对乙酰氨基酚/扑热息痛生物降解产物的影响是安全的,对 HepG2 和 MCF7 的 IC50 值高于对乙酰氨基酚/扑热息痛的 IC50 值 108.5 μg/ml。此外,还进行了体内口服急性单剂量毒性实验,以证实这些体外和硅学毒性比对乙酰氨基酚/扑热息痛低(安全性更高)。
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引用次数: 0
FolE gene expression for folic acid productivity from optimized and characterized probiotic Lactobacillus delbrueckii 优化和表征益生菌德尔布鲁贝克氏乳杆菌叶酸生产率的 FolE 基因表达
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-18 DOI: 10.1186/s43141-023-00603-9
Mohamed Khedr, Fady Sayed Youssef, Noura El-kattan, Mahmoud S. Abozahra, Mohammed N. Selim, Abdullah Yousef, Kamal M. A. Khalil, Alsayed E. Mekky
Lactobacillus delbrueckii was one of the most common milk lactic acid bacterial strains (LAB) which characterized as probiotic with many health influencing properties. Among seven isolates, KH1 isolate was the best producer of folic acid with 100 µg/ml after 48 h of incubation; FolE gene expression after 24 h of incubation was in the highest value in case of KH1 with three folds. Lactose was the best carbon source for this KH1, besides the best next isolates KH80 and KH98. The selected three LAB isolates were identified through 16S rDNA as Lactobacillus delbrueckii. These three isolates have high tolerance against acidic pH 2–3; they give 45, 10, and 22 CFUs at pH 3, besides 9, 6, and 4 CFUs at pH2, respectively. They also have resistance against elevated bile salt range 0.1–0.4%. KH1 recorded 99% scavenging against 97.3% 1000 µg/ml ascorbic acid. Docking study exhibits the binding mode of folic acid which exhibited an energy binding of − 8.65 kcal/mol against DHFR. Folic acid formed four Pi-alkyl, Pi-Pi, and Pi-sigma interactions with Ala9, Ile7, Phe34, and Ile60. Additionally, folic acid interacted with Glu30 and Asn64 by three hydrogen bonds with 1.77, 1.76, and 1.96 Å. LAB isolates have probiotic properties, antioxidant activity, and desired organic natural source for folic acid supplementation that improve hemoglobin that indicated by docking study interaction.
德尔布鲁贝克乳杆菌(Lactobacillus delbrueckii)是最常见的牛奶乳酸菌(LAB)菌株之一,具有多种影响健康的益生特性。在七个分离株中,KH1 分离株的叶酸产量最高,培养 48 小时后达到 100 µg/ml;培养 24 小时后,KH1 的 FolE 基因表达量最高,达到三倍。乳糖是 KH1 的最佳碳源,其次是 KH80 和 KH98。经 16S rDNA 鉴定,所选的三个 LAB 分离物均为德尔布鲁贝克乳杆菌(Lactobacillus delbrueckii)。这三种分离物对 pH 值为 2-3 的酸性具有很高的耐受性;在 pH 值为 3 时,它们分别能产生 45、10 和 22 个 CFU,而在 pH 值为 2 时,则分别能产生 9、6 和 4 个 CFU。它们还对 0.1-0.4% 的胆盐具有抗性。KH1 对 97.3% 1000 µg/ml 抗坏血酸的清除率为 99%。Docking 研究显示了叶酸的结合模式,它与 DHFR 的结合能量为 - 8.65 kcal/mol。叶酸与 Ala9、Ile7、Phe34 和 Ile60 形成了四种 Pi-alkyl、Pi-Pi 和 Pi-sigma 相互作用。此外,叶酸还与 Glu30 和 Asn64 以 1.77、1.76 和 1.96 Å 的三个氢键相互作用。LAB 分离物具有益生特性和抗氧化活性,是叶酸补充剂的理想有机天然来源,可通过对接研究相互作用改善血红蛋白。
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引用次数: 0
Biosoftening of banana pseudostem fiber using cellulase and pectinase enzyme isolated from Aspergillus niger for textile industry 利用从黑曲霉中分离的纤维素酶和果胶酶对香蕉假茎纤维进行生物软化,用于纺织工业
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-18 DOI: 10.1186/s43141-023-00617-3
Manjusha W. A., Josphine J. S., Deepa P. K., Sujatha S., Ahil Raj S.
Nowadays, farmers are facing a lot of problems for the disposal of banana pseudostem waste after the harvesting of banana. Banana pseudostem is a rich source of fiber, which is an alternative source of other natural and synthetic fibers. The banana fibers are biodegradable, and they are expected to be in great demand in the international market. For the textile industry, fibers were extracted using chemical and mechanical methods, but it leads to damage and affects the quality of fibers. So, this study mainly focused on biosoftening of banana pseudostem fiber using crude enzyme produced from Aspergillus niger which is one of the most predominant fungus which can synthesize industrially applicable enzymes and which can soften the surface of banana pseudostem fiber. Through this, biosoftened banana pseudostem fiber can be produced, and the disposal problem of banana pseudostem can be rectified in an eco-friendly manner. The present study was undertaken for the biosoftening of banana pseudostem fiber using crude enzymes isolated from fungal strain. The fungal isolates were subjected to enzyme screening such as cellulase, pectinase, chitinase, peroxidase, and polygalacturonase. The maximum production of enzyme was observed in F2 strain, and it was subjected to crude enzyme production and purification using dialysis and column chromatography. The collected best enzyme fractions were selected for the biosoftening of banana pseudostem fiber. The banana pseudostem fiber was treated with crude enzymes at the time duration of 2, 4, 24, and 48 h. After the treatment, the treated and untreated fibers were evaluated for the mechanical properties and chemical constituent’s analysis. The results revealed that the chemical contents were high during 2- and 4-h-treated fibers. After that, chemical constituents were reduced due to the removal of debris by the action of enzymes. The mechanical properties such as breaking load, breaking extension, tenacity, and diameter of fiber were best in the fibers treated for 2 and 4 h. After 4 h due to the removal of chemical constituents the breaking load and tenacity, diameter will be reduced. SEM results proved that the fiber treated at 4th h showed smooth and softened fiber. This study proved that the crude enzymes isolated from the Aspergillus niger can be effectively soften and increase the quality of banana pseudostem fiber.
如今,农民在收获香蕉后面临着香蕉假茎废弃物处理的诸多问题。香蕉假茎含有丰富的纤维,是其他天然纤维和合成纤维的替代来源。香蕉纤维可生物降解,预计在国际市场上需求量很大。在纺织工业中,纤维的提取采用化学和机械方法,但这会导致纤维受损,影响纤维质量。黑曲霉是最主要的真菌之一,能合成工业用酶,并能软化香蕉假茎纤维的表面。通过这种方法可以生产出生物软化香蕉假茎纤维,并以环保的方式解决香蕉假茎的处理问题。本研究利用从真菌菌株中分离出的粗酶对香蕉假茎纤维进行生物软化。对真菌分离物进行了酶筛选,如纤维素酶、果胶酶、几丁质酶、过氧化物酶和聚半乳糖醛酸酶。F2 菌株的酶产量最高,因此对其进行了粗酶生产,并使用透析和柱层析法进行纯化。收集到的最佳酶馏分被用于香蕉假茎纤维的生物软化。用粗酶处理香蕉假茎纤维的时间分别为 2、4、24 和 48 小时。结果显示,经过 2 和 4 小时处理的纤维化学成分含量较高。之后,由于酶的作用清除了碎屑,化学成分有所减少。经过 2 小时和 4 小时处理的纤维的机械性能,如断裂负荷、断裂延伸率、韧性和纤维直径最好。扫描电镜结果表明,经过 4 小时处理的纤维显示出光滑和软化。这项研究证明,从黑曲霉中分离出来的粗酶可以有效软化香蕉假茎纤维并提高其质量。
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引用次数: 0
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) primer design based on Indonesia SARS-CoV-2 RNA sequence 基于印度尼西亚 SARS-CoV-2 RNA 序列的反转录环介导等温扩增 (RT-LAMP) 引物设计
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-18 DOI: 10.1186/s43141-023-00580-z
Irsyad Ibadurrahman, Suryani, Desriani
The COVID-19 pandemic has highlighted the importance of tracking cases by using various methods such as the Reverse transcription loop-mediated isothermal amplification (RT-LAMP) which is a fast, simple, inexpensive, and accurate mass tracker. However, there have been no reports about the development of RT-LAMP primer designs that use genome sequences of viruses from Indonesia. Therefore, this study aimed to design an RT-LAMP primer using SARS-CoV-2 genome sequences from Indonesia and several other countries representing five continents in the world, as well as genomes from five Variants of Concern (VOC). The results showed that the consensus sequence of 70 SARS-CoV-2 virus sequences was obtained with a length of 29,982 bases. The phylogenetic test confirmed that the consensus sequence had a close kinship with the SARS-CoV-2 Wuhan Isolate. Furthermore, the SimPlot analysis showed that there was a high genetic diversity of sequences from the Coronaviridae tribal virus at base sequences of 1,500–5,000, 6,500–7,500, and 23,300–25,500. A total of 139 sets of primers were obtained from the primer design with 4 sets namely T1_6, T1_9, T4_7, and T4_52 having the best characteristics. Based on the secondary structure analysis test on 4 sets of primers, T1_6 and T1_9 were predicted not to form secondary structures at RT-LAMP operational temperatures. The primer set T1_9 showed better specificity in BLAST NCBI and eLAMP BLAST tests. This study obtained a primer set of T1_9 with base sequence F3: CACTGAGACTCATTGATGCTATG, B3: CCAACCGTCTCTAAGAAACTCT, F2: GTTCACATCTGATTTGGCTACT, F1c: GAAGTCAACTGAACAACACCACCT, B2: CCTTCCTTAAACTTCTCTTCAAGC, B1c: GTGGCTAACTAACATCTTTGGCACT, LB: TGAAAACAAACCCGCCGTCCTTG, which meets the ideal parameters and has the best specificity. Therefore, it is recommended for use in further tests to recognize SARS-CoV-2 from Indonesia, other five continents, as well as five VOCs, including the new Omicron sub-variant.
COVID-19 大流行凸显了使用各种方法追踪病例的重要性,例如反转录环介导等温扩增法(RT-LAMP),这是一种快速、简单、廉价且准确的大规模追踪方法。然而,目前还没有关于利用印度尼西亚病毒基因组序列开发 RT-LAMP 引物设计的报道。因此,本研究旨在利用来自印度尼西亚和代表世界五大洲的其他几个国家的 SARS-CoV-2 基因组序列以及五个关注变体(VOC)的基因组设计 RT-LAMP 引物。结果显示,70 个 SARS-CoV-2 病毒序列的共识序列长度为 29 982 个碱基。系统进化检验证实,该共识序列与 SARS-CoV-2 武汉样本具有近缘关系。此外,SimPlot分析表明,冠状病毒科部落病毒序列的遗传多样性较高,碱基序列分别为1,500-5,000、6,500-7,500和23,300-25,500。引物设计共获得 139 组引物,其中 4 组引物(即 T1_6、T1_9、T4_7 和 T4_52)具有最佳特性。根据对 4 组引物的二级结构分析测试,预测 T1_6 和 T1_9 在 RT-LAMP 操作温度下不会形成二级结构。在 BLAST NCBI 和 eLAMP BLAST 测试中,引物组 T1_9 显示出更好的特异性。本研究得到的 T1_9 引物集的碱基序列为:F3:CACTGAGACTCATTGATGCTATG、B3:CCAACCGTCTCTAAGAAACTCT、F2:GTTCACATCTGATTTGGCTACT、F1c:GAAGTCAACTGAACAACACCACCT、B2:CCTTCCTTAAACTTCTCTTCAAGC、B1c:GTGGCTAACTAACATCTTTGGCACT、LB:TGAAAACAAACCCGCCGTCCTTG,符合理想参数,特异性最好。因此,建议将其用于进一步的检测,以识别来自印度尼西亚、其他五大洲以及包括新的 Omicron 亚变异体在内的五种 VOC 的 SARS-CoV-2 病毒。
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引用次数: 0
In silico analysis of HLA-1 and HLA-2 recognition of a designed recombinant human papillomavirus vaccine based on L1 protein HPV subtype 45 对基于 L1 蛋白 HPV 45 亚型设计的重组人乳头瘤病毒疫苗的 HLA-1 和 HLA-2 识别进行硅学分析
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-13 DOI: 10.1186/s43141-023-00593-8
Asri Sulfianti, Nihayatul Karimah, Astutiati Nurhasanah
Human leukocyte antigen (HLA) can bind and present the processed antigenic peptide derived from the vaccine to the T cell receptor, and this capability is crucial in determining the effectivity of the vaccine to terminate virus-infected cells, activate macrophages, and induce B cells to produce antibodies. A recombinant vaccine candidate based on protein L1 HPV45 was designed and analysed whether it is recognisable by T cells through the binding of their epitopes to HLAs. The study consisted of two parts: part one was the analysis of the L1 recombinant protein binding to HLA-1 and 2 epitopes, whereas part two was the distribution analysis of HPV-linked HLA allele. HLA allele sets found at high frequency in the general population and in specific Indonesian population were listed for the binding analysis of the recombinant L1 HPV45 protein. In part one, immunoepitope servers from IEDB were used to predict the binding of the designed proteins to HLA alleles. The prediction method for MHC-I binding prediction was the NetMHCpan EL 4.1 whilst for MHC-II binding prediction was the Consensus approach. Antigenicity analysis for each peptide was conducted using VaxiJen 2.0 with the threshold 1.0 to select the highly antigenic peptides, and positions of these epitopes in the secondary and tertiary structure of the recombinant protein were also predicted. The percent population coverage of the alleles capable of binding to these epitopes worldwide was also estimated. In part two, the worldwide distribution and frequency of HPV-related HLA-1 and 2 were studied. Two highly antigenic peptides (EEYDLQFIF and KLKFWTVDLK) were recognised by high-frequency HLA-1 alleles in both, the general and Western Javanese. In addition to these two epitopes, a few more peptides are also recognised by the high-frequency Western Javanese HLA-1 alleles, which are not in Weiskopf’s list of high-frequency HLA-1 alleles in the general population. Analysis of the highly antigenic epitopes binding to HLA-DRB1 alleles in general (YIKGTSANM) and Western Javanese (LRRRPTIGP) populations showed that these peptide cores associate to HLA-DRB1*04, albeit the different sub-types, due to the presence of different allele in each population group. Analysis of the epitopes and the positive binding alleles showed on average 25.65% population coverage. The recombinant vaccine candidate based on protein L1 HPV45 is presumed to contain highly antigenic peptides that can bind to high-frequency HLA-1 and 2 alleles present in general and Western Javanese populations. It was expected that the protein is capable of eliciting T cell-mediated responses in both populations; however, in vitro study is needed to prove the protectiveness of the designed recombinant protein.
人类白细胞抗原(HLA)能与 T 细胞受体结合,并将疫苗中经过处理的抗原肽呈现给 T 细胞受体,这种能力对疫苗终止病毒感染细胞、激活巨噬细胞和诱导 B 细胞产生抗体的效果至关重要。我们设计了一种基于蛋白 L1 HPV45 的重组候选疫苗,并分析了 T 细胞是否能通过其表位与 HLAs 结合来识别这种疫苗。研究由两部分组成:第一部分是分析 L1 重组蛋白与 HLA-1 和 2 表位的结合,第二部分是分析与 HPV 相关的 HLA 等位基因的分布。在普通人群和特定印尼人群中发现的高频率 HLA 等位基因集被列出,用于重组 L1 HPV45 蛋白的结合分析。第一部分,使用IEDB的免疫表位服务器预测设计的蛋白质与HLA等位基因的结合情况。MHC-I结合预测的预测方法是NetMHCpan EL 4.1,而MHC-II结合预测的预测方法是共识法。使用 VaxiJen 2.0 对每个肽段进行抗原性分析,阈值为 1.0,以筛选出高抗原性肽段,并预测这些表位在重组蛋白二级和三级结构中的位置。此外,还估算了能与这些表位结合的等位基因在全球的覆盖率。第二部分研究了与 HPV 相关的 HLA-1 和 2 在全球的分布和频率。在普通爪哇人和西方爪哇人中,两个高抗原性肽(EEYDLQFIF 和 KLKFWTVDLK)被高频率的 HLA-1 等位基因识别。除了这两个表位外,还有一些肽也能被西爪哇人的高频 HLA-1 等位基因识别,但它们并不在 Weiskopf 的普通人群高频 HLA-1 等位基因列表中。对普通人群(YIKGTSANM)和西爪哇人(LRRRPTIGP)中与 HLA-DRB1 等位基因结合的高抗原性表位进行的分析表明,这些肽核与 HLA-DRB1*04 相关联,但由于每个人群中存在不同的等位基因,因此亚型也不同。对表位和阳性结合等位基因的分析表明,平均人群覆盖率为 25.65%。据推测,基于蛋白 L1 HPV45 的重组候选疫苗含有高抗原性肽,可与普通人群和西爪哇人群中存在的高频 HLA-1 和 2 等位基因结合。预计该蛋白能够在这两种人群中引起 T 细胞介导的反应;不过,要证明所设计的重组蛋白的保护性,还需要进行体外研究。
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引用次数: 0
A scalable overexpression of a thermostable recombinant poly-histidine tag carboxyl esterase under lambda promoter: purification, characterization, and protein modelling 在λ启动子下可扩展地过表达一种热稳定性重组聚组氨酸标签羧基酯酶:纯化、表征和蛋白质模型
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-12 DOI: 10.1186/s43141-023-00610-w
Nadia A. Soliman, Safaa M. Ali, Mahmoud E. A. Duab, Yasser R. Abdel-Fattah
As a white biotechnological trend, esterases are thought to be among the most active enzymes’ classes in biocatalysis and synthesis of industrially importance organic compounds. Esterases are used in many applications such as the manufacture of pharmaceuticals, cosmetics, leather, textile, paper, food, dairy products, detergents, and treatment of some environmental pollutants. A poly-histidine moiety was added to the C-terminal end of the Geobacillus sp. gene encoding carboxyl esterase (EstB, ac: KJ735452) to facilitate one-step purification. This recombinant protein was successfully expressed in Escherichia coli (E. coli) under control of Lambda promoter (λ). An open reading frame (ORF) of 1500 bps encoding a polypeptide of 499 amino acid residues and a calculated molecular weight (54.7 kD) was identified as carboxyl-esterase B due to its conserved glycine-X-serine-X-glycine motif (G-X-S-X-G) and its high similarity toward other carboxyl esterases, where the 3-D tertiary structure of EstB was determined based on high homology % (94.8) to Est55. The expression was scaled up using 7-L stirred tank bioreactor, where a maximum yield of enzyme was obtained after 3.5 h with SEA 51.76 U/mg protein. The expressed protein was purified until unity using immobilized metal affinity chromatography (IMAC) charged with cobalt and then characterized. The purified enzyme was most active at pH 8.0 and remarkably stable at pH (8–10). Temperature optimum was recorded at 65 °C, and it kept 70% of its activity after 1-h exposure to 60 °C. The active half-live of enzyme was 25 min at 70 °C and a calculated T melting (Tm) at 70 °C. The determined reaction kinetics Michaelis–Menten constant (Km), maximum velocity rate (Vmax), the turnover number (Kcat), and catalytic efficiency (Kcat/Km) of the pure enzyme were found 22.756 mM, 164.47 U/ml (59.6 min−1), and (2.619 mol/ min), respectively. Creation of a recombinant 6 × -His estB derived from a thermophile Geobacillus sp. was performed successfully and then overexpressed under λ-promoter. In a bench scale bioreactor, the overexpression was grown up, followed by one-step purification and biochemical characterization. The recorded promising pH and temperature stability properties suggest that this expressed carboxyl esterase could be used in many industrial sectors.
作为一种白色生物技术趋势,酯酶被认为是生物催化和合成工业重要有机化合物中最活跃的酶类之一。酯酶被广泛应用于制药、化妆品、皮革、纺织品、造纸、食品、乳制品、洗涤剂的生产以及一些环境污染物的处理。为了便于一步纯化,我们在 Geobacillus sp.编码羧基酯酶(EstB,ac: KJ735452)基因的 C 端添加了聚组氨酸分子。这种重组蛋白在 Lambda 启动子(λ)的控制下成功地在大肠杆菌(E. coli)中表达。由于其保守的甘氨酸-X-丝氨酸-X-甘氨酸基序(G-X-S-X-G)及其与其他羧基酯酶的高度相似性,EstB 被鉴定为羧基酯酶 B。使用 7 升搅拌罐生物反应器扩大表达规模,3.5 小时后获得最高产酶量,SEA 为 51.76 U/mg 蛋白。利用带钴的固定金属亲和层析(IMAC)技术将表达的蛋白质纯化至完全一致,然后对其进行表征。纯化的酶在 pH 值为 8.0 时活性最高,在 pH 值(8-10)时非常稳定。最适温度为 65 °C,在 60 °C下暴露 1 小时后仍能保持 70% 的活性。在 70 °C 时,酶的活性半衰期为 25 分钟,计算出的熔融温度(Tm)为 70 °C。测定的纯酶的反应动力学迈克尔-门顿常数(Km)、最大速度(Vmax)、周转数(Kcat)和催化效率(Kcat/Km)分别为 22.756 mM、164.47 U/ml (59.6 min-1) 和 (2.619 mol/min)。从嗜热菌 Geobacillus sp.中成功创建了重组 6 × -His estB,并在λ-启动子下进行了过表达。在台架规模的生物反应器中,过表达菌得到了生长,随后进行了一步纯化和生化鉴定。所记录的良好的 pH 和温度稳定性表明,这种表达的羧基酯酶可用于许多工业部门。
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引用次数: 0
In silico design of an epitope-based vaccine against PspC in Streptococcus pneumoniae using reverse vaccinology 利用反向疫苗学,基于表位的肺炎链球菌 PspC 疫苗的硅设计
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-12 DOI: 10.1186/s43141-023-00604-8
Md. Nahian, Muhammad Shahab, Lincon Mazumder, Jonas Ivan Nobre Oliveira, Tanjina Akhtar Banu, Murshed Hasan Sarkar, Barna Goswami, Ahashan Habib, Shamima Begum, Shahina Akter
Streptococcus pneumoniae is a major pathogen that poses a significant hazard to global health, causing a variety of infections including pneumonia, meningitis, and sepsis. The emergence of antibiotic-resistant strains has increased the difficulty of conventional antibiotic treatment, highlighting the need for alternative therapies such as multi-epitope vaccines. In this study, immunoinformatics algorithms were used to identify potential vaccine candidates based on the extracellular immunogenic protein Pneumococcal surface protein C (PspC). The protein sequence of PspC was retrieved from NCBI for the development of the multi-epitope vaccine (MEV), and potential B cell and T cell epitopes were identified. Linkers including EAAAK, AAY, and CPGPG were used to connect the epitopes. Through molecular docking, molecular dynamics, and immunological simulation, the affinity between MEV and Toll-like receptors was determined. After cloning the MEV construct into the PET28a ( +) vector, SnapGene was used to achieve expression in Escherichia coli. The constructed MEV was discovered to be stable, non-allergenic, and antigenic. Microscopic interactions between ligand and receptor are confirmed by molecular docking and molecular dynamics simulation. The use of an in-silico cloning approach guarantees the optimal expression and translation efficiency of the vaccine within an expression vector. Our study demonstrates the potential of in silico approaches for designing effective multi-epitope vaccines against S. pneumoniae. The designated vaccine exhibits the required physicochemical, structural, and immunological characteristics of a successful vaccine against SPN. However, laboratory validation is required to confirm the safety and immunogenicity of the proposed vaccine design.
肺炎链球菌是一种严重危害全球健康的主要病原体,可引起肺炎、脑膜炎和败血症等多种感染。抗生素耐药菌株的出现增加了传统抗生素治疗的难度,凸显了对多表位疫苗等替代疗法的需求。在这项研究中,免疫信息学算法被用来识别基于细胞外免疫原蛋白肺炎球菌表面蛋白 C(PspC)的潜在候选疫苗。为了开发多表位疫苗(MEV),我们从 NCBI 检索了 PspC 的蛋白质序列,并确定了潜在的 B 细胞和 T 细胞表位。连接剂包括 EAAAK、AAY 和 CPGPG,用于连接表位。通过分子对接、分子动力学和免疫学模拟,确定了 MEV 与 Toll 样受体之间的亲和力。在将 MEV 构建体克隆到 PET28a ( +) 载体后,利用 SnapGene 在大肠杆菌中实现了表达。研究发现,构建的 MEV 具有稳定性、非过敏性和抗原性。分子对接和分子动力学模拟证实了配体和受体之间的微观相互作用。采用体内克隆方法保证了疫苗在表达载体中的最佳表达和翻译效率。我们的研究证明了硅学方法在设计有效的肺炎双球菌多表位疫苗方面的潜力。指定的疫苗在理化、结构和免疫学方面都表现出了成功的 SPN 疫苗所需的特征。不过,还需要进行实验室验证,以确认拟议疫苗设计的安全性和免疫原性。
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引用次数: 0
Correction: Mycosynthesis of silver nanoparticles using marine fungi and their antimicrobial activity against pathogenic microorganisms 更正:利用海洋真菌合成银纳米粒子及其对病原微生物的抗菌活性
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-12-08 DOI: 10.1186/s43141-023-00625-3
Manar A. Basheer, Khaled Abutaleb, Nermine N. Abed, Amal A. I. Mekawey

Correction: J Genet Eng Biotechnol 21, 127 (2023)

https://doi.org/10.1186/s43141-023-00572-z

In the original version of this article [1], affiliations 3 and 4 were transposed due to a typesetting error. The affiliations appear correctly in this erratum, and the original article has been corrected.

  1. Basheer MA, Abutaleb K, Abed NN et al (2023) Mycosynthesis of silver nanoparticles using marine fungi and their antimicrobial activity against pathogenic microorganisms. J Genet Eng Biotechnol 21:127. https://doi.org/10.1186/s43141-023-00572-z

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Authors and Affiliations

  1. National Authority for Remote Sensing and Space Sciences (NARSS), 23 Joseph Tito Street, El‑Nozha El‑Gedida, Cairo, 1564, Egypt

    Manar A. Basheer & Khaled Abutaleb

  2. Agricultural Research Council, Natural Resources and Engineering (ARC-NRE), Pretoria, 0001, South Africa

    Khaled Abutaleb

  3. School of Animal, Plant and Environmental Sciences, University of Witwatersrand, Private Bag X3, Johannesburg, 2050, South Africa

    Khaled Abutaleb

  4. Faculty of Science (Girls Branch), Al-Azhar University Egypt, Cairo, 11884, Nasr City, Egypt

    Nermine N. Abed

  5. The Regional Center of Mycology and Biotechnology, Al-Azhar University, Cairo, 4434010, Egypt

    Amal A. I. Mekawey

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  1. Manar A. BasheerView author publications

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  2. Khaled AbutalebView author publications

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Corresponding author

Correspondence to Manar A. Basheer.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the articl

更正:J Genet Eng Biotechnol 21, 127 (2023)https://doi.org/10.1186/s43141-023-00572-zIn 在本文[1]的原始版本中,由于排版错误,3号和4号的单位被调换了。Basheer MA, Abutaleb K, Abed NN et al (2023) Mycosynthesis of silver nanoparticles using marine fungi and their antimicrobial activity against pathogenic microorganisms.J Genet Eng Biotechnol 21:127. https://doi.org/10.1186/s43141-023-00572-zArticle Google Scholar Download references作者和单位国家遥感和空间科学局(NARSS),23 Joseph Tito Street, El-Nozha El-Gedida, Cairo, 1564, EgyptManar A. Basheer & Khaled NN et al (2023) Mycosynthesis of silver nanoparticles using marine fungi and their anticroicro activity against pathogenic microorganisms.Basheer & Khaled AbutalebAgricultural Research Council, Natural Resources and Engineering (ARC-NRE), Pretoria, 0001, South AfricaKhaled AbutalebSchool of Animal, Plant and Environmental Sciences, University of Witwatersrand, Private Bag X3, Johannesburg, 2050, South AfricaKhaled AbutalebFaculty of Science (Girls Branch), Al-Azhar University Egypt, Cairo, 11884, Nasr City, EgyptNermine N. AbedThe Regional Center of Mycology, Cairo, 11884, Nasr City.AbedThe Regional Center of Mycology and Biotechnology, Al-Azhar University, Cairo, 4434010, EgyptAmal A. I. MekaweyAuthorsManar A. Basheer查看作者发表的文章BasheerView author publications您也可以在PubMed Google Scholar中搜索该作者Khaled AbutalebView author publications您也可以在PubMed Google Scholar中搜索该作者Nermine N. AbedView author publications您也可以在PubMed Google Scholar中搜索该作者Amal A. I. MekaweyView author publications您也可以在PubMed Google Scholar中搜索该作者Corresponding authorCorrespondence to Manar A. Basheer.开放存取本文采用知识共享署名 4.0 国际许可协议进行许可,该协议允许以任何媒介或格式使用、共享、改编、分发和复制本文,只要您适当注明原作者和来源,提供知识共享许可协议的链接,并说明是否进行了修改。本文中的图片或其他第三方材料均包含在文章的知识共享许可协议中,除非在材料的署名栏中另有说明。如果材料未包含在文章的知识共享许可协议中,且您打算使用的材料不符合法律规定或超出许可使用范围,您需要直接从版权所有者处获得许可。要查看该许可的副本,请访问 http://creativecommons.org/licenses/by/4.0/.Reprints and PermissionsCite this articleBasheer, M.A., Abutaleb, K., Abed, N.N. et al. Correction:利用海洋真菌合成银纳米粒子及其对病原微生物的抗菌活性。J Genet Eng Biotechnol 21, 164 (2023). https://doi.org/10.1186/s43141-023-00625-3Download citationPublished: 08 December 2023DOI: https://doi.org/10.1186/s43141-023-00625-3Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative.
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引用次数: 0
The Future of Biotechnology and Genetic Engineering in Plants 植物生物技术和基因工程的未来
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2019-03-29 DOI: 10.1201/9780429187643-6
Y. Tourte
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引用次数: 0
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Journal of Genetic Engineering and Biotechnology
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