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Corrigendum to “Defining the molecular pathology and consequent phenotypes in Egyptian HB patients” [J. Genet. Eng. Biotechnol. 19(1) (2021) 75] 对 "确定埃及乙型肝炎患者的分子病理学及其表型 "的更正[J. Genet. Eng. Biotechnol.
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-02 DOI: 10.1016/j.jgeb.2024.100374
Ghada Y. El-Kamah , Rehab M. Mosaad , Mohamed B. Taher , Khalda S. Amr
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引用次数: 0
Production performance analysis of sheep MSTN gene C2361T locus 绵羊 MSTN 基因 C2361T 位点的生产性能分析
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-03-27 DOI: 10.1016/j.jgeb.2024.100372
Yuan Pan , Siyi Li , Qiu Zhang , Jiaqi Li , Chenyu Song , Lingchao Kong , Yining Liu , Sibing Hou , Shuaitong Li , Qingkun Liu , Decui Xia , Zeying Wang

The myostatin (MSTN) gene exhibits significant nucleotide sequence variations in sheep, impacting growth characteristics and muscular traits of the body. However, its influence on specific growth traits in some sheep remains to be further elucidated. This study utilized single nucleotide polymorphism sequence analysis to investigate the role of the MSTN gene in meat production performance across four sheep breeds: Charolais sheep, Australian White sheep, crossbreeds of Australian White and Small-tailed Han, and crossbreeds of Charolais and Small-tailed Han. At a SNP locus of the MSTN gene, the C2361T site was identified, with three genotypes detected: CC, CT, and TT, among which CC predominated. Gene substitution effect analysis revealed that replacing C with T could elevate the phenotypic value. Comparative analysis of data from different genotypes within the same breed highlighted the superiority of CC and TT genotypes in phenotypic values, underscoring the significance of specific genotypes in influencing key traits. Contrasting the performance of different genotypes across breeds, Charolais sheep and Charolais Han hybrids demonstrated superiority across multiple indicators, offering valuable insights for breeding new sheep varieties. Analysis of gender effects on growth characteristics indicated that ewes exhibited significantly wider chest, waist, and hip widths compared to rams, while rams displayed better skeletal growth and muscle development. Additionally, the MSTN gene also exerted certain effects on lamb growth characteristics, with the CC genotype closely associated with weight. These findings not only contribute crucial insights for sheep breeding but also pave the way for future research exploring the interaction of this gene with others.

绵羊的肌生长抑素(MSTN)基因表现出明显的核苷酸序列变异,影响着绵羊的生长特性和肌肉特征。然而,该基因对某些绵羊特定生长性状的影响仍有待进一步阐明。本研究利用单核苷酸多态性序列分析,研究了四种绵羊的 MSTN 基因在肉类生产性能中的作用:夏洛莱绵羊、澳大利亚白绵羊、澳大利亚白绵羊和小尾寒羊杂交种以及夏洛莱绵羊和小尾寒羊杂交种。在 MSTN 基因的 SNP 位点上,发现了 C2361T 位点,并检测到三种基因型:CC、CT 和 TT:其中以 CC 型为主。基因替换效应分析表明,用 T 替换 C 可提高表型值。对同一品种中不同基因型的数据进行比较分析后发现,CC 和 TT 基因型在表型值上更胜一筹,这凸显了特定基因型对关键性状的重要影响。通过对比不同品种不同基因型的表现,夏洛莱绵羊和夏洛莱汉杂交种在多个指标上都表现出了优势,为培育绵羊新品种提供了宝贵的启示。性别对生长特性影响的分析表明,与公羊相比,母羊的胸宽、腰围和臀宽明显更宽,而公羊的骨骼生长和肌肉发育更好。此外,MSTN 基因对羔羊的生长特性也有一定影响,CC 基因型与体重密切相关。这些发现不仅为绵羊育种提供了重要启示,也为今后探索该基因与其他基因的相互作用铺平了道路。
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引用次数: 0
Uncovering the presence of CVPD disease in citrus varieties of South Sulawesi, Indonesia: A molecular approach 揭示印度尼西亚南苏拉威西岛柑橘品种中存在的 CVPD 疾病:分子方法
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-27 DOI: 10.1016/j.jgeb.2023.100332
Mustika Tuwo , Tutik Kuswinanti , Andi Nasruddin , Elis Tambaru

Background

The citrus vein phloem degeneration (CVPD) disease is one of important diseases that infects citrus plants and threatens global citrus production and quality due to its severe symptoms and rapid spread. In the 2000s, South Sulawesi Province as one of the citrus producers in Indonesia reported CVPD infection. To date, it is still uncertain as to whether the citrus production center has already been rid of the CVPD infection, keeping in mind the low prevalence of certified citrus saplings use and sub-optimal management of plantations by farmers.

Results

Field observation results revealed varied chlorosis symptoms from young to productive cultivation, which certainly makes it appealing to find out the presence of the causative bacterium, as it has yet to be known whether all the leaves with positive chlorosis symptoms carry the bacterium Candidatus Liberibacter asiaticus. Citrus saplings that appear healthy may carry CVPD pathogens as the incubation period of CVPD pathogens in the host plant spans three to five months. Thus, it is necessary to find the right, rapid way to detect the presence of CVPD pathogens in the citrus plant. The most effective method to use is PCR as the bacterium Candidatus L. asiaticus is non-culturable in vitro, but it is detectable using 16S rDNA. Sampling of leaves with CVPD symptoms was conducted purposively from eight varieties in five citrus cultivation locations, i.e., Pangkep, Sidrap, Bantaeng, Luwu Utara, and Kepulauan Selayar Regencies. DNA isolation was carried out following the Genomic DNA Kit (Geneaid) procedure, followed by detection using the specific pathogenic primer pair OI1 (5′ GCG CGT ATG CAA TAC GAG CGG C 3′) and OI2c (5′ GCC TCG CGA CTT CGC AAC CCA T 3′).

Conclusion

The PCR visualization result shows seven positive samples with DNA fragments measuring 1160 bp. The seven samples were samples of the Key lime, tangerine, Mandarin (cv. batu 55), and Mandarin (cv. selayar), each being derived from Sidrap, Luwu Utara, and Bantaeng. The average disease incidence rate was 66.56 %. Based on the field observation results, the insect vector Diaphorina citri was nowhere to be found in the five citrus cultivation locations in South Sulawesi.

背景柑橘脉韧皮部退化病(CVPD)是感染柑橘植株的重要病害之一,因其症状严重、传播迅速而威胁着全球柑橘的产量和质量。2000 年代,作为印度尼西亚柑橘生产国之一的南苏拉威西省报告了 CVPD 感染情况。迄今为止,柑橘生产中心是否已经摆脱了 CVPD 感染仍是一个未知数,因为认证柑橘树苗的使用率很低,而且果农对种植园的管理也不尽人意。看起来健康的柑橘树苗可能携带 CVPD 病原体,因为 CVPD 病原体在寄主植物中的潜伏期长达 3 至 5 个月。因此,有必要找到正确、快速的方法来检测柑橘植物中是否存在 CVPD 病原体。最有效的方法是 PCR,因为 Asiaticus 白色念珠菌无法在体外培养,但可以通过 16S rDNA 检测到。对五个柑橘种植区(即 Pangkep、Sidrap、Bantaeng、Luwu Utara 和 Kepulauan Selayar 地区)的八个品种中出现 CVPD 症状的叶片进行了有目的的采样。按照基因组 DNA 试剂盒(Geneaid)的程序进行 DNA 分离,然后使用特异性病原引物对 OI1(5′ GCG CGT ATG CAA TAC GAG CGG C 3′)和 OI2c(5′ GCC TCG CGA CTT CGC AAC CCA T 3′)进行检测。这 7 个样本分别来自 Sidrap、Luwu Utara 和 Bantaeng 的酸橙、橘子、柑橘(cv. batu 55)和柑橘(cv. selayar)。平均发病率为 66.56%。根据实地观察结果,在南苏拉威西岛的五个柑橘种植地均未发现昆虫媒介 Diaphorina citri。
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引用次数: 0
Genetic diversity and population structure of natural provenances of Sonneratia caseolaris in Vietnam 越南 Sonneratia caseolaris 天然产地的遗传多样性和种群结构
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-23 DOI: 10.1016/j.jgeb.2024.100356
Son Le , Thanh Van Le

Background

Sommeratia caseolaris is considered the most important mangrove species for reforestation and conservation programs. Therefore, the knowledge of genetic diversity and the population structure of the species has important implications both for the conservation of existing genetic resources and development programs. In the present study, the genetic diversity and structure population of eight populations of S. caseolaris from the Northern to the Southern Coast of Vietnam were determined using nine ISSR molecular markers.

Results

Eight populations of the mangrove species Sonneratia caseolaris were sampled across the natural range in Vietnam to evaluate the genetic diversity of the species. Nine ISSR markers were used to analyse 30 individuals from each population. There were moderate to high levels of genetic diversity (I = 0.447; h = 0.300). PCoA analysis gave very similar results to UPGMA dendrogram construction with the eight populations clustered into three genetic groups which mostly aligned with geographical distances among them. AMOVA analysis results indicated that most (81 %) of the genetic variation was within populations.

Conclusion

The current study also indicates the high level of genetic variation existing among and within the natural population of S. caseolaris in Vietnam. These results open new perspectives towards the conservation of the species' genetic resources and their future use in conservation and reforestation programs.

背景Sommeratia caseolaris被认为是重新造林和保护计划中最重要的红树林物种。因此,了解该物种的遗传多样性和种群结构对现有遗传资源的保护和发展计划都具有重要意义。本研究使用 9 个 ISSR 分子标记测定了从越南北部到南部海岸的 8 个 S. caseolaris 种群的遗传多样性和种群结构。使用 9 个 ISSR 标记分析了每个种群的 30 个个体。遗传多样性达到了中高水平(I = 0.447;h = 0.300)。PCoA 分析的结果与 UPGMA 树枝图的构建结果非常相似,八个种群被聚类为三个遗传组,这些遗传组大多与它们之间的地理距离一致。AMOVA分析结果表明,大多数遗传变异(81%)发生在种群内部。这些结果为保护该物种的遗传资源及其未来在保护和重新造林计划中的应用开辟了新的前景。
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引用次数: 0
Enhancing in vitro regeneration via somatic embryogenesis and Fusarium wilt resistance of Egyptian cucumber (Cucumis sativus L.) cultivars 通过体细胞胚胎发生提高埃及黄瓜(Cucumis sativus L.)栽培品种的体外再生能力和镰刀菌枯萎病抗性
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-23 DOI: 10.1016/j.jgeb.2024.100360
Hamdy M. Hamza , Rana H. Diab , Ismael A. Khatab , Reda M. Gaafar , Mohamed Elhiti

Background

Somatic embryogenesis offers a reliable method for cucumber (Cucumis sativus L.) regeneration and genetic enhancement against Fusarium wilt. This study aimed to establish a tailored somatic embryogenesis system for Egyptian cultivars, fostering genetic improvements and Fusarium wilt-resistance lines.

Results

Employing the Optimal Arbitrary Design (OAD) approach, we optimized the induction medium, initiating prolific embryogenic calli (53.3 %) at 1 mg/L 2,4-D. The cotyledonary leaf (CL) was the preferred explant, showing 60 % embryogenic callus development. Bieth Alpha exhibited higher responsiveness, generating ∼ 18 somatic embryos per explant compared to Prince's ∼ 10. Somatic embryogenesis system validation used quantitative RT-PCR, showing Cucumis sativus splicing factor 3B subunit (CUS1) and an embryogenesis marker gene expression exclusively within embryogenic calli and mainly during embryogenesis initiation. Evaluating fungal toxin filtrate concentrations for selecting embryogenic calli, the S2 selection (25 % filtrate, four subculture cycles) was chosen for somatic embryo development. To gauge the ramifications of selection at the genetic stratum, an in-depth analysis was executed. A cluster analysis grounded in ISSR banding patterns revealed a distinct separation between in vivo-cultivated plants of the two cultivars and regenerated plants devoid of pathogen filtrate treatment or those regenerated post-filtrate treatment. This segregation distinctly underscores the discernible genetic impact of the selection process.

Conclusions

The highest embryogenic capacity (53.3%) was achieved in this study by optimizing the induction stage, which demonstrated the optimal concentrations of BA and 2,4-D for induced proembryonic masses. Moreover, consistent gene expression throughout both stages of embryogenesis suggests that our system unequivocally follows the somatic embryogenesis pathway.

背景体细胞胚胎发生是黄瓜(Cucumis sativus L.)再生和抗镰刀菌枯萎病遗传改良的可靠方法。本研究旨在为埃及栽培品种建立一个量身定制的体细胞胚胎发生系统,促进遗传改良和抗镰刀菌枯萎病品系的培育。结果采用最优任意设计(OAD)方法,我们对诱导培养基进行了优化,在 1 mg/L 2,4-D 的条件下,胚胎发生胼胝体(53.3%)开始大量繁殖。子叶(CL)是首选的外植体,显示出 60% 的胚性胼胝体发育。Bieth Alpha 的反应性更高,每个外植体可产生 18 ∼ 18 个体细胞胚,而 Prince 的反应性为 10 ∼ 10 个。体细胞胚胎发生系统验证采用了定量 RT-PCR,结果表明 Cucumis sativus 剪接因子 3B 亚基(CUS1)和胚胎发生标记基因只在胚胎发生胼胝体中表达,且主要在胚胎发生起始阶段表达。在评估用于选择胚胎发生胼胝体的真菌毒素滤液浓度时,选择了 S2 选择(25% 滤液,四个亚培养周期)用于体细胞胚胎发育。为了评估基因层选择的影响,我们进行了深入分析。以 ISSR 带型为基础的聚类分析显示,两个栽培品种的体内栽培植株与未经病原体滤液处理或滤液处理后再生的植株之间存在明显的分离。结论本研究通过优化诱导阶段实现了最高的胚胎发生能力(53.3%),证明了 BA 和 2,4-D 诱导原胚质量的最佳浓度。此外,胚胎发生两个阶段的基因表达一致,表明我们的系统明确遵循体细胞胚胎发生途径。
{"title":"Enhancing in vitro regeneration via somatic embryogenesis and Fusarium wilt resistance of Egyptian cucumber (Cucumis sativus L.) cultivars","authors":"Hamdy M. Hamza ,&nbsp;Rana H. Diab ,&nbsp;Ismael A. Khatab ,&nbsp;Reda M. Gaafar ,&nbsp;Mohamed Elhiti","doi":"10.1016/j.jgeb.2024.100360","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100360","url":null,"abstract":"<div><h3>Background</h3><p>Somatic embryogenesis offers a reliable method for cucumber (<em>Cucumis sativus</em> L.) regeneration and genetic enhancement against Fusarium wilt. This study aimed to establish a tailored somatic embryogenesis system for Egyptian cultivars, fostering genetic improvements and Fusarium wilt-resistance lines.</p></div><div><h3>Results</h3><p>Employing the Optimal Arbitrary Design (OAD) approach, we optimized the induction medium, initiating prolific embryogenic calli (53.3 %) at 1 mg/L 2,4-D. The cotyledonary leaf (CL) was the preferred explant, showing 60 % embryogenic callus development. Bieth Alpha exhibited higher responsiveness, generating ∼ 18 somatic embryos per explant compared to Prince's ∼ 10. Somatic embryogenesis system validation used quantitative RT-PCR, showing <em>Cucumis sativus</em> splicing factor 3B subunit (<em>CUS1</em>) and an embryogenesis marker gene expression exclusively within embryogenic calli and mainly during embryogenesis initiation. Evaluating fungal toxin filtrate concentrations for selecting embryogenic calli, the S2 selection (25 % filtrate, four subculture cycles) was chosen for somatic embryo development. To gauge the ramifications of selection at the genetic stratum, an in-depth analysis was executed. A cluster analysis grounded in ISSR banding patterns revealed a distinct separation between <em>in vivo</em>-cultivated plants of the two cultivars and regenerated plants devoid of pathogen filtrate treatment or those regenerated post-filtrate treatment. This segregation distinctly underscores the discernible genetic impact of the selection process.</p></div><div><h3>Conclusions</h3><p>The highest embryogenic capacity (53.3%) was achieved in this study by optimizing the induction stage, which demonstrated the optimal concentrations of BA and 2,4-D for induced proembryonic masses. Moreover, consistent gene expression throughout both stages of embryogenesis suggests that our system unequivocally follows the somatic embryogenesis pathway.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100360"},"PeriodicalIF":3.5,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000635/pdfft?md5=cf3bc10f225c5c63a04450898a99b8ee&pid=1-s2.0-S1687157X24000635-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139942237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Human exons and introns classification using pre-trained Resnet-50 and GoogleNet models and 13-layers CNN model 使用预训练的 Resnet-50 和 GoogleNet 模型以及 13 层 CNN 模型进行人类外显子和内含子分类
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-21 DOI: 10.1016/j.jgeb.2024.100359
Feriel Ben Nasr Barber, Afef Elloumi Oueslati

Background:

Examining functions and characteristics of DNA sequences is a highly challenging task. When it comes to the human genome, which is made up of exons and introns, this task is more challenging. Human exons and introns contain millions to billions of nucleotides, which contributes to the complexity observed in this sequences. Considering how complicated the subject of genomics is, it is obvious that using signal processing techniques and deep learning tools to build a strong predictive model can be very helpful for the development of the research of the human genome.

Results:

After representing human exons and introns with color images using Frequency Chaos Game Representation, two pre-trained convolutional neural network models (Resnet-50 and GoogleNet) and a proposed CNN model having 13 hidden layers were used to classify our obtained images. We have reached a value of 92% for the accuracy rate for Resnet-50 model in about 7 h for the execution time, a value of 91.5% for the accuracy rate for the GoogleNet model in 2 h and a half for the execution time. For our proposed CNN model, we have reached 91.6% for the accuracy rate in 2 h and 37 min.

Conclusions:

Our proposed CNN model is faster than the Resnet-50 model in terms of execution time. It was able to slightly exceed the GoogleNet model for the accuracy rate value.

背景:研究 DNA 序列的功能和特征是一项极具挑战性的任务。人类基因组由外显子和内含子组成,因此这项工作更具挑战性。人类的外显子和内含子包含数百万到数十亿个核苷酸,这就造成了序列的复杂性。考虑到基因组学这一课题的复杂性,利用信号处理技术和深度学习工具建立一个强大的预测模型显然对人类基因组研究的发展大有裨益。结果:在使用频率混沌博弈表示法用彩色图像表示人类外显子和内含子后,我们使用了两个预先训练好的卷积神经网络模型(Resnet-50 和 GoogleNet)和一个拥有 13 个隐藏层的拟议 CNN 模型来对获得的图像进行分类。在大约 7 小时的执行时间内,Resnet-50 模型的准确率达到 92%;在 2 个半小时的执行时间内,GoogleNet 模型的准确率达到 91.5%。结论:就执行时间而言,我们提出的 CNN 模型比 Resnet-50 模型更快。结论:就执行时间而言,我们提出的 CNN 模型比 Resnet-50 模型更快,其准确率也略高于 GoogleNet 模型。
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引用次数: 0
Foliar application of plant-derived peptides decreases the severity of leaf rust (Puccinia triticina) infection in bread wheat (Triticum aestivum L.) 叶面喷施植物源肽可降低面包小麦(Triticum aestivum L.)叶锈病(三尖杉核菌)感染的严重程度
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-15 DOI: 10.1016/j.jgeb.2024.100357
Urbashi Panthi , Brent McCallum , Igor Kovalchuk , Christof Rampitsch , Ana Badea , Zhen Yao , Andriy Bilichak

Background

Screening and developing novel antifungal agents with minimal environmental impact are needed to maintain and increase crop production, which is constantly threatened by various pathogens. Small peptides with antimicrobial and antifungal activities have been known to play an important role in plant defense both at the pathogen level by suppressing its growth and proliferation as well as at the host level through activation or priming of the plant’s immune system for a faster, more robust response against fungi. Rust fungi (Pucciniales) are plant pathogens that can infect key crops and overcome resistance genes introduced in elite wheat cultivars.

Results

We performed an in vitro screening of 18 peptides predominantly of plant origin with antifungal or antimicrobial activity for their ability to inhibit leaf rust (Puccinia triticina, CCDS-96-14-1 isolate) urediniospore germination. Nine peptides demonstrated significant fungicidal properties compared to the control. Foliar application of the top three candidates, β-purothionin, Purothionin-α2 and Defensin-2, decreased the severity of leaf rust infection in wheat (Triticum aestivum L.) seedlings. Additionally, increased pathogen resistance was paralleled by elevated expression of defense-related genes.

Conclusions

Identified antifungal peptides could potentially be engineered in the wheat genome to provide an alternative source of genetic resistance to leaf rust.

背景筛选和开发对环境影响最小的新型抗真菌剂是保持和提高作物产量的需要,而作物产量一直受到各种病原体的威胁。众所周知,具有抗菌和抗真菌活性的小肽在植物防御中发挥着重要作用,既能在病原体水平上抑制其生长和增殖,又能在宿主水平上激活或启动植物的免疫系统,从而对真菌做出更快、更有力的反应。锈菌(Pucciniales)是一种植物病原体,可感染主要农作物并克服小麦优良品种中引入的抗性基因。结果 我们对主要来源于植物的 18 种具有抗真菌或抗菌活性的多肽进行了体外筛选,以确定它们抑制叶锈病(三尖杉锈菌,CCDS-96-14-1 分离物)脲原双孢子萌发的能力。与对照组相比,九种肽具有显著的杀菌特性。叶面喷施前三种候选肽(β-purothionin、Purothionin-α2 和 Defensin-2)可降低小麦(Triticum aestivum L.)幼苗感染叶锈病的严重程度。此外,病原体抗性的增强还与防御相关基因表达的提高有关。
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引用次数: 0
Characterization of phenylalanine ammonia lyase and revealing flavonoid biosynthesis in Gymnema sylvestre R. Br through transcriptomic approach 通过转录组学方法鉴定苯丙氨酸氨裂解酶并揭示 Gymnema sylvestre R. Br 中黄酮类化合物的生物合成过程
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-13 DOI: 10.1016/j.jgeb.2023.100344
Kuldeepsingh A. Kalariya, Ravina R. Mevada, Manish Das

Background

Gymnema sylvestre R.Br. is famous medicinal plant among diabetics for its gymnemic acid content. It also contains flavonoids, which are an essential component in various other products. Though some molecular information on the biosynthesis of gymnemic acid, polyoxypregnane, micro RNAs and photosynthetic efficiency is available, there is no gene level information available on the biosynthesis of flavonoids in this plant. RNA was extracted from winter-collected Gymnema sylvestre leaves and cDNA libraries were prepared and used for next generation sequencing. De novo transcriptome assembly were prepared and Coding DNA Sequences (CDS) of 13 major genes involved in flavonoids biosynthesis were identified from transcriptome data. Phenylalanine ammonia lyase gene containing full-length CDS was employed for in silico protein modelling and subsequent quality assessment. These models were then compared against publicly available databases. To confirm the identification of these genes, a similarity search was conducted using the NCBI BLAST tool.

Results

Therefore, in the present study, an effort has been made to provide molecular insights into flavonoid biosynthesis pathway by examining the expressed transcripts in G.sylvestre. Gene sequences of total thirteen major genes viz., phenylalanine ammonia lyase, 4-coumarate CoA ligase, cinnamic acid 4-hydroxylase, shikimate O-hydroxycinnamoyl transferase, coumaroyl quinate (coumaroyl shikimate) 3′-monooxygenase, caffeoyl-CoA O-methyltransferase, chalcone synthase, chalcone isomerase, naringenin 3-dioxygenase, flavanol synthase, flavonoid 3′-monooxygenase, Flavanone 7-O-glucoside 2″-O-beta-L-rhyamnosyltransferase and leucoanthocyanidin dioxygenase were identified and a putative pathway of flavonoids biosynthesis has been illustrated based on transcriptome data.

Conclusions

This transcriptome study has contributed gene-level insights into the biosynthesis of flavonoids in plants as a whole and represents the first report within a non-model plant, Gymnema sylvestre perticullarly.

背景Gymnema sylvestre R.Br.是糖尿病患者中著名的药用植物,因其含有石膏酸。它还含有黄酮类化合物,而黄酮类化合物是其他各种产品的重要成分。虽然目前已有一些关于石膏酸、聚氧孕烷、微 RNA 和光合效率生物合成的分子信息,但还没有关于该植物中黄酮类化合物生物合成的基因水平信息。从冬季采集的裸冠菊叶片中提取 RNA,制备 cDNA 文库并用于新一代测序。准备了新的转录组,并从转录组数据中确定了参与类黄酮生物合成的 13 个主要基因的编码 DNA 序列(CDS)。含有全长 CDS 的苯丙氨酸氨裂解酶基因被用于硅学蛋白质建模和随后的质量评估。然后将这些模型与公开数据库进行比较。为了确认这些基因的身份,使用 NCBI BLAST 工具进行了相似性搜索。结果因此,在本研究中,我们通过研究鹅掌楸中表达的转录本,努力从分子角度揭示黄酮类化合物的生物合成途径。共有十三个主要基因的基因序列,即苯丙氨酸氨裂解酶、4-香豆酸 CoA 连接酶、肉桂酸 4-羟化酶、莽草酸 O-羟基肉桂酰转移酶、香豆酰醌(香豆酰莽草酸)3′-单加氧酶、咖啡酰-CoA O-甲基转移酶、查尔酮合成酶、查尔酮异构酶、柚皮苷 3-二加氧酶、根据转录组数据,确定了黄烷醇合成酶、黄酮 3′-单氧化酶、黄烷酮 7-O-Glucoside 2″-O-beta-L-rhyamnosyltransferase 和白花青素二氧化酶,并说明了黄酮类化合物生物合成的推定途径。结论这项转录组研究有助于在基因水平上深入了解黄酮类化合物在整个植物中的生物合成过程,是对非模式植物裸冠菊(Gymnema sylvestre perticullarly)的首次报道。
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引用次数: 0
Expression and scale-up production of recombinant human papillomavirus type 52 L1 protein in methylotrophic yeast Hansenula polymorpha 重组人乳头瘤病毒 52 型 L1 蛋白在养甲酵母 Hansenula polymorpha 中的表达和放大生产
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-12 DOI: 10.1016/j.jgeb.2023.100342
Sheila Chairunnisa , Apon Zaenal Mustopa , Budiman Bela , Moh Egy Rahman Firdaus , Shasmita Irawan , Rosyida Khusniatul Arifah , Herman Irawan , Maritsa Nurfatwa , Rifqiyah Nur Umami , Nurlaili Ekawati , Ai Hertati , Nurhasni Hasan

Background

Human papillomavirus (HPV) vaccination is one of the crucial national vaccination programs aimed at reducing the prevalence of the diseases associated with HPV infections, which continue to pose a global health concern. However, a significant disparity exists in the distribution of HPV vaccine, particularly in low-middle income countries where the cost of HPV vaccine becomes a major obstacle. Thus, it is essential to ensure the availability of an economically feasible HPV vaccine, necessitating immediate efforts to enhance the cost-effectiveness of vaccine production. This study aimed to develop an efficient production system for the recombinant HPV type 52 L1 protein as HPV vaccine material using methylotrophic yeast Hansenula polymorpha expression system.

Results

This study presents an in-depth examination of the expression and scale-up production of HPV type 52 L1 protein using DASGIP® parallel bioreactor system. The pHIPX4 plasmid, which is regulated by the MOX promoter, generates stable clones that express the target protein. Cultivation employing the synthetic medium SYN6(10) with controlled parameters (e.g. temperature, pH, feeding strategy, and aeration) produces 0.15 µg/mL of HPV type 52 L1 protein, suggesting a possibility for scaling up to a higher production level.

Conclusion

The scale-up production of HPV type 52 L1 protein using Hansenula polymorpha expression system described in this study provides an opportunity for an economical manufacturing platform for the development of the HPV vaccine.

背景人乳头瘤病毒(HPV)疫苗接种是重要的国家疫苗接种计划之一,旨在降低与人乳头瘤病毒感染相关的疾病的发病率,这些疾病继续构成全球健康问题。然而,HPV 疫苗的分配存在很大差异,尤其是在中低收入国家,HPV 疫苗的费用成为了主要障碍。因此,确保提供经济上可行的人乳头瘤病毒疫苗至关重要,必须立即努力提高疫苗生产的成本效益。本研究旨在利用养甲酵母Hansenula polymorpha表达系统开发一种高效的重组HPV 52型L1蛋白生产系统,作为HPV疫苗材料。受 MOX 启动子调控的 pHIPX4 质粒能产生表达目标蛋白的稳定克隆。采用合成培养基 SYN6(10),并控制其参数(如温度、pH 值、进料策略和通气)培养,可产生 0.15 µg/mL 的 HPV 52 型 L1 蛋白,这表明有可能扩大到更高的生产水平。
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引用次数: 0
Bioinformatics approach for prediction and analysis of the Non-Structural Protein 4B (NSP4B) of the Zika virus 预测和分析寨卡病毒非结构蛋白 4B (NSP4B) 的生物信息学方法
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-02 DOI: 10.1016/j.jgeb.2023.100336
Mohamed E. Hasan , Aya Samir , Magdy M. Khalil , Medhat W. Shafaa

Background

The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number (A0A024B7W1), Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools.

Results

The systematic in silico technique, ThreaDom, had only predicted one domain (4 – 190) of NSP4B. I-TASSER, and Alphafold were ranked as the best servers for full-length 3-D protein structure predictions of NSP4B, where the predicted models were evaluated quantitatively using benchmarked metrics including C-score (-3.43), TM-score (0.77949), RMSD (2.73), and Z-score (1.561). The functional and protein binding motifs were realized using motif databases, secondary and surface accessibility predictions combined with Post-Translational Modification Sites (PTMs) prediction. Two highly conserved protein-binding motifs (Flavi NS4B and Bacillus papRprotein), together with three (PTMs) (Casein Kinase II, Myristyl site, and ASN-Glycosylation site) were predicted utilizing the Motif scan and Scanprosite servers. These patterns and PTMs were associated with NSP4B's role in triggering the development of the viral replication complex and its participation in the localization of NS3 and NS5 on the membrane. Only one hit from Structural Classification of Protein (SCOP) matched the protein sequence at positions 10 to 397 and was categorized six-hairpin glycosidases superfamily according to CATH (Class, Architecture, Topology, and Homology). Integrating this NSP4B information with the templates' SCOP and CATH annotations achieves it easier to attribute structure–function/evolution links to both previously known and recently discovered protein structures.

背景寨卡病毒的非结构蛋白(NSP)4B含有251个氨基酸,来自(ZIKV/Human/POLG_ZIKVF),登录号为(A0A024B7W1)。为了了解蛋白质在自然界中折叠的物理基础并解决蛋白质结构预测的难题,Ab-initio 和比较建模是至关重要的工具。I-TASSER和Alphafold被评为NSP4B全长三维蛋白质结构预测的最佳服务器,预测模型的定量评估指标包括C-score (-3.43)、TM-score (0.77949)、RMSD (2.73)和Z-score (1.561)。利用主题数据库、二级和表面可及性预测以及翻译后修饰位点(PTMs)预测实现了功能性和蛋白质结合主题。利用图案扫描(Motif scan)和扫描位点(Scanprosite)服务器预测了两个高度保守的蛋白质结合图案(弗拉维NS4B和芽孢杆菌papR蛋白)以及三个PTMs(酪蛋白激酶II、肉豆蔻基位点和ASN-糖基化位点)。这些模式和 PTM 与 NSP4B 在触发病毒复制复合体的发展及其参与 NS3 和 NS5 在膜上的定位有关。只有一个来自蛋白质结构分类(SCOP)的结果与第 10 至 397 位的蛋白质序列相匹配,并根据 CATH(类别、结构、拓扑和同源性)被归类为六发夹糖苷酶超家族。将 NSP4B 信息与模板的 SCOP 和 CATH 注释相结合,可以更容易地将结构-功能/进化联系归因于以前已知和最近发现的蛋白质结构。
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引用次数: 0
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Journal of Genetic Engineering and Biotechnology
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