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Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2 探索先进的基因组学和免疫信息学技术,以确定抗击 SARS-CoV-2 的药物和疫苗靶点
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-16 DOI: 10.1016/j.jgeb.2024.100439
Syed Luqman Ali , Awais Ali , Waseef Ullah , Abdulaziz Alamri , Elham Mohammed Khatrawi , Gulzira Sagimova , Aigul Almabayeva , Farida Rakhimzhanova , Gulsum Askarova , Fatima Suleimenova , Nabras Al-Mahrami , Prasanta Kumar Parida
The coronavirus that causes serious acute respiratory syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still a major problem in public health and biomedicine. Even if there is no cure for it, the infection is still progressing naturally, and the only time that optimal treatment choices, such as doxycycline, work is at the beginning of the infection. Our project is structured into two critical parts: the first focuses on the identification of potential drug targets, and the second on vaccine design, both aimed at exploring new ways to treat the disease. Initially, cytoplasmic proteins identified through subtractive analysis underwent comprehensive evaluation for potential drug targeting, focusing on metabolic pathways, homology prediction, drugability assessment, essentiality, and protein–protein interactions. Subsequently, surface proteins underwent rigorous assessment for allergenicity, antigenicity, physiochemical attributes, conserved regions, protein interactions, and identification of B and T cell epitopes. Molecular docking and immunological simulation analyses were then employed to develop and characterize a multi-epitope vaccine, integrating findings from the aforementioned evaluations. Findings from the study point to six proteins as potential critical therapeutic targets for SARS-CoV-2, each of which is involved in a distinct metabolic process. The reverse vaccinology analysis suggested that the following proteins could be used as vaccine candidates: sp|P05106, sp|O00187, sp|Q9NYK1, sp|P05556, sp|P09958, and sp|Q9HC29. Four multi-epitope vaccine named as SARS-COV-2-, C1, C2, C3, and C4 was designed by utilizing different adjuvants and eighteen B cell overlapped epitopes which were predicted from top ranked protiens. Based on immune simulation study, the vaccine exhibited adequate immune-reactivity and favorable encounters with toll-type receptors (TLR4, TLR8, HLA, etc ACE), Among them the SARS-COV-2-C2 showed best binding affinity of which all receptors. Findings from this study could be a game-changer in the quest to develop a vaccine and medication that effectively combat SARS-CoV-2. It is necessary to do additional experimental analyses, nevertheless.
导致严重急性呼吸系统综合征的冠状病毒。严重急性呼吸系统综合征冠状病毒 2(SARS-CoV-2)仍然是公共卫生和生物医学领域的一大难题。即使无法治愈,感染仍在自然发展,只有在感染初期,强力霉素等最佳治疗选择才能发挥作用。我们的项目分为两个关键部分:第一部分侧重于识别潜在的药物靶点,第二部分侧重于疫苗设计,目的都是探索治疗这种疾病的新方法。首先,对通过减法分析确定的细胞质蛋白质进行全面评估,以确定潜在的药物靶点,重点是代谢途径、同源性预测、可药性评估、必需性以及蛋白质与蛋白质之间的相互作用。随后,对表面蛋白的过敏性、抗原性、理化属性、保守区域、蛋白质相互作用以及 B 细胞和 T 细胞表位的鉴定进行了严格评估。然后利用分子对接和免疫学模拟分析,结合上述评估结果,开发多表位疫苗并确定其特性。研究结果表明,六种蛋白质是 SARS-CoV-2 的潜在关键治疗靶点,每种蛋白质都参与了不同的代谢过程。反向疫苗学分析表明,以下蛋白质可用作候选疫苗:sp|P05106、sp|O00187、sp|Q9NYK1、sp|P05556、sp|P09958 和 sp|Q9HC29。通过使用不同的佐剂和从排名靠前的原蛋白中预测出的 18 个 B 细胞重叠表位,设计出了四种多表位疫苗,分别命名为 SARS-COV-2-、C1、C2、C3 和 C4。根据免疫模拟研究,疫苗表现出了足够的免疫反应性,并与收费型受体(TLR4、TLR8、HLA 等 ACE)发生了良好的接触,其中 SARS-COV-2-C2 在所有受体中表现出了最佳的结合亲和力。这项研究的结果可能会改变研制有效抗击 SARS-CoV-2 的疫苗和药物的进程。不过,还需要进行更多的实验分析。
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引用次数: 0
Association of plasma microRNAs with COVID-19 severity and outcome 血浆微RNA与COVID-19严重程度和预后的关系
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-14 DOI: 10.1016/j.jgeb.2024.100433
Sohair Salem , Randa Lotfy , Noha Eltaweel , Mohamed Elbadry

Objective

As one of the remarkable host responses to SARS-CoV-2 infection, circulating microRNAs (miRNAs) represent important diagnostic and prognostic diseases biomarkers. The study is a step towards highlighting the role of miRNAs in COVID-19 pathogenesis and severity.

Methods

In this case-control study, miRCURY LNA miRNA PCR plasma panel (168 miRNAs) was applied and the expression of the altered miRNAs was then analysed by quantitative real time PCR for 120 COVID-19 patients (30 mild, 30 moderate, 30 severe, and 30 critical) and 30 healthy subjects.

Results

The initial screening showed that 30 miRNAs displayed altered expression, out of them, only eleven miRNAs (miR-885-5p, miR-141-3p, miR-21-5p, miR-127-3p, miR-99b-5p, let-7d-3p, miR-375, miR-1260a, miR-139-5p, miR-28-5p and miR-34a-5p) were dysregulated in the plasma of COVID-19 patients; all of them were significantly overexpressed. By applying ROC curve analysis, AUC for the eleven miRNAs were ranged from 0.65 to 0.83, and the AUC for the combined miRNAs was 0.93. Ten miRNAs (miR-141-3p, miR-181a-5p, miR-221-3p, miR-223-5p, miR99b-5p, Let-7d-3p, miR-375, miR-199a-5p, miR-139-5p and miR-28-5p) exhibited a significant change in their expression between different severity groups. Patients with positive outcome were found to have increased miR-375 and decreased miR-99b-5p expression levels. Bioinformatic prediction showed that, out of the eleven dysregulated miRNAs, five miRNAs (miR-139-5p, −34a-5p, −28-5p, −21-5p and −885-5p) have the ability to regulate at least two genes related to COVID-19 according to KEGG database.

Conclusion

miRNAs are dysregulated in COVID-19 patients and associated with severity degree and patients’ outcome.
目的 作为宿主对 SARS-CoV-2 感染的显著反应之一,循环微RNA(miRNA)是诊断和预后疾病的重要生物标志物。方法在这项病例对照研究中,研究人员应用 miRCURY LNA miRNA PCR 血浆样本(168 个 miRNAs),然后对 120 名 COVID-19 患者(30 名轻度患者、30 名中度患者、30 名重度患者和 30 名危重患者)和 30 名健康受试者的 miRNAs 表达进行实时定量 PCR 分析。结果初步筛选显示,有30个miRNA的表达发生了改变,其中只有11个miRNA(miR-885-5p、miR-141-3p、miR-21-5p、miR-127-3p、miR-99b-5p、let-7d-3p、miR-375、miR-1260a、miR-139-5p、miR-28-5p和miR-34a-5p)在COVID-19患者的血浆中表达失调,而且所有这些miRNA都显著过表达。应用 ROC 曲线分析,11 个 miRNA 的 AUC 在 0.65 至 0.83 之间,合并 miRNA 的 AUC 为 0.93。十个 miRNA(miR-141-3p、miR-181a-5p、miR-221-3p、miR-223-5p、miR99b-5p、Let-7d-3p、miR-375、miR-199a-5p、miR-139-5p 和 miR-28-5p)的表达在不同严重程度组别之间有显著变化。结果为阳性的患者的 miR-375 表达水平升高,miR-99b-5p 表达水平降低。生物信息学预测显示,根据 KEGG 数据库,在 11 个表达失调的 miRNAs 中,有 5 个 miRNAs(miR-139-5p、-34a-5p、-28-5p、-21-5p 和 -885-5p)能够调控至少两个与 COVID-19 相关的基因。
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引用次数: 0
Impact of homologous overexpression of PR10a gene on improving salt stress tolerance in transgenic Solanum tuberosum 同源过表达 PR10a 基因对提高转基因茄科植物耐盐胁迫能力的影响
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-13 DOI: 10.1016/j.jgeb.2024.100437
Moemen S. Hanafy , Abeer F. Desouky , Mohsen S. Asker , Eman R. Zaki
Abiotic stresses severely affected crop productivity and considered to be a major yield limiting factor for crop plant. The tolerance to these stresses is a very complex phenomenon involving a wide array of molecular, biochemical and physiological changes in plant cells. Therefore, it is challenging to understand the molecular basis of abiotic stress tolerance to manipulate it for improving abiotic stress tolerance of major crops. Biotechnological approaches and genetic engineering including homologous gene overexpression can be implemented to understand gene functions under well-defined conditions. The Pathogenesis-related proteins (PR10) such as PR10a play multiple roles in biotic and abiotic stress tolerance and, hence, plant development. A PR10a gene from potato cv. Deseree was introduced into three cultivars of potato (Solanum tuberosum L.) by Agrobacterium tumefaciens-mediated genetic transformation. Transgenic plants were selected on a medium containing 1.0 mg/l phosphinothricin (PPT) and confirmed by polymerase chain reaction (PCR), herbicide (BASTA®) leaf paint assay, and Real-Time- quantitative PCR analyses (qPCR). All of the selected transformants showed completely tolerance to the application of PPT application. Experiments designed for testing salt tolerance revealed that there was enhanced salt tolerance of the transgenic lines in vitro in terms of morphological (plant FW, plant DW and plant height) and antioxidant activates as compared to the non-transgenic control plants. qRT-PCR showed that the expression of PR10a gene in the transgenic potato is higher than that in non-transgenic control under salt stress. The relative PR10a gene-expression patterns in the transgenic plants shed lights into the molecular response of homologues overexpressed PR10a potato to salt-stress conditions. The obtained results provide insights on the fact that PR10a plays a major role regarding salt stress tolerance in potato plants.
非生物胁迫严重影响作物产量,被认为是限制作物产量的主要因素。对这些胁迫的耐受性是一个非常复杂的现象,涉及植物细胞中一系列分子、生化和生理变化。因此,了解非生物胁迫耐受性的分子基础并加以操纵以提高主要作物的非生物胁迫耐受性是一项挑战。生物技术方法和基因工程(包括同源基因过表达)可用于了解基因在明确条件下的功能。致病相关蛋白(PR10)(如 PR10a)在生物和非生物胁迫耐受性以及植物生长发育中发挥着多重作用。来自马铃薯变种 Deseree 的 PR10a 基因被引入到三种栽培品种中。通过农杆菌介导的基因转化,将来自马铃薯变种 Deseree 的 PR10a 基因导入马铃薯(Solanum tuberosum L.)的三个栽培品种中。在含有 1.0 mg/l 磷霉素(PPT)的培养基上筛选转基因植株,并通过聚合酶链式反应(PCR)、除草剂(BASTA®)叶片涂抹检测和实时定量 PCR 分析(qPCR)进行确认。所有被选中的转化株都表现出对 PPT 应用的完全耐受性。为测试耐盐性而设计的实验表明,与非转基因对照植物相比,转基因品系在离体形态(植株全长、植株直径和植株高度)和抗氧化活性方面的耐盐性都有所增强。转基因植株中 PR10a 基因的相对表达模式揭示了同源物过表达 PR10a 马铃薯对盐胁迫条件的分子响应。研究结果揭示了 PR10a 在马铃薯植物耐盐胁迫中的重要作用。
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引用次数: 0
Scaled codon usage similarity index: A comprehensive resource for crop plants 标度密码子使用相似性指数:作物植物的综合资源
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-13 DOI: 10.1016/j.jgeb.2024.100441
Taniya Bargoti , Divya Pratap Nain , Rajesh Kumar , Amit Kumar Awasthi , Deepali Singh , Vikrant Nain
Over the past three decades species-specific codon usage bias has been used to optimize heterologous gene expression in the target host. However, synthesizing codon optimized gene for multiple species is not achievable due to the prohibitive expense of DNA synthesis. To address this challenge, grouping species with similar codon usage can reduce the need for species-specific codon optimised gene synthesis. We introduced Scaled Codon Usage Similarity (SCUS) index to standardize species similarity assessments based on codon usage profiles. By analysing the SCUS index of 77 plant nuclear genomes from 13 families, we identified codon usage patterns and similarities. We developed an online SCUS index database and a Consensus Relative Synonymous Codon Usage (CRSCU) calculator, available at https://pcud.plantcodon.info. The CRSCU calculator helps determine the most suitable codon usage pattern among two or more species. The SCUS index and CRSCU calculator will facilitate the development of multi-species expression systems, enabling the efficient expression of a single synthetic gene across various crop species. This innovation paves the way for cost-effective and efficient heterologous gene expression across diverse crop species.
在过去的三十年中,物种特异性密码子使用偏差已被用于优化异源基因在目标宿主中的表达。然而,由于 DNA 合成费用过高,为多个物种合成密码子优化基因是不可能实现的。为了应对这一挑战,将密码子用法相似的物种分组,可以减少对特定物种密码子优化基因合成的需求。我们引入了标度密码子使用相似性(SCUS)指数,根据密码子使用情况对物种相似性评估进行标准化。通过分析来自 13 个科的 77 个植物核基因组的 SCUS 指数,我们确定了密码子使用模式和相似性。我们开发了一个在线 SCUS 指数数据库和一个共识相对同义密码子使用率(CRSCU)计算器,可在 https://pcud.plantcodon.info 上查阅。CRSCU 计算器有助于确定两个或多个物种之间最合适的密码子使用模式。SCUS 指数和 CRSCU 计算器将促进多物种表达系统的开发,使单个合成基因在不同作物物种间高效表达成为可能。这项创新为在不同作物物种间进行经济高效的异源基因表达铺平了道路。
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引用次数: 0
In silico and cheminformatics prediction with experimental validation of an adipogenesis cocktail, sorafenib with rosiglitazone for HCC dedifferentiation 通过硅学和化学信息学预测以及实验验证脂肪生成鸡尾酒、索拉非尼和罗格列酮对 HCC 的去分化作用
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-12 DOI: 10.1016/j.jgeb.2024.100429
Aya Anis , Ahmed M. Mostafa , Mariam S. Kerema , Nadia M. Hamdy , Ahmed S. Sultan

Purpose

Hepatocellular carcinoma (HCC) resistance to sorafenib treatment and other treatment strategies causes a higher mortality rate in patients diagnosed with HCC.
Research question.
HCC often develops resistance to sorafenib treatment and other therapies, leading to increased mortality rates in diagnosed patients. Herein, we propose a combined therapeutic approach using rosiglitazone, a key factor in cellular differentiation, along with adipogenesis inducers such as dexamethasone, IBMX, and insulin. Additionally, we included sorafenib, a primary drug for liver cancer treatment, in this combination cocktail and carried out the differentiation process in the presence of sorafenib.

Results

Our study demonstrates that this combination induces the formation of adipocytes from HCC cells over several days under specific conditions and steps. Conclusion. findings suggest that supplementing sorafenib with rosiglitazone and adipogenesis inducers may potentially transform HCC cells into adipocyte-like cells. Fat could be “the good” in the story of liver cancer alleviation, demonstrating the role of rosiglitazone.
目的肝细胞癌(HCC)对索拉非尼治疗和其他治疗策略产生耐药性,导致确诊的 HCC 患者死亡率升高。研究问题:HCC 经常对索拉非尼治疗和其他疗法产生耐药性,导致确诊患者死亡率升高。在此,我们提出了一种联合治疗方法,使用罗格列酮(细胞分化的关键因素)以及地塞米松、IBMX 和胰岛素等脂肪生成诱导剂。此外,我们还将治疗肝癌的主要药物索拉非尼纳入了这一组合鸡尾酒中,并在索拉非尼存在的情况下进行了分化过程。结果我们的研究表明,在特定条件和步骤下,这一组合可在数天内诱导 HCC 细胞形成脂肪细胞。结论:研究结果表明,索拉非尼与罗格列酮和脂肪生成诱导剂的互补作用有可能将 HCC 细胞转化为类脂肪细胞。脂肪可能是缓解肝癌的 "良药",这证明了罗格列酮的作用。
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引用次数: 0
Correlation and regression analysis of GH and IGF-1 genes in Liaoning cashmere goats with body size and other production performance 辽宁绒山羊 GH 和 IGF-1 基因与体型及其他生产性能的相关性和回归分析
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-12 DOI: 10.1016/j.jgeb.2024.100440
Yining Liu , Lingchao Kong , Siyi Li , Lingjun Nie , Junjie Gao , Shuaitong Li , Yuan Pan , Qingkun Liu , Zeying Wang
Liaoning cashmere goat is an important livestock breed in the world. Its economic value is not only reflected in the production of high-quality cashmere, but also its meat production performance is increasingly attracting attention. In order to more comprehensively explore the economic traits of Liaoning cashmere goats, we mainly carry out research on increasing the body size and meat production performance of Liaoning cashmere goats. In the early stage, through multi-omics joint analysis of muscle tissues at different parts and different developmental stages, the important functional genes GH and IGF-1 for growth and development were determined. Then, genotyping of DNA in the experimental population and correlation analysis between SNP and production performance were carried out by PCR-seq. One SNP site G350A was detected in the GH gene. Only one genotype AG was identified in rams. In ewes, the GG genotype is the dominant genotype for body size and production performance, and the AG genotype is the dominant genotype for slaughter production performance. One SNP site C5464T was detected in the IGF-1 gene. In rams, the TT genotype is the dominant genotype for body size and slaughter production performance. In ewes, the CT genotype is the dominant genotype for body size and slaughter production performance. The dominant haplotype combination for body size and slaughter production performance of rams is AGTT. The dominant haplotype combination for body size production performance of ewes is GGCT, and the dominant haplotype combination for slaughter performance is AGCT. This study provides a theoretical basis for genetic improvement and breeding programs of Liaoning cashmere goats.
辽宁绒山羊是世界上重要的畜牧品种。其经济价值不仅体现在优质羊绒的生产上,其产肉性能也日益受到人们的关注。为了更全面地发掘辽宁绒山羊的经济性状,我们主要开展了辽宁绒山羊体型增大和产肉性能的研究。前期,通过对不同部位、不同发育阶段的肌肉组织进行多组学联合分析,确定了生长发育的重要功能基因 GH 和 IGF-1。然后,通过 PCR-seq 对实验群体的 DNA 进行基因分型,并分析 SNP 与生产性能之间的相关性。在 GH 基因中检测到一个 SNP 位点 G350A。在公羊中只发现了一种基因型 AG。在母羊中,GG 基因型是体型和生产性能的显性基因型,AG 基因型是屠宰生产性能的显性基因型。在 IGF-1 基因中检测到一个 SNP 位点 C5464T。在公羊中,TT 基因型是体型和屠宰生产性能的显性基因型。在母羊中,CT 基因型是体型和屠宰生产性能的显性基因型。公羊体型和屠宰生产性能的显性单倍型组合是 AGTT。母羊体型生产性能的显性单倍型组合为 GGCT,屠宰性能的显性单倍型组合为 AGCT。该研究为辽宁羊绒山羊的遗传改良和育种计划提供了理论依据。
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引用次数: 0
Genomic insights into Duchene muscular dystrophy: Analysis of 1250 patients reveals 30% novel genetic patterns and 6 novel variants 杜氏肌肉萎缩症的基因组学研究:对 1250 名患者的分析揭示了 30% 的新遗传模式和 6 个新变体
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-11 DOI: 10.1016/j.jgeb.2024.100436
Khalda Amr , Nagia Fahmy , Ghada El-Kamah
Duchenne muscular dystrophy (DMD/BMD) is the most common type of muscular dystrophy, together with Becker muscular dystrophy represent more than half of all cases. DMD is a single-gene, X-linked recessive disorder that predominantly affects boys, causing progressive muscle deterioration and eventually leading to fatal cardiopulmonary complications. This study aimed to implement a cost-effective molecular diagnostic method using the SALSA MLPA Kit (probe mixes 034 and 035) to screen a large group of Egyptian DMD patients. The study included 1250 clinically diagnosed DMD males, following complete family history, pedigree analyses and an accurate clinical examination and laboratory investigations mainly considering high levels of creatine phosphokinase (>2000 U/L). We also analysed the carrier status of 100 mothers of 100 probands to gauge the inherited mutation through their patients with familial disease. The negative results of MLPA were further analysed with NGS for ten patients and the results were validated for novel missense mutations, phenotype-genotype correlations were analysed using PolyPhen2 and mutation taster.
Results SALSA MLPA analysis confirmed the diagnoses in 733/1250 (58.6 %) DMD patients and the remaining of 517/1250 (41.4%) were negative. DMD patients having large deletions were 632/1250 (50.6%) while duplications occurred in 101/1250 (8%). The most common single exon deletion was 45 (50/632, 7.9%). In addition, 163 different deletion and duplication patterns were characterized among positive MLPA analyses. 30% of our studied cohort exhibited new patterns of rearragements in addition to seven cases of double deletion and duplication rearrangements identified, within nine patients. Using NGS, for small mutations detection, revealed six novel and three previously reported mutations among screened ten patients.
In conclusion, our findings expand the spectrum of known DMD mutations by offering an effective diagnostic method and identifying novel point mutations through NGS analysis. We recommend using NGS to uncover uncharacterized mutations in patients who test negative with MLPA, which could contribute to the treatment of DMD.
杜兴氏肌肉萎缩症(DMD/BMD)是最常见的肌肉萎缩症类型,与贝克氏肌肉萎缩症一起占所有病例的一半以上。DMD是一种单基因、X连锁隐性遗传疾病,主要影响男孩,导致进行性肌肉退化,最终引发致命的心肺并发症。本研究旨在使用 SALSA MLPA 套件(探针混合物 034 和 035)实施一种经济有效的分子诊断方法,筛查一大批埃及 DMD 患者。该研究纳入了 1250 名临床诊断为 DMD 的男性患者,他们都经过了完整的家族史、血统分析和准确的临床检查,实验室检查主要考虑了肌酸磷酸激酶的高水平(2000 U/L)。我们还分析了 100 位疑似患者的 100 位母亲的携带者状况,以通过她们的家族性疾病患者来判断遗传突变。结果 SALSA MLPA 分析确诊了 733/1250 例(58.6%)DMD 患者,其余 517/1250 例(41.4%)为阴性。632/1250(50.6%)例 DMD 患者存在大量缺失,101/1250(8%)例 DMD 患者存在重复。最常见的单外显子缺失为 45 个(50/632,7.9%)。此外,在阳性的 MLPA 分析中,有 163 种不同的缺失和重复模式。我们的研究队列中有 30% 的患者表现出了新的重排模式,此外还在 9 名患者中发现了 7 例双缺失和重复重排。总之,我们的研究结果扩大了已知 DMD 突变的范围,提供了一种有效的诊断方法,并通过 NGS 分析确定了新的点突变。我们建议使用 NGS 发现 MLPA 检测阴性患者的未定性突变,这将有助于 DMD 的治疗。
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引用次数: 0
DNA phenotyping and mapping intragenic deletion mutations in Fanconi anemia: Patterns and diagnostic inferences 范可尼贫血症的 DNA 表型和基因内缺失突变图谱:模式和诊断推论
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-08 DOI: 10.1016/j.jgeb.2024.100435
Rehab Mosaad , Ghada El-Kamah , Maha Eid , Khalda Amr

Background

Fanconi anemia is a genetically heterogeneous recessive disorder distinguished by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and disturbed DNA repair. To date, Fanconi anemia complementation group (FANC) includes 23 FANC genes identified of which, FANCA gene is the most commonly mutated. The mutation spectrum of the FANCA gene is highly heterogeneous with large intragenic deletions due to Alu elements-mediated recombination.
The study aimed to identify different deletion mutations on FANCA gene in Egyptian Fanconi anemia patients by multiplex ligation-dependent probe amplification (MLPA) technique to define the spectrum of FA molecular pathology as a step for disease control. The study included 80 FA patients (36 females and 44 males) whose ages ranged from 4 months to 17 years descending from unrelated consanguineous families referred to the Hereditary Blood Disorders Clinic, National Research Centre (NRC), Egypt. Patients were diagnosed with classical clinical presentation of FA and were confirmed by chromosomal breakage using Diepoxybutane (DEB).

Results

The common clinical presentation in our FA patients were the presence of café au lait spots with hyperpigmentation in 65/80 (81%) followed by skeletal defects in 40/80 (50%). MLPA revealed a total of five different intragenic homozygous deletions of FANCA gene in 16 /80 (20%) patients, among them two deletion patterns were novel.

Conclusion

Molecular analysis using MLPA could detect pathogenic mutations in 20% of FA patients, our study generated considerable data on causative mutations that was used for genetic counseling and prenatal diagnosis.
背景范可尼贫血症是一种遗传异质性隐性疾病,主要表现为细胞遗传不稳定、对DNA交联剂过敏、染色体断裂增加和DNA修复障碍。迄今为止,范可尼贫血症互补基因组(FANC)已发现 23 个 FANC 基因,其中 FANCA 基因是最常见的突变基因。该研究旨在通过多重连接依赖性探针扩增(MLPA)技术鉴定埃及范可尼贫血症患者 FANCA 基因上的不同缺失突变,从而确定范可尼贫血症的分子病理学谱,为疾病控制迈出一步。该研究包括80名转诊至埃及国家研究中心(NRC)遗传性血液病诊所的范可尼贫血患者(36名女性和44名男性),他们来自无血缘关系的近亲家庭,年龄从4个月到17岁不等。患者被诊断为典型的FA临床表现,并通过使用二氧丁烷(DEB)进行染色体断裂确诊。结果FA患者的常见临床表现为65/80(81%)的患者出现咖啡斑和色素沉着,其次是40/80(50%)的患者出现骨骼缺陷。MLPA显示,16/80(20%)例患者的FANCA基因共有5种不同的基因内同源缺失,其中2种缺失模式是新的。结论使用MLPA进行分子分析可在20%的FA患者中检测到致病突变,我们的研究为遗传咨询和产前诊断提供了大量的致病突变数据。
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引用次数: 0
Correlation and regression analysis of KRT35 and TCHHL1 functional genes for cashmere fineness in Liaoning cashmere goats KRT35 和 TCHHL1 功能基因与辽宁绒山羊羊绒细度的相关性和回归分析
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-11-06 DOI: 10.1016/j.jgeb.2024.100434
Weihang Hong , Hua Ma , Lingjun Nie , Shuaitong Li , Lingchao Kong , Ran Duan , Qingyu Yuan , Qiying Zhan , Jinghan Wang , Yuyan Cong , Zeying Wang
Liaoning cashmere goat (LCG) is the world’s highest cashmere producing white cashmere goat. It has the characteristics of long cashmere fiber, high net cashmere rate, moderate cashmere fineness, white cashmere, strong size, strong adaptability, stable genetic performance, and good effect in improving middle and low production cashmere goat. It is known as “National treasure of China”. With LCG as the paternal parent, five new local breeds have been cultivated, which has made outstanding contributions to the improvement and breeding of Chinese cashmere goat breeds. LCG cashmere has moderate fineness (the average fineness of cashmere of LCG population is about 16 µm).However, as a slightly coarse textile raw material, we hope to identify the key genes regulating cashmere fineness through PCR-seq and MLR, in order to reduce cashmere fineness.We collected and extracted DNA from the blood of Liaoning cashmere goats, designed primers, PCR amplification, and Statistical analysis. It was found that the the AA genotype of the G3667A locus of the KRT35 gene, CT genotype of the T615C locus of the TCHHL1 gene in bucks and the CC genotype of does, as well as CT genotype of the T615C locus of the TCHHL1 gene in bucks and the CC genotype of does are dominant genotypes in cashmere fineness. The dominant haplotype combination with multiple factors and effects of cashmere fineness has been determined to be CTGG in bucks and TTGG in does. There was a significant linear regression relationship between the fineness of cashmere in LCG and the cashmere rate and cashmere quantity. There is a significant linear regression relationship between the fineness of LCG and the cashmere rate and cashmere quantity. CF = 0.001SQ-0.71CY + 20.784 (R2 = 0.818) in buck and CF = 0.001SQ-0.767CY + 22.009 (R2 = 0.863) in doe. Conclusion: The AA genotype of KRT35 gene, CT genotype of TCHHL1 gene in bucks and CC genotype of does can be used as molecular markers to assist in the selection of cashmere fineness.
辽宁绒山羊(LCG)是世界上产绒量最高的白绒山羊。它具有绒纤维长、净绒率高、绒细度适中、绒毛洁白、体型健壮、适应性强、遗传性能稳定、改良中低产绒山羊效果好等特点。被誉为 "中国国宝"。以 LCG 为父本,培育出了 5 个地方新品种,为中国绒山羊品种改良和育种做出了突出贡献。LCG山羊绒的细度适中(LCG种群山羊绒的平均细度约为16微米),但作为一种略粗的纺织原料,我们希望通过PCR-seq和MLR找出调控山羊绒细度的关键基因,以降低山羊绒的细度。结果发现,KRT35基因 G3667A位点的AA基因型、TCHHL1基因T615C位点的CT基因型(公山羊)和CC基因型(母山羊)以及TCHHL1基因T615C位点的CT基因型(公山羊)和CC基因型(母山羊)是羊绒细度的显性基因型。在多种因素和羊绒细度影响下,公鹿的显性单倍型组合被确定为 CTGG,母鹿的显性单倍型组合被确定为 TTGG。LCG 羊绒细度与羊绒率和羊绒量之间存在明显的线性回归关系。LCG 的细度与羊绒率和羊绒量之间存在明显的线性回归关系。公鹿的 CF = 0.001SQ-0.71CY + 20.784 (R2 = 0.818),母鹿的 CF = 0.001SQ-0.767CY + 22.009 (R2 = 0.863)。结论KRT35 基因的 AA 基因型、公鹿 TCHHL1 基因的 CT 基因型和母鹿的 CC 基因型可用作分子标记,帮助选择羊绒细度。
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Mapping proteomic response to salinity stress tolerance in oil crops: Towrads enhanced plant resilience 绘制油料作物耐盐碱胁迫的蛋白质组响应图:韬光养晦增强植物抗逆性
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-10-30 DOI: 10.1016/j.jgeb.2024.100432
Sarah Alrajeh , Muhammad Naveed Khan , Aidhya Irhash Putra , Dhafar N. Al-ugaili , Khalid H. Alobaidi , Othman Al Dossary , Jameel R. Al-Obaidi , Azi Azeyanty Jamaludin , Mohammed Yahya Allawi , Bilal Salim Al-Taie , Norafizah Abdul Rahman , Norasfaliza Rahmad
Exposure to saline environments significantly hampers the growth and productivity of oil crops, harmfully affecting their nutritional quality and suitability for biofuel production. This presents a critical challenge, as understanding salt tolerance mechanisms in crops is key to improving their performance in coastal and high-salinity regions. Our content might be read more properly: This review assembles current knowledge on protein-level changes related to salinity resistance in oil crops. From an extensive analysis of proteomic research, featured here are key genes and cellular pathways which react to salt stress. The literature evinces that cutting-edge proteomic approaches − such as 2D-DIGE, IF-MS/MS, and iTRAQ − have been required to reveal protein expression patterns in oil crops under salt conditions. These studies consistently uncover dramatic shifts in protein abundance associated with important physiological activities including antioxidant defence, stress-related signalling pathways, ion homeostasis, and osmotic regulation. Notably, proteins like ion channels (SOS1, NHX), osmolytes (proline, glycine betaine), antioxidant enzymes (SOD, CAT), and stress-related proteins (HSPs, LEA) play central roles in maintaining cellular balance and reducing oxidative stress. These findings underline the complex regulatory networks that govern oil crop salt tolerance. The application of this proteomic information can inform breeding and genetic engineering strategies to enhance salt resistance. Future research should aim to integrate multiple omics data to gain a comprehensive view of salinity responses and identify potential markers for crop improvement.
暴露在盐碱环境中会严重影响油料作物的生长和产量,损害其营养质量和生物燃料生产的适宜性。这是一个严峻的挑战,因为了解作物的耐盐机制是提高它们在沿海和高盐度地区表现的关键。我们的内容可能更适合阅读:这篇综述汇集了目前有关油料作物耐盐性相关蛋白质水平变化的知识。通过对蛋白质组研究的广泛分析,本文介绍了对盐胁迫做出反应的关键基因和细胞通路。文献表明,要揭示油料作物在盐分条件下的蛋白质表达模式,需要采用最先进的蛋白质组学方法,如二维-DIGE、IF-MS/MS 和 iTRAQ。这些研究不断发现蛋白质丰度的巨大变化与重要的生理活动有关,包括抗氧化防御、应激相关信号通路、离子平衡和渗透调节。值得注意的是,离子通道(SOS1、NHX)、渗透溶质(脯氨酸、甘氨酸甜菜碱)、抗氧化酶(SOD、CAT)和应激相关蛋白(HSPs、LEA)等蛋白质在维持细胞平衡和减少氧化应激方面发挥着核心作用。这些发现强调了油料作物耐盐性的复杂调控网络。应用这些蛋白质组信息可以为育种和基因工程策略提供信息,从而提高耐盐性。未来的研究应着眼于整合多种 omics 数据,以全面了解盐度反应,并确定用于作物改良的潜在标记物。
{"title":"Mapping proteomic response to salinity stress tolerance in oil crops: Towrads enhanced plant resilience","authors":"Sarah Alrajeh ,&nbsp;Muhammad Naveed Khan ,&nbsp;Aidhya Irhash Putra ,&nbsp;Dhafar N. Al-ugaili ,&nbsp;Khalid H. Alobaidi ,&nbsp;Othman Al Dossary ,&nbsp;Jameel R. Al-Obaidi ,&nbsp;Azi Azeyanty Jamaludin ,&nbsp;Mohammed Yahya Allawi ,&nbsp;Bilal Salim Al-Taie ,&nbsp;Norafizah Abdul Rahman ,&nbsp;Norasfaliza Rahmad","doi":"10.1016/j.jgeb.2024.100432","DOIUrl":"10.1016/j.jgeb.2024.100432","url":null,"abstract":"<div><div>Exposure to saline environments significantly hampers the growth and productivity of oil crops, harmfully affecting their nutritional quality and suitability for biofuel production. This presents a critical challenge, as understanding salt tolerance mechanisms in crops is key to improving their performance in coastal and high-salinity regions. Our content might be read more properly: This review assembles current knowledge on protein-level changes related to salinity resistance in oil crops. From an extensive analysis of proteomic research, featured here are key genes and cellular pathways which react to salt stress. The literature evinces that cutting-edge proteomic approaches − such as 2D-DIGE, IF-MS/MS, and iTRAQ − have been required to reveal protein expression patterns in oil crops under salt conditions. These studies consistently uncover dramatic shifts in protein abundance associated with important physiological activities including antioxidant defence, stress-related signalling pathways, ion homeostasis, and osmotic regulation. Notably, proteins like ion channels (SOS1, NHX), osmolytes (proline, glycine betaine), antioxidant enzymes (SOD, CAT), and stress-related proteins (HSPs, LEA) play central roles in maintaining cellular balance and reducing oxidative stress. These findings underline the complex regulatory networks that govern oil crop salt tolerance. The application of this proteomic information can inform breeding and genetic engineering strategies to enhance salt resistance. Future research should aim to integrate multiple omics data to gain a comprehensive view of salinity responses and identify potential markers for crop improvement.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 4","pages":"Article 100432"},"PeriodicalIF":3.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553736","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}
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Journal of Genetic Engineering and Biotechnology
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