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Role of gene interactions in the pathophysiology of skeletal dysplasias: A case report in Colombia 基因相互作用在骨骼发育不良病理生理学中的作用:哥伦比亚的病例报告
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-01 DOI: 10.1016/j.jgeb.2023.100350
Nathalie Yepes Madrid , Lina Johanna Moreno Giraldo

Background

Genome association studies have shown that gene-gene interactions or epistasis play a crucial role in identifying the etiology, prognosis, and treatment response of many complex diseases beyond their main effects. Skeletal dysplasias are a heterogeneous group of congenital bone and cartilage disorders with a genetic and gen-gen interaction etiology. The current classification of skeletal dysplasias distinguishes 461 diseases in 42 groups, and the incidence of all skeletal dysplasias is more than 1 in every 5000 newborns. The objective is to present the case of a patient with four variants that generates gen-gen interactions in the skeletal dysplasia.

Case presentation

A 1-year-old male patient was diagnosed with skeletal dysplasia based on prenatal ultrasound showing micromelia and pyelocalyceal dilation. Postnatal physical examination revealed body disproportion and involvement of other organs and systems.

Materials and Methods

A sequencing study and deletions/duplications analysis were performed for 358 candidate genes associated with skeletal dysplasia.

The GeneMANIA interface was used to evaluate the expression network of genes associated with each other for the gen-gen interaction.

Results

Four pathogenic variants were obtained two heterozygous variants with pathogenic significance in SLC26A, one heterozygous pathogenic variant in CLCN7 and another heterozygous pathogenic variant in CEP120.

The GeneMANIA interface reveals 77.64% physical interactions, 8.01% co-expression, 5.37% prediction, 3.63% co-localization, 2.87% genetic interactions, 1.88% route of action, and 0.60% shared protein domains.

Discussion and Conclusions

These results suggest that the interaction between these genes affects the activity of the inorganic anion exchanger, leading to disorganization of collagen fibers, early mineralization, and decreased assembly of fibronectin in the bone extracellular matrix. Identifying gene-gene interactions is a fundamental step in understanding proper cell function and thus understanding the pathophysiology of many complex human diseases, improving diagnosis, and the possibilities of new personalized therapies.

背景基因组关联研究表明,基因与基因之间的相互作用或外显子在确定许多复杂疾病的病因、预后和治疗反应方面起着关键作用,而不是主要作用。骨骼发育不良是一组具有遗传和基因-基因相互作用病因的先天性骨骼和软骨疾病。目前的骨骼发育不良分类将 461 种疾病分为 42 组,所有骨骼发育不良的发病率超过每 5000 个新生儿中就有 1 例。病例介绍一名 1 岁的男性患者在产前超声检查中发现小骨畸形和肾盂扩张,被诊断为骨骼发育不良。材料与方法对358个与骨骼发育不良相关的候选基因进行了测序研究和缺失/重复分析。结果在 SLC26A 中获得了两个具有致病意义的杂合变异,在 CLCN7 中获得了一个杂合致病变异,在 CEP120 中获得了另一个杂合致病变异。GeneMANIA界面显示了77.64%的物理相互作用、8.01%的共表达、5.37%的预测、3.63%的共定位、2.87%的遗传相互作用、1.88%的作用途径和0.60%的共享蛋白结构域。讨论与结论这些结果表明,这些基因之间的相互作用会影响无机阴离子交换子的活性,导致骨细胞外基质中胶原纤维的紊乱、早期矿化和纤维连接蛋白的组装减少。确定基因与基因之间的相互作用是了解细胞正常功能的一个基本步骤,从而了解许多复杂的人类疾病的病理生理学,改善诊断,并为新的个性化疗法提供可能性。
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引用次数: 0
Efficacy of Event MON 87460 in drought-tolerant maize hybrids under optimal and managed drought-stress in eastern and southern africa 在非洲东部和南部最佳干旱胁迫和可控干旱胁迫条件下,耐旱玉米杂交种MON 87460事件的功效
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-02-01 DOI: 10.1016/j.jgeb.2024.100352
Caleb O. Obunyali , Kiru Pillay , Barbara Meisel , Eric N. Ndou , Kingstone Mashingaidze , Julius Pyton Sserumaga , Godfrey Asea , Murenga Mwimali , Regina Tende , Yoseph Beyene , Stephen Mugo , Emmanuel Okogbenin , Sylvester O. Oikeh

Background

Frequent drought events due to climate change have become a major threat to maize (Zea mays L.) production and food security in Africa. Genetic engineering is one of the ways of improving drought tolerance through gene introgression to reduce the impact of drought stress in maize production. This study aimed to evaluate the efficacy of Event MON 87460 (CspB; DroughtGard®) gene in more than 120 conventional drought-tolerant maize hybrids in Kenya, South Africa, and Uganda for 3–6 years under managed drought-stress and optimal conditions and establish any additional yield contribution or yield penalties of the gene in traited hybrids relative to their non-traited isohybrids. Germplasm used in the study were either MON 87460 traited un-adapted (2008–2010), adapted traited DroughtTEGO® (2011–2013) or a mix of both under confined field trials.

Results

Results showed significant yield differences (p < 0.001) among MON 87460 traited and non-traited hybrids across well-watered and managed drought-stress treatments. The gene had positive and significant effect on yield by 36–62% in three hybrids (CML312/CML445; WMA8101/CML445; and CML312/S0125Z) relative to non-traited hybrids under drought, and without significant yield penalty under optimum-moisture conditions in Lutzville, South Africa. Five traited hybrids (WMA2003/WMB4401; CML442/WMB4401; CML489/WMB4401; CML511/CML445; and CML395/WMB4401) had 7–13% significantly higher yield than the non-traited isohybrids out of 34 adapted DroughtTEGO® hybrids with same background genetics in the three countries for ≥ 3 years. The positive effect of MON 87460 was mostly observed under high drought-stress relative to low, moderate, or severe stress levels.

Conclusion

This study showed that MON 87460 transgenic drought tolerant maize hybrids could effectively tolerate drought and shield farmers against severe yield loss due to drought stress. The study signified that development and adoption of transgenic drought tolerant maize hybrids can cushion against farm yield losses due to drought stress as part of an integrated approach in adaptation to climate change effects.

背景气候变化导致的频繁干旱已成为非洲玉米(Zea mays L.)生产和粮食安全的主要威胁。基因工程是通过基因导入提高耐旱性以减少干旱胁迫对玉米生产影响的方法之一。本研究旨在评估事件 MON 87460(CspB;DroughtGard®)基因在肯尼亚、南非和乌干达 120 多个常规耐旱玉米杂交种中的功效,该杂交种在管理干旱胁迫和最适条件下已种植 3-6 年,并确定了该基因在转基因杂交种中相对于未转基因同系杂交种的额外产量贡献或产量惩罚。研究中使用的种质是MON 87460转基因非适应性种质(2008-2010年)、适应性转基因DroughtTEGO®种质(2011-2013年)或两者在封闭田间试验中的混合种质。结果结果表明,MON 87460转基因杂交种和非转基因杂交种在水分充足和干旱胁迫管理条件下的产量差异显著(p <0.001)。在南非卢茨维尔,该基因在干旱条件下对三个杂交种(CML312/CML445;WMA8101/CML445;CML312/S0125Z)的产量产生了积极而显著的影响,相对于未转录的杂交种产量提高了 36-62%,而在最适水分条件下没有显著的产量损失。在这三个国家的 34 个背景遗传相同的 DroughtTEGO® 改良杂交种中,有 5 个转性杂交种(WMA2003/WMB4401;CML442/WMB4401;CML489/WMB4401;CML511/CML445;和 CML395/WMB4401)的产量比未转性的同系杂交种显著高出 7-13%,时间≥ 3 年。结论这项研究表明,MON 87460 转基因抗旱玉米杂交种能有效抗旱,保护农民免受干旱胁迫造成的严重产量损失。这项研究表明,作为适应气候变化影响的综合方法的一部分,开发和采用转基因耐旱玉米杂交种可以减轻干旱胁迫造成的农业产量损失。
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引用次数: 0
Identification of cuproptosis-related lncRNAs signature for predicting the prognosis in patients with kidney renal clear cell carcinoma 鉴定杯突相关lncRNAs特征以预测肾透明细胞癌患者的预后
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-30 DOI: 10.1016/j.jgeb.2023.100338
Ya He , Hongxia Zhang , Jingang Li , Hui Zhou , Fei Wang , Guangliang Zhang , Yuetao Wen

Background

Kidney renal clear cell carcinoma (KIRC), with low survival rate, is the most frequent subtype of renal cell carcinoma. Recently, more and more studies indicate that cuproptosis-related genes (CRGs) and long non-coding RNAs (lncRNAs) play a vital role in the occurrence and development of many types of cancers. However, the roles of cuproptosis-related lncRNAs (CRlncRNAs) in the KIRC was uncertain.

Results

In our study, CRlncRNAs were obtained by coexpression between differentially expressed and prognostic CRGs and differentially expressed and prognostic lncRNAs, and an 8-CRlncRNAs (AC007743.1, AC022915.1, AP005136.4, APCDD1L-DT, HAGLR, LINC02027, MANCR and SMARCA5-AS1) risk model was established according to least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression. This risk model could differentiate immune cell infiltration, immune function and gene mutation.

Conclusions

This 8-CRlncRNAs risk model may be promising for the clinical prediction of prognoses, tumor immune, immunotherapy response and chemotherapeutic response in KIRC patients.

背景肾透明细胞癌(KIRC)生存率低,是肾细胞癌中最常见的亚型。最近,越来越多的研究表明,杯突相关基因(CRGs)和长非编码 RNAs(lncRNAs)在多种癌症的发生和发展中起着重要作用。结果在我们的研究中,通过差异表达和预后的 CRGs 与差异表达和预后的 lncRNAs 的共表达获得了 CRlncRNAs,并得到了 8 个 CRlncRNAs(AC007743.1、AC022915.1、AP005136.4、APCDD1L-DT、HAGLR、LINC02027、MANCR和SMARCA5-AS1)的风险模型。结论 该 8-CRlncRNAs 风险模型有望用于 KIRC 患者预后、肿瘤免疫、免疫治疗反应和化疗反应的临床预测。
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引用次数: 0
Aggrecan-related bone disorders; a novel heterozygous ACAN variant associated with spondyloepimetaphyseal dysplasia expanding the phenotypic spectrum and review of literature Aggrecan相关骨病;与脊柱软骨骺软骨发育不良相关的新型杂合子ACAN变体扩大了表型谱并回顾了相关文献
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-30 DOI: 10.1016/j.jgeb.2023.100341
Hoda A. Ahmed , R. Elhossini , M. Aglan , Khalda Amr

Background

Spondyloepimetaphyseal dysplasias (SEMD) are a large group of skeletal disorders represented by abnormalities of vertebrae in addition to epiphyseal and metaphyseal areas of bones. Several genes have been identified underlying different forms. ACAN gene mutations were found to cause Aggrecan-related bone disorders (spondyloepimetaphyseal dysplasias,spondyloepiphyseal dysplasias, familial osteochondritis dissecans and short stature syndromes). This study aims to find the disease causing variant in Egyptian patient with SEMD using whole exome sequencing.

Methods

Whole-exome sequencing was performed for an Egyptian male patient who presented with short stature, clinical and radiological features suggestive of unclassified SEMD.

Results

The study identified a novel de novo heterozygous ACAN gene variant (c.7378G>A; p.Gly2460Arg) in G3 domain. Mutations in ACAN gene have been more commonly associated with short stature than SEMD. The phenotype of our patient was intermediate in severity between spondyloepiphyseal dysplasia presentation; Kimberley type(SEDK) and Spondyloepimetaphyseal dysplasias Aggrecan (SEMDAG)

Conclusions

Whole exome sequencing revealed a novel de novo ACAN gene variant in patient with SEDK. The clinical and skeletal phenotype of our patient was much severe than those reported originally and showed more metaphyseal involvement. To the best of our knowledge, two previous studies reported a heterozygous variant in ACAN with spondyloepiphyseal dysplasia presentation; Kimberley type.

背景软骨骺软骨发育不良(SEMD)是一大类骨骼疾病,除骨骺和骨骺区域外,椎骨也有异常。目前已确定了几种不同形式的潜在基因。研究发现,ACAN 基因突变可导致与 Aggrecan 相关的骨骼疾病(脊柱软骨骺软骨发育不良、脊柱软骨骺软骨发育不良、家族性骨软骨炎和身材矮小综合征)。本研究旨在通过全外显子组测序找到埃及 SEMD 患者的致病变异基因。方法对一名埃及男性患者进行了全外显子组测序,该患者表现为身材矮小,临床和影像学特征提示为未分类的 SEMD。与 SEMD 相比,ACAN 基因突变更常与身材矮小相关。我们患者的表型在严重程度上介于脊柱骺软骨发育不良金伯利型(SEDK)和脊柱骺软骨发育不良阿格雷康型(SEMDAG)之间。我们患者的临床和骨骼表型比最初报道的严重得多,并显示出更多的骺端受累。据我们所知,之前有两项研究报道了 ACAN 基因的杂合变异与脊柱软骨发育不良的表现;Kimberley 型。
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引用次数: 0
Elucidating the evolution of monkeypox virus genomes through phylo-geo-network and haplogroup analysis 通过植物地理网络和单倍群分析阐明猴痘病毒基因组的进化过程
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-28 DOI: 10.1016/j.jgeb.2023.100346
Taslima Nasrin , Md Samim Hassan , Muzaffar Iqbal , Amar Yousif , Mehboob Hoque , Nemat Ali , Safdar Ali

Background

As the world settles down from the COVID-19 pandemic, many countries are faced with an unexpected outbreak of monkeypox infection. Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is an enveloped, double stranded DNA virus belonging to the Poxviridae family. Presently, we construct and analyze the phylo-geo-network and the corresponding haplogroups. Presently, we performed the haplogroup analysis with their defining mutations and phylogenetic lineage study along with geographical distributions with the aim to understand the evolutionary path of the MPXV across the world.

Results

Information about 719 full length genomes of MPXV were collected from GISAID repository and the sequences extracted from NCBI. The alignment of 719 MPXV genomes and their subsequent analysis revealed a total of 1530 segregating sites of which 330 were parsimony informative (PI) sites. The variations had a positive value of Tajima’s D statistic indicating some mutations being prevalent and hence balancing selection. A total of 39 haplogroups were observed in the phylo-geo-network and their defining mutations along with the evolutionary path has been discussed. The phylo-geo-network revealed the nodal haplogroup is represented by GISAID ID 13889450, haplogroup A1, an isolate from Germany, having a total of 296 identical sequences in the study incident across 22 countries. The localized evolution is highlighted by country specific sequences and haplogroups. USA had a total of 58 genomes and 13 haplogroups as compared to Peru (89 genomes, 7 haplogroups) and Germany (26 genomes, 6 haplogroups).

Conclusions

The evolution of MPXV can be happening in a localized manner and hence accumulation of variations in the MPXV genomes needs to be monitored in order to be prepared for any possible threats.

背景 随着全球从 COVID-19 大流行中恢复过来,许多国家都面临着猴痘感染的意外爆发。猴痘是由猴痘病毒(MPXV)引起的人畜共患疾病,MPXV是一种包膜双链DNA病毒,属于痘病毒科。目前,我们正在构建和分析植物地理网络和相应的单倍群。结果从 GISAID 数据库中收集了 719 个 MPXV 全长基因组的信息,并从 NCBI 中提取了序列。通过对 719 个 MPXV 基因组进行比对和随后的分析,共发现了 1530 个分离位点,其中 330 个位点具有参照信息(PI)。这些变异的田岛 D 统计量为正值,表明一些突变是普遍存在的,从而平衡了选择。在植物地理网络中总共观察到 39 个单倍群,并讨论了这些单倍群的突变及其进化路径。植物地理网络显示,节点单倍群以 GISAID ID 13889450 为代表,单倍群 A1 来自德国,在 22 个国家的研究事件中总共有 296 个相同序列。特定国家的序列和单倍群凸显了本地化进化。与秘鲁(89 个基因组,7 个单倍群组)和德国(26 个基因组,6 个单倍群组)相比,美国共有 58 个基因组和 13 个单倍群组。
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引用次数: 0
Screening of miRNAs as prognostic biomarkers and their associated hub targets across Hepatocellular carcinoma using survival-based bioinformatics approach 利用基于生存期的生物信息学方法筛选作为肝细胞癌预后生物标志物的 miRNA 及其相关枢纽靶点
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-24 DOI: 10.1016/j.jgeb.2023.100337
Prithvi Singh , Rubi Solanki , Alvea Tasneem , Simran Suri , Harleen Kaur , Sapna Ratan Shah , Ravins Dohare

Background

The hepatocellular carcinoma (HCC) incident rate is gradually increasing yearly despite all the research and efforts taken by scientific communities and governing bodies. Approximately 90% of all liver cancer cases belong to HCC. Usually, HCC patients approach the treatment in the late stages of this malignancy which becomes the primary cause of high mortality rate. The knowledge about molecular pathogenesis of HCC is limited and needs more attention from researchers to identify the driver genes and miRNAs, which causes to translate this information into clinical practice. Therefore, the key regulators identification of miRNA-mRNA regulatory network is essential to identify HCC-associated genes.

Methodology

We extracted microRNA (miRNA) and messenger RNA (mRNA) expression datasets of normal and tumor HCC patient samples from UCSC Xena followed by identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Univariate and multivariate cox-proportional hazard models were utilized to identify DEMs having significant association with overall survival (OS). Kaplan-Meier (KM) plotter was used to validate the presence of prognostic DEMs. A risk-score model was used to evaluate the effectiveness of KM-plotter validated DEMs combination on risk of samples. Target DEGs of prognostic miRNAs were identified via sources such as miRTargetLink and miRWalk followed by their validation in an external microarray cohort and enrichment analysis.

Results

562 DEGs and 388 DEMs were identified followed by seven prognostic miRNAs (i.e., miR-19a, miR-19b, miR-30d-5p, miR-424-5p, miR-3677-5p, miR-3913-5p, miR-7705) post univariate, multivariate, risk-score model evaluation and KM-plotter analyses. ANLN, MRO, CPEB3 were their targets and were also validated in GSE84005 dataset.

Conclusions

The findings of this study decipher that most significant miRNAs and their identified target genes have association with apoptosis, inflammation, cell cycle regulation and cancer-related pathways, which appear to contribute to HCC pathogenesis and therefore, the discovery of new targets.

背景尽管科学界和管理机构进行了各种研究和努力,但肝细胞癌(HCC)的发病率仍在逐年上升。约 90% 的肝癌病例属于 HCC。通常,HCC 患者在恶性肿瘤晚期才开始接受治疗,这也是导致高死亡率的主要原因。目前,人们对 HCC 分子发病机制的了解还很有限,需要研究人员更多地关注如何识别驱动基因和 miRNA,从而将这些信息转化为临床实践。方法我们从 UCSC Xena 提取了正常和肿瘤 HCC 患者样本的 microRNA(miRNA)和信使 RNA(mRNA)表达数据集,然后鉴定了差异表达基因(DEGs)和差异表达 miRNA(DEMs)。利用单变量和多变量cox-比例危险模型来确定与总生存期(OS)有显著关联的DEMs。Kaplan-Meier (KM) plotter用于验证预后DEMs的存在。风险评分模型用于评估KM-plotter验证的DEMs组合对样本风险的影响。通过 miRTargetLink 和 miRWalk 等来源确定了预后 miRNA 的靶 DEGs,然后在外部微阵列队列中进行了验证和富集分析、miR-19a、miR-19b、miR-30d-5p、miR-424-5p、miR-3677-5p、miR-3913-5p、miR-7705)进行单变量、多变量、风险评分模型评估和 KM 绘图仪分析。结论这项研究的结果揭示了大多数重要的 miRNAs 及其确定的靶基因与细胞凋亡、炎症、细胞周期调控和癌症相关通路有关,这些通路似乎有助于 HCC 的发病机制,因此需要发现新的靶点。
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引用次数: 0
Meta-analysis of biodynamic (BD) preparations reveal the bacterial population involved in improving soil health, crop yield and quality 对生物动力(BD)制剂的元分析揭示了参与改善土壤健康、作物产量和质量的细菌群体
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-24 DOI: 10.1016/j.jgeb.2023.100345
Supriya Vaish , Sumit K. Soni , Balvindra Singh , Neelima Garg , Iffat Zareen Ahmad , Muthukumar Manoharan , Ajaya Kumar Trivedi

Background

Bacterial community found in biodynamic preparations (BD500–BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them.

Results

Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501.

Conclusion

The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.

背景在生物动力制剂(BD500-BD507)中发现的细菌群落有助于改善土壤健康、植物发育、产量和质量。本研究对这些制剂进行了元基因组学调查,以确定细菌群落及其功能多样性。结果使用 Illumina MiSeq 平台进行了元基因组测序,该平台采用了新一代测序(NGS)技术,以了解生物动力制剂中的细菌群落及其功能多样性。BD 制剂的 NGS 数据显示,蛋白菌门的最大操作分类单元(OTU)出现在 BD506(23429 个),其次分别是 BD505(22712 个)和 BD501(21591 个)。此外,BD506 的未分类门(16657)和属(16657)也最高。BD501 的α多样性最高(1095 个 OTU),BD507 最低(257 个 OTU)。此外,在 BD506 和 BD501 中,碳水化合物代谢、异生物降解、膜转运功能、能量代谢和酶活性这五大代谢功能组的 OTU 也很丰富。因此,这些制剂可能被认为更有效。调查还发现,细菌的数量变化很大,这可以解释为什么 BD 制剂在实地使用时效果很好。有鉴于此,BD 制剂可用于未开发的细菌群落,促进可持续农业生产。
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引用次数: 0
Subtractive genomics study of Xanthomonas oryzae pv. Oryzae reveals repurposable drug candidate for the treatment of bacterial leaf blight in rice 对黄单胞菌(Xanthomonas oryzae pv. Oryzae)的基因组学子研究发现了可用于治疗水稻细菌性叶枯病的候选药物
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-23 DOI: 10.1016/j.jgeb.2024.100353
Ishtiaque Ahammad , Tabassum Binte Jamal , Anika Bushra Lamisa , Arittra Bhattacharjee , Nayeematul Zinan , Md. Zahid Hasan Chowdhury , Shah Mohammad Naimul Islam , Kazi Md. Omar Faruque , Zeshan Mahmud Chowdhury , Mohammad Uzzal Hossain , Keshob Chandra Das , Chaman Ara Keya , Md Salimullah

Background

Xanthomonas oryzae pv. oryzae is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental compounds and chemical agents have been tested against X. oryzae pv. oryzae, still no approved drug is available. In this study, a subtractive genomic approach was used to identify potential therapeutic targets and repurposible drug candidates that could control of bacterial leaf blight in rice plants.

Results

The entire proteome of the pathogen underwent an extensive filtering process which involved removal of the paralogous proteins, rice homologs, non-essential proteins. Out of the 4382 proteins present in Xoo proteome, five hub proteins such as dnaA, dnaN, recJ, ruvA, and recR were identified for the druggability analysis. This analysis led to the identification of dnaN-encoded Beta sliding clamp protein as a potential therapeutic target and one experimental drug named [(5R)-5-(2,3-dibromo-5-ethoxy-4hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid that can be repurposed against it. Molecular docking and 100 ns long molecular dynamics simulation suggested that the drug can form stable complexes with the target protein over time.

Conclusion

Findings from our study indicated that the proposed drug showed potential effectiveness against bacterial leaf blight in rice caused by X. oryzae pv. oryzae. It is essential to keep in consideration that the procedure for developing novel drugs can be challenging and complicated. Even the most promising results from in silico studies should be validated through further in vitro and in vivo investigation before approval.

背景黄单胞菌(X. oryzae pv. oryzae)是一种植物病原体,可引起水稻最严重的细菌性病害之一,即细菌性叶枯病,对全球水稻生产构成重大威胁。尽管已针对 X. oryzae pv. oryzae 试验了多种化合物和化学制剂,但仍没有获得批准的药物。结果病原体的整个蛋白质组经过了广泛的筛选过程,包括去除旁系蛋白、水稻同源蛋白和非必要蛋白。在 Xoo 蛋白质组的 4382 个蛋白质中,确定了五个中心蛋白,如 dnaA、dnaN、recJ、ruvA 和 recR,用于可药性分析。分析结果表明,dnaN编码的Beta滑动钳蛋白是一个潜在的治疗靶点,一种名为[(5R)-5-(2,3-二溴-5-乙氧基-4-羟基苄基)-4-氧代-2-硫酮-1,3-噻唑烷-3-基]乙酸的实验药物可用于治疗该靶点。分子对接和 100 ns 长的分子动力学模拟表明,该药物可与目标蛋白质形成稳定的复合物。必须考虑到,开发新型药物的过程可能具有挑战性和复杂性。即使是最有希望的硅学研究结果,也应通过进一步的体外和体内研究加以验证,然后才能获得批准。
{"title":"Subtractive genomics study of Xanthomonas oryzae pv. Oryzae reveals repurposable drug candidate for the treatment of bacterial leaf blight in rice","authors":"Ishtiaque Ahammad ,&nbsp;Tabassum Binte Jamal ,&nbsp;Anika Bushra Lamisa ,&nbsp;Arittra Bhattacharjee ,&nbsp;Nayeematul Zinan ,&nbsp;Md. Zahid Hasan Chowdhury ,&nbsp;Shah Mohammad Naimul Islam ,&nbsp;Kazi Md. Omar Faruque ,&nbsp;Zeshan Mahmud Chowdhury ,&nbsp;Mohammad Uzzal Hossain ,&nbsp;Keshob Chandra Das ,&nbsp;Chaman Ara Keya ,&nbsp;Md Salimullah","doi":"10.1016/j.jgeb.2024.100353","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100353","url":null,"abstract":"<div><h3>Background</h3><p><em>Xanthomonas oryzae</em> pv. <em>oryzae</em> is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental compounds and chemical agents have been tested against <em>X. oryzae</em> pv. <em>oryzae</em>, still no approved drug is available. In this study, a subtractive genomic approach was used to identify potential therapeutic targets and repurposible drug candidates that could control of bacterial leaf blight in rice plants.</p></div><div><h3>Results</h3><p>The entire proteome of the pathogen underwent an extensive filtering process which involved removal of the paralogous proteins, rice homologs, non-essential proteins. Out of the 4382 proteins present in <em>Xoo</em> proteome, five hub proteins such as dnaA, dnaN, recJ, ruvA, and recR were identified for the druggability analysis. This analysis led to the identification of dnaN-encoded Beta sliding clamp protein as a potential therapeutic target and one experimental drug named [(5R)-5-(2,3-dibromo-5-ethoxy-4hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid that can be repurposed against it. Molecular docking and 100 ns long molecular dynamics simulation suggested that the drug can form stable complexes with the target protein over time.</p></div><div><h3>Conclusion</h3><p>Findings from our study indicated that the proposed drug showed potential effectiveness against bacterial leaf blight in rice caused by <em>X. oryzae</em> pv. <em>oryzae</em>. It is essential to keep in consideration that the procedure for developing novel drugs can be challenging and complicated. Even the most promising results from <em>in silico</em> studies should be validated through further <em>in vitro</em> and <em>in vivo</em> investigation before approval.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000520/pdfft?md5=c9355b6b58b7db3e5f5d21d6fd2e7041&pid=1-s2.0-S1687157X24000520-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549102","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
The role of zygotic genome activation in genetic−related reproductive medicine: Technological perspective, religious and bioethical concerns, challenges and benefits 子代基因组激活在遗传相关生殖医学中的作用:技术视角、宗教和生物伦理问题、挑战和益处
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-23 DOI: 10.1016/j.jgeb.2023.100340
Nameer Hashim Qasim , Abzal Zhumagaliuly , Rabiga Khozhamkul , Fakher Rahim

Zygotic Genome Activation (ZGA) is a crucial developmental milestone in early embryogenesis, marking the transition from maternal to embryonic control of development. This process, which varies in timing across species, involves the activation of the embryonic genome, paving the way for subsequent cell differentiation and organismal development. Recent advances in genomics and reproductive medicine have highlighted the potential of ZGA in the realm of genetic screening, providing a window into the genetic integrity of the developing embryo at its earliest stages. The intersection of ZGA and genetic screening primarily emerges in the context of preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS). These techniques, often employed during assisted reproductive technologies, aim to detect potential genetic abnormalities or chromosomal imbalances before embryo implantation. Given that ZGA represents the onset of embryonic gene expression, understanding its intricacies can significantly enhance the accuracy and predictive power of these screening processes. With the advent of next-generation sequencing and other high-throughput genomic techniques, detailed mapping of the transcriptomic changes during ZGA has become feasible. Such advancements have deepened our insights into the dynamics of early embryonic development and the onset of genetic disorders. As our knowledge in this realm expands, it promises to revolutionize our capabilities in detecting, understanding, and potentially rectifying genetic anomalies at the earliest stages of human life, thereby optimizing reproductive outcomes.

胚胎基因组激活(ZGA)是早期胚胎发生过程中一个重要的发育里程碑,标志着发育从母体控制过渡到胚胎控制。这一过程的时间因物种而异,涉及胚胎基因组的激活,为随后的细胞分化和机体发育铺平道路。基因组学和生殖医学的最新进展凸显了 ZGA 在基因筛选领域的潜力,为了解发育中胚胎最初阶段的基因完整性提供了一个窗口。ZGA 与基因筛查的交叉点主要出现在胚胎植入前基因诊断 (PGD) 和胚胎植入前基因筛查 (PGS) 中。这些技术通常在辅助生殖技术中使用,旨在胚胎植入前检测潜在的遗传异常或染色体不平衡。鉴于 ZGA 代表着胚胎基因表达的开始,了解其复杂性可大大提高这些筛查过程的准确性和预测能力。随着下一代测序和其他高通量基因组技术的出现,详细绘制 ZGA 期间转录组变化的图谱已变得可行。这些进展加深了我们对早期胚胎发育动态和遗传疾病发病的了解。随着我们在这一领域的知识不断扩展,有望彻底改变我们在人类生命最初阶段检测、了解和纠正遗传异常的能力,从而优化生殖结果。
{"title":"The role of zygotic genome activation in genetic−related reproductive medicine: Technological perspective, religious and bioethical concerns, challenges and benefits","authors":"Nameer Hashim Qasim ,&nbsp;Abzal Zhumagaliuly ,&nbsp;Rabiga Khozhamkul ,&nbsp;Fakher Rahim","doi":"10.1016/j.jgeb.2023.100340","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100340","url":null,"abstract":"<div><p>Zygotic Genome Activation (ZGA) is a crucial developmental milestone in early embryogenesis, marking the transition from maternal to embryonic control of development. This process, which varies in timing across species, involves the activation of the embryonic genome, paving the way for subsequent cell differentiation and organismal development. Recent advances in genomics and reproductive medicine have highlighted the potential of ZGA in the realm of genetic screening, providing a window into the genetic integrity of the developing embryo at its earliest stages. The intersection of ZGA and genetic screening primarily emerges in the context of preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS). These techniques, often employed during assisted reproductive technologies, aim to detect potential genetic abnormalities or chromosomal imbalances before embryo implantation. Given that ZGA represents the onset of embryonic gene expression, understanding its intricacies can significantly enhance the accuracy and predictive power of these screening processes. With the advent of next-generation sequencing and other high-throughput genomic techniques, detailed mapping of the transcriptomic changes during ZGA has become feasible. Such advancements have deepened our insights into the dynamics of early embryonic development and the onset of genetic disorders. As our knowledge in this realm expands, it promises to revolutionize our capabilities in detecting, understanding, and potentially rectifying genetic anomalies at the earliest stages of human life, thereby optimizing reproductive outcomes.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015111/pdfft?md5=e35c9f60af6785557151e565d6527c79&pid=1-s2.0-S1687157X23015111-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549082","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
Emergence of carbapenem resistant gram-negative pathogens with high rate of colistin resistance in Egypt: A cross sectional study to assess resistance trends during the COVID-19 pandemic 埃及出现耐碳青霉烯类革兰氏阴性病原体,对可乐定耐药率高:评估 COVID-19 大流行期间耐药性趋势的横断面研究
IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-01-23 DOI: 10.1016/j.jgeb.2024.100351
Fatma A. Afify , Ahmed H. Shata , Nirmeen Aboelnaga , Dina Osama , Salma W. Elsayed , Nehal A. Saif , Shaimaa F. Mouftah , Sherine M. Shawky , Ahmed A. Mohamed , Omar Loay , Mohamed Elhadidy

The current study investigated the temporal phenotypic and genotypic antimicrobial resistance (AMR) trends among multi-drug resistant and carbapenem-resistant Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa recovered from Egyptian clinical settings between 2020 and 2021. Bacterial identification and antimicrobial sensitivity of 111 clinical isolates against a panel of antibiotics were performed. Molecular screening for antibiotic resistance determinants along with integrons and associated gene cassettes was implemented. An alarming rate (98.2%) of these isolates were found to be phenotypically resistant to carbapenem. Although 23.9 % K. pneumoniae isolates were phenotypically resistant to colistin, no mobile colistin resistance (mcr) genes were detected. Among carbapenem-resistant isolates, blaNDM and blaOXA-48-like were the most prevalent genetic determinants and were significantly overrepresented among K. pneumoniae. Furthermore, 84.78% of K. pneumoniae isolates co-produced these two carbapenemase genes. The plasmid-mediated quinolone resistance genes (qnrS and qnrB) were detected among the bacterial species and were significantly more prevalent among K. pneumoniae. Moreover, Class 1 integron was detected in 82% of the bacterial isolates. This study alarmingly reveals elevated resistance to last-resort antibiotics such as carbapenems as well as colistin which impose a considerable burden in the health care settings in Egypt. Our future work will implement high throughput sequencing-based antimicrobial resistance surveillance analysis for characterization of novel AMR determinants. This information could be applied as a step forward to establish a robust antibiotic stewardship program in Egyptian clinical settings, thereby addressing the rising challenges of AMR.

本研究调查了 2020 年至 2021 年期间从埃及临床环境中回收的耐多药和耐碳青霉烯类抗菌药物(AMR)的表型和基因型趋势。对 111 例临床分离菌进行了细菌鉴定并确定了其对一系列抗生素的抗菌敏感性。对抗生素耐药性决定因子以及整合子和相关基因盒进行了分子筛选。结果发现,这些分离菌株中有98.2%对碳青霉烯类具有表型耐药性。虽然 23.9% 的肺炎克雷伯菌分离株对可乐定具有表型耐药性,但未检测到移动可乐定耐药性(mcr)基因。在耐碳青霉烯类的分离株中,blaNDM 和 blaOXA-48-like 是最普遍的基因决定因子,在肺炎克雷伯菌中的比例明显偏高。此外,84.78%的肺炎克雷伯菌分离株同时产生这两种碳青霉烯酶基因。质粒介导的喹诺酮类药物耐药基因(qnrS 和 qnrB)在细菌种类中均有检出,且在肺炎克雷伯菌中明显较多。此外,在 82% 的细菌分离物中检测到了 1 类整合子。这项研究令人震惊地揭示了对碳青霉烯类和可乐定等最后一种抗生素的耐药性升高,这给埃及的医疗机构造成了相当大的负担。我们今后的工作将以高通量测序为基础进行抗菌药耐药性监测分析,以确定新型 AMR 决定因素的特征。这些信息可用于在埃及临床环境中建立健全的抗生素管理计划,从而应对日益严峻的 AMR 挑战。
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引用次数: 0
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Journal of Genetic Engineering and Biotechnology
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