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Investigating the role of prognostic mitophagy-related genes in non-small cell cancer pathogenesis via multiomics and network-based approach. 通过多组学和基于网络的方法研究与丝裂吞噬相关的预后基因在非小细胞癌发病机制中的作用。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-21 DOI: 10.1007/s13205-024-04127-y
Prithvi Singh, Gulnaz Tabassum, Mohammad Masood, Saleha Anwar, Mansoor Ali Syed, Kapil Dev, Md Imtaiyaz Hassan, Mohammad Mahfuzul Haque, Ravins Dohare, Indrakant Kumar Singh

As one of the most prevalent malignancies, lung cancer displays considerable biological variability in both molecular and clinical characteristics. Lung cancer is broadly categorized into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) with the latter being most prevalent. The primary histological subtypes of NSCLC are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In the present work, we primarily extracted mRNA count data from a publicly accessible database followed by differentially expressed genes (DEGs) and differentially expressed mitophagy-related genes (DEMRGs) identification in case of both LUAD and LUSC cohorts. Next, we identified important DEMRGs via clustering approach followed by enrichment, survival, and mutational analyses. Lastly, the finalized prognostic biomarker was validated using wet-lab experimentations. Primarily, we obtained 986 and 1714 DEGs across LUAD and LUSC cohorts. Only 7 DEMRGs from both cohorts had significant membership values as indicated by the clustering analysis. Most significant pathway, Gene Ontology (GO)-biological process (BP), GO-molecular function (MF), GO-cellular compartment (CC) terms were macroautophagy, GTP metabolic process, magnesium ion binding, mitochondrial outer membrane. Among all, only TDRKH reported significant overall survival (OS) and 14% amplification across LUAD patients. Lastly, we validated TDRKH via immunohistochemistry (IHC) and semi-quantitative polymerase chain reaction (PCR). In conclusion, our findings advocate for the exploration of TDRKH and their genetic alterations in precision oncology therapeutic approaches for LUAD, emphasizing the potential for target-driven therapy and early diagnostics.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04127-y.

作为最常见的恶性肿瘤之一,肺癌在分子和临床特征方面都表现出相当大的生物差异性。肺癌大致分为小细胞肺癌(SCLC)和非小细胞肺癌(NSCLC),后者最为常见。非小细胞肺癌的主要组织学亚型是肺腺癌(LUAD)和肺鳞癌(LUSC)。在本研究中,我们首先从一个可公开访问的数据库中提取了 mRNA 计数数据,然后对 LUAD 和 LUSC 队列中的差异表达基因(DEGs)和差异表达有丝分裂相关基因(DEMRGs)进行了鉴定。接下来,我们通过聚类方法确定了重要的 DEMRGs,然后进行了富集、生存和突变分析。最后,我们通过湿实验室实验对最终确定的预后生物标志物进行了验证。首先,我们在 LUAD 和 LUSC 队列中分别获得了 986 个和 1714 个 DEGs。聚类分析显示,两个队列中只有 7 个 DEMRGs 具有显著的成员值。最重要的通路、基因本体(GO)-生物过程(BP)、GO-分子功能(MF)、GO-细胞区室(CC)术语是大自噬、GTP 代谢过程、镁离子结合、线粒体外膜。其中,只有 TDRKH 在 LUAD 患者的总生存率(OS)和 14% 的扩增率方面具有显著性。最后,我们通过免疫组化(IHC)和半定量聚合酶链反应(PCR)对 TDRKH 进行了验证。总之,我们的研究结果主张在LUAD的肿瘤精准治疗方法中探索TDRKH及其基因改变,强调靶向驱动治疗和早期诊断的潜力:在线版本包含补充材料,可在 10.1007/s13205-024-04127-y.获取。
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引用次数: 0
In silico analysis of R2R3-MYB transcription factors in the basal eudicot model, Aquilegia coerulea. 基生裸子植物模型 Aquilegia coerulea 中 R2R3-MYB 转录因子的硅学分析。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-29 DOI: 10.1007/s13205-024-04119-y
Banisha Phukela, Hanna Leonard, Yuval Sapir

R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, Aquilegia coerulea is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized Arabidopsis thaliana R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as A. thaliana R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus Aquilegia. AqcoeR2R3-MYB genes are present in all seven chromosomes of A. coerulea, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in A. coerulea. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04119-y.

R2R3-MYBs是一类重要的转录因子,调控整个植物界的关键发育过程;然而,迄今为止还没有对Ranunculaceae(毛茛科)早期分化的裸子植物支系中的R2R3-MYBs进行过全面的分析。本研究选取 Aquilegia coerulea 作为研究对象,通过分析 R2R3-MYBs 的基因组分布、组织结构、基因结构、理化性质、蛋白质结构、进化和可能的扩展模式,了解 R2R3-MYBs 的保守和分化程度。全基因组分析表明,根据全长蛋白质序列的系统进化分析,存在 82 个推定同源物,分为 21 个亚群。该结构域在所有同源物中基本保持不变,与拟南芥 R2R3-MYB 的特征差异很小。当使用全长蛋白质序列时,系统发生树的拓扑结构保持不变,表明 R2R3-MYB 的进化仅由结构域区域驱动。同一亚群中存在相似的外显子-内含子结构和保守基团也证明了这一点。此外,通过将 AqcoeR2R3-MYB 成员与单子叶植物和核心裸子植物进行比较,发现了一些功能支系的进化扩展,如大连油菜 R2R3-MYB 亚群 6(SG6),它是花色素生物合成和花色的上游调控因子。SG6 类基因在被子植物中的进化历史重建突显了 Aquilegia 属中发生的独立复制事件。AqcoeR2R3-MYB基因存在于A. coerulea的所有七条染色体中,其中大部分是局部和节段复制的结果。对这些重复基因对的选择分析表明,除一个基因对外,其他基因对均有纯化选择,而对 R2R3-MYB 的理化分析表明,MYB 之间存在差异,表明其功能多样化。这项研究为进一步研究旁系拷贝及其在 A. coerulea 不同花性状进化中可能扮演的角色铺平了道路。它为基础裸子植物中 R2R3-MYBs 的功能基因组研究奠定了基础,并促进了被子植物之间的比较研究。这项工作还为破译支配花形态多样性的新型遗传调控途径提供了一个框架:在线版本包含补充材料,可查阅 10.1007/s13205-024-04119-y。
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引用次数: 0
Bioremediation of metal cyanide complexes from electroplating wastewater for long-term application using Agrobacterium tumefaciens SUTS 1 and Pseudomonas monteilii SUTS 2. 利用农杆菌 SUTS 1 和假单胞菌 SUTS 2 对电镀废水中的金属氰化物络合物进行生物修复,以便长期应用。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-29 DOI: 10.1007/s13205-024-04122-3
Nootjalee Supromin, Siraporn Potivichayanon

The purpose of this study was to investigate the optimum conditions, including aerobic and anoxic conditions, for operating a long-term bioreactor system to decrease the toxicity of industrial electroplating wastewater effluents containing metal cyanide using Agrobacterium tumefaciens SUTS 1 and Pseudomonas monteilii SUTS 2. The initial results revealed that bacteria performed better under aerobic conditions than under anoxic conditions. An aerobic bioreactor system was subsequently set up in a long-term study lasting 30 days under optimum operating conditions. Both mixed-culture bacteria and indigenous bacteria promoted the high-efficiency treatment of cyanide and metals in the first 7 days of the study. When the system had high removal rates, cyanide removal was greater than that of zinc, copper, nickel, and chromium (CN- > Zn > Cu > Ni > Cr), with removal efficiencies of 96.67%, 93.93%, 74.17%, 63.43%, and 44.65%, respectively, with residual concentrations of 0.15 ± 0.01, 0.24 ± 0.005, 0.03 ± 0.002, 18.41 ± 0.06 and 14.26 ± 0.15 mg/L, respectively. The cell concentration in the bioreactor increased to approximately 107 CFU/mL over 30 days from initial cell concentrations of 6.15 × 105 CFU/mL and 1.05 × 103 CFU/mL for the mixed culture and indigenous inoculation, respectively. These results implied that the bacteria were resistant to heavy metal toxicity. The addition of an appropriate carbon source with sufficient aeration to a bioreactor resulted in increased cyanide degradation.

本研究的目的是调查长期运行生物反应器系统的最佳条件,包括好氧和缺氧条件,以便利用农杆菌 SUTS 1 和假单胞菌 SUTS 2 降低含有金属氰化物的工业电镀废水的毒性。 初步结果显示,细菌在好氧条件下的表现优于缺氧条件。随后,在最佳操作条件下进行了为期 30 天的长期研究,建立了一个好氧生物反应器系统。在研究的前 7 天,混合培养细菌和本地细菌都促进了氰化物和金属的高效处理。当系统具有高去除率时,氰化物的去除率高于锌、铜、镍和铬(CN- > Zn > Cu > Ni > Cr),去除率分别为 96.67%、93.93%、74.17%、63.43% 和 44.65%,残留浓度分别为 0.15 ± 0.01、0.24 ± 0.005、0.03 ± 0.002、18.41 ± 0.06 和 14.26 ± 0.15 mg/L。生物反应器中的细胞浓度在 30 天内从混合培养和本地接种的初始细胞浓度分别为 6.15 × 105 CFU/mL 和 1.05 × 103 CFU/mL,增加到约 107 CFU/mL。这些结果表明,细菌对重金属毒性具有抗性。在生物反应器中加入适当的碳源和充分的通气可提高氰化物的降解。
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引用次数: 0
Composition and diversity of endophytic bacterial communities in the tubers of Pinellia ternata from different regions and their effects on succinate biosynthesis based on high-throughput sequencing. 基于高通量测序的不同地区半夏块茎内生细菌群落的组成和多样性及其对琥珀酸生物合成的影响。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-06 DOI: 10.1007/s13205-024-04108-1
Peng Zhang, Wei Ding, Heng Zheng

In this study, high-throughput sequencing (HTS) technology was used to investigate the composition and diversity of endophytic bacteria and their effects on succinic acid biosynthesis in P. ternata tubers from three different geographical locations (MS, SL, and ZT). A total of 1777 amplicon sequence variants (ASVs) were annotated, and the diversity and composition of endophytic bacteria in P. ternata tubers were significantly different among different regions. The ZT samples presented the highest α diversity, and the Shannon diversity, richness, and Pielou evenness index were all ZT > MS > SL. Co-occurrence network analysis revealed that endophytic bacterial groups such as Stenotrophomonas, Pseudomonas, Mycobacterium, and Chryseomicrobium were key groups in the endophytic bacterial interaction network, indicating that they play a role in maintaining community stability. In addition, some endophytic bacteria were associated with the biosynthesis of succinic acid, a key bioactive compound in P. ternata. The succinate content was positively correlated with the genera Brevundimonas, Ensifer, Nocardioides, and Paenibacillus, while it was negatively correlated with the genera Lentimicrobium, Anaerovorax, and Pajaroellobacter. These findings highlight the key role of endophytic bacteria in regulating the efficacy of P. ternata. These findings provide key information for further elucidating the mechanism by which endophytic bacteria affect the synthesis of bioactive compounds.

本研究采用高通量测序(HTS)技术研究了三个不同地理位置(MS、SL和ZT)的P. ternata块茎中内生细菌的组成和多样性及其对琥珀酸生物合成的影响。共注释了 1777 个扩增子序列变异(ASVs),不同地区 P. ternata 块茎中内生细菌的多样性和组成存在显著差异。ZT 样品的 α 多样性最高,香农多样性、丰富度和 Pielou 均匀度指数均为 ZT > MS > SL。共生网络分析显示,内生细菌群(如 Stenotrophomonas、Pseudomonas、Mycobacterium 和 Chryseomicrobium)是内生细菌相互作用网络中的关键群,表明它们在维持群落稳定性方面发挥作用。此外,一些内生细菌与琥珀酸的生物合成有关,琥珀酸是 P. ternata 的一种关键生物活性化合物。琥珀酸含量与 Brevundimonas 属、Ensifer 属、Nocardioides 属和 Paenibacillus 属呈正相关,而与 Lentimicrobium 属、Anaerovorax 属和 Pajaroellobacter 属呈负相关。这些发现凸显了内生细菌在调节 P. ternata 的功效方面所起的关键作用。这些发现为进一步阐明内生细菌影响生物活性化合物合成的机制提供了关键信息。
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引用次数: 0
Genetic diversity of the fungal community that contributes to the sensory quality of coffee beverage after carbonic maceration and fermentation. 真菌群落的遗传多样性有助于提高碳酸浸渍和发酵后咖啡饮料的感官质量。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-19 DOI: 10.1007/s13205-024-04099-z
Thaynara Lorenzoni Entringer, José Maria Rodrigues da Luz, Tomás Gomes Reis Veloso, Lucas Louzada Pereira, Karen Mirella Souza Menezes, Dério Brioschi Júnior, Maria Catarina Megumi Kasuya, Marliane de Cássia Soares da Silva

Understanding the effects of microorganisms on coffee fermentation is crucial to ensure sensory quality and food security. The analysis of the dynamics of the microbial community during fermentation can contribute to a better understanding of the beneficial and harmful effects of microorganisms and help select starter cultures to improve coffee quality. Furthermore, the anaerobic environment produced by carbonic maceration of the coffee fruits inhibits aerobic respiratory processes and stimulates fermentative metabolism, modulating the microbial community during coffee fermentation. This study evaluated the effects of carbonic maceration in the fungal community dynamics during the fermentation of Coffea arabica fruits at 18, 28, and 38 °C for 24, 48, 72, 96, and 120 h. Fungal diversity was accompanied by high-throughput sequencing (NGS) of the Internal Transcribed Spacer (ITS) region. During the coffee fermentation, the fungal community changed over time, with the most significant changes occurring at 18 and 28 °C after 72 h. However, at 38 °C, there were greater variations in fungal composition and fungal diversity was highest after 120 h. The yeast Pichia cephalocereana was predominant in the fermentations. These results indicated that temperature and fermentation conditions influence the fungal community during coffee fermentation. Lower temperatures might favor a more stable microbial environment, while higher temperatures lead to more intense changes. Thus, our data from NGS can help in the identification, isolation, and metabolic characterization of fungi for the fermentation of coffee fruits.

了解微生物对咖啡发酵的影响对于确保感官质量和食品安全至关重要。分析发酵过程中微生物群落的动态有助于更好地了解微生物的有益和有害影响,并帮助选择启动培养物以提高咖啡质量。此外,咖啡果实碳酸浸渍产生的厌氧环境会抑制有氧呼吸过程,刺激发酵代谢,从而调节咖啡发酵过程中的微生物群落。本研究评估了碳酸浸渍对阿拉比卡咖啡果实在 18、28 和 38 °C 温度下发酵 24、48、72、96 和 120 小时期间真菌群落动态的影响。在咖啡发酵过程中,真菌群落随着时间的推移而变化,在 18 和 28 °C 温度下,72 小时后的变化最为显著;但在 38 °C 温度下,真菌组成的变化更大,120 小时后真菌多样性最高。这些结果表明,温度和发酵条件会影响咖啡发酵过程中的真菌群落。较低的温度可能有利于更稳定的微生物环境,而较高的温度则会导致更剧烈的变化。因此,我们从 NGS 中获得的数据有助于咖啡果实发酵过程中真菌的鉴定、分离和代谢特征描述。
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引用次数: 0
Genome sequencing of Caridina pseudogracilirostris and its comparative analysis with malacostracan crustaceans. Caridina pseudogracilirostris 的基因组测序及其与 malacostracan 甲壳类的比较分析。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-23 DOI: 10.1007/s13205-024-04121-4
NandhaGopal SoundharaPandiyan, Carlton Ranjith Wilson Alphonse, Subramoniam Thanumalaya, Samuel Gnana Prakash Vincent, Rajaretinam Rajesh Kannan

The Caridina pseudogracilirostris is commonly found in the brackish waters of the southwestern coastal regions of India. This study provides a comprehensive genomic investigation of the shrimp species C. pseudogracilirostris, offering insights into its genetic makeup, evolutionary dynamics, and functional annotations. The genomic DNA was isolated from tissue samples, sequenced using next-generation sequencing (NGS), and stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Accession No: PRJNA847710). De novo sequencing indicated a genome size of 1.31 Gbp with a low heterozygosity of about 0.81%. Repeat masking and annotation revealed that repeated elements constitute 24.60% of the genome, with simple sequence repeats (SSRs) accounting for 7.26%. Gene prediction identified 14,101 genes, with functional annotations indicating involvement in critical biological processes such as development, cellular function, immunological responses, and reproduction. Furthermore, phylogenetic analysis revealed genomic links among Malacostraca species, indicating gene duplication as a strategy for genetic diversity and adaptation. C. pseudogracilirostris has 1,856 duplicated genes, reflecting a distinct genomic architecture and evolutionary strategy within the Malacostraca branch. These findings enhance our understanding of the genetic characteristics and evolutionary relationships of C. pseudogracilirostris, providing significant insights into the overall evolutionary dynamics of the Malacostraca group.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04121-4.

假梭子蟹(Caridina pseudogracilirostris)常见于印度西南沿海地区的咸水中。本研究对对虾物种C. pseudogracilirostris进行了全面的基因组调查,深入了解了其基因组成、进化动态和功能注释。基因组 DNA 从组织样本中分离出来,使用新一代测序技术(NGS)进行测序,并存储在美国国家生物技术信息中心(NCBI)的序列读取档案(SRA)数据库中(登录号:PRJNA847710)。从头测序显示基因组大小为 1.31 Gbp,杂合度低,约为 0.81%。重复屏蔽和注释显示,重复元素占基因组的 24.60%,其中简单序列重复(SSR)占 7.26%。基因预测确定了 14 101 个基因,其功能注释表明这些基因参与发育、细胞功能、免疫反应和繁殖等关键生物过程。此外,系统发育分析还揭示了孔雀鱼物种之间的基因组联系,表明基因复制是实现遗传多样性和适应性的一种策略。C. pseudogracilirostris有1,856个重复基因,反映了孔雀鱼分支内部独特的基因组结构和进化策略。这些发现加深了我们对C. pseudogracilirostris的遗传特征和进化关系的理解,为我们深入了解Malacostraca类群的整体进化动态提供了重要依据:在线版本包含补充材料,可查阅 10.1007/s13205-024-04121-4。
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引用次数: 0
Ex vivo and miniaturized in vitro models to study microbiota-gut-brain axis. 研究微生物群-肠-脑轴的体外和微型体外模型。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-24 DOI: 10.1007/s13205-024-04126-z
Vinod Kumar Yata

The microbiota-gut-brain axis involves complex bidirectional communication through neural, immune, and endocrine pathways. Microbial metabolites, such as short-chain fatty acids, influence gut motility and brain function by interacting with gut receptors and modulating hormone release. Additionally, microbial components such as lipopolysaccharides and cytokines can cross the gut epithelium and the blood-brain barrier, impacting immune responses and cognitive function. Ex vivo models, which preserve gut tissue and neural segments, offer insight into localized gut-brain communication by allowing for detailed study of nerve excitability in response to microbial signals, but they are limited in systemic complexity. Miniaturized in vitro models, including organ-on-chip platforms, enable precise control of the cellular environment and simulate complex microbiota-host interactions. These systems allow for the study of microbial metabolites, immune responses, and neuronal activity, providing valuable insights into gut-brain communication. Despite challenges such as replicating long-term biological processes and integrating immune and hormonal systems, advancements in bioengineered platforms are enhancing the physiological relevance of these models, offering new opportunities for understanding the mechanisms of the microbiota-gut-brain axis. This review aims to describe the ex vivo and miniaturized in vitro models which are used to mimic the in vivo conditions and facilitate more precise studies of gut brain communication.

微生物群-肠道-大脑轴涉及通过神经、免疫和内分泌途径进行复杂的双向交流。微生物代谢产物(如短链脂肪酸)通过与肠道受体相互作用并调节激素释放,从而影响肠道蠕动和大脑功能。此外,脂多糖和细胞因子等微生物成分可穿过肠道上皮和血脑屏障,影响免疫反应和认知功能。体外模型保留了肠道组织和神经节段,可以详细研究神经兴奋性对微生物信号的反应,从而深入了解局部肠道与大脑的交流,但其系统复杂性有限。微型体外模型,包括器官芯片平台,可以精确控制细胞环境,模拟复杂的微生物-宿主相互作用。这些系统可以研究微生物代谢物、免疫反应和神经元活动,为了解肠脑交流提供宝贵的信息。尽管存在复制长期生物过程以及整合免疫和激素系统等挑战,但生物工程平台的进步正在提高这些模型的生理相关性,为了解微生物群-肠-脑轴的机制提供了新的机会。本综述旨在介绍体内外模型和微型体外模型,这些模型可用于模拟体内条件,促进更精确的肠脑交流研究。
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引用次数: 0
PFusionDB: a comprehensive database of plant-specific fusion transcripts. PFusionDB:植物特异性融合转录本综合数据库。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-28 DOI: 10.1007/s13205-024-04132-1
Ajay Arya, Simran Arora, Fiza Hamid, Shailesh Kumar

Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of Arabidopsis thaliana, Oryza sativa japonica, Oryza sativa indica, and Cicer arietinum respectively. Here, a total of 76,599 (Arabidopsis thaliana), 35,480 (Oryza sativa japonica), 72,099 (Oryza sativa indica), and 9524 (Cicer arietinum) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04132-1.

融合转录本(FTs)是众所周知的癌症生物标志物,但在植物中的研究相对不足。在此,我们开发了一个新颖的植物特异性融合转录本数据库 PFusionDB (www.nipgr.ac.in/PFusionDB)。它是一个全面的数据库,分别包含拟南芥、粳稻、籼稻和黑麦的 1280、637、697 和 181 份 RNA-Seq 样本中检测到的 80170、39108、83330 和 11500 个独特融合基因。其中,共有 76599 个融合转录本(拟南芥)、35480 个融合转录本(粳稻)、72099 个融合转录本(籼稻)和 9524 个融合转录本(菊苣)是非重复性的,即只在一个样本中发现。FTs 的鉴定共使用了五种工具,即 EricScript-Plants、STAR-Fusion、TrinityFusion、SQUID 和 MapSplice。在 PFusionDB 中,融合事件的基本信息包括亲代基因信息、连接序列、融合转录本的表达水平、断点坐标、链信息、组织类型、处理信息、融合类型、PFusionDB ID 和序列读取档案(SRA)ID。此外,还有两个搜索模块:此外,还有两个搜索模块:"简单搜索 "和 "高级搜索",以及下载数据的 "浏览 "选项,方便用户使用。另外还有三个不同的模块,即 "BLASTN"、"SW Align "和 "Mapping",用于有效地将查询序列映射和比对到 FT。PFusionDB 是深入研究错综复杂的植物融合转录本世界的重要资源,为研究人员提供了进一步探索和分析的基础。数据库网址:www.nipgr.ac.in/PFusionDB.Supplementary 信息:在线版本包含补充材料,可查阅 10.1007/s13205-024-04132-1。
{"title":"PFusionDB: a comprehensive database of plant-specific fusion transcripts.","authors":"Ajay Arya, Simran Arora, Fiza Hamid, Shailesh Kumar","doi":"10.1007/s13205-024-04132-1","DOIUrl":"10.1007/s13205-024-04132-1","url":null,"abstract":"<p><p>Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of <i>Arabidopsis thaliana</i>, <i>Oryza sativa japonica</i>, <i>Oryza sativa indica</i>, and <i>Cicer arietinum</i> respectively. Here, a total of 76,599 (<i>Arabidopsis thaliana</i>), 35,480 (<i>Oryza sativa japonica</i>), 72,099 (<i>Oryza sativa indica</i>), and 9524 (<i>Cicer arietinum</i>) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04132-1.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11519250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Simultaneous detection of novel goose parvovirus and novel duck reovirus by SYBR Green I-based duplex real-time quantitative polymerase chain reaction. 利用基于 SYBR Green I 的双工实时定量聚合酶链式反应同时检测新型鹅细小病毒和新型鸭细小病毒。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-11-03 DOI: 10.1007/s13205-024-04139-8
Yimin Wang, Yong Wang, Zhuangli Bi, Yuhan Liu, Chunchun Meng, Jie Zhu, Guangqing Liu, Chuanfeng Li

Co-infection with novel goose parvovirus (NGPV) and novel duck reovirus (NDRV) is common, significantly impeding duck growth and resulting in considerable economic losses within the duck farming industry. To facilitate rapid and accurate diagnosis and differentiation of these two viruses, this study developed a SYBR Green I-based duplex real-time quantitative polymerase chain reaction (qPCR) assay. This assay enabled the simultaneous detection of NGPV and NDRV by exploiting their distinct melting temperatures (Tm): 78.5 ± 0.50 °C for NGPV and 84.5 ± 0.50 °C for NDRV. No amplification was observed for other prevalent non-target duck viruses. The intra- and inter-assay coefficients of variation were less than 1.75%. The assay showed good performance with the same detection limit of 102 copies/μL for both NGPV and NDRV. The results of the clinical testing indicated that 45.3% (34/75) of the samples tested positive for NGPV, while 38.7% (29/75) were positive for NDRV. Notably, 13.3% (10/75) exhibited co-infection. These results revealed that the sensitivity of the developed method exceed that of conventional polymerase chain reaction (PCR). The developed method for the identifying of NGPV and NDRV shows good specificity, sensitivity, and repeatability, rendering it an effective tool for the simultaneous detection of co-infection with NGPV and NDRV.

新型鹅副粘病毒(NGPV)和新型鸭再病毒(NDRV)的混合感染很常见,严重阻碍了鸭子的生长,给养鸭业造成了巨大的经济损失。为了快速准确地诊断和区分这两种病毒,本研究开发了一种基于 SYBR Green I 的双工实时定量聚合酶链反应(qPCR)检测方法。通过利用 NGPV 和 NDRV 不同的熔解温度 (Tm),该检测方法可同时检测这两种病毒:NGPV 为 78.5 ± 0.50 °C,NDRV 为 84.5 ± 0.50 °C。其他流行的非目标鸭病毒未发现扩增。测定内和测定间的变异系数均小于 1.75%。该检测方法性能良好,对 NGPV 和 NDRV 的检测限均为 102 拷贝/μL。临床检测结果表明,45.3%(34/75)的样本对 NGPV 检测呈阳性,38.7%(29/75)的样本对 NDRV 检测呈阳性。值得注意的是,13.3%(10/75)的样本表现出合并感染。这些结果表明,所开发方法的灵敏度超过了传统的聚合酶链反应(PCR)。所开发的鉴定 NGPV 和 NDRV 的方法具有良好的特异性、灵敏度和重复性,是同时检测 NGPV 和 NDRV 共同感染的有效工具。
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引用次数: 0
Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India. 印度东北部香蕉自然感染的香蕉条纹 MY 病毒和香蕉条纹 IM 病毒的新基因变种。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-23 DOI: 10.1007/s13205-024-04113-4
Richa Rai, Yumlembam Rupert Anand, Sapam Monteshori, Damini Diksha, Saurabh Kumar Dubey, Virendra Kumar Baranwal, Susheel Kumar Sharma

Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.

从印度东北部地区(NER)表现出不同症状的香蕉植株中发现了不同的香蕉条纹病毒(BSV)。利用滚动圈扩增(RCA)技术,鉴定了 7 个外显香蕉条纹 MY 病毒(BSMYV)分离株(包括 2 个新型变体)和 2 个新型香蕉条纹 IM 病毒(BSIMV)分离株的完整基因组序列。新型 BSMYV 基因变体除了常见的条斑病症状外,还与新萌发叶片上的明显坏死、花序梗扭曲、假茎内部坏死有关。在完整的基因组核苷酸序列中,BSMYV-IN4 和 IN5 与其他 BSMYV 的同一性为 77-79%,而 BSMYV-IN7 和 IN8 的同一性为 77-97%。本研究首次报道了感染三倍体香蕉杂交种的两种香蕉条纹IM病毒(BSIMV-IN1和-IN2)的完整基因组,这两种病毒表现出叶片扭曲、莲座状生长迟缓和坏死,与参考BSIMV基因组(GenBank登录号:HQ593112)有87%的序列相同性。基于完整基因组的系统发育推断表明,BSMYV-IN4 和 IN5 在 BSMYV 群体中的位置是不同的,而且是一致的。对保守的 RT/RNase H 核苷酸(nt)序列进行配对比较发现,BSMYV-IN7 和 IN4 分离物与 BSMYV (AY805074) 的同一性分别为 85% 和 97%,与 BSMYV-IN6、IN9 和 IN10 的 nt 同一性最高,为 100%。BSIMV-IN1和IN2的RT/RNase H nt序列与BSIMV(HQ593112)的同一性为98%,但基于完整基因组被鉴定为BSIMV的新变种。对 BSMYV 和 BSIMV 分离物 ORFIII 多聚蛋白中相对同义密码子使用(RSCU)模式的分析表明,AGA 和 AGG(精氨酸)是最常出现的高比例密码子(>1.5),在这两个物种的基因组中进化保守。36 个 BSV 基因组中共检测到 14 个重组事件,重组断点主要位于 ORFI、III 和 IGR 基因组区域。一个新的系统发生群由支系 I 中的 BSMYV-IN4 和 IN5 组成,该系统发生群可能来自于类似于香蕉条纹 VN 病毒(BSVNV;AY750155)和香蕉条纹 GF 病毒(BSGFV;KJ013507)分离株的亲本之间的异源重组。本研究最终报告了印度东北部香蕉杂交种感染 BSMYV 和 BSIMV 的不同基因和症状变种的情况。
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引用次数: 0
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3 Biotech
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