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Biotechnological advances in microbial synthesis of gold nanoparticles: Optimizations and applications. 微生物合成金纳米粒子的生物技术进展:优化与应用。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-07 DOI: 10.1007/s13205-024-04110-7
Jyoti Verma, Chitranjan Kumar, Monica Sharma, Sangeeta Saxena

This review discusses the eco-friendly and cost-effective biosynthesis of gold nanoparticles (AuNPs) in viable microorganisms, focusing on microbes-mediated AuNP biosynthesis. This process suits agricultural, environmental, and biomedical applications, offering renewable, eco-friendly, non-toxic, sustainable, and time-efficient methods. Microorganisms are increasingly used in green technology, nanotechnology, and RNAi technology, but several microorganisms have not been fully identified and characterized. Bio-nanotechnology offers eco-friendly and sustainable solutions for nanomedicine, with microbe-mediated nanoparticle biosynthesis producing AuNPs with anti-oxidation activity, stability, and biocompatibility. Ultrasmall AuNPs offer rapid distribution, renal clearance, and enhanced permeability in biomedical applications. The review explores nano-size dependent biosynthesis of AuNPs by bacteria, fungi, and viruses revealing their non-toxic, non-genotoxic, and non-oxidative properties on human cells. AuNPs with varying sizes and shapes, from nitrate reductase enzymes, have shown potential as a promising nano-catalyst. The synthesized AuNPs, with negative charge capping molecules, have demonstrated antibacterial activity against drug-resistant Pseudomonas aeruginosa, and Acinetobacter baumannii strains, and were non-toxic to Vero cell lines, indicating potential antibiotic resistance treatments. A green chemical method for the biosynthesis of AuNPs using reducing chloroauric acid and Rhizopus oryzae protein extract has been described, demonstrating excellent stability and strong catalytic activity. AuNPs are eco-friendly, non-toxic, and time-efficient, making them ideal for biomedical applications due to their antioxidant, antidiabetic, and antibacterial properties. In addition to the biomedical application, the review also highlights the role of microbially synthesized AuNPs in sustainable management of plant diseases, and environmental bioremediation.

本综述讨论了在有生命力的微生物中以生态友好和具有成本效益的方式进行金纳米粒子(AuNPs)的生物合成,重点是微生物介导的 AuNPs 生物合成。这一工艺适合农业、环境和生物医学应用,提供了可再生、生态友好、无毒、可持续和省时的方法。微生物在绿色技术、纳米技术和 RNAi 技术中的应用越来越广泛,但有几种微生物尚未得到充分鉴定和表征。生物纳米技术为纳米医学提供了生态友好和可持续的解决方案,微生物介导的纳米粒子生物合成产生了具有抗氧化活性、稳定性和生物相容性的 AuNPs。超小 AuNPs 在生物医学应用中具有快速分布、肾脏清除和更强的渗透性。这篇综述探讨了细菌、真菌和病毒根据纳米尺寸进行的 AuNPs 生物合成,揭示了它们对人体细胞无毒、无遗传毒性和无氧化作用的特性。来自硝酸还原酶酶的不同大小和形状的 AuNPs 已显示出作为一种前景广阔的纳米催化剂的潜力。合成的带有负电荷封端分子的 AuNPs 对耐药性铜绿假单胞菌和鲍曼不动杆菌菌株具有抗菌活性,而且对 Vero 细胞系无毒,表明具有治疗抗生素耐药性的潜力。该研究介绍了一种利用还原性氯金酸和根瘤菌蛋白提取物生物合成 AuNPs 的绿色化学方法,该方法具有极佳的稳定性和较强的催化活性。AuNPs 具有环保、无毒、省时等特点,因其抗氧化、抗糖尿病和抗菌特性而成为生物医学应用的理想选择。除生物医学应用外,该综述还强调了微生物合成的 AuNPs 在植物病害可持续管理和环境生物修复方面的作用。
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引用次数: 0
Multifunctional gold nanoparticles for cancer theranostics. 用于癌症治疗的多功能金纳米粒子。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-14 DOI: 10.1007/s13205-024-04086-4
Donald A Fernandes

The diagnosis and treatment of cancer can often be challenging requiring more attractive options. Some types of cancers are more aggressive than others and symptoms for many cancers are subtle, especially in the early stages. Nanotechnology provides high sensitivity, specificity and multimodal capability for cancer detection, treatment and monitoring. In particular, metal nanoparticles (NPs) such as gold nanoparticles (AuNPs) are attractive nanosystems for researchers interested in bioimaging and therapy. The size, shape and surface of AuNPs can be modified for improving targeting and accumulation in cancer cells, for example through introduction of ligands and surface charge. The interactions of AuNPs with electromagnetic radiation (e.g., visible-near-infrared, X-rays) can be used for photothermal therapy and radiation therapy, through heat generated from light absorption and emission of Auger electrons, respectively. The subsequent expansion and high X-ray attenuation from AuNPs can be used for enhancing contrast for tumor detection (e.g., using photoacoustic, computed tomography imaging). Multi-functionality can be further extended through covalent/non-covalent functionalization, for loading additional imaging/therapeutic molecules for combination therapy and multimodal imaging. In order to cover the important aspects for designing and using AuNPs for cancer theranostics, this review focuses on the synthesis, functionalization and characterization methods that are important for AuNPs, and presents their unique properties and different applications in cancer theranostics.

癌症的诊断和治疗往往具有挑战性,需要更具吸引力的选择。某些类型的癌症比其他类型的癌症更具侵袭性,许多癌症的症状并不明显,尤其是在早期阶段。纳米技术为癌症检测、治疗和监测提供了高灵敏度、高特异性和多模式能力。尤其是金属纳米粒子(NPs),如金纳米粒子(AuNPs),对于对生物成像和治疗感兴趣的研究人员来说是一种极具吸引力的纳米系统。AuNPs 的大小、形状和表面可以通过引入配体和表面电荷等方式进行修饰,以提高在癌细胞中的靶向性和蓄积性。AuNPs 与电磁辐射(如可见光-近红外和 X 射线)的相互作用可分别通过光吸收和奥杰电子发射产生的热量用于光热疗法和放射治疗。AuNPs 随后产生的膨胀和高 X 射线衰减可用于增强肿瘤检测的对比度(例如,利用光声学和计算机断层扫描成像)。还可通过共价/非共价功能化进一步扩展其多功能性,装载额外的成像/治疗分子,用于联合治疗和多模式成像。为了涵盖设计和使用 AuNPs 进行癌症治疗的重要方面,本综述重点介绍对 AuNPs 十分重要的合成、功能化和表征方法,并介绍 AuNPs 的独特性质及其在癌症治疗中的不同应用。
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引用次数: 0
Novel sulfamethoxazole and 1-(2-fluorophenyl) piperazine derivatives as potential apoptotic and antiproliferative agents by inhibition of BCL2; design, synthesis, biological evaluation, and docking studies. 新型磺胺甲噁唑和 1-(2-氟苯基)哌嗪衍生物通过抑制 BCL2 而成为潜在的凋亡和抗增生药物;设计、合成、生物学评价和对接研究。
IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 Epub Date: 2024-10-15 DOI: 10.1007/s13205-024-04111-6
Nagalakshmamma Vadabingi, Venkataswamy Mallepogu, Rani E Mallapu, Chiranjeevi Pasala, Sumithra Poreddy, Poojitha Bellala, Umamaheswari Amineni, Suresh Reddy Cirandur, Balaji Meriga

In the present study, a novel series of sulfamethoxazole and 1-(2-fluorophenyl) piperazine derivatives were designed, synthesized and characterized by FTIR, IH NMR,13C NMR, Mass spectrometry, CHN data, and evaluated for their efficiency as BCL2 inhibitors that could lead to potential antiproliferative activity. The ten newly synthesized compounds were screened for their therapeutic activity using MDA-MB-231 breast cancer cell lines. All the test compounds exhibited moderate to high cytotoxic activity in MTT assay. Among them, compounds 3e and 6b exhibited promising antitumor activity, as evidenced by their IC50 values of 16.98 and 17.33 μM respectively. In addition, both compounds 3e and 6b displayed potential antioxidant and apoptosis induction properties. The qRT-PCR analysis showed down regulation of BCL2 expression and up regulation of Casp3 expression in 3e and 6b treated MDA-MB-231 cells. Further, the interaction between critical amino acids of the active domains of BCL2 and 3e and 6b was evaluated by MD simulation, and the results reflected the potent inhibitory activities of 3e and 6b. In summary, the novel compounds 3e and 6b demonstrate their potent anti-cancer properties by inducing apoptosis and selectively targeting BCL2 and caspases-3.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04111-6.

本研究设计、合成了一系列新型磺胺甲噁唑和 1-(2-氟苯基)哌嗪衍生物,并通过傅立叶变换红外光谱(FTIR)、IH NMR、13C NMR、质谱分析和 CHN 数据对其进行了表征,评估了它们作为 BCL2 抑制剂的效率,这可能会导致潜在的抗增殖活性。利用 MDA-MB-231 乳腺癌细胞系对这十种新合成的化合物进行了治疗活性筛选。在 MTT 试验中,所有受试化合物都表现出中等到较高的细胞毒性活性。其中,化合物 3e 和 6b 的 IC50 值分别为 16.98 和 17.33 μM,显示出良好的抗肿瘤活性。此外,化合物 3e 和 6b 还具有潜在的抗氧化和诱导细胞凋亡的特性。qRT-PCR 分析表明,在 3e 和 6b 处理的 MDA-MB-231 细胞中,BCL2 表达下调,Casp3 表达上调。此外,通过 MD 模拟评估了 BCL2 活性域的关键氨基酸与 3e 和 6b 之间的相互作用,结果显示 3e 和 6b 具有很强的抑制活性。总之,新型化合物 3e 和 6b 通过诱导细胞凋亡和选择性靶向 BCL2 和 caspases-3 显示了其强大的抗癌特性:在线版本包含补充材料,可查阅 10.1007/s13205-024-04111-6。
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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
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
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
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。
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引用次数: 0
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3 Biotech
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