A microscopy-based image analysis pipeline for the quantification of germination of filamentous fungi

IF 2.4 3区生物学 Q3 GENETICS & HEREDITY

Fungal Genetics and Biology Pub Date : 2025-02-01 DOI:10.1016/j.fgb.2024.103942

Sébastien C. Ortiz, Thomas Easter, Clara Valero, Michael J. Bromley, Margherita Bertuzzi

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引用次数: 0

Abstract

Germination is the fundamental process whereby fungi transition from the dormant and stress resistant spores into actively replicating cells such as hyphae. Germination is essential for fungal colonization of new environments and pathogenesis, yet this differentiation process remains relatively poorly understood. For filamentous fungi, the study of germination has been limited by the lack of high-throughput, temporal, low cost, and easy-to-use methods of quantifying germination. To this end we have developed an image analysis pipeline to automate the quantification of germination from microscopy images. We have optimized this tool for the fungal pathogen Aspergillus fumigatus and demonstrated its potential applications by evaluating different strains, germination inhibitors, and auxotrophic and antifungal resistant mutants. Finally, we have expanded this tool to a variety of filamentous fungi and developed an easy-to-use web app for the fungal research community.

Abstract Image

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基于显微镜的丝状真菌萌发定量图像分析管道。

萌发是真菌从休眠和抗胁迫孢子转变为积极复制细胞（如菌丝）的基本过程。萌发对真菌在新环境中的定植和发病机制至关重要，但这种分化过程仍然相对知之甚少。对于丝状真菌，由于缺乏高通量、时间、低成本和易于使用的发芽定量方法，对其萌发的研究一直受到限制。为此，我们开发了一个图像分析流水线，以自动定量从显微镜图像发芽。我们优化了该工具用于真菌病原体烟曲霉，并通过评估不同菌株，发芽抑制剂，营养不良和抗真菌抗性突变体来证明其潜在的应用。最后，我们将这个工具扩展到各种丝状真菌，并为真菌研究社区开发了一个易于使用的web应用程序。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Fungal Genetics and Biology 生物-遗传学

CiteScore

6.20

自引率

3.30%

发文量

审稿时长

85 days

期刊介绍： Fungal Genetics and Biology, formerly known as Experimental Mycology, publishes experimental investigations of fungi and their traditional allies that relate structure and function to growth, reproduction, morphogenesis, and differentiation. This journal especially welcomes studies of gene organization and expression and of developmental processes at the cellular, subcellular, and molecular levels. The journal also includes suitable experimental inquiries into fungal cytology, biochemistry, physiology, genetics, and phylogeny. Fungal Genetics and Biology publishes basic research conducted by mycologists, cell biologists, biochemists, geneticists, and molecular biologists. Research Areas include: • Biochemistry • Cytology • Developmental biology • Evolutionary biology • Genetics • Molecular biology • Phylogeny • Physiology.