scholarly journals A fully automated pipeline for the dynamic at‐line morphology analysis of microscale Aspergillus cultivation

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Roman Jansen ◽  
Kira Küsters ◽  
Holger Morschett ◽  
Wolfgang Wiechert ◽  
Marco Oldiges
Keyword(s):  
Filamentous Fungi ◽  
High Throughput ◽  
Automated Image Analysis ◽  
Height Velocity ◽  
Pellet Size ◽  
Application Study ◽  
Liquid Handling ◽  
Morphology Analysis ◽  
Development And Utilization ◽  
Increasing Demand

Abstract Background Morphology, being one of the key factors influencing productivity of filamentous fungi, is of great interest during bioprocess development. With increasing demand of high-throughput phenotyping technologies for fungi due to the emergence of novel time-efficient genetic engineering technologies, workflows for automated liquid handling combined with high-throughput morphology analysis have to be developed. Results In this study, a protocol allowing for 48 parallel microbioreactor cultivations of Aspergillus carbonarius with non-invasive online signals of backscatter and dissolved oxygen was established. To handle the increased cultivation throughput, the utilized microbioreactor is integrated into a liquid handling platform. During cultivation of filamentous fungi, cell suspensions result in either viscous broths or form pellets with varying size throughout the process. Therefore, tailor-made liquid handling parameters such as aspiration/dispense height, velocity and mixing steps were optimized and validated. Development and utilization of a novel injection station enabled a workflow, where biomass samples are automatically transferred into a flow through chamber fixed under a light microscope. In combination with an automated image analysis concept, this enabled an automated morphology analysis pipeline. The workflow was tested in a first application study, where the projected biomass area was determined at two different cultivation temperatures and compared to the microbioreactor online signals. Conclusions A novel and robust workflow starting from microbioreactor cultivation, automated sample harvest and processing via liquid handling robots up to automated morphology analysis was developed. This protocol enables the determination of projected biomass areas for filamentous fungi in an automated and high-throughput manner. This measurement of morphology can be applied to describe overall pellet size distribution and heterogeneity.

Rectal organoid morphology analysis (ROMA) as a promising diagnostic tool in cystic fibrosis

Thorax ◽  
2021 ◽  
pp. thoraxjnl-2020-216368
Author(s):  
Senne Cuyx ◽  
Anabela Santo Ramalho ◽  
Nikky Corthout ◽  
Steffen Fieuws ◽  
Eva Fürstová ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Image Analysis ◽  
Diagnostic Tool ◽  
Automated Image Analysis ◽  
Sweat Chloride ◽  
Morphology Analysis ◽  
Morphological Differences ◽  
Two Parameters ◽  
Analysis Protocol

Diagnosing cystic fibrosis (CF) when sweat chloride is not in the CF range and less than 2 disease-causing CFTR mutations are found requires physiological CFTR assays, which are not always feasible or available. We developed a new physiological CFTR assay based on the morphological differences between rectal organoids from subjects with and without CF. In organoids from 167 subjects with and 22 without CF, two parameters derived from a semi-automated image analysis protocol (rectal organoid morphology analysis, ROMA) fully discriminated CF subjects with two disease-causing mutations from non-CF subjects (p<0.001). ROMA, feasible at all ages, can be centralised to improve standardisation.

scholarly journals Integrating Molecular Biology and Bioinformatics Education

2018 ◽  
Author(s):  
Boas Pucker ◽  
Hanna Marie Schilbert ◽  
Sina Franziska Schumacher
Keyword(s):  
Molecular Biology ◽  
Cooperative Learning ◽  
Peer Review ◽  
High Throughput ◽  
Teaching Method ◽  
Integrated Education ◽  
High Throughput Data ◽  
Wet Lab ◽  
Bioinformatics Education ◽  
Increasing Demand

Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand for scientists with a combined background in both fields, the education in dry lab and wet lab is often separated. This work describes an example of integrated education with focus on genomics and transcriptomics. Participants learn computational and molecular biology methods in the same practical course. Peer-review is applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. Evaluation results indicate acceptance and appreciation of this approach.

scholarly journals Integrating Molecular Biology and Bioinformatics Education

2018 ◽  
Author(s):  
Boas Pucker ◽  
Hanna Marie Schilbert ◽  
Sina Franziska Schumacher
Keyword(s):  
Molecular Biology ◽  
Cooperative Learning ◽  
Peer Review ◽  
High Throughput ◽  
Teaching Method ◽  
Integrated Education ◽  
High Throughput Data ◽  
Wet Lab ◽  
Bioinformatics Education ◽  
Increasing Demand

Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand for scientists with a combined background in both fields, the education in dry lab and wet lab is often separated. This work describes an example of integrated education with focus on genomics and transcriptomics. Participants learn computational and molecular biology methods in the same practical course. Peer-review is applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. Evaluation results indicate acceptance and appreciation of this approach.

scholarly journals Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch in European winter wheat

2018 ◽  
Author(s):  
Steven Yates ◽  
Alexey Mikaberidze ◽  
Simon Krattinger ◽  
Michael Abrouk ◽  
Andreas Hund ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Winter Wheat ◽  
High Throughput ◽  
Quantitative Resistance ◽  
Small Chromosome ◽  
Snp Markers ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Limiting Factor

Accurate, high-throughput phenotyping for quantitative traits is the limiting factor for progress in plant breeding. We developed automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform a GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four resistance traits. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.

scholarly journals High-throughput microfluidic micropipette aspiration device to probe time-scale dependent nuclear mechanics in intact cells

Lab on a Chip ◽  
2019 ◽  
Vol 19 (21) ◽  
pp. 3652-3663 ◽  
Author(s):  
Patricia M. Davidson ◽  
Gregory R. Fedorchak ◽  
Solenne Mondésert-Deveraux ◽  
Emily S. Bell ◽  
Philipp Isermann ◽  
...  
Keyword(s):  
Image Analysis ◽  
High Throughput ◽  
Time Scale ◽  
Viscoelastic Properties ◽  
Micropipette Aspiration ◽  
Automated Image Analysis ◽  
Cell Nuclei ◽  
Intact Cells ◽  
Nuclear Mechanics ◽  
Analysis Platform

We report the development, validation, and application of an easy-to-use microfluidic micropipette aspiration device and automated image analysis platform that enables high-throughput measurements of the viscoelastic properties of cell nuclei.

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