Integrating Molecular Biology and Bioinformatics Education

10.20944/preprints201811.0183.v1 ◽

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.

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Integrating Molecular Biology and Bioinformatics Education

Journal of Integrative Bioinformatics ◽

10.1515/jib-2019-0005 ◽

2019 ◽

Vol 16 (3) ◽

Cited By ~ 4

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

AbstractCombined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand of scientists with a combined background in both fields, the education of dry and wet lab subjects are often still separated. This work describes an example of integrated education with a focus on genomics and transcriptomics. Participants learned computational and molecular biology methods in the same practical course. Peer-review was applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. The positive evaluation results indicate that this approach was accepted by the participants and would likely be suitable for wider scale application.

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Faculty Opinions recommendation of Finding disease genes: a fast and flexible approach for analyzing high-throughput data.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13277014.14635129 ◽

2011 ◽

Author(s):

Alejandro Schaffer

Keyword(s):

High Throughput ◽

Disease Genes ◽

Flexible Approach ◽

High Throughput Data

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Robust and Efficient Parametric Spectral Density Estimation for High-Throughput Data

Technometrics ◽

10.1080/00401706.2021.1884134 ◽

2021 ◽

pp. 1-22

Author(s):

Martin Lysy ◽

Feiyu Zhu ◽

Bryan Yates ◽

Aleksander Labuda

Keyword(s):

Spectral Density ◽

Density Estimation ◽

High Throughput ◽

Spectral Density Estimation ◽

High Throughput Data

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

Fungal Biology and Biotechnology ◽

10.1186/s40694-021-00109-4 ◽

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.

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Science Teachers’ Perceptions and Self-Efficacy Beliefs Related to Integrated Science Education

Education Sciences ◽

10.3390/educsci11060272 ◽

2021 ◽

Vol 11 (6) ◽

pp. 272

Author(s):

Outi Haatainen ◽

Jaakko Turkka ◽

Maija Aksela

Keyword(s):

Science Education ◽

Science Teachers ◽

Self Efficacy ◽

Online Survey ◽

Teaching Method ◽

Survey Study ◽

Integrated Education ◽

Integrated Science ◽

Teachers Perceptions ◽

Key Factor

To understand how integrated science education (ISE) can be transferred into successful classroom practices, it is important to understand teachers’ perceptions and self-efficacy. The focus of this study is twofold: (1) to understand how teachers perceive ISE and (2) to assess if science teachers’ perceptions of and experiences with integrated education correlate with their views on self-efficacy in relation to ISE. Ninety-five Finnish science teachers participated in an online survey study. A mixed method approach via exploratory factor analysis and data-driven content analysis was used. Self-efficacy emerged as a key factor explaining teachers’ perceptions of and their lack of confidence in implementing ISE as well as their need for support. In addition, teachers regarded ISE as a relevant teaching method, but challenging to implement, and teachers primarily applied integrated approaches irregularly and seldom. Furthermore, teachers’ experiences with integrated activities and collaboration correlated with their views on integrated education and self-efficacy. These findings indicate teachers need support to better understand and implement ISE.

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