2025 > Detecting rhizosphere pH dynamics

Kanwar, P., Altmeisch, S., & Bauer, P. (2025). Quantitative tools for analyzing rhizosphere pH dynamics: localized and integrated approaches. Biology Methods and Protocols, 10(1), bpaf026.

https://doi.org/10.1093/biomethods/bpaf026

The study introduces two complementary electrode-based methods—localized and integrated rhizosphere pH measurement—to capture spatially precise and system-wide pH changes around plant roots. These techniques enhance accuracy and scalability, enabling detailed analysis of how genetic and environmental factors influence rhizosphere pH and nutrient availability.

2025 > Machine-aided phenotyping in alkaline calcareous soil

Knopf, M., & Bauer, P. (2025). An affordable non-invasive validated machine-aided phenotyping pipeline identifies phenotypic variation of stress resilience in alkaline calcareous soil across the life cycle in Arabidopsis thaliana.

https://www.biorxiv.org/content/10.1101/2025.03.02.641020v1

This study describes how accurate machine-aided phenotyping can be employed to characterize growth responses of Arabidopsis thaliana lines in artificially created alkaline and calcareous soil conditions. The approach allows fast and non-destructive comparison of different plant lines in challenging conditions.

Applied in:

• Mohr, I., Eutebach, M., Knopf, M. C., Schommen, N., Gratz, R., Angrand, K., ... & Ivanov, R. (2024). The small ARF-like 2 GTPase TITAN5 is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER (Journal of Cell Science, V.137(23).

2025 > PlugNSeq: An Easy, Rapid, and Streamlined mRNA-Seq Data Analysis Pipeline Empowering Insightful Exploration with Well-Annotated Organisms, Requiring Minimal Bioinformatic Expertise

PlugNSeq is a streamlined mRNA-Seq data analysis pipeline. It requires only basic knowledge in working with a PC. The protocol is compatible with Linux, Mac OS, and Windows. It includes automated preprocessing of the reads as well as transcript quantification, and statistical analyses, producing all the important key tables and figures. These results form an excellent starting point for further exploration. The protocol is easy to execute and yet, important parameters can be adapted. Therefore, this pipeline enables efficient but still flexible RNA-seq analysis with minimal bioinformatics expertise.

Mai H.J. (2025) https://dx.doi.org/10.17504/protocols.io.4r3l2qjo3l1y/v1

2024 > Microscopic characterization of light-controlled nuclear condensates

This study shows how fluorescence microscopy-based techniques can be used to determine quantitative and qualitative characteristics of condensates, e.g. size, mobility and form of condensates, as well as transcription factor complexes forming inside condensates, and furthermore colocalization with plant nuclear body markers.

Trofimov K, Gratz R, Ivanov R, Stahl Y, Bauer P, Brumbarova T. FER-like iron deficiency-induced transcription factor (FIT) accumulates in nuclear condensates. J Cell Biol. 2024 Apr 1;223(4): doi: 10.1083/jcb.202311048. 

2023 > High-Throughput Plant Gene Expression Analysis by 384-Format Reverse Transcription-Quantitative PCR for Investigating Plant Iron Homeostasis

This protocol provides a detailed guide for accurate high-throughput plant gene expression analysis using a 384-well plate format. It demonstrates how gene expression analysis of different types of iron deficiency marker genes is used to investigate regulatory hierarchies.

Ngigi, M.N., Bauer, P. (2023). High-Throughput Plant Gene Expression Analysis by 384-Format Reverse Transcription-Quantitative PCR for Investigating Plant Iron Homeostasis. In: Jeong, J. (eds) Plant Iron Homeostasis. Methods in Molecular Biology, vol 2665.

https://doi.org/10.1007/978-1-0716-3183-6_1

Applied in:

• Mohr, I., Eutebach, M., Knopf, M. C., Schommen, N., Gratz, R., Angrand, K., … & Ivanov, R. (2024). The small ARF-like 2 GTPase TITAN5 is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER 1. Journal of Cell Science, 137(23).

• Ngigi M, Khan M, Remus R, Gupta S.K, Bauer P. Age-dependent differential iron deficiency responses of rosette leaves during reproductive stages in Arabidopsis thaliana. bioRxiv. Accepted in Journal of Experimental Botany.

• Lichtblau DM, Baby D, Khan M, Trofimov K, Ari Y, Schwarz B, et al. (2024) The small iron-deficiency-induced protein OLIVIA and its relation to the bHLH transcription factor POPEYE. PLoS ONE 19, (14).

2023 > Black sheep, dark horses, and colorful dogs: a review on the current state of the Gene Ontology with respect to iron homeostasis in Arabidopsis thaliana

In this review, we present plant physiology-relevant gene sets for gene set enrichment analysis (GSEA) related to iron homeostasis. As the current Gene Ontology lacks comprehensive coverage of this topic, we recommend using these curated lists instead (check out particularly Suppl. Table 23). An accompanying R script facilitates GSEA with these gene sets.

Mai, H. J., Baby, D., & Bauer, P. (2023). Black sheep, dark horses, and colorful dogs: a review on the current state of the Gene Ontology with respect to iron homeostasis in Arabidopsis thaliana. Frontiers in Plant Science, 14, 1204723.

2016 > Analyzing iron deficiency response gene regulation in Arabidopsis thaliana (96 format)

Abdallah H.B., Bauer P. (2016); Quantitative Reverse Transcription-qPCR-Based Gene Expression Analysis in Plants. Methods Mol. Biol. 1363: 9-24

2016 > Detecting ROS stress responses in plants 

Brumbarova T., Le C.T., Bauer P. (2016) Hydrogen Peroxide Measurement in Arabidopsis Root Tissue Using Amplex Red. BioProtocols 6(21) DOI: doi.org/10.21769/BioProtoc.1999

2014 > Detecting iron accumulation in plants 

Brumbarova T., Ivanov R. (2014); Perls Staining for Histochemical Detection of Iron in Plant Samples. BioProtocols 4(18) DOI: https://doi.org/10.21769/BioProtoc.1245

2009 > Basics for analyzing iron deficiency response gene regulation in Arabidopsis thaliana (96 format)

Klatte M. and Bauer P. (2009); Accurate real-time reverse transcription quantitative PCR. Methods Mol. Biol. 479: 61-77