Rich-Griffin, C. | bioRxiv Science

bioRxiv2022

Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data

With continually improved instrumentation, Fourier transform infrared (FTIR) microspectroscopy can now be used to capture thousands of high-resolution spectra for chemical characterisation of a sample. The spatially resolved nature of this method lends itself well to histological characterisation of complex biological specimens. However, commercial software currently available can make joint analysis of multiple samples challenging and, for large datasets, computationally infeasible. In order to overcome these limitations, we have developed Photizo - an open-source Python library for spectral analysis which includes functions for pre-processing, visualisation and downstream analysis, including principal component analysis, clustering, macromolecular quantification and biochemical mapping. This library can be used for analysis of spectroscopy data without a spatial component, as well as spatially-resolved data, such as data obtained via infrared (IR) microspectroscopy in scanning mode and IR imaging by focal plane array (FPA) detector. Contactcdendrou@well.ox.ac.uk

bioinformatics↗

bioRxiv2021

The plant circadian clock gene LHY influences Medicago truncatula nodulation

Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which are factories of metabolic activity. We discovered that the circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY) affects nodulation in Medicago truncatula. By carrying out expression analysis of transcripts over time in nodules we found that the clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. Rhythmic transcripts in root nodules include a subset of Nodule-specific Cysteine Rich peptides (NCRs) that have the LHY-bound conserved Evening Element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis. HighlightsO_LIThe circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY) impacts on successful Medicago truncatula-rhizobial symbiosis C_LIO_LIThe plant clock coordinates rhythmic patterns of metabolic and regulatory activity in nodules and drives rhythmic expression of a subset of Nodule-specific Cysteine Rich (NCR) genes. C_LIO_LIRhythmic expression of NCRs may be important for temporal coordination of bacterial activity with plant host rhythms to ensure optimal symbiosis. C_LI

plant biology↗