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FBES/OEB/SenPEP weather station

We have a weather station at our experimental field that I look after. It started collecting data in 2015 and in 2020 it had a large upgrade. There is a full description of the equipment and measurements at https://viikki-stn.r4photobiology.info/.

Photograph of the station
The weather station in November 2020

Differently to standard meteorological stations data are logged for most variables at 1 min intervals, as means of 12 measurements taken at 5 s intervals. Hourly and daily summaries are also stored.

Currently the station logs more than 40 variables, a few of them from multiple sensors. Special emphasis is on solar radiation, with measurements of photon irradiance for UV-B, UV-A, blue, red and far-red, and global energy irradiance. Differently to measurements of  erythemal, i.e., biologically effective UV radiation more commonly available, UV-A and UV-B irradiances are measured separately and without applying a spectral weighting function.

With the most recent upgrade we started measurements of the profile of soil temperature, water content and electrical conductivity. Surface temperature is measured on vegetation and/or bare soil with non-contact (infrared) sensors.

The usual air temperature, water vapour pressure, atmospheric pressure, wind speed, wind direction and rainfall are also recorded. The data are available on request. The radiation data for the winter period are less reliable than for the growth season, and there are also some gaps in past winters for all variables.

 

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Cryptochromes and stomatal opening

Our recent paper, included in Fang Wang’s thesis:

Fang Wang, T Matthew Robson, Jorge J Casal, Alexey Shapiguzov, Pedro J Aphalo (2020) Contributions of cryptochromes and phototropins to stomatal opening through the day. Functional Plant Biology, 47, 226-238. DOI: https://doi.org/10.1071/FP19053.

The role of phototropins in stomatal opening in response to blue light in well documented in the literature. Reports of a role for cryptochromes in this response have been few, and to some extent contradictory. Most studies on the daily patterns of stomatal opening date from the time when well described photoreceptor mutants were not yet available, so using these mutants was expected to reveal new features of stomatal responses.

Continue reading “Cryptochromes and stomatal opening”

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NEW BOOK: Learn R: As a Language

My book Learn R: As a Language was published some weeks ago by Chapman & Hall / CRC in the “The R Series”.

ISBN 9780367182533

As I a side note, I have typeset the whole book using R and LaTeX using the same approach as for reproducible data analyses. All code examples are run and their textual and graphical outputs generated each time the camera ready PDF is built. This ensures that all code is functional and that all output is up-to-date at the time the PDF is generated. In the spirit of openness and reproducibility, the source files used for generating the book PDF are available through the public Git repository at https://bitbucket.org/aphalo/learnr-book-crc/.

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R for photobiology packages

I have published through CRAN a suite of R packages for calculation and plotting tasks commonly needed in photobiology. Additional information and on-line documentation are available at The R for Photobiology Website.

This is open source, free to use and modify software that aims to make it easier for all photobiologists to do calculations correctly and play with example data. In addition, the example data facilitates the production of original illustrations for use in teaching and text books.

Continue reading “R for photobiology packages”

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UVR8 is an UV-B and UV-A photoreceptor

Our two recent papers:

Neha Rai, Susanne Neugart, Yan Yan, Fang Wang, Sari M Siipola, Anders V Lindfors, Jana Barbro Winkler, Andreas Albert, Mikael Brosché, Tarja Lehto, Luis O Morales, Pedro J Aphalo (2019) How do cryptochromes and UVR8 interact in natural and simulated sunlight? Journal of Experimental Botany, 70, 4975–4990. https://doi.org/10.1093/jxb/erz236

Neha Rai, Andrew O’Hara, Daniel Farkas, Omid Safronov, Khuanpiroon Ratanasopa, Fang Wang, Anders V. Lindfors, Gareth I. Jenkins, Tarja Lehto, Jarkko Salojärvi, Mikael Brosché, Åke Strid, Pedro J. Aphalo, Luis O. Morales (2020) The photoreceptor UVR8 mediates the perception of both UV‐B and UV‐A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes. Plant, Cell & Environment, https://doi.org/10.1111/pce.13752

In these two recent publications we have shown that UVR8, previously described as an ultravioltet-B (UV-B, 280-315 nm) photoreceptor, in sunlight functions both as an ultraviolet-A (UV-A, 315-400 nm) and UV-B photoreceptor. Although UVR8 presents maximal absorption at the boundary between ultraviolet-C (UV-C, <280 nm) and UV-B, the shape of the solar spectrum in the ultraviolet region, characterized by a very steep slope, allows the UVR8 protein to absorb nearly as many UV-A photons as UV-B photons, and obviously no photons in the UV-C as they are not present in sunlight at ground level.

Normalized spectral absoorbance of UVR8 protein in vitro (From Rai et al.. 2020).

Continue reading “UVR8 is an UV-B and UV-A photoreceptor”

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Measuring campaign in the Alps

I joined a field measuring campaign organized by my collaborator T. Matthew Robson (see Matt’s CanSEE website for information on the research project) with the participation of José Ignacio García Plazaola and Beatriz Fernandez-Marin from the University of the Basque-Country.

Matthew described the aim of our work as:

By characterising the patterns of response to UV radiation in terms of the photoprotection and UV-screening of plants across a diversity of species, we hope to better understand how and why these response evolved and what environmental cues underpin their induction.

We spent the last weeks of May the at 2100 m a.s.l. in the Alps at the Jardin Botanique du Lautaret measuring solar radiation and the responses of plants to it. I did some measurements of solar radiation but spent most of the time photographing plants and lichens to record their optical properties in the ultraviolet-A, visible and near-infrared regions of the spectrum.

Villar-d’Arêne, French Alps, 2100 m a.s.l.

Several of the photographs I took of site, crew, plants and lichens available at my photography website in a post published earlier today (as I have the server set up for easy creation of galleries). These photographs are stored at Flickr.

Matthew has also written a post about the trip and project in his blog.

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Perspectives on plant UV-research and its applications

An article, titled “A perspective on ecologically relevant plant-UV research and its practical application”, to be included in the PPS special issue, has been published on-line. It originated on discussions at the second UV4Plants Network meeting held in Bled last year, but writing and editing continued for several months. The article has been published under open access and is available through PPS’ web site. Several members of our research group and some of our collaborators are co-authors.

The graphical and text abstracts are reproduced below.

Graphical abstract from the article. Copyrighted (c) 2019.

Abstract

Plants perceive ultraviolet-B (UV-B) radiation through the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8), and initiate regulatory responses via associated signalling networks, gene expression and metabolic pathways. Various regulatory adaptations to UV-B radiation enable plants to harvest information about fluctuations in UV-B irradiance and spectral composition in natural environments, and to defend themselves against UV-B exposure. Given that UVR8 is present across plant organs and tissues, knowledge of the systemic signalling involved in its activation and function throughout the plant is important for understanding the context of specific responses. Fine-scale understanding of both UV-B irradiance and perception within tissues and cells requires improved application of knowledge about UV-attenuation in leaves and canopies, warranting greater consideration when designing experiments. In this context, reciprocal crosstalk among photoreceptor-induced pathways also needs to be considered, as this appears to produce particularly complex patterns of physiological and morphological response. Through crosstalk, plant responses to UV-B radiation go beyond simply UV-protection or amelioration of damage, but may give cross-protection over a suite of environmental stressors. Overall, there is emerging knowledge showing how information captured by UVR8 is used to regulate molecular and physiological processes, although understanding of upscaling to higher levels of organisation, i.e. organisms, canopies and communities remains poor. Achieving this will require further studies using model plant species beyond Arabidopsis, and that represent a broad range of functional types. More attention should also be given to plants in natural environments in all their complexity, as such studies are needed to acquire an improved understanding of the impact of climate change in the context of plant-UV responses. Furthermore, broadening the scope of experiments into the regulation of plant-UV responses will facilitate the application of UV radiation in commercial plant production. By considering the progress made in plant-UV research, this perspective highlights prescient topics in plant-UV photobiology where future research efforts can profitably be focussed. This perspective also emphasises burgeoning interdisciplinary links that will assist in understanding of UV-B effects across organisational scales and gaps in knowledge that need to be filled so as to achieve an integrated vision of plant responses to UV-radiation.

 

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Faba bean accessions from Sweden and Ecuador

Faba bean’s wild ancestors grew in the Mediterranean region. Domestication took place about 10000 BC, most likely in what is currently Northern Israel. The wild ancestor grew in this region. Consequently, faba bean is one of the oldest or “founder” crops cultivated from the very start of agriculture. Nowadays it is an important source of protein and widely grown in cool and temperate regions. From the Mediterranean region it spread to other regions including the Americas and Northern Europe.

Faba beans have been under cultivation at high elevation in equatorial South America since the times of the Spanish conquest, i.e. for a few hundred years. Faba bean spread to the North much earlier, as their is evidence for its cultivation in Sweden already during the Stone Age.

In these two regions environmental conditions during the growing season are very different with respect to exposure to ultraviolet radiation, while temperatures are similar as the effects  of latitude and elevation are opposite. Comparing accessions from these two regions should shed light on adaptive traits conferring tolerance to UV exposure. Our first publication from this line of research has been published on-line in the journal Photochemical and Photobiological Sciences and will be part of a special issue, as well as included in Yan Yan’s thesis.

The most obvious difference is in the flavonoid composition, in particular the level of glycosilation of Kamferols.

The article Responses of flavonoid profile and associated gene expression to solar blue and UV radiation in two accessions of Vicia faba L. from contrasting UV environments describes the differences between a selection from the Swedish cultivar Aurora and a selection from an Ecuatorian land race. The article has been published under open access. We reproduce here the abstract an one figure.

Fig. 4 Kaempferol profiles of accessions Aurora and ILB938 of V. faba grown in sunlight under four filters. Top, molar concentrations (μmol g−1) of individual kaempferol glycosides per unit leaf dry mass. Values are means ± SE of four replicate blocks, 163 sampled plants in total. Bottom, principal component analysis (PCA) of the kaempferol glycoside profile. The ellipses show 0.95 confidence regions assuming bivariate t distribution. The first two principal components together explain 70% of the variance. All kaempferol compounds are shown with their labels.

Abstract

Blue light and UV radiation shape a plant’s morphology and development, but accession-dependent responses under natural conditions are unclear. Here we tested the hypothesis that two faba bean (Vicia faba L.) accessions adapted to different latitudes and altitudes vary in their responses to solar blue and UV light. We measured growth, physiological traits, phenolic profiles and expression of associated genes in a factorial experiment combining two accessions (Aurora, a Swedish cultivar adapted to high latitude and low altitude; ILB938, from the Andean region of Colombia and Ecuador, adapted to low latitude and high altitude) and four filter treatments created with plastic sheets: 1. transparent as control; 2. attenuated short UV (290–350 nm); 3. attenuated UV (290–400 nm); 4. attenuated blue and UV light. In both accessions, the exclusion of blue and UV light increased plant height and leaf area, and decreased transcript abundance of ELONGATED HYPOCOTYL 5 (HY5) and TYROSINE AMINOTRANSFERASE 3 (TAT3). Blue light and short UV induced the accumulation of epidermal and whole-leaf flavonoids, mainly quercetins, and the responses in the two accessions were through different glycosides. Filter treatments did not affect kaempferol concentration, but there were more tri-glycosides in Aurora and di-glycosides in ILB938. Furthermore, fewer quercetin glycosides were identified in ILB938. The transcript abundance was consistently higher in Aurora than in ILB938 for all seven investigated genes: HY5, TAT3, CHALCONE SYNTHASE (CHS), CHALCONE ISOMERASE (CHI), DON-GLUCOSYLTRANSFERASE 1 (DOGT1), ABA INSENSITIVE 2 (ABI2), AUXIN-INDUCIBLE 2–27 (IAA5). The two largest differences in transcript abundance between the two accessions across treatments were 132-fold in CHS and 30-fold in DOGT1 which may explain the accession-dependent glycosylation patterns. Our findings suggest that agronomic selection for adaptation to high altitude may favour phenotypes with particular adaptations to the light environment, including solar UV and blue light.

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Visible and UV-A radiation in greenhouses

Different cladding materials transmit different amounts of ultraviolet radiation, and we cannot see this with our eyes. The following UVA photographs give an idea of how different parts of the same greenhouse may differ without we being able to see it.

Roof of a greenhouse seen in visible light.
Roof of a greenhouse seen in UVA radiation.

Light distribution in greenhouses is not spatially even, neither irradiance (“intensity”) nor spectrum (colour) are uniform in space. Ventilation openings, supporting structures, differences in cladding materials and shade screens affect both. To some extent these patches move as the position of the sun moves, but not necessarily enough to even-out light conditions over the whole area of a greenhouse compartment. Other factors affecting the amount of radiation transmitted are the cleanliness of the cladding surface, and the angle between incoming direct solar radiation and the surface of the cladding. An example of how closed and open roof vents affect illumination.  Two visible light photographs taken only a few minutes apart under fully clear sky conditions around 2 pm solar time.

Visible light closed vents and open shade screen.
Visible, open vents and closed shade screen.

Paired photographs in UV-A radiation.

UVA radiation, closed vents and open shade screen.
UVA radiation, open vents and closed shade screen.

This highlights why design of experiments, and correct randomisation in space and time are crucial when using greenhouses in research or at early stages of crop breeding.