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.
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).
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.
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.
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.
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.
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.
A currently ongoing surprising event affecting what I considered one of my least important articles (https://doi.org/10.19232/uv4pb.2016.1.92), has made me rethink how search engines and the internet affect the impact of publications.
Among web site developers “SEO” is considered a very important factor in being successful in “drawing traffic or page reads” to a site. SEO means search-engine optimisation. For web pages, it involves much more than subjectively choosing suitable words for titles. In a way it is like reverse engineering how research engines like Google work, so as to write web pages in a way such that they will appear near the top of searches as frequently as possible. There exist different types of tools and software to help in the task of achieving good “SEO” and even companies that offer for a payment SEO for websites. My thoughts are: do we need similar tools for SEO of research papers? Needed or not, a more important question is how much do the properties of the algorithms used by search engines affect the impact of the articles we write? I do not know the answers, but I think these are important questions.
What is the incident? To me it looks like a snowball effect, helped by accidental good SEO. I wrote a short review of a book in the UV4Plants Bulletin (http://bulletin.uv4plants.org) and as it is allowed, made it available through ResearchGate. It is being read and being followed and recommended… but much more than what would seem to me to be reasonable, to the point that it has already been on two weeks according to ResearchGate the most read article from a Finnish author! and more than once the most read forestry article worldwide (although neither the Bulletin, nor the reviewed book, have anything to do with forestry).
University of Helsinki
