Solar UV radiation and microbial life in the atmosphere.

Many microorganisms are alive while suspended in the atmosphere, and some seem to be metabolically active during their time there. One of the most important factors threatening their life and activity is solar ultraviolet (UV) radiation. Quantitative understanding of the spatial and temporal survival patterns in the atmosphere, and of the ultimate deposition of microbes to the surface, is limited by a number factors some of which are discussed here. These include consideration of appropriate spectral sensitivity functions for biological damage (e.g. inactivation), and the estimation of UV radiation impingent on a microorganism suspended in the atmosphere. We show that for several bacteria (E. coli, S. typhimurium, and P. acnes) the inactivation rates correlate well with irradiances weighted by the DNA damage spectrum in the UV-B spectral range, but when these organisms show significant UV-A (or visible) sensitivities, the correlations become clearly non-linear. The existence of these correlations enables the use of a single spectrum (here DNA damage) as a proxy for sensitivity spectra of other biological effects, but with some caution when the correlations are strongly non-linear. The radiative quantity relevant to the UV exposure of a suspended particle is the fluence rate at an altitude above ground, while down-welling irradiance at ground-level is the quantity most commonly measured or estimated in satellite-derived climatologies. Using a radiative transfer model that computes both quantities, we developed a simple parameterization to exploit the much larger irradiance data bases to estimate fluence rates, and present the first fluence-rate based climatology of DNA-damaging UV radiation in the atmosphere. The estimation of fluence rates in the presence of clouds remains a particularly challenging problem. Here we note that both reductions and enhancements in the UV radiation field are possible, depending mainly on cloud optical geometry and prevailing solar zenith angles. These complex effects need to be included in model simulations of the atmospheric life cycle of the organisms.

Evolution of the Z-scheme of photosynthesis: a perspective.

The concept of the Z-scheme of oxygenic photosynthesis is in all the textbooks. However, its evolution is not. We focus here mainly on some of the history of its biophysical aspects. We have arbitrarily divided here the 1941-2016 period into three sub-periods: (a) Origin of the concept of two light reactions: first hinted at, in 1941, by James Franck and Karl Herzfeld; described and explained, in 1945, by Eugene Rabinowitch; and a clear hypothesis, given in 1956 by Rabinowitch, of the then available cytochrome experiments: one light oxidizing it and another reducing it; (b) Experimental discovery of the two light reactions and two pigment systems and the Z-scheme of photosynthesis: Robert Emerson's discovery, in 1957, of enhancement in photosynthesis when two light beams (one in the far-red region, and the other of shorter wavelengths) are given together than when given separately; and the 1960 scheme of Robin Hill & Fay Bendall; and

Effects of Ca addition on the uptake, translocation, and distribution of Cd in Arabidopsis thaliana.

Cadmium (Cd) pollution poses a risk to human health for its accumulation in soil and crops, but this can be alleviated by calcium (Ca) addition. However, its mechanism remains unclear yet. In this study, Arabidopsis thaliana was used to explore the alleviating effects of Ca on Cd toxicity and its specific function during uptake, upward-translocation, and distribution of Cd. Supplementing plants with 5mM CaCl2 alleviated the intoxication symptoms caused by 50µM CdCl2, such as smaller leaves, early bolting and root browning. Ca addition decreased uptake of Cd, possibly by reducing the physical adsorption of Cd since the root cell membrane was well maintained and lignin deposition was decreased as well, and by decreasing symplastic Cd transport. Expression of the genes involved (AtZIP2 and AtZIP4) was also decreased. In addition, Ca accumulated in the plant shoot to help facilitating the upward-translocation of Cd, with evidence of higher translocation factor and expression of genes that were involved in Ca transport (AtPCR1) and Cd xylem loading (AtHMA2 and AtHMA4). Dithizone-staining of Cd in leaves showed that in Cd+Ca-treated plants, Ca addition initially protected the leaf stomata by preventing Cd from entering guard cells, but with prolonged Cd treatment facilitated the Cd accumulation around trichomes and maybe its excretion. We conclude that Ca promotes the upward-translocation of Cd and changes its distribution in leaves. The results may have relevance for bioremediation.

In photosynthesis, oxygen comes from water: from a 1787 book for women by Monsieur De Fourcroy.

It is now well established that the source of oxygen in photosynthesis is water. The earliest suggestion previously known to us had come from René Bernard Wurmser (1930). Here, we highlight an earlier report by Monsieur De Fourcroy (1787), who had already discussed the broad outlines of such a hypothesis in a book on Chemistry written for women. We present here a free translation of a passage from this book, with the original text in French as an Appendix.

Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots.

OBJECTIVES: To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants. RESULTS: A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched. CONCLUSIONS: The in-house protein database is a feasible and innovative strategy for proteomic research on non-model plants.

Thermal emissivity of avian eggshells.

The hypothesis has been tested that evolution has resulted in lower thermal emissivity of eggs of birds breeding openly in cold climates than of eggs of birds that nest under protective covering or in warmer climates. Directional thermal emissivity has been estimated from directional-hemispherical reflectance spectra. Due to several methodological difficulties the absolute emissivity is not accurately determined, but differences between species are obvious. Most notably, small waders of the genus Calidris, breeding in cold climates on the tundra, and in most cases with uniparental nest attendance, have low directional emissivity of their eggshells, about 0.92 when integration is carried out for wavelengths up to 16µm. Species belonging to Galloanserinae have the highest directional emissivity, about 0.96, of their eggs. No differences due to climate or breeding conditions were found within this group. Eggs of most other birds tested possess intermediate emissivity, but the values for Pica pica and Corvus corone cornix are as low as for Calidris. Large species-dependent differences in spectral reflectance were found at specific wavelengths. For instance, at 4.259µm the directional-hemispherical reflectance for galliforms range from 0.05 to 0.09, while for Fratercula arctica and Fulmarus glacialis it is about 0.3. The reflection peaks at 6.5 and 11.3µm due to calcite are differentially attenuated in different species. In conclusion, the hypothesis that evolution has resulted in lower thermal emissivity of bird eggs being exposed in cold climates is not supported by our results. The emissivity is not clearly related to nesting habits or climate, and it is unlikely that the small differences observed are ecologically important. The spectral differences between eggs that nevertheless exist should be taken into account when using infrared thermometers for estimating the surface temperature of avian eggs.

Trs130 participates in autophagy through GTPases Ypt31/32 in Saccharomyces cerevisiae.

Trs130 is a specific component of the transport protein particle II complex, which functions as a guanine nucleotide exchange factor (GEF) for Rab GTPases Ypt31/32. Ypt31/32 is known to be involved in autophagy, although the precise mechanism has not been thoroughly studied. In this study, we investigated the potential involvement of Trs130 in autophagy and found that both the cytoplasm-to-vacuole targeting (Cvt) pathway and starvation-induced autophagy were defective in a trs130ts (trs130 temperature-sensitive) mutant. Mutant cells could not transport Atg8 and Atg9 to the pre-autophagosomal structure/phagophore assembly site (PAS) properly, resulting in multiple Atg8 dots and Atg9 dots dispersed in the cytoplasm. Some dots were trapped in the trans-Golgi. Genetic studies showed that the effect of the Trs130 mutation was downstream of Atg5 and upstream of Atg1, Atg13, Atg9 and Atg14 on the autophagic pathway. Furthermore, overexpression of Ypt31 or Ypt32, but not of Ypt1, rescued autophagy defects in trs130ts and trs65ts (Trs130-HA Trs120-myc trs65Δ) mutants. Our data provide mechanistic insight into how Trs130 participates in autophagy and suggest that vesicular trafficking regulated by GTPases/GEFs is important in the transport of autophagy proteins from the trans-Golgi to the PAS.

Community dynamics of arbuscular mycorrhizal fungi in high-input and intensively irrigated rice cultivation systems.

Application of a mycorrhizal inoculum could be one way to increase the yield of rice plants and reduce the application of fertilizer. We therefore studied arbuscular mycorrhizal fungi (AMF) in the roots of wetland rice (Oryza sativa L.) collected at the seedling, tillering, heading, and ripening stages in four paddy wetlands that had been under a high-input and intensively irrigated rice cultivation system for more than 20 years. It was found that AMF colonization was mainly established in the heading and ripening stages. The AMF community structure was characterized in rhizosphere soils and roots from two of the studied paddy wetlands. A fragment covering the partial small subunit (SSU), the whole internal transcribed spacer (ITS), and the partial large subunit (LSU) rRNA operon regions of AMF was amplified, cloned, and sequenced from roots and soils. A total of 639 AMF sequences were obtained, and these were finally assigned to 16 phylotypes based on a phylogenetic analysis, including 12 phylotypes from Glomeraceae, one phylotype from Claroideoglomeraceae, two phylotypes from Paraglomeraceae, and one unidentified phylotype. The AMF phylotype compositions in the soils were similar between the two surveyed sites, but there was a clear discrepancy between the communities obtained from root and soil. The relatively high number of AMF phylotypes at the surveyed sites suggests that the conditions are suitable for some species of AMF and that they may have an important function in conventional rice cultivation systems. The species richness of root-colonizing AMF increased with the growth of rice, and future studies should consider the developmental stages of this crop in the exploration of AMF function in paddy wetlands.

Teaching about photosynthesis with simple equipment: analysis of light-induced changes in fluorescence and reflectance of plant leaves.

Solar energy absorbed by plants results in either reflection or absorption. The latter results in photosynthesis, fluorescence, or heat. Measurements of fluorescence changes have been used for monitoring processes associated with photosynthesis. A simple method to follow changes in leaf fluorescence and leaf reflectance associated with nonphotochemical quenching and light acclimation of leaves is described. The main equipment needed consists of a green-light emitting laser pointer, a digital camera, and a personal computer equipped with the camera acquisition software and the programs ImageJ and Excel. Otherwise, only commonly available cheap materials are required.

Margareta Ryberg (1946-2012): a personal tribute.

We pay tribute to the life and work of Margareta Ryberg (1946-2012). She was an expert on the different forms of protochlorophyll(ide), their protein partners, and their transformations in angiosperms; on the structural aspects, and the nature of prolamellar bodies, as well as on the localization of light-dependent NADPH:protochlorophyllide oxido-reductase. She was a great teacher, who also loved gardening and handicraft. But above all, she was a beloved wife, mother, grandmother, and friend who will be deeply missed.

Ecological importance of the thermal emissivity of avian eggshells.

Breeding birds have to divide their time between egg incubation and foraging. Particularly in cases when only one parent incubates the eggs, and especially in cold climates, the cooling of the eggs during absence from the nest may be problematic. In the present study we find that the thermal emissivity of eggshells may be ecologically important, and that an evolutionary pressure towards lower emissivity for exposed eggs in cold climates exists. We plan to experimentally compare emissivities among species in a future study.

Environmental effects of ozone depletion and its interactions with climate change: progress report, 2011.

The parties to the Montreal Protocol are informed by three panels of experts. One of these is the Environmental Effects Assessment Panel (EEAP), which deals with two focal issues. The first focus is the effects of increased UV radiation on human health, animals, plants, biogeochemistry, air quality, and materials. The second focus is on interactions between UV radiation and global climate change and how these may affect humans and the environment. When considering the effects of climate change, it has become clear that processes resulting in changes in stratospheric ozone are more complex than believed previously. As a result of this, human health and environmental problems will be longer-lasting and more regionally variable. Like the other panels, the EEAP produces a detailed report every four years; the most recent was published in 2010 (Photochem. Photobiol. Sci., 2011, 10, 173-300). In the years in between, the EEAP produces less detailed and shorter progress reports, which highlight and assess the significance of developments in key areas of importance to the parties. The next full quadrennial report will be published in 2014-2015.

Ultraviolet-B radiation and nitrogen affect nutrient concentrations and the amount of nutrients acquired by above-ground organs of maize.

UV-B radiation effects on nutrient concentrations in above-ground organs of maize were investigated at silking and maturity at different levels of applied nitrogen under field conditions. The experiment simulated a 20% stratospheric ozone depletion over Portugal. At silking, UV-B increased N, K, Ca, and Zn concentrations, whereas at maturity Ca, Mg, Zn, and Cu increased and N, P and Mn decreased in some plant organs. Generally, at maturity, N, Ca, Cu, and Mn were lower, while P, K, and Zn concentrations in stems and nitrogen-use efficiency (NUE) were higher in N-starved plants. UV-B and N effects on shoot dry biomass were more pronounced than on nutrient concentrations. Nutrient uptake decreased under high UV-B and increased with increasing N application, mainly at maturity harvest. Significant interactions UV-B x N were observed for NUE and for concentration and mass of some elements. For instance, under enhanced UV-B, N, Cu, Zn, and Mn concentrations decreased in leaves, except on N-stressed plants, whereas they were less affected by N nutrition. In order to minimize nutritional, economical, and environmental negative consequences, fertiliser recommendations based on element concentration or yield goals may need to be adjusted.

Phosphorus-arsenic interaction in the 'soil-plant-microbe' system and its influence on arsenic pollution.

Elevated arsenic (As) in soil is of public concern due to the carcinogenicity. Phosphorus (P) strongly influences the adsorption, absorption, transport, and transformation of As in the soil and in organisms due to the similarity of the chemical properties of P and As. In soil, P, particularly inorganic P, can release soil-retained As (mostly arsenate) by competing for adsorption sites. In plant and microbial systems, P usually reduces As (mainly arsenate) uptake and affects As biotransformation by competing for As transporters. The intensity and pattern of PAs interaction are highly dependent on the forms of As and P, and strongly influenced by various biotic and abiotic factors. An understanding of the PAs interaction in 'soil-plant-microbe' systems is of great value to prevent soil As from entering the human food chain. Here, we review PAs interactions and the main influential factors in soil, plant, and microbial subsystems and their effects on the As release, absorption, transformation, and transport in the 'soil-plant-microbe' system. We also analyze the application potential of P fertilization as a control for As pollution and suggest the research directions that need to be followed in the future.

UV-B-induced DNA damage mediates expression changes of cell cycle regulatory genes in Arabidopsis root tips.

Even though a number of studies have shown that UV-B radiation inhibits plant growth and regulates the cell cycle progress, little is known about the molecular and cellular mechanisms. Here, we developed a synchronous root-tip cell system to investigate expression changes of cell cycle marker genes and DNA damage under UV-B radiation. Expression analysis of cell cycle marker genes revealed that G1-to-S transition in root-tip cells was accomplished within 6 h. In the in vivo synchronous root-tip cells, high level of UV-B radiation (0.45 W m(-2)) induced expression changes of the cell cycle regulatory genes. Genes involved in G1-to-S transition, Histone H4 and E2Fa, were down-regulated by UV-B radiation during 2-6 h; whereas transcripts for KRP2, a negative regulator of G1-to-S transition, were up-regulated by UV-B at 2 h. The peak time for transcript level of CYCD3;1, a positive factor in G1-to-S transition, was delayed by UV-B radiation. Interestingly, a medium level of UV-B radiation (0.25 W m(-2)) did not change the expression of these genes in root tip cells from wild type. However, cell cycle regulatory genes were greatly affected in uvh1 mutant, which exhibited higher content of cyclobutane pyrimidine dimers (CPDs). Ascorbic acid treatment did not change the expression pattern of cell cycle regulatory genes that were affected by high-level UV-B. Our results implied that UV-B-induced DNA damage results in the delay of G1-to-S transition of plant cell cycle. UV-B-induced G1-to-S arrest may be a protective mechanism that prevents cells with damaged DNA from dividing and may explain the plant growth inhibition under increased solar UV-B radiation.

Is the action spectrum for the UV-induced production of previtamin D3 in human skin correct?

The universally recognised action spectrum for the UV-induced conversion of 7-dehydrocholesterol to previtamin D(3) in human skin was published in 1982, and indicates a maximum at about 297 nm with essentially no production above 315 nm. This work represents a milestone in research on vitamin D, but limitations in the original data should be recognised. Various findings have arisen in recent years which cast doubts on the accuracy of the action spectrum and its application for spectral weighting in calculations of effective UV doses. In conclusion, the construction of an entirely new computational model to predict previtamin D levels is recommended.

Environmental effects of ozone depletion and its interactions with climate change: progress report, 2009.

The parties to the Montreal Protocol are informed by three panels of experts. One of these is the Environmental Effects Assessment Panel (EEAP), which deals with UV radiation and its effects on human health, animals, plants, biogeochemistry, air quality and materials. Since 2000, the analyses and interpretation of these effects have included interactions between UV radiation and global climate change. When considering the effects of climate change, it has become clear that processes resulting in changes in stratospheric ozone are more complex than believed previously. As a result of this, human health and environmental problems will likely be longer-lasting and more regionally variable. Like the other panels, the EEAP produces a detailed report every four years; the most recent was that for 2006 (Photochem. Photobiol. Sci., 2007, 6, 201-332). In the years in between, the EEAP produces a less detailed and shorter progress report, as is the case for this present one for 2009. A full quadrennial report will follow for 2010.

Peptidoglycan in eukaryotes: Unanswered questions.

Peptidoglycan has been retained in chloroplasts that have evolved from cyanobacteria along some evolutionary tracks, but has seemingly been quickly eliminated during evolution of others. It has been eliminated in Rhodophyta, Chlorophyta, Pteridophyta and Spermatophyta, but has been retained in streptophyte algae, Glaukophyta, and Lycophyta. In this article questions emerging from this are raised, and for some of them answers are suggested.

UV radiation: balancing risks and benefits.

We use action spectra published by the International Commission on Illumination to examine diurnal, seasonal and latitudinal variations in erythemally weighted (sunburning) UV-a health risk, and vitamin D-weighted UV-a health benefit. Vitamin D-weighted UV is more strongly dependent on ozone and solar zenith angle. Consequently, its diurnal, seasonal and geographic variability is more pronounced than for erythemally weighted UV. We then investigate relationships between the two quantities. An algorithm is developed and used to relate vitamin D production to the widely used UV index, to help the public to optimize their exposure to UV radiation. In the summer at noon, there should at mid-latitudes be sufficient UV to photosynthesize optimal vitamin D in approximately 1 min for full body exposure, whereas skin damage occurs after approximately 15 min. Further, while it should be possible to photosynthesize vitamin D in the winter at mid-latitudes, the amount of skin that must be exposed is larger than from the hands and face alone. This raises the question of whether the action spectrum for vitamin D production is correct, since studies have reported that production of vitamin D is not possible in the winter at mid-latitudes.