Is UV-induced DNA damage greater at higher elevation?

Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.

Thermal compensation reduces DNA damage from UV radiation

Increases in ultraviolet radiation (UVR) correlate spatially and temporally with global amphibian population declines and interact with other stressors such as disease and temperature. Declines have largely occurred in high-altitude areas associated with greater UVR and cooler temperatures. UVR is a powerful mutagenic harming organisms largely by damaging DNA. When acutely exposed to UVR at cool temperatures, amphibian larvae have increased levels of DNA damage. Amphibians may compensate for the depressive effects of temperature on DNA damage through acclimatisation, but it is unknown whether they have this capacity. We reared striped marsh frog larvae (Limnodynastes peronii) in warm (25 °C) and cool (15 °C) temperatures under a low or moderate daily dose of UVR (10 and 40 μW cm-2 UV-B for 1 h at midday, respectively) for 18-20 days and then measured DNA damage resulting from an acute high UVR dose (80 μW cm-2 UV-B for 1.5 h) at a range of temperatures (10, 15, 20, 25, and 30 °C). Larvae acclimated to 15 °C and exposed to UVR at 15 °C completely compensated UVR-induced DNA damage compared with 25 °C acclimated larvae exposed to UVR at 25 °C. Additionally, warm-acclimated larvae had higher DNA damage than cold-acclimated larvae across test temperatures, which indicated a cost of living in warmer temperatures. Larvae reared under elevated UVR levels showed no evidence of UVR acclimation resulting in lower DNA damage following high UVR exposure. Our finding that thermal acclimation in L. peronii larvae compensated UVR-induced DNA damage at low temperatures suggested that aquatic ectotherms living in cool temperatures may be more resilient to high UVR than previously realised. We suggested individuals or species with less capacity for thermal acclimation of DNA repair mechanisms may be more at risk if exposed to changing thermal and UVR exposure regimes.

Maintenance of a fruit colour polymorphism along an elevational gradient in the Southern Alps of New Zealand

Many plants produce colour-polymorphic fruits. However, the processes responsible for the evolution and maintenance of fruit colour polymorphisms are poorly understood. We investigated the fruit colour polymorphism in Gaultheria depressa var. novae-zealandiae (Ericaceae), a predominantly bird-dispersed, alpine shrub from New Zealand, by testing whether colour morph frequencies vary geographically to maximise fruit-foliage colour contrasts. We also conducted a seed germination experiment to test whether fruit colour morphs vary in their susceptibility to UV damage. Results showed that 'red' fruits were more abundant at lower elevations, while 'white' fruits were predominant at higher elevations. Leaf colours shifted from 'green' in appearance at lower elevations to 'red' at higher elevations. Analyses of fruit-foliage colour contrasts showed that 'red' fruits were more conspicuous at lower elevations, and 'white' fruits were more conspicuous at higher elevations, which was consistent with the hypothesis that colour morph frequencies vary geographically to maximise their conspicuousness to dispersers. However, 'red' fruits were generally more conspicuous than 'white' fruits, regardless of elevation, indicating that the maintenance of the polymorphism could not be attributed to fruit-foliage colour contrasts alone. The seed germination experiment showed that 'white' fruits were more resistant to UV damage, suggesting the preponderance of 'white' fruited individuals in the landscape results from a greater degree of protection from UV damage. The fruit colour polymorphism in Gaultheria depressa var. novae-zealandiae therefore appears to be maintained by trade-offs between conspicuousness to dispersers and tolerance to UV damage, advocating a pluralistic approach to the problem in the future.

Prevalence of Keratoconus and Keratoconus Suspect among Patients Seeking Refractive Surgery in Syria

PURPOSE

The purpose of this study was to determine the prevalence of keratoconus (KC) and keratoconus suspect (KCS) among patients seeking refractive surgery in Syria.

METHODS

This is a retrospective multicenter screening study. The study was conducted in Damascus University, Tishreen University, and Tartous Specialist Eye Center (a private center). Data were collected from refractive surgery candidates referred for preoperative evaluation before laser in situ keratomileusis, photorefractive keratectomy, intrastromal corneal rings, and phakic intraocular lens implantation. Corneal parameters were obtained by Scheimpflug-Placido tomography, Sirius (CSO, Italy).

RESULTS

A total of 1479 patients were included in this analysis. The prevalence rates of KC and KCS were 18.19% (269/1479) and 13.52% (200/1479), respectively. In addition, patients with KC were found to have higher percentages of eye rubbing and astigmatism than suspect and normal (P < 0.0001).

CONCLUSION

High prevalence rate of KC was found among patients seeking refractive surgery in Syria. Although this study was carried out on a highly selective population, it may reflect a high prevalence rate in a general population in Syria.

Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika (Ochotona princeps)

High-elevation environments have lower atmospheric oxygen content, reduced temperatures, and higher levels of UV radiation than found at lower elevations. As such, species living at high elevations must overcome these challenges to survive, grow, and reproduce. American pikas (Ochotona princeps) are alpine lagomorphs that are habitat specialists typically found at elevations >2,000 m. Previous research has shown putative evidence for high-elevation adaptation; however, investigations to date have been limited to a fraction of the genome. Here, we took a comparative genomics approach to identify putative regions under selection using a chromosomal reference genome assembly for the American pika relative to 8 other mammalian species targeted based on phylogenetic relatedness and (dis)similarity in ecology. We first identified orthologous gene groups across species and then extracted groups containing only American pika genes as well as unclustered pika genes to inform functional enrichment analyses; among these, we found 141 enriched terms with many related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. We identified 15 significantly expanded gene families within the American pika across all orthologous gene groups that displayed functionally enriched terms associated with hypoxia adaptation. We further detected 196 positively selected genes, 41 of which have been associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. In particular, OXNAD1, NRDC, and those genes critical in DNA repair represent important targets for future research to examine their functional implications in the American pika, especially as they may relate to adaptation to rapidly changing environments.

Prevalence of Keratoconus in a Population-Based Study in Syria

Aim

To determine the prevalence and associations of keratoconus (KC) in a university student population in Syria.

Methods

A prospective multicentre cross-sectional cohort study was conducted at two universities in Syria. Student volunteers were recruited from Tishreen University (Latakia governorate) and Damascus University (Damascus governorate). All participants underwent a comprehensive ocular examination. Placido/Scheimpflug-based corneal imaging using the Sirius (CSO, Florence. Italy), and a questionnaire to evaluate the baseline characteristics and medical history, as well as to highlight possible risk factors of KC. Univariate and bivariate analyses were performed.

Results

The estimated prevalence of KC among all subjects was 1.43% (n = 12). A strong association between eye rubbing and keratoconus was found (OR 9.33, 95% CI 2.94–29.63, P < 0.001). Damascus University participants had a higher prevalence of KC than Tishreen University. However, the difference was not statistically significant.

Conclusion

The prevalence of keratoconus in this Syrian student population was 1.43%. The results of this study demonstrate a high prevalence of keratoconus in the study population. Early detection of keratoconus through screening may yield benefits in preventing devastating sequelae of KC in populations with a high prevalence.

Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas

Primates have adapted to numerous environments and lifestyles, but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of hematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared to baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult hemoglobin but found that gelada hemoglobin does not exhibit markedly altered oxygenation properties compared to lowland primates. We also found that geladas at high altitude do not exhibit elevated blood hemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research.

Exposure to UV-B Radiation Leads to Increased Deposition of Cell Wall-Associated Xerocomic Acid in Cultures of Serpula himantioides

Many fungi are thought to have developed morphological and physiological adaptations to cope with exposure to UV-B radiation, but in most species, such responses and their protective effects have not been explored. Here, we study the adaptive response to UV-B radiation in the widespread, saprotrophic fungus Serpula himantioides, frequently found colonizing coniferous wood in nature. We report the morphological and chemical responses of S. himantioides to controlled intensities of UV-B radiation, under in vitro culture conditions. Ultraviolet radiation induced a decrease in the growth rate of S. himantioides but did not cause gross morphological changes. Instead, we observed accumulation of pigments near the cell wall with increasing intensities of UV-B radiation. Nuclear magnetic resonance (NMR) and high-performance liquid chromatography-mass spectrometry (HPLC-MS) analyses revealed that xerocomic acid was the main pigment present, both before and after UV-B exposure, increasing from 7 mg/liter to 15 mg/liter after exposure. We show that xerocomic acid is a photoprotective metabolite with strong antioxidant abilities, as evidenced by DPPH (2,2-diphenyl-1-picrylhydrazyl), ABTS [2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt], and oxygen radical absorbance capacity (ORAC) assays. Finally, we assessed the capacity of xerocomic acid as a photoprotective agent on HEK293 cells and observed better photoprotective properties than those of β-carotene. Xerocomic acid is therefore a promising natural product for development as a UV-protective ingredient in cosmetic and pharmaceutical products.IMPORTANCE Our study shows the morphological and chemical responses of S. himantioides to controlled doses of UV-B radiation under in vitro culture conditions. We found that increased biosynthesis of xerocomic acid was the main strategy adopted by S. himantioides against UV-B radiation. Xerocomic acid showed strong antioxidant and photoprotective abilities, which has not previously been reported. Our results indicate that upon UV-B exposure, S. himantioides decreases its hyphal growth rate and uses this energy instead to increase the biosynthesis of xerocomic acid, which is allocated near the cell wall. This metabolic switch likely allows xerocomic acid to efficiently defend S. himantioides from UV radiation through its antioxidant and photoprotective properties. The findings further suggest that xerocomic acid is a promising candidate for development as a cosmetic ingredient to protect against UV radiation and should therefore be investigated in depth in the near future both in vitro and in vivo.

Survival and ice nucleation activity of Pseudomonas syringae strains exposed to simulated high-altitude atmospheric conditions

Pseudomonas syringae produces highly efficient biological ice nuclei (IN) that were proposed to influence precipitation by freezing water in clouds. This bacterium may be capable of dispersing through the atmosphere, having been reported in rain, snow, and cloud water samples. This study assesses its survival and maintenance of IN activity under stressing conditions present at high altitudes, such as UV radiation within clouds. Strains of the pathovars syringae and garcae were compared to Escherichia coli. While UV-C effectively inactivated these cells, the Pseudomonas were much more tolerant to UV-B. The P. syringae strains were also more resistant to radiation from a solar simulator, composed of UV-A and UV-B, while only one of them suffered a decline in IN activity at −5 °C after long exposures. Desiccation at different relative humidity values also affected the IN, but some activity at −5 °C was always maintained. The pathovar garcae tended to be more resistant than the pathovar syringae, particularly to desiccation, though its IN were found to be generally more sensitive. Compared to E. coli, the P. syringae strains appear to be better adapted to survival under conditions present at high altitudes and in clouds.

How can the natural radiation background affect DNA integrity in angiosperm plant species at different altitudes in Rila Mountain (Southwest Bulgaria)?

Climate changes and anthropogenic factors are the main factors contributing to the destruction of natural ecosystems. The aim of this study was to investigate the extent to which wild plants adapt to UV, gamma background, and gross beta activity, as well as the possible damage that can be recorded in plants growing at different altitudes in Rila Mountain. We used physicochemical, cytogenetic, and molecular methods. Our investigations were done on the nine plant species characteristic of the ecosystems in Rila Mountain at three altitudes: 1500 m, 1782 m, and 2925 m. The registered beta activity in the plants did not depend on the altitude of the habitats. Our results showed that wild plant species differ in their tolerance to the combined effect of UV and IR radiation as well as climate factors. The genotype plays a more important role than the difference in the habitat altitude. The comet assay adapted by us for these plant species showed that the DNA of Epilobium angustifolium L. (Onagraceae) growing at 1500 m was more susceptible to damage than that of Dactylis glomerata L. (Poaceae). Both these species growing at 1782 m did not show any increase in DNA damage evaluated as the level of DNA migration. The level of DNA damage in Pedicularis orthantha Griseb. (Orobanchaceae) at 2925 m was comparable to that at a lower altitude. Regarding the formation of micronuclei, grass species were more sensitive to UV- and IR-induced DNA damage than cereals. Our data imply the existence of specific protective mechanisms developed by plants to overcome DNA damage induced by stress factors.

Plasticity of functional traits and optimality of biomass allocation in elevational ecotypes of Arabidopsis halleri grown at different soil nutrient availabilities

In mountainous areas, plant distribution is constrained by various environmental stresses. Plasticity and constancy in plant functional traits may relate to optimal strategies at respective habitats and to ecotypic differentiation along elevation. Although plant biomass allocation has been extensively studied in relation to adaptation to soil nutrient availability along elevation, its optimality is still poorly understood. We examined soil nutrient availability in the field and conducted growth analysis for two elevational ecotypes of Arabidopsis halleri grown under different nutrient availabilities. We determined plasticity in morphological and physiological traits and evaluated optimal biomass allocation using an optimality model. Our field investigation indicated that soil nitrogen (N) availability increased rather than decreased with increasing elevation. Our growth analysis revealed that lowland ecotype was more plastic in morphological variables and N concentrations, whereas the highland ecotype was more plastic in other physiological variables such as the net assimilation rate (NAR). The leaf mass ratio (LMR) in the lowland ecotype was moderately plastic at the whole range of N availabilities, whereas LMR in the highland ecotype was very plastic at higher N availabilities only. The optimality model indicated that the LMR of the lowland ecotype was nearly optimal throughout the range of studied N availabilities, whereas that of the highland ecotype was suboptimal at low N availability. These results suggest that highland ecotype is adapted only to high N availability, whereas the lowland ecotype is adapted to a relatively wide range of N availabilities as a result of natural selection in their respective habitats. We conclude that an adaptive differentiation has occurred between the two ecotypes and plasticity in the biomass allocation is directly related to its optimization in changing environments.

Ultraviolet-B-induced DNA damage and ultraviolet-B tolerance mechanisms in species with different functional groups coexisting in subalpine moorlands

High doses of ultraviolet-B (UV-B; 280-315 nm) radiation can have detrimental effects on plants, and especially damage their DNA. Plants have DNA repair and protection mechanisms to prevent UV-B damage. However, it remains unclear how DNA damage and tolerance mechanisms vary among field species. We studied DNA damage and tolerance mechanisms in 26 species with different functional groups coexisting in two moorlands at two elevations. We collected current-year leaves in July and August, and determined accumulation of cyclobutane pyrimidine dimer (CPD) as UV-B damage and photorepair activity (PRA) and concentrations of UV-absorbing compounds (UACs) and carotenoids (CARs) as UV-B tolerance mechanisms. DNA damage was greater in dicot than in monocot species, and higher in herbaceous than in woody species. Evergreen species accumulated more CPDs than deciduous species. PRA was higher in Poaceae than in species of other families. UACs were significantly higher in woody than in herbaceous species. The CPD level was not explained by the mechanisms across species, but was significantly related to PRA and UACs when we ignored species with low CPD, PRA and UACs, implying the presence of another effective tolerance mechanism. UACs were correlated negatively with PRA and positively with CARs. Our results revealed that UV-induced DNA damage significantly varies among native species, and this variation is related to functional groups. DNA repair, rather than UV-B protection, dominates in UV-B tolerance in the field. Our findings also suggest that UV-B tolerance mechanisms vary among species under evolutionary trade-off and synergism.

Effect of UV-B radiation on the antibody response of fish - implication on high altitude fish culture

Literally, all living forms are either directly or indirectly dependent upon sun for energy. Radiation from sun is differentiated into several components of a spectrum based on the wavelength. Ultraviolet (UV) radiation may be one of the infamous radiations emitted by the sun. Ozone depletion is another critical factor by which UV induced ill-effects are intensified. Though there are numerous studies on effects of UV radiation on terrestrial organisms, its effect on freshwater and aquaculture ecosystems has been largely neglected. Here, we report that enhanced UV irradiation may suppress the primary and secondary antibody responses to a soluble protein antigen in fish. Fishes exposed for longer periods (80min) were particularly very sensitive to infection, as shown by our sensitivity index.

Beyond xeroderma pigmentosum: DNA damage and repair in an ecological context. A tribute to James E. Cleaver

The ability to repair DNA is a ubiquitous characteristic of life on Earth and all organisms possess similar mechanisms for dealing with DNA damage, an indication of a very early evolutionary origin for repair processes. James E. Cleaver's career (initiated in the early 1960s) has been devoted to the study of mammalian ultraviolet radiation (UVR) photobiology, specifically the molecular genetics of xeroderma pigmentosum and other human diseases caused by defects in DNA damage recognition and repair. This work by Jim and others has influenced the study of DNA damage and repair in a variety of taxa. Today, the field of DNA repair is enhancing our understanding of not only how to treat and prevent human disease, but is providing insights on the evolutionary history of life on Earth and how natural populations are coping with UVR-induced DNA damage from anthropogenic changes in the environment such as ozone depletion.