Isoprene hotspots at the Western Coast of Antarctic Peninsula during MASEC′16

Isoprene (C5H8) plays an important role in the formation of surface ozone (O3) and the secondary organic aerosol (SOA) which contributed to the climate change. This study aims to determine hourly distribution of tropospheric isoprene over the Western Coast of Antarctic Peninsula (WCAP) during the Malaysian Antarctic Scientific Expedition Cruise 2016 (MASEC′16). In-situ measurements of isoprene were taken using a custom-built gas chromatography with photoionization detector, known as iDirac. Biological parameters such as chlorophyll a (chl-a) and particulate organic carbon (POC) were compared to the in-situ isoprene measurements. Significant positive correlation was observed between isoprene and POC concentrations (r2 = 0.67, p < 0.001), but not between isoprene and chl-a. The hotspots of isoprene over maritime Antarctic were then were investigated using NAME dispersion model reanalysis. Measurements showed that isoprene mixing ratio were the highest over region of King George Island, Deception Island and Booth Island with values of ∼5.0, ∼0.9 and ∼5.2 ppb, respectively. Backward trajectory analysis showed that air masses may have lifted the isoprene emitted by marine algae. We believe our findings provide valuable data set of isoprene estimation over the under sampled WCAP

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Field Evaluation of Arbuscular Mycorrhizal Fungal Colonization in Bacillus thuringiensis Toxin-Expressing (Bt) and Non-Bt Maize

The cultivation of genetically engineered Bacillus thuringiensis toxin-expressing (Bt) maize continues to increase worldwide, yet the effects of Bt crops on arbuscular mycorrhizal fungi (AMF) in soil are poorly understood. In this field experiment, we investigated the impact of seven different genotypes of Bt maize and five corresponding non-Bt parental cultivars on AMF and evaluated plant growth responses at three different physiological time points. Plants were harvested 60 days (active growth), 90 days (tasseling and starting to produce ears), and 130 days (maturity) after sowing, and data on plant growth responses and percent AMF colonization of roots at each harvest were collected. Spore abundance and diversity were also evaluated at the beginning and end of the field season to determine whether the cultivation of Bt maize had a negative effect on AMF propagules in the soil. Plant growth and AMF colonization did not differ between Bt and non-Bt maize at any harvest period, but AMF colonization was positively correlated with leaf chlorophyll content at the 130-day harvest. Cultivation of Bt maize had no effect on spore abundance and diversity in Bt versus non-Bt plots over one field season. Plot had the most significant effect on total spore counts, indicating spatial heterogeneity in the field. Although previous greenhouse studies demonstrated that AMF colonization was lower in some Bt maize lines, our field study did not yield the same results, suggesting that the cultivation of Bt maize may not have an impact on AMF in the soil ecosystem under field conditions

Evidence of reduced arbuscular mycorrhizal fungal colonization in multiple lines of Bt maize

Premise of the Study: Insect-resistant Bacillus thuringiensis (Bt) maize is widely cultivated, yet few studies have examined the interaction of symbiotic arbuscular mycorrhizal fungi (AMF) with different lines of Bt maize. As obligate symbionts, AMF may be sensitive to genetic changes within a plant host. Previous evaluations of the impact of Bt crops on AMF have been inconsistent, and because most studies were conducted under disparate experimental conditions, the results are difficult to compare. Methods: We evaluate AMF colonization in nine Bt maize lines, differing in number and type of engineered trait, and five corresponding near-isogenic parental (P) base hybrids in greenhouse microcosms. Plants were grown in 50% local agricultural soil with low levels of fertilization, and AMF colonization was evaluated at 60 and 100 d. Nontarget effects of Bt cultivation on AMF colonization were tested in a subsequently planted crop, Glycine max, which was seeded into soil that had been preconditioned for 60 d with Bt or P maize. Key Results: We found that Bt maize had lower levels of AMF colonization in their roots than did the non-Bt parental lines. However, reductions in AMF colonization were not related to the expression of a particular Bt protein. There was no difference in AMF colonization in G. max grown in the Bt- or P-preconditioned soil. Conclusions: These findings are the first demonstration of a reduction in AMF colonization in multiple Bt maize lines grown under the same experimental conditions and contribute to the growing body of knowledge examining the unanticipated effects of Bt crop cultivation on nontarget soil organisms

Assessing the Potential of Land Use Modification to Mitigate Ambient NO2 and Its Consequences for Respiratory Health

Understanding how local land use and land cover (LULC) shapes intra-urban concentrations of atmospheric pollutants—and thus human health—is a key component in designing healthier cities. Here, NO2 is modeled based on spatially dense summer and winter NO2 observations in Portland-Hillsboro-Vancouver (USA), and the spatial variation of NO2 with LULC investigated using random forest, an ensemble data learning technique. The NO2 random forest model, together with BenMAP, is further used to develop a better understanding of the relationship among LULC, ambient NO2 and respiratory health. The impact of land use modifications on ambient NO2, and consequently on respiratory health, is also investigated using a sensitivity analysis. We find that NO2 associated with roadways and tree-canopied areas may be affecting annual incidence rates of asthma exacerbation in 4–12 year olds by +3000 per 100,000 and -1400 per 100,000, respectively. Our model shows that increasing local tree canopy by 5% may reduce local incidences rates of asthma exacerbation by 6%, indicating that targeted local tree-planting efforts may have a substantial impact on reducing city-wide incidence of respiratory distress. Our findings demonstrate the utility of random forest modeling in evaluating LULC modifications for enhanced respiratory health

Limits to Sexual Reproduction in Geothermal Bryophytes

Previous research suggests that while sexual reproduction generally increases with environmental stress it may decrease with extreme stress, at the edge of eukaryotic life. In this study, we explored the limits to sexual reproduction in an extremophile, bryophyte system to ultimately understand the processes that limit sexual reproduction. We used field data from geothermal sites at Lassen Volcanic National Park, California, to demonstrate that sexual reproduction, as measured by the number of sporophytes per shoot, decreases with increasing environmental stress. We found that the number of sporophytes per shoot is positively correlated with distance from geothermal features. When Pohlia nutans plants were transplanted to mesic conditions, high numbers of gametoecia and sporophytes were produced, regardless of where along the environmental stress gradient plants originated, suggesting that physiological stress rather than local adaptation is constraining sexual reproduction in this extremophile system. We discuss our results with respect to previous work on sex in extreme environments

Reducing the Negative Human-Health Impacts of Bioenergy Crop Emissions through Region-Specific Crop Selection

An expected global increase in bioenergy-crop cultivation as an alternative to fossil fuels will have consequences on both global climate and local air quality through changes in biogenic emissions of volatile organic compounds (VOCs). While greenhouse gas emissions may be reduced through the substitution of next-generation bioenergy crops such as eucalyptus, giant reed, and switchgrass for fossil fuels, the choice of species has important ramifications for human health, potentially reducing the benefits of conversion due to increases in ozone (O3) and fine particulate matter (PM2.5) levels as a result of large changes in biogenic emissions. Using the Community Earth System Model we simulate the conversion of marginal and underutilized croplands worldwide to bioenergy crops under varying future anthropogenic emissions scenarios. A conservative global replacement using high VOCemitting crop profiles leads to modeled population-weighted O3 increases of 5–27 ppb in India, 1–9 ppb in China, and 1–6 ppb in the United States, with peak PM2.5 increases of up to 2 μg m−3 . We present a metric for the regional evaluation of candidate bioenergy crops, as well as results for the application of this metric to four representative emissions profiles using four replacement scales (10–100% maximum estimated available land). Finally, we assess the total health and climate impacts of biogenic emissions, finding that the negative consequences of using high-emitting crops could exceed 50% of the positive benefits of reduced fossil fuel emissions in value

Effects of Sex and Mycorrhizal Fungi on Gas Exchange in the Dioecious Salt Marsh Grass Distichlis Spicata

Premise of research. In dioecious plant species, males and females often differ in physiology, and mycorrhizal fungal relationships are likely to influence these differences. However, few data are available on the potential role of mycorrhizal fungi in altering sex-specific physiology and population sex ratios of dioecious plant species. Methodology. In this study, we measured leaf gas exchange in a multifactorial greenhouse experiment with and without mycorrhizal fungal additions and under field conditions in Distichlis spicata, a dioecious C4 salt marsh grass, displaying extreme spatial sex ratio variation. Pivotal results. We found a significant interaction between gas exchange, plant sex, and mycorrhizal fungal infection. Specifically, females but not males had significantly lower transpiration rates and higher water use efficiency (WUE) in treatments with increased mycorrhizal fungi. Additionally, field data showed similar WUE between plants at female-majority sites and male-majority sites, despite significantly lower rates of net assimi- lation and stomatal conductance in plants at female-majority sites. Conclusions. Our results suggest that the higher WUE associated with increased mycorrhizal fungi in female D. spicata plants may be an important physiological attribute enabling female success in the higher-stress salt- water environment contributing to the spatial segregation of the sexes observed in this dioecious species

Sex-Specific Morphological and Physiological Differences in the Moss Ceratodon purpureus (Dicranales)

Background and Aims: Dioecy and sexual dimorphism occur in many terrestrial plant species but are especially widespread among the bryophytes. Despite the prevalence of dioecy in non-vascular plants, surprisingly little is known about how fine-scale sex-specific cell and leaf morphological traits are correlated with sex-specific physiology and population sex ratios. Such data are critical to understanding the inter-relationship between sex-specific morphological and physiological characters and how their relationship influences population structure. In this study, these data types were assessed to determine how they vary across three populations within one moss species and whether fine-scale morphological traits scale up to physiological and sex ratio characteristics. Methods: Twenty cell-, leaf- and canopy-level traits and two photochemical measurements were compared between sexes and populations of the dioecious moss Ceratodon purpureus. Field population-expressed sex ratios were obtained for the same populations. Key Results: Male and female plants differed in cell, leaf and photochemical measures. These sexual dimorphisms were female biased, with females having larger and thicker leaves and greater values for chlorophyll fluorescence-based, leaf photochemistry measurements than males. Female traits were also more variable than male traits. Interestingly, field population sex ratios were significantly male biased in two study populations and female biased in the third study population. Conclusions: The results demonstrate that the larger morphology and the greater physiological output of female C. purpureus gametophytes compared with males occurs across populations and is likely to have significant effects on resource allocation and biotic interactions. However, this high level of dimorphism does not explain population sex ratio variation in the three study populations tested. This research lays the groundwork for future studies on how differential sex-specific variation in cell and leaf traits influences bryophyte plant fitness

Urban Forested Parks and Tall Tree Canopies Contribute to Macrolichen Epiphyte Biodiversity in Urban Landscapes

Land use changes through urbanization can dramatically impact floral and faunal species-specific survival and alter patterns of regional biodiversity. These changes can lead to complex, ecosystem scale interactions that yield both positive and negative impacts on urban and ex-urban biota. The Pacific Northwest region is one of the most rapidly urbanizing areas of the United States, with the human population estimated to increase more than fifty percent by 2050. Despite rapid population growth in the Pacific Northwest and a forest system known to provide extraordinary ecosystem services, relatively little is known about how human activities affect urban tree biology and the services these trees provide. Specifically, little is known about how urbanization impacts tall tree canopy epiphyte communities, a unique and sensitive component of Pacific Northwest trees which are known to contribute essential ecosystem functions. Here, we revisit a historic study of urban epiphytic lichen communities, initially conducted 18 years ago in Portland, Oregon, USA. Additionally, to compare ground and canopy-based survey methods and to gain a broader understanding of urban epiphytic communities, we comprehensively investigated the biodiversity of stratified urban canopy epiphyte lichen communities, for the first time. Our results show that tall, urban conifer trees and urban parks and forested areas can provide both heterogeneous and stratified habitats for urban-tolerant epiphytic lichens. We found significant and highly eutrophied lichen communities in all epiphytic surveys, suggesting that continued urbanization in the Portland metro region may further impact these communities despite overall gains in regional air quality during the 18 year study period. Our results support the distinct homogenization of urban epiphytic lichen communities, suggesting that it may be necessary to expand beyond measures of biodiversity to consider community composition and functional biodiversity in assessments of the ecology and potential ecosystem services of epiphyte communities within urbanizing landscapes