Kinetic resolution of ligand binding to the alpha and beta chains within human hemoglobin.

Nitric oxide has been used as a chain-specific, spin label of unliganded heme groups present in kinetic mixtures of human hemoglobin and n-butyl isocyanide. In these experiments, deoxyhemoglobin was reacted with n-butyl isocyanide for a controlled time and then mixed rapidly with a high concentration of nitric oxide to fill residual, unoccupied heme sites. The final mixture was frozen immediately after formation to prevent any displacement of bound isonitrile. The EPR spectrum of the frozen sample was resolved into alpha and beta nitric oxide components; these reflect the relative proportions of alpha- and beta-heme sites which were unoccupied by n-butyl isocyanide. Individual time courses for the alpha and beta subunits were obtained by varying the time between the formation of the isonitrile/hemoglobin mixture and its reaction with nitric oxide. At pH 7.0 only the beta chain time course exhibits an initial rapid phase; the alpha chain time course is monophasic, exhibiting almost, exponential behavior. This result shows unequivocally that the beta-hemes within deoxyhemoglobin react much more rapidly with n-butyl isocyanide than the alpha hemes.     

Complementarity and Area-Efficiency in the Prioritization of the Global Protected Area Network

Complementarity and cost-efficiency are widely used principles for protected area network design. Despite the wide use and robust theoretical underpinnings, their effects on the performance and patterns of priority areas are rarely studied in detail. Here we compare two approaches for identifying the management priority areas inside the global protected area network: 1) a scoring-based approach, used in recently published analysis and 2) a spatial prioritization method, which accounts for complementarity and area-efficiency. Using the same IUCN species distribution data the complementarity method found an equal-area set of priority areas with double the mean species ranges covered compared to the scoring-based approach. The complementarity set also had 72% more species with full ranges covered, and lacked any coverage only for half of the species compared to the scoring approach. Protected areas in our complementarity-based solution were on average smaller and geographically more scattered. The large difference between the two solutions highlights the need for critical thinking about the selected prioritization method. According to our analysis, accounting for complementarity and area-efficiency can lead to considerable improvements when setting management priorities for the global protected area network.     

Uncertainty and Sensitivity in the Carbon Footprint of Shopping Bags

Carbon footprints for several shopping bag alternatives (polyethylene, paper, cotton, biodegradable modified starch, and recycled polyethylene) were compared with life cycle assessment. Stochastic uncertainty analysis was used to study the sensitivity of the comparison to scenario and parameter uncertainty. On the basis of the results, we could give only a few robust conclusions without choosing a waste treatment scenario or limiting the parameter space. Given the scenario of current waste infrastructure in Finland, recycled polyethylene bags seem to be the most preferable (?7 to 24 g CO₂ eq./bag) and biodegradable bags the least preferable (38 to 60 g CO₂ eq./bag) option. In each analyzed waste treatment scenario, a few parameters dominated the uncertainty of results. Most of these parameters were downstream of the shopping bag manufacturing (consumer behavior, landfill conditions, method of waste combustion, etc.). The choice of waste treatment scenario had a greater effect on the ranking of bags than parameter uncertainty within scenarios. This result highlights the importance of including several scenarios in comparative life cycle assessments.     

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

Understanding how genetic variation affects distinct cellular phenotypes, such as gene expression levels, alternative splicing and DNA methylation levels, is essential for better understanding of complex diseases and traits. Furthermore, how inter-individual variation of DNA methylation is associated to gene expression is just starting to be studied. In this study, we use the GenCord cohort of 204 newborn Europeans’ lymphoblastoid cell lines, T-cells and fibroblasts derived from umbilical cords. The samples were previously genotyped for 2.5 million SNPs, mRNA-sequenced, and assayed for methylation levels in 482,421 CpG sites. We observe that methylation sites associated to expression levels are enriched in enhancers, gene bodies and CpG island shores. We show that while the correlation between DNA methylation and gene expression can be positive or negative, it is very consistent across cell-types. However, this epigenetic association to gene expression appears more tissue-specific than the genetic effects on gene expression or DNA methylation (observed in both sharing estimations based on P-values and effect size correlations between cell-types). This predominance of genetic effects can also be reflected by the observation that allele specific expression differences between individuals dominate over tissue-specific effects. Additionally, we discover genetic effects on alternative splicing and interestingly, a large amount of DNA methylation correlating to alternative splicing, both in a tissue-specific manner. The locations of the SNPs and methylation sites involved in these associations highlight the participation of promoter proximal and distant regulatory regions on alternative splicing. Overall, our results provide high-resolution analyses showing how genome sequence variation has a broad effect on cellular phenotypes across cell-types, whereas epigenetic factors provide a secondary layer of variation that is more tissue-specific. Furthermore, the details of how this tissue-specificity may vary across inter-relations of molecular traits, and where these are occurring, can yield further insights into gene regulation and cellular biology as a whole.     

Estimating population characteristics of two saproxylic beetles: a mark-recapture approach

Using a mark-release-recapture technique we describe adult sex ratios, recapture rates and other sample characteristics of two saproxylic species: the nationally threatened longhorn beetle Leptura (Rutpela) maculata (Coleoptera: Cerambycidae) and the common L. quadrifasciata in southeastern Finland over two summers. Over 350 individuals of L. maculata and 150 individuals of L. quadrifasciata were captured on floral resource or in flight, and marked each summer. For L. maculata, the sex ratio was male-biased (2:1), whereas for L. quadrifasciata the bias was less clear. For both species, the male-bias may reflect behavioral differences between sexes, rather than true population differences. The proportion of recaptured individuals was low and varied between 7 and 33% depending on the species and year, which allowed us to estimate population parameters only for L. maculata in 2006. A model which assumed constant survival, but time-dependent catchability and entrance probability from a larger superpopulation, fit the data best. The precision of the total population size estimates were reasonable for all the models tested (coefficient of variation = 7–14%). Based on the estimated local adult population size (mean ± 95% confidence interval = 865 ± 131), and the current distribution area of L. maculata, we infer that the species is not in immediate risk of extinction in Finland. Our analysis shows that mark-recapture technique can provide precise estimates of adult population size of saproxylic beetles which have different adult and larval habitats, and thus be useful in assessing extinction risk and monitoring population trends.     

Helper component proteinase of the genus Potyvirus is an interaction partner of translation initiation factors eIF(iso)4E and eIF4E and contains a 4E binding motif

The multifunctional helper component proteinase (HCpro) of potyviruses (genus Potyvirus; Potyviridae) shows self-interaction and interacts with other potyviral and host plant proteins. Host proteins that are pivotal to potyvirus infection include the eukaryotic translation initiation factor eIF4E and the isoform eIF(iso)4E, which interact with viral genome-linked protein (VPg). Here we show that HCpro of Potato virus A (PVA) interacts with both eIF4E and eIF(iso)4E, with interactions with eIF(iso)4E being stronger, as judged by the data of a yeast two-hybrid system assay. A bimolecular fluorescence complementation assay on leaves of Nicotiana benthamiana showed that HCpro from three potyviruses (PVA, Potato virus Y, and Tobacco etch virus) interacted with the eIF(iso)4E and eIF4E of tobacco (Nicotiana tabacum); interactions with eIF(iso)4E and eIF4E of potato (Solanum tuberosum) were weaker. In PVA-infected cells, interactions between HCpro and tobacco eIF(iso)4E were confined to round structures that colocalized with 6K2-induced vesicles. Point mutations introduced to a 4E binding motif identified in the C-terminal region of HCpro debilitated interactions of HCpro with translation initiation factors and were detrimental to the virulence of PVA in plants. The 4E binding motif conserved in HCpro of potyviruses and HCpro-initiation factor interactions suggest new roles for HCpro and/or translation factors in the potyvirus infection cycle.     

Epistatic selection between coding and regulatory variation in human evolution and disease

Interaction (nonadditive effects) between genetic variants has been highlighted as an important mechanism underlying phenotypic variation, but the discovery of genetic interactions in humans has proved difficult. In this study, we show that the spectrum of variation in the human genome has been shaped by modifier effects of cis-regulatory variation on the functional impact of putatively deleterious protein-coding variants. We analyzed 1000 Genomes population-scale resequencing data from Europe (CEU [Utah residents with Northern and Western European ancestry from the CEPH collection]) and Africa (YRI [Yoruba in Ibadan, Nigeria]) together with gene expression data from arrays and RNA sequencing for the same samples. We observed an underrepresentation of derived putatively functional coding variation on the more highly expressed regulatory haplotype, which suggests stronger purifying selection against deleterious coding variants that have increased penetrance because of their regulatory background. Furthermore, the frequency spectrum and impact size distribution of common regulatory polymorphisms (eQTLs) appear to be shaped in order to minimize the selective disadvantage of having deleterious coding mutations on the more highly expressed haplotype. Interestingly, eQTLs explaining common disease GWAS signals showed an enrichment of putative epistatic effects, suggesting that some disease associations might arise from interactions increasing the penetrance of rare coding variants. In conclusion, our results indicate that regulatory and coding variants often modify the functional impact of each other. This specific type of genetic interaction is detectable from sequencing data in a genome-wide manner, and characterizing these joint effects might help us understand functional mechanisms behind genetic associations to human phenotypes-including both Mendelian and common disease.     

Global change synergies and trade‐offs between renewable energy and biodiversity

Reliance on fossil fuels is causing unprecedented climate change and is accelerating environmental degradation and global biodiversity loss. Together, climate change and biodiversity loss, if not averted urgently, may inflict severe damage on ecosystem processes, functions and services that support the welfare of modern societies. Increasing renewable energy deployment and expanding the current protected area network represent key solutions to these challenges, but conflicts may arise over the use of limited land for energy production as opposed to biodiversity conservation. Here, we compare recently identified core areas for the expansion of the global protected area network with the renewable energy potential available from land‐based solar photovoltaic, wind energy and bioenergy (in the form of Miscanthus × giganteus). We show that these energy sources have very different biodiversity impacts and net energy contributions. The extent of risks and opportunities deriving from renewable energy development is highly dependent on the type of renewable source harvested, the restrictions imposed on energy harvest and the region considered, with Central America appearing at particularly high potential risk from renewable energy expansion. Without restrictions on power generation due to factors such as production and transport costs, we show that bioenergy production is a major potential threat to biodiversity, while the potential impact of wind and solar appears smaller than that of bioenergy. However, these differences become reduced when energy potential is restricted by external factors including local energy demand. Overall, we found that areas of opportunity for developing solar and wind energy with little harm to biodiversity could exist in several regions of the world, with the magnitude of potential impact being particularly dependent on restrictions imposed by local energy demand. The evidence provided here helps guide sustainable development of renewable energy and contributes to the targeting of global efforts in climate mitigation and biodiversity conservation.