Modelled effects of rising CO2 concentration and climate change on native perennial grass and sown grass-legume pastures

Native perennial grass and sown grass-legume pastures are an important agricultural and environmental resource. We investigated the impact of rising carbon dioxide concentration ([CO2]) and projected climate changes on these pasture ecosystems in southeastern Tasmania, Australia, using a biophysical simulation model, EcoMod. The model consists of interdependent modules that describe soil physicochemical and hydrological characteristics, and pasture growth and senescence, with fluxes described by empirical and mechanistic equations. Our simulations showed that in native pastures, projected climate change increased the biomass of C-4 grasses, with limited impact upon C-3 grasses, a trend reversed by rising [CO2]. In sown pastures, projected climate change decreased the biomass of perennial rye grass Lolium perenne and total biomass markedly by 2070, whilst subterranean clover Trifolium subterraneum biomass increased. Subterranean clover biomass changed little with increased [CO2] alone, whereas perennial rye grass biomass increased. Responses across pastures reflected species' tolerances to environmental factors, with projected climate change generally having more of an impact on biomass than rising [CO2]. Changes in both [CO2] and climate led to a reduction in protein content and digestibility. Soil inorganic nutrient concentrations decreased with increasing [CO2] and increased with projected climate change. Further simulations should investigate whether these patterns are robust for different sites and alternative environmental futures. Our results reinforce the need to pursue adaptation strategies in response to environmental change in order to maintain productive pasture ecosystems

A Recoding Method to Improve the Humoral Immune Response to an HIV DNA Vaccine

This manuscript describes a novel strategy to improve HIV DNA vaccine design. Employing a new information theory based bioinformatic algorithm, we identify a set of nucleotide motifs which are common in the coding region of HIV, but are under-represented in genes that are highly expressed in the human genome. We hypothesize that these motifs contribute to the poor protein expression of gag, pol, and env genes from the c-DNAs of HIV clinical isolates. Using this approach and beginning with a codon optimized consensus gag gene, we recode the nucleotide sequence so as to remove these motifs without modifying the amino acid sequence. Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version. We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model. Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine

A population-based study of the clinical expression of the hemochromatosis gene

Background and Methods: Hereditary hemochromatosis is associated with homozygosity for the C282Y mutation in the hemochromatosis (HFE) gene on chromosome 6, elevated serum transferrin saturation, and excess iron deposits throughout the body. To assess the prevalence and clinical expression of the HFE gene, we conducted a population-based study in Busselton, Australia. In 1994, we obtained blood samples for the determination of serum transferrin saturation and ferritin levels and the presence or absence of the C282Y mutation and the H63D mutation (which may contribute to increased hepatic iron levels) in 3011 unrelated white adults. We evaluated all subjects who had persistently elevated transferrin-saturation values (45 percent or higher) or were homozygous for the C282Y mutation. We recommended liver biopsy for subjects with serum ferritin levels of 300 ng per milliliter or higher. The subjects were followed for up to four years. Results: Sixteen of the subjects (0.5 percent) were homozygous for the C282Y mutation, and 424 (14.1 percent) were heterozygous. The serum transferrin saturation was 45 percent or higher in 15 of the 16 who were homozygous; in 1 subject it was 43 percent. Four of the homozygous subjects had previously been given a diagnosis of hemochromatosis, and 12 had not. Seven of these 12 patients had elevated serum ferritin levels in 1994; 6 of the 7 had further increases in 1998, and 1 had a decrease, although the value remained elevated. The serum ferritin levels in the four other homozygous patients remained in the normal range. Eleven of the 16 homozygous subjects underwent liver biopsy; 3 had hepatic fibrosis, and 1, who had a history of excessive alcohol consumption, had cirrhosis and mild microvesicular steatosis. Eight of the 16 homozygous subjects had clinical findings that were consistent with the presence of hereditary hemochromatosis, such as hepatomegaly, skin pigmentation, and arthritis. Conclusions: In a population of white adults of northern European ancestry, 0.5 percent were homozygous for the C282Y mutation in the HFE gene. However, only half of those who were homozygous had clinical features of hemochromatosis, and one quarter had serum ferritin levels that remained normal over a four-year period

Small RNA analysis in Sindbis virus infected human HEK293 cells

In contrast to the defence mechanism of RNA interference (RNAi) in plants and invertebrates, its role in the innate response to virus infection of mammals is a matter of debate. Since RNAi has a well-established role in controlling infection of the alphavirus Sindbis virus (SINV) in insects, we have used this virus to investigate the role of RNAi in SINV infection of human cells

Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing

Human Tudor-SN is involved in the degradation of hyper-edited inosine-containing microRNA precursors, thus linking the pathways of RNA interference and editing. Tudor-SN contains four tandem repeats of staphylococcal nuclease-like domains (SN1–SN4) followed by a tudor and C-terminal SN domain (SN5). Here, we showed that Tudor-SN requires tandem repeats of SN domains for its RNA binding and cleavage activity. The crystal structure of a 64-kD truncated form of human Tudor-SN further shows that the four domains, SN3, SN4, tudor and SN5, assemble into a crescent-shaped structure. A concave basic surface formed jointly by SN3 and SN4 domains is likely involved in RNA binding, where citrate ions are bound at the putative RNase active sites. Additional modeling studies provide a structural basis for Tudor-SN's preference in cleaving RNA containing multiple I·U wobble-paired sequences. Collectively, these results suggest that tandem repeats of SN domains in Tudor-SN function as a clamp to capture RNA substrates

Carbon myopia: the urgent need for integrated social, economic and environmental action in the livestock sector

Livestock have long been integral to food production systems, often not by choice but by need. While our knowledge of livestock greenhouse gas emissions (GHG) mitigation has evolved, the prevailing focus has been - somewhat myopically on technology applications associated with mitigation.Here, we (1) examine the global distribution of livestock GHG emissions, (2) explore social, economic and environmental co-benefits and trade-offs associated with mitigation interventions, and (3) critique approaches for quantifying GHG emissions.This review uncovered many insights. First, while GHG emissions from ruminant livestock are greatest in low and middle-income countries (LMIC; globally, 66% of emissions are produced by Latin America and the Caribbean, East and southeast Asia, and south Asia), the majority of mitigation strategies are designed for developed countries. This serious concern is heightened by the fact that 80% of growth in global meat production over the next decade will occur in LMIC. Second, few studies concurrently assess social, economic and environmental aspects of mitigation. Of the 54 interventions reviewed, only 16 had triple-bottom line benefit with medium-high mitigation potential. Third, while efforts designed to stimulate adoption of strategies allowing both emissions reduction (ER) and carbon sequestration (CS) would achieve the greatest net emissions mitigation, CS measures have greater potential mitigation and co-benefits.The scientific community must shift attention away from the prevailing myopic lens on carbon, towards more holistic, systems-based, multi-metric approaches that carefully consider the raison d'être for livestock systems. Consequential life-cycle assessments and systems-aligned socio-economic planetary boundaries offer useful starting points that may uncover leverage points and cross-scale emergent properties. Derivation of harmonised, globally-reconciled sustainability metrics requires iterative dialogue between stakeholders at all levels. Greater emphasis on the simultaneous characterisation of multiple sustainability dimensions would help avoid situations where progress made in one area causes maladaptive outcomes in other areas

Basic Amino Acid Mutations in the Nuclear Localization Signal of Hibiscus Chlorotic Ringspot Virus p23 Inhibit Virus Long Distance Movement

10.1371/journal.pone.0074000PLoS ONE89-POLN

Top Quarks as a Window to String Resonances

We study the discovery potential of string resonances decaying to $t\bar{t}$ final state at the LHC. We point out that top quark pair production is a promising and an advantageous channel for studying such resonances, due to their low Standard Model background and unique kinematics. We study the invariant mass distribution and angular dependence of the top pair production cross section via exchanges of string resonances. The mass ratios of these resonances and the unusual angular distribution may help identify their fundamental properties and distinguish them from other new physics. We find that string resonances for a string scale below 4 TeV can be detected via the $t\bar{t}$ channel, either from reconstructing the $t\bar{t}$ semi-leptonic decay or recent techniques in identifying highly boosted tops.Comment: 22 pages, 6 figure