Bioenergy and the importance of land use policy in a carbon-constrained world

Policies aimed at limiting anthropogenic climate change would result in significant transformations of the energy and land-use systems. However, increasing the demand for bioenergy could have a tremendous impact on land use, and can result in land clearing and deforestation. Wise et al. (2009a,b) analyzed an idealized policy to limit the indirect land use change emissions from bioenergy. The policy, while effective, would be difficult, if not impossible, to implement in the real world. In this paper, we consider several different land use policies that deviate from this first-best, using the Joint Global Change Research Institute’s Global Change Assessment Model (GCAM). Specifically, these new frameworks are (1) a policy that focuses on just the above-ground or vegetative terrestrial carbon rather than the total carbon, (2) policies that focus exclusively on incentivizing and protecting forestland, and (3) policies that apply an economic penalty on the use of biomass as a proxy to limit indirect land use change emissions. For each policy, we examine its impact on land use, land-use change emissions, atmospheric CO2 concentrations, agricultural supply, and food prices

eIF1A/eIF5B Interaction Network and its Functions in Translation Initiation Complex Assembly and Remodeling

Eukaryotic translation initiation is a highly regulated process involving multiple steps, from 43S pre-initiation complex (PIC) assembly, to ribosomal subunit joining. Subunit joining is controlled by the G-protein eukaryotic translation initiation factor 5B (eIF5B). Another protein, eIF1A, is involved in virtually all steps, including subunit joining. The intrinsically disordered eIF1A C-terminal tail (eIF1A-CTT) binds to eIF5B Domain-4 (eIF5B-D4). The ribosomal complex undergoes conformational rearrangements at every step of translation initiation; however, the underlying molecular mechanisms are poorly understood. Here we report three novel interactions involving eIF5B and eIF1A: (i) a second binding interface between eIF5B and eIF1A; (ii) a dynamic intramolecular interaction in eIF1A between the folded domain and eIF1A-CTT; and (iii) an intramolecular interaction between eIF5B-D3 and -D4. The intramolecular interactions within eIF1A and eIF5B interfere with one or both eIF5B/eIF1A contact interfaces, but are disrupted on the ribosome at different stages of translation initiation. Therefore, our results indicate that the interactions between eIF1A and eIF5B are being continuously rearranged during translation initiation. We present a model how the dynamic eIF1A/eIF5B interaction network can promote remodeling of the translation initiation complexes, and the roles in the process played by intrinsically disordered protein segments

Topology and Regulation of the Human eIF4A/4G/4H Helicase Complex in Translation Initiation

SummaryThe RNA helicase eIF4A plays a key role in unwinding of mRNA and scanning during translation initiation. Free eIF4A is a poor helicase and requires the accessory proteins eIF4G and eIF4H. However, the structure of the helicase complex and the mechanisms of stimulation of eIF4A activity have remained elusive. Here we report the topology of the eIF4A/4G/4H helicase complex, which is built from multiple experimentally observed domain-domain contacts. Remarkably, some of the interactions are continuously rearranged during the ATP binding/hydrolysis cycle of the helicase. We show that the accessory proteins modulate the affinity of eIF4A for ATP by interacting simultaneously with both helicase domains and promoting either the closed, ATP-bound conformation or the open, nucleotide-free conformation. The topology of the complex and the spatial arrangement of the RNA-binding surfaces offer insights into their roles in stimulation of helicase activity and the mechanisms of mRNA unwinding and scanning

Functional asymmetry and chemical reactivity of CsoR family persulfide sensors

CstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily. While CstR regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens, other dithiol-containing CsoR proteins respond to host derived Cu(I) toxicity, sometimes in the same bacterial cytoplasm, but without regulatory crosstalk in cells. It is not clear what prevents this crosstalk, nor the extent to which RSS sensors exhibit specificity over other oxidants. Here, we report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, which together with the first crystallographic structure of a CstR and comprehensive mass spectrometry-based kinetic profiling experiments, reveal new insights into the molecular basis of RSS specificity in CstRs. We find that the more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. Moreover, our CstR crystal structure is markedly asymmetric and chemical reactivity experiments reveal the functional impact of this asymmetry. Substitution of the Asn wedge between the resolving and the attacking thiol with Ala significantly decreases asymmetry in the crystal structure and markedly impacts the distribution of species, despite adopting the same global structure as the parent repressor. Companion NMR, SAXS and molecular dynamics simulations reveal that the structural and functional asymmetry can be traced to fast internal dynamics of the tetramer. Furthermore, this asymmetry is preserved in all CstRs and with all oxidants tested, giving rise to markedly distinct distributions of crosslinked products. Our exploration of the sequence, structural, and kinetic features that determine oxidant-specificity suggest that the product distribution upon RSS exposure is determined by internal flexibility.Fil: Fakhoury, Joseph N. Indiana University; Estados UnidosFil: Zhang, Yifan. Indiana University; Estados UnidosFil: Edmonds, Katherine A. Indiana University; Estados UnidosFil: Bringas, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Luebke, Justin L. Indiana University; Estados UnidosFil: Gonzalez Gutierrez, Giovanni. Indiana University; Estados UnidosFil: Capdevila, Daiana Andrea. Indiana University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Giedroc, David Peter. Indiana University; Estados Unido

How to fragment peralkaline rhyolites: Observations on pumice using combined multi-scale 2D and 3D imaging

Peralkaline rhyolites are volatile-rich magmas that typically erupt in continental rift settings. The high alkali and halogen content of these magmas results in viscosities two to three orders of magnitude lower than in calc-alkaline rhyolites. Unless extensive microlite crystallisation occurs, the calculated strain rates required for fragmentation are unrealistically high, yet peralkaline pumices from explosive eruptions of varying scales are commonly microlite-free. Here we present a combined 2D scanning electron microscopy and 3D X-ray microtomography study of peralkaline rhyolite vesicle textures designed to investigate fragmentation processes. Microlite-free peralkaline pumice textures from Pantelleria, Italy, strongly resemble those from calc-alkaline rhyolites on both macro and micro scales. These textures imply that the pumices fragmented in a brittle fashion and that their peralkaline chemistry had little direct effect on textural evolution during bubble nucleation and growth. We suggest that the observed pumice textures evolved in response to high decompression rates and that peralkaline rhyolite magmas can fragment when strain localisation and high bubble overpressures develop during rapid ascent

Climate policy implications for agricultural water demand

Energy, water and land are scarce resources, critical to humans. Developments in each affect the availability and cost of the others, and consequently human prosperity. Measures to limit greenhouse gas concentrations will inevitably exact dramatic changes on energy and land systems and in turn alter the character, magnitude and geographic distribution of human claims on water resources. We employ the Global Change Assessment Model (GCAM), an integrated assessment model to explore the interactions of energy, land and water systems in the context of alternative policies to limit climate change to three alternative levels: 2.5 Wm-2 (445 ppm CO2-e), 3.5 Wm-2 (535 ppm CO2-e) and 4.5 Wm-2 (645 ppm CO2-e). We explore the effects of two alternative land-use emissions mitigation policy options—one which taxes terrestrial carbon emissions equally with fossil fuel and industrial emissions, and an alternative which only taxes fossil fuel and industrial emissions but places no penalty on land-use change emissions. We find that increasing populations and economic growth could be anticipated to almost triple demand for water for agricultural systems across the century even in the absence of climate policy. In general policies to mitigate climate change increase agricultural demands for water still further, though the largest changes occur in the second half of the century, under both policy regimes. The two policies examined profoundly affected both the sources and magnitudes of the increase in irrigation water demands. The largest increases in agricultural irrigation water demand occurred in scenarios where only fossil fuel emissions were priced (but not land-use change emission) and were primarily driven by rapid expansion in bioenergy production. In these scenarios water demands were large relative to present-day total available water, calling into question whether it would be physically possible to produce the associated biomass energy. We explored the potential of improved water delivery and irrigation system efficiencies. These could potentially reduce demands substantially. However, overall demands remained high under our fossil-fuel-only tax policy. In contrast, when all carbon was priced, increases in agricultural water demands were smaller than under the fossil-fuel-only policy and were driven primarily by increased demands for water by non-biomass crops such as rice. Finally we estimate the geospatial pattern of water demands and find that regions such as China, India and other countries in south and east Asia might be expected to experience greatest increases in water demands

Reduced Regional Cerebral Blood Flow Relates to Poorer Cognition in Older Adults With Type 2 Diabetes

Type 2 diabetes mellitus (T2DM) increases risk for dementia, including Alzheimer’s disease (AD). Many previous studies of brain changes underlying cognitive impairment in T2DM have applied conventional structural magnetic resonance imaging (MRI) to detect macrostructural changes associated with cerebrovascular disease such as white matter hyperintensities or infarcts. However, such pathology likely reflects end-stage manifestations of chronic decrements in cerebral blood flow (CBF). MRI techniques that measure CBF may (1) elucidate mechanisms that precede irreversible parenchymal damage and (2) serve as a marker of risk for cognitive decline. CBF measured with arterial spin labeling (ASL) MRI may be a useful marker of perfusion deficits in T2DM and related conditions. We examined associations among T2DM, CBF, and cognition in a sample of 49 well-characterized nondemented older adults. Along with a standard T1-weighted scan, a pseudocontinuous ASL sequence optimized for older adults (by increasing post-labeling delays to allow more time for the blood to reach brain tissue) was obtained on a 3T GE scanner to measure regional CBF in FreeSurfer derived regions of interest. Participants also completed a neuropsychological assessment. Results showed no significant differences between individuals with and without T2DM in terms of cortical thickness or regional brain volume. However, adjusting for age, sex, comorbid vascular risk factors, and reference CBF (postcentral gyrus) older adults with T2DM demonstrated reduced CBF in the hippocampus, and inferior temporal, inferior parietal, and frontal cortices. Lower CBF was associated with poorer memory and executive function/processing speed. When adjusting for diabetes, the significant associations between lower regional CBF and poorer executive function/processing speed remained. Results demonstrate that CBF is reduced in older adults with T2DM, and suggest that CBF alterations likely precede volumetric changes. Notably, relative to nondiabetic control participants, those with T2DM showed lower CBF in predilection sites for AD pathology (medial temporal lobe and inferior parietal regions). Findings augment recent research suggesting that perfusion deficits may underlie cognitive decrements frequently observed among older adults with T2DM. Results also suggest that CBF measured with ASL MRI may reflect an early and important marker of risk of cognitive impairment in T2DM and related conditions