Choices in land representation materially affect modeled biofuel carbon intensity estimates.

Estimates of biofuel carbon intensity are uncertain and depend on modeled land use change (LUC) emissions. While analysts have focused on economic and agronomic assumptions affecting the quantity of land converted, researchers have paid less attention to how models classify land into broad categories and designate some categories as ineligible for LUC. To explore the effect of these land representation attributes, we use three versions of a global human and Earth systems model, GCAM, and compute the "carbon intensity of land-use change" (CI-LUC) from increased U.S. corn ethanol production. We consider uncertainty in model parameters along with the choice of land representation and find the latter is one of the most influential parameters on estimated CI-LUC. A version of the model that protects 90% of non-commercial land reduced estimated CI-LUC by an average of 32% across Monte Carlo trials compared to our baseline model. Another version that mimics the GTAP-BIO-ADV land representation, which protects all non-commercial land, reduced CI-LUC by an average of 19%. The results of this experiment demonstrate that land representation in biofuel LUC models is an important determinant of CI-LUC.

Optimized Methodology for the Calculation of Electrostriction from First-Principles.

In this work a new method for the calculation of the electrostrictive properties of materials using density functional theory is presented. The method relies on the thermodynamical equivalence, in a dielectric, of the quadratic mechanical responses (stress or strain) to applied electric stimulus (electric or polarization fields) to the strain or stress dependence of its dielectric susceptibility or stiffness tensors. Comparing with current finite-field methodologies for the calculation of electrostriction, it is demonstrated that this presented methodology offers significant advantages of efficiency, robustness, and ease of use. These advantages render tractable the high throughput theoretical investigation into the largely unknown electrostrictive properties of materials, and the microscopic origins of giant electrostriction.

Dynamic Linking of Upstream Energy and Freight Demands for Bio and Fossil Energy Pathways in the Global Change Analysis Model.

Comprehensive study of the environmental impacts associated with demand for an energy resource or carrier in any one sector requires a full consideration of the direct and indirect impacts on the rest of the regional and global energy system. Biofuels are especially complex since they have feedbacks to both the energy system and to regional and global crop markets. In this study, we present a strategy for dynamically including the upstream energy and transportation links to the Global Change Analysis Model. We incorporate the following inter-sectoral linkages: energy inputs to crop production, energy inputs to fossil resource production, and freight transport requirements of energy and agricultural commodities. We assess the implications of explicitly including these links by measuring the global impacts of increased corn ethanol demand in the United States with and without these links included. Although the net global impact of the upstream links on energy and emissions are relatively modest in the scenarios analyzed, the inclusion of these links illustrates interesting trade-offs in energy and transportation demand among fossil fuel and agriculture sectors. We find that the increment in agricultural energy driven by the additional biofuel production associated with the corn ethanol shock is higher than the decrease of energy associated with the displaced fossil fuel consumption. However, this effect is compensated by the reduction in freight transportation requirements of energy. These sectoral interactions suggest that this level of modeling detail could be important in evaluating future analytical questions.

Electronic and excitonic properties of ultrathin (In,Ga)N layers: the role of alloy and monolayer width fluctuations.

We present an atomistic theoretical analysis of the electronic and excitonic properties of ultrathin, monolayer thick wurtzite (In,Ga)N embedded in GaN. Our microscopic investigation reveals that (i) alloy fluctuations within the monolayer lead to carrier localization effects that dominate the electronic and optical properties of these ultrathin systems and that (ii) excitonic binding energies in these structures exceed the thermal energy at room temperature, enabling excitonic effects to persist even at elevated temperatures. Our theoretical findings are consistent with, and provide an explanation for, literature experimental observations of (i) broad photoluminescence linewidth and (ii) excitonic effects contributing to the radiative recombination process at elevated temperatures. When accounting for small structural inhomogeneities, such as local thickness fluctuations of one monolayer, "indirect" excitons may be found, with electrons and holes independently localized in different spatial positions. This result also provides further arguments for experimentally observed effects such as (i) non-exponential decay curves in time dependent photoluminescence spectra and (ii) the "S"-shape temperature dependence of the photoluminescence peak energies. Overall, our results provide fundamental understanding, on an atomistic level, of the electronic and optical properties of ultrathin, quasi 2D (In,Ga)N monolayers embedded in GaN, and offer guidance for the tailoring of their properties for potential future device applications.

KSRP modulation of GAP-43 mRNA stability restricts axonal outgrowth in embryonic hippocampal neurons.

The KH-type splicing regulatory protein (KSRP) promotes the decay of AU-rich element (ARE)-containing mRNAs. Although KSRP is expressed in the nervous system, very little is known about its role in neurons. In this study, we examined whether KSRP regulates the stability of the ARE-containing GAP-43 mRNA. We found that KSRP destabilizes this mRNA by binding to its ARE, a process that requires the presence of its fourth KH domain (KH4). Furthermore, KSRP competed with the stabilizing factor HuD for binding to these sequences. We also examined the functional consequences of KSRP overexpression and knockdown on the differentiation of primary hippocampal neurons in culture. Overexpression of full length KSRP or KSRP without its nuclear localization signal hindered axonal outgrowth in these cultures, while overexpression of a mutant protein without the KH4 domain that has less affinity for binding to GAP-43's ARE had no effect. In contrast, depletion of KSRP led to a rise in GAP-43 mRNA levels and a dramatic increase in axonal length, both in KSRP shRNA transfected cells and neurons cultured from Ksrp(+/-) and Ksrp(-/-) embryos. Finally we found that overexpression of GAP-43 rescued the axonal outgrowth deficits seen with KSRP overexpression, but only when cells were transfected with GAP-43 constructs containing 3' UTR sequences targeting the transport of this mRNA to axons. Together, our results suggest that KSRP is an important regulator of mRNA stability and axonal length that works in direct opposition to HuD to regulate the levels of GAP-43 and other ARE-containing neuronal mRNAs.

Increased expression of axogenesis-related genes and mossy fibre length in dentate granule cells from adult HuD overexpressor mice.

The neuronal RNA-binding protein HuD plays a critical role in the post-transcriptional regulation of short-lived mRNAs during the initial establishment and remodelling of neural connections. We have generated transgenic mice overexpressing this protein (HuD-Tg) in adult DGCs (dentate granule cells) and shown that their mossy fibres contain high levels of GAP-43 (growth-associated protein 43) and exhibit distinct morphological and electrophysiological properties. To investigate the basis for these changes and identify other molecular targets of HuD, DGCs from HuD-Tg and control mice were collected by LCM (laser capture microscopy) and RNAs analysed using DNA microarrays. Results show that 216 known mRNAs transcripts and 63 ESTs (expressed sequence tags) are significantly up-regulated in DGCs from these transgenic mice. Analyses of the 3'-UTRs (3'-untranslated regions) of these transcripts revealed an increased number of HuD-binding sites and the presence of several known instability-conferring sequences. Among these, the mRNA for TTR (transthyretin) shows the highest level of up-regulation, as confirmed by qRT-PCR (quantitative reverse transcription-PCR) and ISH (in situ hybridization). GO (gene ontology) analyses of up-regulated transcripts revealed a large over-representation of genes associated with neural development and axogenesis. In correlation with these gene expression changes, we found an increased length of the infrapyramidal mossy fibre bundle in HuD-Tg mice. These results support the notion that HuD stabilizes a number of developmentally regulated mRNAs in DGCs, resulting in increased axonal elongation.

Oligodendrocyte progenitors reversibly exit the cell cycle and give rise to astrocytes in response to interferon-γ.

Oligodendrocyte-type 2 astrocyte progenitor cells (O-2A/OPCs) populate the CNS and generate oligodendrocytes and astrocytes in vitro and in vivo. Understanding how O-2A/OPCs respond to their environment is crucial to understanding how these cells function in the CNS and how to best promote their therapeutic proliferation and differentiation. We show that interferon-γ (IFN-γ) was not toxic to highly purified perinatal or adult rat O-2A/OPCs. IFN-γ treatment led to downregulation of PDGFR-α (platelet-derived growth factor receptor-α) and Ki-67 and decreased self-renewal in clonal populations. IFN-γ also significantly increased the proportion of cells in the G(0)/G(1) phase of the cell cycle, decreased BrdU (5-bromo-2'-deoxyuridine) incorporation, and led to increased expression of the cell cycle inhibitors Rb and p27(kip1). Although p27(kip1) expression was not necessary for IFN-γ-mediated quiescence, its upstream regulator IRF-1 was required. The quiescent state of O-2A/OPCs caused by IFN-γ was reversible as the withdrawal of IFN-γ allowed O-2A/OPCs to appropriately respond to both proliferation and differentiation signals. Differentiation into oligodendrocytes induced by either thyroid hormone or CNTF was also abrogated by IFN-γ. This inhibition was specific to the oligodendrocyte pathway, as O-2A/OPC differentiation into astrocytes was not inhibited. IFN-γ alone also led to the generation of GFAP-positive astrocytes in a subset of O-2A/OPCs. Together, these results demonstrate a reversible inhibitory effect of IFN-γ on O-2A/OPC proliferation with a concomitant generation of astrocytes. We propose that neuroinflammation involving increased IFN-γ can reduce progenitor numbers and inhibit differentiation, which has significant clinical relevance for injury repair, but may also contribute to the generation of astrocytes.

[Local treatment of chronic skin wounds in a Swiss out-patient wound centre 2010]. / Lokale Behandlung von chronischen Hautwunden an einer Schweizerischen Wundambulanz 2010.

In Switzerland around 30,000 patients suffer from chronic skin wounds. Appropriate topical wound care along with treatment of the causes of the wounds enables to heal a lot of these patients and to avoid secondary disease such as infections. Thereby, the final goal of wound care is stable reepithelisation. Based on experience with chronic leg ulcers mainly in our out-patient wound centre, we give a survey of the wound dressings we actually use and discuss their wound-phase adapted application. Furthermore, we address the two tissue engineering products reimbursed in Switzerland, Apligraf and EpiDex, as well as the biological matrix product Oasis. The crucial question, which treatment options will be offered in future to the wound patients by our health regulatory and insurance systems, is open to debate.

Alterations in mossy fiber physiology and GAP-43 expression and function in transgenic mice overexpressing HuD.

HuD is a neuronal RNA-binding protein associated with the stabilization of mRNAs for GAP-43 and other neuronal proteins that are important for nervous system development and learning and memory mechanisms. To better understand the function of this protein, we generated transgenic mice expressing human HuD (HuD-Tg) in adult forebrain neurons. We have previously shown that expression of HuD in adult dentate granule cells results in an abnormal accumulation of GAP-43 mRNA via posttranscriptional mechanisms. Here we show that this mRNA accumulation leads to the ectopic expression of GAP-43 protein in mossy fibers. Electrophysiological analyses of the mossy fiber to CA3 synapse of HuD-Tg mice revealed increases in paired-pulse facilitation (PPF) at short interpulse intervals and no change in long-term potentiation (LTP). Presynaptic calcium transients at the same synapses exhibited faster time constants of decay, suggesting a decrease in the endogenous Ca(2+) buffer capacity of mossy fiber terminals of HuD-Tg mice. Under resting conditions, GAP-43 binds very tightly to calmodulin sequestering it and then releasing it upon PKC-dependent phosphorylation. Therefore, subsequent studies examined the extent of GAP-43 phosphorylation and its association to calmodulin. We found that despite the increased GAP-43 expression in HuD-Tg mice, the levels of PKC-phosphorylated GAP-43 were decreased in these animals. Furthermore, in agreement with the increased proportion of nonphosphorylated GAP-43, HuD-Tg mice showed increased binding of calmodulin to this protein. These results suggest that a significant amount of calmodulin may be trapped in an inactive state, unable to bind free calcium, and activate downstream signaling pathways. In conclusion, we propose that an unregulated expression of HuD disrupts mossy fiber physiology in adult mice in part by altering the expression and phosphorylation of GAP-43 and the amount of free calmodulin available at the synaptic terminal.

Coordinated expression of HuD and GAP-43 in hippocampal dentate granule cells during developmental and adult plasticity.

Previous work from our laboratory demonstrated that the RNA-binding protein HuD binds to and stabilizes the GAP-43 mRNA. In this study, we characterized the expression of HuD and GAP-43 mRNA in the hippocampus during two forms of neuronal plasticity. During post-natal development, maximal expression of both molecules was found at P5 and their levels steadily decreased thereafter. At P5, HuD was also present in the subventricular zone, where it co-localized with doublecortin. In the adult hippocampus, the basal levels of HuD and GAP-43 were lower than during development but were significantly increased in the dentate gyrus after seizures. The function of HuD in GAP-43 gene expression was confirmed using HuD-KO mice, in which the GAP-43 mRNA was significantly less stable than in wild type mice. Altogether, these results demonstrate that HuD plays a role in the post-transcriptional control of GAP-43 mRNA in dentate granule cells during developmental and adult plasticity.

Behavioral teratogenicity induced by nonforced maternal nicotine consumption.

Prenatal nicotine exposure (PNE) has been associated with increased prevalence of attention deficit hyperactivity disorder (ADHD), major depressive disorder (MDD) and substance abuse in exposed children and adolescents. Whether these syndromes are caused by nicotine exposure, or genetic and psychosocial adversities associated with maternal smoking is not completely clear. Animal models suggest a direct impact of PNE. However, the fact that nicotine is forcefully administrated in these paradigms raises some questions about the specificity of these findings. Pregnant C57BI/6J mice were allowed to choose drinking saccharin/nicotine solutions or pure water. Controls could choose saccharin solutions or pure water. Offspring were tested in spontaneous locomotion, fear-associated learning (trace conditioning), addictive (conditioned place preference), and depression-like (learned helplessness) behaviors. There was no significant difference in weight or pup number between the prenatal treatment groups. A significant effect of PNE was observed on spontaneous locomotion, preference for a cocaine-associated place, and latency to escape in the learned helplessness paradigm. Surprisingly, PNE mice exhibited an increased learning of trace-conditioned fear-associated cues. The hyperlocomotive behavior reported in animal models of PNE is not likely an artifact of forceful nicotine administration. The increased prevalence of ADHD, MDD and substance abuse observed in PNE children and adolescents is probably caused by direct behavioral teratogenic effects of PNE. The role of PNE as a risk factor of syndromes associated to increased learning of fear-associated cues such as post-traumatic stress disorder (PTSD) warrants further evaluation.

Associative and spatial learning and memory deficits in transgenic mice overexpressing the RNA-binding protein HuD.

HuD is a neuronal specific RNA-binding protein associated with the stabilization of short-lived mRNAs during brain development, nerve regeneration and synaptic plasticity. To investigate the functional significance of this protein in the mature brain, we generated transgenic mice overexpressing HuD in forebrain neurons under the control of the alphaCaMKinII promoter. We have previously shown that one of the targets of HuD, GAP-43 mRNA, was stabilized in neurons in the hippocampus, amygdala and cortex of transgenic mice. Animals from two independent lines expressing different levels of the transgene were subjected to a battery of behavioral tests including contextual fear conditioning and the Morris water maze. Our results show that although HuD is increased after learning and memory, constitutive HuD overexpression impaired the acquisition and retention of both cued and contextual fear and the ability to remember the position of a hidden platform in the Morris water maze. No motor-sensory abnormalities were observed in HuD transgenic mice, suggesting that the poor performance of the mice in these tests reflect a true cognitive impairment. We conclude that posttranscriptional regulation of gene expression by stabilization of specific mRNAs may have to be restricted temporally and spatially for proper acquisition and storage of memories.

In vivo post-transcriptional regulation of GAP-43 mRNA by overexpression of the RNA-binding protein HuD.

HuD is a neuronal-specific RNA-binding protein that binds to and stabilizes the mRNAs of growth-associated protein-43 (GAP-43) and other neuronal proteins. HuD expression increases during brain development, nerve regeneration, and learning and memory, suggesting that this protein is important for controlling gene expression during developmental and adult plasticity. To examine the function of HuD in vivo, we generated transgenic mice overexpressing human HuD under the control of the calcium-calmodulin-dependent protein kinase IIalpha promoter. The transgene was expressed at high levels throughout the forebrain, including the hippocampal formation, amygdala and cerebral cortex. Using quantitative in situ hybridization, we found that HuD overexpression led to selective increases in GAP-43 mRNA in hippocampal dentate granule cells and neurons in the lateral amygdala and layer V of the neorcortex. In contrast, GAP-43 pre-mRNA levels were unchanged or decreased in the same neuronal populations. Comparison of the levels of mature GAP-43 mRNA and pre-mRNA in the same neurons of transgenic mice suggested that HuD increased the stability of the transcript. Confirming this, mRNA decay assays revealed that the GAP-43 mRNA was more stable in brain extracts from HuD transgenic mice than non-transgenic littermates. In conclusion, our results demonstrate that HuD overexpression is sufficient to increase GAP-43 mRNA stability in vivo.

Fetal alcohol exposure alters GAP-43 phosphorylation and protein kinase C responses to contextual fear conditioning in the hippocampus of adult rat offspring.

BACKGROUND: The growth- and plasticity-associated protein GAP-43 plays a significant role in the establishment and remodeling of neuronal connections. We have previously shown that GAP-43 levels, protein kinase C (PKC) activity, and GAP-43 phosphorylation increase during contextual fear conditioning and that fetal alcohol exposure (FAE) decreases PKC activity and GAP-43 phosphorylation in the hippocampus of adult offspring. Drawing on these observations, we hypothesized that FAE manifests its cognitive impairment by disrupting PKC activation and membrane translocation, thereby decreasing GAP-43 phosphorylation and function. METHODS: Three groups of pregnant rat dams (FAE and two control diet groups) were placed on different diet regimens. Offspring from each of these groups were placed into each of four test groups, a contextual fear conditioned (CFC) group, a naïve unhandled group, and two nonlearning stress control groups. Hippocampi were dissected, homogenized, and used to prepare a cytosolic and a membrane fraction. These fractions were probed for total GAP-43, PKC-phosphorylated GAP-43, and several PKC subtypes. PKC activity also was measured in total homogenates. RESULTS: Compared with both control diet groups, FAE animals showed a deficit in the activation of PKC in the hippocampus at 24 hr but not at 1.5 hr after CFC. Likewise, we found that the amount of GAP-43 and its phosphorylation were decreased 24 hr after CFC in FAE rats but not at early times after training. Analysis of the translocation of various PKC isoforms revealed that FAE animals had decreased levels of membrane-bound PKC beta2 and PKC epsilon 24 hr after CFC. CONCLUSIONS: Considering the role of PKC activation and GAP-43 phosphorylation in synaptic plasticity, our results suggest that deficient translocation of PKC beta2 and PKC epsilon in the hippocampus may mediate the electrophysiological and behavioral deficits observed in fetal alcohol exposed animals.

Crystallization and preliminary X-ray analysis of native and selenomethionine 2-hydroxybiphenyl 3-monooxygenase.

2-hydroxybiphenyl 3-monooxygenase (HbpA; EC 1.14.13.44) from Pseudomonas azelaica HBP1 was produced in Escherichia coli both as native and SeMet-labelled protein. The two enzymes were purified to homogeneity and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 108.6, b = 196.8, c = 79.3 A, beta = 97.7 degrees for the native protein and a = 108.3, b = 196.8, c = 79.0 A, beta = 97.8 degrees for SeMet HbpA. Crystal-packing considerations led to the assumption of two HbpA subunits per asymmetric unit, which corresponds to a V(M) value of 3.3 A(3) Da(-1) and a solvent content of 62%. The crystals were radiation-sensitive and only had a lifespan of about 120 s when exposed to synchrotron radiation on an undulator beamline. To obtain complete data sets, data were collected from 23 native and 26 derivative crystals. The high-resolution limit was 2.0 A for native and 2.25 A for SeMet HbpA.