Tracking current and forecasting future land-use impacts of agricultural value chains. 67th Discussion Forum on Life Cycle Assessment, 3rd of November 2017, Zurich,Switzerland

The 67th Discussion Forum on Life Cycle Assessment (LCA), organised by partners of the European project RELIEF (RELIability of product Environmental Footprints), focused on methods for better understanding the impacts of land use linked to agricultural value chains. The first session of the forum was dedicated to methods that help in retrospective tracking of land use within complex supply chains. Novel approaches were presented for the integration of increasingly available spatially located land use data into LCA. The second session focused on forward-looking projections of land use change and included emerging, predictive methods for the modelling of land change. The third session considered impact assessment methods related to the use of land and their application together with land change modelling approaches. Discussions throughout the day centred on opportunities and challenges arising from integrating spatially located land use information into Life Cycle Assessment. Increasing amounts of spatially located land use data are becoming available and this could potentially increase the robustness and specificity of Life Cycle Assessment. However, the use of such data can be computationally expensive and requires the development of skills (i.e. use of geographical information systems (GIS) and model coding) within the LCA community. Land change modelling and ecosystem service modelling are associated with considerable uncertainty which must be communicated appropriately to stakeholders and decision-makers when interpreting results from an LCA. The new approaches were found to challenge aspects of the traditional LCA approach—particularly the division between the life cycle inventory and impact assessment and the assumption of linearity between scale and impacts when deriving characterisation factors. The presentations from the DF-67 are available for download (www.lcaforum.ch), and video recordings can be accessed online (http://www.video.ethz.ch/events/lca/2017/autumn/67th.html).     

Follistatin antagonizes transforming growth factor-beta3-induced epithelial-mesenchymal transition in vitro: implications for murine palatal development supported by microarray analysis

Abstract Epithelial–mesenchymal transition (EMT) is involved in normal embryonic development as well as in tumor progression and invasiveness. This process is also known to be a crucial step in palatogenesis during fusion of the bi-lateral palatal processes. Disruption of this step results in a cleft palate, which is among the most frequent birth defects in humans. A number of genes and encoded proteins have been shown to play a role in this developmental stage. The central role is attributed to the cytokine transforming growth factor-β3 (TGF-β3), which is expressed in the medial edge epithelium (MEE) already before the fusion process. The MEE covers the tips of the growing palatal shelves and eventually undergoes EMT or programmed cell death (apoptosis). TGF-β3 is described to induce EMT in embryonic palates. With regard to the early expression of this molecule before the fusion process, it is not well understood which mechanisms prevent the TGF-β3 producing epithelial cells from undergoing differentiation precociously. We used the murine palatal fusion to study the regulation of EMT. Specifically, we analyzed the MEE for the expression of known antagonists of TGF-β molecules using in situ hybridization and detected the gene coding for Follistatin to be co-expressed with TGF-β3. Further, we could show that Follistatin directly binds to TGF-β3 and that it completely blocks TGF-β3-induced EMT of the normal murine mammary gland (NMuMG) epithelial cell line in vitro . In addition, we analyzed the gene expression profile of NMuMG cells during TGF-β3-induced EMT by microarray hybridization, detecting strong changes in the expression of apoptosis-regulating genes.     

Intermittent Preventive Treatment in Pregnant Women Is Associated with Increased Risk of Severe Malaria in Their Offspring

Background

In areas of widespread sulfadoxine-pyrimethamine resistance, intermittent treatment in pregnancy (IPTp) fails to prevent placental malaria (PM) and may exacerbate drug resistant infections. Because PM predicts increased susceptibility to parasitemia during infancy, we hypothesized that IPTp would also increase susceptibility to malaria infection and disease in the offspring.

Methods

In a birth cohort from NE Tanzania, we evaluated the association between maternal IPTp use and risk of parasitemia and severe malaria in the offspring. Using Cox Proportional Hazards Models as well as Generalized Estimating Equations, we evaluated the effects of IPTp on the entire cohort and on subgroups stratified by PM status at delivery.

Results and Conclusions

Offspring of PM+ women who received IPTp had a dose-dependent decrease in time to first parasitemia (AHR = 2.13, p = 0.04 [95%CI: 1.04, 4.38]). Among all offspring, IPTp was associated with earlier first severe malaria episode (AHR = 2.32, p = 0.02 [95%CI: 1.12, 4.78]) as well as increased overall odds of severe malaria (AOR = 2.31, p = 0.03 [95%CI: 1.09, 4.88]). Cost-benefit analyses of IPTp regimens should consider the long term effects on offspring in addition to pregnancy outcomes.     

The Effect of Chemical Chaperones on the Assembly and Stability of HIV-1 Capsid Protein

Chemical chaperones are small organic molecules which accumulate in a broad range of organisms in various tissues under different stress conditions and assist in the maintenance of a correct proteostasis under denaturating environments. The effect of chemical chaperones on protein folding and aggregation has been extensively studied and is generally considered to be mediated through non-specific interactions. However, the precise mechanism of action remains elusive. Protein self-assembly is a key event in both native and pathological states, ranging from microtubules and actin filaments formation to toxic amyloids appearance in degenerative disorders, such as Alzheimer''s and Parkinson''s diseases. Another pathological event, in which protein assembly cascade is a fundamental process, is the formation of virus particles. In the late stage of the virus life cycle, capsid proteins self-assemble into highly-ordered cores, which encapsulate the viral genome, consequently protect genome integrity and mediate infectivity. In this study, we examined the effect of different groups of chemical chaperones on viral capsid assembly in vitro, focusing on HIV-1 capsid protein as a system model. We found that while polyols and sugars markedly inhibited capsid assembly, methylamines dramatically enhanced the assembly rate. Moreover, chemical chaperones that inhibited capsid core formation, also stabilized capsid structure under thermal denaturation. Correspondingly, trimethylamine N-oxide, which facilitated formation of high-order assemblies, clearly destabilized capsid structure under similar conditions. In contrast to the prevailing hypothesis suggesting that chemical chaperones affect proteins through preferential exclusion, the observed dual effects imply that different chaperones modify capsid assembly and stability through different mechanisms. Furthermore, our results indicate a correlation between the folding state of capsid to its tendency to assemble into highly-ordered structures.     

Maturation of locust corpora allata during the reproductive cycle: Effect of reserpine on allatotropic activity,juvenile hormone-III biosynthesis,and oocyte development

Reserpine, at doses of 20–175 μg per g body weight, severely retards oogenesis in newly emerged adult female migratory locusts (Locusta migratoria migratorioides) but does not increase mortality during the first 9 days and only slightly delays somatic growth. Total protein, and hemolymph vitellogenin content particularly, are significantly reduced in reserpine-treated locusts. The synthesis of juvenile hormone III (JH-III) following adult emergence, essential for induction of vitellogenesis and subsequent oogenesis, is dependent on the maturation and activation of the corpora allata (CA). CA of 7- to 8-day-old female locusts, treated with reserpine at day 1 after adult emergence, are only marginally active in vitro and are only slightly stimulated by an allatotropic factor. The basal activity and response of CA from the reserpine-treated locusts resembles that of newly emerged locusts, suggesting that reserpine specifically retards the initial maturation of the locust CA. Recovery of basal CA activity is evident on days 12–13 in reserpine-treated locusts, but responsiveness to the allatotropic factor is not recovered. Starvation of newly emerged females for 3 days and subsequent feeding did not effect ooctye development or CA activity. Cerebral content of the allatotropic factor, assayed on days 7–8, is not reduced by the reserpine treatment.     

Glass‐Type Polyamorphism in Li‐Garnet Thin Film Solid State Battery Conductors

Ceramic Li₇La₃Zr₂O₁₂ garnet materials are promising candidates for the electrolytes in solid state batteries due to their high conductivity and structural stability. In this paper, the existence of “polyamorphism” leading to various glass‐type phases for Li‐garnet structure besides the known crystalline ceramic ones is demonstrated. A maximum in Li‐conductivity exists depending on a frozen thermodynamic glass state, as exemplified for thin film processing, for which the local near range order and bonding unit arrangement differ. Through processing temperature change, the crystallization and evolution through various amorphous and biphasic amorphous/crystalline phase states can be followed for constant Li‐total concentration up to fully crystalline nanostructures. These findings reveal that glass‐type thin film Li‐garnet conductors exist for which polyamorphism can be used to tune the Li‐conductivity being potential new solid state electrolyte phases to avoid Li‐dendrite formation (no grain boundaries) for future microbatteries and large‐scale solid state batteries.     

Structural features that predict real-value fluctuations of globular proteins

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective combinations of features for predicting the real value of residue fluctuations using the support vector regression (SVR). It was found that some structural features have higher correlation than crystallographic B‐factors with fluctuations observed in MD trajectories. Moreover, SVR that uses combinations of static structural features showed accurate prediction of fluctuations with an average Pearson's correlation coefficient of 0.669 and a root mean square error of 1.04 Å. This correlation coefficient is higher than the one observed in predictions by the Gaussian network model (GNM). An advantage of the developed method over the GNMs is that the former predicts the real value of fluctuation. The results help improve our understanding of relationships between protein structure and fluctuation. Furthermore, the developed method provides a convienient practial way to predict fluctuations of proteins using easily computed static structural features of proteins. Proteins 2012; © 2012 Wiley Periodicals, Inc.     

Cytoskeletal Components Define Protein Location to Membrane Microdomains

The plasma membrane is an important compartment that undergoes dynamic changes in composition upon external or internal stimuli. The dynamic subcompartmentation of proteins in ordered low-density (DRM) and disordered high-density (DSM) membrane phases is hypothesized to require interactions with cytoskeletal components. Here, we systematically analyzed the effects of actin or tubulin disruption on the distribution of proteins between membrane density phases. We used a proteomic screen to identify candidate proteins with altered submembrane location, followed by biochemical or cell biological characterization in Arabidopsis thaliana. We found that several proteins, such as plasma membrane ATPases, receptor kinases, or remorins resulted in a differential distribution between membrane density phases upon cytoskeletal disruption. Moreover, in most cases, contrasting effects were observed: Disruption of actin filaments largely led to a redistribution of proteins from DRM to DSM membrane fractions while disruption of tubulins resulted in general depletion of proteins from the membranes. We conclude that actin filaments are necessary for dynamic movement of proteins between different membrane phases and that microtubules are not necessarily important for formation of microdomains as such, but rather they may control the protein amount present in the membrane phases.Living cells need borders and molecular compartments for biochemical reactions and storage of metabolites. The plasma membrane therefore is a prerequisite for the evolution of different life forms. It consists of a phospholipid bilayer into which proteins and special lipid species such as sterols, sphingolipids, and glycolipids are inserted. The first complex model of plasma membrane was proposed in 1972 by Jonathan Singer and Garth Nicolson (1), replacing the concept of the plasma membrane as a strict protein–lipid–protein sandwich that was generally accepted until then. In Singer and Nicolson''s model, the cell membrane is a two-dimensionally oriented viscous solution in which the membrane constituents are orientated in the most thermodynamically favorable manner, hiding hydrophobic hydrocarbon chains inside the lipid bilayer and exposing polar and ionic groups to the aqueous phase. This fluid mosaic model also implied that membrane proteins as well as lipid components are distributed in a homogeneous lipid bilayer at long range, but they can form specific aggregates and phases at short range, which were also termed “lipid rafts” or membrane microdomains.Over the past 30 years, it has become evident that the plasma membrane is not such a homogeneous structure as it was initially proposed. We now know that the lipid bilayer is asymmetric (2) and that the free diffusion of membrane proteins is restricted by their interactions with intracellular and extracellular components (3). More recently, Simons and Ikonen suggested that large ordered phases, enriched with cholesterol and sphingolipids, emerge within the plasma membrane and that they function as platforms for enrichment of certain proteins while excluding others (4). This current membrane model suggests that the mixture of sterols and polar lipids within the plasma membrane can appear in two distinct phases: liquid disordered (L_d) and liquid ordered (L_o) phase (5). In this view, the so-called membrane microdomains are considered to be part of the L_o phase. Based on work on model membranes, it is suggested that lateral segregation of components into L_d and L_o phases occurs spontaneously (6) with the self-associating properties between sterols and highly saturated hydrocarbon chains of phopsho- and sphingolipids as the main driving force (7). Additionally, it is suggested that also specific lipid-protein and protein-protein interactions are essential for the formations of membrane domains as well as for stabilization of smaller nanodomains which subsequently may cause formation of larger platforms. In contrast to the animal cells, in plants these membrane microdomains seem to be rather immobile (8), possibly due to their attachment to the outer cell wall. More recently, it became obvious that membrane microdomains within a single cell are highly diverse and of different compositions (9). Generally, in the plant model, organisms'' plasma membrane microdomains turned out to be important in plant defense (10, 11), cell polarity (12, 13), and general signaling properties of the plasma membrane (14, 15).The cytoskeleton was identified as an essential cellular component with important roles in membrane topography, bordering, trafficking, and organelle movement (16). Single particle tracking in mammalian cells revealed that the transferrin receptor and macroglobulin receptor demonstrate normal Brownian diffusion but only within a specific membrane compartment (17). Two hypothetical models were proposed in order to explain this phenomenon (supplemental Fig. 1). Direct interactions between transmembrane proteins and cytoskeleton are suggested to creates a barrier, called “fence,” where cytosolic parts of transmembrane proteins collides with cytoskeletal components, limiting their diffusion to certain areas. These molecules can jump over the “fence” to a neighboring compartment, possibly due to the dynamic nature of the interaction of membrane proteins and cytoskeleton, where they are again temporally trapped (17). This phenomenon was recently described also in A. thaliana where the interplay between membrane microdomains and microtubules plays a role in secondary cell wall formation (reviewed in (18)). The second model assumes, additionally, that particular transmembrane proteins are anchored to and lined up along cytoskeleton and act as “pickets” to arrest free diffusion of other membrane components, including nontransmembrane proteins, within the enclosed compartment (19).For plants, the composition of these sterol-rich membranes phases was analyzed in several biochemical studies (14, 20–22). Thereby, low-density preparations of plasma membrane fractions after treatment with nonionic detergents (DRM¹ fractions) were considered as a biochemical representation enriched in cellular membrane ordered phases or microdomains. Proteomic studies in mammalian cells consistently reported that the DRM fraction is highly enriched with several cytoskeletal proteins such as actin, tubulin, myosin, dynamin, actinin, and supervillin (23–25). Additionally, the level of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a lipid connecting the plasma membrane to actin filaments, was also significantly elevated in DRM preparations (26). Treatment with microtubule and actin depolymerizing agent results in drastic loss of many signaling proteins from these DRM fractions prepared from adult rat cardiac myocytes (27) or human embryonic retinal cells (28).Based on this knowledge, we propose two hypothetical models for the relationship between cytoskeleton and membrane microdomains for plant cells: (i) Actin filaments and microtubules could be important in the membrane phase separation or formation of the membrane microdomains themselves. In this case, disruption of the cytoskeleton would cause a lack of phase segregation in the plasma membrane. (ii) The cytoskeleton is only important for the incorporation of specific protein into the sterol-enriched regions but not for the general formation of these phase separations. This view implies that phase separations or membrane microdomains would still be present after cytoskeleton disruption but their protein composition can be different. Another possible scenario is (iii) that cytoskeletal elements serve as anchors for membrane microdomains at particular position in the plasma membrane, so the absence of these anchors would cause the increased mobility of microdomains (supplemental Fig. 1).The primary aim of this study was to characterize the interplay between cytoskeletal components and different membrane phases (microdomains) in A. thaliana suspension cell cultures. To reach this goal, biochemical and proteomic approaches were combined with confocal microscopy and activity assays measuring the influence of actin or tubulin disruption on the composition, localization, and biochemical properties of the sterol-enriched membrane microdomains. Thereby, for biochemical analyses, low-density detergent-resistant membrane fractions are analyzed as containing cellular sterol-rich membrane compartments.     

Histone H3 lysine 27 acetylation is altered in colon cancer

Background

Histone post-translational modifications (PTMs) play an important role in the regulation of the expression of genes, including those involved in cancer development and progression. However, our knowledge of PTM patterns in human tumours is limited.

Methods

MS-based analyses were used to quantify global alterations of histone PTMs in colorectal cancer (CRC) samples. Histones isolated from 12 CRCs and their corresponding normal mucosa by acidic extraction were separated by SDS-PAGE and analysed by liquid chromatography-mass spectrometry.

Results

Among 96 modified peptides, 41 distinct PTM sites were identified, of which 7, 13, 11, and 10 were located within the H2A, H2B, H3, and H4 sequences, respectively, and distributed among the amino-terminal tails and the globular domain of the four histones. Modification intensities were quantified for 33 sites, of which 4 showed significant (p-value ≤ 0.05) differences between CRC tissues and healthy mucosa samples. We identified histone H3 lysine 27 acetylation (H3K27Ac) as a modification upregulated in CRC, which had not been shown previously.

Conclusions

The present results indicate the usefulness of a bottom-up proteomic approach for the detection of histone modifications at a global scale. The differential abundance of H3K27Ac mark in CRC, a PTM associated with active enhancers, suggests its role in regulating genes whose expression changes in CRC.     

Experimental Myocardial Infarction Induces Altered Regulatory T Cell Hemostasis,and Adoptive Transfer Attenuates Subsequent Remodeling

Background

Ischemic cardiac damage is associated with upregulation of cardiac pro-inflammatory cytokines, as well as invasion of lymphocytes into the heart. Regulatory T cells (Tregs) are known to exert a suppressive effect on several immune cell types. We sought to determine whether the Treg pool is influenced by myocardial damage and whether Tregs transfer and deletion affect cardiac remodeling.

Methods and Results

The number and functional suppressive activity of Tregs were assayed in mice subjected to experimental myocardial infarction. The numbers of splenocyte-derived Tregs in the ischemic mice were significantly higher after the injury than in the controls, and their suppressive properties were significantly compromised. Compared with PBS, adoptive Treg transfer to mice with experimental infarction reduced infarct size and improved LV remodeling and functional performance by echocardiography. Treg deletion with blocking anti-CD25 antibodies did not influence infarct size or echocardiographic features of cardiac remodeling.

Conclusion

Treg numbers are increased whereas their function is compromised in mice with that underwent experimental infarction. Transfer of exogeneous Tregs results in attenuation of myocardial remodeling whereas their ablation has no effect. Thus, Tregs may serve as interesting potential interventional targets for attenuating left ventricular remodeling.