Comparison of the defensive elicitation activity of cerato-populin and cerato-platanin: a structural model

Plants can defend themselves from potential pathogenic microorganisms relying on a complex interplay of signaling pathways: activation of the MAPK cascade, transcription of defense related genes, production of reactive oxygen species, nitric oxide and synthesis of other defensive compounds such as phytoalexins. These events are triggered by the recognition of pathogen’s effectors (effector-triggered immunity) or PAMPs (PAMP-triggered immunity). The Cerato Platanin Family (CPF) members are Cys-rich proteins secreted and localized on fungal cell walls, involved in several aspects of fungal development and pathogen-host interactions. Although more than hundred genes of the CPF have been identified and analyzed, the structural and functional characterization of the expressed proteins has been restricted only to few members of the family. Interestingly, those proteins have been shown to bind chitin with diverse affinity and after foliar treatment they elicit defensive mechanisms in host and non-host plants. This property turns cerato platanins into interesting candidates, worth to be studied to develop new fungal elicitors with applications in sustainable agriculture. This study focus on cerato-platanin (CP), core member of the family and on the orthologous cerato-populin (Pop1). The latter shows an identity of 62% and an overall homology of 73% with respect to CP. Both proteins are able to induce MAPKs phosphorylation, production of reactive oxygen species and nitric oxide, overexpression of defense’s related genes, programmed cell death and synthesis of phytoalexins. CP, however, when compared to Pop1, induces a faster response and, in some cases, a stronger activity on plane leaves. Aim of the present research is to verify if the dissimilarities observed in the defense elicitation activity of these proteins can be associated to their structural and dynamic features. Taking advantage of the available CP NMR structure, Pop1’s 3D one was obtained by homology modeling. Experimental residual dipolar couplings and 1H, 15N, 13C resonance assignments were used to validate the model. Previous works on CPF members, addressed the highly conserved random coil regions (loops b1-b2 and b2-b3) as sufficient and necessary to induce necrosis in plants’ leaves: that region was investigated in both Pop1 and CP. In the two proteins the loops differ, in their primary sequence, for few mutations and an insertion with a consequent diversification of the proteins’ electrostatic surface. A set of 2D and 3D NMR experiments was performed to characterize both the spatial arrangement and the dynamic features of the loops. NOE data revealed a more extended network of interactions between the loops in Pop1 than in CP. In addition, in Pop1 we identified a salt bridge Lys25/Asp52 and a strong hydrophobic interaction between Phe26/Trp53. These structural features were expected not only to affect the loops’ spatial arrangement, but also to reduce the degree of their conformational freedom. Relaxation data and the order parameter S2 indeed highlighted reduced flexibility, in particular for loop b1-b2 of Pop1. In vitro NMR experiments, where Pop1 and CP were titrated with oligosaccharides, supported the hypothesis that the loops structural and dynamic differences may be responsible for the different chitin-binding properties of the two proteins: CP selectively binds tetramers of chitin in a shallow groove on one side of the barrel defined by loops b1-b2, b2-b3 and b4-b5, Pop1, instead, interacts in a non-specific fashion with oligosaccharides. Because the region involved in chitin-binding is also responsible for the defense elicitation activity, possibly being recognized by plant's receptors, it is reasonable to expect that those structural and dynamic modifications may also justify the different extent of defense elicitation. To test that hypothesis, the initial steps of a protocol aimed to the identify a receptor for CP, in silico, are presented.

Extended theory about the allocation of time: Description and application to the increase in the retirement age policies

This paper revises mainstream economic models which include time use in an explicit and endogenous manner, suggesting a extended theory which escape from the main problem existing in the literature. In order to do it, we start by presenting in section 2 the mainstream time use models in economics, showing their main features. Once this is done, we introduce the reader in the main problems this kind of well established models imply, within section 3, being the most highlighted the problem of joint production. Subsequently, we propose an extended theory which solves the problem of joint production; this is extensively described in section 4. Last, but not least, we apply this model to offer a time use analysis of the effect of a policy which increases the retirement age in a life-cycle perspective for a representative individual.

An extended Herschel drop-out source in the center of AS1063: a normal dusty galaxy at z=6.1 or SZ substructures?

In the course of our 870 μm APEX/LABOCA follow-up of the Herschel Lensing Survey we have detected a source in AS1063 (RXC J2248.7-4431) that has no counterparts in any of the Herschel PACS/SPIRE bands, it is a Herschel “drop-out” with S_870/S_500 ≥ 0.5. The 870 μm emission is extended and centered on the brightest cluster galaxy, suggesting either a multiply imaged background source or substructure in the Sunyaev-Zel’dovich increment due to inhomogeneities in the hot cluster gas of this merging cluster. We discuss both interpretations with emphasis on the putative lensed source. Based on the observed properties and on our lens model we find that this source may be the first submillimeter galaxy (SMG) with a moderate far-infrared (FIR) luminosity (L_FIR < 10^12 L_⊙) detected so far at z > 4. In deep HST observations we identified a multiply imaged z ~ 6 source and measured its spectroscopic redshift to be z = 6.107 with VLT/FORS. This source may be associated with the putative SMG, but it is most likely offset spatially by 10−30 kpc and they may be interacting galaxies. With a FIR luminosity in the range [5−15] × 10^11 L_⊙ corresponding to a star formation rate in the range [80−260] M_⊙ yr^-1, this SMG would be more representative of the z > 4 dusty galaxies than the extreme starbursts detected so far. With a total magnification of ~25 it would open a unique window to the normal dusty galaxies at the end of the epoch of reionization.

Exponential decay of spin-spin correlation between distant defect states produced by contour hydrogenation of polycyclic aromatic hydrocarbon molecules

The first few low-lying spin states of alternant polycyclic aromatic hydrocarbon (PAH) molecules of several shapes showing defect states induced by contour hydrogenation have been studied both by ab initio methods and by a precise numerical solution of Pariser-Parr-Pople (PPP) interacting model. In accordance with Lieb's theorem, the ground state shows a spin multiplicity equal to one for balanced molecules, and it gets larger values for imbalanced molecules (that is, when the number of π electrons on both subsets is not equal). Furthermore, we find a systematic decrease of the singlet-triplet splitting as a function of the distance between defects, regardless of whether the ground state is singlet or triplet. For example, a splitting smaller than 0.001 eV is obtained for a medium size C46H28 PAH molecule (di-hydrogenated [11]phenacene) showing a singlet ground state. We conclude that π electrons unbound by lattice defects tend to remain localized and unpaired even when long-range Coulomb interaction is taken into account. Therefore they show a biradical character (polyradical character for more than two defects) and should be studied as two or more local doublets. The implications for electron transport are potentially important since these unpaired electrons can trap traveling electrons or simply flip their spin at a very small energy cost.

Exports and Capacity Constraints: A smooth transition regression model for six euro-area countries. CEPS Working Document No. 395/May 2014

The significant gains in export market shares made in a number of vulnerable euro-area crisis countries have not been accompanied by an appropriate improvement in price competitiveness. This paper argues that, under certain conditions, firms consider export activity as a substitute for serving domestic demand. The strength of the link between domestic demand and exports is dependent on capacity constraints. Our econometric model for six euro-area countries suggests domestic demand pressure and capacity-constraint restrictions as additional variables of a properly specified export equation. As an innovation to the literature, we assess the empirical significance through the logistic and the exponential variant of the non-linear smooth transition regression model. We find that domestic demand developments are relevant for the short-run dynamics of exports in particular during more extreme stages of the business cycle. A strong substitutive relationship between domestic and foreign sales can most clearly be found for Spain, Portugal and Italy, providing evidence of the importance of sunk costs and hysteresis in international trade.

The EU-Turkey Customs Union: A model for Future Euro-Med Integration. MEDPRO Technical Report No. 9/March 2012

This paper studying the 1995 EU-Turkey Customs Union (CU) reveals that the CU has been a major instrument of integration of the Turkish economy into the EU and global markets, offering powerful tools to reform the Turkish economy. Turkish producers of industrial goods are protected by tariffs from external competition to exactly the same extent as EU producers, and they face competition from duty-free imports of industrial goods from world-class pan-European firms. In return, Turkish industrial producers have duty-free market access to the European Economic Area, which was recently extended to certain Mediterranean countries. Trade liberalisation achieved through the CU has thus successfully moved the Turkish economy from a government-controlled regime to a market-based one, and Turkish producers of industrial goods have performed remarkably well. The paper further shows that market access conditions for Turkish producers are determined, in addition to tariffs, by standards, conformity assessment procedures, competition policy, industrial property rights and contingent protectionism measures. The CU also offered Turkey the opportunity to establish new institutions, and modernise and upgrade rules and disciplines required for the elimination of technical barriers to trade, and for the implementation of the EU’s competition, industrial property rights, and contingent protectionism policies.

Establishment of a confluent monolayer model with human primary trophoblast cells: novel insights into placental glucose transport

STUDY HYPOTHESIS Using optimized conditions, primary trophoblast cells isolated from human term placenta can develop a confluent monolayer in vitro, which morphologically and functionally resembles the microvilli structure found in vivo. STUDY FINDING We report the successful establishment of a confluent human primary trophoblast monolayer using pre-coated polycarbonate inserts, where the integrity and functionality was validated by cell morphology, biophysical features, cellular marker expression and secretion, and asymmetric glucose transport. WHAT IS KNOWN ALREADY Human trophoblast cells form the initial barrier between maternal and fetal blood to regulate materno-fetal exchange processes. Although the method for isolating pure human cytotrophoblast cells was developed almost 30 years ago, a functional in vitro model with primary trophoblasts forming a confluent monolayer is still lacking. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Human term cytotrophoblasts were isolated by enzymatic digestion and density gradient separation. The purity of the primary cells was evaluated by flow cytometry using the trophoblast-specific marker cytokeratin 7, and vimentin as an indicator for potentially contaminating cells. We screened different coating matrices for high cell viability to optimize the growth conditions for primary trophoblasts on polycarbonate inserts. During culture, cell confluency and polarity were monitored daily by determining transepithelial electrical resistance (TEER) and permeability properties of florescent dyes. The time course of syncytia-related gene expression and hCG secretion during syncytialization were assessed by quantitative RT-PCR and enzyme-linked immunosorbent assay, respectively. The morphology of cultured trophoblasts after 5 days was determined by light microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Membrane makers were visualized using confocal microscopy. Additionally, glucose transport studies were performed on the polarized trophoblasts in the same system. MAIN RESULTS AND THE ROLE OF CHANCE During 5-day culture, the highly pure trophoblasts were cultured on inserts coated with reconstituted basement membrane matrix . They exhibited a confluent polarized monolayer, with a modest TEER and a size-dependent apparent permeability coefficient (Papp) to fluorescently labeled compounds (MW ∼400-70 000 Da). The syncytialization progress was characterized by gradually increasing mRNA levels of fusogen genes and elevating hCG secretion. SEM analyses confirmed a confluent trophoblast layer with numerous microvilli, and TEM revealed a monolayer with tight junctions. Immunocytochemistry on the confluent trophoblasts showed positivity for the cell-cell adhesion molecule E-cadherin, the tight junction protein 1 (ZO-1) and the membrane proteins ATP-binding cassette transporter A1 (ABCA1) and glucose transporter 1 (GLUT1). Applying this model to study the bidirectional transport of a non-metabolizable glucose derivative indicated a carrier-mediated placental glucose transport mechanism with asymmetric kinetics. LIMITATIONS, REASONS FOR CAUTION The current study is only focused on primary trophoblast cells isolated from healthy placentas delivered at term. It remains to be evaluated whether this system can be extended to pathological trophoblasts isolated from diverse gestational diseases. WIDER IMPLICATIONS OF THE FINDINGS These findings confirmed the physiological properties of the newly developed human trophoblast barrier, which can be applied to study the exchange of endobiotics and xenobiotics between the maternal and fetal compartment, as well as intracellular metabolism, paracellular contributions and regulatory mechanisms influencing the vectorial transport of molecules. LARGE-SCALE DATA Not applicable. STUDY FUNDING AND COMPETING INTERESTS This study was supported by the Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, Switzerland, and the Swiss National Science Foundation (grant no. 310030_149958, C.A.). All authors declare that their participation in the study did not involve factual or potential conflicts of interests.

Use of Extended Characteristics of Locomotion and Feeding Behavior for Automated Identification of Lame Dairy Cows.

This study was carried out to detect differences in locomotion and feeding behavior in lame (group L; n = 41; gait score ≥ 2.5) and non-lame (group C; n = 12; gait score ≤ 2) multiparous Holstein cows in a cross-sectional study design. A model for automatic lameness detection was created, using data from accelerometers attached to the hind limbs and noseband sensors attached to the head. Each cow's gait was videotaped and scored on a 5-point scale before and after a period of 3 consecutive days of behavioral data recording. The mean value of 3 independent experienced observers was taken as a definite gait score and considered to be the gold standard. For statistical analysis, data from the noseband sensor and one of two accelerometers per cow (randomly selected) of 2 out of 3 randomly selected days was used. For comparison between group L and group C, the T-test, the Aspin-Welch Test and the Wilcoxon Test were used. The sensitivity and specificity for lameness detection was determined with logistic regression and ROC-analysis. Group L compared to group C had significantly lower eating and ruminating time, fewer eating chews, ruminating chews and ruminating boluses, longer lying time and lying bout duration, lower standing time, fewer standing and walking bouts, fewer, slower and shorter strides and a lower walking speed. The model considering the number of standing bouts and walking speed was the best predictor of cows being lame with a sensitivity of 90.2% and specificity of 91.7%. Sensitivity and specificity of the lameness detection model were considered to be very high, even without the use of halter data. It was concluded that under the conditions of the study farm, accelerometer data were suitable for accurately distinguishing between lame and non-lame dairy cows, even in cases of slight lameness with a gait score of 2.5.

Age model of ODP Site 113-697 (Table 2)

We examined diatom preservation patterns in Pliocene age sediments of Jane Basin (ODP Site 697) and compared them with diatom distribution in more northerly sites at various sectors of the Southern Ocean. Our data from Site 697, as well as other sites from around the Southern Ocean, support the view that there was significant ice growth on Antarctica during the late Pliocene. DSDP Site 514 in the Atlantic sector shows increased relative abundance of Eucampia antarctica, an ice-related form, in the upper part of the Gauss Chron with a larger increase just above it. With one exception, all sites included in the present study show increased relative abundance of E. antarctica in the upper part of the Gauss. Our view that there was ice growth on Antarctica during the late Gauss Chron is supported by the results from ODP Site 697. While diatoms are present and percent opal is high in the early and middle Gauss Chron (suggesting more open-ocean conditions), late Gauss sediments contain low percentages of opal and few or no diatoms. This is also true for the early Matuyama Chron. If we accept spring and summer sea-ice cover as the major suppressant of diatom productivity in the Southern Ocean, then we conclude that sea-ice covered the region around Site 697 through much of the year during this interval. Further, the absence of diatoms and the low percentages of opal in middle and late Matuyama chron sediments suggests increased sea-ice cover over the Jane Basin during this time. Although warmer openocean intervals are inferred for intervals near the Olduvai and Jaramillo Subchrons, most of the Matuyama Chron was marked by extensive sea-ice cover with low seasonal contrast. Our results for the early part of the Brunhes Chron are similar, at least for the Jane Basin. During this time, sea-ice cover over the basin apparently extended well into the growing season. In contrast, the later Brunhes Chron is marked by alternating open water (during the growing season) and extensive, almost year-round, sea-ice.

A Kinetic Vlasov Model for Plasma Simulation Using Discontinuous Galerkin Method on Many-Core Architectures

Thesis (Ph.D.)--University of Washington, 2016-03

Seismically-Induced Rock-Slope Failure: Numerical Investigation using the Bonded Particle Model

Thesis (Ph.D.)--University of Washington, 2016-06

Angiotensin II facilitates autoregulation in the perfused mouse kidney: An optimized in vitro model for assessment of renal vascular and tubular function

Background and Aims: We have optimized the isolated perfused mouse kidney (IPMK) model for studying renal vascular and tubular function in vitro using 24-28 g C57BL6J mice; the wild type controls for many transgenic mice. Methods and Results: Buffer composition was optimized for bovine serum albumin concentration (BSA). The effect of adding erythrocytes on renal function and morphology was assessed. Autoregulation was investigated during stepped increases in perfusion pressure. Perfusion for 60 min at 90-110 mmHg with Krebs bicarbonate buffer containing 5.5% BSA, and amino acids produced functional parameters within the in vivo range. Erythrocytes increased renal vascular resistance (3.8 +/- 0.2 vs 2.4 +/- 0.1 mL/min.mmHg, P < 0.05), enhanced sodium reabsorption (FENa = 0.3 +/- 0.08 vs 1.5 +/- 0.7%, P < 0.05), produced equivalent glomerular filtration rates (GFR; 364 +/- 38 vs 400 +/- 9 muL/min per gkw) and reduced distal tubular cell injury in the inner stripe (5.8 +/- 1.7 vs 23.7 +/- 3.1%, P < 0.001) compared to cell free perfusion. The IPMK was responsive to vasoconstrictor (angiotensin II, EC50 100 pM) and vasodilator (methacholine, EC50 75 nM) mediators and showed partial autoregulation of perfusate flow under control conditions over 65-85 mmHg; autoregulatory index (ARI) of 0.66 +/- 0.11. Angiotensin II (100 pM) extended this range (to 65-120 mmHg) and enhanced efficiency (ARI 0.21 +/- 0.02, P < 0.05). Angiotensin II facilitation was antagonized by methacholine (ARI 0.76 +/- 0.08) and papaverine (ARI 0.91 +/- 0.13). Conclusion: The IPMK model is useful for studying renal physiology and pathophysiology without systemic neurohormonal influences.

Quantum-gate characterization in an extended Hilbert space

We describe an approach for characterizing the process performed by a quantum gate using quantum process tomography, by first modeling the gate in an extended Hilbert space, which includes nonqubit degrees of freedom. To prevent unphysical processes from being predicted, present quantum process tomography procedures incorporate mathematical constraints, which make no assumptions as to the actual physical nature of the system being described. By contrast, the procedure presented here assumes a particular class of physical processes, and enforces physicality by fitting the data to this model. This allows quantum process tomography to be performed using a smaller experimental data set, and produces parameters with a direct physical interpretation. The approach is demonstrated by example of mode matching in an all-optical controlled-NOT gate. The techniques described are general and could be applied to other optical circuits or quantum computing architectures.

A new approach to control of MIMO processes with static nonlinearities using an extended IMC framework

In this paper, a new control design method is proposed for stable processes which can be described using Hammerstein-Wiener models. The internal model control (IMC) framework is extended to accommodate multiple IMC controllers, one for each subsystem. The concept of passive systems is used to construct the IMC controllers which approximate the inverses of the subsystems to achieve dynamic control performance. The Passivity Theorem is used to ensure the closed-loop stability. (c) 2005 Elsevier Ltd. All rights reserved.