Cathepsin S dominates autoantigen processing in human thymic dendritic cells

The interaction of developing thymocytes with peptide-MHC complexes on thymic antigen presenting cells (APC) is crucial for T cell development, both for positive selection of "useful" thymocytes as well as negative selection of autoreactive thymocytes to prevent autoimmunity. The peptides presented on MHC II molecules are generated by lysosomal proteases such as the cathepsins. At the same time, lysosomal proteases will also destroy other potential T cell epitopes from self-antigens. This will lead to a lack of presentation on negatively selecting thymic antigen presenting cells and consequently, escape of autoreactive T cells recognizing these epitopes. In order to understand the processes that govern generation or destruction of self-epitopes in thymic APC, we studied the antigen processing machinery and epitope processing in the human thymus. We find that each type of thymic APC expresses a different signature of lysosomal proteases, providing indirect evidence that positive and negative selection of CD4(+) T cells might occur on different sets of peptides, in analogy to what has been proposed for CD8(+) T cells. We also find that myeloid dendritic cells (DC) are more efficient in processing autoantigen than plasmacytoid DC. In addition, we observed that cathepsin S plays a central role in processing of the autoantigens myelin basic protein and proinsulin in thymic dendritic cells. Cathepsin S destroyed a number of known T cell epitopes, which would be expected to result in lack of presentation and consequently, escape of autoreactive T cells. Cathepsin S therefore appears to be an important factor that influences selection of autoreactive T cells.

Missing Links in the Proposed EU Data Protection Regulation and Cloud Computing Scenarios: A Brief Overview

Applying location-focused data protection law within the context of a location-agnostic cloud computing framework is fraught with difficulties. While the Proposed EU Data Protection Regulation has introduced a lot of changes to the current data protection framework, the complexities of data processing in the cloud involve various layers and intermediaries of actors that have not been properly addressed. This leaves some gaps in the regulation when analyzed in cloud scenarios. This paper gives a brief overview of the relevant provisions of the regulation that will have an impact on cloud transactions and addresses the missing links. It is hoped that these loopholes will be reconsidered before the final version of the law is passed in order to avoid unintended consequences.

THE ROLE OF TYROSINE PHOSPHORYLATION IN THE FUNCTIONS OF THE TUMOR SUPPRESSOR GPRC5A

The retinoic acid inducible G protein coupled receptor family C group 5 type A (GPRC5A) is expressed preferentially in normal lung tissue but its expression is suppressed in the majority of human non-small cell lung cancer cell lines and tissues. This differential expression has led to the idea that GPRC5A is a potential tumor suppressor. This notion was supported by the finding that mice with a deletion of the Gprc5a gene develop spontaneous lung tumors. However, there are various tumor cell lines and tissue samples, including lung, that exhibit higher GPRC5A expression than normal tissues and some reports by other groups that GPRC5A transfection increased cell growth and colony formation. Obviously, GPRC5A has failed to suppress the development of the tumors and the growth of the cell lines where its expression is not suppressed. Since no mutations were detected in the coding sequence of GPRC5A in 20 NSCLC cell lines, it’s possible that GPRC5A acts as a tumor suppressor in the context of some cells but not in others. Alternatively, we raised the hypothesis that the GPRC5A protein may be inactivated by posttranslational modification(s) such as phosphorylation. It is well established that Serine/Threonine phosphorylation of G protein coupled receptors leads to their desensitization and in a few cases Tyrosine phosphorylation of GPCRs has been linked to internalization. Others reported that GPRC5A can undergo tyrosine phosphorylation in the cytoplasmic domain after treatment of normal human mammary epithelial cells (HMECs) with epidermal growth factor (EGF) or Heregulin. This suggested that GPRC5A is a substrate of EGFR. Therefore, we hypothesized that tyrosine phosphorylation of GPRC5A by activation of EGFR signaling may lead to its inactivation. To test this hypothesis, we transfected human embryo kidney (HEK) 293 cells with GPRC5A and EGFR expression vectors and confirmed that GPRC5A can be tyrosine phosphorylated after activation of EGFR by EGF. Further, we found that EGFR and GPRC5A can interact either directly or through other proteins and that inhibition of the EGFR kinase activity decreased the phosphorylation of GPRA5A and the interaction between GPRC5A and EGFR. In c-terminal of GPRC5A, There are four tyrosine residues Y317, Y320, Y347, Y350. We prepared GPRC5A mutants in which all four tyrosine residues had been replaced by phenylalanine (mutant 4F) or each individual Tyr residue was replaced by Phe and found that Y317 is the major site for EGFR mediated phosphorylation in the HEK293T cell line. We also found that EGF can induce GPRC5A internalization both in H1792 transient and stable cell lines. EGF also partially inactivates the suppressive function of GPRC5A on cell invasion activity and anchorage-independent growth ability of H1792 stable cell lines. These finding support our hypothesis that GPRC5A may be inactivated by posttranslational modification- tyrosine phosphorylation.

Influence of microphysical schemes on atmospheric water in the Weather Research and Forecasting model

This study examines how different microphysical parameterization schemes influence orographically induced precipitation and the distributions of hydrometeors and water vapour for midlatitude summer conditions in the Weather Research and Forecasting (WRF) model. A high-resolution two-dimensional idealized simulation is used to assess the differences between the schemes in which a moist air flow is interacting with a bell-shaped 2 km high mountain. Periodic lateral boundary conditions are chosen to recirculate atmospheric water in the domain. It is found that the 13 selected microphysical schemes conserve the water in the model domain. The gain or loss of water is less than 0.81% over a simulation time interval of 61 days. The differences of the microphysical schemes in terms of the distributions of water vapour, hydrometeors and accumulated precipitation are presented and discussed. The Kessler scheme, the only scheme without ice-phase processes, shows final values of cloud liquid water 14 times greater than the other schemes. The differences among the other schemes are not as extreme, but still they differ up to 79% in water vapour, up to 10 times in hydrometeors and up to 64% in accumulated precipitation at the end of the simulation. The microphysical schemes also differ in the surface evaporation rate. The WRF single-moment 3-class scheme has the highest surface evaporation rate compensated by the highest precipitation rate. The different distributions of hydrometeors and water vapour of the microphysical schemes induce differences up to 49 W m−2 in the downwelling shortwave radiation and up to 33 W m−2 in the downwelling longwave radiation.

Coherence and phase locking in the scalp EEG and between LORETA model sources, and microstates as putative mechanisms of brain temporo-spatial functional organization

Brain electric mechanisms of temporary, functional binding between brain regions are studied using computation of scalp EEG coherence and phase locking, sensitive to time differences of few milliseconds. However, such results if computed from scalp data are ambiguous since electric sources are spatially oriented. Non-ambiguous results can be obtained using calculated time series of strength of intracerebral model sources. This is illustrated applying LORETA modeling to EEG during resting and meditation. During meditation, time series of LORETA model sources revealed a tendency to decreased left-right intracerebral coherence in the delta band, and to increased anterior-posterior intracerebral coherence in the theta band. An alternate conceptualization of functional binding is based on the observation that brain electric activity is discontinuous, i.e., that it occurs in chunks of up to about 100 ms duration that are detectable as quasi-stable scalp field configurations of brain electric activity, called microstates. Their functional significance is illustrated in spontaneous and event-related paradigms, where microstates associated with imagery- versus abstract-type mentation, or while reading positive versus negative emotion words showed clearly different regions of cortical activation in LORETA tomography. These data support the concept that complete brain functions of higher order such as a momentary thought might be incorporated in temporal chunks of processing in the range of tens to about 100 ms as quasi-stable brain states; during these time windows, subprocesses would be accepted as members of the ongoing chunk of processing.

CONFORMATIONAL DYNAMICS OF K-RAS AND H-RAS PROTEINS: IS THERE FUNCTIONAL SPECIFICITY AT THE CATALYTIC DOMAIN?

Ras proteins serve as crucial signaling modulators in cell proliferation through their ability to hydrolyze GTP and exist in a GTP “on” state and GTP “off” state. There are three different human Ras isoforms: H-ras, N-ras and K-ras (4A and 4B). Although their sequence identity is very high at the catalytic domain, these isoforms differ in their ability to activate different effectors and hence different signaling pathways. Much of the previous work on this topic has attributed this difference to the hyper variable region of Ras proteins, which contains most of the sequence variance among the isoforms and encodes specificity for differential distribution in the membrane. However, we hypothesize that sequence variation on lobe II of Ras catalytic domain alters dynamics and leads to differential preference for different effectors or modulators. In this work, we used all atom molecular dynamics to analyze the dynamics in the catalytic domain of H-ras and K-ras. We have also analyzed the dynamics of a transforming mutant of H-ras and K-ras and further studied the dynamics of an effectorselective mutant of H-ras. Collectively we have determined that wild type K-ras is more dynamic than H-ras and that the structure of the effector binding loop more closely resembles that of the T35S Raf-selective mutant, possibly giving us a new view and insight into the v mode of effector specificity. Furthermore we have determined that specific mutations at the same location perturb the conformational equilibrium differently in H-ras and K-ras and that an enhanced oncogenic potential may arise from different structural perturbations for each point mutation of a specific isoform.

Ice rafted debris in the Nordic Seas

A continuous 3.5 Myr IRD record was produced from Ocean Drilling Program (ODP) Site 907. A timescale based on magnetic polarity chrons, oxygen isotope stratigraphy (for the last 1Myr) and orbital tuning was developed. The record documents a stepwise inception of large-scale glacial cycles in the Nordic Seas region, the first being a marked expansion of the Greenland ice sheet at 3.3 Ma. A second step occurred at 2.74 Ma by an expansion of large scale ice sheets in the Northern Hemisphere. Ice sheet variability around the Nordic Seas was tightly coupled to global ice volume over the past 3.3 Myr. Between 3 and 1 Ma, most of the variance of the IRD signal is in the 41 kyr band, whereas the last 1 Myr is characterized by stronger 100 kyr variance. The Gamma Ray Porosity Evaluator (GRAPE) density record is closely linked with IRD variations and documents sub orbital variability resembling the late Quaternary Heinrich/Bond cycles.

Radiolarians in the Sea of Okhotsk

To assess the relationship of radiolarian production, species distribution in water and surface sediment to water-mass characteristics, biological productivity and export regimes in the Sea of Okhotsk (SOk) we accomplished a quantitative analysis of radiolarian assemblages obtained from 35 surface-sediment samples and 115 plankton samples recording the radiolarian depth distribution in the upper 1000 m of the water column at 23 locations. This study augments the knowledge on the autecological demands of radiolarians dwelling in a specific hydrographic and biological environment, and extracts new information on the significance of radiolarians for the assessment of past oceanographic and climatic development in high latitudes. Highest radiolarian accumulation rates and seasonal radiolarian standing stocks are encountered in the western part of the SOk close to Sakhalin, marking the environmental conditions in this area as most favorable for radiolarian production. Maximum standing stocks occur during summer, indicating that the radiolarian signal preserved in the sediment record is mainly produced during this season when the mesopelagic biomass is at highest activity. We identified seven radiolarian species and groups related to specific water-mass characteristics, depth habitats, and productivity regimes. Of those, Dictyophimus hirundo and Cycladophora davisiana are most prominent in the Sea of Okhotsk Intermediate Water (200-1000 m), the latter representing an indicator of the occurrence of cold and well ventilated intermediate/deep water and enhanced export of organic matter from a highly productive ocean surface. While Antarctissa (?) sp. 1 is typically related to the cold-water Sea of Okhotsk Dicothermal Layer (SODL), ranging between 50 and 150 m water depth, the surface waters above the SODL affected by strong seasonal variability are inhabited predominantly by taxa belonging to the Spongodiscidae, having a broad environmental tolerance. Taxa only found in the sediment record show that the plankton study did not cover all assemblages occurring in the modern SOk. This accounts for an assemblage restricted to the western Kurile Basin and apparently related to environmental conditions influenced by North Pacific and Japan Sea waters. Other important taxa include species of the Plagoniidae group, representing the most prominent contributors to the SOk plankton and surface sediments. These radiolarians show a more opportunistic occurrence and are indicative of high nutrient supply in a hydrographic environment characterized by pronounced stratification enhancing heterotrophic activity and phytodetritus export.

Simulated transition to agropastoralism in the Indus valley 7500-3000 BC

The Indus Valley Civilization (IVC) was one of the first great civilizations in prehistory. This bronze age civilization flourished from the end of the fourth millennium BC. It disintegrated during the second millennium BC; despite much research effort, this decline is not well understood. Less research has been devoted to the emergence of the IVC, which shows continuous cultural precursors since at least the seventh millennium BC. To understand the decline, we believe it is necessary to investigate the rise of the IVC, i.e., the establishment of agriculture and livestock, dense populations and technological developments 7000-3000 BC. Although much archaeologically typed information is available, our capability to investigate the system is hindered by poorly resolved chronology, and by a lack of field work in the intermediate areas between the Indus valley and Mesopotamia. We thus employ a complementary numerical simulation to develop a consistent picture of technology, agropastoralism and population developments in the IVC domain. Results from this Global Land Use and technological Evolution Simulator show that there is (1) fair agreement between the simulated timing of the agricultural transition and radiocarbon dates from early agricultural sites, but the transition is simulated first in India then Pakistan; (2) an independent agropas- toralism developing on the Indian subcontinent; and (3) a positive relationship between archeological artifact richness and simulated population density which remains to be quantified.

Rates of nitrogen cycling and chemo-autotrophy in the cold-water coral Lophelia pertusa

Cold-water corals (CWC) are widely distributed around the world forming extensive reefs at par with tropical coral reefs. They are hotspots of biodiversity and organic matter processing in the world's deep oceans. Living in the dark they lack photosynthetic symbionts and are therefore considered to depend entirely on the limited flux of organic resources from the surface ocean. While symbiotic relations in tropical corals are known to be key to their survival in oligotrophic conditions, the full metabolic capacity of CWC has yet to be revealed. Here we report isotope tracer evidence for efficient nitrogen recycling, including nitrogen assimilation, regeneration, nitrification and denitrification. Moreover, we also discovered chemoautotrophy and nitrogen fixation in CWC and transfer of fixed nitrogen and inorganic carbon into bulk coral tissue and tissue compounds (fatty acids and amino acids). This unrecognized yet versatile metabolic machinery of CWC conserves precious limiting resources and provides access to new nitrogen and organic carbon resources that may be essential for CWC to survive in the resource-depleted dark ocean.

Chemical and isotopic compositions of Archean magmatic and metasedimentary rocks and minerals from the Podolia domain, Ukrainian Shield

Zircons from the oldest magmatic and metasedimentary rocks in the Podolia domain of the Ukrainian shield were studied and dated by the U-Pb method on a NORDSIM secondary-ion mass spectrometer. Age of zircon cores in enderbite gneisses sampled in the Kazachii Yar and Odessa quarries on the opposite banks of the Yuzhnyi Bug River reaches 3790 Ma. Cores of terrigenous zircons in quartzites from the Odessa quarry as well as in garnet gneisses from the Zaval'e graphite quarry have age within 3650-3750 Ma. Zircon rims record two metamorphic events around 2750-2850 Ma and 1900-2000 Ma. Extremely low U content in zircons of the second age group indicates conditions of the granulite facies metamorphism in Paleoproterozoic within the Podolia domain. Measured data on orthorocks (enderbite-gneiss) and metasedimentary rocks unambiguously suggest existence of the ancient Paleoarchean crust in the Podolia (Dniester-Bug) domain of the Ukrainian shield. They contribute in our knowledge of scales of formation and geochemical features of the primordial crust.

Including hardware/software co-design in the ASSERT model driven engineering process.

Abstract. The ASSERT project de?ned new software engineering methods and tools for the development of critical embedded real-time systems in the space domain. The ASSERT model-driven engineering process was one of the achievements of the project and is based on the concept of property- preserving model transformations. The key element of this process is that non-functional properties of the software system must be preserved during model transformations. Properties preservation is carried out through model transformations compliant with the Ravenscar Pro?le and provides a formal basis to the process. In this way, the so-called Ravenscar Computational Model is central to the whole ASSERT process. This paper describes the work done in the HWSWCO study, whose main objective has been to address the integration of the Hardware/Software co-design phase in the ASSERT process. In order to do that, non-functional properties of the software system must also be preserved during hardware synthesis. Keywords : Ada 2005, Ravenscar pro?le, Hardware/Software co-design, real- time systems, high-integrity systems, ORK

Structural homologies with ATP- and folate-binding enzymes in the crystal structure of folylpolyglutamate synthetase

Folylpolyglutamate synthetase, which is responsible for the addition of a polyglutamate tail to folate and folate derivatives, is an ATP-dependent enzyme isolated from eukaryotic and bacterial sources, where it plays a key role in the retention of the intracellular folate pool. Here, we report the 2.4-Å resolution crystal structure of the MgATP complex of the enzyme from Lactobacillus casei. The structural analysis reveals that folylpolyglutamate synthetase is a modular protein consisting of two domains, one with a typical mononucleotide-binding fold and the other strikingly similar to the folate-binding enzyme dihydrofolate reductase. We have located the active site of the enzyme in a large interdomain cleft adjacent to an ATP-binding P-loop motif. Opposite this site, in the C domain, a cavity likely to be the folate binding site has been identified, and inspection of this cavity and the surrounding protein structure suggests that the glutamate tail of the substrate may project into the active site. A further feature of the structure is a well defined Ω loop, which contributes both to the active site and to interdomain interactions. The determination of the structure of this enzyme represents the first step toward the elucidation of the molecular mechanism of polyglutamylation of folates and antifolates.

Identification by mass spectrometry of the phosphorylated residue responsible for activation of the catalytic domain of myosin I heavy chain kinase, a member of the PAK/STE20 family

Myosin I heavy chain kinase from Acanthamoeba castellanii is activated in vitro by autophosphorylation (8–10 mol of P per mol). The catalytically active C-terminal domain produced by trypsin cleavage of the phosphorylated kinase contains 2–3 mol of P per mol. However, the catalytic domain expressed in a baculovirus–insect cell system is fully active as isolated without autophosphorylation in vitro. We now show that the expressed catalytic domain is inactivated by incubation with acid phosphatase and regains activity upon autophosphorylation. The state of phosphorylation of all of the hydroxyamino acids in the catalytic domain were determined by mass spectrometry of unfractionated protease digests. Ser-627 was phosphorylated in the active, expressed catalytic domain, lost its phosphate when the protein was incubated with phosphatase, and was rephosphorylated when the dephosphorylated protein was incubated with ATP. No other residue was significantly phosphorylated in any of the three samples. Thus, phosphorylation of Ser-627, which is in the same position as the Ser and Thr residues that are phosphorylated in many other kinases, is necessary and sufficient for full activity of the catalytic domain. Ser-627 is also phosphorylated when full-length, native kinase is activated by autophosphorylation.

Human deoxycytidine kinase is located in the cell nucleus

Human deoxyribonucleoside kinases are required for the pharmacological activity of several clinically important anticancer and antiviral nucleoside analogs. Human deoxycytidine kinase and thymidine kinase 1 are described as cytosolic enzymes in the literature, whereas human deoxyguanosine kinase and thymidine kinase 2 are believed to be located in the mitochondria. We expressed the four human deoxyribonucleoside kinases as fusion proteins with the green fluorescent protein to study their intracellular locations in vivo. Our data showed that the human deoxycytidine kinase is located in the cell nucleus and the human deoxyguanosine kinase is located in the mitochondria. The fusion proteins between green fluorescent protein and thymidine kinases 1 and 2 were both predominantly located in the cytosol. Site-directed mutagenesis of a putative nuclear targeting signal, identified in the primary structure of deoxycytidine kinase, completely abolished nuclear import of the protein. Reconstitution of a deoxycytidine kinase-deficient cell line with the wild-type nuclear or the mutant cytosolic enzymes both restored sensitivity toward anticancer nucleoside analogs. This paper reports that a deoxyribonucleoside kinase is located in the cell nucleus and we discuss the implications for deoxyribonucleotide synthesis and phosphorylation of nucleoside analogs.