Contemporaneous fluctuations in T cell responses to persistent herpes virus infections

The classical paradigm for T cell dynamics suggests that the resolution of a primary acute virus infection is followed by the generation of a long-lived pool of memory T cells that is thought to be highly stable. Very limited alteration in this repertoire is expected until the immune system is re-challenged by reactivation of latent viruses or by cross-reactive pathogens. Contradicting this view, we show here that the T cell repertoire specific for two different latent herpes viruses in the peripheral blood displayed significant contemporaneous co-fluctuations of virus-specific CD8(+) T cells. The coordinated responses to two different viruses suggest that the fluctuations within the T cell repertoire may be driven by sub-clinical viral reactivation or a more generalized 'bystander' effect. The later contention was supported by the observation that, while absolute number of CD3(+) T cells and their subsets and also the cell surface phenotype of antigen-specific T cells remained relatively constant, a loss of CD62L expression in the total CD8(+) T cell population was coincident with the expansion of tetramer-positive virus-specific T cells. This study demonstrates that the dynamic process of T cell expansion and contractions in persistent viral infections is not limited to the acute phase of infection, but also continues during the latent phase of infection.

Evaluating trends in abundance of immature green turtles, Chelonia mydas, in the Greater Caribbean

Many long-lived marine species exhibit life history traits. that make them more vulnerable to overexploitation. Accurate population trend analysis is essential for development and assessment of management plans for these species. However, because many of these species disperse over large geographic areas, have life stages inaccessible to human surveyors, and/or undergo complex developmental migrations, data on trends in abundance are often available for only one stage of the population, usually breeding adults. The green turtle (Chelonia mydas) is one of these long-lived species for which population trends are based almost exclusively on either numbers of females that emerge to nest or numbers of nests deposited each year on geographically restricted beaches. In this study, we generated estimates of annual abundance for juvenile green turtles at two foraging grounds in the Bahamas based on long-term capture-mark-recapture (CMR) studies at Union Creek (24 years) and Conception Creek (13 years), using a two-stage approach. First, we estimated recapture probabilities from CMR data using the Cormack-Jolly-Seber models in the software program MARK; second, we estimated annual abundance of green turtles. at both study sites using the recapture probabilities in a Horvitz-Thompson type estimation procedure. Green turtle abundance did not change significantly in Conception Creek, but, in Union Creek, green turtle abundance had successive phases of significant increase, significant decrease, and stability. These changes in abundance resulted from changes in immigration, not survival or emigration. The trends in abundance on the foraging grounds did not conform to the significantly increasing trend for the major nesting population at Tortuguero, Costa Rica. This disparity highlights the challenges of assessing population-wide trends of green turtles and other long-lived species. The best approach for monitoring population trends may be a combination of (1) extensive surveys to provide data for large-scale trends in relative population abundance, and (2) intensive surveys, using CMR techniques, to estimate absolute abundance and evaluate the demographic processes' driving the trends.

A polytope DNA vaccine elicits multiple effector and memory CTL responses and protects against human papillomavirus 16 E7-expressing tumour

Vaccine-induced CD8 T cells directed to tumourspecific antigens are recognised as important components of protective and therapeutic immunity against tumours. Where tumour antigens have pathogenic potential or where immunogenic epitopes are lost from tumours, development of subunit vaccines consisting of multiple individual epitopes is an attractive alternative to immunising with whole tumour antigen. In the present study we investigate the efficacy of two DNA-based multiepitope('polytope') vaccines containing murine (H-2(b)) and human (HLA-A* 0201)-restricted epitopes of the E7 oncoprotein of human papillomavirus type 16, in eliciting tumour-protective cytotoxic T-lymphocyte (CTL) responses. We show that the first of these polytopes elicited powerful effector CTL responses ( measured by IFN-gamma ELISpot) and long-lived memory CTL responses ( measured by functional CTL assay and tetramers) in immunised mice. The responses could be boosted by immunisation with a recombinant vaccinia virus expressing the polytope. Responses induced by immunisation with polytope DNA alone partially protected against infection with recombinant vaccinia virus expressing the polytope. Complete protection was afforded against challenge with an E7-expressing tumour, and reduced growth of nascent tumours was observed. A second polytope differing in the exact composition and order of CTL epitopes, and lacking an inserted endoplasmic reticulum targeting sequence and T-helper epitope, induced much poorer CTL responses and failed to protect against tumour challenge. These observations indicate the validity of a DNA polytope vaccine approach to human papillomavirus E7 - associated carcinoma, and underscore the importance of design in polytope vaccine construction.

Efficient -tensor determination and NH assignment of paramagnetic proteins

Anisotropic magnetic susceptibility tensors chi of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the chi-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D N-15-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable chi-tensor anisotropy parameters from 2D spectra of uniformly N-15-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit epsilon from E. coli DNA polymerase III in complex with the subunit theta and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.

Timing and chemistry of fluid-flow events in the Lawn Hill Platform, Northern Australia

Mudrocks and carbonates of the Isa superbasin in the Lawn Hill platform in northern Australia host major base metal sulfide mineralization, including the giant strata-bound Century Zn-Pb deposit. Mineral paragenesis, stable isotope, and K-Ar dating studies demonstrate that long-lived structures such as the Termite Range fault acted as hot fluid conduits several times during the Paleoproterozoic and Mesoproterozoic in response to major tectonic events. Illite and chlorite crystallinity studies suggest the southern part of the platform has experienced higher temperatures (up to 300 degrees C) than similar stratigraphic horizons in the north. The irregular downhole variation of illite crystallinity values provides further information oil the thermal regime in the basin and shows that clay formation was controlled not only by temperature increase with depth but also by high water/rock ratios along relatively permeable zones. K-Ar dating of illite, in combination with other data, may indicate three major thermal events in the central and northern Lawn Hill platform Lit 1500, 1440 to 1400, and 1250 to 1150 Ma. This study did not detect the earlier Century base metal mineralizing event at 1575 Ma. 1500 Ma ages are recorded only in the south and correspond to the age of the Late Isan orogeny and deposition of the Lower Roper superbasin. They may reflect exhumation of a provenance region. The 1440 to 1300 Ma ages are related to fault reactivation and a thermal pulse at similar to 1440 to 1400 Ma possibly accompanied by fluid flow, with subsequent enhanced cooling possibly due to thermal relaxation or further crustal exhumation. The youngest thermal and/or fluid-flow event at 1250 to 1150 Ma is recorded mainly to the cast of the Tern-lite Range fault and may be related to the assembly of the Rodinian supercontinent. Fluids in equilibrium with illite that formed over a range of temperatures, at different times in different parts of the platform. have relatively uniform oxygen isotope compositions and more variable hydrogen isotope compositions (delta O-18 = 3.5-9.7 parts per thousand V-SMOW; delta D = -94 to -36 parts per thousand V-SMOW). The extent of the 180 enrichment and the variably depleted hydrogen isotope compositions suggest the illite interacted with deep-basin hypersaline brines that were composed of evaporated seawater and/or highly evolved meteoric water. Siderite is the most abundant iron-rich gangue phase in the Century Zn-Pb deposit, which is surrounded by all extensive ferroan carbonate alteration halo. Modeling suggests that the ore siderite formed at temperatures of 120 degrees to 150 degrees C, whereas siderite and ankerite in the alteration halo formed at temperatures of 150 degrees to 180 degrees C. The calculated isotopic compositions of the fluids are consistent with O-18-rich basinal brines and mixed inorganic and organic carbon Sources (6180 = 3-10 parts per thousand V-SMOW, delta C-13 = -7 to -3 parts per thousand V-PDB). in the northeast Lawn Hill platform carbonate-rich rocks preserve marine to early diagenetic carbon and oxygen isotope compositions, whereas ferroan carbonate cements in siltstones and shales in the Desert Creek borehole are O-18 and C-13 depleted relative to the sedimentary carbonates. The good agreement between temperature estimates from illite crystallinity and organic reflectance (160 degrees-270 degrees C) and inverse correlation with carbonate delta O-18 values indicates that organic maturation and carbonate precipitation in the northeast Lawn Hill platform resulted from interaction with the 1250 to 1150 Ma fluids. The calculated isotopic compositions of the fluid are consistent with evolved basinal brine (delta O-18 = 5.1-9.4 parts per thousand V-SMOW; delta C-13 = -13.2 to -3.7 parts per thousand V-PDB) that contained a variable organic carbon component from the oxidation and/or hydrolysis of organic matter in the host sequence. The occurrence of extensive O-18- and C-13-depleted ankerite and siderite alteration in Desert Creek is related to the high temperature of the 1250 to 1150 Ma fluid-flow event in the northeast Lawn Hill platform, in contrast to the lower temperature fluids associated with the earlier Century Zn-Pb deposit in the central Lawn Hill platform.

Measurement of productivity index with dynamic DEA

Fare, Grosskopf, Norris and Zhang developed a non-parametric productivity index, Malmquist index, using data envelopment analysis (DEA). The Malmquist index is a measure of productivity progress (regress) and it can be decomposed to different components such as 'efficiency catch-up' and 'technology change'. However, Malmquist index and its components are based on two period of time which can capture only a part of the impact of investment in long-lived assets. The effects of lags in the investment process on the capital stock have been ignored in the current model of Malmquist index. This paper extends the recent dynamic DEA model introduced by Emrouznejad and Thanassoulis and Emrouznejad for dynamic Malmquist index. This paper shows that the dynamic productivity results for Organisation for Economic Cooperation and Development countries should reflect reality better than those based on conventional model.

Transglutaminase 2 is involved in autophagosome maturation

Autophagy is a highly conserved cellular process responsible for the degradation of long-lived proteins and organelles. Autophagy occurs at low levels under normal conditions, but it is enhanced in response to stress, e.g. nutrient deprivation, hypoxia, mitochondrial dysfunction and infection. "Tissue" transglutaminase (TG2) accumulates, both in vivo and in vitro, to high levels in cells under stressful conditions. Therefore, in this study, we investigated whether TG2 could also play a role in the autophagic process. To this end, we used TG2 knockout mice and cell lines in which the enzyme was either absent or overexpressed. The ablation of TG2 protein both in vivo and in vitro, resulted in an evident accumulation of microtubule-associated protein 1 light chain 3 cleaved isoform II (LC3 II) on pre-autophagic vesicles, suggesting a marked induction of autophagy. By contrast, the formation of the acidic vesicular organelles in the same cells was very limited, indicating an impairment of the final maturation of autophagolysosomes. In fact, the treatment of TG2 proficient cells with NH4Cl, to inhibit lysosomal activity, led to a marked accumulation of LC3 II and damaged mitochondria similar to what we observed in TG2-deficient cells. These data indicate a role for TG2-mediated post-translational modifications of proteins in the maturation of autophagosomes accompanied by the accumulation of many damaged mitochondria.

Spatiotemporal optical bullets in two-dimensional fiber arrays and their stability

Long-lived light bullets fully localized in both space and time can be generated in novel photonic media such as multicore optical fiber or waveguide arrays. In this paper we present detailed theoretical analysis on the existence and stability of the discrete-continuous light bullets using a very generic model that occurs in a number of applications.

Dynamic variability in adaptive systems

One of the reasons for using variability in the software product line (SPL) approach (see Apel et al., 2006; Figueiredo et al., 2008; Kastner et al., 2007; Mezini & Ostermann, 2004) is to delay a design decision (Svahnberg et al., 2005). Instead of deciding on what system to develop in advance, with the SPL approach a set of components and a reference architecture are specified and implemented (during domain engineering, see Czarnecki & Eisenecker, 2000) out of which individual systems are composed at a later stage (during application engineering, see Czarnecki & Eisenecker, 2000). By postponing the design decisions in such a manner, it is possible to better fit the resultant system in its intended environment, for instance, to allow selection of the system interaction mode to be made after the customers have purchased particular hardware, such as a PDA vs. a laptop. Such variability is expressed through variation points which are locations in a software-based system where choices are available for defining a specific instance of a system (Svahnberg et al., 2005). Until recently it had sufficed to postpone committing to a specific system instance till before the system runtime. However, in the recent years the use and expectations of software systems in human society has undergone significant changes.Today's software systems need to be always available, highly interactive, and able to continuously adapt according to the varying environment conditions, user characteristics and characteristics of other systems that interact with them. Such systems, called adaptive systems, are expected to be long-lived and able to undertake adaptations with little or no human intervention (Cheng et al., 2009). Therefore, the variability now needs to be present also at system runtime, which leads to the emergence of a new type of system: adaptive systems with dynamic variability.

Trichloroethylene fate and transport studies and biodegradation kinetics in the saturated zone

Permeable reactive barriers (PRB) are constructed from soil solid amendments to support the growth of bacteria that are capable of degrading organic contaminants. The objective of this study was to identify low-cost soil solid amendments that could retard the movement of trichloroethylene (TCE) while serving as long-lived carbon sources to foster its biodegradation in shallow groundwater through the use of a PRB. The natural amendments high in organic carbon content such as eucalyptus mulch, compost, wetland peat, organic humus were compared based on their geophysical characteristics, such as pHw, porosity and total organic carbon (TOC), and as well as TCE sorption potentials. The pHw values were within neutral range except for pine bark mulch and wetland peat. All other geophysical characteristics of the amendments showed suitability for use in a PRB. While the Freundlich model showed better fit for compost and pine bark mulch, the linear sorption model was adequate for eucalyptus mulch, wetland peat and Everglades muck within the concentration range studied (0.2-0.8 mg/L TCE). According to these results, two composts and eucalyptus mulch were selected for laboratory column experiments to evaluate their effectiveness at creating and maintaining conditions suitable for TCE anaerobic dechlorination. The columns were monitored for pH, ORP, TCE degradation, longevity of nutrients and soluble TOC to support TCE dechlorination. Native bacteria in the columns had the ability to convert TCE to DCEs; however, the inoculation with the TCE-degrading culture greatly increased the rate of biodegradation. This caused a significant increase in by-product concentration, mostly in the form of DCEs and VC followed by a slow degradation to ethylene. Of the tested amendments eucalyptus mulch was the most effective at supporting the TCE dechlorination. The experimental results of TCE sequential dechlorination took place in eucalyptus mulch and commercial compost from Savannah River Site columns were then simulated using the Hydrus-1D model. The simulations showed good fit with the experimental data. The results suggested that sorption and degradation were the dominant fate and transport mechanisms for TCE and DCEs in the column, supporting the use of these amendments in a permeable reactive barrier to remediate the TCE.

Inter-subjective and transnational racial effects: The role of the United States in the formation and evolution of the collective perception and racial relations in Cuba, 1898–1902

Since the arrival of the first African slaves to Cuba in 1524, the issue of race has had a long-lived presence in the Cuban national discourse. However, despite Cuba’s colonial history, it has often been maintained by some historians that race relations in Cuba were congenial with racism and racial discrimination never existing as deep or widespread in Cuba as in the United States (Cannon, 1983, p. 113). In fact, it has been argued that institutionalized racism was introduced into Cuban society with the first U.S. occupation, during 1898–1902 (Cannon, 1983, p. 113). This study of Cuba investigates the influence of the United States on the development of race relations and racial perceptions in post-independent Cuba, specifically from 1898-1902. These years comprise the time period immediately following the final fight for Cuban Independence, culminating with the Cuban-Spanish-American War and the first U.S. occupation of Cuba. By this time, the Cuban population comprised Africans as well as descendants of Africans, White Spanish people, indigenous Cubans, and offspring of the intermixing of the groups. This research studies whether the United States’ own race relations and racial perceptions influenced the initial conflicting race relations and racial perceptions in early and post-U.S. occupation Cuba. This study uses a collective interpretative framework that incorporates a national level of analysis with a race relations and racial perceptions focus. This framework reaches beyond the traditionally utilized perspectives when interpreting the impact of the United States during and following its intervention in Cuba. Attention is given to the role of the existing social, political climate within the United States as a driving influence of the United States’ involvement with Cuba. This study reveals that emphasis on the role of the United States as critical to the development of Cuba’s race relations and racial perceptions is credible given the extensive involvement of the U.S. in the building of the early Cuban Republic and U.S. structures serving as models for reconstruction. U.S. government formation in Cuba aligned with a governing system reflecting the existing governing codes of the U.S. during that time period.

(Table S1) Brominated flame retardant concentrations in an ice core from Holtedahlfonna, Svalbard

Brominated flame retardants (BFRs) have been found in Arctic wildlife, lake sediment, and air. To identify the atmospheric BFR deposition history on Svalbard, Norway, we analyzed 19 BFRs, including hexabromocyclododecane (HBCD), 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE), decabromodiphenyl ethane (DBDPE), pentabromoethylbenzene (PBEB),and 15 polybrominated diphenyl ether congeners (PBDE) in the upper 34 m of an ice core (representing 1953-2005) from Holtedahlfonna, the western-most ice sheet on Svalbard. All of the non-PBDE compounds were detected in nearly continuous profiles in the core. Seven PBDEs were not observed above background (28,47,66,100,99,154,153), while 4 were found in 1 or 2 of 6 segments (17,85,138,183). BDEs-49,71,190,209 had nearly continuous profiles but only BDE-209 in large amounts. The greatest inputs were HBCD and BDE-209, 910, and 320 pg/cm**2/yr from 1995-2005. DBDPE, BTBPE, and PBEB show nearly continuous input growth in recent core segments, but all were <6 pg/cm**2/yr. Long-range atmospheric processes may have moved these particle-bound BFRs to the site, probably during the Arctic haze season. Average air mass trajectories over 10 years show >75% of atmospheric flow to Holtedahlfonna coming from Eurasia during haze periods (March and April).

Suspended paticulate matter and respiration experiments of Laternula elliptica in Potter Cove, King George Island, Western Antarctic Peninsula

Recent rapid changes of air temperature on the western side of the Antarctic Peninsula results in increased sediment discharge and ice scouring frequencies in coastal regions. These changes are bound to especially affect slow growing, sessile filter feeders such as the Antarctic bivalve, Laternula elliptica, a long-lived and abundant key species with circumpolar distribution. We investigated the effect of sedimentation and ice scouring on small/young and large/old individuals at two closely located stations, distinctly influenced by both types of disturbance. Small individuals dealt better with disturbance in terms of their respiratory response to sediment exposure, reburrowing ability, and survival after injury, compared to larger animals. At the more disturbed station L. elliptica population density was lower, but larger animals reburrowed faster after iceberg disturbance and reduced their metabolic rate under strong sediment coverage, compared to larger animals of the less disturbed station, indicating that an adaptation or learning response to both types of disturbance may be possible. Smaller individuals were not influenced. Laternula elliptica seems capable of coping with the rapidly changing environmental conditions. Due to a decrease in population density and mean population lifespan, L. elliptica could however lose its key role in the bentho-pelagic carbon flux in areas of high sediment deposition.

A Viking Age maritime haven: a reassessment of the island settlement at Beginish, Co. Kerry

The results of O'Kelly’s excavations on Beginish Island are reassessed and it is proposed that there was a long-lived settlement there that functioned as a Viking-age maritime way-station. This re-evaluation is conducted in the light of recent scholarship on the nature of Scandinavian and Hiberno-Scandinavian settlement in Ireland and, in part, is based on the finds that have emerged on Beginish since the conclusion of the excavations there. The site is considered in the context of its location on the sea route that joined Hiberno-Scandinavian Cork with Limerick, and it is suggested that other such way-stations await.

Lead/Calcium profiles in the common time window 1770-2010 of the three Arctica islandica shells

In the study, we establish centennial records of anthropogenic lead pollution at different locations in the North Atlantic (Iceland, USA, and Europe) by means of lead deposited in shells of the long-lived bivalve Arctica islandica. Due to local oceanographic and geological conditions we conclude that the lead concentrations in the Icelandic shell reflect natural influxes of lead into Icelandic waters. In comparison, the lead profile of the US shell is clearly driven by anthropogenic lead emissions transported from the continent to the ocean by westerly surface winds. Lead concentrations in the European North Sea shell, in contrast, are dominantly driven by local lead sources resulting in a much less conspicuous 1970s gasoline lead peak. In conclusion, the lead profiles of the three shells are driven by different influxes of lead, and yet, all support the applicability of Pb/Ca analyses of A. islandica shells to reconstruct location specific anthropogenic lead pollution.