Overnight Resting of PBMC Changes Functional Signatures of Antigen Specific T- Cell Responses: Impact for Immune Monitoring within Clinical Trials

Polyfunctional CD4 or CD8 T cells are proposed to represent a correlate of immune control for persistent viruses as well as for vaccine mediated protection against infection. A well-suited methodology to study complex functional phenotypes of antiviral T cells is the combined staining of intracellular cytokines and phenotypic marker expression using polychromatic flow cytometry. In this study we analyzed the effect of an overnight resting period at 37°C on the quantity and functionality of HIV-1, EBV, CMV, HBV and HCV specific CD4 and CD8 T-cell responses in a cohort of 21 individuals. We quantified total antigen specific T cells by multimer staining and used 10-color intracellular cytokine staining (ICS) to determine IFNγ, TNFα, IL2 and MIP1β production. After an overnight resting significantly higher numbers of functionally active T cells were detectable by ICS for all tested antigen specificities, whereas the total number of antigen specific T cells determined by multimer staining remained unchanged. Overnight resting shifted the quality of T-cell responses towards polyfunctionality and increased antigen sensitivity of T cells. Our data suggest that the observed effect is mediated by T cells rather than by antigen presenting cells. We conclude that overnight resting of PBMC prior to ex vivo analysis of antiviral T-cell responses represents an efficient method to increase sensitivity of ICS-based methods and has a prominent impact on the functional phenotype of T cells.     

Nitric oxide formation by Escherichia coli. Dependence on nitrite reductase,the NO-sensing regulator Fnr,and flavohemoglobin Hmp

Nitric oxide (NO) is a key signaling and defense molecule in biological systems. The bactericidal effects of NO produced, for example, by macrophages are resisted by various bacterial NO-detoxifying enzymes, the best understood being the flavohemoglobins exemplified by Escherichia coli Hmp. However, many bacteria, including E. coli, are reported to produce NO by processes that are independent of denitrification in which NO is an obligatory intermediate. We demonstrate using an NO-specific electrode that E. coli cells, grown anaerobically with nitrate as terminal electron acceptor, generate significant NO on adding nitrite. The periplasmic cytochrome c nitrite reductase (Nrf) is shown, by comparing Nrf+ and Nrf- mutants, to be largely responsible for NO generation. Surprisingly, an hmp mutant did not accumulate more NO but, rather, failed to produce detectable NO. Anaerobic growth of the hmp mutant was not stimulated by nitrate, and the mutant failed to produce periplasmic cytochrome(s) c, leading to the hypothesis that accumulating NO in the absence of Hmp inactivates the global anaerobic regulator Fnr by reaction with the [4Fe-4S]2+ cluster (Cruz-Ramos, H., Crack, J., Wu, G., Hughes, M. N., Scott, C., Thomson, A. J., Green, J., and Poole, R. K. (2002) EMBO J. 21, 3235-3244). Fnr thus failed to up-regulate nitrite reductase. The model is supported by the inability of an fnr mutant to generate NO and by the restoration of NO accumulation to hmp mutants upon introducing a plasmid encoding Fnr* (D154A) known to confer activity in the presence of oxygen. A cytochrome bd-deficient mutant retained NO-generating activity. The present study reveals a critical balance between NO-generating and -detoxifying activities during anaerobic growth.     

The association between blood coagulation activity and lung function: a population-based study

Background

Increased in susceptibility to thrombotic disease may be associated with lower lung function. If causal, this association may suggest an area for development of new interventions for lung disease. The aim of this study was to investigate the association between blood coagulation activation as measured by plasma d-dimers and lung function.

Methodology/Principal Findings

We conducted a cross-sectional study on 2463 randomly selected adults in 1991 and followed up 1252 of these individuals in 2000. Plasma D-dimer levels, a marker of activity of blood coagulation pathways, were analysed in the baseline 1991 samples. There was an inverse cross-sectional association between plasma D-dimer and Forced Expiratory Volume in one second, with a decrease of 71 ml per µg FEU/ml increment in plasma D-dimer (95% confidence intervals CI: −135 to −6), and a decrease in Forced Vital Capacity (97 ml per µg FEU/ml increase in D-dimer, 95%CI: −170 to −24). These associations were attenuated after adjustment for serum highly sensitive CRP. No association was observed between plasma D-dimer and the decline in lung function between 1991 and 2000.

Conclusions/Significance

The cross-sectional findings are consistent with the hypothesis that activation of blood coagulation pathways is associated with decreased lung function, and that systemic inflammation may contribute to this relation. However, the lack of an association with decline in lung function suggests that clotting pathways that involve d-dimers may not be a promising therapeutic target for new interventions for respiratory disease.     

Soil biota,carbon cycling and crop plant biomass responses to biochar in a temperate mesocosm experiment

Plant and Soil - Shifts of plant community composition with enhanced atmospheric nitrogen (N) deposition in grasslands have occurred globally. Despite extensive studies on the effects of enhanced N...     

Mycobacterium tuberculosis inhibits the NLRP3 inflammasome activation via its phosphokinase PknF

Mycobacterium tuberculosis (Mtb) has evolved to evade host innate immunity by interfering with macrophage functions. Interleukin-1β (IL-1β) is secreted by macrophages after the activation of the inflammasome complex and is crucial for host defense against Mtb infections. We have previously shown that Mtb is able to inhibit activation of the AIM2 inflammasome and subsequent pyroptosis. Here we show that Mtb is also able to inhibit host cell NLRP3 inflammasome activation and pyroptosis. We identified the serine/threonine kinase PknF as one protein of Mtb involved in the NLRP3 inflammasome inhibition, since the pknF deletion mutant of Mtb induces increased production of IL-1β in bone marrow-derived macrophages (BMDMs). The increased production of IL-1β was dependent on NLRP3, the adaptor protein ASC and the protease caspase-1, as revealed by studies performed in gene-deficient BMDMs. Additionally, infection of BMDMs with the pknF deletion mutant resulted in increased pyroptosis, while the IL-6 production remained unchanged compared to Mtb-infected cells, suggesting that the mutant did not affect the priming step of inflammasome activation. In contrast, the activation step was affected since potassium efflux, chloride efflux and the generation of reactive oxygen species played a significant role in inflammasome activation and subsequent pyroptosis mediated by the Mtb pknF mutant strain. In conclusion, we reveal here that the serine/threonine kinase PknF of Mtb plays an important role in innate immune evasion through inhibition of the NLRP3 inflammasome.     

Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species’ extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.     

Cyclic hydrostatic pressure and cotton particles stimulate synthesis by human lung macrophages of cytokines in vitro

Background

Inhalation of particulates is a leading cause of the development of lung diseases and current understanding of the complex relationship between lung metabolism and airborne particulates is incomplete. It is well established that mechanical load is important in the development of the lung and in lung cell differentiation. The interaction between particle exposure and physical forces on alveolar macrophages is a physiologically relevant issue, but as yet understudied. This study examines the effect of cyclic hydrostatic pressure and cotton particles on synthesis of cytokines by human alveolar macrophages.

Methods

Alveolar macrophages were obtained from patients with lung disease, either from lavage samples or from lung tissue resection. The commonly used cell line THP-1 was included in the experiments. Cell cultures were exposed to cotton particles and/cyclic hydrostatic pressure (3 or 5 psi); control cultures were exposed to medium only. TNFα, IL-1β and IL-6 were assayed in the culture media using specific ELISAs. Cells were characterized using morphology and markers specific for macrophages (Jenner/Giemsa staining, CD14 and CD68).

Results

Exposure to cotton particles stimulated cytokine synthesis by macrophages from all three sources; exposure to cyclic hydrostatic pressure alone did not stimulate cytokine synthesis significantly. However, the combination of both particles and cyclic hydrostatic pressure increased the simulation of cytokine synthesis still further. Cell characterization demonstrated that the large majority of cells had a macrophage morphology and were positive for CD14 and CD68.

Conclusion

These data suggest an interaction between cyclic hydrostatic pressure and particulate exposure, which increases alveolar macrophage cytokine production. This interaction was only observed at the higher cyclic hydrostatic pressure. However, in patient samples, there was considerable variation in the amount by which secretion of an individual cytokine increased and there was also variation in the mechanosensitivity of cells from the three different sources. Cyclic hydrostatic pressure, therefore, may be an important modulator of the response of alveolar macrophages to cotton particles, but the source of the cells may be a confounding factor which demands further investigation.     

Long-term patterns of fruit production in five forest types of the South Carolina upper coastal plain

Fleshy fruit is a key food resource for many vertebrates and may be particularly important energy source to birds during fall migration and winter. Hence, land managers should know how fruit availability varies among forest types, seasons, and years. We quantified fleshy fruit abundance monthly for 9 years (1995–2003) in 56 0.1-ha plots in 5 forest types of South Carolina's upper Coastal Plain, USA. Forest types were mature upland hardwood and bottomland hardwood forest, mature closed-canopy loblolly (Pinus taeda) and longleaf pine (P. palustris) plantation, and recent clearcut regeneration harvests planted with longleaf pine seedlings. Mean annual number of fruits and dry fruit pulp mass were highest in regeneration harvests (264,592 ± 37,444 fruits; 12,009 ± 2,392 g/ha), upland hardwoods (60,769 ± 7,667 fruits; 5,079 ± 529 g/ha), and bottomland hardwoods (65,614 ± 8,351 fruits; 4,621 ± 677 g/ha), and lowest in longleaf pine (44,104 ± 8,301 fruits; 4,102 ± 877 g/ha) and loblolly (39,532 ± 5,034 fruits; 3,261 ± 492 g/ha) plantations. Fruit production was initially high in regeneration harvests and declined with stand development and canopy closure (1995–2003). Fruit availability was highest June–September and lowest in April. More species of fruit-producing plants occurred in upland hardwoods, bottomland hardwoods, and regeneration harvests than in loblolly and longleaf pine plantations. Several species produced fruit only in 1 or 2 forest types. In sum, fruit availability varied temporally and spatially because of differences in species composition among forest types and age classes, patchy distributions of fruiting plants both within and among forest types, fruiting phenology, high inter-annual variation in fruit crop size by some dominant fruit-producing species, and the dynamic process of disturbance-adapted species colonization and decline, or recovery in recently harvested stands. Land managers could enhance fruit availability for wildlife by creating and maintaining diverse forest types and age classes. © 2012 The Wildlife Society.     

CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA

Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approaches using full-length proteins in the budding yeast system. We find that the C-terminal tail of Asf1 enhances the interaction of Asf1 with CAF-1. Surprisingly, although H3/H4 also enhances the interaction of Asf1 with the CAF-1 subunit Cac2, H3/H4 forms a tight complex with CAF-1 exclusive of Asf1, with an affinity weaker than Asf1–H3/H4 or H3/H4–DNA interactions. Unlike Asf1, monomeric CAF-1 binds to multiple H3/H4 dimers, which ultimately promotes the formation of (H3/H4)₂ tetramers on DNA. Thus, transition of H3/H4 from the Asf1-associated dimer to the DNA-associated tetramer is promoted by CAF-1-induced H3/H4 oligomerization.     

Bioethanol potential from miscanthus with low ILUC risk in the province of Lublin,Poland

Increasing production of biofuels has led to concerns about indirect land‐use change (ILUC). So far, significant efforts have been made to assess potential ILUC effects. But limited attention has been paid to strategies for reducing the extent of ILUC and controlling the type of LUC. This case study assesses five key ILUC mitigation measures to quantify the low‐ILUC‐risk production potential of miscanthus‐based bioethanol in Lublin province (Poland) in 2020. In 2020, a total area of 196 to 818 thousand hectare of agricultural land could be made available for biomass production by realizing above‐baseline yield developments (95–413 thousand ha), increased food chain efficiencies (9–30 thousand ha) and biofuel feedstock production on underutilized lands (92–375 thousand ha). However, a maximum 203–269 thousand hectare is considered legally available (not protected) and biophysically suitable for miscanthus production. The resulting low‐ILUC‐risk bioethanol production potential ranges from 12 to 35 PJ per year. The potential from this region alone is higher than the national Polish target for second‐generation bioethanol consumption of 9 PJ in 2020. Although the sustainable implementation potential may be lower, the province of Lublin could play a key role in achieving this target. This study shows that the mitigation or prevention of ILUC from bioenergy is only possible when an integrated perspective is adopted on the agricultural and bioenergy sectors. Governance and policies on planning and implementing ILUC mitigation are considered vital for realizing a significant bioenergy potential with low ILUC risk. One important aspect in this regard is monitoring the risk of ILUC and the implementation of ILUC mitigation measures. Key parameters for monitoring are land use, land cover and crop yields.