Biotic Regulation of CO<Subscript>2</Subscript> Uptake–Climate Responses: Links to Vegetation Properties

Identifying the plant traits and patterns of trait distribution in communities that are responsible for biotic regulation of CO₂ uptake–climate responses remains a priority for modeling terrestrial C dynamics. We used remotely sensed estimates of gross primary productivity (GPP) from plots planted to different combinations of perennial grassland species in order to determine links between traits and GPP–climate relationships. Climatic variables explained about 50% of the variance in temporal trends in GPP despite large variation in CO₂ uptake among seasons, years, and plots of differing composition. GPP was highly correlated with contemporary changes in net radiation (Rn) and precipitation deficit (potential evapotranspiration minus precipitation) but was negatively correlated with precipitation summed over 210 days prior to flux measurements. Plots differed in GPP–Rn and GPP–water (deficit, precipitation) relationships. Accounting for differences in GPP–climate relationships explained an additional 11% of variance in GPP. Plot differences in GPP–Rn and GPP–precipitation slopes were linked to differences in community-level light-use efficiency (GEE*). Plot differences in GPP–deficit slopes were linked to differences in a species abundance-weighted index of specific leaf area (SLA). GEE* and weighted SLA represent vegetation properties that may regulate how CO₂ uptake responds to climatic variation in grasslands.     

Strong diversifying selection on domains of the Plasmodium falciparum apical membrane antigen 1 gene

The surface-accessible ectodomain region of the Plasmodium falciparum apical membrane antigen 1 (AMA1) is a malaria vaccine candidate. The amino acid sequence may be under selection from naturally acquired immune responses, and previous analyses with a small number of allele sequences indicate a non-neutral pattern of nucleotide variation. To investigate whether there is selection to maintain polymorphism within a population, and to identify the parts of the ectodomain under strongest selection, a sample of 51 alleles from a single endemic population was studied. Analyses using Fu and Li's D and F tests, Tajima's D test, and the McDonald-Kreitman test (with the chimpanzee parasite P. reichenowi as outgroup) show significant departure from neutrality and indicate the selective maintenance of alleles within the population. There is also evidence of a very high recombination rate throughout the sequence, as estimated by the recombination parameter, C, and by the rapid decline in linkage disequilibrium with increasing nucleotide distance. Of the three domains (I-III) encoding structures determined by disulfide bonds, the evidence of selection is strongest for Domains I and III. We predict that these domains in particular are targets of naturally acquired protective immune responses in humans.     

Plant invasions differentially affected by diversity and dominant species in native‐ and exotic‐dominated grasslands

Plant invasions are an increasingly serious global concern, especially as the climate changes. Here, we explored how plant invasions differed between native‐ and novel exotic‐dominated grasslands with experimental addition of summer precipitation in Texas in 2009. Exotic species greened up earlier than natives by an average of 18 days. This was associated with a lower invasion rate early in the growing season compared to native communities. However, invasion rate did not differ significantly between native and exotic communities across all sampling times. The predictors of invasion rate differed between native and exotic communities, with invasion being negatively influenced by species richness in natives and by dominant species in exotics. Interestingly, plant invasions matched the bimodal pattern of precipitation in Temple, Texas, and did not respond to the pulse of precipitation during the summer. Our results suggest that we will need to take different approaches in understanding of invasion between native and exotic grasslands. Moreover, with anticipated increasing variability in precipitation under global climate change, plant invasions may be constrained in their response if the precipitation pulses fall outside the normal growing period of invaders.     

Stomatal density and aperture length in four plant species grown across a subambient CO2 gradient

Stomatal density, stomatal aperture length, area/leaf, and number of stomata/leaf were measured after the annual C₃ agronomic grasses oats (Avena sativa) and wheat (Triticum aestivum), the C, woody legume honey mesquite (Prosopis glandulosa), and the perennial C₄ grass little bluestem (Schizachyrium scoparium) were grown across a subambient carbon dioxide concentration ([CO₂]) gradient from near 200 to 350 μmol/mol in a growth chamber. The purpose was to determine if the size and density of stomata vary in response to atmospheric [CO₂] during growth, across a subambient [CO₂] range representative of the doubling that has occurred since the last ice age. Changes in stomatal density and aperture length with increasing [CO₂] were small when detected. Stomatal density decreased on adaxial flag leaf surfaces of wheat, and aperture length increased slightly with [CO₂], Leaf area and number of stomata/flag leaf increased by similar proportions with [CO₂] in two wheat cultivars. No consistent relationship between [CO₂] and stomatal density or size was detected in mesquite, oats, or little bluestem. We conclude that individual plants of these species lack the plasticity to significantly alter stomatal density and aperture length in response to increasing atmospheric [CO₂] in a single generation (annuals) or growing season (perennials).     

CO2‐caused change in plant species composition rivals the shift in vegetation between mid‐grass and tallgrass prairies

Atmospheric CO₂ enrichment usually changes the relative contributions of plant species to biomass production of grasslands, but the types of species favored and mechanisms by which change is mediated differ among ecosystems. We measured changes in the contributions of C₃ perennial forbs and C₄ grasses to aboveground biomass production of tallgrass prairie assemblages grown along a field CO₂ gradient (250–500 μmol mol^?1) in central Texas USA. Vegetation was grown on three soil types and irrigated each season with water equivalent to the growing season mean of precipitation for the area. We predicted that CO₂ enrichment would increase the forb contribution to community production, and favor tall‐grasses over mid‐grasses by increasing soil water content and reducing the frequency with which soil water fell below a limitation threshold. CO₂ enrichment favored forbs over grasses on only one of three soil types, a Mollisol. The grass fraction of production increased dramatically across the CO₂ gradient on all soils. Contribution of the tall‐grass Sorghastrum nutans to production increased at elevated CO₂ on the two most coarse‐textured of the soils studied, a clay Mollisol and sandy Alfisol. The CO₂‐caused increase in Sorghastrum was accompanied by an offsetting decline in production of the mid‐grass Bouteloua curtipendula. Increased CO₂ favored the tall‐grass over mid‐grass by increasing soil water content and apparently intensifying competition for light or other resources (Mollisol) or reducing the frequency with which soil water dipped below threshold levels (Alfisol). An increase in CO₂ of 250 μmol mol^?1 above the pre‐industrial level thus led to a shift in the relative production of established species that is similar in magnitude to differences observed between mid‐grass and tallgrass prairies along a precipitation gradient in the central USA. By reducing water limitation to plants, atmospheric CO₂ enrichment may alter the composition and even structure of grassland vegetation.     

Tissue-Specific Differences in PD-1 and PD-L1 Expression during Chronic Viral Infection: Implications for CD8 T-Cell Exhaustion

The PD-1/PD-L pathway plays a major role in regulating T-cell exhaustion during chronic viral infections in animal models, as well as in humans, and blockade of this pathway can revive exhausted CD8⁺ T cells. We examined the expression of PD-1 and its ligands, PD-L1 and PD-L2, in multiple tissues during the course of chronic viral infection and determined how the amount of PD-1 expressed, as well as the anatomical location, influenced the function of exhausted CD8 T cells. The amount of PD-1 on exhausted CD8 T cells from different anatomical locations did not always correlate with infectious virus but did reflect viral antigen in some tissues. Moreover, lower expression of PD-L1 in some locations, such as the bone marrow, favored the survival of PD-1^Hi exhausted CD8 T cells, suggesting that some anatomical sites might provide a survival niche for subpopulations of exhausted CD8 T cells. Tissue-specific differences in the function of exhausted CD8 T cells were also observed. However, while cytokine production did not strictly correlate with the amount of PD-1 expressed by exhausted CD8 T cells from different tissues, the ability to degranulate and kill were tightly linked to PD-1 expression regardless of the anatomical location. These observations have implications for human chronic infections and for therapeutic interventions based on blockade of the PD-1 pathway.Chronic viral infections are often associated with CD8⁺ T-cell dysfunction (30). This dysfunction, termed exhaustion, includes defects in the ability to produce antiviral cytokines, poor cytotoxicity, a loss of antigen-independent self-renewal, and the inability to vigorously re-expand following antigen exposure (30). These functional deficiencies contrast with the highly functional memory CD8⁺ T cells that are generated after acute infection and maintained via interleukin-7 (IL-7)- and IL-15-mediated homeostatic proliferation (30). During chronic viral infections, T-cell exhaustion often correlates with poor control of viral replication (3, 8, 38, 39). Thus, there is considerable interest in developing strategies to reverse exhaustion and restore function in virus-specific CD8⁺ T cells during chronic infections.Recent studies have revealed an important role for the negative regulatory molecule PD-1 in CD8 T-cell exhaustion during chronic viral infections (29). PD-1, a member of the CD28/CTLA-4 family of costimulatory/coinhibitory receptors, contains both ITIM and ITSM motifs in the intracellular tail and can deliver negative signals, at least partly via recruitment of the phosphatase Shp-2 (29). A role for PD-1 in regulating T-cell responses to chronic viral infections was first observed using lymphocytic choriomeningitis virus (LCMV) infection of mice, where PD-1 was found to be highly expressed on exhausted CD8⁺ T cells from chronically infected animals but not on functional memory CD8⁺ T cells from mice that had cleared an acute strain of the virus (3). In vivo blockade of the PD-1 pathway led to a dramatic increase in the number of virus-specific CD8⁺ T cells, improved functionality of these cells, and enhanced control of viral replication (3). These observations were extended to human chronic viral infections, and a series of studies have demonstrated that human immunodeficiency virus (HIV)-, hepatitis C virus (HCV)-, and HBV-specific CD8⁺ T cells upregulate PD-1 in humans compared to CD8⁺ T cells specific for nonpersisting viruses such as influenza virus or vaccinia virus (6-8, 24, 26, 32, 33, 42). Increasing PD-1 expression also correlates with disease status during HIV infection (8, 42). In vitro blockade of PD-1-PD-L interactions can reinvigorate exhausted virus-specific T-cell responses in humans and appears to have a prominent impact on proliferative expansion and/or prevention of apoptosis in these cases (9, 24, 32). Finally, recent results from in vivo blockade in the macaque simian immunodeficiency virus (SIV) infection model demonstrated the effectiveness of blocking PD-1 in primates during chronic viral infection (36). In these studies, PD-1 blockade enhanced virus-specific T and B-cell responses, lowered viral load, and improved the survival of chronically infected animals. Thus, PD-1 has emerged as not only a major regulator of T-cell exhaustion and viral control during chronic infection but also as an important potential therapeutic target.Despite these important studies and the clear impact of PD-1 blockade on the reversal of T-cell exhaustion, important questions remain. For example, previous work has demonstrated that PD-1 expression is not uniform on subsets of exhausted CD8 T cells (4). However, the expression of PD-1 on exhausted CD8 T cells in multiple tissues, and the relationship between PD-1 expression in these tissues to viral load, the PD-1 ligands and function has not been examined. Given the nonlymphoid accumulation of virus-specific CD8 T cells during chronic viral infections (11, 39) and the predilection of many important chronic infections for replicating in anatomically restricted locations (e.g., HCV and the liver, HIV and mucosal tissues, etc.), the dynamics of PD-1 expression by exhausted CD8 T cells outside the blood and spleen could have important therapeutic implications.In the present study we examined these issues using the mouse model of LCMV infection. Our results demonstrate that exhausted CD8 T cells have a wide range of PD-1 expression in different tissues of chronically infected mice. Virus-specific CD8 T cells in some anatomical locations such as the liver, brain, and bone marrow (BM) expressed high PD-1 for substantially longer than virus-specific CD8⁺ T cells from the spleens or blood of the same mice. Although PD-1 expression in the spleen correlated well with reduced gamma interferon (IFN-γ) and tumor necrosis factor (TNF) production, the PD-1^Hi virus-specific CD8⁺ T cells from the BM remained capable of producing antiviral cytokines ex vivo. In contrast, a strong negative correlation between PD-1 expression and cytotoxicity existed for exhausted CD8 T cells from all tissues tested. PD-L1 expression was high in the spleen, whereas in the BM antigen-presenting cell (APC) populations expressed lower amounts of PD-L1. Survival of PD-1^Hi CD8⁺ T cells from the BM was decreased in the presence of splenic APCs, suggesting that different tissue microenvironments in vivo could selectively support the persistence of PD-1^Hi exhausted CD8 T cells. Since PD-1 expression differs by anatomical location, these observations suggest that PD-1 blockade in vivo will have varying impacts on exhausted CD8 T cells from different tissues or anatomical locations. These observations have implications for human chronic infections such as HBV, HCV, and HIV.     

Two directions of plasticity in the sensory-deprived adult cortex

Damage or deprivation of a localized region of the skin surface has been shown to induce a selective expansion of adjacent skin surface representations in the adult somatosensory cortex. Here, we use repeated optical imaging in conjunction with single unit recordings to assess the plasticity of a single whisker's functional representation in the adult rat. We observed a large-scale expansion of a single whisker's functional representation following innocuous removal of all neighboring whiskers. Surprisingly, the same manipulation can also induce a large-scale contraction of the representation if the animal is removed from its home cage and given a brief opportunity to use its whiskers for active exploration of a different environment. Both the expansion and contraction reverse upon regrowth of the deprived whiskers. Thus, allowing the animal to use its deprived receptor organ in active exploration can determine the direction of plasticity in the adult cortex.     

Chemical and Thermal Unfolding of a Global Staphylococcal Virulence Regulator with a Flexible C-Terminal End

SarA, a Staphylococcus aureus-specific dimeric protein, modulates the expression of numerous proteins including various virulence factors. Interestingly, S. aureus synthesizes multiple SarA paralogs seemingly for optimizing the expression of its virulence factors. To understand the domain structure/flexibility and the folding/unfolding mechanism of the SarA protein family, we have studied a recombinant SarA (designated rSarA) using various in vitro probes. Limited proteolysis of rSarA and the subsequent analysis of the resulting protein fragments suggested it to be a single-domain protein with a long, flexible C-terminal end. rSarA was unfolded by different mechanisms in the presence of different chemical and physical denaturants. While urea-induced unfolding of rSarA occurred successively via the formation of a dimeric and a monomeric intermediate, GdnCl-induced unfolding of this protein proceeded through the production of two dimeric intermediates. The surface hydrophobicity and the structures of the intermediates were not identical and also differed significantly from those of native rSarA. Of the intermediates, the GdnCl-generated intermediates not only possessed a molten globule-like structure but also exhibited resistance to dissociation during their unfolding. Compared to the native rSarA, the intermediate that was originated at lower GdnCl concentration carried a compact shape, whereas, other intermediates owned a swelled shape. The chemical-induced unfolding, unlike thermal unfolding of rSarA, was completely reversible in nature.     

Revisiting the use of Iprodione and Trichoderma in the integrated management of onion white rot

The biocontrol properties of Trichoderma species are well documented, but their effectiveness in antagonism of the problematic Sclerotium cepivorum, the causal agent of white rot in Allium species, appears limited with reports of significant control only relating to deliberately-mutated strains of Trichoderma. Our previous studies have indicated the possibility of using selected naturally-occurring strains of the antagonist in the suppression of other diseases; now in vitro and controlled environment in vivo studies have indicated that a degree of control of Onion White Rot is possible, and that the selected antagonist strains can be used in integrated treatments with Iprodione to good effect. The possible value of such treatments is considered in light of other approaches to the suppression of this continuing problem.