Signatures of competition and strain structure within the major blood‐stage antigen of Plasmodium falciparum in a local community in Ghana

The concept of niche partitioning has received considerable theoretical attention at the interface of ecology and evolution of infectious diseases. Strain theory postulates that pathogen populations can be structured into distinct nonoverlapping strains by frequency‐dependent selection in response to intraspecific competition for host immune space. The malaria parasite Plasmodium falciparum presents an opportunity to investigate this phenomenon in nature, under conditions of high recombination rate and extensive antigenic diversity. The parasite's major blood‐stage antigen, PfEMP1, is encoded by the hyperdiverse var genes. With a dataset that includes thousands of var DBLα sequence types sampled from asymptomatic cases within an area of high endemicity in Ghana, we address how var diversity is distributed within isolates and compare this to the distribution of microsatellite allelic diversity within isolates to test whether antigenic and neutral regions of the genome are structured differently. With respect to var DBLα sequence types, we find that on average isolates exhibit significantly lower overlap than expected randomly, but that there also exists frequent pairs of isolates that are highly related. Furthermore, the linkage network of var DBLα sequence types reveals a pattern of nonrandom modularity unique to these antigenic genes, and we find that modules of highly linked DBLα types are not explainable by neutral forces related to var recombination constraints, microsatellite diversity, sampling location, host age, or multiplicity of infection. These findings of reduced overlap and modularity among the var antigenic genes are consistent with a role for immune selection as proposed by strain theory. Identifying the evolutionary and ecological dynamics that are responsible for the nonrandom structure in P. falciparum antigenic diversity is important for designing effective intervention in endemic areas.     

T-Cell Regulation in Lepromatous Leprosy

Regulatory T (T_reg) cells are known for their role in maintaining self-tolerance and balancing immune reactions in autoimmune diseases and chronic infections. However, regulatory mechanisms can also lead to prolonged survival of pathogens in chronic infections like leprosy and tuberculosis (TB). Despite high humoral responses against Mycobacterium leprae (M. leprae), lepromatous leprosy (LL) patients have the characteristic inability to generate T helper 1 (Th1) responses against the bacterium. In this study, we investigated the unresponsiveness to M. leprae in peripheral blood mononuclear cells (PBMC) of LL patients by analysis of IFN-γ responses to M. leprae before and after depletion of CD25⁺ cells, by cell subsets analysis of PBMC and by immunohistochemistry of patients'' skin lesions. Depletion of CD25⁺ cells from total PBMC identified two groups of LL patients: 7/18 (38.8%) gained in vitro responsiveness towards M. leprae after depletion of CD25⁺ cells, which was reversed to M. leprae-specific T-cell unresponsiveness by addition of autologous CD25⁺ cells. In contrast, 11/18 (61.1%) remained anergic in the absence of CD25⁺ T-cells. For both groups mitogen-induced IFN-γ was, however, not affected by depletion of CD25⁺ cells. In M. leprae responding healthy controls, treated lepromatous leprosy (LL) and borderline tuberculoid leprosy (BT) patients, depletion of CD25⁺ cells only slightly increased the IFN-γ response. Furthermore, cell subset analysis showed significantly higher (p = 0.02) numbers of FoxP3⁺ CD8⁺CD25⁺ T-cells in LL compared to BT patients, whereas confocal microscopy of skin biopsies revealed increased numbers of CD68⁺CD163⁺ as well as FoxP3⁺ cells in lesions of LL compared to tuberculoid and borderline tuberculoid leprosy (TT/BT) lesions. Thus, these data show that CD25⁺ T_reg cells play a role in M. leprae-Th1 unresponsiveness in LL.     

Linear forms of plasmid DNA are superior to supercoiled structures as active templates for gene expression in plant protoplasts

Introduction of the plasmids pUC8CaMVCAT and pNOSCAT into plant protoplasts is known to result in transient expression of the chloramphenicol acetyl transferase (CAT) gene. Also, transfection with the plasmid pDO432 results in transient appearance of the luciferase enzyme. In the present work we have used these systems to study the effect of DNA topology on the expression of the above recombinant genes. Linear forms of the above plasmids exhibited much higher activity in supporting gene expression than their corresponding super-coiled structures. CAT activity in protoplasts transfected with the linear forms of pUC8CaMVCAT and pNOSCAT was up to ten-fold higher than that observed in protoplasts transfected by the supercoiled template of these plasmids. This effect was observed in protoplasts derived from two different lines of Petunia hybrida and from a Nicotiana tabacum cell line. Transfection with the relaxed form of pUC8CaMVCAT resulted in very low expression of the CAT gene.Northern blot analysis revealed that the amount of poly(A)⁺ RNA extracted from protoplasts transformed with the linear forms of the DNA was about 10-fold higher than that found in protoplasts transformed with supercoiled DNA.Southern blot analysis revealed that about the same amounts of supercoiled and linear DNA molecules were present in nuclei of transfected protoplasts. No significant quantitative differences have been observed between the degradation rates of the various DNA templates used.     

Structure of carbohydrate-bound polynuclear iron oxyhydroxide nanoparticles in parenteral formulations

Intravenous iron therapy is used to treat anemia associated with chronic kidney disease. The chemical structures of parenteral iron agents have not been characterized in detail, and correlations between structure, efficiency of iron delivery, and toxicity via catalysis of oxygen-derived free radical creation remain to be established. In this study, two formulations of parenteral iron have been characterized by absorption spectroscopy, X-ray diffraction analysis (XRD), transmission electron microscopy (TEM), atomic force microscopy (AFM), and elemental analysis. The samples studied were Venofer (Iron Sucrose Injection, USP) and Ferrlecit (Sodium Ferric Gluconate in Sucrose Injection). The 250-800-nm absorption spectra and the XRD patterns showed that both formulations contain a mineral core composed of iron oxyhydroxide in the beta-FeOOH mineral polymorph known as akaganeite. This was further confirmed for each formulation by imaging using TEM and AFM. The average core size for the nanoparticles, after dialysis to remove unbound or loosely bound carbohydrate, was approximately 3+/-2 nm for the iron-sucrose, and approximately 2+/-1 nm for the iron-gluconate. Each of the nanoparticles consists of a mineral core, surrounded by a layer of bound carbohydrate. The overall diameter of the average bead in the dialyzed preparations was approximately 7+/-4 nm for the iron-sucrose, and 3+/-1 nm for the iron-gluconate. Undialyzed preparations have particles with larger average sizes, depending on the extent of dilution of unbound and loosely bound carbohydrate. At a dilution corresponding to a final Fe concentration of 5 mg/mL, the average particle diameter in the iron-sucrose formulation was approximately 22+/-9 nm, whereas that of the iron-gluconate formulation was approximately 12+/-5 nm.     

Isolation,characterization, and structure of the folded interphase genome of Drosophila melanogaster

The intact interphase genome of Drosophila melanogaster has been isolated by sucrose gradient centrifugation after gentle lysis of tissue culture cells in 0.9 M NaCl-0.4% Nonidet P40. The nonviscous folded DNA sediments as a single broad 5000S peak in a complex with RNA (a fraction of the nuclear nascent RNA) and protein (all of the four intranucleosome histones: H2A, H2B, H3, and H4).The folded DNA is supercoiled and can be relaxed to slower sedimenting forms either by intercalating ethidium or by nicking with DNAase I. Incomplete DNAase treatment gives partially relaxed complexes, indicating that each nick relaxes only a stretch of DNA (defined as a supercoiled DNA loop) without affecting the superhelical content of the rest of the genome. The concentration of superhelices in the Drosophila folded DNA is the same as in the E. coli and SV40 closed circular DNAs—that is, about one negative turn every 200 base pairs (bp) in 0.15 M NaCl at 26°C. The estimated average size of the supercoiled DNA loops, about 85,000 bp, equals the size of the larger Drosophila chromomeres.Ethidium intercalation in 0.9 M NaCl both removes the negative superhelical turns and dissociates the four histones from the DNA. The four histones are dissociated in equimolar concentrations, and the relative proportion of histones displaced from the DNA is a function of ethidium concentration. The histones are completely dissociated from the folded DNA at the ethidium concentration which removes all of the negative superhelices. Thus the data strongly suggest that the rotation of the Watson Crick helix which accompanies ethidium intercalation causes the loss of nucleosomes from the DNA.The results are interpreted in terms of a model for the folded Drosophila genome which has the DNA constrained (by both protein-DNA and RNA-DNA interactions) into independent supercoiled loops containing on the average 400 nucleosomes per loop. Each nucleosome is composed of a histone core with the DNA wound around it in a 360° left-handed toroidal supercoil; each nucleosome toroidal supercoil plus its relaxed internucleosome DNA contains, on the average, 200 bp.     

Formation of electrochemically reduced graphene oxide on melamine electrografted layers and its application toward the determination of methylxanthines

The current study describes the electrografting of 2,4-diamino-1,3,5-triazine (AT) groups at the surfaces of glassy carbon electrode (GCE) and indium tin oxide (ITO) through in situ diazotization of melamine. The presence of AT groups at the surface of the electrode was confirmed by X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV). Furthermore, graphene oxide (GO) was self-assembled on AT grafted GCE. The oxygen functional groups present on the surface of GO were electrochemically reduced to form an electrochemically reduced graphene oxide (ERGO) on AT grafted electrode surface. Raman spectra show the characteristic D and G bands at 1340 and 1605 cm⁻¹, respectively, which confirms the successful attachment of GO on AT grafted surface, and the ratio of D and G bands was increased after the electrochemical reduction of GO. EIS shows that the electron transfer reaction of [Fe(CN)₆]^3−/4− was higher at the ERGO modified electrode than at bare, AT grafted, and GO modified GCEs. The electrocatalytic activity of ERGO was investigated toward the oxidation of methylxanthines. It shows excellent electrocatalytic activity toward these methylxanthines by not only shifting their oxidation potentials toward less positive potentials but also enhancing their oxidation currents.     

Chemical Discrimination and Aggressiveness via Cuticular Hydrocarbons in a Supercolony-Forming Ant,Formica yessensis

Background

Territorial boundaries between conspecific social insect colonies are maintained through nestmate recognition systems. However, in supercolony-forming ants, which have developed an extraordinary social organization style known as unicoloniality, a single supercolony extends across large geographic distance. The underlying mechanism is considered to involve less frequent occurrence of intraspecific aggressive behaviors, while maintaining interspecific competition. Thus, we examined whether the supercolony-forming species, Formica yessensis has a nestmate recognition system similar to that of the multicolonial species, Camponotus japonicus with respect to the cuticular hydrocarbon-sensitive sensillum (CHC sensillum), which responds only to non-nestmate CHCs. We further investigated whether the sensory system reflects on the apparent reduced aggression between non-nestmates typical to unicolonial species.

Methodology/Principal Findings

F. yessensis constructs supercolonies comprising numerous nests and constitutes the largest supercolonies in Japan. We compared the within-colony or between-colonies’ (1) similarity in CHC profiles, the nestmate recognition cues, (2) levels of the CHC sensillar response, (3) levels of aggression between workers, as correlated with geographic distances between nests, and (4) their genetic relatedness. Workers from nests within the supercolony revealed a greater similarity of CHC profiles compared to workers from colonies outside it. Total response of the active CHC sensilla stimulated with conspecific alien CHCs did not increase as much as in case of C. japonicus, suggesting that discrimination of conspecific workers at the peripheral system is limited. It was particularly limited among workers within a supercolony, but was fully expressed for allospecific workers.

Conclusions/Significance

We demonstrate that chemical discrimination between nestmates and non-nestmates in F. yessensis was not clear cut, probably because this species has only subtle intraspecific differences in the CHC pattern that typify within a supercolony. Such an incomplete chemical discrimination via the CHC sensilla is thus an important factor contributing to decreased occurrence of intraspecific aggressive behavior especially within a supercolony.     

Assessing the effects of architectural variations on light partitioning within virtual wheat–pea mixtures

Background and Aims

Predicting light partitioning in crop mixtures is a critical step in improving the productivity of such complex systems, and light interception has been shown to be closely linked to plant architecture. The aim of the present work was to analyse the relationships between plant architecture and light partitioning within wheat–pea (Triticum aestivum–Pisum sativum) mixtures. An existing model for wheat was utilized and a new model for pea morphogenesis was developed. Both models were then used to assess the effects of architectural variations in light partitioning.

Methods

First, a deterministic model (L-Pea) was developed in order to obtain dynamic reconstructions of pea architecture. The L-Pea model is based on L-systems formalism and consists of modules for ‘vegetative development’ and ‘organ extension’. A tripartite simulator was then built up from pea and wheat models interfaced with a radiative transfer model. Architectural parameters from both plant models, selected on the basis of their contribution to leaf area index (LAI), height and leaf geometry, were then modified in order to generate contrasting architectures of wheat and pea.

Key results

By scaling down the analysis to the organ level, it could be shown that the number of branches/tillers and length of internodes significantly determined the partitioning of light within mixtures. Temporal relationships between light partitioning and the LAI and height of the different species showed that light capture was mainly related to the architectural traits involved in plant LAI during the early stages of development, and in plant height during the onset of interspecific competition.

Conclusions

In silico experiments enabled the study of the intrinsic effects of architectural parameters on the partitioning of light in crop mixtures of wheat and pea. The findings show that plant architecture is an important criterion for the identification/breeding of plant ideotypes, particularly with respect to light partitioning.     

Remote sensing reveals long-term effects of caribou on tundra vegetation

Declining use and abandonment of traditional ranges by migratory caribou (Rangifer tarandus) have often been related to density-dependent depletion of summer forage. The Pen Islands caribou herd (R. t. caribou), Ontario and Manitoba, Canada, numbered in the thousands on its traditional summer tundra range during the 1980s, but then declined in that region. We postulated that increased caribou abundance over three decades negatively affected phytomass, given that under the exploitation ecosystem hypothesis (EEH), grazers limit the amount of primary production if few predators are present. We tested this prediction using the Normalized Difference Vegetation Index (NDVI), as a proxy for phytomass available to caribou. We lagged caribou abundance in the explanatory model by the number of years (4–7) between peak caribou abundance and minimum NDVI. NDVI was negatively related to caribou abundance lagged by 6 years, and growing degree days explained much of the annual variation in NDVI. Precipitation was not an important predictor in the model. Our study is the first to apply NDVI to support the EEH for caribou. We propose that this method could be used over broad scales to shed light on limiting factors for migratory caribou across the circumpolar North.