CD1 molecules efficiently present antigen in immature dendritic cells and traffic independently of MHC class II during dendritic cell maturation

Upon exposure to Ag and inflammatory stimuli, dendritic cells (DCs) undergo a series of dynamic cellular events, referred to as DC maturation, that involve facilitated peptide Ag loading onto MHC class II molecules and their subsequent transport to the cell surface. Besides MHC molecules, human DCs prominently express molecules of the CD1 family (CD1a, -b, -c, and -d) and mediate CD1-dependent presentation of lipid and glycolipid Ags to T cells, but the impact of DC maturation upon CD1 trafficking and Ag presentation is unknown. Using monocyte-derived immature DCs and those stimulated with TNF-alpha for maturation, we observed that none of the CD1 isoforms underwent changes in intracellular trafficking that mimicked MHC class II molecules during DC maturation. In contrast to the striking increase in surface expression of MHC class II on mature DCs, the surface expression of CD1 molecules was either increased only slightly (for CD1b and CD1c) or decreased (for CD1a). In addition, unlike MHC class II, DC maturation-associated transport from lysosomes to the plasma membrane was not readily detected for CD1b despite the fact that both molecules were prominently expressed in the same MIIC lysosomal compartments before maturation. Consistent with this, DCs efficiently presented CD1b-restricted lipid Ags to specific T cells similarly in immature and mature DCs. Thus, DC maturation-independent pathways for lipid Ag presentation by CD1 may play a crucial role in host defense, even before DCs are able to induce maximum activation of peptide Ag-specific T cells.     

Molecular phylogenetic analysis of the avian malarial parasite Plasmodium (Novyella) juxtanucleare

Plasmodium (Novyella) juxtanucleare is a widely distributed parasite that primarily infects chickens (Gallus gallus domesticus). All species of Novyella are characterized by very small schizonts, which in the case of P. juxtanucleare are always found juxtaposed to the erythrocyte nucleus, hence its name. Nearly complete small-subunit ribosomal RNA sequences have been obtained from 2 isolates of this species, and comparisons with other Plasmodium species have been made. Phylogenetic analysis reveals that this parasite is closely related to other avian-infecting Plasmodium species and that molecular relationships among the avian-infecting plasmodia do not correspond to their morphology-based subgeneric classifications.     

Interferon-regulated pathways that control hepatitis B virus replication in transgenic mice

We previously showed that the intrahepatic induction of cytokines such as alpha/beta interferon (IFN-alpha/beta) and gamma interferon (IFN-gamma) inhibits hepatitis B virus (HBV) replication noncytopathically in the livers of transgenic mice. The intracellular pathway(s) responsible for this effect is still poorly understood. To identify interferon (IFN)-inducible intracellular genes that could play a role in our system, we crossed HBV transgenic mice with mice deficient in IFN regulatory factor 1 (IRF-1), the double-stranded RNA-activated protein kinase (PKR), or RNase L (RNase L) (IRF-1(-/-), PKR(-/-), or RNase L(-/-) mice, respectively), three well-characterized IFN-inducible genes that mediate antiviral activity. We showed that unmanipulated IRF-1(-/-) or PKR(-/-) transgenic mice replicate HBV in the liver at slightly higher levels than the respective controls, suggesting that both IRF-1 and PKR individually appear to mediate signals that modulate HBV replication under basal conditions. These same animals were responsive to the antiviral effects of the IFN-alpha/beta inducer poly(I-C) or recombinant murine IFN-gamma, suggesting that under these conditions, either the IRF-1 or the PKR genes can mediate the antiviral activity of the IFNs or other IFN-inducible genes mediate the antiviral effects. Finally, RNase L(-/-) transgenic mice were undistinguishable from controls under basal conditions and after poly(I-C) or IFN-gamma administration, suggesting that RNase L does not modulate HBV replication in this model.     

Costs of phenotypic plasticity

Phenotypically plastic organisms display alternative phenotypes in different environments. It is widely appreciated that possessing alternative phenotypes can affect fitness. However, some investigators have suggested that simply carrying the ability to be plastic could also affect fitness. Evolutionary models suggest that high costs of plasticity could constrain the evolution of optimal phenotypes. However, costs (and limits) of plasticity are primarily hypothetical. Little empirical evidence exists to show that increased plasticity leads to reduced growth and development, leads to increased developmental instability, or limits the ability of organisms to produce more extreme phenotypes. I used half-sib families of larval wood frogs (Rana sylvatica) reared in outdoor mesocosms to examine how tadpoles altered behavioral, morphological, and life-historical traits in response to larval dragonfly predators (Anax longipes). The predators induced lower activity and the development of relatively large tails and small bodies in wood frogs. As a result, wood frogs experienced reduced growth and development. I then examined whether tadpole sibships with higher plasticity experienced fitness costs (above and beyond the costs of expressing a particular phenotype) and whether they were limited in producing extreme phenotypes. Fitness effects of plasticity were widespread. Depending on the trait examined and the environment experienced, increased plasticity had either positive effects, negative effects, or no effects on tadpole mass, development, and survivorship. I found no relationship between increased plasticity and greater developmental instability. There was also no evidence that sibships with increased plasticity produced less extreme phenotypes; the most extreme trait states were always produced by the most plastic genotypes. This work suggests that costs of plasticity may be pervasive in nature and may substantially impact the evolution of optimal phenotypes in organisms that live in heterogeneous environments.     

Breaking barriers through collaboration: the example of the Cell Migration Consortium

Understanding complex integrated biological processes, such as cell migration, requires interdisciplinary approaches. The Cell Migration Consortium, funded by a Large-Scale Collaborative Project Award from the National Institute of General Medical Science, develops and disseminates new technologies, data, reagents, and shared information to a wide audience. The development and operation of this Consortium may provide useful insights for those who plan similarly large-scale, interdisciplinary approaches.     

CYP3A4-V and prostate cancer in African Americans: causal or confounding association because of population stratification?

CYP3A4-V, an A to G promoter variant associated with prostate cancer in African Americans, exhibits large differences in allele frequency between populations. Given that the African American population is genetically heterogeneous because of its African ancestry and subsequent admixture with European Americans, case-control studies with African Americans are highly susceptible to spurious associations. To test for association with prostate cancer, we genotyped CYP3A4-V in 1376 (2 N) chromosomes from prostate cancer patients and age- and ethnicity-matched controls representing African Americans, Nigerians, and European Americans. To detect population stratification among the African American samples, 10 unlinked genetic markers were genotyped. To correct for the stratification, the uncorrected association statistic was divided by the average of association statistics across the 10 unlinked markers. Sharp differences in CYP3A4-V frequencies were observed between Nigerian and European American controls (0.87 and 0.10, respectively; P<0.0001). African Americans were intermediate (0.66). An association uncorrected for stratification was observed between CYP3A4-V and prostate cancer in African Americans (P=0.007). A nominal association was also observed among European Americans (P=0.02) but not Nigerians. In addition, the unlinked genetic marker test provided strong evidence of population stratification among African Americans. Because of the high level of stratification, the corrected P-value was not significant (P=0.25). Follow-up studies on a larger dataset will be needed to confirm whether the association is indeed spurious; however, these results reveal the potential for confounding of association studies by using African Americans and the need for study designs that take into account substructure caused by differences in ancestral proportions between cases and controls.     

Ontogenetic Variation in the Diurnal Food and Habitat Associations of an Endemic and an Exotic Fish in Floodplain Ponds: Consequences for Niche Partitioning

In floodplain ponds with low piscivore abundance, both endemic Midgley's gudgeons, Hypseleotris sp. 5, and exotic mosquitofish, Gambusia holbrooki, showed significant ontogenetic variation in the use of food and space. Small gudgeons were generally associated with surface and benthic habitats, then restricted their distribution to benthic habitats at a size of approximately 24mm (standard length). The ontogenetic variation in mosquitofish habitat use was less discrete, and could be described as a tendency for larger individuals to be associated with the bottom of the littoral macrophyte beds than with the surface of the macrophyte beds or surface of the limnetic zone. Small gudgeons exhibited high spatial overlap with mosquitofish within the surface habitats of the ponds. All size-class/species comparisons showed significant partitioning of food resources, however, the diets of small gudgeons and mosquitofish were very similar. Therefore, juvenile gudgeons may have to pass through a similar spatial and trophic niche to introduced mosquitofish before recruiting to the adult stage. Possible mechanisms driving the ontogenetic variation in gudgeon and mosquitofish habitat use are discussed. This paper demonstrates that ontogenetic niche shifts at fine spatial scales can affect our interpretation of interactions between native and introduced fishes.     

Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria

Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply in the Planctomycetales. Here we describe a new genus and species of anaerobic ammonium oxidizing planctomycetes, discovered in a wastewater treatment plant (wwtp) treating landfill leachate in Pitsea, UK. The biomass from this wwtp showed high anammox activity (5.0 +/- 0.5 nmol/mg protein/min) and produced hydrazine from hydroxylamine, one of the unique features of anammox bacteria. Eight new planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass. Four of these were affiliated to known anammox 16S rRNA gene sequences, but branched much closer to the root of the planctomycete line of descent. Fluorescence in situ hybridization (FISH) with oligonucleotide probes specific for these new sequences showed that two species (belonging to the same genus) together made up > 99% of the planctomycete population which constituted 20% of the total microbial community. The identification of these organisms as typical anammox bacteria was confirmed with electron microscopy and lipid analysis. The new species, provisionally named Candidatus "Scalindua brodae" and "Scalindua wagneri" considerably extend the biodiversity of the anammox lineage on the 16S rRNA gene level, but otherwise resemble known anammox bacteria. Simultaneously, another new species of the same genus, Candidatus "Scalindua sorokinii", was detected in the water column of the Black Sea, making this genus the most widespread of all anammox bacteria described so far.     

Dinucleotide repeats in the Drosophila and human genomes have complex,length-dependent mutation processes

We use methods of maximum likelihood estimation to fit several microsatellite mutation models to the observed length distribution of dinucletoide repeats in the Drosophila and human genomes. All simple models are rejected by this procedure. Two new models, one with quadratic and another with piecewise linear slippage rates, have the best fits and agree with recent experimental studies by predicting that long microsatellites have a bias toward contractions.