Phylogeny,niche conservatism and the latitudinal diversity gradient in mammals

Biologists have long searched for mechanisms responsible for the increase in species richness with decreasing latitude. The strong correlation between species richness and climate is frequently interpreted as reflecting a causal link via processes linked to energy or evolutionary rates. Here, we investigate how the aggregation of clades, as dictated by phylogeny, can give rise to significant climate–richness gradients without gradients in diversification or environmental carrying capacity. The relationship between climate and species richness varies considerably between clades, regions and time periods in a global-scale phylogenetically informed analysis of all terrestrial mammal species. Many young clades show negative richness–temperature slopes (more species at cooler temperatures), with the ages of these clades coinciding with the expansion of temperate climate zones in the late Eocene. In carnivores, we find steeply positive richness–temperature slopes in clades with restricted distributions and tropical origins (e.g. cat clade), whereas widespread, temperate clades exhibit shallow, negative slopes (e.g. dog–bear clade). We show that the slope of the global climate–richness gradient in mammals is driven by aggregating Chiroptera (bats) with their Eutherian sister group. Our findings indicate that the evolutionary history should be accounted for as part of any search for causal links between environment and species richness.     

Directional Spread of Surface-Associated Retroviruses Regulated by Differential Virus-Cell Interactions

The spread of viral infections involves the directional progression of virus particles from infected cells to uninfected target cells. Prior to entry, the binding of virus particles to specific cell surface receptors can trigger virus surfing, an actin-dependent lateral transport of viruses toward the cell body (M. J. Lehmann et al., J. Cell Biol. 170:317-325, 2005; M. Schelhaas, et al., PLoS Pathog. 4:e1000148, 2008; J. L. Smith, D. S. Lidke, and M. A. Ozbun, Virology 381:16-21, 2008). Here, we have used live-cell imaging to demonstrate that for cells chronically infected with the gammaretrovirus murine leukemia virus in which receptor has been downregulated, a significant portion of completely assembled virus particles are not immediately released into the supernatant but retain long-term association with the cell surface. Retention can be attributed, at least in part, to nonspecific particle attachment to cell surface glycosylaminoglycans. In contrast to virus surfing, viruses retained at the surface of infected cells undergo a lateral motility that is random and actin independent. This diffusive motility can be abruptly halted and converted into inward surfing after treatment with Polybrene, a soluble cation that increases virus-cell adsorption. In the absence of Polybrene, particle diffusion allows for an outward flow of viruses to the infected cell periphery. Peripheral particles are readily captured by and transmitted to neighboring uninfected target cells in a directional fashion. These data demonstrate a surface-based mechanism for the directional spread of viruses regulated by differential virus-cell interactions.Virus transmission from cell to cell critically contributes to the rapid spreading of viral infections (27). In the case of enveloped viruses, virus transmission generally involves an extracellular phase that is initiated by the budding and pinching off of viral particles from the producer cell prior to transmission to target cells and ends with cell entry by membrane fusion. The extracellular transmission phase can follow a cell-free mechanism, or, alternatively, the virus may be passed on at contacts established between infected and noninfected target cells. Strong evidence, particularly for retroviruses such as human immunodeficiency virus (HIV) and human T-cell leukemia virus (HTLV), points to a more efficient mode of transmission under conditions when cells directly contact each other (13, 16). Consistently, morphological studies indicate a strong accumulation of viral antigens and viral particles at the site of cell-cell contact (2, 13, 16, 19), and the direct transfer of viral particles has been directly documented in living cells (12, 30). Broad cell-cell contacts, designated virological synapses because of a resemblance to immunological synapses, as well as thin, filopodial or nanotube contacts have been described (8, 12, 14, 26, 30, 33). It has been suggested that an efficient coordination of assembly and entry at sites of cell-cell contact contributes to the overall efficiency of cell-to-cell transmission (15, 16, 23). Indeed, four-dimensional imaging of cell-to-cell transmission of murine leukemia virus (MLV) in living cells revealed that virus assembly can be polarized toward sites of cell-cell contact (14). In addition, uninfected cells may capture cell-free virus and pass it on to susceptible cells without themselves becoming infected. This pathway, first observed for HIV and dendritic cells, can facilitate efficient cell-to-cell transfer of surface virus to susceptible T cells (3, 9, 19, 36).Here, we provide details of a surface-based transfer mechanism that contributes to the directional cell-to-cell spread of MLV. Using live-cell imaging, we show that newly assembled virus particles can be retained at the plasma membrane of chronically infected fibroblasts in which receptor has been downregulated from the cell surface. Viruses retained at the cell surface exhibit a lateral diffusive motility, a behavior that we call virus “surfacing.” Virus surfacing in the cell periphery provided for contact-mediated transmission to receptor-expressing cells. Our data suggest a general mechanism wherein differential virus-cell interactions occurring at the cell surface contribute to the vectorial spread of viral infection.     

Partial medial meniscectomy and rotational differences at the knee during walking

Loss of meniscal function due to injury or partial meniscectomy is common and represents a significant risk factor for premature osteoarthritis. The menisci can influence the transverse plane movements (anterior–posterior (AP) translation and internal–external (IE) rotation) of the knee during walking. While walking is the most frequent activity of daily living, the kinematic differences at the knee during walking associated with the meniscal injury are not well understood. This study examined the influence of partial medial meniscectomy (PMM) on the kinematics and kinetics of the knee during the stance phase of gait by testing the differences in anterior–posterior translation, internal–external rotation, knee flexion range of movement, peak flexion/extension moments, and adduction moments between the PMM and healthy contralateral limbs. Ten patients (45±9 years old, height 1.75±0.06 m, weight 76.7±13.5 kg) who had undergone partial medial meniscectomy (33±100 months post-op) in one limb with a healthy contralateral limb were tested during normal walking. The contralateral limb was compared to a matched control group and no differences were found. The primary kinematic difference was a significantly greater external rotation (3.2°) of the tibia that existed through stance phase, with 8 of 10 subjects demonstrating the same pattern. The PMM subjects also exhibited significantly lower peak flexion and extension moments in their PMM limbs. The altered rotational position found likely results in changes of tibio-femoral contact during walking and could cause the type of degenerative changes found in the articular cartilage following meniscal injury.     

Extended Structures in RNA Folding Intermediates Are Due to Nonnative Interactions Rather than Electrostatic Repulsion

RNA folding occurs via a series of transitions between metastable intermediate states for Mg²⁺ concentrations below those needed to fold the native structure. In general, these folding intermediates are considerably less compact than their respective native states. Our previous work demonstrates that the major equilibrium intermediate of the 154-residue specificity domain (S-domain) of the Bacillus subtilis RNase P RNA is more extended than its native structure. We now investigate two models with falsifiable predictions regarding the origins of the extended intermediate structures in the S-domains of the B. subtilis and the Escherichia coli RNase P RNA that belong to different classes of P RNA and have distinct native structures. The first model explores the contribution of electrostatic repulsion, while the second model probes specific interactions in the core of the folding intermediate. Using small-angle X-ray scattering and Langevin dynamics simulations, we show that electrostatics plays only a minor role, whereas specific interactions largely account for the extended nature of the intermediate. Structural contacts in the core, including a nonnative base pair, help to stabilize the intermediate conformation. We conclude that RNA folding intermediates adopt extended conformations due to short-range, nonnative interactions rather than generic electrostatic repulsion of helical domains. These principles apply to other ribozymes and riboswitches that undergo functionally relevant conformational changes.     

Immunological characteristics correlating with clinical response to immunotherapy in patients with advanced metastatic melanoma

Current treatment options for advanced metastatic melanoma are limited to experimental regimen that provide poor survival outcomes. Immunotherapy is a promising alternative and we recently reported a clinical trial in which 6 out of 19 patients enrolled had objective clinical responses to a fully autologous melanoma/dendritic cell vaccine. The mechanism of the vaccine is not well understood, but we hypothesized that general immunocompetence may be a determinant of clinical response. We therefore examined the immune status of an expanded series of 21 patients who displayed varying clinical responses to the melanoma/dendritic cell vaccine. Immunocompetence was assessed using in vitro assays of lymphocyte function: survival, proliferation and cytokine responses to mitogen stimulation as well as T-cell receptor zeta expression and lymphocyte subset analysis. Although lymphocytes from patients mostly performed comparably to age-matched and sex-matched controls, in some assays we identified significant differences between complete clinical responders and other patients, both before and following vaccination. Surprisingly, before vaccination, only lymphocytes from clinical responder patients showed impaired in vitro survival. Following vaccination, T lymphocyte survival improved and cells recovered their ability to produce the Th1-associated cytokines TNF and IFN-gamma in response to anti-CD3 stimulation in vitro. No increase in Th1 cytokine production was observed in lymphocytes from patients who experienced partial clinical responses or progressive disease. We conclude that, before vaccination, patients who go on to have complete responses have immune characteristics suggestive of high cell turnover and low Th1-associated cytokine production, and that these can be reversed with vaccination. These results have potential implications for future immunotherapeutic strategies.     

High-affinity ligand probes of CD22 overcome the threshold set by cis ligands to allow for binding, endocytosis, and killing of B cells

CD22 (Siglec-2) is a key regulator of B cell signaling whose function is modulated by interaction with extracellular glycan ligands mediated through its N-terminal Ig domain. Its preferred ligand is the sequence Sia alpha2-6Gal that is abundantly expressed on N-linked glycans of B cell glycoproteins, and by binding to CD22 in cis causes CD22 to appear "masked" from binding to synthetic sialoside probes. Yet, despite the presence of cis ligands, CD22 redistributes to sites of cell contact by binding to trans ligands on neighboring cells. In this study, we demonstrate the dynamic equilibrium that exists between CD22 and its cis and trans ligands, using a high-affinity multivalent sialoside probe that competes with cis ligands and binds to CD22 on native human and murine B cells. Consistent with the constitutive endocytosis reported for CD22, the probes are internalized once bound, demonstrating that CD22 is an endocytic receptor that can carry ligand-decorated "cargo" to intracellular compartments. Conjugation of the sialoside probes to the toxin saporin resulted in toxin uptake and toxin-mediated killing of B lymphoma cell lines, suggesting an alternative approach for targeting CD22 for treatment of B cell lymphomas.     

Vitamin B1 de novo synthesis in the human malaria parasite Plasmodium falciparum depends on external provision of 4-amino-5-hydroxymethyl-2-methylpyrimidine

Vitamin B1 (thiamine) is an essential cofactor for several key enzymes of carbohydrate metabolism. Mammals have to salvage this crucial nutrient from their diet to complement their deficiency of de novo synthesis. In contrast, bacteria, fungi, plants and, as reported here, Plasmodium falciparum, possess a vitamin B1 biosynthesis pathway. The plasmodial pathway identified consists of the three vitamin B1 biosynthetic enzymes 5-(2-hydroxy-ethyl)-4-methylthiazole (THZ) kinase (ThiM), 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP)/HMP-P kinase (ThiD) and thiamine phosphate synthase (ThiE). Recombinant PfThiM and PfThiD proteins were biochemically characterised, revealing K(m)app values of 68 microM for THZ and 12 microM for HMP. Furthermore, the ability of PfThiE for generating vitamin B1 was analysed by a complementation assay with thiE-negative E. coli mutants. All three enzymes are expressed throughout the developmental blood stages, as shown by Northern blotting, which indicates the presence of the vitamin B1 biosynthesis enzymes. However, cultivation of the parasite in minimal medium showed a dependency on the provision of HMP or thiamine. These results demonstrate that the human malaria parasite P. falciparum possesses active vitamin B1 biosynthesis, which depends on external provision of thiamine precursors.