The Highly Conserved Layer-3 Component of the HIV-1 gp120 Inner Domain Is Critical for CD4-Required Conformational Transitions

The trimeric envelope glycoprotein (Env) of human immunodeficiency virus type 1 (HIV-1) mediates virus entry into host cells. CD4 engagement with the gp120 exterior envelope glycoprotein subunit represents the first step during HIV-1 entry. CD4-induced conformational changes in the gp120 inner domain involve three potentially flexible topological layers (layers 1, 2, and 3). Structural rearrangements between layer 1 and layer 2 have been shown to facilitate the transition of the envelope glycoprotein trimer from the unliganded to the CD4-bound state and to stabilize gp120-CD4 interaction. However, our understanding of CD4-induced conformational changes in the gp120 inner domain remains incomplete. Here, we report that a highly conserved element of the gp120 inner domain, layer 3, plays a pivot-like role in these allosteric changes. In the unliganded state, layer 3 modulates the association of gp120 with the Env trimer, probably by influencing the relationship of the gp120 inner and outer domains. Importantly, layer 3 governs the efficiency of the initial gp120 interaction with CD4, a function that can also be fulfilled by filling the Phe43 cavity. This work defines the functional importance of layer 3 and completes a picture detailing the role of the gp120 inner domain in CD4-induced conformational transitions in the HIV-1 Env trimer.     

Root carbon inputs to the rhizosphere stimulate extracellular enzyme activity and increase nitrogen availability in temperate forest soils

The exudation of carbon (C) by tree roots stimulates microbial activity and the production of extracellular enzymes in the rhizosphere. Here, we investigated whether the strength of rhizosphere processes differed between temperate forest trees that vary in soil organic matter (SOM) chemistry and associate with either ectomycorrhizal (ECM) or arbuscular mycorrhizal (AM) fungi. We measured rates of root exudation, microbial and extracellular enzyme activity, and nitrogen (N) availability in samples of rhizosphere and bulk soil influenced by four temperate forest tree species (i.e., to estimate a rhizosphere effect). Although not significantly different between species, root exudation ranged from 0.36 to 1.10 g C m^?2 day^?1, representing a small but important transfer of C to rhizosphere microbes. The magnitude of the rhizosphere effects could not be easily characterized by mycorrhizal associations or SOM chemistry. Ash had the lowest rhizosphere effects and beech had the highest rhizosphere effects, representing one AM and one ECM species, respectively. Hemlock and sugar maple had equivalent rhizosphere effects on enzyme activity. However, the form of N produced in the rhizosphere varied with mycorrhizal association. Enhanced enzyme activity primarily increased amino acid availability in ECM rhizospheres and increased inorganic N availability in AM rhizospheres. These results show that the exudation of C by roots can enhance extracellular enzyme activity and soil-N cycling. This work suggests that global changes that alter belowground C allocation have the potential to impact the form and amount of N to support primary production in ECM and AM stands.     

HIV-1 Vpr-mediated G2 arrest involves the DDB1-CUL4AVPRBP E3 ubiquitin ligase

Human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) has been shown to cause G2 cell cycle arrest in human cells by inducing ATR-mediated inactivation of p34cdc2, but factors directly engaged in this process remain unknown. We used tandem affinity purification to isolate native Vpr complexes. We found that damaged DNA binding protein 1 (DDB1), viral protein R binding protein (VPRBP), and cullin 4A (CUL4A)--components of a CUL4A E3 ubiquitin ligase complex, DDB1-CUL4A(VPRBP)--were able to associate with Vpr. Depletion of VPRBP by small interfering RNA impaired Vpr-mediated induction of G2 arrest. Importantly, VPRBP knockdown alone did not affect normal cell cycle progression or activation of ATR checkpoints, suggesting that the involvement of VPRBP in G2 arrest was specific to Vpr. Moreover, leucine/isoleucine-rich domain Vpr mutants impaired in their ability to interact with VPRBP and DDB1 also produced strongly attenuated G2 arrest. In contrast, G2 arrest-defective C-terminal Vpr mutants were found to maintain their ability to associate with these proteins, suggesting that the interaction of Vpr with the DDB1-VPRBP complex is necessary but not sufficient to block cell cycle progression. Overall, these results point toward a model in which Vpr could act as a connector between the DDB1-CUL4A(VPRBP) E3 ubiquitin ligase complex and an unknown cellular factor whose proteolysis or modulation of activity through ubiquitination would activate ATR-mediated checkpoint signaling and induce G2 arrest.     

Enhanced Tethered-Particle Motion Analysis Reveals Viscous Effects

Tethered-particle motion experiments do not require expensive or technically complex hardware, and increasing numbers of researchers are adopting this methodology to investigate the topological effects of agents that act on the tethering polymer or the characteristics of the polymer itself. These investigations depend on accurate measurement and interpretation of changes in the effective length of the tethering polymer (often DNA). However, the bead size, tether length, and buffer affect the confined diffusion of the bead in this experimental system. To evaluate the effects of these factors, improved measurements to calibrate the two-dimensional range of motion (excursion) versus DNA length were carried out. Microspheres of 160 or 240 nm in radius were tethered by DNA molecules ranging from 225 to 3477 basepairs in length in aqueous buffers containing 100 mM potassium glutamate and 8 mM MgCl₂ or 10 mM Tris-HCl and 200 mM KCl, with or without 0.5% Tween added to the buffer, and the motion was recorded. Different buffers altered the excursion of beads on identical DNA tethers. Buffer with only 10 mM NaCl and >5 mM magnesium greatly reduced excursion. Glycerol added to increase viscosity slowed confined diffusion of the tethered beads but did not change excursion. The confined-diffusion coefficients for all tethered beads were smaller than those expected for freely diffusing beads and decreased for shorter tethers. Tethered-particle motion is a sensitive framework for diffusion experiments in which small beads on long leashes most closely resemble freely diffusing, untethered beads.     

Aneuploidy, centrosome alteration and securin overexpression as features of pituitary somatotroph and lactotroph adenomas

OBJECTIVE: To verify the presence of numerical chromosomal aberrations (NCAs) in different types of pituitary adenomas (PAs) and to investigate 2 of the mechanisms that are possibly related to aneuploidies in PAs: securin overexpression and centrosome alterations. STUDY DESIGN: Twenty-one PAs of different types were analyzed with interphase fluorescence in situ hybridization (FISH) on paraffin sections with centromeric probes for chromosomes 2, 3, 8, 11 and 12. In all cases, the immunohistochemical expression of securin was evaluated and the number of cells with abnormal nuclear shape recorded. The ultrastructural study of centrosomes was performed in a subset of 12 tumors. RESULTS: At interphase FISH analysis, growth hormone (GH)-cell and prolactin (PRL)-cell PAs showed multiple chromosome gains and a low frequency of chromosome losses, suggesting a hyperdiploid chromosome assessment. In contrast, in the other types of PAs a lower frequency of NCAs was observed. In addition, when compared to other types of PAs, GH-cell and PRL-cell adenomas showed overexpression of securin and a higher number of both cells with abnormal nuclear shape and cells with centrosomes. CONCLUSION: Somatotroph and lactotroph adenomas are characterized by aneuploidy, abnormal nuclear shape and centrosome amplification, which are possibly related to securin overexpression.     

Increased mercury in forest soils under elevated carbon dioxide

Fossil fuel combustion is the primary anthropogenic source of both CO₂ and Hg to the atmosphere. On a global scale, most Hg that enters ecosystems is derived from atmospheric Hg that deposits onto the land surface. Increasing concentrations of atmospheric CO₂ may affect Hg deposition to terrestrial systems and storage in soils through CO₂-mediated changes in plant and soil properties. We show, using free-air CO₂ enrichment (FACE) experiments, that soil Hg concentrations are almost 30% greater under elevated atmospheric CO₂ in two temperate forests. There were no direct CO₂ effects, however, on litterfall, throughfall or stemflow Hg inputs. Soil Hg was positively correlated with percent soil organic matter (SOM), suggesting that CO₂-mediated changes in SOM have influenced soil Hg concentrations. Through its impacts on SOM, elevated atmospheric CO₂ may increase the Hg storage capacity of soils and modulate the movement of Hg through the biosphere. Such effects of rising CO₂, ones that transcend the typically studied effects on C and nutrient cycling, are an important next phase for research on global environmental change.     

Photochemistry of dyes and fluorochromes used in biology and medicine: some physicochemical background and current applications

An overview of the basic principles of photochemistry is presented to facilitate discussion of fluorescence, quenching and quantum yields. These topics in turn provide the foundation for an account of fluorescence spectroscopy and its application to microscopy. A brief overview of light microscopy and the application of fluorescence microscopy is given. The influences of molecular features, such as aromatic character and substitution patterns, on color and fluorescence are described. The concept of color fading is considered with particular reference to its effect on microscopic preparations. A survey of representative fluorescent probes is provided, and their sensitivity, application, and limitations are described. The phototoxicity of fluorescent molecules is discussed using biomembranes and DNA as examples of targets of toxicity. Photodynamic therapy, a relatively new clinical application of phototoxicity, is described. Both anticancer and antimicrobial applications are noted, and an assessment is given of the current ideas on the ideal physicochemical properties of the sensitizing agents for such applications.     

The nitrogen budget of a pine forest under free air CO2 enrichment

Elevated concentrations of atmospheric CO₂ increase plant biomass, net primary production (NPP) and plant demand for nitrogen (N). The demand for N set by rapid plant growth under elevated CO₂ could be met by increasing soil N availability or by greater efficiency of N uptake. Alternatively, plants could increase their nitrogen-use efficiency (NUE), thereby maintaining high rates of growth and NPP in the face of nutrient limitation. We quantified dry matter and N budgets for a young pine forest exposed to 4 years of elevated CO₂ using free-air CO₂ enrichment technology. We addressed three questions: Does elevated CO₂ increase forest NPP and the demand for N by vegetation? Is demand for N met by greater uptake from soils, a shift in the distribution of N between plants, microbes, and soils, or increases in NUE under elevated CO₂? Will soil N availability constrain the NPP response of this forest as CO₂ fumigation continues? A step-function increase in atmospheric CO₂ significantly increased NPP during the first 4 years of this study. Significant increases in NUE under elevated CO₂ modulated the average annual requirement for N by vegetation in the first and third growing seasons under elevated CO₂; the average stimulation of NPP in these years was 21% whereas the average annual stimulation of the N requirement was only 6%. In the second and fourth growing seasons, increases in NPP increased the annual requirement for N by 27-33%. Increases in the annual requirement for N were largely met by increases in N uptake from soils. Retranslocation of nutrients prior to senescence played only a minor role in supplying the additional N required by trees growing under elevated CO₂. NPP was highly correlated with between-plot variation in the annual rate of net N mineralization and CO₂ treatment. This demonstrates that NPP is co-limited by C availability, as CO₂ from the atmosphere, and N availability from soils. There is no evidence that soil N mineralization rates have increased under elevated CO₂. The correlation between NPP and N mineralization rates and the increase in the annual requirement for N in certain years imply that soil N availability may control the long-term productivity response of this ecosystem to elevated CO₂. Although we have no evidence suggesting that NPP is declining in response to >4 years of CO₂ fumigation, if the annual requirement of N continues to be stimulated by elevated CO₂, we predict that the productivity response of this forest ecosystem will decline over time.