Site-Specific Structural Variations Accompanying Tubular Assembly of the HIV-1 Capsid Protein

The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurements on HIV-1 CA tubes that provide new information regarding changes in molecular structure that accompany CA self-assembly, local dynamics within CA tubes, and possible mechanisms for the generation of lattice curvature. This information is contained in site-specific assignments of signals in two- and three-dimensional solid-state NMR spectra, conformation-dependent ¹⁵N and ¹³C NMR chemical shifts, detection of highly dynamic residues under solution NMR conditions, measurements of local variations in transverse spin relaxation rates of amide ¹H nuclei, and quantitative measurements of site-specific ¹⁵N–¹⁵N dipole–dipole couplings. Our data show that most of the CA sequence is conformationally ordered and relatively rigid in tubular assemblies and that structures of the N-terminal domain (NTD) and the C-terminal domain (CTD) observed in solution are largely retained. However, specific segments, including the N-terminal β-hairpin, the cyclophilin A binding loop, the inter-domain linker, segments involved in intermolecular NTD–CTD interactions, and the C-terminal tail, have substantial static or dynamical disorder in tubular assemblies. Other segments, including the 3₁₀-helical segment in CTD, undergo clear conformational changes. Structural variations associated with curvature of the CA lattice appear to be localized in the inter-domain linker and intermolecular NTD–CTD interface, while structural variations within NTD hexamers, around local 3-fold symmetry axes, and in CTD–CTD dimerization interfaces are less significant.     

Interactions Among Fuel Management,Species Composition,Bark Beetles,and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin

Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their long-term interactions with future climate change are poorly understood. Droughts and the associated moisture deficit contribute to the onset of bark beetle outbreaks although outbreak extent and severity is dependent upon the density of host trees, wildfire, and forest management. Our objective was to estimate the effects of climate change and bark beetle outbreaks on ecosystem carbon dynamics over the next century in a western US forest. Specifically, we hypothesized that (a) bark beetle outbreaks under climate change would reduce net ecosystem carbon balance (NECB) and increase uncertainty and (b) these effects could be ameliorated by fuels management. We also examined the specific tree species dynamics—competition and release—that determined NECB response to bark beetle outbreaks. Our study area was the Lake Tahoe Basin (LTB), CA and NV, USA, an area of diverse forest types encompassing steep elevation and climatic gradients and representative of mixed-conifer forests throughout the western United States. We simulated climate change, bark beetles, wildfire, and fuels management using a landscape-scale stochastic model of disturbance and succession. We simulated the period 2010–2100 using downscaled climate projections. Recurring droughts generated conditions conducive to large-scale outbreaks; the resulting large and sustained outbreaks significantly increased the probability of LTB forests becoming C sources over decadal time scales, with slower-than-anticipated landscape-scale recovery. Tree species composition was substantially altered with a reduction in functional redundancy and productivity. Results indicate heightened uncertainty due to the synergistic influences of climate change and interacting disturbances. Our results further indicate that current fuel management practices will not be effective at reducing landscape-scale outbreak mortality. Our results provide critical insights into the interaction of drivers (bark beetles, wildfire, fuel management) that increase the risk of C loss and shifting community composition if bark beetle outbreaks become more frequent.     

Retrograde Traffic Out of the Yeast Vacuole to the TGN Occurs via the Prevacuolar/Endosomal Compartment

A large number of trafficking steps occur between the last compartment of the Golgi apparatus (TGN) and the vacuole of the yeast Saccharomyces cerevisiae. To date, two intracellular routes from the TGN to the vacuole have been identified. Carboxypeptidase Y (CPY) travels through a prevacuolar/endosomal compartment (PVC), and subsequently on to the vacuole, while alkaline phosphatase (ALP) bypasses this compartment to reach the same organelle. Proteins resident to the TGN achieve their localization despite a continuous flux of traffic by continually being retrieved from the distal PVC by virtue of an aromatic amino acid–containing sorting motif. In this study we report that a hybrid protein based on ALP and containing this retrieval motif reaches the PVC not by following the CPY sorting pathway, but instead by signal-dependent retrograde transport from the vacuole, an organelle previously thought of as a terminal compartment. In addition, we show that a mutation in VAC7, a gene previously identified as being required for vacuolar inheritance, blocks this trafficking step. Finally we show that Vti1p, a v-SNARE required for the delivery of both CPY and ALP to the vacuole, uses retrograde transport out of the vacuole as part of its normal cellular itinerary.     

The art of cobbling a running pump—Will human embryonic stem cells mend broken hearts?

The heart is one of the least regenerative organs in the body, and highly vulnerable to the increasing incidence of cardiovascular diseases in an aging world population. Cell-based approaches aimed at cardiac repair have recently caused great public excitement. But clinical trials of patients’ own skeletal myoblasts or bone marrow cells for transplantation have been disappointing. Human embryonic stem cells (hESCs) form bona fide cardiomyocytes in vitro which are readily generated in mass culture and are being tested in animal models of heart damage. The early results, while encouraging, underscore that much remains to be done. This review focuses on the many challenges that remain before hESCs-mediated repair of the human heart becomes a reality.     

Temporal and spatial trends in heavy metal concentrations in the marine mussel Mytilus edulis from the Western Scheldt estuary (The Netherlands)

Since the first North Sea Conference (1984, Bremen), all countries bordering the North Sea made commitments to reduce discharge of hazardous substances into the North Sea. From Belgium and The Netherlands, large reductions (upto 90) in heavy metal emissions from land-based sources have been reported between 1985 and 2000. Recently, some studies in the Western Scheldt estuary (WS) have shown that total metal concentration in the water, sediments and suspended particles have decreased compared to levels in the 70s. However, data on aquatic organisms is still very limited and it is therefore difficult to confirm whether the reductions in pollution input and generally improving water quality in the WS have a corresponding impact on the levels of heavy metals in aquatic organisms. The current study measured metal concentrations in the soft tissues of mussels, Mytilus edulis (known to be good indicators of environmental metal pollution) during the period 1996–2002. Spatial (salinity and pollution gradients), temporal and seasonal variations were also studied. Results showed a down-stream decreasing trend for the metals studied (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn) during all sampling campaigns. There was also a significant seasonal effect on tissue metal concentrations, with a peak observed around spring in both WS and the nearby less polluted Eastern Scheldt (ES). On temporal trends, a clear drop of metals in mussels was observed in the early 80s coinciding with the start of the efforts to reduce chemical pollution input into the North Sea. Since those early reductions, metal concentrations in mussels generally remained unchanged upto mid 90s. However, in recent times metal concentration in mussels have increased significantly, for example Cd in 2002 was almost 10 times the values in 1983 and similar to levels seen during the peak in the 70s. Other metals also increased in the 90s also reaching levels seen in the 70s. As there is no indication of recent increase in metal input into the estuary, we suggest that increased metal concentrations observed in mussels in recent years especially in the upper estuary are most likely a result of changes in physical and chemical speciation and metal bioavailability. Such changes may be caused by changes in some water quality parameters in the estuary (i.e. increased dissolved oxygen, concentration of organic matter), resulting in conditions that favour releases of sediment-bound metals into the water column. The relationship between metal content and season showed very similar annual profiles in the polluted WS and less polluted ES. Thus, seasonal variations in metal concentrations appear to be largely controlled by biological processes, while total body burdens are dependent on environmental levels and bioavailability.