Binding of HIV-1 Vpr Protein to the Human Homolog of the Yeast DNA Repair Protein RAD23 (hHR23A) Requires Its Xeroderma Pigmentosum Complementation Group C Binding (XPCB) Domain as Well as the Ubiquitin-associated 2 (UBA2) Domain

The human homolog of the yeast DNA repair protein RAD23, hHR23A, has been found previously to interact with the human immunodeficiency virus, type 1 accessory protein Vpr. hHR23A is a modular protein containing an N-terminal ubiquitin-like (UBL) domain and two ubiquitin-associated domains (UBA1 and UBA2) separated by a xeroderma pigmentosum complementation group C binding (XPCB) domain. All domains are connected by flexible linkers. hHR23A binds ubiquitinated proteins and acts as a shuttling factor to the proteasome. Here, we show that hHR23A utilizes both the UBA2 and XPCB domains to form a stable complex with Vpr, linking Vpr directly to cellular DNA repair pathways and their probable exploitation by the virus. Detailed structural mapping of the Vpr contacts on hHR23A, by NMR, revealed substantial contact surfaces on the UBA2 and XPCB domains. In addition, Vpr binding disrupts an intramolecular UBL-UBA2 interaction. We also show that Lys-48-linked di-ubiquitin, when binding to UBA1, does not release the bound Vpr from the hHR23A-Vpr complex. Instead, a ternary hHR23A·Vpr·di-Ub^K48 complex is formed, indicating that Vpr does not necessarily abolish hHR23A-mediated shuttling to the proteasome.     

A method for quantitative analysis of spatially variable physiological processes across leaf surfaces

Many physiological processes are spatially variable across leaf surfaces. While maps of photosynthesis, stomatal conductance, gene expression, water transport, and the production of reactive oxygen species (ROS) for individual leaves are readily obtained, analytical methods for quantifying spatial heterogeneity and combining information gathered from the same leaf but with different instruments are not widely used. We present a novel application of tools from the field of geographical imaging to the multivariate analysis of physiological images. Procedures for registration and resampling, cluster analysis, and classification provide a general framework for the analysis of spatially resolved physiological data. Two experiments were conducted to illustrate the utility of this approach. Quantitative analysis of images of chlorophyll fluorescence and the production of ROS following simultaneous exposure of soybean leaves to atmospheric O₃ and soybean mosaic virus revealed that areas of the leaf where the operating quantum efficiency of PSII was depressed also experienced an accumulation of ROS. This correlation suggests a causal relationship between oxidative stress and inhibition of photosynthesis. Overlaying maps of leaf surface temperature and chlorophyll fluorescence following a photoinhibition treatment indicated that areas with low operating quantum efficiency of PSII also experienced reduced stomatal conductance (high temperature). While each of these experiments explored the covariance of two processes by overlaying independent images gathered with different instruments, the same procedures can be used to analyze the covariance of information from multiple images. The application of tools from geographic image analysis to physiological processes occurring over small spatial scales will help reveal the mechanisms generating spatial variation across leaves.     

Contribution of above‐ and belowground bioenergy crop residues to soil carbon

GHG mitigation by bioenergy crops depends on crop type, management practices, and the input of residue carbon (C) to the soil. Perennial grasses may increase soil C compared to annual crops because of more extensive root systems, but it is less clear how much soil C is derived from above‐ vs. belowground inputs. The objective of this study was to synthesize the existing knowledge regarding soil C inputs from above‐ and belowground crop residues in regions cultivated with sugarcane, corn, and miscanthus, and to predict the impact of residue removal and tillage on soil C stocks. The literature review showed that aboveground inputs to soil C (to 1‐m depth) ranged from 70% to 81% for sugarcane and corn vs. 40% for miscanthus. Modeled aboveground C inputs (to 30 cm depth) ranged from 54% to 82% for sugarcane, but were 67% for miscanthus. Because 50% of observed miscanthus belowground biomass is below 30 cm depth, it may be necessary to increase the depth of modeled soil C dynamics to reconcile modeled belowground C inputs with measured. Modeled removal of aboveground corn residue (25–100%) resulted in C stock reduction in areas of corn–corn–soybean rotation under conventional tillage, while no‐till management lessoned this impact. In sugarcane, soil C stocks were reduced when total aboveground residue was removed at one site, while partial removal of sugarcane residue did not reduce soil C stocks in either area. This study suggests that aboveground crop residues were the main C‐residue source to the soil in the current bioethanol sector (corn and sugarcane) and the indiscriminate removal of crop residues to produce cellulosic biofuels can reduce soil C stocks and reduce the environmental benefits of bioenergy. Moreover, a switch to feedstocks such as miscanthus with more allocation to belowground C could increase soil C stocks at a much faster rate.     

Edaphic limitations to growth and photosynthesis in Sierran and Great Basin vegetation

Summary Soils derived from hydrothermally altered andesite support unique communities of Sierran conifers (Pinus ponderosa Laws. and P. jeffreyi Grev. and Balf.) amongst sagebrush (Artemisia tridentata Nutt.) vegetation in the western Great Basin. Plants grown in soil derived from hydrothermally altered bedrock had lower growth rates, total biomass, and net photosynthetic rates than plants grown in soil derived from unaltered andesite of the same formation. Total dry mass was 10 to 28% lower for conifers grown in altered soil whereas dry mass of Artemisia tridentata and Bromus tectorum L. was reduced by over 90%. Results from a nutrient amendment experiment indicated that low phosphorus was the dominant limitation in altered soil, and phosphorus-deficiency affected growth primarily by limiting leaf area development rather than direct inhibition of photosynthesis. The proportionately greater reduction of biomass for Artemisia and Bromus grown in altered soil supports our hypothesis that Great Basin vegetation is excluded from altered soil by intolerance to nutrient deficiency. The Sierran conifers growing on this rock type are therefore free of competition for water with Great Basin vegetation and are able to persist in an exceptionally dry climate.     

Altered dynamics of forest recovery under a changing climate

Forest regeneration following disturbance is a key ecological process, influencing forest structure and function, species assemblages, and ecosystem–climate interactions. Climate change may alter forest recovery dynamics or even prevent recovery, triggering feedbacks to the climate system, altering regional biodiversity, and affecting the ecosystem services provided by forests. Multiple lines of evidence – including global‐scale patterns in forest recovery dynamics; forest responses to experimental manipulation of CO₂, temperature, and precipitation; forest responses to the climate change that has already occurred; ecological theory; and ecosystem and earth system models – all indicate that the dynamics of forest recovery are sensitive to climate. However, synthetic understanding of how atmospheric CO₂ and climate shape trajectories of forest recovery is lacking. Here, we review these separate lines of evidence, which together demonstrate that the dynamics of forest recovery are being impacted by increasing atmospheric CO₂ and changing climate. Rates of forest recovery generally increase with CO₂, temperature, and water availability. Drought reduces growth and live biomass in forests of all ages, having a particularly strong effect on seedling recruitment and survival. Responses of individual trees and whole‐forest ecosystems to CO₂ and climate manipulations often vary by age, implying that forests of different ages will respond differently to climate change. Furthermore, species within a community typically exhibit differential responses to CO₂ and climate, and altered community dynamics can have important consequences for ecosystem function. Age‐ and species‐dependent responses provide a mechanism by which climate change may push some forests past critical thresholds such that they fail to recover to their previous state following disturbance. Altered dynamics of forest recovery will result in positive and negative feedbacks to climate change. Future research on this topic and corresponding improvements to earth system models will be a key to understanding the future of forests and their feedbacks to the climate system.     

Studies on the transposition rates of mobile genetic elements in a natural population of Drosophila melanogaster

In an isolated population of Drosophila melanogaster on Ishigaki Island the chromosomal distribution of several retrotransposons, including copia, 412, 297, 17.6, I, and jockey elements, was examined by in situ hybridization. In this population the cosmopolitan inversion, In(2L)t, is known to exist in high frequency. One major haplotype concerning the occupied sites of the transposable elements was identified in the In(2L)t-carrying chromosomes. This haplotype is suggested to be the ancestral one. The age of the inversion in this local population was estimated to be 1,400 generations. The transposition rates of these elements were estimated based on the age of the inversion and the number of the elements lost and gained. The excision rates were in the range from 9.13 x 10(-5) to 2.25 x 10(-4) per site per generation. They were similar each other in the copia-like elements as well as in the LINE-like elements. The rate was higher in the copia-like elements than in the LINE-like elements. Insertions occurred in the range from 6.79 x 10(-4) to 9.05 x 10(-4) per element per generation. It is herein shown that both insertions and excisions occurred at a significantly higher rate in this population than in the laboratory.      

Contribution of photosynthetic rate to growth and reproduction in Amaranthus hybridus

While it is known that genetic variation for photosynthetic and growth traits exists in natural populations, the functional significance of this variation remains unclear, particularly for photosynthetic traits. To test the hypothesis that photosynthetic rate has direct effects on reproduction as well as contributing indirectly to reproduction through effects on growth, we compared wild-type Amaranthus hybridus families to those with a single gene mutation that confers a lower photosynthetic rate. Wild-type and photosynthetic-mutant families were grown in competitive and non-competitive environments and we compared size, biomass allocation, architecture, and reproduction at three developmental stages. To assess the contributions of individual growth traits to reproduction, we calculated covariances between standardized traits and relative fitness (selection differentials), and compared selection between the two biotypes. Finally, we used path analysis to calculate the indirect effects of photosynthetic rate on fitness through growth. The size, allocation, and architecture of photosynthetic mutants did not differ from those of the wild type in either the competitive or non-competitive environment, with the exception that they were taller by the last developmental stage. However, the reproductive biomass of the photosynthetic mutants was significantly reduced compared to the wild type. In the competitive environment, the wild type achieved greater fitness because, while similar in size to the mutants, at any given size it produced more reproductive biomass. This suggests that photosynthetic rate affected the linkage between plant size and reproduction and is evidence of an indirect contribution to fitness. In the non-competitive environment, there were fewer differences in selection differentials between the two plant genotypes, suggesting fewer indirect effects. Path analysis showed that variation in photosynthetic biotype had indirect effects on reproductive biomass, via growth traits, and that there were no direct effects. Photosynthetic rate appears to have fitness consequences primarily through multiple contributions to growth throughout development. Received: 27 March 1998 / Accepted: 28 August 1998     

Insect herbivory in an intact forest understory under experimental CO2 enrichment

Human-induced increases in atmospheric CO₂ concentration have the potential to alter the chemical composition of plant tissue, and thereby affect the amount of tissue consumed by herbivorous arthropods. At the Duke Forest free-air concentration enrichment (FACE) facility in North Carolina (FACTS–1 research facility), we measured the amount of leaf tissue damaged by insects and other herbivorous arthropods during two growing seasons in a deciduous forest understory continuously exposed to ambient (360 l l^–1) and elevated (~560 µl l^–1) CO₂ conditions. In 1999, there was a significant interaction between CO₂ and species such that winged elm (Ulmus alata) showed lower herbivory in elevated CO₂ plots, whereas red maple (Acer rubra) and sweetgum (Liquidambar styraciflua) did not. In 2000, our results did not achieve statistical significance but the magnitude of the result was consistent with the 1999 results. In 1999 and 2000, we found a decline (10–46%) in community-level herbivory in elevated CO₂ plots driven primarily by reductions in herbivory on elm. The major contribution to total leaf damage was from missing tissue (66% of the damaged tissue), with galls, skeletonized, and discolored tissue making smaller contributions. It is unclear whether the decline in leaf damage is a result of altered insect populations, altered feeding, or a combination. We were not able to quantify insect populations, and our measurements did not resolve an effect of elevated CO₂ on leaf chemical composition (total nitrogen, carbon, C/N, sugars, phenolics, starch). Despite predictions from a large number of single-species studies that herbivory may increase under elevated CO₂, we have found a decrease in herbivory in a naturally established forest understory exposed to a full suite of insect herbivores and their predators.