Mutations Altering a Structurally Conserved Loop-Helix-Loop Region of a Viral Packaging Motor Change DNA Translocation Velocity and Processivity

Many double-stranded DNA viruses employ ATP-driven motors to translocate their genomes into small, preformed viral capsids against large forces resisting confinement. Here, we show via direct single-molecule measurements that a mutation T194M downstream of the Walker B motif in the phage λ gpA packaging motor causes an 8-fold reduction in translocation velocity without substantially changing processivity or force dependence, whereas the mutation G212S in the putative C (coupling) motif causes a 3-fold reduction in velocity and a 6-fold reduction in processivity. Meanwhile a T194M pseudorevertant (T194V) showed a near restoration of the wild-type dynamics. Structural comparisons and modeling show that these mutations are in a loop-helix-loop region that positions the key residues of the catalytic motifs, Walker B and C, in the ATPase center and is structurally homologous with analogous regions in chromosome transporters and SF2 RNA helicases. Together with recently published studies of SpoIIIE chromosome transporter and Ded1 RNA helicase mutants, these findings suggest the presence of a structurally conserved region that may be a part of the mechanism that determines motor velocity and processivity in several different types of nucleic acid translocases.     

Recombinant adeno-associated virus type 2-mediated gene delivery into the <Emphasis Type="Italic">Rpe65</Emphasis><Superscript>-/-</Superscript> knockout mouse eye results in limited rescue

Background  

Leber's congenital amaurosis (LCA) is a severe form of retinal dystrophy. Mutations in the RPE65 gene, which is abundantly expressed in retinal pigment epithelial (RPE) cells, account for approximately 10–15% of LCA cases. In this study we used the high turnover, and rapid breeding and maturation time of the Rpe65 ^-/- knockout mice to assess the efficacy of using rAAV-mediated gene therapy to replace the disrupted RPE65 gene. The potential for rAAV-mediated gene treatment of LCA was then analyzed by determining the pattern of RPE65 expression, the physiological and histological effects that it produced, and any improvement in visual function.     

Population genetic variation in gene expression is associated with phenotypic variation in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Background

The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits.

Results

We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes, 20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2.

Conclusions

Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

     

Effects of flooding and drought on stomatal activity, transpiration, photosynthesis, water potential and water channel activity in strawberry stolons and leaves

Transpiration, xylem water potential and water channel activity were studied in developing stolons and leaves of strawberry (Fragaria × ananassa Duch.) subjected to drought or flooding, together with morphological studies of their stomata and other surface structures. Stolons had 0.12 stomata mm^–2 and a transpiration rate of 0.6 mmol H₂O m^–2 s^–1, while the leaves had 300 stomata mm^–2 and a transpiration rate of 5.6 mmol H₂O m^–2 s^–1. Midday water potentials of stolons were always less negative than in leaves enabling nutrient ion and water transport via or to the strawberry stolons. Drought stress, but not flooding, decreased stolon and leaf water potential from –0.7 to –1 MPa and from –1 to –2 MPa, respectively, with a concomitant reduction in stomatal conductance from 75 to 30 mmol H₂O m^–2 s^–1. However, leaf water potentials remained unchanged after flooding. Similarly, membrane vesicles derived from stolons of flooded strawberry plants showed no change in water channel activity. In these stolons, turgor may be preserved by maintaining root pressure, an electrochemical and ion gradient and xylem differentiation, assuming water channels remain open. By contrast, water channel activity was reduced in stolons of drought stressed strawberry plants. In every case, the effect of flooding on water relations of strawberry stolons and leaves was less pronounced than that of drought which cannot be explained by increased ABA. Stomatal closure under drought could be attributed to increased delivery of ABA from roots to the leaves. However, stomata closed more rapidly in leaves of flooded strawberry despite ABA delivery from the roots in the xylem to the leaves being strongly depressed. This stomatal closure under flooding may be due to release of stress ethylene. In the relative absence of stomata from the stolons, cellular (apoplastic) water transport in strawberry stolons was primarily driven by water channel activity with a gradient from the tip of the stolon to the base, concomitant with xylem differentiation and decreased water transport potential from the stolon tip to its base. Reduced water potential in the stolons under drought are discussed with respect to reduced putative water channel activity.     

Comparing Effects of Nutrients on Algal Biomass in Streams in Two Regions with Different Disturbance Regimes and with Applications for Developing Nutrient Criteria

Responses of stream algal biomass to nutrient enrichment were studied in two regions where differences in hydrologic variability cause great differences in herbivory. Around northwestern Kentucky (KY) hydrologic variability constrains invertebrate biomass and their effects on algae, but hydrologic stability in Michigan (MI) streams permits accrual of high herbivore densities and herbivory of benthic algae. Multiple indicators of algal biomass and nutrient availability were measured in 104 streams with repeated sampling at each site over a 2−month period. Many measures of algal biomass and nutrient availability were positively correlated in both regions, however the amount of variation explained varied with measures of biomass and nutrient concentration and with region. Indicators of diatom biomass were higher in KY than MI, but were not related to nutrient concentrations in either region. Chl a and % area of substratum covered by Cladophora were positively correlated to nutrient concentrations in both regions. Cladophora responded significantly more to nutrients in MI than KY. Total phosphorus (TP) and total nitrogen (TN) explained similar amounts of variation in algal biomass, and not significantly more variation in biomass than dissolved nutrient concentrations. Low N:P ratios in the benthic algae indicated N as well as P may be limiting their accrual. Most observed responses in benthic algal biomass occurred in nutrient concentrations between 10 and 30 μg TP l⁻¹ and between 400 and 1000 μg TN l⁻¹.     

Spatial Segregation of Congeneric Invaders in Central Pennsylvania, USA

Carduus acanthoides and Carduus nutans (plumeless and musk thistles) are among the most noxious weeds in the United States of America, presenting a serious challenge in cropping and pasture systems. Unfortunately, a lack of detailed spatial distribution information hampers both our ability to understand the factors affecting their invasive success, and the effectiveness of monitoring and management efforts. To examine patterns of distribution and co-occurrence at a local level, we sampled a 5000 km² area of central Pennsylvania that cut a transect across known areas of C. acanthoides and C. nutans infestation. A number of potential environmental explanatory variables were recorded and analyzed to examine whether they correlated with observed species distribution patterns. Patterns of forest density and spatial aggregation of the thistles were the primary covariates that significantly impacted both species’ distributions. The survey established that the frequency of sightings for each species diminished as the ranges converged, with only brief overlap: the two species are strongly negatively correlated in space. Understanding environmental correlates of infestation and the pattern of spatial dissociation of these two invasive species is an important step towards an improved understanding of the mechanisms underlying their invasive potential, and hence towards effective weed control.