Structure-based design of irreversible, tripeptidyl human rhinovirus 3C protease inhibitors containing N-methyl amino acids.

Tripeptide-derived molecules incorporating N-methyl amino acid residues and C-terminal Michael acceptor moieties were evaluated as irreversible inhibitors of the cysteine-containing human rhinovirus 3C protease (3CP). Such compounds displayed good 3CP inhibition activity (k(obs)/[I] up to 610,000 M(-1) s(-1)) and potent in vitro antiviral properties (EC50 approaching 0.03 microM) when tested against HRV serotype-14.     

Inducing condensed tannin production in Colophospermum mopane: Absence of response to soil N and P fertility and physical damage

The effects of available soil N and P and the effect of simulated browsing (leave removal) on foliar condensed tannin (CT) concentration were tested on young Colophospermum mopane (J. Kirk ex Benth) J. Leonard (Mopane) plants. Although clear differences in growth occurred between different levels of soil N, no differences in foliar CT concentration were found. Changes in available soil P and physical damage did not affect the plant growth or chemical composition. The complete absence of response of CT concentration to physical damage and soil nutrients may be related to the age of the trees in this study. It is proposed that existing theories on the interaction between soil properties and carbon based defences in trees are expanded, to include the potential responses of young trees to different soil nutrient levels.     

Histopathology and PR-protein markers provide insight into adult plant resistance to stripe rust of wheat

Stripe rust, caused by Puccinia striiformis f. sp. tritici , is a serious disease of wheat. The spring wheat cultivar Kariega expresses complete adult plant resistance to stripe rust, whereas Avocet S is susceptible. In former studies, quantitative trait loci (QTL) analysis of doubled haploid lines derived from a Kariega × Avocet S cross revealed two major QTL ( QYr.sgi-7D and QYr.sgi-2B.1 ) and two minor QTL ( QYr.sgi-1A and QYr.sgi-4A.1 ) responsible for the adult resistance of Kariega in the field. Avocet S contains none of these QTL. In the present study, stripe rust development was compared, by means of fluorescence and confocal laser scanning microscopy, in flag leaves of Kariega, Avocet S and six doubled haploid (DH) lines, containing all four, none or one QTL. Depending on the QTL present, the infection types of the DH lines ranged from resistant to fully susceptible. No differences in fungal growth were observed during the first 5 days post inoculation (dpi), whereas the mean length of the fungal colonies started to differ at 6 dpi. Interestingly, MP 51 carrying QYr.sgi-7D responded with lignification to the fungal growth without restricting it, whereas MP 35 containing QYr.sgi-2B.1 did not show lignified host tissue, but fungal growth was restricted. RT PCR experiments with sequences of pathogenesis-related (PR) proteins resulted in a slightly stronger induction of PR 1, 2 and 5, known markers for the hypersensitive reaction, and peroxidases in MP 51, whereas a second band for chitinases was detected in MP 35 only.     

Strategies for antiviral resistance in transgenic plants

Genetic engineering offers a means of incorporating new virus resistance traits into existing desirable plant cultivars. The initial attempts to create transgenes conferring virus resistance were based on the pathogen-derived resistance concept. The expression of the viral coat protein gene in transgenic plants was shown to induce protective effects similar to classical cross protection, and was therefore distinguished as 'coat-protein-mediated' protection. Since then, a large variety of viral sequences encoding structural and non-structural proteins were shown to confer resistance. Subsequently, non-coding viral RNA was shown to be a potential trigger for virus resistance in transgenic plants, which led to the discovery of a novel innate resistance in plants, RNA silencing. Apart from the majority of pathogen-derived resistance strategies, alternative strategies involving virus-specific antibodies have been successfully applied. In a separate section, efforts to combat viroids in transgenic plants are highlighted. In a final summarizing section, the potential risks involved in the introduction of transgenic crops and the specifics of the approaches used will be discussed.     

Will the Three Gorges Dam affect the underwater light climate of <Emphasis Type="Italic">Vallisneria spiralis</Emphasis> L. and food habitat of Siberian crane in Poyang Lake?

Almost 95% of the entire population of the Siberian crane (Grus leucogeranus) winter in Poyang Lake, China, where they forage on the tubers of the submerged aquatic macrophyte Vallisneria spiralis. The Three Gorges Dam on the Yangtze River may possibly affect this food source of the Siberian crane by affecting the light intensity reaching the top of the V. spiralis canopy. In this study, the photosynthetically active radiation at the top of the V. spiralis canopy (PAR_tc) in Lake Dahuchi was modeled from 1998 to 2006, and the potential impacts of changes in water level and turbidity on the underwater light climate of V. spiralis were analyzed. PAR_tc was calculated from incident irradiance while the losses due to reflection at the water surface, absorption, and scattering within the water column were taken into consideration. The results indicated significant differences in PAR_tc between years. Six years of water level and Secchi disk depth records revealed a seasonal switching of the lake from a turbid state at low water levels in autumn, winter, and spring to a clear state at high water levels during the monsoon in summer. The highest PAR_tc occurred at intermediate water levels, which were reached when the Yangtze River forces Lake Dahuchi out of its turbid state in early summer and the water becomes clear. The intended operation of the Three Gorges Dam, which will increase water levels in May and June, may advance the moment when Lake Dahuchi switches from turbid to clear. We suggest that this might increase production of V. spiralis and possibly improve the food habitat conditions for wintering Siberian crane in Poyang Lake.

Scale-sensitive landscape complementation determines habitat suitability for a territorial generalist

Evaluating habitat suitability is often complex, as habitat effects may be scale‐dependent, critical resources may be spatially segregated, and resource availability may also depend on intra‐ and inter‐specific interactions. Using analyses that spanned multiple years and spatial scales, we investigated habitat requirements of a territorial generalist, the common raven Corvus corax, in a relatively pristine woodland, Bia?owie?a Forest (E Poland). We compiled data from multiple raven surveys conducted between 1985 and 2001. Ravens were regularly distributed over the entire study area but declined in density over 50% within the 16 yr interval. In the same period game and forest management significantly reduced ungulate densities and likely diminished the habitat quality with regard to food supply, especially carrion. To better understand habitat requirements of ravens we studied breeding performance in relation to three different habitat types across multiple scales: open areas, coniferous‐dominated forest, and deciduous‐dominated forest. We found a prominent dissimilarity between raven nesting and foraging habitats highlighting the importance of resource complementation for ravens. On a fine scale, large old pines were exclusively selected as nesting trees and nesting areas were generally coniferous‐dominated. However, at increasingly broader scales, coniferous habitats were negatively associated with raven reproductive success as those habitats likely provide a lower food supply. Only where the coniferous nesting areas at smaller scales were complemented with high percentages of deciduous forests and open areas at broader scales did the breeding performance increase. In addition to habitat composition, intra‐specific interactions were important determinants of reproductive performance and very successful neighbors decreased reproductive performance of a focal pair. Most of previous studies have investigated resource complementation in terms of habitat edges or proximity of complementing resource patches. Our study demonstrates that the concept of landscape complementation also applies to gradients in landscape composition and emphasizes the importance of scales and intraspecific interactions in habitat analyses.     

Non-invasive imaging of mouse hepatitis coronavirus infection reveals determinants of viral replication and spread in vivo

Bioluminescence imaging (BLI) is a powerful new method to study virus dissemination in the live animal. Here we used this method to monitor the spatial and temporal progression of mouse hepatitis coronavirus (MHV) infection in mice using luciferase-expressing viruses. Upon intranasal inoculation, virus replication could initially be observed in the nasal cavity and the cervical lymph nodes, after which the infection spread to the brain and frequently to the eyes. The kinetics of virus spread to and clearance from the brain appeared to depend on the inoculation dose. After intraperitoneal inoculation, virus replication was predominantly observed in the liver and occasionally in the intestines, but interestingly also in the tail and paws. BLI thus elucidated new anatomic locations of virus replication. Furthermore, MHV dissemination was shown to be critically depended on the viral spike protein, but also on the mouse strain used. Widespread dissemination was observed in mice lacking a functional type I interferon response. The importance of the type I interferon system in limiting viral spread was also demonstrated by the administration of type I interferons to mice. Our results provide new insights in coronavirus pathogenesis and demonstrate the potential of BLI to study coronavirus–host interactions in vivo .     

Viral Load Levels Measured at Set-Point Have Risen Over the Last Decade of the HIV Epidemic in the Netherlands

Background

HIV-1 RNA plasma concentration at viral set-point is associated not only with disease outcome but also with the transmission dynamics of HIV-1. We investigated whether plasma HIV-1 RNA concentration and CD4 cell count at viral set-point have changed over time in the HIV epidemic in the Netherlands.

Methodology/Principal Findings

We selected 906 therapy-naïve patients with at least one plasma HIV-1 RNA concentration measured 9 to 27 months after estimated seroconversion. Changes in HIV-1 RNA and CD4 cell count at viral set-point over time were analysed using linear regression models. The ATHENA national observational cohort contributed all patients who seroconverted in or after 1996; the Amsterdam Cohort Studies (ACS) contributed seroconverters before 1996. The mean of the first HIV-1 RNA concentration measured 9–27 months after seroconversion was 4.30 log₁₀ copies/ml (95% CI 4.17–4.42) for seroconverters from 1984 through 1995 (n = 163); 4.27 (4.16–4.37) for seroconverters 1996–2002 (n = 232), and 4.59 (4.52–4.66) for seroconverters 2003–2007 (n = 511). Compared to patients seroconverting between 2003–2007, the adjusted mean HIV-1 RNA concentration at set-point was 0.28 log₁₀ copies/ml (95% CI 0.16–0.40; p<0.0001) and 0.26 (0.11–0.41; p = 0.0006) lower for those seroconverting between 1996–2002 and 1984–1995, respectively. Results were robust regardless of type of HIV-1 RNA assay, HIV-1 subtype, and interval between measurement and seroconversion. CD4 cell count at viral set-point declined over calendar time at approximately 5 cells/mm³/year.

Conclusion

The HIV-1 RNA plasma concentration at viral set-point has increased over the last decade of the HIV epidemic in the Netherlands. This is accompanied by a decreasing CD4 cell count over the period 1984–2007 and may have implications for both the course of the HIV infection and the epidemic.     

Multiple loss-of-function 5-O-glucosyltransferase alleles revealed in Vitis vinifera,but not in other Vitis species

Key message

Wild and loss-of-function alleles of the 5 - O - glucosyltransferase gene responsible for synthesis of diglucoside anthocyanins in Vitis were characterized. The information aids marker development for tracking this gene in grape breeding.

Abstract

Anthocyanins in red grapes are present in two glycosylation states: monoglucoside (3-O-glucoside) and diglucoside (3, 5-di-O-glucoside). While monoglucoside anthocyanins are present in all pigmented grapes, diglucoside anthocyanins are rarely found in the cultivated grape species Vitis vinifera. Biochemically 3-O-glucoside anthocyanins can be converted into 3,5-di-O-glucoside anthocyanins by a 5-O-glucosyltransferase. In this study, we surveyed allelic variation of the 5-O-glucosyltransferase gene (5GT) in 70 V. vinifera ssp. vinifera cultivars, 52 V. vinifera ssp. sylvestris accessions, 23 Vitis hybrid grapes, and 22 accessions of seven other Vitis species. Eighteen 5GT alleles with apparent loss-of-function mutations, including seven premature stop codon mutations and six frameshift indel mutations, were discovered in V. vinifera, but not in the other Vitis species. A total of 36 5GT alleles without apparent loss-of-function mutations (W-type) were identified. These W-type alleles were predominantly present in wild Vitis species, although a few of them were also found in some V. vinifera accessions. We further evaluated some of these 5GT alleles in producing diglucoside anthocyanins by analyzing the content of diglucoside anthocyanins in a set of representative V. vinifera cultivars. Through haplotype network analysis we revealed that V. vinifera ssp. vinifera and its wild progenitor V. vinifera ssp. sylvestris shared many loss-of-function 5GT alleles and extensive divergence of the 5GT alleles was evident within V. vinifera. This work advances our understanding of the genetic diversity of 5GT and provides a molecular basis for future marker-assisted selection for improving this important wine quality trait.     

Herbaceous production in South India—limiting factors and implications for large herbivores

This study’s goal was to better understand the growth pattern and limitations of the herbaceous production that supports South India’s rich large herbivore grazer assemblage. We conducted a fully factorial nitrogen and water (three levels each) treatment field experiment in the herbivore rich South Indian Western Ghats region to determine the seasonal pattern and the extent to which nitrogen and water availability limit herbaceous production. Graminoid production was found to be nitrogen limited. Despite low rainfall, additional water did not significantly increase overall biomass production nor extend growth in the dry season. Accumulated standing biomass was highest in the late wet season (November) and lowest in the dry season (May). Leaf nitrogen was highest in the early wet season (June) and lowest in the late dry season (March). Grazing had a positive effect on grass production by extending the growing season. Biomass production and graminoid leaf nitrogen concentration levels in the study area were similar to other tropical areas in the world. Also similar to other tropical large herbivore areas, the dry season poses an annual challenge for large herbivores in the study area —particularly the smaller bodied species—to satisfy their nutrient requirements.