The locus encoding an oligomorphic family of <Emphasis Type="Italic">MHC-A</Emphasis> alleles (<Emphasis Type="Italic">Mane-A</Emphasis>*06/<Emphasis Type="Italic">Mamu-A</Emphasis>*05) is present at high frequency in several macaque species

Several macaques species are used for HIV pathogenesis and vaccine studies, and the characterization of their major histocompatibility complex (MHC) class I genes is required to rigorously evaluate the cellular immune responses induced after immunization and/or infection. In this study, we demonstrate that the gene expressing the Mane-A*06 allele of pig-tailed macaques is an orthologue of the locus encoding the Mamu-A*05 allele family in rhesus macaques. Analysis of the distribution of this locus in a cohort of 63 pig-tailed macaques revealed that it encodes an oligomorphic family of alleles, highly prevalent (90%) in the pig-tailed macaque population. Similarly, this locus was very frequently found (62%) in a cohort of 80 Indian rhesus macaques. An orthologous gene was also detected in cynomolgus monkeys originating from four different geographical locations, but was absent in two African monkey species. Expression analysis in pig-tailed macaques revealed that the Mane-A*06 alleles encoded by this locus are transcribed at 10- to 20-fold lower levels than other MHC-A alleles (Mane-A*03 or Mane-A*10). Despite their conservation and high prevalence among Asian macaque species, the alleles of the Mane-A*06 family and, by extension their orthologues in rhesus and cynomolgus monkeys, may only modestly contribute to cellular immune responses in macaques because of their low level of expression.     

A NEW SPECIES OF THE WOMBAT WARENDJA FROM LATE MIOCENE DEPOSITS AT RIVERSLEIGH, NORTH-WEST QUEENSLAND, AUSTRALIA

Abstract:  A new species of the plesiomorphic wombat Warendja is described. Warendja encorensis sp. nov., the second species to be attributed to this genus, is known from a single fossil locality (Encore Site) at Riversleigh, north-west Queensland. Specimens of W. encorensis are limited to isolated teeth, two mandibular fragments and a maxillary fragment. Two molars preserve the unworn crown morphology. Encore Site has been estimated to be late Miocene in age, making these the only known specimens of Warendja to be clearly older than Pleistocene. Warendja encorensis is also the first described species of wombat from Miocene deposits to which hypselodont teeth have been attributed. It differs from W. wakefieldi in its larger size, distribution of enamel, and in details of the incisor and premolar morphology.     

Genetic selection for a highly functional cysteine-less membrane protein using site saturation mutagenesis

We describe an efficient method for generating highly functional membrane proteins with variant amino acids at defined positions that couples a modified site saturation strategy with functional genetic selection. We applied this method to the production of a cysteine-less variant of the Crithidia fasciculata inosine-guanosine permease CfNT2 to facilitate biochemical studies using thiol-specific modifying reagents. Of 10 endogenous cysteine residues in CfNT2, two cannot be replaced with serine or alanine without loss of function. High-quality single- and double-mutant libraries were produced by combining a previously reported site saturation mutagenesis scheme based on the Stratagene Quikchange method with a novel gel purification step that effectively eliminated template DNA from the products. Following selection for functional complementation in Saccharomyces cerevisiae cells auxotrophic for purines, several highly functional noncysteine substitutions were efficiently identified at each desired position, allowing the construction of cysteine-less variants of CfNT2 that retained wild-type affinity for inosine. This combination of an improved site saturation mutagenesis technique and positive genetic selection provides a simple and efficient means to identify functional and perhaps unexpected amino acid variants at a desired position.     

免疫进化算法在建立地位指数曲线模型中的应用

选择Schumacher方程构建优势高和地位指数均能写成显式表达式的多形地位指数曲线模型,以同时兼顾优势高和地位指数的估测误差最小为目标函数,采用免疫进化算法求解参数．实例分析表明：该文建立的多形地位指数曲线模型能够客观地反映不同立地下优势高的生长规律,且误差小,应用方便．     

Predicting spacing behavior and mating systems of solitary cervids: a study of hog deer and Indian muntjac

This study investigates the validity of current theory for predicting ecological and allometric effects on space use, social structure and mating systems of poorly known solitary cervids, based on a comparative analysis of radio-telemetry data on hog deer Axis porcinus (N=32) and Indian muntjac Muntiacus muntjak (N=28). The larger and sexually size-dimorphic hog deer inhabit highly productive alluvial floodplains, where resource distribution is patchy and spatiotemporally unpredictable. As predicted for this species, site fidelity was low and range sizes varied among sex and age groups and among seasons. Hog deer were probably non-territorial, as home range sizes seemed too large to be exclusive when taking into account their high population density. Extensive movements of adult males during the rut implied "roaming" as a mating strategy. The smaller, forest-dwelling and sexually size-monomorphic muntjacs inhabit a more uniform and stable habitat. As predicted, muntjacs exhibited higher site fidelity than hog deer, and no seasonal variations in home range sizes. Adults exhibited relatively large home range overlap, both inter- and intrasexually. Hence, strict territoriality did not occur, but their well-defined home ranges and high site fidelity indicated some form of site-specific dominance. In conclusion, habitat characteristics were appropriate predictors of home range sizes and site fidelity. Body mass appeared to be a suitable predictor of intraspecific patterns in space use but a poor predictor of interspecific patterns, probably due to a confounding effect of habitat productivity.     

Disturbance persistence in managed grasslands: shifts in aboveground community structure and the weed seed bank

The length of time and form in which disturbances persist in systems depends on the intensity and frequency of disturbance and on the abilities of resident species to recover from such events. In grazed grasslands, trampling by large mammalian herbivores can periodically facilitate weed establishment by exposing patches of bare ground but whether an intense soil disturbance event results in a temporary increase in weed abundance or a persistent weed problem remains unclear. In May 2002, cattle trampling following heavy rain caused severe damage to nine-month old, rotationally grazed, cool-season pastures (Midwest USA). In September 2002, we compared the aboveground composition of paddocks (i.e., fenced pasture sections) that were heavily disturbed to those that received no damage. Relative to undisturbed paddocks, forage species relative cover was 17% lower in disturbed paddocks, and weed species and bare ground relative cover was 61% and 100% higher, respectively. By September 2004, paddock types did not differ in all aboveground community components. However, the abundance and species richness of weed seeds in the soil seed bank averaged respectively 82% and 30% higher in disturbed paddocks between 2003 and 2004. These findings indicate that a spatially extensive, intense soil disturbance event may soon become undetectable in components of aboveground pasture structure but can persist as an augmented weed seed bank. Because of high weed seed bank longevity, disturbances to formerly disturbed pastures would likely result in higher weed recruitment, with more species represented, than in those which lack previous disturbance. Disturbance history may thus be a useful predictor of weed community composition following subsequent disturbance. Based on empirical data supporting this proposition, we recommend that grassland managers explicitly incorporate disturbance history into dynamic management planning and do not rely exclusively on aboveground characters to evaluate the invasion status or colonization potential of an area by undesirable plants. We emphasize that the ecological legacies of past soil disturbance events cannot only influence the contemporary patterns and processes of grasslands, but importantly, affect their compositional trajectories following subsequent perturbation.     

Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I--usefulness in SAGE

While it has been demonstrated that AdoMet is required for DNA cleavage by Type III restriction enzymes, here we show that in the presence of exogenous AdoMet, the head-to-head oriented recognition sites are cleaved only on a supercoiled DNA. On a linear DNA, exogenous AdoMet strongly drives methylation while inhibiting cleavage reaction. Strikingly, AdoMet analogue sinefungin results in cleavage at all recognition sites irrespective of the topology of DNA. The cleavage reaction in the presence of sinefungin is ATP dependent. The site of cleavage is comparable with that in the presence of AdoMet. The use of EcoP15I restriction in presence of sinefungin as an improved tool for serial analysis of gene expression is discussed.     

Allosteric Inhibition of the Epithelial Na+ Channel through Peptide Binding at Peripheral Finger and Thumb Domains

The epithelial Na⁺ channel (ENaC) mediates the rate-limiting step in transepithelial Na⁺ transport in the distal segments of the nephron and in the lung. ENaC subunits are cleaved by proteases, resulting in channel activation due to the release of inhibitory tracts. Peptides derived from these tracts inhibit channel activity. The mechanism by which these intrinsic inhibitory tracts reduce channel activity is unknown, as are the sites where these tracts interact with other residues within the channel. We performed site-directed mutagenesis in large portions of the predicted periphery of the extracellular region of the α subunit and measured the effect of mutations on an 8-residue inhibitory tract-derived peptide. Our data show that the inhibitory peptide likely binds to specific residues within the finger and thumb domains of ENaC. Pairwise interactions between the peptide and the channel were identified by double mutant cycle experiments. Our data suggest that the inhibitory peptide has a specific peptide orientation within its binding site. Extended to the intrinsic inhibitory tract, our data suggest that proteases activate ENaC by removing residues that bind at the finger-thumb domain interface.     

Root and stem partitioning of Pinus taeda

We measured root and stem mass at three sites (Piedmont (P), Coastal Plain (C), and Sandhills (S)) in the southeastern United States. Stand density, soil texture and drainage, genetic makeup and environmental conditions varied with site while differences in tree size at each site were induced with fertilizer additions. Across sites, root mass was about one half of stem mass when estimated on a per hectare basis. Stem mass per hectare explained 91% of the variation in root mass per hectare, while mean tree diameter at breast height (D), site, and site by measurement year were significant variables explaining an additional 6% of the variation in root mass per hectare. At the S site, the root:stem ratio decreased from 0.7 to 0.5 when mean tree D increased from 10 to 22 cm. At the P and C sites, where mean root:stem ratios were 0.40 and 0.47, respectively, no significant slope in the root:stem to mean tree D relationship was found over a more narrow range in mean tree D (12–15 and 12–18 cm, respectively). Roots were observed in the deepest layers measured (190, 190, and 290 cm for the P, C, and S sites, respectively); however, the asymptotically decreasing root mass per layer indicated the bulk of roots were measured. Root growth relative to stem growth would need to change with increased mean tree D to explain the results observed here. While these changes in growth rate among plant components may differ across sites, stem mass alone does a good job of estimating root mass across sites.     

Light environment under Rhododendron maximum thickets and estimated carbon gain of regenerating forest tree seedlings

Canopy tree recruitment is inhibited by evergreen shrubs in many forests. In the southern Appalachian mountains of the USA, thickets of Rhododendron maximum L. restrict dominant canopy tree seedling survival and persistence. Using R. maximum as a model system, we examined available light under the thickets and the photosynthetic responses of seedlings of canopy tree species. We tested the hypothesis that the additional shading from under R. maximum drives carbon gain in seedlings below the threshold for growth and survival. A reduction in light under the thicket was found where canopy openness (derived from canopy photographs) under R. maximum was half the amount measured in forest without R. maximum. R.␣maximum also reduced direct radiation by 50% and diffuse radiation by 12–29% compared to forest without the shrub layer. Mean mid-day PPFD (photosynthetically active photon flux density between 1000 and 1400 h) under R. maximum (obtained from quantum sensors) was below 10 mol m⁻² s⁻¹ on both clear and overcast days and the amount of sunflecks greater than 10 mol m⁻² s⁻¹ PPFD was only 0–20 min per day. In contrast, forest without R. maximum received a mean PPFD of 18–25 mol m⁻² s⁻¹ on clear days and a cumulative sunfleck duration of 100–220 min per day in all sky conditions. Consistent with light availability between the sites, daily carbon gain in Quercus rubra L. seedlings was lower in forest with R. maximum compared to forest where the shrub was absent. The presence of the shrub layer also significantly suppressed average mid-day photosynthesis of both Q. rubra and Prunus serotina Ehrt. seedlings on 8 out of 11 measurement dates. However, parameters derived from light response curves between seedlings growing in forest sites with or without a thicket of R. maximum was significantly different only in A _max (maximum photosynthetic rate), indicating a lack of further acclimation to the deeper shade under R. maximum. While the additional shade cast by R. maximum is sufficient to prevent the regeneration of tree seedlings under this shrub, there was sufficient heterogeneity in light under the thicket to imply that deep shade only partially explains the complete inhibition of regenerating canopy trees under R. maximum.