The effects of truncating long-range forces on protein dynamics

This paper considers the effects of truncating long-range forces on protein dynamics. Six methods of truncation that we investigate as a function of cutoff criterion of the long-range potentials are (1) a shifted potential; (2) a switching function; (3) simple atom-atom truncation based on distance; (4) simple atom-atom truncation based on a list which is updated periodically (every 25 steps); (5) simple group-group truncation based on distance; and (6) simple group-group truncation based on a list which is updated periodically (every 25 steps). Based on 70 calculations of carboxymyoglobin we show that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. Evaluation of the different methods is based on comparison of a simulation's rms fluctuation about the average coordinates, the rms deviation from the average coordinates of a no cutoff simulation and from the X-ray structure of the protein. The simulations in which long-range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 A, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function are investigated by varying the range over which electrostatic interactions are switched off. Results using a short switching function that switches off the potential over a short range of distances are poor for all cutoff distances. A switching function over a 5-9 A range gives reasonable results for a distance-dependent dielectric, but not using a constant dielectric. Both the atom-atom and group-group truncation methods based on distance shows large rms deviation and fluctuation for short cutoff distances, while for cutoff distances of 11 A or greater, reasonable results are achieved. Although comparison of these to distance-based truncation methods show surprisingly larger rms deviations for the group-group truncation, contrary to simulation studies of aqueous ionic solutions. The results of atom-atom or group-group list-based simulations generally appear to be less stable than the distance-based simulations, and require more frequent velocity scaling or stronger coupling to a heat bath.     

Long-Term Ecosystem Effects of Sand-Binding Vegetation in the Tengger Desert, Northern China

The planting of sand‐binding vegetation in the Shapotou region at the southeastern edge of the Tengger Desert began in 1956. Over the past 46 years, it has not only insured the smooth operation of the Baotou–Lanzhou railway in the sand dune section but has also played an important role in the restoration of the local eco‐environment; therefore, it is viewed as a successful model for desertification control and ecological restoration along the transport line in the arid desert region of China. Long‐term monitoring and focused research show that within 4–5 years of establishment of sand‐binding vegetation, the physical surface structure of the sand dunes stabilized, and inorganic soil crusts formed by atmospheric dust gradually turned into microbiotic crusts. Among the organisms comprising these crusts are cryptogams such as desert algae and mosses. In the 46 years since establishing sand‐binding vegetation, some 24 algal species occurred in the crusts. However, only five moss species were identified, which was fewer than the species number in the crust of naturally fixed sand dunes. Other results of the planting were that near‐surface wind velocity in the 46‐year‐old vegetation area was reduced by 54.2% compared with that in the moving sand area; soil organic matter increased from 0.06% in moving sand dunes to 1.34% in the 46‐year‐old vegetation area; the main nutrients N, P, K, etc., in the desert ecosystem increased; soil physicochemical properties improved; and soil‐forming processes occurred in the dune surface layer. Overall, establishment of sand‐binding vegetation significantly impacted soil water cycles, creating favorable conditions for colonization by many herbaceous species. These herbaceous species, in turn, facilitated the colonization and persistence of birds, insects, soil animals, and desert animals. Forty‐six years later, some 28 bird species and 50 insect species were identified in the vegetated dune field. Thus, establishment of a relatively simple community of sand‐binding species led to the transformation of the relatively barren dune environment into a desert ecosystem with complex structure, composition, and function. This restoration effort shows the potential for short‐term manipulation of environmental variables (i.e., plant cover via artificial vegetation establishment) to begin the long‐term process of ecological restoration, particularly in arid climates, and demonstrates several techniques that can be used to scientifically monitor progress in large‐scale restoration projects.     

Effects of selected insecticides on Cotesia plutellae, endoparasitoid of Plutella xylostella

Effects of field dosages ofselected insecticides to Cotesiaplutellae (Kurdjumov) (Hymenoptera: Braconidae), a larval endoparasitoidof Plutella xylostella L. (Lepidoptera: Plutellidae), wereinvestigated under laboratory conditions.Emergence of adult C. plutellae frominsecticide-treated pupae was not significantlydifferent from the control treatment. Contacttoxicity to C. plutellae adults variedgreatly among the insecticides in a paperresidue contact bioassay. Threeazadirachtin-based insecticides, Agroneem(4.8 mg a.i.liter^–1), Neemix (20 mga.i.liter^–1) and Ecozin (20 mgai.liter^–1) caused 11.1, 16.7 and 5.6%adult mortality, respectively. Of fourcommercial Bacillus thuringiensis (Bt)insecticides examined (all at 1.2 mga.i.liter^–1), Crymax and Xentari had noeffect on adult parasitoids, whereas Mattchcaused 5.6% mortality, and Dipel caused 11.1%mortality. Indoxacarb (53 mg a.i.liter^–1),-cyhalothrin (28 mg a.i.liter^–1) andspinosad (53 mg a.i.liter^–1) caused 100,88.5 and 50% adult mortalities, respectively.Low adult mortality (0–5.6%) was recorded fromingestion of azadirachtin-based, Btinsecticides and indoxacarb, compared with100% adult mortality in treatments of spinosador -cyhalothrin. Compared with the watercontrol, ingestion of azadirachtin-basedinsecticides significantly reduced parasitismby 50–57%, and Bt insecticides by 8–25%.However, ingestion of these insecticides didnot affect longevity of male and femaleparasitoid adults with one exception; femalelongevity was significantly reduced in theindoxacarb treatment. Insecticide residuescaused considerable mortality of C.plutellae adults, 39 and 44% mortality causedby 10 d old indoxacarb and -cyhalothrin,respectively, and 24 and 0% mortality causedby 7 and 10 d old residues of spinosad,respectively.     

Alternative stable states and regional community structure

Many models of local species interactions predict the occurrence of priority effects due to alternative stable equilibria (ASE). However, few empirical examples of ASE have been shown. One possible explanation for the disparity is that local ASE are difficult to maintain regionally in patch dynamic models. Here we examine two possible mechanisms for regional coexistence of species engaged in local ASE. Biotically generated heterogeneity (e.g., habitat modification that favors further invasion by conspecifics) results in regional exclusion of one species at equilibrium. In contrast, abiotic heterogeneity due to spatial variation in resource supply ratios generates local-scale ASE and ensures regional coexistence with sufficiently broad environmental gradients. Abiotic heterogeneity can result in a species that is the dominant competitor over some of its range being excluded if the area where it is dominant is too small. Biotic heterogeneity can lead to alternative stable landscapes or regional priority effects, while abiotic heterogeneity results in regional determinism. Broad environmental gradients in resource supply favor regional coexistence of species that exhibit local ASE.     

GENETIC AND SOCIAL INHERITANCE OF BODY AND EGG SIZE IN THE BARNACLE GOOSE (BRANTA LEUCOPSIS)

We present heritability estimates for final size of body traits and egg size as well as phenotypic and genetic correlations between body and egg traits in a recently established population of the barnacle goose (Branta leucopsis) in the Baltic area. Body traits as well as egg size were heritable and, hence, could respond evolutionarily to phenotypic selection. Genetic correlations between body size traits were significantly positive and of similar magnitude or higher than the corresponding phenotypic correlations. Heritability estimates for tarsus length obtained from full-sib analyses were higher than those obtained from midoffspring-midparent regressions, and this indicates common environment effects on siblings. Heritabilities for tarsus length obtained from midoffspring-mother regressions were significantly higher than estimates from midoffspring-father regressions. The results suggest that this discrepancy is not caused by maternal effects through egg size, nor by extra-pair fertilizations, but by a socially inherited foraging site fidelity in females.     

我国湖泊与海水鱼类养殖的环境效应和基于生态系统的渔业管理

在我国,鱼类养殖是一项重要的商业活动。鱼类养殖在过去几十年的快速发展过程中,对水环境产生了重要影响。研究表明:鱼类养殖对养殖区鱼、浮游生物、水生植物群落结构和水质变化有重要影响。现在,几乎所有的鱼类养殖系统都在一定程度上受到了损害。随着人们环境保护意识的增强,鱼类养殖的环境效应和渔业管理问题已引起了社会的广泛关注,渔业管理不再仅仅是通过开发资源以获取最高产量。面临挑战,人们应该采取切实可行的步骤,从传统的渔业管理转变到基于生态系统的渔业管理,将渔业纳入生态系统管理以保障养殖业的可持续发展。     

Structure and function of the Gondwanian hemoglobin of Pseudaphritis urvillii, a primitive notothenioid fish of temperate latitudes

The suborder Notothenioidei dominates the Antarctic ichthyofauna. The non-Antarctic monotypic family Pseudaphritidae is one of the most primitive families. The characterization of the oxygen-transport system of euryhaline Pseudaphritis urvillii is herewith reported. Similar to most Antarctic notothenioids, this temperate species has a single major hemoglobin (Hb 1, over 95% of the total). Hb 1 has strong Bohr and Root effects. It shows two very uncommon features in oxygen binding: At high pH values, the oxygen affinity is exceptionally high compared to other notothenioids, and subunit cooperativity is modulated by pH in an unusual way, namely the curve of the Hill coefficient is bell-shaped, with values approaching 1 at both extremes of pH. Molecular modeling, electronic absorption and resonance Raman spectra have been used to characterize the heme environment of Hb 1 in an attempt to explain these features, particularly in view of some potentially important nonconservative replacements found in the primary structure. Compared to human HbA, no major changes were found in the structure of the proximal cavity of the alpha-chain of Hb 1, although an altered distal histidyl and heme position was identified in the models of the beta-chain, possibly facilitated by a more open heme pocket due to reduced steric constraints on the vinyl substituent groups. This conformation may lead to the hemichrome form identified by spectroscopy in the Met state, which likely fulfils a potentially important physiological role.     

Fixed effect genetic analysis of a diallel cross in dry beans (Phaseolus vulgaris L.)

Summary A full diallel cross among four diverse homozygous strains of dry edible beans (Phaseolus vulgaris L.) was evaluated for yield, protein content, and culinary quality traits in the F₂ and F₃ generations in two locations. Interpretation of diallel effects [Method 1 Model I] using a fixed-effect genetic model made it possible to combine data from two generations into a single analysis and quantify the relative contributions of additive and dominance genetic effects to general (GCA) and specific (SCA) combining abilities. GCA was found to arise from three potential sources: additive effects, dominance interactions at homozygous loci, and average dominance interactions in hybrids involving the parent in question. SCA was found to be a function solely of dominance. Additive effects were the primary determinant of GCA and were highly significant. Specific dominance interactions were significant for seed yield, cooked bean moisture content, and texture but not for protein content. Texture was the only trait for which the additive-dominance model failed to provide an adequate fit to the data, suggesting that texture is significantly affected by epistatic interaction. One cross (Brazil-2 × Sanilac) was identified that exhibited a large heterotic effect for seed yield although the parents' additive effects were nonsignificant. Such a nicking effect was attributed to complementation between the two parents.Cooperative investigations of the Agricultural Research Service, U.S. Department of Agriculture and Michigan State University, East Lansing, MI 48824. Part of a thesis submitted by the senior author in partial fulfillment of the requirements for the Ph.D. degree at Michigan State University. Approved for publication by the Michigan Agricultural Experiment Station as Journal Article No. 11791. Research supported by USAID under a Title XII Bean/Cowpea CRSP and cooperative with Washington State University, Pullman, WA99164     

海岸带复合梨园的光能分布与利用规律

采用方格法和分层法相结合的技术对江苏省如东县棉花原种场林网保护区内13年生梨园的树冠结构特征和光能分布与利用规律进行了系统研究。结果表明:梨树叶幕光能分布状况直接受叶面积系数、树冠结构、太阳位置及光强的影响。各层叶幕中的光合有效辐射(PAR)分布随自然光照条件的变化而改变,其日平均透光率大小和PAR日变化范围均从叶幕外围向内膛随累积叶面积系数(LAI)的增加而减弱;不同生长时期及不同天气变化下树冠光能分布存在明显的差异性;树冠结构与累积LAI对PAR的分布及利用率具有决定性的影响。在生产实践中,通过密度调控、整形修剪等农业技术措施,维持成年梨园盛果期高效光合生产的叶幕厚度在2.5m以上,有效LAI为4左右,是增强梨树光合生产能力、提高产量和品质的有效措施。     

The contribution of cacao agroforests to the conservation of lower canopy ant and beetle diversity in Indonesia

The ongoing destruction of tropical rainforests has increased the interest in the potential value of tropical agroforests for the conservation of biodiversity. Traditional, shaded agroforests may support high levels of biodiversity, for some groups even approaching that of undisturbed tropical forests. However, it is unclear to what extent forest fauna is represented in this diversity and how management affects forest fauna in agroforests. We studied lower canopy ant and beetle fauna in cacao agroforests and forests in Central Sulawesi, Indonesia, a region dominated by cacao agroforestry. We compared ant and beetle species richness and composition in forests and cacao agroforests and studied the impact of two aspects of management intensification (the decrease in shade tree diversity and in shade canopy cover) on ant and beetle diversity. The agroforests had three types of shade that represented a decrease in tree diversity (high, intermediate and low diversity). Species richness of ants and beetles in the canopies of the cacao trees was similar to that found in lower canopy forest trees. However, the composition of ant and beetle communities differed greatly between the agroforest and forest sites. Forest beetles suffered profoundly from the conversion to agroforests: only 12.5% of the beetle species recorded in the forest sites were also found in the agroforests and those species made up only 5% of all beetles collected from cacao. In contrast, forest ants were well represented in agroforests, with 75% of all species encountered in the forest sites also occurring on cacao. The reduction of shade tree diversity had no negative effect on ants and beetles on cacao trees. Beetle abundances and non-forest ant species richness even increased with decreasing shade tree diversity. Thinning of the shade canopy was related to a decrease in richness of forest ant species on cacao trees but not of beetles. The contrasting responses of ants and beetles to shade tree management emphasize that conservation plans that focus on one taxonomic group may not work for others. Overall ant and beetle diversity can remain high in shaded agroforests but the conservation of forest ants and beetles in particular depends primarily on the protection of natural forests, which for forest ants can be complemented by the conservation of adjacent shaded cacao agroforests.