Protein side chain conformation predictions with an MMGBSA energy function

The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an “MMGBSA” energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803–819. © 2016 Wiley Periodicals, Inc.     

Correlations of pelvis state to foot placement do not imply within-step active control

Experimental studies of human walking have shown that within an individual step, variations in the center of mass (CoM) state can predict corresponding variations in the next foot placement. This has been interpreted by some to indicate the existence of active control in which the nervous system uses the CoM state at or near mid-stance to regulate subsequent foot placement. However, the passive dynamics of the moving body and/or moving limbs also contribute (perhaps strongly) to foot placement, and thus to its variation. The extent to which correlations of CoM state to foot placement reflect the effects of within-step active control, those of passive dynamics, or some combination of both, remains an important and still open question. Here, we used an open-loop-stable 2D walking model to show that this predictive ability cannot by itself be taken as evidence of within-step active control. In our simulations, we too find high correlations between the CoM state and subsequent foot placement, but these correlations are entirely due to passive dynamics as our system has no active control, either within a step or between steps. This demonstrates that any inferences made from such correlations about within-step active control require additional supporting evidence beyond the correlations themselves. Thus, these within-step predictive correlations leave unresolved the relative importance of within-step active control as compared to passive dynamics, meaning that such methods should be used to characterize control in human walking only with caution.     

Toward ecologically explicit null models of nestedness

A community is "nested" when species assemblages in less rich sites form nonrandom subsets of those at richer sites. Conventional null models used to test for statistically nonrandom nestedness are under- or over-restrictive because they do not sufficiently isolate ecological processes of interest, which hinders ecological inference. We propose a class of null models that are ecologically explicit and interpretable. Expected values of species richness and incidence, rather than observed values, are used to create random presence-absence matrices for hypothesis testing. In our examples, based on six datasets, expected values were derived either by using an individually based random placement model or by fitting empirical models to richness data as a function of environmental covariates. We describe an algorithm for constructing unbiased null matrices, which permitted valid testing of our null models. Our approach avoids the problem of building too much structure into the null model, and enabled us to explicitly test whether observed communities were more nested than would be expected for a system structured solely by species-abundance and species-area or similar relationships. We argue that this test or similar tests are better determinants of whether a system is truly nested; a nested system should contain unique pattern not already predicted by more fundamental ecological principles such as species-area relationships. Most species assemblages we studied were not nested under these null models. Our results suggest that nestedness, beyond that which is explained by passive sampling processes, may not be as widespread as currently believed. These findings may help to improve the utility of nestedness as an ecological concept and conservation tool.     

Morphological variation between non‐native lake‐ and stream‐dwelling pumpkinseed Lepomis gibbosusin the Iberian Peninsula

The objective of this study was to test if morphological differences in pumpkinseed Lepomis gibbosus found in their native range (eastern North America) that are linked to feeding regime, competition with other species, hydrodynamic forces and habitat were also found among stream‐ and lake‐ or reservoir‐dwelling fish in Iberian systems. The species has been introduced into these systems, expanding its range, and is presumably well adapted to freshwater Iberian Peninsula ecosystems. The results show a consistent pattern for size of lateral fins, with L. gibbosus that inhabit streams in the Iberian Peninsula having longer lateral fins than those inhabiting reservoirs or lakes. Differences in fin placement, body depth and caudal peduncle dimensions do not differentiate populations of L. gibbosus from lentic and lotic water bodies and, therefore, are not consistent with functional expectations. Lepomis gibbosus from lotic and lentic habitats also do not show a consistent pattern of internal morphological differentiation, probably due to the lack of lotic–lentic differences in prey type. Overall, the univariate and multivariate analyses show that most of the external and internal morphological characters that vary among populations do not differentiate lotic from lentic Iberian populations. The lack of expected differences may be a consequence of the high seasonal flow variation in Mediterranean streams, and the resultant low‐ or no‐flow conditions during periods of summer drought.     

Shallow-soil endemics: adaptive advantages and constraints of a specialized root-system morphology

Worldwide, many rare plant species occur in shallow-soil, drought-prone environments. For most of these species, the adaptations required to be successful in their own habitats, as well as their possible consequences for establishment and persistence in others, are unknown. Here, two rare Hakea (Proteaceae) species confined to shallow-soil communities in mediterranean-climate south-western Australia were compared with four congeners commonly occurring on deeper soils. Seedlings were grown for 7 months in a glasshouse in individual 1.8 x 0.2-m containers, to allow for unconstrained root development. In addition, a reciprocal transplant experiment was carried out. The rare Hakea species differed consistently from their common congeners in their spatial root placement. They invested more in deep roots and explored the bottom of the containers much more quickly. In the reciprocal transplant experiment they showed increased survival in their own habitat, but not in others. This research suggests that shallow-soil endemics have a specialized root system that allows them to explore a large rock surface area, thereby presumably increasing their chance to locate cracks in the underlying rock. However, this root-system morphology may be maladaptive on deeper soils, providing a possible explanation for the restricted distribution of many shallow-soil endemics.     

An evaluation of carbon disulphide as a sulphur fertilizer and as a nitrification inhibitor

There was little release of extractable SO₄-S during four weeks from CS₂ applied by injecting into two S-deficient soils. In this incubation experiment, the rate of CS₂ was 30 μg S g⁻, placement was injection at 9 cm depth, soil temperature was 20°C, and soil moisture tension was 33 kPa. The yield of barley forage after seven weeks in the greenhouse showed only small increases from 10 or 30 μg S g⁻¹ of CS₂ as compared to Na₂SO₄, on the two soils. While CS₂ supplied little plant available S in the short term, it was an effective inhibitor of nitrification. In the laboratory, or in the field, the injection of CS₂ (with N fertilizers) at a point 9 cm into the soils either stopped or reduced nitrification. In one laboratory experiment, 35 μg of CS₂ g⁻¹ of soil with urea reduced nitrification for at least four weeks; and in another experiment 20 μg of CS₂ g⁻¹ of soil with aqua NH₃ nearly or completely inhibited nitrification at 20 days. In two field experiments, 3 and 12 μg of CS₂ g⁻¹ of soil (or 6 and 24 kg ha⁻¹) with aqua NH₃ inhibited nitrification from October to the subsequent May. In addition, CS₂ reduced the amount of ammonium produced from the soil N, both in these two field experiments and in the laboratory experiments. That is to say, CS₂ injected at a point, inhibited both nitrification and ammonification. In other field experiments, CS₂ at a rate of 10 kg ha⁻¹ was injected in bands 9 cm deep with urea in October, and by May there was still reduced nitrification. Less than half of the fall-applied urea alone was recovered as mineral N, but with the application of CS₂ the recovery was increased to three-quarters. The yield and N uptake of barley grain was increased where fall-applied banded urea or aqua NH₃ received banded CS₂, (NH₄)₂CS₃, or K₂CS₃. The average increase in yield from fall-applied fertilizer, from inhibitor with fall-applied fertilizer, and from spring-applied fertilizer was 800, 1370, and 1900 kg ha⁻¹, respectively. In the same order, the apparent % recovery of fertilizer N in grain was 24, 42, and 60.     

Deep placement of Mn fertiliser on a sandy soil increased grain yield and reduced split seed in Lupinus angustifolius

Experiments were conducted over two years with Lupinus angustifolius L. on a site with acid sandy soil near Esperance, Western Australia to determine if deep placed manganese fertilizer increases lupin grain yield. Manganese at 4 and 8 kg ha⁻¹ was placed below the surface immediately before sowing at 4, 20 and 30 cm and 4, 8, 12, 16 and 20 cm in 1987 and 1988 respectively. Foliar Mn applied at 1 kg ha⁻¹ when the first order laterals were in mid-flowering stage, was also compared. Increasing the depth of Mn placement increased grain yield in both years. The deepest placed Mn increased grain yields by 255 kg ha⁻¹ (10%) and 430 kg ha⁻¹ (106%) in year 1 and year 2 over the shallow (4 cm) placed Mn. The higher responses to deep placed Mn occurred in year 2, the year with the driest spring and most intense aphid infestations. Foliar applied Mn was as effective as most deep placed Mn treatments, except for the highest rate (8 kg ha⁻¹) at the greatest depth (20 cm) in year 2. The higher rate of applied Mn gave the best grain yields. This revised version was published online in June 2006 with corrections to the Cover Date.     

胆道支架置入联合介入化疗对恶性胆道梗阻患者肝功能及预后的影响

目的:研究胆道支架置入联合介入化疗对恶性胆道梗阻患者肝功能及预后的影响,为临床治疗提供依据。方法:选取2013年2月到2015年2月我院收治的恶性胆道梗阻患者90例,按照随机数字表法将患者分为Ⅰ组、Ⅱ组和Ⅲ组,每组30例,Ⅰ组给予胆道支架置入联合介入化疗,Ⅱ组给予单纯胆道支架置入,Ⅲ组给予保守治疗,比较三组治疗前、后肝功能、并发症、支架通畅率及生存期。结果:治疗前三组谷草转氨酶(AST)、谷丙转氨酶(ALT)、γ-谷氨酰转移酶(r-GT)比较无统计学意义(P0.05),治疗后Ⅰ组和Ⅱ组AST、ALT和r-GT均显著改善,与治疗前和Ⅲ组比较差异具有统计学意义(P0.05),且I组显著优于Ⅱ组,比较差异具有统计学意义(P0.05),Ⅲ组治疗后AST、ALT和r-GT与治疗前比较差异无统计学意义(P0.05);Ⅰ组、Ⅱ组和Ⅲ组并发症发生率比较无统计学意义(P0.05);Ⅰ组术后3个月、6个月和12个月支架通畅率均显著高于Ⅱ组,比较差异具有统计学意义(P0.05);I组生存期显著高于Ⅱ组和Ⅲ组,Ⅱ组高于Ⅲ组,比较差异具有统计学意义(P0.05)。结论:胆道支架置入联合介入化疗治疗恶性胆道梗阻具有较好效果,能明显改善患者肝功,延长患者生存期。     

Partial Root Drying Effects on Biomass Production in Brassica napus and the Significance of Root Responses

Partial root drying (PRD) has been shown to stimulate stomatal-closure response and improve water-use efficiency and thus biomass production and grain yield under water deficiency. While most studies focus on above-ground responses to PRD, we examined how root responses contributed to effects of partial root drying. In particular, in two experiments with oilseed rape (Brassica napus L.) we investigated whether roots were able to forage for patchily distributed water, and how this affected plant growth compared with uniform watering and alternate watering (in which different parts of the roots receive water alternately). The first pot experiment was carried out in the greenhouse and the second outside under a rain-shelter in which also the watering amount was varied. The results indicate that B. napus roots were able to forage for fixed water patches by selective root placement. In the first experiment with small plants, root foraging was equally effective as enhanced water-use efficiency under alternate watering. Both treatments resulted in about 10% higher shoot biomass compared with uniform watering. Alternate watering generally outperformed uniform watering in the second experiment, but the success depended on the time of harvest and the water supply level. Measurements indicated that only the alternate watering regime effectively reduced stomatal conductance, but lead to a higher shoot biomass only under more severe (50%) rather than under milder water deficiency (70% of a well watered control). Water deficiency strongly reduced leaf initiation rates and leaf sizes in B. napus, but for a given level of water supply the supply pattern (uniform control, fixed patchy or alternate watering) hardly influenced these growth parameters. Although also in the second experiment, the plants selectively placed their roots in the wet parts of the pot, root foraging was not as effective as in the first experiment. Possible reasons for these discrepancies are discussed as well as their implications for the application of PRD effects for crop growth.