Community-wide assessment of protein-interface modeling suggests improvements to design methodology

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.     

Mesostructure of fibrillar bovine serum albumin gels

The mesostructure of bovine serum albumin (BSA) at low pH was investigated. Rheological measurements were performed to determine the critical percolation concentration (c_p). A decreasing c_p with increasing ionic strength was found. Fibrils with a contour length of about 100–300 nm were found using transmission electron microscopy. The measured conversion of monomers into fibrils was independent of ionic strength (0.20–0.30 M). Dilution of BSA samples showed that the aggregation process is reversible and that there exists a critical concentration for the self-assembly of BSA. We explain the decreasing c_p with increasing ionic strength in terms of an adjusted random contact model.     

温度对鳙幼鱼疲劳引起的生理变化和游泳能力的影响研究(英文)

鳙(花鲢)在自然环境中分布于中国南部流域至阿穆尔河,是重要的经济性鱼类,具江湖生殖洄游特性。大坝建设阻碍了其洄游产卵繁殖通道,导致自然环境中其繁殖力的下降,需要有效的过鱼设施帮助鳙通过大坝等水流屏障。为了设计高效的鱼道引导鳙通过,本文通过自制密封的鱼类游泳实验装置,研究了鳙幼鱼游泳能力。测定了5个温度(5、10、15、20和25℃)下鳙幼鱼的临界游泳速度。通过测定不同温度下,疲劳前后血清总蛋白(TP)、血糖(GLU)和甘油三酯(TG)含量,评价疲劳运动引起的生理胁迫。结果表明,在试验温度范围内,随着温度的升高,临界游泳速度显著提高(P0.05)。25℃时临界游泳速度最大,为7.01 BL/s(1.19 m/s)。在疲劳运动后,血清总蛋白、血糖和甘油三酯含量显著升高(P0.05)。水温低于15℃与高于15℃相比,鳙疲劳运动后血清总蛋白、血糖和甘油三酯含量显著升高。以鳙幼鱼为研究对象,研究了非适宜温度环境和疲劳运动胁迫下鱼类的生理反应。以期为鱼类生理学研究和渔业保护管理等领域提供理论依据,为制定有效的鱼道提供数据参考。     

棉花临界需氮量动态定量模型

在大田栽培条件下,于江苏南京和河南安阳两个生态区设置棉花氮素水平试验,基于作物临界氮浓度稀释模型和干物质动态累积模型,建立了棉花花后动态临界氮吸收速率、临界氮需求量的定量化模型.结果表明,两生态区的临界最大氮吸收速率均出现在花后42 d,分别为5.3和4.4 kg·hm^-2·d^-1,临界快速氮累积期分别在花后的23～59 d和23～61 d,安阳的最大临界日需氮量明显大于南京.根据模型得到：安阳生态区适宜施氮量在240～360 kg·hm^-2 之间,且360 kg·hm^-2 条件下其氮累积接近临界需求,南京生态区240 kg·hm^-2施氮量的氮累积与临界值相近.两区域基肥施用量分别占总施肥量的26%和27%,且适宜的追肥时间应在花后22 d左右.由于模型的建立是基于不同氮处理试验,有合理可靠的生理依据,为定量确定不同气候区域的动态施肥量提供了理论依据.     

Bacterial adsorption to thermoresponsive polymer surfaces

The ability of microorganisms to `recognise' a change in the hydrophobicity/hydrophilicity balance of the surface was demonstrated using thermoresponsive poly(N-isopropylacrylamide) co-polymers with different Lower Critical Solution Temperatures. The polymers were grafted onto hydrolysed glass under well controlled conditions and the adhesion was followed using ¹³C-labelled Listeria monocytogenes. Attachment of the bacteria was found to be directly affected by the polymer transition from a hydrophilic to a hydrophobic state but by less than one order of magnitude.     

Subharmonics increase the auditory impact of female koala rejection calls

Although non‐linear phenomena are common in human and non‐human animal vocalisations, their functional relevance remains poorly understood. One theory posits that non‐linear phenomena generate unpredictability in vocalisations, which increases the auditory impact of vocal signals, and makes animals less likely to habituate to call repetition. Female koalas (Phascolarctos cinereus) produce vocal signals when they reject male copulation attempts that contain relatively high levels of non‐linear phenomena, and thus may function as attention grabbing vocal signals during the breeding season. To test this hypothesis, we used playback experiments: firstly, to determine whether female rejection calls induce heightened behavioural responses in free‐ranging male koalas during the breeding season, and secondly, to examine how the relative amount of non‐linear phenomena in rejection calls influences male behavioural response. The results show that male koalas look for longer towards speakers broadcasting playback sequences of male bellows followed by a series of female rejection calls than those broadcasting only male bellows. In addition, female rejection call sequences with more subharmonics, higher harmonics‐to‐noise ratios, and less biphonation produced the greatest male looking responses. Our findings support the hypothesis that female koala rejection calls function to grab male attention during the breeding season, and indicate that subharmonics are the main acoustic feature that increases the auditory impact of these vocal signals.     

硒对水稻的生态毒理效应及临界指标研究

通过土壤添加硒盆栽试验,研究了黄棕壤不同浓度Se对水稻生物量、叶绿素含量、抗氧化酶系统的影响.结果表明,低浓度Se(<8mg·kg^-1)对水稻根和地上生物量、叶绿素a含量、叶绿素a/b有促进作用,并整体提高了作物抗氧化酶系统,使MDA下降,SOD、CAT、POD、GSHPx活性相应提高.而高浓度Se(>16mg·kg^-1)对水稻根和地上生物量、叶绿素a含量、叶绿素a/b有明显的抑制作用,对抗氧化酶系统产生胁迫效应,使GSHPx明显上升,MDA上升,SOD、CAT、POD酶活性明显下降.各项生理指标与土壤Se处理浓度之间相关分析表明,土壤Se浓度与地上部干重相对百分率、根干重百分率、叶绿素a/b、MDA、SOD、CAT、POD之间有显著相关性.比较胁迫效应10%值的临界指标EC10值表明,作物地上部干重抑制率作为土壤临界值制定的依据更为可靠,EC10为21mg·kg^-1.     

Heteroskedasticity as a leading indicator of desertification in spatially explicit data

Regime shifts are abrupt transitions between alternate ecosystem states including desertification in arid regions due to drought or overgrazing. Regime shifts may be preceded by statistical anomalies such as increased autocorrelation, indicating declining resilience and warning of an impending shift. Tests for conditional heteroskedasticity, a type of clustered variance, have proven powerful leading indicators for regime shifts in time series data, but an analogous indicator for spatial data has not been evaluated. A spatial analog for conditional heteroskedasticity might be especially useful in arid environments where spatial interactions are critical in structuring ecosystem pattern and process. We tested the efficacy of a test for spatial heteroskedasticity as a leading indicator of regime shifts with simulated data from spatially extended vegetation models with regular and scale‐free patterning. These models simulate shifts from extensive vegetative cover to bare, desert‐like conditions. The magnitude of spatial heteroskedasticity increased consistently as the modeled systems approached a regime shift from vegetated to desert state. Relative spatial autocorrelation, spatial heteroskedasticity increased earlier and more consistently. We conclude that tests for spatial heteroskedasticity can contribute to the growing toolbox of early warning indicators for regime shifts analyzed with spatially explicit data.     

Combination stem cell therapy using dental pulp stem cells and human umbilical vein endothelial cells for critical hindlimb ischemia

Narrowing of arteries supplying blood to the limbs provokes critical hindlimb ischemia (CLI). Although CLI results in irreversible sequelae, such as amputation, few therapeutic options induce the formation of new functional blood vessels. Based on the proangiogenic potentials of stem cells, in this study, it was examined whether a combination of dental pulp stem cells (DPSCs) and human umbilical vein endothelial cells (HUVECs) could result in enhanced therapeutic effects of stem cells for CLI compared with those of DPSCs or HUVECs alone. The DPSCs+ HUVECs combination therapy resulted in significantly higher blood flow and lower ischemia damage than DPSCs or HUVECs alone. The improved therapeutic effects in the DPSCs+ HUVECs group were accompanied by a significantly higher number of microvessels in the ischemic tissue than in the other groups. In vitro proliferation and tube formation assay showed that VEGF in the conditioned media of DPSCs induced proliferation and vessel-like tube formation of HUVECs. Altogether, our results demonstrated that the combination of DPSCs and HUVECs had significantly better therapeutic effects on CLI via VEGF-mediated crosstalk. This combinational strategy could be used to develop novel clinical protocols for CLI proangiogenic regenerative treatments.