Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Synthesis and biological characterization of new aryloxyindole-4,9-diones as potent trypanosomicidal agents

A new indole-4,9-dione and their phenoxy derivatives were synthesized and evaluated in vitro against the epimastigote form of Trypanosoma cruzi, Y strain. All of these novel compounds were found to be extremely potent and selective that the standard drug nifurtimox. Interestingly, phenoxyindole-4,9-dione 9d displayed excellent nanomolar inhibitory activity, IC₅₀ = 20 nM, and high selectivity index, SI = 625. In silico studies using MOE program were performed to generate a preliminary pharmacophore model.     

Raking Kappa: Describing Potential Impact of Marginal Distributions on Measures of Agreement

Several authors have noted the dependence of kappa measures of inter-rater agreement on the marginal distributions of contingency tables displaying the joint ratings. This paper introduces a smoothed version of kappa computed after raking the table to achieve pre-specified marginal distributions. A comparison of kappa with raked kappa for various margins can indicate the extent of the dependence on the margins, and can indicate how much of the lack of agreement is due to marginal heterogeneity.     

A new species of Megalonychidae (Mammalia, Xenarthra) from the Quaternary of Poço Azul (Bahia, Brazil)

The new genus and species Ahytherium aureum (Mammalia, Xenarthra, Megalonychidae) from the Quaternary of Poço Azul (Bahia, Brazil) is described. It is the first Brazilian megalonychid known from reasonably complete and well-preserved remains. Purported Brazilian megalonychids described in the past, such as Ocnopus gracilis and Xenocnus cearesis, are noted as belonging to other sloth clades, and the acceptance by past paleontologists of the existence of ‘strange’ megalonychids in Brazil is shown to be erroneous. Ahytherium aureum, in fact, exhibits typical megalonychid morphology. It differs from other known members of Megalonychidae in several characters, including a markedly shortened, but high rostral region, with dorsally inflated frontals, wide zygomatic processes of the frontal, narrow, blade-like and anterolaterally oriented lacrimals, curved, slender and oval caniniforms, gracile humerus with less developed deltopectoral shelf, and relatively distal position of the greater trochanter of the femur. A second specimen from São Paolo state is tentatively assigned to the new genus and species.     

Feral cat diet and impact on sooty terns at Juan de Nova Island, Mozambique Channel

Feral cat Felis catus predation on seabirds has been well documented; however, details regarding shifts in feral cat diet in relation to seabird availability, seabird predation rate and impact on seabird population dynamics are scarce. Here, we present data documenting a seasonal shift in feral cat diet at Juan de Nova Island, Mozambique Channel. We also quantify sooty tern Sterna fuscata predation by feral cats and examine the impact on sooty terns over both the short term (by removing individual cats from sub-colonies) and over the longer term by highlighting their influence on population growth rate ( λ ) using a deterministic matrix model. Cat diet shifted dramatically from insects, rats and mice outside the tern breeding season to primarily terns when terns were breeding. The predation rate of sooty terns at Juan de Nova was estimated at 5.94 terns cat⁻¹ day⁻¹, with a proportion of these (22%) being killed without being consumed ('surplus kills'). When only one cat was removed from each sub-colony, tern predation declined tenfold in the short term. From our matrix model, the annual growth rate for sooty terns was 1.01 in the absence of cat predation. It remained above one until a predation impact equivalent to approximately three times the estimated cat density (12.04 per km²) was incorporated. Our results demonstrate that cats preferentially predate and have an impact on breeding sooty terns at Juan de Nova, and that an increase in cat density could lead to negative effects on population growth, despite the large breeding tern population.     

Signalling of information that is neither cryptic nor private

It is commonly assumed that in order for animal signals to be advantageous, the information being signalled could not have been obtained otherwise, and is therefore ‘cryptic’ or ‘private’. Here, we suggest a scenario in which individuals can gain an advantage by signalling ‘public’ information that is neither cryptic nor private. In that scenario, signalling increases the efficiency with which that ‘public’ information is transmitted. We formalize our idea with a game in which offspring can signal their condition to their parents. Specifically, we consider a resource‐strapped parent who can only invest in one of its two offspring, and we allow offspring the chance to influence parental investment through a signal. A parent in the game seeks to invest in the higher‐quality offspring, which it could identify either through a publicly available cue, such as body size, or by relying on a signal provided by the offspring. We find that if the signal can convey information about offspring quality more efficiently than cues, then signalling of condition between offspring and parents can be favoured by selection, even though parents could potentially have acquired the same information from the cue. Our results suggest that the biological function of signals may be broader than currently considered, and provide a scenario where low cost signalling can be favoured. More generally, efficiency benefits could explain signalling across a range of biological and economic scenarios.     

2001-2010年疏勒河流域植被净初级生产力时空变化及其与气候因子的关系

通过改进的光能利用率CASA模型估算2001-2010年间疏勒河流域陆地生态系统的净第一性生产力（NPP），采用线性趋势分析、变异系数和Hurst指数等方法，分析了NPP的时空变化特征及其与气候因子的相关性。结果表明：①疏勒河流域NPP的空间分布具有明显差异，空间上呈现西北低、东南高的趋势，且具有较明显的经向"条带"分布特征，2001-2010年，NPP平均值为102.26 gC m^-2 a^-1。②2001-2010年，疏勒河流域NPP总体呈增长趋势，年际波动较大，NPP明显增加的区域占总面积25.15%，明显减小的区域约占11.93%。③Hurst指数分析显示，疏勒河流域NPP变化的同向特征强于反向特征，其中持续改善地区占总面积的78.3%，21.7%的区域将由改善转为退化。④在年尺度上，降水是植被NPP变化的主要影响因素，NPP与降水呈弱的正相关关系，与温度相关性不显著；在月尺度上，温度是NPP变化的主要控制因子。疏勒河流域NPP对气候因子不存在明显的时滞和累积效应。     

吉林蛟河针阔混交林树木生长的空间关联格局

以吉林蛟河21.12hm2(660m×320m)针阔混交林样地为对象,利用2009年和2014年森林生长观测数据,研究树木生长的空间自相关格局及其生境影响机制。在样地生境型划分结果的基础上,采用Ripley's L(r)函数分析不同生境型中树木种群空间分布特征;利用标记相关函数分析不同生境型中树木生长特征的空间关联格局。研究结果表明:(1)红松(生境型3:1—5m)、蒙古栎(生境型3:1—3m)、胡桃楸(生境型2:1—2m;生境型3:1—7m)、黄檗(生境型2:1—3m;生境型4:1—5m)、水曲柳(生境型3:1—2m;生境型4:1—2m)、瘤枝卫矛(生境型2:1—15m)在特定生境和空间尺度上呈随机分布,但空间格局仍以聚集性分布为主;其余10个物种则在全部0—30m尺度上呈聚集分布。(2)标记相关函数分析显示春榆、毛榛、色木槭、瘤枝卫矛和千金榆的径向生长至少在一个生境中表现出正相关格局;暴马丁香、胡桃楸、裂叶榆、瘤枝卫矛、水曲柳、紫椴、糠椴、毛榛、色木槭和白牛槭的径向生长至少在一个生境中表现出负相关格局;红松、黄檗、蒙古栎和簇毛槭的径向生长在全部尺度上均未检测到显著的空间关联格局。因此,不同树种径向生长的空间自相关特征不同,树种生长特征的空间关联格局具有明显的生境依赖性。