Survey of chemical speciation of trace elements using synchrotron radiation

Information concerning the chemical state of trace elements in biological systems generally has not been available. Such information for toxic elements and metals in metalloproteins could prove extremely valuable in the elucidation of their metabolism and other biological processes. The shielding of core electrons by binding electrons affect the energy required for creating inner-shell holes. Furthermore, the molecular binding and symmetry of the local environment of an atom affect the absorption spectrum in the neighborhood of the absorption edge. X-ray absorption near-edge structure (XANES) using synchrotron radiation excitation can be used to provide chemical speciation information for trace elements at concentrations as low as 10 ppm. The structure and position of the absorption curve in the region of an edge can yield vital data about the local structure and oxidation state of the trace element in question. Data are most easily interpreted by comparing the observed edge structure and position with those of model compounds of the element covering the entire range of possible oxidation states. Examples of such analyses will be reviewed.     

A continuum model to study the internal fluctuations in globular proteins

The salient features of the differential equation model to study protein dynamics are presented with results for 19 proteins.     

Do salt bridges stabilize proteins? A continuum electrostatic analysis

The electrostatic contribution to the free energy of folding was calculated for 21 salt bridges in 9 protein X-ray crystal structures using a continuum electrostatic approach with the DELPHI computer-program package. The majority (17) were found to be electrostatically destabilizing; the average free energy change, which is analogous to mutation of salt bridging side chains to hydrophobic isosteres, was calculated to be 3.5 kcal/mol. This is fundamentally different from stability measurements using pKa shifts, which effectively measure the strength of a salt bridge relative to 1 or more charged hydrogen bonds. The calculated effect was due to a large, unfavorable desolvation contribution that was not fully compensated by favorable interactions within the salt bridge and between salt-bridge partners and other polar and charged groups in the folded protein. Some of the salt bridges were studied in further detail to determine the effect of the choice of values for atomic radii, internal protein dielectric constant, and ionic strength used in the calculations. Increased ionic strength resulted in little or no change in calculated stability for 3 of 4 salt bridges over a range of 0.1-0.9 M. The results suggest that mutation of salt bridges, particularly those that are buried, to "hydrophobic bridges" (that pack at least as well as wild type) can result in proteins with increased stability. Due to the large penalty for burying uncompensated ionizable groups, salt bridges could help to limit the number of low free energy conformations of a molecule or complex and thus play a role in determining specificity (i.e., the uniqueness of a protein fold or protein-ligand binding geometry).     

植物水分来源稳定氢氧同位素偏移研究进展

稳定氢氧同位素技术能有效计算植物根系水分吸收量,确定植物水分来源贡献,评估植物水分利用策略,是生态水文学探究大气-植被-土壤系统水分传输过程机制的有效工具。然而土壤与木质部水稳定氢氧同位素比值(δ²H和δ¹⁸O)偏移造成植物水分来源贡献率计算偏差,引起氢氧同位素结果差异的原因尚不明晰。该文首先简要介绍氢氧稳定同位素比值偏移现象,其次沿水分在土壤-植物-大气连续体中的传输路径构建梳理框架,系统阐述了3个界面(植物-大气界面、土壤-大气界面和根系-土壤界面)与2个空间(植物体和土壤层)中引起δ²H与δ¹⁸O偏移的自然效应,同时概述了土壤与木质部样品提取与测定技术中引起δ²H与δ¹⁸O偏差的人为效应。最后,根据现有研究进展提出主要问题,从获取同位素时空数据,微尺度同位素偏移原因,提取与测定技术的优化三方面指出未来的发展方向。     

Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories.

This paper explores the dependence of the molecular dynamics (MD) trajectory of a protein molecule on the titration state assigned to the molecule. Four 100-ps MD trajectories of bovine pancreatic trypsin inhibitor (BPTI) were generated, starting from two different structures, each of which was held in two different charge states. The two starting structures were the X-ray crystal structure and one of the solution structures determined by NMR, and the charge states differed only in the ionization state of N terminus. Although it is evident that the MD simulations were too short to sample fully the equilibrium distribution of structures in each case, standard Poisson-Boltzmann titration state analysis of the resulting configurations shows general agreement between the overall titration behavior of the protein and the charge state assumed during MD simulation: at pH 7, the total net charge of the protein resulting from the titration analysis is consistently lower for the protein with the N terminus assumed to be neutral than for the protein with the N terminus assumed to be charged. For most of the ionizable residues, the differences in the calculated pKaS among the four trajectories are statistically negligible and remain in good agreement with the data obtained by crystal structure titration and by experiment. The exceptions include the N terminus, which responds directly to the change of its imposed charge; the C terminus, which in the NMR structure interacts strongly with the former; and a few other residues (Arg 1, Glu 7, Tyr 35, and Arg 42) whose pKaS reflect the initial structure and the limited trajectory lengths. This study illustrates the importance of the careful assignment of protonation states at the start of MD simulations and points to the need for simulation methods that allow for the variation of the protonation state in the calculation of equilibrium properties.     

Use of stream order and biological indices to assess water quality in the Osage and Black river basins of Missouri

Significant variations in four biological measures of water quality with stream order and river basin were demonstrated for streams of the Black and Osage river basins of Missouri. Water quality criteria specific for each order and basin were then developed.Benthic macroinvertebrates from springs and stream orders 3–8 in the two river basins were sampled quarterly for one year with riffle nets and artificial substrate samplers. A total of 548 samples were taken at 137 stations. The average annual macroinvertebrate density, index of diversity, number of taxa, and number of mayfly and stonefly taxa were determined for each station. These measures showed significant differences (p < 0.05) across stream order within and between the two river basins. Total taxa, total mayfly and stonefly taxa, and diversity were highest in orders 4 and 5 with decreased values in lower and higher stream orders. Maximum organism densities occurred in intermediate order streams. These differences were attributed to the succession of physical changes from headwaters to mouth within each river and to the unique geomorphology of each catchment basin.Water quality criteria based on three of the four measures described above (with 95% confidence limits) were established for each stream order in each river basin. Criteria for the Osage River basin were then used to identify three streams in the basin affected by environmental disturbances (stream impoundment, channelization and sewage discharge). The use of order- and basin-specific criteria assures that the biological differences between streams caused by environmental disturbance can be distinguished from the natural biological differences between streams of different orders and drainages.     

The cosmopolitics of flow and healing in north‐central Timor‐Leste

In north central Timor‐Leste, multi‐sensory ecological engagement is deeply entangled with conceptualisations of and approaches to people’s wellbeing. How people understand human health and wellbeing is closely related to how they understand nature or more particularly human/nature relations and distinctions across multiple timescales. Working through complex cosmopolitics and activated through cross‐temporal more‐than‐human ‘mutualities of being’, kinship networks are attuned to relational flows between ‘bodies’ and things. Rather than concentrating on the disjunctions created by the differences in the natures of beings or their ritual separation, this paper examines how relational flows between such ‘bodies’ and things open up cosmopolitical spaces for the creation and negotiation of intergenerational wellbeing.     

Is population subdivision different from speciation? From phylogeography to species delimitation

Species‐level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model‐based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.     

人为干扰对溪流鱼类功能多样性及其纵向梯度格局的影响

溪流鱼类多样性沿着河流纵向梯度的空间分布规律已得到大量报道, 但这些研究大多聚焦基于物种组成的分类α多样性, 而有关分类β多样性和功能多样性的纵向梯度分布规律及其对人类干扰的响应研究较少。本文以青弋江上游3条人为干扰程度不同的河源溪流为研究区域, 比较研究了人为干扰对溪流鱼类功能α和β多样性及其纵向梯度分布格局的影响。结果显示, 人类干扰改变了河源溪流鱼类功能多样性的纵向梯度格局——由线性变化变为二项式分布。此外, 我们发现, 人为干扰导致土著种被本地入侵种取代, 且较强的土地利用和水污染排放可能增大环境的不连续性, 而群落周转和嵌套变化往往取决于环境的变化。尽管功能β多样性由嵌套成分主导, 但周转成分占比相对于人为干扰较小的溪流而言明显增加。人为干扰显著改变了受干扰溪流鱼类的物种组成和功能多样性, 且功能多样性的纵向梯度格局在不同的多样性指标上存在差异。本研究强调, 在评估人为干扰下多样性的变化时, 需要从多方面考虑, 包括空间尺度和多样性指标等。