Prediction of protein-protein binding free energies

We present an energy function for predicting binding free energies of protein-protein complexes, using the three-dimensional structures of the complex and unbound proteins as input. Our function is a linear combination of nine terms and achieves a correlation coefficient of 0.63 with experimental measurements when tested on a benchmark of 144 complexes using leave-one-out cross validation. Although we systematically tested both atomic and residue-based scoring functions, the selected function is dominated by residue-based terms. Our function is stable for subsets of the benchmark stratified by experimental pH and extent of conformational change upon complex formation, with correlation coefficients ranging from 0.61 to 0.66.     

昆仑岩黄耆(豆科)在中国的分布

报道了豆科Leguminosae昆仑岩黄耆Hedysarum krassnovii B．Fedtsch．在中国的分布。昆仑岩黄耆与近缘种红花岩黄耆H.multijugum Maxim.形态易混淆,但以其小叶3-9×3-7mm;旗瓣倒卵形,顶端凹陷约2mm深;翼瓣狭披针形;龙骨瓣近半圆形或矩圆形;花萼二唇彤;荚果具1-2节荚等性状易于区分。另外,此二种的物候期、生境及地理分布亦有区别。     

Bacterial biosurfactant increases ex situ biodiesel bioremediation in clayey soil

The contamination of soils by oily compounds has several environmental impacts, which can be reversed through bioremediation, using biosurfactants as auxiliaries in the biodegradation process. In this study, we aimed to perform ex situ bioremediation of biodiesel-contaminated soil using biosurfactants produced by Bacillus methylotrophicus. A crude biosurfactant was produced in a whey-based culture medium supplemented with nutrients and was later added to biodiesel-contaminated clayey soil. The produced lipopeptide biosurfactant could reduce the surface tension of the fermentation broth to 30.2 mN/m. An increase in the microbial population was observed in the contaminated soil; this finding can be corroborated by the finding of increased CO₂ release over days of bioremediation. Compared with natural attenuation, the addition of a lower concentration of the biosurfactant (0.5% w/w in relation to the mass of diesel oil) to the soil increased biodiesel removal by about 16% after 90 days. The added biosurfactant did not affect the retention of the contaminant in the soil, which is an important factor to be considered when applying in situ bioremediation technologies.

     

PCB-153 Shows Different Dynamics of Mobilisation from Differentiated Rat Adipocytes during Lipolysis in Comparison with PCB-28 and PCB-118

Background

Polychlorinated biphenyls (PCBs) are persistent organic pollutants. Due to their lipophilic character, they are preferentially stored within the adipose tissue. During the mobilisation of lipids, PCBs might be released from adipocytes into the bloodstream. However, the mechanisms associated with the release of PCBs have been poorly studied. Several in vivo studies followed their dynamics of release but the complexity of the in vivo situation, which is characterised by a large range of pollutants, does not allow understanding precisely the behaviour of individual congeners. The present in vitro experiment studied the impact of (i) the number and position of chlorine atoms of PCBs on their release from adipocytes and (ii) the presence of other PCB congeners on the mobilisation rate of such molecules.

Methodology/Principal Findings

Differentiated rat adipocytes were used to compare the behaviour of PCB-28, -118 and -153. Cells were contaminated with the three congeners, alone or in cocktail, and a lipolysis was then induced with isoproterenol during 12 hours. Our data indicate that the three congeners were efficiently released from adipocytes and accumulated in the medium during the lipolysis. Interestingly, for a same level of cell lipids, PCB-153, a hexa-CB with two chlorine atoms in ortho-position, was mobilised slower than PCB-28, a tri-CB, and PCB-118, a penta-CB, which are both characterised by one chlorine atom in ortho-position. It suggests an impact of the chemical properties of pollutants on their mobilisation during periods of negative energy balance. Moreover, the mobilisation of PCB congeners, taken individually, did not seem to be influenced by the presence of other congeners within adipocytes.

Conclusion/Significance

These results not only highlight the obvious mobilisation of PCBs from adipocytes during lipolysis, in parallel to lipids, but also demonstrate that the structure of congeners defines their rate of release from adipocytes.     

Current Concepts and Future Directions in Differentiated Thyroid Cancer

This paper provides an overview on the biology, monitoring and management of differentiated thyroid cancer (DTC), with particular attention to issues of relevance to clinical chemistry. The incidence of DTC appears to be increasing and management strategies are evolving as we learn more about its natural history and response to therapy. Clinical chemistry techniques play a central role in these protocols. Technical limitations inherent in current monitoring tools can hamper follow-up, although progress is being made. The molecular basis of DTC is being delineated with the potential to develop new strategies for diagnosis, monitoring and management of this condition.     

Hyperbaric oxygen inhibits neutrophil infiltration and reduces postischemic brain injury in rats

Reversible occlusion of the middle cerebral artery (MCA) was used to test hypothesis that hyperbaric oxygen inhibits the neutrophile infiltration into the ischemic brain thus reducing the brain injury. Treatment with hyperbaric oxygen prior to ischemia or during MCA occlusion significantly reduced neutrophile infiltration, motor disorders, and cerebral infarction volume.     

“山水林田湖草沙生命共同体”耦合框架、模型与展望

“山水林田湖草沙生命共同体”系统保护与修复是我国生态文明建设的重要内容。明确生命共同体的耦合机制,是科学地进行生态保护和修复工作的关键。针对当前生命共同体耦合机制不清、理论和方法不健全的问题,从耦合的视角出发,在小流域尺度上单一生态系统内部生态要素的耦合、流域尺度上不同生态系统之间的耦合、区域尺度上人与自然的耦合三个方面进行整合,在此基础上探讨了多尺度山水林田湖草沙耦合理论,提出了一般性的山水林田湖草沙耦合理论框架。梳理并比较了当前主要的生态系统模型、景观模型、统计学模型以及复合生态系统的多模型耦合方法,综合提出了一个适用于"山水林田湖草沙生命共同体"耦合研究方法。对进一步完善山水林田湖草沙一体化保护修复提出了建议,包括：一是构建多源信息数据库,推进定量化耦合机制研究;二是开展全生命周期监测与评估,探索适应性治理路径;三是强化多元主体参与,完善协同保护机制。     

Effects of transmural pressure and wall shear stress on LDL accumulation in the arterial wall: a numerical study using a multilayered model

The accumulation of low-density lipoprotein (LDL) is recognized as one of the main contributors in atherogenesis. Mathematical models have been constructed to simulate mass transport in large arteries and the consequent lipid accumulation in the arterial wall. The objective of this study was to investigate the influences of wall shear stress and transmural pressure on LDL accumulation in the arterial wall by a multilayered, coupled lumen-wall model. The model employs the Navier-Stokes equations and Darcy's Law for fluid dynamics, convection-diffusion-reaction equations for mass balance, and Kedem-Katchalsky equations for interfacial coupling. To determine physiologically realistic model parameters, an optimization approach that searches optimal parameters based on experimental data was developed. Two sets of model parameters corresponding to different transmural pressures were found by the optimization approach using experimental data in the literature. Furthermore, a shear-dependent hydraulic conductivity relation reported previously was adopted. The integrated multilayered model was applied to an axisymmetric stenosis simulating an idealized, mildly stenosed coronary artery. The results show that low wall shear stress leads to focal LDL accumulation by weakening the convective clearance effect of transmural flow, whereas high transmural pressure, associated with hypertension, leads to global elevation of LDL concentration in the arterial wall by facilitating the passage of LDL through wall layers.     

Vesicles carry most exocyst subunits to exocytic sites marked by the remaining two subunits, Sec3p and Exo70p

Exocytosis in the budding yeast Saccharomyces cerevisiae occurs at discrete domains of the plasma membrane. The protein complex that tethers incoming vesicles to sites of secretion is known as the exocyst. We have used photobleaching recovery experiments to characterize the dynamic behavior of the eight subunits that make up the exocyst. One subset (Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, and Exo84p) exhibits mobility similar to that of the vesicle-bound Rab family protein Sec4p, whereas Sec3p and Exo70p exhibit substantially more stability. Disruption of actin assembly abolishes the ability of the first subset of subunits to recover after photobleaching, whereas Sec3p and Exo70p are resistant. Immunogold electron microscopy and epifluorescence video microscopy indicate that all exocyst subunits, except for Sec3p, are associated with secretory vesicles as they arrive at exocytic sites. Assembly of the exocyst occurs when the first subset of subunits, delivered on vesicles, joins Sec3p and Exo70p on the plasma membrane. Exocyst assembly serves to both target and tether vesicles to sites of exocytosis.