A link surgery spectral sequence in monopole Floer homology

To a link L⊂S³, we associate a spectral sequence whose E² page is the reduced Khovanov homology of L and which converges to a version of the monopole Floer homology of the branched double cover. The pages Ek for k?2 depend only on the mutation equivalence class of L. We define a mod 2 grading on the spectral sequence which interpolates between the δ-grading on Khovanov homology and the mod 2 grading on Floer homology. We also derive a new formula for link signature that is well adapted to Khovanov homology.More generally, we construct new bigraded invariants of a framed link in a 3-manifold as the pages of a spectral sequence modeled on the surgery exact triangle. The differentials count monopoles over families of metrics parameterized by permutohedra. We utilize a connection between the topology of link surgeries and the combinatorics of graph-associahedra. This also yields simple realizations of permutohedra and associahedra, as refinements of hypercubes.     

Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study

We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree–Fock (HF)/6‐31G*, HF/6‐31G**, second‐order Møller–Plesset perturbation (MP2)/6‐31G*, and MP2/6‐31G** levels for three Src homology 3 (SH3) domains and five proline‐recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline‐rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline‐rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

土壤和沉积物中持久性有机污染物分析的不确定度评估

土壤和沉积物中POPs分析过程中的不确定度来源于样品制备、运输和保存、前处理和分析4个环节.土壤经四分法采样、均质化制样、快速溶剂萃取、多层符合硅胶柱净化、GC/MS分析.以p,p'-DDT为例,评定了各环节不确定度的大小,结果表明:样品前处理的不确定度分量对合成不确定度的贡献最大,约占90.6%;样品制备、保存和分析...     

Persistent organochlorines in human breast milk from Al-Sharkia Governorate,Egypt

In the present study, 23 human breast milk samples were collected in January 2009 from Fakous city, Al-Sharkia Governorate, Egypt. The samples were analysed for organochlorine pesticides such as dichlorodiphenyltrichloroethane (DDT) and its metabolites, α, β, and γ-hexachlorocyclohexane (HCH) isomers. The average concentrations of ΣHCHs and ΣDDTs were 225 and 1315?ng?g^?1 lipid respectively. There was no significant difference between the levels of OCP and mother age, while there was a significant difference and correlation between the levels of OCP and the number of times the mother had breast fed (primiparae and multiparae) (p?<?0.05). The results suggested that DDT is still entering the environment depending on the observed ratio of DDE/DDT. The levels of OCP in human milk elucidated that we need to do more regular pollutant monitoring programs.     

Development and Evaluation of Sampling and Analytical Techniques for Investigating Air-Water Exchange of Chemicals

Abstract

Gas exchange across the air-water interface is one of the three major transport pathways for atmospheric inputs of organic pollutants in the Great Lakes. It is essential to advance our knowledge of the air-water exchange processes to improve our understanding of the environmental pathways and fate of a variety of persistent and toxic chemicals. Two complementary prototype devices were developed and tested for direct characterization of air-water exchange processes. One was a sparger device which was used to determine the (truly) dissolved concentration of a given chemical in water, and hence its potential for diffusive transfer at the air-water interface. The other was a flux chamber with which the chemical mass transfer rate from the water surface to the atmosphere (or vice versa) was determined. Ambient air and air from the sparger and flux chamber were collected/concentrated on multi-bed adsorbent tubes, followed by thermal desorption GC-MS analysis. Collected water samples were filtered and then concentrated on adsorbent tubes which were subject to similar thermal desorption GC-MS analytical procedures. The combination of these techniques provides a useful means for the estimation of the mass transfer rates of chemicals across the air-water interface.     

Internet resources in GPCR modelling1

G-Protein coupled receptors (GPCRs), one of the most important families of drug targets, belong to the super family of integral membrane proteins characterized by seven transmembrane helices. Because they are difficult to crystallize, the three dimensional structure of these receptors have not yet been determined by X-ray crystallography, except one. In the absence of a 3-D structure, in-silico approaches for solving the structure of this class of proteins are widely used and provide valuable information for structure based drug design. There are several web servers and computer programs available that automate the modelling process of GPCRs. Some of these include Modeller, Swiss-Model server, Homer, etc. Using these tools reliable homology models of human histamine H1 receptor (HRH1) and thrombin receptor (PAR-1) have been generated which explain the binding mode of the standard antagonists of these receptors and may be useful in designing their novel antagonists.     

Donaldson's theorem,Heegaard Floer homology,and knots with unknotting number one

We establish an obstruction to unknotting an alternating knot by a single crossing change. The obstruction is lattice-theoretic in nature, and combines Donaldson's diagonalization theorem with an obstruction developed by Ozsváth and Szabó using Heegaard Floer homology. As an application, we enumerate the alternating 3-braid knots with unknotting number one, and show that each has an unknotting crossing in its standard alternating diagram.     

Restriction to compact subgroups in the cyclic homology of reductive p-adic groups

Restriction of functions from a reductive p-adic group G to its compact subgroups defines an operator on the Hochschild and cyclic homology of the Hecke algebra of G. We study the commutation relations between this operator and others coming from representation theory: Jacquet functors, idempotents in the Bernstein centre, and characters of admissible representations.     

In silico models for predicting vector control chemicals targeting Aedes aegypti

Human arboviral diseases have emerged or re-emerged in numerous countries worldwide due to a number of factors including the lack of progress in vaccine development, lack of drugs, insecticide resistance in mosquitoes, climate changes, societal behaviours, and economical constraints. Thus, Aedes aegypti is the main vector of the yellow fever and dengue fever flaviviruses and is also responsible for several recent outbreaks of the chikungunya alphavirus. As for the other mosquito species, the A. aegypti control relies heavily on the use of insecticides. However, because of increasing resistance to the different families of insecticides, reduction of Aedes populations is becoming increasingly difficult. Despite the unquestionable utility of insecticides in fighting mosquito populations, there are very few new insecticides developed and commercialized for vector control. This is because the high cost of the discovery of an insecticide is not counterbalanced by the ‘low profitability’ of the vector control market. Fortunately, the use of quantitative structure–activity relationship (QSAR) modelling allows the reduction of time and cost in the discovery of new chemical structures potentially active against mosquitoes. In this context, the goal of the present study was to review all the existing QSAR models on A. aegypti. The homology and pharmacophore models were also reviewed. Specific attention was paid to show the variety of targets investigated in Aedes in relation to the physiology and ecology of the mosquito as well as the diversity of the chemical structures which have been proposed, encompassing man-made and natural substances.     

细胞死亡蛋白的三维结构及活性位点的理论研究

利用同源模建和分子动力学模拟方法,构建了细胞死亡蛋白（CED-10）的三维结构,并预测了其可能的活性位点,为细胞死亡蛋白家族催化机理的深入研究提供了、重要的参考信息．