The order of the differentials in the Atiyah-Hirzebruch spectral sequence

LetF _* be the homology theory corresponding to a spectrumF and consider the Atiyah-Hirzebruch spectral sequenceE _s,t ² H _s (X; _t F) F _s+t (X) for a bounded below spectrum (or CW-complex)X. This paper shows that the images of the differentials d _s,t ^r :E _s,t ^r E _s ^{–r,t+r–1r} in this spectral sequence are always torsion groupsof finite exponent and that this exponent isbounded in a very universal way: we prove the existence of integersR _r forr2 such thatR _r d _s,t ^r =0 for any spectrumF, for any bounded below spectrumX and for all integersr2,s andt. The interesting point is that these upper boundsR _r for the additive order of the differentials d _s,t ^r dependonly onr, and that the result holds without any hypothesis on the spectrumF. In certain special cases, this implies that the spectral sequence collapses and even that the extension problems given by itsE -term are trivial.     

Topological entropy for geodesic flows on fibre bundles over rationally hyperbolic manifolds

Let be the total space of a fibre bundle with base a simply connected manifold whose loop space homology grows exponentially for a given coefficient field. Then we show that for any Riemannian metric on , the topological entropy of the geodesic flow of is positive. It follows then, that there exist closed manifolds with arbitrary fundamental group, for which the geodesic flow of any Riemannian metric on has positive topological entropy.

     

Recovery of known T-cell epitopes by computational scanning of a viral genome

A new computational method (EpiDock) is proposed for predicting peptide binding to class I MHC proteins, from the amino acid sequence of any protein of immunological interest. Starting from the primary structure of the target protein, individual three-dimensional structures of all possible MHC-peptide (8-, 9- and 10-mers) complexes are obtained by homology modelling. A free energy scoring function (Fresno) is then used to predict the absolute binding free energy of all possible peptides to the class I MHC restriction protein. Assuming that immunodominant epitopes are usually found among the top MHC binders, the method can thus be applied to predict the location of immunogenic peptides on the sequence of the protein target. When applied to the prediction of HLA-A^*0201-restricted T-cell epitopes from the Hepatitis B virus, EpiDock was able to recover 92% of known high affinity binders and 80% of known epitopes within a filtered subset of all possible nonapeptides corresponding to about one tenth of the full theoretical list.The proposed method is fully automated and fast enough to scan a viral genome in less than an hour on a parallel computing architecture. As it requires very few starting experimental data, EpiDock can be used: (i) to predict potential T-cell epitopes from viral genomes (ii) to roughly predict still unknown peptide binding motifs for novel class I MHC alleles.     

The sequence homologies of cytochromes P-450 and active-site geometries

Summary The amino acid sequence alignment of 16 cytochrome P-450 proteins representative of the major families is reported. The sequence matching process has been carried out on the basis of maximum homology by residue type, retention of secondary structure and minimization of deletions/insertions except where additional loop regions exist. From the starting point of known reported sequence homology matching from the literature, a realignment on the basis of conserved residues involved in both structure and function gives rise to a self-consistent set of sequences which correlates with known mechanistic and structural data. Once fitted, these archetypal sequences form a straightforward template for the alignment of all P-450 subfamilies. Computer modelling of the active-site regions constructed from homology with the bacterial form of the enzyme (P-450_CAM) evinces the correct substrate specificity. Furthermore, the construction of the macromolecular assembly of components of the cytochrome P-450 system on the microsomal endoplasmic reticular membrane is presented from the evidence of site-directed mutagenesis, analysis by molecular probes, X-ray crystallography and molecular modelling.     

铝酸盐紫色长时发光材料的研制

采用高温固相法制备了紫色长时发光材料CaAl2O4∶Eu2 , Nd3 . 研究了原料配比、激活剂和助熔剂含量、烧结温度、保温时间、还原气氛等对材料长时发光性能的影响. 当原料中Ca和Al的摩尔比为1.0∶2.3, 激活剂Eu2 含量为0.005 mol/mol, 助熔剂含量为1.6% (质量分数), 烧结温度为1350 ℃, 保温时间为4 h, 在氢气气氛下还原时, 所制得的材料的长时发光性能最佳. 当在原料中掺杂了辅助激活剂Nd3 后, 发光材料的初始发光亮度和发光时间都有了明显的提高.     

CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data

We describe CHASE, a novel algorithm for automated de novo sequencing based on the mass spectrometric (MS) fragmentation analysis of tryptic peptides. This algorithm is used for protein identification from sequence similarity criteria and consists of four steps: (1) derivatization of tryptic peptides at the N-terminus with a negatively charged reagent; (2) post-source decay (PSD) fragmentation analysis of peptides; (3) interpretation of the mass peaks with the CHASE algorithm and reconstruction of the amino acid sequence; (4) transfer of these data to software for protein identifications based on sequence homology (Basic Local Alignment Search Tool, BLAST). This procedure deduced the correct amino acid sequence of tryptic peptide samples and also was able to deduce the correct sequence from difficult mass patterns and identify the amino acid sequence. This allows complete automation of the process starting from MS fragmentation of complex peptide mixtures at low concentration (e.g. from silver-stained gel bands) to identification of the protein. We also show that if PSD data are collected in a single spectrum (instead of the segmented mode offered by conventional matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrumentation), the complete workflow from MS-PSD data acquisition to similarity-based identification can be completely automated. This strategy may be applied to proteomic studies for protein identification based on automated de novo sequencing instead of MS or tandem MS patterns. We describe the Charge Assisted Sequencing Engine (CHASE) algorithm, the working protocol, the performance of the algorithm on spectra from MALDI-TOFMS and the data comparison between a TOF and a TOF-TOF instrument.     

Lambda-Opérations sur l''Homologie d''une Algèbre de Lie de Matrices

One extends lambda operations from the cyclic homology of A to the homology of the Lie algebra gl(A) using exterior powers of matrices. One shows a formula of giving their behavior with respect to the direct sum of matrices. It uses the coproduct and the structure of ring object induced by the tensor product of matrices.     

Homology of the configuration spaces of quasi-equilateral polygon linkages

We consider the configuration space of quasi-equilateral polygon linkages with vertices each edge having length except for one fixed edge having length in the Euclidean plane In this paper, we determine .

     

The Homology of Partitions with an Even Number of Blocks

Let denote the subposet obtained by selecting even ranks in the partition lattice . We show that the homology of has dimension , where is the tangent number. It is thus an integral multiple of both the Genocchi number and an André or simsun number. Using the general theory of rank-selected homology representations developed in [22], we show that, for the special case of , the character of the symmetric group S _2n on the homology is supported on the set of involutions. Our proof techniques lead to the discovery of a family of integers b _i(n), 2 i n, defined recursively. We conjecture that, for the full automorphism group S _2n, the homology is a sum of permutation modules induced from Young subgroups of the form , with nonnegative integer multiplicity b _i(n). The nonnegativity of the integers b _i(n) would imply the existence of new refinements, into sums of powers of 2, of the tangent number and the André or simsun number a _n(2n).Similarly, the restriction of this homology module to S _2n–1 yields a family of integers d _i(n), 1 i n – 1, such that the numbers 2^–i d _i(n) refine the Genocchi number G _2n . We conjecture that 2^–i d _i(n) is a positive integer for all i.Finally, we present a recursive algorithm to generate a family of polynomials which encode the homology representations of the subposets obtained by selecting the top k ranks of , 1 k n – 1. We conjecture that these are all permutation modules for S _2n .