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901.
902.
The individual haplotyping problem is a computing problem of reconstructing two haplotypes for an individual based on several optimal criteria from one's fragments sequencing data. This paper is based on the fact that the length of a fragment and the number of the fragments covering a SNP (single nucleotide polymorphism) site are both very small compared with the length of a sequenced region and the total number of the fragments and introduces the parameterized haplotyping problems. With m fragments whose maximum length is k(1), n SNP sites and the number of the fragments covering a SNP site no more than k(2), our algorithms can solve the gapless MSR (Minimum SNP Removal) and MFR (Minimum Fragment Removal) problems in the time complexity O(nk(1)k(2) + m log m + nk(2) + mk(1)) and O(mk(2)(2) + mk(1) k(2) + m log m + nk(2) + mk(1))respectively. Since, the value of k(1) and k(2) are both small (about 10) in practice, our algorithms are more efficient and applicable compared with the algorithms of V. Bafna et al. of time complexity O(mn(2)) and O(m(2)n + m(3)), respectively. 相似文献
903.
A novel pathway of HMGB1-mediated inflammatory cell recruitment that requires Mac-1-integrin 总被引:3,自引:0,他引:3
Orlova VV Choi EY Xie C Chavakis E Bierhaus A Ihanus E Ballantyne CM Gahmberg CG Bianchi ME Nawroth PP Chavakis T 《The EMBO journal》2007,26(4):1129-1139
High-mobility group box 1 (HMGB1) is released extracellularly upon cell necrosis acting as a mediator in tissue injury and inflammation. However, the molecular mechanisms for the proinflammatory effect of HMGB1 are poorly understood. Here, we define a novel function of HMGB1 in promoting Mac-1-dependent neutrophil recruitment. HMGB1 administration induced rapid neutrophil recruitment in vivo. HMGB1-mediated recruitment was prevented in mice deficient in the beta2-integrin Mac-1 but not in those deficient in LFA-1. As observed by bone marrow chimera experiments, Mac-1-dependent neutrophil recruitment induced by HMGB1 required the presence of receptor for advanced glycation end products (RAGE) on neutrophils but not on endothelial cells. In vitro, HMGB1 enhanced the interaction between Mac-1 and RAGE. Consistently, HMGB1 activated Mac-1 as well as Mac-1-mediated adhesive and migratory functions of neutrophils in a RAGE-dependent manner. Moreover, HMGB1-induced activation of nuclear factor-kappaB in neutrophils required both Mac-1 and RAGE. Together, a novel HMGB1-dependent pathway for inflammatory cell recruitment and activation that requires the functional interplay between Mac-1 and RAGE is described here. 相似文献
904.
905.
Xie P 《Archives of biochemistry and biophysics》2007,457(1):73-84
Based on the available crystal structure a model is presented for the polymerization activity and switching transition between polymerase and exonuclease sites of a DNA polymerase molecular motor. Using the model, the fast polymerization rate for correctly base-paired DNA and much reduced polymerization rate after an incorporation of a mismatched base can be well explained. The dependences of the polymerization rate and exonuclease rate on mechanical tension acting on the DNA template are studied. The switching rates between the two sites are analyzed. All the results show good quantitative agreement with the available experimental results. 相似文献
906.
Xie ZR Yang HT Liu WC Hwang MJ 《Biochemical and biophysical research communications》2007,358(3):722-726
Oscillatory gene expression plays an important role in somite segmentation during the early developmental stages of vertebrates. Recent experimental studies have shown that microRNA can regulate gene expression by stimulating degradation of mRNA and/or repression of translation. In this communication, we incorporate miRNA into a previous mathematical model of gene expression with delayed negative feedback and demonstrate how this modified model can elucidate the possible effect of miRNA on the oscillatory gene expression. Our finding suggests that miRNA maybe a destabilizing or stabilizing factor in the dynamics of gene expression depending on the severity of its effect on mRNA degradation. Our finding provides testable hypothesis for experimental biologists to further investigate miRNA's increasing functional roles in regulating cellular processes and development. 相似文献
907.
Cyanobacteria blooms (especially Microcystis spp.) are thought to alter dominance of large-sized daphnids into small-sized metazoan zooplankton. However, several field
investigations show different phenomena. Laboratory experiments were conducted based on the hypothesis that different Microcystis spp. concentrations would influence competitive outcomes using two algal combinations of different concentrations and four
species of cladocerans. In the algal combination of 50 mg l−1 colonial Microcystis spp. + 1 mg l−1
Scenedesmus obliquus (fresh weight), Daphnia carinata was absent during the experiment in competition with other cladocerans. Decreasing colonial Microcystis spp. concentration (10 mg l−1) resulted in a shift from dominance by small-sized cladocerans to dominance by D. carinata. No significant effects of different concentrations of colonial Microcystis spp. on competitive outcomes were shown among three small-sized cladocerans. These results support the idea that cyanobacteria
concentration affects the dominance status of large-bodied daphnid. 相似文献
908.
Yu Xie Hao-Han Wu Yong Cui Long Pan Rong Fan Yang-Chao Tian Liu-Si Sheng 《Inorganica chimica acta》2007,360(5):1669-1677
Three homochiral metal-organic coordination networks [Co2(l-Trp)2(Py)6] · Py · (ClO4)2 (1), [Ni(l-Trp)(Py)3] · H2O · ClO4 (2) and [Co2(l-Trp)(INT)2(H2O)2(ClO4)] (3), all containing natural amino acid l-HTrp (l-typtophan), were hydrothermally synthesized and structurally characterized. The compounds 1 and 2 crystallize in the orthorhombic space group C2221, with a = 10.731(2) Å, b = 19.709(4) Å, c = 27.365(6) Å and Z = 4 for 1 and a = 10.710(10) Å, b = 20.088(18) Å, c = 27.63(3) Å and Z = 8 for 2, respectively. The compound 3 has the monoclinic space group P21, with a = 8.1934(14) Å, b = 13.209(2) Å, c = 12.464(2) Å, β = 104.107(3)° and Z = 2. Both 1 and 2 consist of 1D helical chains. Compound 3 is composed of 2D networks, which further assemble into a 3D supramolecular structure via weak interlayer interactions. The optically pure amino acid l-HTrp plays an important role leading to homochiral structures reported here. 相似文献
909.
910.
The approval of using monoclonal antibodies as a targeted therapy in the management of patients with B cell lymphoma has led to new treatment options for this group of patients. Production ofmonoclonal antibodies by the traditional hybridoma technology is costly, and the resulting murine antibodies often have the disadvantage of triggering human anti-mouse antibody (HAMA) response. Therefore recombinant Fab antibodies generated by the phage display technology can be a suitable alternative in managing B cell lymphoma. In this study, we extracted total RNA from spleen cells of BALB/c mice immunized with human B lymphoma cells, and used RT-PCR to amplify cDNAs coding for the κ light chains and Fd fragments of heavy chains. After appropriate restriction digests, these cDNA fragments were successively inserted into the phagemid vector pComb3H-SS to construct an immunized Fab phage display library. The diversity of the constructed library was approximately 1.94× 10^7. Following five rounds of biopanning, soluble Fab antibodies were produced from positive clones identified by ELISA. From eight positive clones, FabC06, FabC21, FabC43 and FabC59 were selected for sequence analysis. At the level of amino acid sequences, the variable heavy domains (VH) and variable light domains (VL) were found to share 88-92% and 89-94% homology with sequences coded by the corresponding murine germline genes respectively. Furthermore, reactivity with membrane proteins of the B cell lymphoma was demonstrated by immunohistochemistry and western blotting. These immunized Fab antibodies may provide a valuable tool for further study of B cell lymphoma and could also contribute to the improvement of disease therapy. 相似文献