A pyrimidine dimer-DNA glycosylase activity associated with the v gene product of bacterophage T4

Mutations in the v gene of bacteriophage T4 are associated with a marked increase in sensitivity to killing by UV radiation at 254 nm, but not to a variety of other forms of base damage to DNA. Early studies from this laboratory provided evidence for a role of the v gene in the excision of pyrimidine dimers (PD) from DNA. Specifically, it was shown that extracts of T4v+-infected Escherichia coli catalyse the formation of single-strand breaks (nicks) and/or alkali-labile sites in UIV-irradiated duplex DNA. Comparable hydrolysis of phosphodiester bonds is not observed with extracts of E. coli infected with the mutant T4v1 (ref. 5). The product of the v gene has been extensively purified in a number of laboratories; however, convincing evidence of purification to physical homogeneity has not yet been presented.     

Cloning of cDNAs for cellular proteins that bind to the retinoblastoma gene product

The E7 transforming protein of human papilloma virus-16 binds to the retinoblastoma gene product (pRb) through a nine-amino-acid segment of E7 (21-29). This segment of E7 is homologous to the pRb-binding domains of the simian virus 40 large T and adenovirus E1A transforming proteins. Each of these viral transforming proteins bind to the same region of pRb. To isolate cellular proteins that interact with this viral protein-binding domain on pRb, we used recombinant pRb to screen a human complementary DNA expression library. Two cDNAs were isolated that encode retinoblastoma binding proteins (RBP-1 and RBP-2). We report here that these RBP genes exist in separate loci and produce discrete messenger RNAs. The predicted amino-acid sequence of these genes showed no homology to known proteins, but both RBPs contain the pRb binding motif conserved between E7, large T and E1A14. In vitro expression of the RBP cDNAs yielded proteins that specifically bound to pRb. Recombinant E7 protein, the E7 21-29 peptide and the homologous RBP-1 peptide inhibited RBP-pRb binding. Mutations introduced into the putative pRb-binding segment in RBP-1 impaired its binding activity. These studies indicate that the cellular RBP-1, RBP-2 and viral E7 proteins interact with pRb through similar domains.     

Local degradation of fibronectin at sites of expression of the transforming gene product pp60src

Local degradation of extracellular fibronectin, a major extracellular adhesive protein, is believed to play an important part in the migration of cells through the extracellular matrix during tumour invasion, morphogenetic movement and trophoblast implantation. Fibronectin is lost from the cell surface after transformation with Rous sarcoma virus (RSV). By using fluorescent and radiolabelled probes covalently coupled to the surface of substrata, we have recently identified a proteolytic activity that is expressed in RSV-transformed cells and is involved in the local degradation of fibronectin at cell-substratum contact sites. Here, we extend the relevance of these findings and gain some insight into the cellular functions of pp60src, the transforming gene product of RSV. We show that newly expressed viral pp60src is localized at the cytoplasmic surface of the cell membrane, corresponding to the cell contact sites where degradation of extracellular fibronectin occurs.     

Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9

Specific modifications to histones are essential epigenetic markers---heritable changes in gene expression that do not affect the DNA sequence. Methylation of lysine 9 in histone H3 is recognized by heterochromatin protein 1 (HP1), which directs the binding of other proteins to control chromatin structure and gene expression. Here we show that HP1 uses an induced-fit mechanism for recognition of this modification, as revealed by the structure of its chromodomain bound to a histone H3 peptide dimethylated at Nzeta of lysine 9. The binding pocket for the N-methyl groups is provided by three aromatic side chains, Tyr21, Trp42 and Phe45, which reside in two regions that become ordered on binding of the peptide. The side chain of Lys9 is almost fully extended and surrounded by residues that are conserved in many other chromodomains. The QTAR peptide sequence preceding Lys9 makes most of the additional interactions with the chromodomain, with HP1 residues Val23, Leu40, Trp42, Leu58 and Cys60 appearing to be a major determinant of specificity by binding the key buried Ala7. These findings predict which other chromodomains will bind methylated proteins and suggest a motif that they recognize.     

Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle.

We report here the determination and refinement to 1.9 A resolution by X-ray cryo-crystallography the structure of HLA-Aw68. The averaged image from the collection of bound, endogenous peptides clearly shows the atomic structure at the first three and last two amino acids in the peptides but no connected electron density in between. This suggests that bound peptides, held at both ends, take alternative pathways and could be of different lengths by bulging out in the middle. Peptides eluted from HLA-Aw68 include peptides of 9, 10 and 11 amino acids, a direct indication of the length heterogeneity of tightly bound peptides. Peptide sequencing shows relatively conserved 'anchor' residues at position 2 and the carboxy-terminal residue. Conserved binding sites for the peptide N and C termini at the ends of the class I major histocompatibility complex binding groove are apparently dominant in producing the long half-lives of peptide binding and the peptide-dependent stabilization of the class I molecule's structure.     

Sequences at the somatic recombination sites of immunoglobulin light-chain genes.

The entire nucleotide sequence of a 1.7-kilobase embryonic DNA fragment containing five joining (J) DNA segments for mouse immunoglobulin kappa chain gene has been determined. Each J DNA segment can encode amino acid residues 96--108. Comparison of one of the five J DNA sequences with those of an embryonic variable (V) gene and a complete kappa chain gene permitted localisation of a precise recombination site. The 5'-flanking regions of J DNA segments could form an inverted stem structure with the 3'-non-coding region of embryonic V genes. This hypothetical structure and gel-blotting analysis of total embryo and myeloma DNA suggest that the somatic recombination may be accompanied by excision of an entire DNA segment between a V gene and a J DNA segment. Antibody diversity may in part be generated by modulation of the precise recombination sites.     

Turbo乘积码的重复译码算法

主要是针对TPC译码算法进行研究,依据对数似然概率(LLR)和最大后验准则的原理,推导出对数似然概率估算的近似公式,形成TPC重复软译码纠错算法,并通过软件实现.     

贵州省云台山林下鸟类捕获与雾网放置场所的关系

为了探究林下鸟类调查时雾网放置场所选择的问题,2011年9月-2012年8月用网捕法对贵州省云台山林下鸟类进行调查．将雾网放置在林缘、林窗和林下3类生境中,共捕获鸟类3目12科25种231只．全年3种生境之间的鸟类数量（P=0．033）、种类（P=0．005）和生物量（P=0．007）3个特征数存在显著差异,3个特征数均表现出林缘和林窗生境之间无显著差异,但林缘和林窗生境均显著高于林下生境．Shannon-Wiener指数和专有种（指仅在某种生境被捕获的鸟类）均表现为从林缘、林窗、林下依次下降的特点．对森林林下鸟类进行网捕法调查时,应该将更多的网场选择在林缘和林窗生境,而不是林下生境．     

The mec-4 gene is a member of a family of Caenorhabditis elegans genes that can mutate to induce neuronal degeneration.

Three dominant mutations of mec-4, a gene needed for mechanosensation, cause the touch-receptor neurons of Caenorhabditis elegans to degenerate. With deg-1, another C. elegans gene that can mutate to induce neuronal degeneration and that is similar in sequence, mec-4 defines a new gene family. Cross-hybridizing sequences are detectable in other species, raising the possibility that degenerative conditions in other organisms may be caused by mutations in similar genes. All three dominant mec-4 mutations affect the same amino acid. Effects of amino-acid substitutions at this position suggest that steric hindrance may induce the degenerative state.     

The products of the Drosophila gap genes hunchback and Krüppel bind to the hunchback promoters

The first zygotic genes to be expressed during early Drosophila development are the gap genes. Their role is to read and interpret coarse positional information deposited in the egg by the mother and to refine it by cross-regulatory interactions and by controlling a class of pair-rule genes. Little is known about the molecular mechanisms by which the three cloned gap genes carry out their genetically defined functions. Here we report that the Krüppel (Kr) gene product (Kr) binds to the sequence AAGGGGTTAA, whereas the hunchback (hb) gene product (Hb) recognizes the consensus ACNCAAAAAANTA. We have identified binding sites for these proteins upstream of the two hb promoters, which we suggest could mediate the repression of hb by Kr and perhaps allow hb to influence its own expression.     

Similarity of the product of the Drosophila neurogenic gene big brain to transmembrane channel proteins.

Cells in the neurogenic region of Drosophila embryos are initially bipotential; they can become either neuroblasts or epidermoblasts. Cell-cell interaction seems to play an important part in this developmental decision, which involves the function of a group of genes (the neurogenic genes). Loss-of-function mutations in any of the neurogenic genes result in nervous system hyperplasia and epidermal hypoplasia. Of the six known zygotic neurogenic genes, big brain (bib) is unique in several aspects. Most notably, all the other known neurogenic genes seem to fit into a cascade defined by genetic interactions, whereas bib does not show any detectable interaction with them. To understand how bib functions, we have now cloned the bib genomic and complementary DNAs. The predicted bib product shows significant sequence similarity to a family of transmembrane proteins, some of which form channels permeable to small molecules. Together with genetic studies, our results indicate that the bib product may mediate intercellular communication in a pathway separate from the one involving the products of the other neurogenic genes.     

AID is required to initiate Nbs1/gamma-H2AX focus formation and mutations at sites of class switching.

Class switch recombination (CSR) is a region-specific DNA recombination reaction that replaces one immunoglobulin heavy-chain constant region (Ch) gene with another. This enables a single variable (V) region gene to be used in conjunction with different downstream Ch genes, each having a unique biological activity. The molecular mechanisms that mediate CSR have not been defined, but activation-induced cytidine deaminase (AID), a putative RNA-editing enzyme, is required for this reaction. Here we report that the Nijmegen breakage syndrome protein (Nbs1) and phosphorylated H2A histone family member X (gamma-H2AX, also known as gamma-H2afx), which facilitate DNA double-strand break (DSB) repair, form nuclear foci at the Ch region in the G1 phase of the cell cycle in cells undergoing CSR, and that switching is impaired in H2AX-/- mice. Localization of Nbs1 and gamma-H2AX to the Igh locus during CSR is dependent on AID. In addition, AID is required for induction of switch region (S mu)-specific DNA lesions that precede CSR. These results place AID function upstream of the DNA modifications that initiate CSR.     

A product of the prune locus of Drosophila is similar to mammalian GTPase-activating protein.

The X-linked prune (pn) eye-colour mutation of Drosophila melanogaster has a highly specific, complementary lethal interaction with the conditional dominant Killer of prune (awdK-pn) mutation. Although awdK-pn flies have no apparent phenotype on their own, pn awdK-pn double mutants die as second or third larval instars. The awd locus encodes a nucleoside diphosphate kinase, an enzyme that catalyses the transfer of high-energy phosphate bonds between nucleoside diphosphates and nucleoside triphosphates, which is essential for the normal development of Drosophila. Analysis of the pn locus has suggested that the complementary DNA, TcD37, encodes a putative pn+ product. Here we report the nucleotide sequence of TcD37 and the similarity of its deduced protein product to the catalytic domain of mammalian GTPase-activating proteins (GAPs); GAPs stimulate the GTPase activity of Ras (ref. 6), which are plasma membrane-bound proteins involved in the regulation of cell proliferation and differentiation. These results suggest that the Drosophila TcD37 protein participates in a biochemical pathway similar to that of Ras and GAPs in mammals and yeast. We propose that the interaction between pn and awd is due to a neomorphic mutation that enhances the ability of AwdK-pn nucleoside diphosphate kinase to induce a regulatory GTPase into a GTP-bound 'on' state, whereas Pn modulates the activity of this GTPase either by switching it to a GDP-bound 'off' state or by interfering with its effector function.     

对比法在判定终点名次中的应用

对比法是一项新的终点裁判方法,是计算机数据排列的基本原理在终点裁判工作中的应用。本文介绍了这种方法并指出其理论依据。