High throughput detection of small genomic insertions or deletions by Pyrosequencing

Small insertions or deletions of nucleotides are common polymorphic variations in the human genome and can result in a predisposition to disease. However, high throughput methods for detecting these variations are limited. This report describes a method to detect this variation based on sequencing the boundaries of nucleotide alterations using the Pyrosequencing technique. This method can optimally detect up to 100 base pair nucleotide insertions and deletions, and also complicated genomic rearrangements.     

An integrated physical and genetic map of the nematode<Emphasis Type="Italic"> Pristionchus pacificus</Emphasis>

The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of the P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes.Communicated by G. Jürgens     

Immunohistochemical localization of leukemia inhibitory factor, interleukins 1 and 6 at the primary implantation site in the rhesus monkey

Blastocyst implantation and placentation involve localized inflammatory type of responses at and around the site of nidation. In the present study, the likely involvement of inflammatory cytokines, namely, leukemia inhibitory factor (LIF), interleukins 1 alpha and 1 beta (IL-1alpha and IL-1beta) and IL-6 at the primary implantation site of the rhesus monkey was examined immunocytochemically during lacunar (n=6) and villous (n=8) stages of gestation. Trophoblast cells and extraembryonic mesenchymal cells were immunopositive for LIF and IL-1alpha. The distribution of IL-1beta and IL-6 in trophoblast cells was low in lacunar stage samples, however, a higher degree of immunopositivity for IL-6 was observed in villous stage samples. Decidual cells were immunopositive for all the cytokines studied. In lacunar stage samples, plaque cells adjacent to implanted nidus were immunopositive for all the cytokines examined, and the degree of their immunoprecipitation increased, except that of IL-1beta, during the villous stage. Luminal and glandular epithelial cells were immunopositive for LIF, IL-1alpha, IL-1beta and IL-6 in lacunar and in villous stage samples. LIF immunopositivity was detected in endothelial cells of blood vessels within and below chorionic plate and cytotrophoblast shell, while vascular smooth muscle cells were positive for all the cytokines studied. The temporo-spatial characteristics of LIF, IL-1alpha, IL-1beta and IL-6 protein expressions in primary implantation sites of the rhesus monkey suggest that these pro-inflammatory cytokines play specific roles in regulating trophoblast cell proliferation, differentiation, invasion and associated maternal tissue remodelling during early gestation.     

Are mice calorically restricted in nature?

An important question about traditional caloric restriction (CR) experiments on laboratory mice is how food intake in the laboratory compares with that of wild mice in nature. Such knowledge would allow us to distinguish between two opposing views of the anti-aging effect of CR--whether CR represents, in laboratory animals, a return to a more normal level of food intake, compared with excess food consumption typical of laboratory conditions or whether CR represents restriction below that of animals living in nature, i.e. the conditions under which house mice evolved. To address this issue, we compared energy use of three mouse genotypes: (1) laboratory-selected mouse strains (= laboratory mice), (2) house mice that were four generations or fewer removed from the wild (= wild-derived mice) and (3) mice living in nature (= wild mice). We found, after correcting for body mass, that ad libitum fed laboratory mice eat no more than wild mice. In fact, under demanding natural conditions, wild mice eat even more than ad libitum fed laboratory mice. Laboratory mice do, however, eat more than wild-derived mice housed in similar captive conditions. Therefore, laboratory mice have been selected during the course of domestication for increased food intake compared with captive wild mice, but they are not particularly gluttonous compared with wild mice in nature. We conclude that CR experiments do in fact restrict energy consumption beyond that typically experienced by mice in nature. Therefore, the retarded aging observed with CR is not due to eliminating the detrimental effects of overeating.     

Cerebellar granule cell Cre recombinase expression

The cerebellum maintains balance and orientation, refines motor action, stores motor memories, and contributes to the timing aspects of cognition. We generated two mouse lines for making Cre recombinase-mediated gene disruptions largely confined to adult cerebellar granule cells. For this purpose we chose the GABA(A) receptor alpha6 subunit gene, whose expression marks this cell type. Here we describe mouse lines expressing Cre recombinase generated by 1) Cre knocked into the native alpha6 subunit gene by homologous recombination in embryonic stem cells; and 2) Cre recombined into an alpha6 subunit gene carried on a bacterial artificial chromosome (BAC) genomic clone. The fidelity of Cre expression was tested by crossing the mouse lines with the ROSA26 reporter mice. The particular alpha6BAC clone we identified will be valuable for delivering other gene products to cerebellar granule cells.     

转基因动物整合位点的研究进展

转基因动物整合位点克隆及相关序列特征研究是探索外源基因整合机制和整合稳定性的重要手段。转基因整合位点序列的克隆方法主要有：个体基因组文库筛选法、反向PCR法、热不对称交互式PCR法和质粒回收法。4种方法各有优缺点,可根据不同条件选用。克隆到的整合位点序列表明,整合位点可能存在一定的共同特征。 Integration Sites of Transgenes in Transgenic Animals WU Bo,ZHU Zuo-Yan State Key Laboratory of Freshwater Ecology and Biotechnology,Institute of Hydrobiology, Chinese Academy of Science,Wuhan 430072,China Abstract:To study the mechanism of transgene ' s integration in the host genome,first step is to clone the integration-site sequence.The method employed for this purpose includes selection from genomic pool,IPCR,TAIL-PCR and plasmid rescued.Different method fits different cases depending on how the transgenics have been produced.The data of integration-site sequences showed some similar features existed. Key words：transgene; integration site; clone method     

Enzymatic function of loop movement in enolase: preparation and some properties of H159N,H159A,H159F,and N207A enolases

The hypothesis that His159 in yeast enolase moves on a polypeptide loop to protonate the phosphoryl of 2-phosphoglycerate to initiate its conversion to phosphoenolpyruvate was tested by preparing H159N, H159A, and H159F enolases. These have 0.07%–0.25% of the native activity under standard assay conditions and the pH dependence of maximum velocities of H159A and H159N mutants is markedly altered. Activation by Mg²⁺ is biphasic, with the smaller Mg²⁺ activation constant closer to that of the catalytic Mg²⁺ binding site of native enolase and the larger in the mM range in which native enolase is inhibited. A third Mg²⁺ may bind to the phosphoryl, functionally replacing proton donation by His159. N207A enolase lacks an intersubunit interaction that stabilizes the closed loop(s) conformation when 2-phosphoglycerate binds. It has 21% of the native activity, also exhibits biphasic Mg²⁺ activation, and its reaction with the aldehyde analogue of the substrate is more strongly inhibited than is its normal enzymatic reaction. Polypeptide loop(s) closure may keep a proton from His159 interacting with the substrate phosphoryl oxygen long enough to stabilize a carbanion intermediate.     

Conservation of the syntenies between porcine chromosome 7 and human chromosomes 6, 14 and 15 demonstrated by radiation hybrid mapping and linkage analysis

Comparative mapping studies facilitate the identification of genes located in quantitative trait locus (QTL) regions in domestic animals by utilizing information from the human genome. Radiation hybrid (RH) mapping is effective for this purpose because of its high resolution in ordered gene mapping on chromosomes. We constructed an RH map of pig chromosome 7, by adding 23 markers associated with genes. This RH map clearly demonstrated the mosaic of homology between pig chromosome 7 (SSC7) and human chromosomes 6, 14 and 15 at a 'gene' level, and was confirmed by linkage analysis. Clarification of the homology of SSC7 to human chromosomes will contribute to the elucidation of the gene(s) responsible for QTL detected on this chromosome.     

Inhibition of nicotinoprotein (NAD+-containing) alcohol dehydrogenase by trans-4-(N,N-dimethylamino)-cinnamaldehyde binding to the active site

Ethanol oxidation by nicotinoprotein alcohol dehydrogenase (np-ADH) from the bacterium Amycolatopsis methanolica is inhibited by trans-4-(N,N-dimethylamino)-cinnamaldehyde through direct binding to the catalytic zinc ion in a substrate-like geometry. This binding is accompanied by a characteristic red shift of the aldehyde absorbance from 398 nm to 467 nm. Np-ADH is structurally related to mammalian ADH class I, and a model of np-ADH shows how the cinnamaldehyde derivative can be accommodated in the active site of the nicotinoprotein, correlating the structural and enzymological data.