DNA fiber mapping techniques for the assembly of high-resolution physical maps.

High-resolution physical maps are indispensable for directed sequencing projects or the finishing stages of shotgun sequencing projects. These maps are also critical for the positional cloning of disease genes and genetic elements that regulate gene expression. Typically, physical maps are based on ordered sets of large insert DNA clones from cosmid, P1/PAC/BAC, or yeast artificial chromosome (YAC) libraries. Recent technical developments provide detailed information about overlaps or gaps between clones and precisely locate the position of sequence tagged sites or expressed sequences, and thus support efforts to determine the complete sequence of the human genome and model organisms. Assembly of physical maps is greatly facilitated by hybridization of non-isotopically labeled DNA probes onto DNA molecules that were released from interphase cell nuclei or recombinant DNA clones, stretched to some extent and then immobilized on a solid support. The bound DNA, collectively called "DNA fibers," may consist of single DNA molecules in some experiments or bundles of chromatin fibers in others. Once released from the interphase nuclei, the DNA fibers become more accessible to probes and detection reagents. Hybridization efficiency is therefore increased, allowing the detection of DNA targets as small as a few hundred base pairs. This review summarizes different approaches to DNA fiber mapping and discusses the detection sensitivity and mapping accuracy as well as recent achievements in mapping expressed sequence tags and DNA replication sites.     

苜蓿叶片水杨酸含量与其蓟马抗性的关系

采用不同抗蓟马特性的苜蓿品系,于不同蓟马虫口密度下测定苜蓿水杨酸含量和虫害程度,以明确苜蓿叶片水杨酸含量与其抗蓟马特性的关系.结果表明,苜蓿叶片游离态、结合态水杨酸含量均与苜蓿抗蓟马特性密切相关;高抗品系(抗蓟马品系)的水杨酸初始含量(0.539 mg·g-1)高于低抗品系(0.403 mg·g-1);与较低抗品系相比,高抗品系受害器官(叶)水杨酸含量随虫口密度和危害点面积的增大而增加相对缓慢,而随危害指数的增大而增加较快(3.84倍).可见,水杨酸主要是间接增强苜蓿对蓟马的抗性;高抗蓟马苜蓿品系能通过快速获得较高水杨酸含量来阻碍被危害伤口的扩大,降低其受危害程度,促使自身产量和品质提高.     

Seed set in Sorghum stipoideum,and not fire,determines the timing of breeding by Gouldian finches (Erythrura gouldiae)

Seeds of native grasses are an important food source for granivorous finches throughout the tropical savannas of northern Australia. The iconic Gouldian finch (Erythrura gouldiae), a threatened species endemic to these savanna grasslands, relies almost exclusively on the grass seeds of annual Sorghum spp. when breeding, and appears to time breeding with the availability of these seeds. Fire is common throughout the savanna grasslands of northern Australia and has the potential to alter Sorghum spp. seed germination and plant reproductive phenology which in turn could alter the Gouldian finch breeding phenology window. This study examines if the temporal relationship between breeding by Gouldian finches in the north‐east Kimberley region of Australia relates to fire and Sorghum stipoideum seed phenology. The availability of S. stipoideum seed was monitored at Gouldian finch breeding sites in association with local fire history and Gouldian finch breeding data. The effect of experimental fire (heat and smoke) on S. stipoideum seed dormancy and germination was also investigated. We found that the first heavy rainfalls preceded germination of S. stipoideum in November/December. Synchronous seed set by S. stipoideum plants the following March/April coincided with the start and duration of the Gouldian finch breeding season. The timing of dry season fires had no relationship with seed dormancy or the phenology of seed germination and seed set. Nor did the effects of smoke or heat affect seed dormancy and germination. These findings support the importance of the seed phenology of annual grass species, such as S. stipoideum, to breeding Gouldian finches, and also suggest that the occurrence of fire at a breeding site in the previous year does not alter the S. stipoideum seed or finch breeding window. The implications of these results for threatened Gouldian finch ecology and management are discussed in relation to previously published fire impacts on S. stipoideum seed nutrition and finch breeding site selection.     

Labeling of the centromeric region on human chromosome 8 by in situ hybridization

Summary Probe DNA that binds preferentially to the centromeric region of human chromosomes 8 was synthesized. Alpha satellite probe DNA molecules were selectively amplified from sorter-purified human chromosomes 8 by in vitro DNA amplification using the polymerase chain reaction (PCR). Probe labeling was performed during PCR by incorporation of biotinylated deoxyuridine. In situ hybridization of unpurified probe DNA comprised of alpha satellite monomer and higher molecular weight DNA fragments with metaphase chromosome spreads showed binding to the centromeric regions of numerous chromosomes. However, blocking with unlabeled total human alphoid DNA dramatically reduced crosshybridization to chromosomes other than 8. Under these conditions, the degenerate probe DNA allowed unambiguous visualization of domains occupied by centromeric DNA of chromosome 8 in metaphase spreads and interphase cell nuclei, thus greatly facilitating the detection of numerical chromosome aberrations in tumor cells. In situ hybridization of size-fractionated alpha satellite DNA identified the monomeric fraction as the major cause of crosshybridization. Alpha satellite dimers and higher molecular weight DNA fragments showed relatively high specificity for human chromosomes 8.     

A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.

Tissue-specific patterns of methylated deoxycytidine residues in the mammalian genome are preserved by postreplicative methylation of newly synthesized DNA. DNA methyltransferase (MTase) is here shown to associate with replication foci during S phase but to display a diffuse nucleoplasmic distribution in non-S phase cells. Analysis of DNA MTase-beta-galactosidase fusion proteins has shown that association with replication foci is mediated by a novel targeting sequence located near the N-terminus of DNA MTase. This sequence has the properties expected of a targeting sequence in that it is not required for enzymatic activity, prevents proper targeting when deleted, and, when fused to beta-galactosidase, causes the fusion protein to associate with replication foci in a cell cycle-dependent manner.     

Inhibition of IKK-2 by 2-[(aminocarbonyl)amino]-5-acetylenyl-3-thiophenecarboxamides

A series of 21 novel 2-[(aminocarbonyl)amino]-5-acetylenyl-3-thiophenecarboxamides were synthesized and evaluated for the inhibition of IKK-2. In spite of their often modest activity on the enzyme, six selected analogs showed significant inhibition of the production of inflammatory cytokine IL-8 in IL-1beta stimulated rheumatoid arthritis-derived synovial fibroblasts, demonstrating their potential usefulness as NF-kappaB regulators.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Combined immunophenotyping and FISH with sex chromosome-specific DNA probes for the detection of chimerism in epidermal Langerhans cells after sex-mismatched bone marrow transplantation

 Langerhans cells (LC) of the skin represent bone marrow-derived dendritic antigen-presenting cells and are therefore important in pathophysiological processes such as rejection, graft-versus-host disease, and graft-versus-leukemia-reaction after bone marrow transplantation (BMT). For understanding of these diseases, the evaluation of the chimeric status of LC following BMT is of great interest. To analyze the sex chromosome constitution of LC in the skin, we established a modified and refined technique of combined immunophenotyping and fluorescence in situ hybridization (FISH) and investigated frozen sections of skin biopsies from nine patients after allogeneic sex-mismatched BMT and of two healthy donors for control. LC were specifically labeled using a fluorescent CD1a antibody and hybridized simultaneously with X and Y chromosome-specific DNA probes. The results of this practical application on nine leukemia patients show the appearance of donor-type LC and the persistence of host-type LC at various times (36 up to 1395 days) after sex-mismatched BMT. Complete chimerism of LC could not be detected in any case. The frequency of recipient-specific LC ranged from 7% to 92% and showed no correlation with time postgrafting. We conclude from our results of 1461 analyzed LC that combined immunophenotyping and interphase cytogenetic analysis by FISH is the method of choice for the assessment of chimerism in a particular cell type after sex-mismatched BMT. Its practical application on other tissues affected by BMT-related pathophysiological processes reveals further knowledge of the time-dependent course of chimeric patterns after BMT. Accepted: 18 July 1996     

CHLOROPLAST DEVELOPMENT AND ULTRESTRUCTURE IN THE FRESHWATER RED ALGA BATRACHOSPERMUM1

Chloroplast development and ultrastructure of the freshwater red alga Batrachospermum moniliforme are described. Chloroplasts develop from proplastids which have a double-membraned chloroplast envelope and a parallel double-membraned outer photo-synthetic lamella. Of these 2 double-membraned structures of the proplastid, only the outermost pho-tosynthetic lamella functions in production of further lamellae. The mature chloroplast consists of 2 or more concentric lamellae and a variable number of nonconcentric lamellae. These lamellae are not dense, uninterrupted sheets as described for other red algae, but are largely constructed of tubules, lying side by side, that form interrupted lamellar sheets. The possible physiological significance of lamellar interruptions in providing path-ways for movement of materials in the chloroplast stroma is discussed.