Showing papers on "Genomics published in 1990"

Direct detection and automated sequencing of individual alleles after electrophoretic strand separation: identification of a common nonsense mutation in exon 9 of the human lipoprotein lipase gene

Abstract: Large-scale screening by direct sequencing of DNA to detect molecular variants remains a laborious endeavor whose difficulty is compounded by heterozygosity. We show that mobility shifts of single-stranded DNA electrophoresed under nondenaturing conditions can be used not only to detect variants (Orita,M. et al., 1989, Genomics, 5, 874-879), but also to separate and sequence directly individual alleles. In this manner, we have identified a common variant of human lipoprotein lipase resulting from a nonsense mutation in exon 9 of the gene. Whether this variant is of functional significance remains to be determined.

The transfer of cytoplasmic and nuclear genomes by somatic hybridisation.

Abstract: For somatic hybridisation between two species to be successful, specific regenerability, compatibility and selection criteria must be met. The development of new methodologies has reduced the reliance on auxotrophic and albino mutants in selection strategies. Somatic hybridisation allows the transfer of chloroplast, mitochondrial or nuclear genomes in a single-step procedure and can extend the transfer boundaries defined by sexual hybridisation. Cytoplasmic genomes can be transferred over wider genetic distances than nuclear genomes. We consider the transfer of the three genomes but with particular emphasis on chloroplasts. Strategies for chloroplast transfer are reviewed. When no selection strategies for a particular chloroplast are utilised the regenerated plant will have chloroplasts from either one of the parents, but not a mixture of both. The rapid sorting out can be explained by the changes in plastid numbers that occur in the first few divisions. Biased segregation can frequently be related to an unequal input of plastids but, in some cases, plastid-mitochondrial-nuclear incompatibilities are presumably involved and more studies of the callus stage are required to identify these phenomena. Chloroplast DNA recombination is rare, consistent with known inheritance patterns and the relative conservation of the chloroplast genome. Stable heteroplasmy of chloroplasts as a result of somatic hybridisation has not been reported, although chloroplast DNA heteroplasmy occurs naturally in some species. Mitochondria can be transferred in a similar fashion to chloroplasts but, as their numbers are higher, their segregation is less likely to be complete in the regenerated plant. There are many reports of mitochondrial DNA recombination and cloned fragments containing sites of intergenomic recombination have been obtained. It appears that fusion between these organelles is common. Interspecific somatic hybridisation within a genus can produce nuclear hybrid plants that can be part of a breeding program to provide novel sources of germplasm. Aneuploids rather than amphiploids may be produced as a result of chromosome loss during the culture phase. Nuclear hybrids from wider crosses are usually infertile. However asymmetric somatic hybridisation offers the possibility of incorporating nuclear genetic material from more diverse sources. Somatic hybridisation has an important rc le in complementing conventional breeding in providing the gross genetic structure of chloroplast, mitochondrial and nuclear genomes. Specific gene transfer technologies can fine-tune the genomes thus provided.

Sampling strategies for distances between DNA sequences.

Abstract: An international effort is now underway to obtain the DNA sequence for the entire human genome (Watson and Jordan, 1989, Genomics 5, 654-656; Barnhart, 1989, Genomics 5, 657-660) This Human Genome Initiative will generate sequence data from several species other than humans, and will result in several copies per species of at least some regions of the genome Although the project has generated much interest, it is but one aspect of the widespread effort to generate DNA sequence data Published sequences are collected in common databases, and release 63 of GenBank in March 1990 contained 40,127,752 bases from 33,337 reported sequences (News from GenBank 3; Mountain View, California: Intelligenetics, Inc, 1990) Large though this database is, it is only about 1% of the number of bases in the human genome Interpretations of data of such magnitude are going to require the collaborative efforts of biometricians and molecular biologists, and an aim of this paper is to show that there is also a role for readers of this journal in the design of surveys of DNA sequences Discussion here will center on the use of sequence data in evolutionary studies, where some region of DNA is sequenced in several different species The object is to infer the evolutionary history of that particular region, or of the species themselves Statistical issues in the very important studies on sequences to locate and characterize regions responsible for human diseases will not be addressed here We will discuss appropriate ways of measuring distances between DNA sequences and of predicting the sampling properties of the distances There are procedures for inferring evolutionary histories for a set of elements that depend on a matrix of distances between each pair of elements, and the precision of resulting trees must be influenced by the precision of the distances We will show that account needs to be taken of two sampling processes--the sampling of sequences by the investigator ("statistical sampling"), and the sampling of genetic material involved in the formation of offspring from a parental population ("genetic sampling")

Genome Analysis in Domestic Animals

Abstract: Chromatin organization in interphase on the organization of animal genomes - ubiquitous interspersion of repetitive DNA sequences screening and cloning of genes for application in animal genetics and animal breeding techniques, strategies and stages of DNA sequencing computer-aided analysis of biomolecular sequence and structure in genome research linkage studies and mapping gene and chromosome homologies in different species.

Molecular approaches to the study of plant biosystematics

Abstract: Genetic relationships among organisms can be estimated from the pattern of DNA sequence change between hereditary molecules. The methods of molecular biology are increasingly being employed in systematic and evolutionary research to study genetic relationships and phylogeny. The investigator is faced with a variety of choices in initiating research in 'molecular biosystematics'. First, a gene or genome that provides a level of genetic resolution appropriate for the materials under study must be selected. Common choices in plants include the chloroplast genome (cpDNA) or components of the chloroplast genome, the nuclear ribosomal RNA genes (rDNA), or nuclear-encoded, single-copy genes. A second consideration is that several methods can be employed to provide direct or indirect measures of DNA sequence divergence. One widely used method determines genetic divergence based on restriction site changes. Restriction site analyses typically require some knowledge of the physical map of the DNA molecule under study. Empirical studies indicate that restriction site analyses of cpDNA provide good resolution for systematic investigations at or below the family level. A second method that is increasing in importance is DNA sequencing. Until quite recently, DNA sequencing required the molecular cloning of the gene or DNA fragment of interest and the implementation of a 'sequencing strategy' for the production of overlapping sequence runs. Two related technological developments have overcome both of these requirements, when the goal is the repetitive sequencing of a specific gene from a number of taxa. It is now possible to synthesise synthetic oligonucleotides that can be used to prime dideoxy sequencing at virtually any point in the gene of interest, based on previously determined sequence information. The second major innovation is the invention of the polymerase chain reaction technique (PCR). The PCR method permits the direct amplification of DNA fragments from heterogeneous DNA mixtures and thereby circumvents the molecular cloning requirement. Application of the PCR method to chloroplast genes, together with direct primer-mediated sequencing, provides a method for obtaining large data sets. CpDNA sequence data are especially valuable at or above the family level and provide a powerful means of resolving genetic relationships at the deepest levels of plant evolution.

Development of Geminivirus-Based Gene Vectors for Dicotyledonous Plants

Abstract: Geminiviruses are small icosahedral plant viruses that contain circular single-stranded DNA as their genome. In tomato golden mosaic virus (TGMV), a geminivirus that infects dicotyledonous hosts, several genes involved in replication, spread of virus or DNA in plants, and possibly insect transmission have been identified. Gene replacement experiments suggest that useful plant gene expression vectors can be constructed from TGMV. Following the integration of stable master copies of vectors based on TGMV DNA into plant chromosomal DNA, heritable gene amplification of a number of bacterial genes has been demonstrated, suggesting exciting possibilities for similar amplification of plant genes in the future.

The European project for sequencing the yeast genome

Abstract: The 2-year project launched in January 1989 in the framework of the European-Community(EC)funded Bioteehnology Action Programme, was a worldwide premi6re of scientists working concurrently, in their different countries, to determine the sequence of the entire chromosome of a eukaryotic cell. This network of 35 laboratories sequencing the yeast chromosome 11I, has constituted a model that will promote the sequencing of the whole yeast genome in the coming years.

Engineering the Human Genome Project

Abstract: The Human Genome Initiative, a worldwide research effort to analyze the structure of human deoxyribonucleic acid (DNA) and determine the location of all human genes, is discussed. The nature of the task is described, and the technologies needed to construct 'libraries' of overlapping clones of DNA fragments are examined. DNA sequencing methods and technologies are also discussed. The role that the engineer could play in supporting the project by advances in instrumentation is briefly discussed. >