Toward a cDNA map of the human genome

Advances in the Human Genome Project are shaping the strategies for identifying the 50,000-100,000 human genes. High-resolution genetic maps of the human genome combined with sequencing herald an era of rapid regional definition of disease genes. However, only once their chromosome band location is known will the systematic partial sequencing of thousands of random cDNA clones provide the reagents for teh rapid assessment of the genes responsible for the inherited disorders. We now present an approach to the rapid determination of map position and therefore to the creation of a transcribed map of the human genome. Sensitive fluorescence in situ hybridization has been combined with high-resolution chromosome banding and random cDNA sequencing to map 41 cDNAs with an average insert size of <2 kb to single human chromosome bands. The result provide 15 new genes, with database and functional information, as candidates for human disease. These include the large extracellular signal-related kinase (HUMERK), the ERK activator kinase (PRKMK1), a new member of the RAS oncogene family, protein phosphatase 2 regulatory subunit B alpha isoform (PPP2R2A), and a novel human gene with very high homology to a plant membrane transport family. Further, an analysis of expressed genes associated with pseudogenes showed that by using these techniques, it is possible to detect accurately the transcribed locus within a multigene or processed pseudogene family in most cases. These findings suggest that direct cDNA mapping using fluorescence in situ hybridization provides an accurate and rapid approach to the definition of a transcribed map of the human genome. This low-cost, high-resolution (2-5 Mb) mapping greatly enhances the speed with which these genes can be subsequently assigned to contigs. This assignment provides a necessary first step in understanding the relationship of the genes to both acquired and inherited human diseases.     

From genome to proteome: protein map of Haemophilus influenzae

High-resolution two-dimensional (2-D) polyacrylamide gel electrophoresis allows the separation of complex biological mixtures (i.e., several hundred proteins from a bacterial cell lysate) in a single experiment. In this report proteins from Haemophilus influenzae were separated by 2-D gels and analyzed by peptide mass fingerprinting and/or amino acid analysis. By comparing the peptide mass profiles and the amino acid composition with the Haemophilus influenzae database, 119 protein spots were identified. The combination of amino acid analysis and peptide mass fingerprinting is a powerful tool for a rapid and economical identification of a large number of proteins resolved by 2-D gels. Studies on gene regulation and changes of protein expression upon drug treatment require quick and serial analysis techniques to efficiently identify potential new drug targets.     

Integrated map of the Schizosaccharomyces pombe genome

A restriction map of the entire Schizosaccharomyces pombe genome was constructed using two restriction enzymes (BamHI and PstI) that recognize 6 bp. The restriction map contains 420 minimally overlapping clones (miniset) and has 22 gaps. We located 126 genes, marker fragments of DNA (NotI and SfiI linking clones), and 36 transposable elements by hybridization to unique restriction fragments.     

A linkage map of the canine genome

A genetic linkage map of the canine genome has been developed by typing 150 microsatellite markers using 17 three-generation pedigrees, composed of 163 F2 individuals. One hundred and thirty-nine markers were linked to at least one other marker with a lod score > or = 3.0, identifying 30 linkage groups. The largest chromosome had 9 markers spanning 106.1 cM. The average distance between markers was 14.03 cM, and the map covers an estimated 2073 cM. Eleven markers were informative on the mapping panel, but were unlinked to any other marker. These likely represent single markers located on small, distinct canine chromosomes. This map will be the initial resource for mapping canine traits of interest and serve as a foundation for development of a comprehensive canine genetic map.     

A second-generation linkage map of the bovine genome

We report a bovine linkage map constructed with 1236 polymorphic DNA markers and 14 erythrocyte antigens and serum proteins. The 2990-cM map consists of a sex-specific, X chromosome linkage group and 29 sex-averaged, autosomal linkage groups with an average interval size of 2.5 cM. The map contains 627 new markers and 623 previously linked markers, providing a basis for integrating the four published bovine maps. Orientation and chromosomal assignment of all the linkage groups, except BTA20 and BTA22, was provided by 88 markers that were assigned previously to chromosomes. This map provides sufficient marker density for genomic scans of populations segregating quantitative trait loci (QTL) and subsequent implementation of marker-assisted selection (MAS) mating schemes.     

Physical genome map of the unicellular cyanobacterium Synechococcus sp. strain PCC 7002

A physical restriction map of the genome of the cyanobacterium Synechococcus sp. strain PCC 7002 was assembled from AscI, NotI, SalI, and SfiI digests of intact genomic DNA separated on a contour-clamped homogeneous electric field pulsed-field gel electrophoresis system. An average genome size of 2.7 x 10(6) bp was calculated from 21 NotI, 37 SalI, or 27 SfiI fragments obtained by the digestions. The genomic map was assembled by using three different strategies: linking clone analysis, pulsed-field fragment hybridization, and individual clone hybridization to singly and doubly restriction-digested large DNA fragments. The relative positions of 21 genes or operons were determined, and these data suggest that the gene order is not highly conserved between Synechococcus sp. strain PCC 7002 and Anabaena sp. strain PCC 7120.     

Physical and genetic map of the mitochondrial genome of Cryphonectria parasitica Ep155

In the chestnut-blight fungus, Cryphonectria parasitica, a cytoplasmically transmissible (infectious) form of hypovirulence is associated with mitochondrial DNA (mtDNA) mutations that cause respiratory deficiencies. To facilitate the characterization of such mutations, a restriction map including the probable location of 13 genes was constructed for a relatively well-characterized virulent strain of the fungus, Ep155. The physical map is based on the order of all fragments generated by cleavage of the mtDNA by the PstI restriction endonuclease and includes some of the cleavage sites for HindIII, EcoRI, and XbaI. It was constructed from hybridization patterns of cloned mtDNA fragments with Southern blots of mtDNA digested with the four restriction enzymes. On this map, the probable locations of genes commonly found in the mitochondrial genomes of ascomycetes were determined by low-stringency hybridization of cloned Neurospora crassa mitochondrial gene probes to Southern blots of C. parasitica mtDNA. The data indicate that the mtDNA of strain Ep155 is a circular molecule of approximately 157 kbp and ranks among the largest mitochondrial chromosomes observed so far in fungi. The mtDNAs of 11 different C. parasitica isolates range in size from 135 to 157 kbp and in relatedness from 68 to 100 percent, as estimated from restriction-fragment polymorphisms. In addition to the typical mtDNA, the mitochondria of some isolates of the fungus contain double-stranded DNA plasmids consisting of nucleotide sequences not represented in the mtDNA of Ep155.     

Positional cloning without a genome map: using 'Targeted RFLP Subtraction' to isolate dense markers tightly linked to the regA locus of Volvox carteri

The ability to isolate genes defined by mutant phenotypes has fueled the rapid progress in understanding basic biological mechanisms and the causes of inherited diseases. Positional cloning, a commonly used method for isolating genes corresponding to mutations, is most efficiently applied to the small number of model organisms for which high resolution genetic maps exist. We demonstrate a new and generally applicable positional cloning method that obviates the need for a genetic map. The technique is based on Restriction Fragment Length Polymorphism (RFLP) Subtraction, a method that isolates RFLP markers spanning an entire genome. The new method, Targeted RFLP Subtraction (TRS), isolates markers from a specific region by combining RFLP Subtraction with a phenotypic pooling strategy. We used TRS to directly isolate dense markers tightly linked to the regA gene of the eukaryotic green alga Volvox. As a generally applicable method for saturating a small targeted region with DNA markers, TRS should facilitate gene isolation from diverse organisms and accelerate the process of physically mapping specific regions in preparation for sequence analysis.     

Analysis of 94 kb of the chlorella virus PBCV-1 330-kb genome: map positions 88 to 182

Analysis of 94 kb of DNA, located between map positions 88 and 182 kb in the 330-kb chlorella virus PBCV-1 genome, revealed 195 open reading frames (ORFs) 65 codons or longer. One hundred and five of the 195 ORFs were considered major ORFs. Twenty-six of the 105 major ORFs resembled genes in the databases including three chitinases, a chitosanase, three serine/threonine protein kinases, two additional protein kinases, a tyrosine protein phosphatase, two ankyrins, an ornithine decarboxylase, a copper/zinc-superoxide dismutase, a proliferating cell nuclear antigen, a DNA polymerase, a fibronectin-binding protein, the yeast Ski2 protein, an adenine DNA methyltransferase and its corresponding DNA site-specific endonuclease, and an amidase. The genes for the 105 major ORFs were evenly distributed along the genome and, except for one noncoding 1788-nucleotide stretch, the genes were close together. Unexpectedly, a 900-bp region in the 1788-bp noncoding sequence resembled a CpG island.     

Updating displays after imagined object and viewer rotations.

Six experiments compared spatial updating of an array after imagined rotations of the array versus viewer. Participants responded faster and made fewer errors in viewer tasks than in array tasks while positioned outside (Experiment 1) or inside (Experiment 2) the array. An apparent array advantage for updating objects rather than locations was attributable to participants imagining translations of single objects rather than rotations of the array (Experiment 3). Superior viewer performance persisted when the array was reduced to 1 object (Experiment 4); however, an object with a familiar configuration improved object performance somewhat (Experiment 5). Object performance reached near-viewer levels when rotations included haptic information for the turning object. The researchers discuss these findings in terms of the relative differences in which the human cognitive system transforms the spatial reference frames corresponding to each imagined rotation. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The genome of Staphylococcus aureus: a review

The genome of Staphylococcus aureus consists of a single circular chromosome (2.7-2.8 mbp) plus an assortment of extrachromosomal accessory genetic elements: conjugative and nonconjugative plasmids, mobile elements (IS, Tn, Hi), prophages and other variable elements. Plasmids (1-60 kbp) are classified into 4 classes and there are 15 known incompatibility groups. Mobile elements of the genome (0.8-18 kbp) appear in the chromosome or in plasmids of classes II and III. Prophages (45-60 kbp) are integrated in the bacterial chromosome, and they are UV- or mitomycin-inducible. Temperate bacteriophages of S. aureus are members of the Siphoviridae and the serological groups A, B and F occur most frequently. In the paper presented, the characteristics of chromosome, plasmids, transposons and other genetic elements of S. aureus genome are given and an alphabetical list of known genes of this species is included.     

Unpacking the cognitive map: The parallel map theory of hippocampal function.

In the parallel map theory, the hippocampus encodes space with 2 mapping systems. The bearing map is constructed primarily in the dentate gyrus from directional cues such as stimulus gradients. The sketch map is constructed within the hippocampus proper from positional cues. The integrated map emerges when data from the bearing and sketch maps are combined. Because the component maps work in parallel, the impairment of one can reveal residual learning by the other. Such parallel function may explain paradoxes of spatial learning, such as learning after partial hippocampal lesions, taxonomic and sex differences in spatial learning, and the function of hippocampal neurogenesis. By integrating evidence from physiology to phylogeny, the parallel map theory offers a unified explanation for hippocampal function. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Physical and genetic map of the genome of Buchnera, the primary endosymbiont of the pea aphid Acyrthosiphon pisum

The genome of Buchnera, an endosymbiotic bacterium of the pea aphid Acyrthosiphon pisum, was characterized by pulse-field gel electrophoresis (PFGE) as a circular DNA molecule of 657 kb. The enzymes I-CeuI, CpoI, ApaI, SmaI, NaeI, SacII, MluI, FspI, and NruI were used to cleave the DNA of Buchnera into fragments of suitable size for PFGE analysis. A physical map of the Buchnera genome, including restriction fragments from seven of these enzymes, was constructed using double cutting, partial digestion, and hybridization with linking fragments, and 29 genes and operons were localized on the map. In addition, the genomic map of Buchnera was compared with those of Escherichia coli and Haemophilus influenzae. The gene order in Buchnera is more similar to that of E. coli than to H. influenzae. The dramatic shrinkage of the Buchnera genome compared with those of other members of the closely related Enterobacteriaceae family is discussed in terms of evolution under the influence of the intracellular symbiotic association.