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Congenital chloride diarrhea (CLD) gene maps are different from cystic fibrosis transmembrane regulator gene (CFTR). However, CLD gene maps and CFTR have a strong association, with respect to chromosome 7 markers. Allelic linkage are closer between CLD and D7S496 than between CLD and D7S501.

Pulsed-field gel electrophoresis and molecular cloning enable the mapping of the 5rRNA operons of Staphylococcus aureus BB255 in the published map of the NCTC8325 chromosome, at SmaI fragments. One operon that cannot be mapped is linked to a 23-kb SmaI fragment. Chromosomal location of genes not found in NCTC8325 can be obtained with these clones.

The dipeptidyl carboxypeptidase (dcp) gene of Escherichia coli has a 2.9-kb DNA which comprises a 2,043 nucleotide open reading frame. The dcp gene expression is reduced according to the elevated gene copy number and the codon usage pattern. A 78.8% homology exists between the dcp gene and an enzyme from Salmonella typhimurium. The biophysical and biochemical qualities of Escherichia coli can be studied using the dcp gene.

A physical map of the genome of Rhizobium meliloti 1021 was developed to demonstrate its use by localizing 12 previously unmapped transposon insertions in the genome. This map of the genome is the first of a multireplicon member of the Rhizobiaceae family and is also the first physical map of a Rhizobium chromosome. These maps contain AT-rich restriction sites for SwaI, PacI, PmeI, pSym-b and SpeI.

The nucleocapsid protein N and phosphoprotein P interact with each other in vivo, yielding a sensitive assay system that has helped in the mapping of the domains between the two proteins. The two-hybrid systems employed in the study of the specific interaction between the two proteins can also be used in other viral systems and in the study of the interaction between proteins involved in transcription and replication.

Conventional and molecular markers are used to map the locus of an autosomal dominant gene responsible for the exceptionally gradual Wallerian degeneration in a substrain of the mouse inbred strain C57BL or C57BL/Ola. The name and symbol Wallerian degeneration Wld, with the mutant allele Wlds, are assigned to the locus. The locus is mapped to the distal tip of chromosome 4 near the locus of pronatriodilatin.

Associations of tumor susceptibility with alleles of genetic markers distributed across the mouse genome were studied in backcross progeny from a cross of susceptible BALB/c and resistant DBA/2 strains of mice to regionalize genes associated with plasmacytomagnesis. The extensive linkage homology is shared with areas of human chromosome 1 that have been linked to cytogenetic abnormalities in multiple myeloma breast lymphoid and endocrine tumors by the areas of mouse chromosomes 4 and 1 that are correlated with plasmocytoma susceptibility.

A wealth of protein and DNA sequence data is being generated by genome projects and other sequencing efforts. A crucial barrier to deciphering these sequences and understanding the relations among them is the difficulty of detecting subtle local residue patterns common to multiple sequences. Such patterns frequently reflect similar molecular structures and biological properties. A mathematical definition of this 'local multiple alignment' problem suitable for full computer automation has been used to develop a new and sensitive algorithm, based on the statistical method of iterative sampling. This algorithm finds an optimized local alignment model for N sequences in N-linear time, requiring only seconds on current workstations, and allows the simultaneous detection and optimization of multiple patterns and pattern repeats. The method is illustrated as applied to helix-turn-helix proteins, lipocalins, and prenyltransferases., Patterns shared by multiple protein or nucleic acid sequences shed light on molecular structure, function, and evolution. The recognition of such patterns generally relies upon aligning many sequences, a complex, [...]

Escherichia coli bacterial growth on L-lactate induces an L-lactate dehydrogenase synthesis responsible to an lct locus at 80.8 minutes on the chromosomal map. Pathway formation for dehydrogenase synthesis is dependent on three genes which cause formation of a regulator protein, a permease and the L-lactate dehydrogenase. These three genes overlap, and the L-lactate dehydrogenase gene sequence explains the functional similarity between L-lactate dehydrogenase and aerobic glycerol-3-phosphate dehydrogenase.

Phenotypic transition of Candida albicans is genetically analyzed using a SfiI macrorestriction map of the genome from the nonswitching 1006 strain. Restriction maps help localize genes from a specific genome to a specific part of the chromosomes, and also help analyze unclear linkage data. C.albicans is an opportunistic pathogen existing in many animals.

Upstream regulation regions of rRNA in Rhodobacter sphaeroides uses cloning and sequence information on all three existing rRNA operons. Mutants containing one or two rrn operons are studied for upstream regulatory regions by mapping the 5' rRNA ends to localize promoter regions. This is compared with upstream regulation sequences of Escherchia coli.

The structure of linear plasmids of Rhodococcus sp. MR11 and MR22 was examined by defining the physical characteristics of pHG207, which is the smallest of the Aut elements. Restriction maps of pHG207, pHG204 and pHG205 were drawn revealing pHG207 as a derivative of a combination of pHG204 and pHG205. It was proved that the linear plasmid pHG207 has proteins located at both ends connected to the 5' terminals of the DNA plasmid. Inverted terminal repeats were revealed by cloning and nucleotide sequence analysis.

Site directed mutagenesis and high-resolution CD4 structural data were used to obtain elaborate mapping of the class II major histocompatibility complex (MHC) binding site. The residues on every lateral surface of domain 1 and the nearby sections of domain 2 are involved in contacting class II MHC. Apparent MHC contacts go beyond the BED face of domain 1 over the interdomain groove and onto the FG loop of domain 2.

The behavior and genetics of the Drosophila mutant radish (rsh gene) has been characterized. At both early and late times after training, subsequent memory deteriorates quickly, though high initial learning of radish flies is observed in two olfactory discrimination studies. Three hours after training, anesthesia-resistant memory or consolidated memory cannot be identified. The odor cues and electric shock reinforcement, employed in the learning tests, elicit normal locomotor activity and normal sensitivity from the mutant.

Orthologous ion, identified with a common group of cDNA clones, formed the basis of the development of genetic linkage maps for rice and maize genomes. It was possible to determine conserved linkage groups. In certain cases, whole chromosomes or chromosme arms were almost exactly alike in relation to gene content and gene order. More than 72% of the genes duplicated during ancient polyploidization were copied in the maize genome.

The superinfection exclusion gene (sieB) of Salmonella phage P22 was tabulated using phage deletion mutants. The DNA sequence was studied to determine an open reading frame conforming to the deletion tabulations, revealing several differences from earlier sequences and the new sequence with a single open reading frame of 242 codons with six possible translation initiation codons. The second of these six sites was inferred to be the translation initiation site of the sieB gene on the basis of deletion and amber mutant phenotypes. The sieB gene encodes a polypeptide with 192 amino acid residues with a molecular weight of 22,442.

A detailed redefined satellite mapping of chromosome 2 heterochromatin and the distribution of the cloned sequences of the genome of Drosophila melanogaster are presented. Chromosomal experiments were earlier conducted using cloned and sequenced probes. Stringent hybridization policies were used to prevent cross-hybridization between related satellites. The present study used this analysis to rearrange the chromosomes in order to map satellite blocks with special heterochromatic measurements.

A study of the DNA-dependent dimerization of the alpha and beta subunits of an Oxytricha nova, telomere-binding protein, used glycerol gradient sedimentation and chemical cross-linking to analyze subunit interactions. Both subunits exist primarily as monomers in the absence of telomeric DNA, when incubated together, and interact directly with one another to develop a heterodimer, upon binding to DNA. This DNA-dependent dimerization is involved in chromosome mapping as part of the heterodimer and may permit every subunit to execute unique operations as a monomer.

The cloning of the aroA gene of Staphylococcus aureus 8325-4 was undertaken and sequence analysis of directed plasmid insertions of 5 inches on aroA show that aroA is situated in an operon. The operon also includes aroB and aroC genes. Temperature sensitive plasmids were coordinated with 5 inch chromosomes to aroA, which resulted in an Aro phenotype. ORFs encode proteins which are homologous with the aroB and aroF genes of B subtilis. The aroB complements E. Coli.

A 4,400-base pair stretch of DNA starting from the end of the trp operon and including tonB and some open reading frames were compared in Escherichia coli K12 and 36 ECOR strains. Comparative sequencing showed consistency in multilocus enzyme electrophoresis and analyses of restriction fragment length polymorphism suggesting that the observed linear discontinuities are due to recombination. The replacement patterns may be explained by incorporation of small or large entrant DNA fragments or through the cascade hypothesis.

Phylogenetic patterns within Calycadenia were estimated from 18-26S nuclear ribosomal DNA sequences of the internal transcribed spacer (ITS) region in 19 representatives of all species in Calycadenia, including Osmadenia (C.) tenella, and in two outgroup species. In pairwise comparisons among the Calycadenia and Osmadenia sequences, divergence ranged from 0 to 11.2% of nucleotides in ITS 1 and from 0 to 8.6% in ITS 2. Of 62 nucleotide sites with potential phylogenetic information, 51.6% were in ITS 1,46.8% were in ITS 2, and 1.6% were in the 5.8S subunit. A highly resolved, strict consensus tree from Wagner parsimony analysis of these data agrees well with morphological and cytological evidence. This tree suggests that: 1) the monotypic Osmadenia tenella is the sister-group to Calycadenia; 2) the base chromosome number in Calycadenia is n = 7, from which other numbers were derived; 3) species with multiple T-glands on cylindrical bracts and chromosome numbers of n = 5 or 6 (or 7 in C. oppositifolia) form a monophyletic group derived from an n = 7 species similar or identical in genomic structure to C. hooveri or C. villosa; 4) C. spicata (n = 4) is the product of an independent dysploid reduction from n = 7; 5) C. multiglandulosa and C. pauciflora, sensu Keck, are not monophyletic taxa; and 6) loss of chromosomal homology between Calycadenia species, as reflected by meiotic chromosomal association in hybrids, is positively correlated with time since evolutionary divergence. These results offer little evidence of homoplasy in chromosomal and phenotypic characters in Calycadenia and provide further support for the phylogenetic utility of plant ITS sequences.

A study was done on the cloning and chromosomal mapping of an HIV 1 'TATA' element modulatory factor. A 123 kDa cellular protein was identified and found to bind to the HIV 1 TATA element. The protein serves as an element modulatory factor and inhibits the activation of the viral long terminal repeat by the TATA-binding protein in in vitro transcription assays. This modulatory factor contains leucine-zipper amino acid motifs and shows homology in its DNA binding domain with the phage-encoded DNA binding protein Ner.

The genome size of the myxobacterium Stigmatella aurantiaca DW 4/3.1 was determined. Analysis of the fragment pattern after SpeI and AseI restriction of genomic DNA revealed 33 AseI and 25 SpeI restriction fragments. The apparent size of the chromosome was determined to be about 9,350 kbp. Several S. aurantiaca isolates also showed five unique genomic fingerprints and minor genome size variations. The S. erecta chromosome was slightly larger than that of S. aurantiaca .

A locus that ensures complementation of the elevated sister chromatid exchange phenotype is mapped using Bloom syndrome (BSx) cells as recipients for microcell-mediated chromosome transfer. Traditional genetic linkage analysis was useless in mapping gene defects because the rare occurrence of several autosomal recessive disorders, including BSx, ensured the paucity of informative families.

A detailed genetic map of the CobII and CobIII regions in Salmonella typhimuriium involved in cobalamin synthesis was constructed through deletion mapping. Complementation analysis indicated that CobII contains four complementation groups designated cobJKLM, while CobIII contains three complementation groups correspondig to cobU, cobS and cobT genes. Preliminary results suggest that cobJ and cobL are involved in the synthesis of dimethylphenylenediamine (DMPDA), while cobK and cobM gene products convert DMPDA to dimethylbenzimidazole.

The recent ability to sequence whole genomes allows ready access to all genetic material. The approaches outlined here allow automated analysis of sequence for the synthesis of optimal primers in an automated multiplex oligonucleotide synthesizer (AMOS). The efficiency is such that all ORFs for an organism can be amplified by PCR. The resulting amplicons can be used directly in the construction of DNA arrays or can be cloned for a large variety of functional analyses. These tools allow a replacement of single-gene analysis with a highly efficient whole-genome analysis.

The ability to sequence DNA accurately and efficiently has revolutionized biology and medicine and has ushered in the new era of genomic science, the study of genes and genomes. An [...]

Five years since its inception, the Human Genome Project has exceeded all expectations. The organizers have begun research on non-human genetic mapping, while the mapping of human genomes is developing ahead of schedule. Advances in the identification of expressed sequence tags have led to new research on cloning, and the ethical and legal aspects of mapping are being addressed in a professional and timely manner.

Complentation analysis reveals that the cls and nov genes in E. coli are identical. Cls codes for cardiolipin synthase and nov is a novobiocin resistance gene. A cls-bearing plasmid was introduced into a nov-deficient strain and the resulting transformant was able to grow on novobiocin. The cls gene is 1,458 nucleotides long and codes for a 54,574 Da protein.

Physical chromosomal maps of M. gallisepticum are constructed by field inversion gel electrophoresis, which reveals the Mycoplasma virulence at the molecular level. Three deletions in strain ATCC 19610, relative to strain R, suggest the depletion of depletion factors influenced by mutations in virulence-related genes or down regulation of virulence genes.

Mapping of the bovine beta-hemoglobin, albino and lactate dehydrogenase A (LDHA) loci in mammals with a 1.8 kb cDNA clone from human tyrosinase shows that the beta-hemoglobin (HBB) locus is not syntenic with the albino locus but with catalase (CAT). The tyrosinase probe is hybridized to a region syntenic with LDHA loci. Two chromosomal reorganizations are essential to elucidate the chromosomal properties and linkages of the albino locus and CAT, LDHA and HBB in mice, cattle and human species.

A study of the chromosomal mapping of the human QIN gene, which was renamed by the Human Genome Organization Nomenclature Committee as FKH2, revealed that the QIN gene mapped to chromosome region 14q32. Fluorescence in situ hybridization techniques with a human QIN genomic clone refined the localization of human QIN gene to 14q13.

Studies on the soybean germplasm line C1727 reveal that Fap2 locus belongs to the linkage group D of USDA-ARS/ISU soybean molecular genetic map. The location at the locus is between markers A-537 and A-611. It is now possible to characterize the gene controlling palmitate synthesis and construct a map based on cloning experiments, leading to the selection of high palmitate varieties.

The yeast Saccharomyes cerevisiae has a rad 1 missense mutation (rad 1-20), which has been characterized, and is observed to map to an area of the Rad 1 polypeptide needed for Rad 1-Rad 10 complex development. Increased RAD-10 complex gene expression can partially correct the Uv sensitivity of the rad 1-20 mutant, indicating that for nucleotide excision repairs, the Rad 1 and Rad 10 proteins are necessary. Damage-specific incision of DNA involves Rad 1 and Rad 10 proteins as a complex, which is evident because one molecule of the Rad 1 and Rad 10 protein constitutes an endonuclease specific for single-stranded DNA.

The hybridization of common structural motifs of RNA, such as, hairpins, internal loops, bulges, 3'- and 5'-dangling ends, and pseudoknots to isoenergetic microarray probes is presented. The data obtained from isoenergetic microarray mapping could facilitate and improve RNA secondary structure prediction, but combination with chemical and/or enzymatic mapping might provide optimal results.