Genomes and Genes
Summary: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
- Kostichka K, Thomas S, Gibson K, Nagarajan V, Cheng Q. Cloning and characterization of a gene cluster for cyclododecanone oxidation in Rhodococcus ruber SC1. J Bacteriol. 2001;183:6478-86 pubmed
- Kim I, Shim J, Lee K, Hwang W, Kim I, Choi S, et al. Nonribosomal peptide synthase is responsible for the biosynthesis of siderophore in Vibrio vulnificus MO6-24/O. J Microbiol Biotechnol. 2008;18:35-42 pubmed..We also demonstrated that the NRPS genes are important for virulence of the pathogen in a mice model. ..
- Kurdi Haidar B, Heath D, Lennon G, Howell S. Chromosomal localization and genomic structure of the human arsenite-stimulated ATPase (hASNA-I). Somat Cell Mol Genet. 1998;24:307-11 pubmed..Our results indicate that the coding region of hASNA-I consists of 4 exons spanning 6 kb on band 19q13.3. These data will facilitate molecular analysis of the role of hASNA-I in human disease. ..
- Sibthorpe D, Baker A, Gilmartin B, Blackwell J, White J. Comparative analysis of two slc11 (Nramp) loci in Takifugu rubripes. DNA Cell Biol. 2004;23:45-58 pubmed publisher..Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AJ496547/8/9 and AJ496550.]..
- Davidson H, Taylor M, Doherty A, Boyd A, Porteous D. Genomic sequence analysis of Fugu rubripes CFTR and flanking genes in a 60 kb region conserving synteny with 800 kb of human chromosome 7. Genome Res. 2000;10:1194-203 pubmed..The euryhaline killifish CFTR coding sequence is highly homologous to the Fugu sequence, suggesting that upregulation of CFTR in that species in response to salinity may be regulated transcriptionally...
- Kang S, Lebrun M, Farrall L, Valent B. Gain of virulence caused by insertion of a Pot3 transposon in a Magnaporthe grisea avirulence gene. Mol Plant Microbe Interact. 2001;14:671-4 pubmed..grisea genome. The appearance of Pot3 in M. grisea seems to predate the diversification of various host-specific forms of the fungus. ..
- Fernández Martínez L, Del Sol R, Evans M, Fielding S, Herron P, Chandra G, et al. A transposon insertion single-gene knockout library and new ordered cosmid library for the model organism Streptomyces coelicolor A3(2). Antonie Van Leeuwenhoek. 2011;99:515-22 pubmed publisher..To achieve the highest coverage, a new ordered cosmid library was also constructed. Individual cosmids from both the existing and new libraries were disrupted using the Tn5-based mini-transposon Tn5062...
- Gubbels M, Lehmann M, Muthalagi M, Jerome M, Brooks C, Szatanek T, et al. Forward genetic analysis of the apicomplexan cell division cycle in Toxoplasma gondii. PLoS Pathog. 2008;4:e36 pubmed publisher..identified 18 candidate loci, eight of which were independently confirmed using a set of sequenced and arrayed cosmids. For three of these loci we have identified the mutant allele...
- Giorgi D, Rouquier S. Identification of V1R-like putative pheromone receptor sequences in non-human primates. Characterization of V1R pseudogenes in marmoset, a primate species that possesses an intact vomeronasal organ. Chem Senses. 2002;27:529-37 pubmed..These observations raise the possibility that the V1R family has evolved in such a manner in mammals that every species that relies on a VNO-mediated sensory function possesses its own set of functional vomeronasal genes. ..
- Miki S, Matsui K, Kito H, Otsuka K, Ashizawa T, Yasuda N, et al. Molecular cloning and characterization of the AVR-Pia locus from a Japanese field isolate of Magnaporthe oryzae. Mol Plant Pathol. 2009;10:361-74 pubmed publisher..Restriction fragment length polymorphism analysis of this region revealed that this DNA sequence co-segregated with the AVR-Pia locus in a genetic map that was constructed using Chinese isolates. ..
- Ludecke H, Schmidt O, Nardmann J, von Holtum D, Meinecke P, Muenke M, et al. Genes and chromosomal breakpoints in the Langer-Giedion syndrome region on human chromosome 8. Hum Genet. 1999;105:619-28 pubmed..Two genes, OPG and CXIV, which are deleted only in some patients with TRPS II may contribute to the clinical variability of this syndrome...
- Savouret C, Junien C, Gourdon G. Analysis of CTG repeats using DM1 model mice. Methods Mol Biol. 2004;277:185-97 pubmed
- Satola S, Schirmer P, Farley M. Genetic analysis of the capsule locus of Haemophilus influenzae serotype f. Infect Immun. 2003;71:7202-7 pubmed..The chromosomal location of the Hif cap locus and the organization of the flanking sequences differed significantly from previously described division I H. influenzae serotypes. ..
- Pontius J, O Brien S. Genome Annotation Resource Fields--GARFIELD: a genome browser for Felis catus. J Hered. 2007;98:386-9 pubmed
- Philibert R, Winfield S, Damschroder Williams P, Tengstrom C, Martin B, Ginns E. The genomic structure and developmental expression patterns of the human OPA-containing gene (HOPA). Hum Genet. 1999;105:174-8 pubmed..We conclude that the delineation of the function of the HOPA gene locus merits further study. ..
- Dolf G, Schelling C, Stahlberger Saitbekova N, Fu B, Schlapfer J, Yang F. Seven cosmid-derived canine microsatellites. Anim Genet. 2000;31:411-2 pubmed
- Kuzmin I, Geil L, Ge H, Bengtsson U, Duh F, Stanbridge E, et al. Analysis of aberrant methylation of the VHL gene by transgenes, monochromosome transfer, and cell fusion. Oncogene. 1999;18:5672-9 pubmed..Contribution of some putative trans-acting factors cannot be excluded during a period when the aberrant VHL methylation pattern was first generated. ..
- Szalai G, Xie D, Wassenich M, Veres M, Ceci J, Dewey M, et al. Distal and proximal cis-linked sequences are needed for the total expression phenotype of the mouse alcohol dehydrogenase 1 (Adh1) gene. Gene. 2002;291:259-70 pubmed..b>Cosmids containing either 7 kb of upstream and 21 kb of downstream or 12 kb of upstream and 23 kb of downstream sequence ..
- Yanagihara I, Yamagata M, Sakai N, Shukunami C, Kurahashi H, Yamazaki M, et al. Genomic organization of the human chondromodulin-1 gene containing a promoter region that confers the expression of reporter gene in chondrogenic ATDC5 cells. J Bone Miner Res. 2000;15:421-9 pubmed..These results suggest that the element -446/+87 confers the cartilage-specific expression of this gene by some factor(s) other than Sox9, Og12, and Cart-1. ..
- Ferrer M, Beloqui A, Golyshin P. Screening metagenomic libraries for laccase activities. Methods Mol Biol. 2010;668:189-202 pubmed publisher..In this chapter, we provide an overview of screening methods to identify laccase-encoding genes from environmental resources. ..
- Karbarz M, Kalb S, Cotter R, Raetz C. Expression cloning and biochemical characterization of a Rhizobium leguminosarum lipid A 1-phosphatase. J Biol Chem. 2003;278:39269-79 pubmed..leguminosarum symbiosis with plants. Possible orthologs of LpxE are present in some intracellular human pathogens, including Francisella tularensis, Brucella melitensis, and Legionella pneumophila. ..
- Trettel F, Mantuano E, Calabresi V, Veneziano L, Olsen A, Georgescu A, et al. A fine physical map of the CACNA1A gene region on 19p13.1-p13.2 chromosome. Gene. 2000;241:45-50 pubmed..A number of new STSs, whether polymorphic or not, were characterized and physically mapped within this region. Four ESTs were also assigned to cosmids belonging to specific contigs.
- Rojas Jiménez K, Sohlenkamp C, Geiger O, Martinez Romero E, Werner D, Vinuesa P. A ClC chloride channel homolog and ornithine-containing membrane lipids of Rhizobium tropici CIAT899 are involved in symbiotic efficiency and acid tolerance. Mol Plant Microbe Interact. 2005;18:1175-85 pubmed..tropici CIAT899, which, in turn, are contributing to symbiotic performance and acid tolerance...
- Kharel M, Subba B, Basnet D, Woo J, Lee H, Liou K, et al. A gene cluster for biosynthesis of kanamycin from Streptomyces kanamyceticus: comparison with gentamicin biosynthetic gene cluster. Arch Biochem Biophys. 2004;429:204-14 pubmed..The comparative genetic studies of Gm, Km, tobramycin (Tm), and butirosin (Bn) reveal their similar biosynthetic routes and provide a framework for the further biosynthetic studies. ..
- Vuoristo J, Berrettini W, Overhauser J, Prockop D, Ferraro T, Ala Kokko L. Sequence and genomic organization of the human G-protein Golfalpha gene (GNAL) on chromosome 18p11, a susceptibility region for bipolar disorder and schizophrenia. Mol Psychiatry. 2000;5:495-501 pubmed..Knowledge of the sequence and structure of the human GNAL gene provides essential information for further analysis of the GNAL locus at chromosome 18p11 which has been linked to bipolar disorder and schizophrenia. ..
- Shimada K, Nakamura M, Ishida E, Kishi M, Konishi N. Androgen and the blocking of radiation-induced sensitization to Fas-mediated apoptosis through c-jun induction in prostate cancer cells. Int J Radiat Biol. 2003;79:451-62 pubmed..Radiation-induced Fas sensitization in prostate cancer cell was mediated through p53-dependent transactivation of the Fas gene, which can be blocked by androgen stimulation mainly through induction of c-jun. ..
- Fujino M, Adachi K, Kawasaki M, Kitazawa Y, Funeshima N, Okuyama T, et al. Prolonged survival of rat liver allograft with adenoviral gene transfection of human immunodeficiency virus type 1 nef. Liver Transpl. 2003;9:805-13 pubmed..In conclusion, we showed that the nef gene could prolong survival of rat liver allografts, and this result suggested the potential clinical use of its transfection. ..
- Lucas M, Gwillam R, Lepingle A, Lyne M, Rajandream M, Rochet M, et al. Sequence analysis of two cosmids from Schizosaccharomyces pombe chromosome III. Yeast. 2000;16:1519-26 pubmedWe report the complete sequence of two cosmids, SPCC895 (38457 bp insert, EMBL Accession No. AL035247) and SPCC1322 (42068 bp insert, EMBL Accession No. AL035259), localized on chromosome III of the Schizosaccharomyces pombe genome...
- ..This unit discusses the appropriate numerical considerations for both ordinary genomic DNA libraries and subgenomic DNA libraries, and then describes a limited number of appropriate vectors. ..
- Boakes S, Cortes J, Appleyard A, Rudd B, Dawson M. Organization of the genes encoding the biosynthesis of actagardine and engineering of a variant generation system. Mol Microbiol. 2009;72:1126-36 pubmed publisher..Deletion of this gene resulted in the production of deoxy variants of actagardine, demonstrating that the formation of the sulfoxide group is enzyme catalysed and not a spontaneous chemical modification as previously believed. ..
- Dahlin Laborde R, Scolaro E, Romine N, Ramer Tait A, Lei S, Beetham J. Characterization of DNA sequences that confer complement resistance in Leishmania chagasi. Ann N Y Acad Sci. 2008;1149:347-51 pubmed publisher..3) multiple cosmid-transfectants exhibited partial CML resistance; and (4) the sequence for one of the cosmids (Cosmid 51) was determined...
- Bosch R, García Valdés E, Moore E. Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10. Gene. 1999;236:149-57 pubmed..stutzeri AN10 genome. Comparisons also suggest the coexistence of two entire nah upper pathways in a host strain, and further recombination between them. These events could accelerate the evolution of modern catabolic pathways. ..
- Hall D, Bhandarkar S, Wang J. ODS2: a multiplatform software application for creating integrated physical and genetic maps. Genetics. 2001;157:1045-56 pubmed..Other features include the flexibility of storing data in a local file or relational database and the ability to create full or minimum tiling contig maps. ..
- Sabbioni S, Veronese A, Trubia M, Taramelli R, Barbanti Brodano G, Croce C, et al. Exon structure and promoter identification of STIM1 (alias GOK), a human gene causing growth arrest of the human tumor cell lines G401 and RD. Cytogenet Cell Genet. 1999;86:214-8 pubmed
- Cozijnsen A, Howlett B. Characterisation of the mating-type locus of the plant pathogenic ascomycete Leptosphaeria maculans. Curr Genet. 2003;43:351-7 pubmed..The ORF1 transcript is 1.2 kb in the MAT1-1 isolate and 1.0 kb in the MAT1-2 isolate; and probes cross-hybridise weakly. A mating-type PCR assay with three nucleotide primers is developed for L. maculans. ..
- Larbig K, Christmann A, Johann A, Klockgether J, Hartsch T, Merkl R, et al. Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol. 2002;184:6665-80 pubmed
- Martin DeLeon P, Canaff L, Korstanje R, Bhide V, Selkirk M, Hendy G. Rabbit calcium-sensing receptor (CASR) gene: chromosome location and evidence for related genes. Cytogenet Cell Genet. 1999;86:252-8 pubmed
- Tornus D, Floss H. Identification of four genes from the granaticin biosynthetic gene cluster of Streptomyces violaceoruber Tü22 involved in the biosynthesis of L-rhodinose. J Antibiot (Tokyo). 2001;54:91-101 pubmed..Each gene was individually inactivated on a cosmid carrying the entire gra gene cluster and the mutant cosmids were transformed into S. coelicolor CH999...
- McLellan A, Fischer B, Dveksler G, Hori T, Wynne F, Ball M, et al. Structure and evolution of the mouse pregnancy-specific glycoprotein (Psg) gene locus. BMC Genomics. 2005;6:4 pubmed..This information will facilitate functional studies of this complex gene family. ..
- L Etoile N, Coburn C, Eastham J, Kistler A, Gallegos G, Bargmann C. The cyclic GMP-dependent protein kinase EGL-4 regulates olfactory adaptation in C. elegans. Neuron. 2002;36:1079-89 pubmed..A predicted nuclear localization signal within EGL-4 is required for adaptation after longer odor exposure, suggesting that nuclear translocation of EGL-4 triggers late forms of adaptation. ..
- Sarovich D, Pemberton J. pPSX: a novel vector for the cloning and heterologous expression of antitumor antibiotic gene clusters. Plasmid. 2007;57:306-13 pubmed..The inclusion of a lacZalpha multiple cloning site (MCS) allows blue/white screening. pPSX cosmids can be extracted from the host cell with commercial plasmid extraction kits facilitating downstream analysis, ..
- Ridge J, Lin M, Larsen E, Fegan M, McEwan A, Sly L. A multicopper oxidase is essential for manganese oxidation and laccase-like activity in Pedomicrobium sp. ACM 3067. Environ Microbiol. 2007;9:944-53 pubmed..These results suggest that moxBA and its homologues constitute a family of genes encoding an MCO and a predicted component of the Type I secretion system. ..
- Robert V, Prud homme N, Kim A, Bucheton A, Pelisson A. Characterization of the flamenco region of the Drosophila melanogaster genome. Genetics. 2001;158:701-13 pubmed..However, transgenes containing dip1 genomic DNA were not able to rescue flamenco mutant flies. The possible nature of the missing flamenco sequences is discussed. ..
- Hoskisson P, Rigali S, Fowler K, Findlay K, Buttner M. DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor. J Bacteriol. 2006;188:5014-23 pubmed..This suggestion was confirmed by gel mobility shift assays that showed that DevA binds its own promoter region in vitro. ..
- Liu L, Du Z, Zhao H, Liu X, Huang X, Shen J, et al. T to C substitution at -175 or -173 of the gamma-globin promoter affects GATA-1 and Oct-1 binding in vitro differently but can independently reproduce the hereditary persistence of fetal hemoglobin phenotype in transgenic mice. J Biol Chem. 2005;280:7452-9 pubmed..Both the -173 and -175 T to C substitutions may disrupt the complex assembly and result in the reactivation of the gamma-globin gene in adult erythrocytes. ..
- Smith M, Micali O, Hubbard S, Mir Rashed N, Jacobson D, Glass N. Vegetative incompatibility in the het-6 region of Neurospora crassa is mediated by two linked genes. Genetics. 2000;155:1095-104 pubmed..crassa. ..
- Kim M, Park J, Park H, Chung I, Park K. PAC and cosmid contig spanning the HOXA cluster on human chromosome 7p15. Somat Cell Mol Genet. 1998;24:245-8 pubmed..The isolated cosmids contained several consecutive HOX genes of regional group, probably sharing the regulatory processes such as ..
- Bülow H, Berry K, Topper L, Peles E, Hobert O. Heparan sulfate proteoglycan-dependent induction of axon branching and axon misrouting by the Kallmann syndrome gene kal-1. Proc Natl Acad Sci U S A. 2002;99:6346-51 pubmed..We hypothesize that KAL-1 binds by means of a heparan sulfate proteoglycan to its cognate receptor or other extracellular cues to induce axonal branching and axon misrouting. ..
- Robey M, Morgan E, Lodge J, Bolton A, Martin G, Brown N, et al. A new chromosomal locus associated with gut-modulated phenotypes in Salmonella enterica serotype typhimurium. J Med Microbiol. 2002;51:247-63 pubmed..pHC20-2 mapped at c. centisome 25 on the salmonella chromosome close to, but distinct from, SPI-5. ..
- Sun Y, Zhou X, Liu J, Bao K, Zhang G, Tu G, et al. 'Streptomyces nanchangensis', a producer of the insecticidal polyether antibiotic nanchangmycin and the antiparasitic macrolide meilingmycin, contains multiple polyketide gene clusters. Microbiology. 2002;148:361-71 pubmed
- Benos P, Gatt M, Ashburner M, Murphy L, Harris D, Barrell B, et al. From sequence to chromosome: the tip of the X chromosome of D. melanogaster. Science. 2000;287:2220-2 pubmed..2-kilobases of inverted repeats, each composed of a 350-base pair satellite related element. Thus, some aspects of chromosome structure appear to be revealed directly within the DNA sequence itself. ..